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Result Summary
| Number of genes | 36 | |
| Export | ||
Embryo
| Area | Images | Terms |
|---|---|---|
| stage 1-3 |
|
Stage 1-3 Non-Expressed |
| stage 4-5 |
|
Stage 4-5 Expressed Zygotic Zygotic starting stage 4 Blastoderm nuclei Subset blastoderm nuclei Segmented pattern Pair-rule pattern Weak expression (>41ms exp) Localized Subcellular localization patterns Apical localization Apical enrichment Apical clusters |
| stage 6-7 |
|
Stage 6-7 Expressed Zygotic Blastoderm nuclei Subset blastoderm nuclei Segmented pattern Pair-rule pattern Weak expression (>41ms exp) Localized Subcellular localization patterns Basal localization Basal enrichment |
| stage 8-9 |
|
Stage 8-9 Expressed Zygotic Blastoderm nuclei Subset blastoderm nuclei Segmented pattern Pair-rule pattern Weak expression (>41ms exp) Localized |
| stage 10-17 |
|
Stage 10-17 Expressed Zygotic Tracheal system Tracheal pits Segmented pattern Head Blastoderm nuclei |
Larva
| Area | Images | Terms |
|---|---|---|
| fat body |
|
3rd Instar Larval Tissues Fat body Expressed in fat body Fat body allover - Ubiquitous |
| intestine |
|
3rd Instar Larval Tissues Intestine Expressed in midgut Subcellular localization in midgut Midgut - foci Midgut allover Expressed in malpighian tubules Subcellular localization in malpighian tubules Malpighian tubules - foci Malpighian tubules allover Expressed in gastric caeca Gastric caeca allover |
| imaginal discs |
|
3rd Instar Larval Tissues Imaginal discs Not expressed in imaginal discs |
| nervous system |
|
3rd Instar Larval Tissues Nervous system Not expressed in nervous system |
| salivary gland |
|
3rd Instar Larval Tissues Salivary gland Not expressed in salivary glands |
| lymph glands and ring glands |
|
3rd Instar Larval Tissues Lymph Glands and Ring Glands Ring gland Expressed in ring gland Ring gland allover Lymph Glands Not expressed in lymph glands |
Adult
| Area | Images | Terms |
|---|
Comments
| insitu done in 2006 by Eric's group. |
Embryo
| Area | Images | Terms |
|---|---|---|
| stage 1-3 |
|
Stage 1-3 Non-Expressed |
| stage 4-5 |
|
Stage 4-5 Expressed Zygotic Blastoderm nuclei Subset blastoderm nuclei Segmented pattern Pair-rule pattern Localized Subcellular localization patterns Ventral localization Posterior localization Dorsal localization Anterior localization |
| stage 6-7 |
|
Stage 6-7 Expressed Zygotic Blastoderm nuclei Subset blastoderm nuclei Segmented pattern Pair-rule pattern Expression in ectoderm Localized Posterior localization Embryonic localization patterns Ventral localization Dorsal localization Anterior localization |
| stage 8-9 |
|
Stage 8-9 Expressed Zygotic Blastoderm nuclei Subset blastoderm nuclei Segmented pattern Pair-rule pattern Expression in ectoderm Localized Embryonic localization patterns Ventral localization Posterior localization Germ band localization Dorsal localization Anterior localization |
| stage 10-17 |
|
Stage 10-17 Expressed Zygotic Sensory system Malpighian tubules Head Head epidermis Ectoderm Anal pad |
Larva
| Area | Images | Terms |
|---|
Adult
| Area | Images | Terms |
|---|
Comments
| -performed via HCR-FISH using 3 probe sets targeting the RA isoform transcript |
Embryo
| Area | Images | Terms |
|---|---|---|
| stage 1-3 |
|
Stage 1-3 Expressed Ubiquitous Maternal |
| stage 4-5 |
|
Stage 4-5 Expressed Zygotic Zygotic starting stage 4 Blastoderm nuclei Subset blastoderm nuclei Segmented pattern Pair-rule pattern Gap-gene pattern Ubiquitous Maternal |
| stage 6-7 |
|
Stage 6-7 Expressed Zygotic Blastoderm nuclei Subset blastoderm nuclei Segmented pattern Pair-rule pattern |
| stage 8-9 |
|
Stage 8-9 Expressed Zygotic Blastoderm nuclei Subset blastoderm nuclei Segmented pattern Pair-rule pattern Expression in mesoderm Expression in ectoderm |
| stage 10-17 |
|
Stage 10-17 Expressed Zygotic Segmented pattern |
Larva
| Area | Images | Terms |
|---|
Adult
| Area | Images | Terms |
|---|
Comments
| Re-annotated 2014. |
Embryo
| Area | Images | Terms |
|---|---|---|
| stage 1-3 |
|
Stage 1-3 Expressed Weak expression (>41ms exp) Ubiquitous Maternal |
| stage 4-5 |
|
Stage 4-5 Expressed Zygotic Blastoderm nuclei Subset blastoderm nuclei Segmented pattern Pair-rule pattern Localized Subcellular localization patterns Exclusionary patterns Pole cell exclusion Apical localization Apical enrichment Apical clusters Embryonic localization patterns |
| stage 6-7 |
|
Stage 6-7 Expressed Zygotic Blastoderm nuclei Subset blastoderm nuclei Segmented pattern Pair-rule pattern Localized Subcellular localization patterns Exclusionary patterns Apical localization Apical enrichment Apical clusters Embryonic localization patterns Exclusionary patterns Pole cell exclusion |
| stage 8-9 |
|
Stage 8-9 Expressed Zygotic Blastoderm nuclei Subset blastoderm nuclei Segmented pattern Pair-rule pattern Expression in ectoderm Expression in amnioserosa Localized Subcellular localization patterns Perinuclear localization Perinuclear subset of nuclei Nuclei-associated localization Intranuclear accumulation Accumulation nuclear subregion Cytoplasmic foci |
| stage 10-17 |
|
Stage 10-17 Expressed Zygotic Tracheal system Tracheal pits Segmented pattern Oenocytes Muscles-embryo Visceral mesoderm Head Blastoderm nuclei Localized Subcellular localization patterns Perinuclear localization Perinuclear around ectoderm nuclei Foci Small Foci Small Foci in tracheal cells Small Foci in ectoderm |
Larva
| Area | Images | Terms |
|---|---|---|
| fat body |
|
3rd Instar Larval Tissues Fat body Subcellular Localization - Fat body Fat body - Nuclear localization Fat body - Subnuclear localization Cytoplasmic foci-fat body Nascent transcript in fat body Expressed in fat body Fat body allover - Ubiquitous |
| intestine |
|
3rd Instar Larval Tissues Intestine Expressed in midgut Subcellular localization in midgut Midgut - foci Midgut allover Expressed in hindgut Hindgut allover Hindgut - Midgut border Expressed in gastric caeca Gastric caeca allover |
| nervous system |
|
3rd Instar Larval Tissues Nervous system Expressed in brain lobes Optic lobe Brain lobes - Significant area Brain lobes - Foci or dots |
| salivary gland |
|
3rd Instar Larval Tissues Salivary gland Subcellular localization in salivary gland Salivary gland - subnuclear Salivary gland - nuclear dots Salivary gland - Cytoplasmic foci Nascent transcript in salivary gland Expressed in salivary glands Salivary glands allover |
| ovary and testis |
|
Adult Tissues Male reproductive tissues Testis 3rd Instar Larval Tissues Larval Ovary and Testis-Larva Testis allover - Larva |
| lymph glands and ring glands |
|
3rd Instar Larval Tissues Lymph Glands and Ring Glands Ring gland Ring gland - Subcellular localization Ring gland - Cytoplasmic foci Ring gland - Few and small foci Expressed in ring gland Ring gland allover |
Adult
| Area | Images | Terms |
|---|
Comments
| Good probe on gel. |
Embryo
| Area | Images | Terms |
|---|---|---|
| stage 1-3 |
|
Stage 1-3 Expressed Ubiquitous Medium expression (21-40ms exp) Maternal |
| stage 4-5 |
|
Stage 4-5 Expressed Zygotic Zygotic starting stage 4 Blastoderm nuclei Subset blastoderm nuclei Random blastoderm nuclei Ubiquitous Maternal Degraded Degraded partially stage 5 Degraded partially stage 4 Degradation maternal transcripts |
| stage 6-7 |
|
Stage 6-7 Expressed Zygotic Blastoderm nuclei Subset blastoderm nuclei Segmented pattern Pair-rule pattern |
| stage 8-9 |
|
