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Result Summary
| Number of genes | 29 | |
| Export | ||
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 |
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 |
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 Expression in mesoderm Weak expression (>41ms exp) Localized Subcellular localization patterns Cytoplasmic foci Embryonic localization patterns Dorsal localization |
| stage 10-17 |
|
Stage 10-17 Expressed Zygotic Muscles-embryo Visceral mesoderm Specific visceral mesoderm pattern Midgut Hemocytes Foregut Fat body Esophagus CNS Ventral nerve cord Foci - VNC Brain Weak expression (>41ms exp) 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 RC isoform transcript |
| -very nice hemocyte pattern; possible glial cell pattern in CNS; possible ring gland or lymph gland signal on the dorsal region of head; pericardial cells are reported but not clearly observed in this sample |
Embryo
| Area | Images | Terms |
|---|---|---|
| stage 1-3 |
|
Stage 1-3 Expressed Weak expression (>41ms exp) Ubiquitous Maternal Degraded Degraded partially stage 2 Degradation maternal transcripts |
| 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 Random blastoderm nuclei Dorsal blastoderm nuclei Medium expression (21-40ms exp) Localized Subcellular localization patterns Nuclei-associated localization Perinuclear localization Perinuclear subset of nuclei Perinuclear around yolk nuclei Intranuclear accumulation Accumulation nuclear subregion Exclusionary patterns Pole cell exclusion Dorsal localization Cell division apparatus Chromatin associated metaphase Basal localization Basal enrichment Apical localization Embryonic localization patterns |
| stage 6-7 |
|
Stage 6-7 Expressed Zygotic Yolk Nuclei Subset yolk nuclei Random yolk nuclei Localized Subcellular localization patterns Nuclei-associated localization Perinuclear localization Perinuclear subset of nuclei Perinuclear around yolk nuclei Intranuclear accumulation Accumulation nuclear subregion Embryonic localization patterns Dorsal localization |
| stage 8-9 |
|
Stage 8-9 Expressed Zygotic Blastoderm nuclei Subset blastoderm nuclei Expression in neuroblasts Expression in amnioserosa Localized Subcellular localization patterns Perinuclear localization Perinuclear subset of nuclei Other subcellular pattern Nuclei-associated localization Cell junction associated Embryonic localization patterns Dorsal localization |
| stage 10-17 |
|
Stage 10-17 Expressed Zygotic Yolk nuclei Yolk nuclei 'podia' Perinuclear around yolk nuclei Tracheal system Specific tracheal branches Sensory system Segmented pattern Proventriculus PNS Midgut Midgut subset Hindgut Specific hindgut area or cells Midgut hindgut border Head Ectoderm Polarized Ectoderm Dorsal vessel Dorsal vessel specific pattern CNS Ventral nerve cord Blastoderm nuclei Localized Subcellular localization patterns Perinuclear localization Perinuclear polarized Foci Small Foci Small Foci in ectoderm Bigger Foci Cell junction associated Cell extensions or 'podia' |
Larva
| Area | Images | Terms |
|---|
Adult
| Area | Images | Terms |
|---|
Comments
| Good probe. Amazing insitu! Little maternal. |
| Sub-cellular localization at the edges of amnioserosa cells. |
| Great patterns! |
Probe CR43617-RA Links: Permalink
Genes: CR43617
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 Ventral blastoderm nuclei Single stripe Segmented pattern Gap-gene pattern Posterior blastoderm nuclei Dorsal blastoderm nuclei All blastoderm nuclei Ubiquitous Localized Subcellular localization patterns Posterior localization Cytoplasmic foci Basal localization Basal enrichment Apical localization |
| stage 6-7 |
|
Stage 6-7 Expressed Zygotic Blastoderm nuclei Subset blastoderm nuclei Ventral blastoderm nuclei Segmented pattern Gap-gene pattern Posterior blastoderm nuclei Dorsal blastoderm nuclei Ubiquitous Localized Subcellular localization patterns Exclusionary patterns Apical exclusion Cytoplasmic foci Basal localization Basal enrichment Apical localization Posterior localization Embryonic localization patterns Ventral localization Dorsal localization Degraded Degraded partially stage 7 |