Stage 8-9 Expressed Zygotic Blastoderm nuclei Subset blastoderm nuclei Segmented pattern Pair-rule pattern Random blastoderm nuclei |
Larva
| Area | Images | Terms |
|---|
Adult
| Area | Images | Terms |
|---|
Comments
Embryo
| Area | Images | Terms |
|---|---|---|
| stage 1-3 |
|
Stage 1-3 Expressed Weak expression (>41ms exp) Ubiquitous Maternal |
| stage 4-5 |
|
Stage 4-5 Expressed Zygotic Zygotic starting stage 4 Yolk nuclei Subset yolk nuclei Blastoderm nuclei Subset blastoderm nuclei Segmented pattern Gap-gene pattern Strong expression (1-20ms exp) Maternal Localized Subcellular localization patterns Exclusionary patterns Pole cell exclusion Embryonic localization patterns Degraded Degraded completely stage 4 Degradation maternal transcripts |
| stage 6-7 |
|
Stage 6-7 Expressed Zygotic Yolk Nuclei All yolk nuclei Blastoderm nuclei Subset blastoderm nuclei Segmented pattern Gap-gene pattern Expression in ectoderm Strong expression (1-20ms exp) |
| stage 8-9 |
|
Stage 8-9 Expressed Zygotic Blastoderm nuclei Subset blastoderm nuclei Segmented pattern Pair-rule pattern Expression in ectoderm Expression in amnioserosa Strong expression (1-20ms exp) |
| stage 10-17 |
|
Stage 10-17 Expressed Zygotic Yolk nuclei Segmented pattern Ectoderm Amnioserosa |
Larva
| Area | Images | Terms |
|---|---|---|
| intestine |
|
3rd Instar Larval Tissues Intestine Expressed in hindgut Hindgut - Midgut border |
| imaginal discs |
|
3rd Instar Larval Tissues Imaginal discs Not expressed in imaginal discs |
| nervous system |
|
3rd Instar Larval Tissues Nervous system Not expressed in nervous system |
| salivary gland |
|
3rd Instar Larval Tissues Salivary gland Subcellular localization in salivary gland Salivary gland - subnuclear Nascent transcript in salivary gland Expressed in salivary glands |
| lymph glands and ring glands |
|
3rd Instar Larval Tissues Lymph Glands and Ring Glands Ring gland Not expressed in ring gland |
Adult
| Area | Images | Terms |
|---|
Comments
Embryo
| Area | Images | Terms |
|---|---|---|
| stage 1-3 |
|
Stage 1-3 Expressed Weak expression (>41ms exp) Ubiquitous Maternal |
| stage 4-5 |
|
Stage 4-5 Expressed Zygotic Zygotic starting stage 5 Blastoderm nuclei Subset blastoderm nuclei Segmented pattern Pair-rule pattern Gap-gene pattern Weak expression (>41ms exp) Localized Subcellular localization patterns Nuclei-associated localization Intranuclear accumulation Accumulation nuclear subregion Membrane associated Exclusionary patterns Pole cell exclusion Apical localization Apical enrichment Embryonic localization patterns |
| stage 6-7 |
|
Stage 6-7 Expressed Zygotic Blastoderm nuclei Subset blastoderm nuclei Segmented pattern Pair-rule pattern Weak expression (>41ms exp) Localized Subcellular localization patterns Nuclei-associated localization Intranuclear accumulation Accumulation nuclear subregion Exclusionary patterns Embryonic localization patterns Exclusionary patterns Pole cell exclusion |
| stage 8-9 |
|
Stage 8-9 Expressed Zygotic Blastoderm nuclei Subset blastoderm nuclei Segmented pattern Pair-rule pattern Expression in mesoderm Weak expression (>41ms exp) |
| stage 10-17 |
|
Stage 10-17 Expressed Zygotic Ectoderm Blastoderm nuclei |
Larva
| Area | Images | Terms |
|---|
Adult
| Area | Images | Terms |
|---|
Comments
| Good probe on gel. |
Embryo
| Area | Images | Terms |
|---|---|---|
| stage 1-3 |
|
Stage 1-3 Non-Expressed |
| stage 4-5 |
|
Stage 4-5 Expressed Zygotic Zygotic starting stage 4 Blastoderm nuclei Subset blastoderm nuclei Segmented pattern Pair-rule pattern Weak expression (>41ms exp) Localized Subcellular localization patterns Apical localization Apical enrichment Diffuse apical localization Embryonic localization patterns |
| stage 6-7 |
|
Stage 6-7 Expressed Zygotic Blastoderm nuclei Subset blastoderm nuclei Segmented pattern Pair-rule pattern Posterior blastoderm nuclei Weak expression (>41ms exp) Localized Subcellular localization patterns Apical localization Apical enrichment Diffuse apical localization Embryonic localization patterns |
| stage 8-9 |
|
Stage 8-9 Expressed Zygotic Blastoderm nuclei Subset blastoderm nuclei Segmented pattern Pair-rule pattern Weak expression (>41ms exp) |
Larva
| Area | Images | Terms |
|---|
Adult
| Area | Images | Terms |
|---|
Comments
| Re-annotated. |
Probe CG31131-ex Links: Permalink
Genes: CG31131
Embryo
| Area | Images | Terms |
|---|---|---|
| stage 1-3 |
|
Stage 1-3 Non-Expressed |
| stage 4-5 |
|
Stage 4-5 Expressed Zygotic Blastoderm nuclei Subset blastoderm nuclei Segmented pattern Pair-rule pattern Localized Subcellular localization patterns Posterior localization Dorsal localization Anterior localization |
| stage 6-7 |
|
Stage 6-7 Expressed Zygotic Blastoderm nuclei Subset blastoderm nuclei Segmented pattern Pair-rule pattern Localized Posterior localization Embryonic localization patterns Dorsal localization Anterior localization |
| stage 8-9 |
|
Stage 8-9 Expressed Zygotic Blastoderm nuclei Subset blastoderm nuclei Segmented pattern Pair-rule pattern Weak expression (>41ms exp) Ubiquitous Localized Embryonic localization patterns Posterior localization Dorsal localization Anterior localization |
| stage 10-17 |
|
Stage 10-17 Expressed Zygotic Ectoderm Weak expression (>41ms exp) Ubiquitous |
Larva
| Area | Images | Terms |
|---|
Adult
| Area | Images | Terms |
|---|
Comments
| -performed via HCR-FISH using 3 probe sets targeting common exons |
| -modENCODE RNAseq data on FlyBase shows low/no expression, however, we observed strong expression patterns throughout development |
Probe CR46452-RA Links: Permalink
Genes: CR46452
Embryo
| Area | Images | Terms |
|---|---|---|
| stage 1-3 |
Stage 1-3 Non-Expressed |
|
| stage 4-5 |
|
Stage 4-5 Expressed Zygotic Zygotic starting stage 4 Blastoderm nuclei Subset blastoderm nuclei Ventral blastoderm nuclei Segmented pattern Pair-rule pattern Dorsal blastoderm nuclei Ubiquitous Localized Subcellular localization patterns Ventral localization Nuclei-associated localization Perinuclear localization Perinuclear subset of nuclei Exclusionary patterns Pole cell exclusion Apical exclusion Dorsal localization Cytoplasmic foci Basal localization Basal enrichment |
| stage 6-7 |
|
Stage 6-7 Expressed Zygotic Blastoderm nuclei Subset blastoderm nuclei Ventral blastoderm nuclei Segmented pattern Pair-rule pattern Ubiquitous Localized Subcellular localization patterns Nuclei-associated localization Perinuclear localization Perinuclear subset of nuclei Perinuclear around blastoderm nuclei Cytoplasmic foci Embryonic localization patterns Ventral localization Degraded Degraded partially stage 6 |
| stage 8-9 |
|
Stage 8-9 Expressed Zygotic Blastoderm nuclei Subset blastoderm nuclei Segmented pattern Pair-rule pattern Expression in mesoderm Expression in ectoderm Localized Subcellular localization patterns Cytoplasmic foci Embryonic localization patterns Germ band localization Degraded Degraded partially stage 8 Degraded completely stage 9 |
| stage 10-17 |
Stage 10-17 Non-Expressed |
Larva
| Area | Images | Terms |
|---|
Adult
| Area | Images | Terms |
|---|
Comments
| -performed via HCR-FISH using 3 probe sets targeting the RA isoform transcript |
| -interesting 7-stripe pattern observed in the blastoderm/epidermis |
Embryo
| Area | Images | Terms |
|---|---|---|
| stage 1-3 |
|
Stage 1-3 Expressed Ubiquitous Medium expression (21-40ms exp) Maternal |
| stage 4-5 |
|
Stage 4-5 Expressed Maternal Localized Subcellular localization patterns Exclusionary patterns Pole cell exclusion Apical exclusion Embryonic localization patterns Degraded Degraded partially stage 5 Degradation maternal transcripts |
| stage 6-7 |
|
Stage 6-7 Expressed Zygotic Zygotic starting stage 6 Blastoderm nuclei Subset blastoderm nuclei Segmented pattern Pair-rule pattern Gap-gene pattern Localized Subcellular localization patterns Exclusionary patterns Embryonic localization patterns Exclusionary patterns Pole cell exclusion |
| stage 8-9 |
|
Stage 8-9 Expressed Zygotic Blastoderm nuclei Subset blastoderm nuclei Segmented pattern Pair-rule pattern Degraded Degraded partially stage 8 Degradation maternal transcripts |
Larva
| Area | Images | Terms |
|---|
Adult
| Area | Images | Terms |
|---|
Comments
| Re-annotated |
Embryo
| Area | Images | Terms |
|---|---|---|
| stage 1-3 |
|
Stage 1-3 Expressed Ubiquitous Maternal |
| stage 4-5 |
|
Stage 4-5 Expressed Ubiquitous Localized Subcellular localization patterns Nuclei-associated localization Intranuclear accumulation Accumulation in all nuclei |
| stage 6-7 |
|
Stage 6-7 Expressed Zygotic Blastoderm nuclei Subset blastoderm nuclei Segmented pattern Pair-rule pattern Expression in ectoderm Ubiquitous Localized Subcellular localization patterns Nuclei-associated localization Intranuclear accumulation Accumulation in all nuclei |
| stage 8-9 |
|
Stage 8-9 Expressed Zygotic Blastoderm nuclei Subset blastoderm nuclei Segmented pattern Pair-rule pattern Expression in ectoderm Ubiquitous Localized Subcellular localization patterns Nuclei-associated localization Accumulation in all nuclei Embryonic localization patterns Dorsal localization Degraded Degraded partially stage 9 |
| stage 10-17 |
|
Stage 10-17 Expressed Zygotic Midgut Head Head epidermis Ectoderm Brain Ubiquitous Localized Subcellular localization patterns Nuclei-associated localization |
Larva
| Area | Images | Terms |
|---|
Adult
| Area | Images | Terms |
|---|
Comments
| -performed via HCR-FISH using 3 probe sets targeting common exons |
Embryo
| Area | Images | Terms |
|---|---|---|
| stage 1-3 |
|
Stage 1-3 Expressed Ubiquitous Maternal |
| stage 4-5 |
|
Stage 4-5 Expressed Zygotic Blastoderm nuclei Subset blastoderm nuclei Segmented pattern Pair-rule pattern Localized Subcellular localization patterns Ventral localization Posterior localization Dorsal localization Anterior localization |
| stage 6-7 |
|
Stage 6-7 Expressed Zygotic Blastoderm nuclei Subset blastoderm nuclei Segmented pattern Pair-rule pattern Localized Posterior localization Embryonic localization patterns Ventral localization Dorsal localization Anterior localization |
| stage 8-9 |
|
Stage 8-9 Expressed Zygotic Blastoderm nuclei Subset blastoderm nuclei Segmented pattern Pair-rule pattern Localized Embryonic localization patterns Ventral localization Posterior localization Dorsal localization Anterior localization |
| stage 10-17 |
|
Stage 10-17 Expressed Zygotic Tracheal system Tracheal pits Posterior spiracles Muscles-embryo Muscles - subregion Maxillary complex Head Head epidermis Ectoderm Brain |
Larva
| Area | Images | Terms |
|---|
Adult
| Area | Images | Terms |
|---|
Comments
| -performed via HCR-FISH using 3 probe sets targeting the RA isoform transcript |
| -There is no entry for this gene on BDGP, and modENCODE RNAseq data on FlyBase indicates that it is not expressed in the embryo. However, we observed obvious patterns during embryogenesis. Additionally, FlyBase does not have any in-depth characterizations of this gene. |
| -Osi21 does not overlap with any other genes, ruling out the possibility of the targeting of alternative transcripts. BLAST also confirms the specificity of our probes to Osi21. Additionally, no other genes for which probes were designed for on this plate show patterns such as those observed here, ruling out the possibility of cross-contamination during probe preparation. |
| -This may be a result of Osi21's poor characterization or incorrect RNAseq data |
Embryo
| Area | Images | Terms |
|---|---|---|
| stage 1-3 |
|
Stage 1-3 Expressed Weak expression (>41ms exp) Ubiquitous Maternal |
| stage 4-5 |
|
Stage 4-5 Expressed Zygotic Zygotic starting stage 5 Blastoderm nuclei Subset blastoderm nuclei Ventral blastoderm nuclei Segmented pattern Segment polarity pattern Gap-gene pattern Weak expression (>41ms exp) Maternal Localized Subcellular localization patterns Exclusionary patterns Pole cell exclusion Embryonic localization patterns Degraded Degraded completely stage 5 Degradation maternal transcripts |
| stage 6-7 |
|
Stage 6-7 Expressed Zygotic Blastoderm nuclei Subset blastoderm nuclei |
| stage 8-9 |
|
Stage 8-9 Expressed Zygotic Blastoderm nuclei Subset blastoderm nuclei Segmented pattern Pair-rule pattern |
Larva
| Area | Images | Terms |
|---|
Adult
| Area | Images | Terms |
|---|
Comments
| insitu done in 2006 by Eric's group. |
| Need more images to get the full story. |
Embryo
| Area | Images | Terms |
|---|---|---|
| stage 1-3 |
|
Stage 1-3 Expressed Ubiquitous Medium expression (21-40ms exp) Maternal |
| stage 4-5 |
|
Stage 4-5 Expressed Zygotic Zygotic starting stage 4 Blastoderm nuclei Subset blastoderm nuclei Segmented pattern Pair-rule pattern Medium expression (21-40ms exp) Maternal Localized Subcellular localization patterns Exclusionary patterns Pole cell exclusion Apical exclusion Embryonic localization patterns Degraded Degraded completely stage 4 Degradation maternal transcripts |
| stage 6-7 |
|
Stage 6-7 Expressed Zygotic Blastoderm nuclei Subset blastoderm nuclei Segmented pattern Pair-rule pattern Strong expression (1-20ms exp) Localized Subcellular localization patterns Basal localization Basal enrichment Local terms for zygotic transcripts |
| stage 8-9 |
|
Stage 8-9 Expressed Zygotic Blastoderm nuclei Subset blastoderm nuclei Segmented pattern Pair-rule pattern Expression in ectoderm Expression in amnioserosa Strong expression (1-20ms exp) |
| stage 10-17 |
|
Stage 10-17 Expressed Zygotic Segmented pattern Ectoderm Localized |
Larva
| Area | Images | Terms |
|---|
Adult
| Area | Images | Terms |
|---|
Comments
Embryo
| Area | Images | Terms |
|---|---|---|
| stage 1-3 |
|
Stage 1-3 Expressed Ubiquitous Maternal |
| stage 4-5 |
|
Stage 4-5 Expressed Zygotic Blastoderm nuclei Subset blastoderm nuclei Segmented pattern Pair-rule pattern Ubiquitous Localized Subcellular localization patterns Ventral localization Dorsal localization Cytoplasmic foci |
| stage 6-7 |
|
Stage 6-7 Expressed Zygotic Blastoderm nuclei Subset blastoderm nuclei Segmented pattern Pair-rule pattern Localized Subcellular localization patterns Cytoplasmic foci Embryonic localization patterns Ventral localization Dorsal localization |
| stage 8-9 |
|
Stage 8-9 Expressed Zygotic Blastoderm nuclei Subset blastoderm nuclei Segmented pattern Pair-rule pattern Expression in ectoderm Localized Subcellular localization patterns Cytoplasmic foci Embryonic localization patterns Ventral localization Dorsal localization |
| stage 10-17 |
|
Stage 10-17 Expressed Zygotic Sensory system Head Head epidermis Ectoderm CNS Ventral nerve cord Foci - VNC Brain Localized Subcellular localization patterns Foci Small Foci Small Foci in CNS Small Foci in Brain |
Larva
| Area | Images | Terms |
|---|
Adult
| Area | Images | Terms |
|---|
Comments
| -performed via HCR-FISH using 3 probe sets targeting the RA isoform transcript |
Embryo
| Area | Images | Terms |
|---|---|---|
| stage 1-3 |
|
Stage 1-3 Expressed Ubiquitous Maternal |
| stage 4-5 |
|