| stage 8-9 |
|
Stage 8-9 Expressed Zygotic Blastoderm nuclei Subset blastoderm nuclei Ventral blastoderm nuclei Segmented pattern Gap-gene pattern Dorsal blastoderm nuclei Localized Subcellular localization patterns Cytoplasmic foci Embryonic localization patterns Ventral localization Posterior localization Dorsal 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 |
| -posterior single stripe; expression is reported to be similar to the lncRNA "iab4" (CR31271) |
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 Degraded Degraded partially stage 5 |
| stage 6-7 |
|
Stage 6-7 Non-Expressed |
| stage 8-9 |
|
Stage 8-9 Expressed Zygotic Zygotic starting stage 9 Blastoderm nuclei Subset blastoderm nuclei Ventral blastoderm nuclei Expression in ectoderm Dorsal blastoderm nuclei Localized Subcellular localization patterns Cytoplasmic foci Embryonic localization patterns Ventral localization Dorsal localization |
| stage 10-17 |
|
Stage 10-17 Expressed Zygotic Sensory system Proventriculus PNS Muscles-embryo Visceral mesoderm Ectoderm CNS Ventral nerve cord Brain Localized Subcellular localization patterns Foci Small Foci Small Foci in Brain |
Larva
| Area | Images | Terms |
|---|
Adult
| Area | Images | Terms |
|---|
Comments
| -performed via HCR-FISH using 3 probe sets targeting the RK isoform transcript |
| -maternal signal is weak and we are not sure if it is real |
| -signal in the foregut in late stage 11 may be either foregut/proventriculus PR or stomatogastric PR |
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 Yolk Nuclei All yolk nuclei Blastoderm nuclei Subset blastoderm nuclei Ventral blastoderm nuclei Weak expression (>41ms exp) Localized Yolk plasm localization Subcellular localization patterns Nuclei-associated localization Perinuclear localization Perinuclear subset of nuclei Perinuclear around yolk nuclei Cytoplasmic foci Embryonic localization patterns Ventral localization |
| stage 8-9 |
|
Stage 8-9 Expressed Zygotic Yolk nuclei All yolk nuclei Blastoderm nuclei Subset blastoderm nuclei Ventral blastoderm nuclei Expression in ectoderm Expression in API Expression in amnioserosa Dorsal blastoderm nuclei Medium expression (21-40ms exp) Localized Yolk plasm localization Embryonic localization patterns Ventral localization Dorsal localization |
| stage 10-17 |
|
Stage 10-17 Expressed Zygotic Tracheal system Tracheal pits Tracheal lumen Specific tracheal branches Dorsal trunk Segmented pattern Salivary glands Proventriculus Pharynx Head Head epidermis Foregut Ectoderm Amnioserosa Amnioserosa edges Medium expression (21-40ms exp) |
Larva
| Area | Images | Terms |
|---|
Adult
| Area | Images | Terms |
|---|
Comments
| -performed via HCR-FISH using 3 probe sets targeting the RA isoform transcript |
| -diverse ectoderm derived structures such as the salivary gland (and the salivary primordium), amnioserosa, proventriculus, tracheal pits, and epidermis |
| -prior reported expression of hemocytes were not visible in this experiment |
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 Localized Subcellular localization patterns Dorsal localization Basal localization |
| stage 6-7 |
|
Stage 6-7 Expressed Zygotic Blastoderm nuclei Subset blastoderm nuclei Segmented pattern Expression in ectoderm Localized Embryonic localization patterns Dorsal localization |
| stage 8-9 |
|
Stage 8-9 Expressed Zygotic Blastoderm nuclei Subset blastoderm nuclei Segmented pattern Expression in ectoderm Localized Embryonic localization patterns Dorsal localization Anterior localization |
| stage 10-17 |
|
Stage 10-17 Expressed Zygotic Sensory system Head Head epidermis 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 common exons |