Stage 4-5 Expressed Zygotic Blastoderm nuclei Subset blastoderm nuclei Segmented pattern Pair-rule pattern Localized Subcellular localization patterns Ventral localization Posterior localization Dorsal localization Anterior localization |
| stage 6-7 |
|
Stage 6-7 Expressed Zygotic Blastoderm nuclei Subset blastoderm nuclei Segmented pattern Pair-rule pattern Localized Posterior localization Embryonic localization patterns Ventral localization Dorsal localization Anterior localization |
| stage 8-9 |
|
Stage 8-9 Expressed Zygotic Blastoderm nuclei Subset blastoderm nuclei Segmented pattern Pair-rule pattern Localized Embryonic localization patterns Ventral localization Posterior localization Germ band localization Dorsal localization Anterior localization |
| stage 10-17 |
|
Stage 10-17 Expressed Zygotic Sensory system Head Head epidermis Ectoderm |
Larva
| Area | Images | Terms |
|---|
Adult
| Area | Images | Terms |
|---|
Comments
| -performed via HCR-FISH using 3 probe sets targeting the RA isoform transcript |
Embryo
| Area | Images | Terms |
|---|---|---|
| stage 1-3 |
|
Stage 1-3 Expressed Ubiquitous Maternal Localized Subcellular localization patterns Cytoplasmic foci |
| stage 4-5 |
|
Stage 4-5 Expressed Zygotic Zygotic starting stage 5 Localized Subcellular localization patterns Ventral localization Basal localization Basal enrichment Degraded Degradation maternal transcripts |
| stage 6-7 |
|
Stage 6-7 Expressed Zygotic Blastoderm nuclei Subset blastoderm nuclei Expression in ectoderm Localized Subcellular localization patterns Nuclei-associated localization Perinuclear localization Perinuclear subset of nuclei Perinuclear around blastoderm nuclei Basal localization Embryonic localization patterns Ventral localization |
| stage 8-9 |
|
Stage 8-9 Expressed Zygotic Blastoderm nuclei Subset blastoderm nuclei Ventral blastoderm nuclei Segmented pattern Pair-rule pattern Expression in neuroblasts Expression in ectoderm Dorsal blastoderm nuclei Anterior blastoderm nuclei Localized Subcellular localization patterns Cytoplasmic foci Embryonic localization patterns Posterior localization Dorsal localization |
| stage 10-17 |
|
Stage 10-17 Expressed Zygotic Sensory system PNS Neuroblasts Polarized Neuroblasts Head Head epidermis Ectoderm CNS Ventral nerve cord Polarized VNC Perinuclear VNC Brain Localized Subcellular localization patterns Foci Small Foci Small Foci in ectoderm |
Larva
| Area | Images | Terms |
|---|
Adult
| Area | Images | Terms |
|---|
Comments
| -performed via HCR-FISH using 3 probe sets targeting the RA transcript isoform |
| -neat marker for neural precursor formation, appears to not be expressed past stage 13-14 except for 4 small points near the dorsal-posterior region of the ectoderm (possibly tip cells of the Malpighian tubules); clear stomatogastric nervous system primordium expression |
| -images are from two separate experiments under identical conditions for better coverage |
Embryo
| Area | Images | Terms |
|---|---|---|
| stage 1-3 |
|
Stage 1-3 Non-Expressed |
| stage 4-5 |
|
Stage 4-5 Expressed Zygotic Zygotic starting stage 5 Blastoderm nuclei Subset blastoderm nuclei Segmented pattern Gap-gene pattern Posterior blastoderm nuclei Anterior blastoderm nuclei Medium expression (21-40ms exp) |
| stage 6-7 |
|
Stage 6-7 Expressed Zygotic Yolk Nuclei Subset yolk nuclei Posterior yolk nuclei Anterior yolk nuclei Blastoderm nuclei Subset blastoderm nuclei Segmented pattern Pair-rule pattern Gap-gene pattern Medium expression (21-40ms exp) Localized Subcellular localization patterns Cytoplasmic foci Basal localization Basal enrichment Embryonic localization patterns |
| stage 8-9 |
|
Stage 8-9 Expressed Zygotic Blastoderm nuclei Subset blastoderm nuclei Segmented pattern Segment polarity pattern Pair-rule pattern Medium expression (21-40ms exp) Localized Subcellular localization patterns Cytoplasmic foci |
| stage 10-17 |
|
Stage 10-17 Expressed Zygotic Tracheal system Tracheal pits Tracheal lumen Specific tracheal branches Segmented pattern Posterior spiracles Specific posterior spiracle pattern Muscles-embryo Visceral mesoderm Specific visceral mesoderm pattern Hindgut Specific hindgut area or cells Midgut hindgut border Head Ectoderm CNS Ventral nerve cord Nuclear - VNC Foci - VNC Brain Blastoderm nuclei Atrium Localized Subcellular localization patterns Nuclei-associated localization Nuclear in CNS Accumulation nuclear subregion Accumulation entire nucleus Foci Small Foci Small Foci in ectoderm Basal enrichment Basal in hindgut |
Larva
| Area | Images | Terms |
|---|---|---|
| intestine |
|
3rd Instar Larval Tissues Intestine Expressed in proventriculus Subcellular localization in proventriculus Proventriculus foci Nascent transcript in proventriculus Expressed in hindgut Subcellular localization in hindgut Nuclear in hindgut Hindgut - subnuclear localization Nascent transcript in hindgut Hindgut allover |
| imaginal discs |
|
3rd Instar Larval Tissues Imaginal discs Expressed in leg discs Expressed in eye disc Eye disc photo-receptors Eye disc particular pattern |
| nervous system |
|
3rd Instar Larval Tissues Nervous system Expressed in brain lobes Optic lobe Brain lobes - Significant area Brain lobes - Foci or dots |
| ovary and testis |
|
Adult Tissues Male reproductive tissues Testis 3rd Instar Larval Tissues Larval Ovary and Testis-Larva Specific testis expression localization Larval spermatocytes |
Adult
| Area | Images | Terms |
|---|
Comments
| Very interesting patterns! |
| Pre-pair rule pattern |
| Good probe on gel. Borderline between 'not expressed' and 'low expression' at early stages. Very interesting patterns! |
Embryo
| Area | Images | Terms |
|---|---|---|
| stage 1-3 |
|
Stage 1-3 Expressed Ubiquitous Maternal |
| stage 4-5 |
|
Stage 4-5 Expressed Maternal Localized Subcellular localization patterns Exclusionary patterns Pole cell exclusion Embryonic localization patterns Degraded Degraded partially stage 4 Degradation maternal transcripts |
| stage 6-7 |
|
Stage 6-7 Expressed Zygotic Zygotic starting stage 6 Blastoderm nuclei Subset blastoderm nuclei Segmented pattern Localized Subcellular localization patterns Nuclei-associated localization Perinuclear localization Perinuclear subset of nuclei Perinuclear around blastoderm nuclei Intranuclear accumulation Accumulation nuclear subregion Cytoplasmic foci |
| stage 8-9 |
|
Stage 8-9 Expressed Zygotic Blastoderm nuclei Subset blastoderm nuclei Segmented pattern Pair-rule pattern Expression in ectoderm |
| stage 10-17 |
|
Stage 10-17 Expressed Zygotic Tracheal system Tracheal pits Segmented pattern Muscles-embryo Visceral mesoderm Specific visceral mesoderm pattern Head Ectoderm Blastoderm nuclei Atrium Localized Subcellular localization patterns Foci Small Foci Small Foci in tracheal cells Small Foci in head Small Foci in ectoderm |
Larva
| Area | Images | Terms |
|---|
Adult
| Area | Images | Terms |
|---|
Comments
| I wish we had more detailed photos... insitu done many years ago... re-annotated 2014 (rw) |
| Inside some nuclei. |
| Re-annotated 2014. |
Embryo
| Area | Images | Terms |
|---|---|---|
| stage 1-3 |
|
Stage 1-3 Expressed Weak expression (>41ms exp) Ubiquitous Maternal Localized Subcellular localization patterns Cytoplasmic foci |
| stage 4-5 |
|
Stage 4-5 Expressed Zygotic Zygotic starting stage 4 Yolk nuclei Subset yolk nuclei Random yolk nuclei Blastoderm nuclei Subset blastoderm nuclei Segmented pattern Pair-rule pattern Random blastoderm nuclei Weak expression (>41ms exp) Localized Subcellular localization patterns Exclusionary patterns Pole cell exclusion Apical localization Apical enrichment Apical clusters Embryonic localization patterns |
| stage 6-7 |
|
Stage 6-7 Expressed Zygotic Blastoderm nuclei Subset blastoderm nuclei Segmented pattern Pair-rule pattern Weak expression (>41ms exp) Localized Subcellular localization patterns Exclusionary patterns Apical localization Apical enrichment Apical clusters Embryonic localization patterns Exclusionary patterns Pole cell exclusion |
| stage 8-9 |
|
Stage 8-9 Expressed Zygotic Blastoderm nuclei Subset blastoderm nuclei Segmented pattern Pair-rule pattern Expression in neuroblasts Expression in ectoderm Localized Subcellular localization patterns Apical localization Apical enrichment Embryonic localization patterns |
| stage 10-17 |
|
Stage 10-17 Expressed Zygotic Tracheal system Tracheal pits Tracheal lumen Specific tracheal branches Dorsal trunk Neuroblasts Muscles-embryo Visceral mesoderm Specific visceral mesoderm pattern Midgut Hindgut Head Ectoderm Blastoderm nuclei Atrium Amnioserosa Localized Subcellular localization patterns Foci Small Foci Small Foci in other tissues Small Foci in midgut Small Foci in hindgut Small Foci in head Small Foci in ectoderm Small Foci in amnioserosa Apical enrichment Apical enriched hindgut |
Larva
| Area | Images | Terms |
|---|---|---|
| fat body |
|
3rd Instar Larval Tissues Fat body Subcellular Localization - Fat body Fat body - Perinuclear localization Fat body - Nuclear localization Fat body - Subnuclear localization Nascent transcript in fat body Expressed in fat body Fat body allover - Ubiquitous |
| intestine |
|
3rd Instar Larval Tissues Intestine Expressed in proventriculus Subcellular localization in proventriculus Proventriculus foci Nascent transcript in proventriculus Expressed in midgut Subcellular localization in midgut Midgut - Nuclear Midgut - Subnuclear Nascent transcript in midgut Midgut allover Expressed in hindgut Hindgut - Midgut border Expressed in gastric caeca Gastric caeca allover |
| nervous system |
|
3rd Instar Larval Tissues Nervous system Expressed in brain lobes Brain lobes - Significant area |
| ovary and testis |
|
3rd Instar Larval Tissues Larval Ovary and Testis-Larva Ovary allover Expressed in Ovary |
| muscles |
|
3rd Instar Larval Tissues Larval Muscles - larva Expressed in larval muscles-Larva Sub-cellular localization in muscles-Larva Larval Muscles - Cytoplasmic foci Muscles allover - Larva |
Adult
| Area | Images | Terms |
|---|
Comments
| Clear patches of cells close to the invaginating tracheal placodes. |
| Good probe on gel. RNA is allover, with some small but clear foci. |
Embryo
| Area | Images | Terms |
|---|---|---|
| stage 1-3 |
|
Stage 1-3 Non-Expressed |
| stage 4-5 |
|
Stage 4-5 Expressed Weak expression (>41ms exp) Ubiquitous |
| stage 6-7 |
|
Stage 6-7 Expressed Zygotic Blastoderm nuclei Subset blastoderm nuclei Segmented pattern Pair-rule pattern Ubiquitous Localized Subcellular localization patterns Cytoplasmic foci |
| stage 8-9 |
|
Stage 8-9 Expressed Zygotic Blastoderm nuclei Subset blastoderm nuclei Segmented pattern Pair-rule pattern Ubiquitous Localized Embryonic localization patterns Germ band localization |
| stage 10-17 |
|
Stage 10-17 Expressed Zygotic CNS Ventral nerve cord Brain Strong expression (1-20ms exp) |
Larva
| Area | Images | Terms |
|---|
Adult
| Area | Images | Terms |
|---|
Comments
| -performed via HCR-FISH using 3 probe sets targeting common exons |
Embryo
| Area | Images | Terms |
|---|---|---|
| stage 1-3 |
|
Stage 1-3 Non-Expressed Expressed Ubiquitous |
| stage 4-5 |
|
Stage 4-5 Expressed Zygotic Zygotic starting stage 5 Blastoderm nuclei Subset blastoderm nuclei Segmented pattern Pair-rule pattern Localized Subcellular localization patterns Ventral localization Dorsal localization Cytoplasmic foci |
| stage 6-7 |
|
Stage 6-7 Expressed Zygotic Blastoderm nuclei Subset blastoderm nuclei Segmented pattern Pair-rule pattern Localized Embryonic localization patterns Ventral localization Dorsal localization |
| stage 8-9 |
|
Stage 8-9 Expressed Zygotic Blastoderm nuclei Subset blastoderm nuclei Segmented pattern Pair-rule pattern Localized Embryonic localization patterns Ventral localization Germ band localization Dorsal localization |
| stage 10-17 |
|
Stage 10-17 Expressed Zygotic Sensory system Segmented pattern Hindgut Ectoderm Polarized Ectoderm CNS Ventral nerve cord Polarized VNC Brain |
Larva
| Area | Images | Terms |
|---|
Adult
| Area | Images | Terms |
|---|
Comments
| -performed via HCR-FISH using 3 probe sets targeting the RA isoform transcript |
Embryo
| Area | Images | Terms |
|---|---|---|
| stage 1-3 |
|
Stage 1-3 Non-Expressed |
| stage 4-5 |
|
Stage 4-5 Expressed Zygotic Yolk nuclei Blastoderm nuclei Subset blastoderm nuclei Segmented pattern Pair-rule pattern Localized Subcellular localization patterns Dorsal localization |
| stage 6-7 |
|
Stage 6-7 Expressed Zygotic Blastoderm nuclei Subset blastoderm nuclei Segmented pattern Pair-rule pattern Expression in ectoderm Expression in API Localized Embryonic localization patterns Ventral localization Dorsal localization |
| stage 8-9 |
|
Stage 8-9 Expressed Zygotic Blastoderm nuclei Subset blastoderm nuclei Segmented pattern Pair-rule pattern Expression in ectoderm Expression in API Localized Embryonic localization patterns Ventral localization Germ band localization Dorsal localization |
| stage 10-17 |
|
Stage 10-17 Expressed Zygotic Sensory system Midgut Head Head epidermis Ectoderm CNS Ventral nerve cord Foci - VNC Axons Brain |
Larva
| Area | Images | Terms |
|---|
Adult
| Area | Images | Terms |
|---|
Comments
| -performed via HCR-FISH using 3 probe sets targeting the RA isoform transcript |
| -Most signals in the late stages are likely imaginal discs |
| -6 "ring"-like structures on the anterior ventral side are likely the leg discs -2 circles above leg discs on each side are likely wing discs -Band posterior to the VNC is likely the genital disc -small dots located on the late stage midgut may be intestinal stem cells (ISCs) |
| -Other signals in late stages likely correspond to imaginal discs which we cannot identify based on our resolution |
Embryo
| Area | Images | Terms |
|---|---|---|
| stage 1-3 |
|
Stage 1-3 Expressed Ubiquitous Strong expression (1-20ms exp) Maternal |
| stage 4-5 |
|
Stage 4-5 Expressed Zygotic Zygotic starting stage 4 Blastoderm nuclei Subset blastoderm nuclei Segmented pattern Gap-gene pattern Posterior blastoderm nuclei Anterior blastoderm nuclei Localized Subcellular localization patterns Exclusionary patterns Pole cell exclusion Cytoplasmic foci Basal localization Basal enrichment Embryonic localization patterns |
| stage 6-7 |
|
Stage 6-7 Expressed Zygotic Blastoderm nuclei Subset blastoderm nuclei Expression in mesoderm Localized Subcellular localization patterns Basal localization Basal enrichment Embryonic localization patterns |
| stage 8-9 |
|
Stage 8-9 Expressed Zygotic Blastoderm nuclei Subset blastoderm nuclei Ventral blastoderm nuclei Segmented pattern Pair-rule pattern Localized Subcellular localization patterns Exclusionary patterns Apical exclusion Basal localization Basal enrichment Embryonic localization patterns |
| stage 10-17 |
|
Stage 10-17 Expressed Zygotic Yolk nuclei Perinuclear around yolk nuclei Tracheal system Tracheal pits PNS Muscles-embryo Visceral mesoderm Head Ectoderm CNS Ventral nerve cord Foci - VNC Blastoderm nuclei Atrium Localized Subcellular localization patterns Perinuclear localization Foci Small Foci Small Foci in PNS Small Foci in CNS Cell junction associated |
Larva
| Area | Images | Terms |
|---|
Adult
| Area | Images | Terms |
|---|
Comments
| Interesting |
| Low probe on gel. |
| Interesting patterns. Salivary glands, maybe non-specific. |
| Interesting |
Embryo
| Area | Images | Terms |
|---|---|---|
| stage 1-3 |
|
Stage 1-3 Expressed Maternal |
| stage 4-5 |
|
Stage 4-5 Expressed Zygotic Blastoderm nuclei Subset blastoderm nuclei Segmented pattern Pair-rule pattern Strong expression (1-20ms exp) Localized Subcellular localization patterns Ventral localization Exclusionary patterns Pole cell exclusion Dorsal localization |
| stage 6-7 |
|
Stage 6-7 Expressed Zygotic Blastoderm nuclei Subset blastoderm nuclei Ventral blastoderm nuclei Segmented pattern Pair-rule pattern Expression in ectoderm Strong expression (1-20ms exp) Localized Embryonic localization patterns Ventral localization Exclusionary patterns Pole cell exclusion Dorsal localization |
| stage 8-9 |
|
Stage 8-9 Expressed Zygotic Blastoderm nuclei Subset blastoderm nuclei Segmented pattern Pair-rule pattern Strong expression (1-20ms exp) Localized Embryonic localization patterns Ventral localization Germ band localization |
| stage 10-17 |
|
Stage 10-17 Expressed Zygotic Tracheal system Tracheal pits Segmented pattern PNS Optic lobes primordium Head Head epidermis Ectoderm CNS Brain Strong expression (1-20ms exp) |
Larva
| Area | Images | Terms |
|---|
Adult
| Area | Images | Terms |
|---|
Comments
| -performed via HCR-FISH using 3 probe sets targeting the RA isoform transcript |
Embryo
| Area | Images | Terms |
|---|---|---|
| stage 1-3 |
|
Stage 1-3 Non-Expressed |
| stage 4-5 |
|
Stage 4-5 Non-Expressed |
| stage 6-7 |
|
Stage 6-7 Expressed Zygotic Zygotic starting stage 6 Blastoderm nuclei Subset blastoderm nuclei Segmented pattern Pair-rule pattern Expression in ectoderm Localized Embryonic localization patterns Ventral localization Dorsal localization |
| stage 8-9 |
|
Stage 8-9 Expressed Zygotic Blastoderm nuclei Subset blastoderm nuclei Segmented pattern Pair-rule pattern Expression in ectoderm Localized Embryonic localization patterns Ventral localization Dorsal localization |
| stage 10-17 |
|
Stage 10-17 Expressed Zygotic Tracheal system Tracheal pits Sensory system Proventriculus Hindgut Specific hindgut area or cells Foregut Ectoderm Anal pad |
Larva
| Area | Images | Terms |
|---|
Adult
| Area | Images | Terms |
|---|
Comments
| -performed via HCR-FISH using 3 probe sets targeting common exons |
| -Potential weak ventral nerve cord signal |
Embryo
| Area | Images | Terms |
|---|---|---|
| stage 1-3 |
|
Stage 1-3 Expressed Medium expression (21-40ms exp) Maternal Localized Embryonic localization patterns Exclusionary patterns Pole plasm excluded |
| stage 4-5 |
|
Stage 4-5 Expressed Zygotic Zygotic starting stage 5 Blastoderm nuclei Subset blastoderm nuclei Segmented pattern Gap-gene pattern Anterior blastoderm nuclei Maternal Localized Subcellular localization patterns Exclusionary patterns Yolk cortex exclusion Pole cell exclusion Apical exclusion Apical localization Apical enrichment Diffuse apical localization Embryonic localization patterns Degraded Degraded partially stage 4 Degraded completely stage 5 Degradation maternal transcripts |
| stage 6-7 |
|
Stage 6-7 Expressed Zygotic Blastoderm nuclei Subset blastoderm nuclei Segmented pattern Gap-gene pattern Anterior blastoderm nuclei Localized Subcellular localization patterns Apical localization Apical enrichment Diffuse apical localization Embryonic localization patterns |
| stage 8-9 |
|
Stage 8-9 Expressed Zygotic Blastoderm nuclei Subset blastoderm nuclei Segmented pattern Pair-rule pattern Expression in neuroblasts |
| stage 10-17 |
|
Stage 10-17 Expressed Zygotic Tracheal system Tracheal pits Specific tracheal branches Sensory system Segmented pattern PNS Midgut CNS Ventral nerve cord Axons Blastoderm nuclei Localized Subcellular localization patterns Perinuclear localization Perinuclear around PNS nuclei Perinuclear around CNS nuclei Foci Small Foci Small Foci in PNS Small Foci in midgut Cell extensions or 'podia' |
Larva
| Area | Images | Terms |
|---|
Adult
| Area | Images | Terms |
|---|
Comments
Embryo
| Area | Images | Terms |
|---|---|---|
| stage 1-3 |
|
Stage 1-3 Expressed Ubiquitous Maternal Localized Subcellular localization patterns Cytoplasmic foci |
| stage 4-5 |
|
Stage 4-5 Expressed Ubiquitous Maternal Localized Subcellular localization patterns Exclusionary patterns Pole cell exclusion Cytoplasmic foci |
| stage 6-7 |
|
Stage 6-7 Expressed Zygotic Zygotic starting stage 6 Blastoderm nuclei Subset blastoderm nuclei Ventral blastoderm nuclei Segmented pattern Pair-rule pattern Expression in ectoderm Ubiquitous Maternal Localized Yolk plasm localization Yolk cortex localization Yolk cortex enrichment Subcellular localization patterns Nuclei-associated localization Perinuclear localization Perinuclear subset of nuclei Perinuclear around blastoderm nuclei Intranuclear accumulation Accumulation in subset nuclei Cytoplasmic foci Basal localization Basal enrichment Apical localization Apical enrichment Embryonic localization patterns Ventral localization Degraded Degraded partially stage 6 Degradation maternal transcripts |
| stage 8-9 |
|
Stage 8-9 Expressed Zygotic Blastoderm nuclei Subset blastoderm nuclei Segmented pattern Pair-rule pattern Expression in ectoderm Localized Subcellular localization patterns Perinuclear localization Perinuclear around blastoderm nuclei Embryonic localization patterns Ventral localization Dorsal localization |
| stage 10-17 |
|
Stage 10-17 Expressed Zygotic Ring gland Head Head epidermis Ectoderm Localized Subcellular localization patterns Perinuclear localization Perinuclear around ectoderm nuclei Foci Small Foci Small Foci in ectoderm |
Larva
| Area | Images | Terms |
|---|
Adult
| Area | Images | Terms |
|---|
Comments
| -performed via HCR-FISH using 6 probe sets targeting the RA isoform transcript (previously tested with 3 and signals bordered between expressed and non-expressed) |
| -exceptional expression patterning in early epidermis and ring gland |
| -probes are from two different plates (3 sets from each plate); SH-HCR-Plate-1 and SH-HCR-Plate-4 |
Embryo
| Area | Images | Terms |
|---|---|---|
| stage 1-3 |
|
Stage 1-3 Expressed Weak expression (>41ms exp) Ubiquitous Maternal |
| stage 4-5 |
|
Stage 4-5 Expressed Zygotic Zygotic starting stage 4 Blastoderm nuclei Subset blastoderm nuclei Segmented pattern Pair-rule pattern Strong expression (1-20ms exp) Localized Subcellular localization patterns Nuclei-associated localization Perinuclear localization Perinuclear subset of nuclei Perinuclear around blastoderm nuclei Exclusionary patterns Pole cell exclusion Cell division apparatus Chromatin associated metaphase Apical localization Apical enrichment Diffuse apical localization Local terms for zygotic transcripts Embryonic localization patterns |
| stage 6-7 |
|
Stage 6-7 Expressed Zygotic Blastoderm nuclei Subset blastoderm nuclei Segmented pattern Pair-rule pattern Strong expression (1-20ms exp) Localized Subcellular localization patterns Exclusionary patterns Apical localization Apical enrichment Apical clusters Local terms for zygotic transcripts Embryonic localization patterns Exclusionary patterns Pole cell exclusion |
| stage 8-9 |
|
Stage 8-9 Expressed Zygotic Blastoderm nuclei Subset blastoderm nuclei Segmented pattern Pair-rule pattern Expression in neuroblasts Expression in ectoderm Strong expression (1-20ms exp) Localized Subcellular localization patterns Apical localization Apical enrichment Apical Localization Neuroblasts |
| stage 10-17 |
|
Stage 10-17 Expressed Zygotic Segmented pattern PNS CNS Ventral nerve cord Brain Blastoderm nuclei Localized Subcellular localization patterns Perinuclear localization Perinuclear around PNS nuclei Perinuclear around CNS nuclei |
Larva
| Area | Images | Terms |
|---|---|---|
| fat body |
|
3rd Instar Larval Tissues Fat body Expressed in fat body Fat body allover - Ubiquitous |
| intestine |
|
3rd Instar Larval Tissues Intestine Expressed in proventriculus Subcellular localization in proventriculus Proventriculus foci Proventriculus - Few foci Proventriculus allover Expressed in malpighian tubules Subcellular localization in malpighian tubules Malpighian tubules - foci Malpighian tubules allover Expressed in hindgut Subcellular localization in hindgut Hindgut foci Expressed in gastric caeca Subcellular localization in gastric caeca Gastric caeca foci Gastric caeca allover Expressed in esophagus |
| imaginal discs |
|
3rd Instar Larval Tissues Imaginal discs Expressed in wing disc Wing disc pouch Expressed in eye disc Morphogenetic furrow Eye disc few cells - dots Expressed in antennal disc Antennal disc few cells - dots |
| nervous system |
|
3rd Instar Larval Tissues Nervous system Not expressed in nervous system |
| salivary gland |
|
3rd Instar Larval Tissues Salivary gland Subcellular localization in salivary gland Salivary gland - Cytoplasmic foci Salivary gland - Small foci Expressed in salivary glands Salivary glands allover |
| muscles |
|
3rd Instar Larval Tissues Larval Muscles - larva Expressed in larval muscles-Larva Sub-cellular localization in muscles-Larva Larval Muscles - Cytoplasmic foci |
| lymph glands and ring glands |
|
3rd Instar Larval Tissues Lymph Glands and Ring Glands Ring gland Ring gland - Subcellular localization Ring gland - Cytoplasmic foci Expressed in ring gland Ring gland allover Lymph Glands Subcellular localization in lymph glands Lymph Glands - Cytoplasmic foci Expressed in lymph glands Lymph glands all over |
Adult
| Area | Images | Terms |
|---|
Comments
Embryo
| Area | Images | Terms |
|---|---|---|
| stage 1-3 |
|
Stage 1-3 Expressed Weak expression (>41ms exp) Ubiquitous Maternal |
| stage 4-5 |
|
Stage 4-5 Expressed Weak expression (>41ms exp) Maternal Localized Subcellular localization patterns Yolk plasm localization Yolk plasm enrichment Yolk cortex localization Yolk cortex enrichment Pole cell localization Nuclei-associated localization Perinuclear localization Perinuclear subset of nuclei Perinuclear around pole cell nuclei Exclusionary patterns Apical exclusion Basal localization Basal enrichment Embryonic localization patterns |
| stage 6-7 |
|
Stage 6-7 Expressed Weak expression (>41ms exp) Maternal Localized Yolk cortex localization Yolk cortex enrichment Subcellular localization patterns Exclusionary patterns Embryonic localization patterns Exclusionary patterns Pole cell exclusion |
| stage 8-9 |
|
Stage 8-9 Expressed Zygotic Blastoderm nuclei Subset blastoderm nuclei Segmented pattern Pair-rule pattern Expression in ectoderm |
| stage 10-17 |
|
Stage 10-17 Expressed Zygotic Yolk nuclei Inside Yolk nuclei Tracheal system Tracheal lumen Salivary glands Salivary glands lumen Posterior spiracles Pharynx Muscles-embryo Muscles - subregion Midgut Hindgut Specific hindgut area or cells CNS Ventral nerve cord Foci - VNC Axons Blastoderm nuclei Localized Subcellular localization patterns Nuclei-associated localization Accumulation nuclear subregion Foci Small Foci Small Foci in muscle cells Small Foci in hindgut Small Foci in CNS Cell extensions or 'podia' Basal enrichment Basal in hindgut |
Larva
| Area | Images | Terms |
|---|
Adult
| Area | Images | Terms |
|---|
Comments
Embryo
| Area | Images | Terms |
|---|---|---|
| stage 1-3 |
Stage 1-3 Non-Expressed |
|
| stage 4-5 |
Stage 4-5 Non-Expressed |
|
| stage 6-7 |
Stage 6-7 Non-Expressed |
|
| stage 8-9 |
|
Stage 8-9 Expressed Zygotic Zygotic starting stage 8 Blastoderm nuclei Subset blastoderm nuclei Segmented pattern Pair-rule pattern Expression in ectoderm Localized Subcellular localization patterns Nuclei-associated localization Accumulation in subset nuclei Cytoplasmic foci Embryonic localization patterns Ventral localization Dorsal localization |
| stage 10-17 |
|
Stage 10-17 Expressed Zygotic Tracheal system Tracheal pits Segmented pattern Posterior spiracles Head Head epidermis Ectoderm Polarized Ectoderm Ubiquitous Localized Subcellular localization patterns Nuclei-associated localization Nuclear in ectoderm Foci Small Foci Small Foci in ectoderm Bigger Foci Apical enrichment Apical ectoderm |
Larva
| Area | Images | Terms |
|---|
Adult
| Area | Images | Terms |
|---|
Comments
| -performed via HCR-FISH using 6 probe sets targeting the RD isoform transcript (previously tested with 3 and was not detected) |
| -probes are from two different plates (3 sets from each plate); SH-HCR-Plate-1 and SH-HCR-Plate-4 |
| -this gene is very weakly expressed and more probe sets (if using HCR-FISH) should be considered for future retests |
Embryo
| Area | Images | Terms |
|---|---|---|
| stage 1-3 |
|
Stage 1-3 Non-Expressed |
| stage 4-5 |
|
Stage 4-5 Expressed Zygotic Zygotic starting stage 4 Blastoderm nuclei Subset blastoderm nuclei Single stripe Segmented pattern Pair-rule pattern |
| stage 6-7 |
|
Stage 6-7 Expressed Zygotic Blastoderm nuclei Subset blastoderm nuclei Segmented pattern Pair-rule pattern Localized Subcellular localization patterns Basal localization Basal enrichment |
| stage 8-9 |
|
Stage 8-9 Expressed Zygotic Blastoderm nuclei Subset blastoderm nuclei Segmented pattern Pair-rule pattern Localized Subcellular localization patterns Cytoplasmic foci |
| stage 10-17 |
|
Stage 10-17 Expressed Zygotic Segmented pattern Head Ectoderm Blastoderm nuclei Localized Subcellular localization patterns Foci Small Foci Small Foci in ectoderm |
Larva
| Area | Images | Terms |
|---|---|---|
| fat body |
|
3rd Instar Larval Tissues Fat body Subcellular Localization - Fat body Cytoplasmic foci-fat body Expressed in fat body Fat body allover - Ubiquitous |
| intestine |
|
3rd Instar Larval Tissues Intestine Not expressed in the intestine |
| nervous system |
|
3rd Instar Larval Tissues Nervous system Expressed in brain lobes Brain lobes - Foci or dots |
| salivary gland |
|
3rd Instar Larval Tissues Salivary gland Not expressed in salivary glands |
| muscles |
|
3rd Instar Larval Tissues Larval Muscles - larva Expressed in larval muscles-Larva Sub-cellular localization in muscles-Larva Larval Muscles - Cytoplasmic foci Muscles allover - Larva |
Adult
| Area | Images | Terms |
|---|---|---|
| Male reproductive tissues |
|
Adult Tissues Male reproductive tissues Testis Testis Cell type and stage - TE Terminal Epithelium - TE Cytoplasmic in terminal epithelium - TE Spermatogonium-TE Cytoplasmic in spermatogonium-TE Spermatocytes -TE Cytoplasmic in Spermatocytes - TE Spermatids -TE Individualizing Spermatids - TE Cytoplasmic in individualizing spermatids - TE Elongating Spermatids - TE Cytoplasmic in elongating spermatids-TE Early elongating spermatids-TE Cytoplasmic in early elongating spermatids Cyst cells -TE Tail cyst cell - TE Elongating Tail Cyst Cell - TE Elongating Tail Cyst Cell Cytoplasm - TE Subcellularly localized - TE Expression level-TE Expressed Low - TE Distal tip region-TE Expressed in distal tip region - TE Lower expression in tip region Seminal Vesicle Subcellularly localized - SV Lumenal-SV Scattered Foci - SV Cell type - SV Cytoplasmic-SV Membrane enriched - SV Cytoplasmic Foci - SV Ejaculatory Duct Subcellularly localized - ED Expression level-ED Expressed Low - ED Cell type - ED Cytoplasmic-ED Membrane enriched - ED Accessory Gland Subcellularly localized - AG Lumenal - AG Non-particulate - AG Expression level-AG Expressed Low - AG Cell type - AG Secondary cells - AG Cytoplasmic-SC Main cells -AG Cytoplasmic-MC Membrane Enriched-MC |
Comments
| Small, clear foci. |
| Good probe on gel. Some photos from a different day. |
Embryo
| Area | Images | Terms |
|---|---|---|
| stage 1-3 |
|
Stage 1-3 Expressed Ubiquitous Maternal Localized Subcellular localization patterns Cytoplasmic foci |
| stage 4-5 |
|
Stage 4-5 Expressed Zygotic Blastoderm nuclei Subset blastoderm nuclei Ventral blastoderm nuclei Dorsal blastoderm nuclei Anterior blastoderm nuclei All blastoderm nuclei Transiently widespread Ubiquitous Localized Subcellular localization patterns Yolk plasm localization Yolk cortex localization Nuclei-associated localization Intranuclear accumulation Exclusionary patterns Cytoplasmic foci Basal localization Basal enrichment Apical localization Apical enrichment Discrete apical foci Degraded Degradation maternal transcripts |
| stage 6-7 |
|
Stage 6-7 Expressed Zygotic Zygotic starting stage 7 Blastoderm nuclei Subset blastoderm nuclei Ventral blastoderm nuclei Segmented pattern Pair-rule pattern Expression in mesoderm Expression in ectoderm Expression in API Dorsal blastoderm nuclei Anterior blastoderm nuclei All blastoderm nuclei Transiently widespread Localized Subcellular localization patterns Nuclei-associated localization Perinuclear localization Perinuclear subset of nuclei Perinuclear around blastoderm nuclei Intranuclear accumulation Accumulation in subset nuclei Cytoplasmic foci Embryonic localization patterns Ventral localization Dorsal localization |
| stage 8-9 |
|
Stage 8-9 Expressed Zygotic Blastoderm nuclei Subset blastoderm nuclei Segmented pattern Pair-rule pattern Expression in neuroblasts Expression in ectoderm Localized Subcellular localization patterns Perinuclear localization Perinuclear around blastoderm nuclei Nuclei-associated localization Accumulation in subset nuclei Cytoplasmic foci Embryonic localization patterns Ventral localization Posterior localization Germ band localization Dorsal localization Anterior localization |
| stage 10-17 |
|
Stage 10-17 Expressed Zygotic Segmented pattern Optic lobes primordium Neuroblasts Maxillary complex Head Head epidermis Ectoderm Dorsal vessel CNS Ventral nerve cord Perinuclear VNC Nuclear - VNC Foci - VNC Brain Localized Subcellular localization patterns Perinuclear localization Perinuclear around ectoderm nuclei Perinuclear around CNS nuclei Nuclei-associated localization Nuclear in ectoderm Nuclear in CNS Foci Small Foci Small Foci in head Small Foci in ectoderm Small Foci in CNS Small Foci in Brain |
Larva
| Area | Images | Terms |
|---|
Adult
| Area | Images | Terms |
|---|
Comments
| -performed via HCR-FISH using 3 probe sets targeting the RA transcript isoform |
| -very diverse and neat patterns at all stages |
Embryo
| Area | Images | Terms |
|---|---|---|
| stage 1-3 |
|
Stage 1-3 Expressed Weak expression (>41ms exp) Maternal Localized Subcellular localization patterns Cytoplasmic foci Embryonic localization patterns Yolk plasm localization Yolk plasm enrichment Exclusionary patterns Pole plasm excluded |
| stage 4-5 |
|
Stage 4-5 Expressed Zygotic Zygotic starting stage 4 Blastoderm nuclei Subset blastoderm nuclei Segmented pattern Pair-rule pattern Medium expression (21-40ms exp) Localized Subcellular localization patterns Apical localization Apical enrichment Apical clusters |
| stage 6-7 |
|
Stage 6-7 Expressed Zygotic Blastoderm nuclei Subset blastoderm nuclei Segmented pattern Pair-rule pattern Expression in ectoderm |
| stage 8-9 |
|
Stage 8-9 Expressed Zygotic Blastoderm nuclei Subset blastoderm nuclei Segmented pattern Pair-rule pattern Expression in neuroblasts Expression in ectoderm Localized Subcellular localization patterns Perinuclear localization Perinuclear around blastoderm nuclei Nuclei-associated localization Apical localization Apical enrichment Apical Localization Neuroblasts |
| stage 10-17 |
|
Stage 10-17 Expressed Zygotic Sensory system Segmented pattern Salivary glands Salivary glands lumen Ring gland Proventriculus PNS Pharynx Midgut Midgut subset Hindgut Specific hindgut area or cells Head Foregut Ectoderm Polarized Ectoderm CNS Ventral nerve cord Perinuclear VNC Brain Blastoderm nuclei Localized Subcellular localization patterns Perinuclear localization Perinuclear polarized Perinuclear around ectoderm nuclei Perinuclear around CNS nuclei Nuclei-associated localization Nuclear in ectoderm Accumulation entire nucleus |
Larva
| Area | Images | Terms |
|---|
Adult
| Area | Images | Terms |
|---|
Comments
| Neuroblast, interesting. |
| Nice stripes! |
| Lowish, good probe. Very nice insitu! |
Embryo
| Area | Images | Terms |
|---|---|---|
| stage 1-3 |
|
Stage 1-3 Non-Expressed |
| stage 4-5 |
|
Stage 4-5 Expressed Zygotic Zygotic starting stage 4 Blastoderm nuclei Subset blastoderm nuclei Ventral blastoderm nuclei Posterior blastoderm nuclei Anterior blastoderm nuclei Localized Subcellular localization patterns Ventral localization Posterior localization Nuclei-associated localization Perinuclear localization Perinuclear subset of nuclei Perinuclear around blastoderm nuclei Exclusionary patterns Yolk plasm exclusion Pole cell exclusion Cytoplasmic foci Basal localization Basal enrichment Apical localization Apical enrichment Diffuse apical localization Anterior localization |
| stage 6-7 |
|
Stage 6-7 Expressed Zygotic Blastoderm nuclei Subset blastoderm nuclei Ventral blastoderm nuclei Expression in mesoderm Expression in ectoderm Anterior blastoderm nuclei Localized Yolk cortex localization Yolk cortex enrichment Subcellular localization patterns Nuclei-associated localization Perinuclear localization Perinuclear subset of nuclei Perinuclear around blastoderm nuclei Exclusionary patterns Yolk cortex exclusion Basal localization Basal enrichment Apical localization Apical enrichment Diffuse apical localization Posterior localization Embryonic localization patterns Anterior localization |
| stage 8-9 |
|
Stage 8-9 Expressed Zygotic Blastoderm nuclei Subset blastoderm nuclei Segmented pattern Pair-rule pattern Expression in mesoderm Expression in ectoderm Expression in API Localized Subcellular localization patterns Perinuclear localization Perinuclear around blastoderm nuclei Cytoplasmic foci Basal localization Basal enrichment Embryonic localization patterns Ventral localization Germ band localization Dorsal localization Anterior localization Degraded Degraded partially stage 9 |
| stage 10-17 |
|
Stage 10-17 Expressed Zygotic Muscles-embryo Visceral mesoderm Specific visceral mesoderm pattern Muscles - subregion Hindgut Head Foregut Esophagus Ectoderm Localized Subcellular localization patterns Perinuclear localization Perinuclear around muscle nuclei |
Larva
| Area | Images | Terms |
|---|
Adult
| Area | Images | Terms |
|---|
Comments
| -retested using HCR-FISH 2025 for full coverage of late stage expression patterns |
| -performed using 3 probe pairs (HCR-FISH) against the RB isoform |
| -really interesting patterns! |