| -Lateral and ventral spots in the epidermis of late stage samples are likely imaginal discs |
Probe E-spl-malpha-BFM-RA Links: Permalink
Genes: E(spl)malpha-BFM
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 Ventral blastoderm nuclei Localized Subcellular localization patterns Ventral localization Basal localization Basal enrichment |
| stage 6-7 |
|
Stage 6-7 Expressed Zygotic Blastoderm nuclei Subset blastoderm nuclei Ventral blastoderm nuclei Dorsal blastoderm nuclei |
| stage 8-9 |
|
Stage 8-9 Expressed Ubiquitous Localized Embryonic localization patterns Ventral localization Germ band localization Dorsal localization |
| stage 10-17 |
|
Stage 10-17 Expressed Zygotic Muscles-embryo Visceral mesoderm Head Head epidermis Ectoderm |
Larva
| Area | Images | Terms |
|---|
Adult
| Area | Images | Terms |
|---|
Comments
| -Our experiment did not observe the same late stage patterns observed by BDGP (i.e. dorsal vessel, tracheal system, certain epidermal signals) |
| -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 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 Non-Expressed |
| stage 4-5 |
|
Stage 4-5 Expressed Zygotic Zygotic starting stage 5 Blastoderm nuclei Subset blastoderm nuclei Segmented pattern Gap-gene pattern Dorsal blastoderm nuclei Weak expression (>41ms exp) |
| stage 6-7 |
|
Stage 6-7 Expressed Zygotic Blastoderm nuclei Subset blastoderm nuclei Expression in API Dorsal blastoderm nuclei Weak expression (>41ms exp) Localized Embryonic localization patterns Dorsal localization |
| stage 8-9 |
|
Stage 8-9 Expressed Zygotic Blastoderm nuclei Subset blastoderm nuclei Expression in amnioserosa Weak expression (>41ms exp) Localized Subcellular localization patterns Nuclei-associated localization Intranuclear accumulation Accumulation nuclear subregion Embryonic localization patterns Dorsal localization |
| stage 10-17 |
|
Stage 10-17 Expressed Zygotic Posterior spiracles Specific posterior spiracle pattern PNS Oenocytes Midgut Hindgut Specific hindgut area or cells Head CNS Ventral nerve cord Brain Blastoderm nuclei Amnioserosa Localized Subcellular localization patterns Nuclei-associated localization Nuclear in PNS Nuclear in other cells Nuclear in ectoderm Nuclear in CNS Nuclear in amnioserosa Accumulation nuclear subregion |
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 Blastoderm nuclei Subset blastoderm nuclei Ventral blastoderm nuclei Dorsal blastoderm nuclei Anterior blastoderm nuclei Weak expression (>41ms exp) Localized Subcellular localization patterns Ventral localization Other subcellular pattern Nuclei-associated localization Perinuclear localization Perinuclear subset of nuclei Perinuclear around blastoderm nuclei Intranuclear accumulation Accumulation nuclear subregion Exclusionary patterns Pole cell exclusion Dorsal localization Cell division apparatus Other cell division pattern Basal localization Basal enrichment Apical localization Apical enrichment Diffuse apical localization Embryonic localization patterns |
| stage 6-7 |
|
Stage 6-7 Expressed Weak expression (>41ms exp) Localized Subcellular localization patterns Other subcellular pattern Nuclei-associated localization Perinuclear localization Perinuclear subset of nuclei Perinuclear around blastoderm nuclei Intranuclear accumulation Accumulation nuclear subregion Exclusionary patterns Cell division apparatus Apical localization Apical enrichment Discrete apical foci Apical clusters 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 Expression in neuroblasts Expression in amnioserosa Weak expression (>41ms exp) Localized Subcellular localization patterns Perinuclear localization Nuclei-associated localization Cytoplasmic foci Apical localization Apical enrichment Diffuse apical localization Apical Localization Neuroblasts Embryonic localization patterns Ventral localization Dorsal localization |
| stage 10-17 |
|
Stage 10-17 Expressed Zygotic PNS Fat body Fat body- specific region Fat body polarized Dorsal vessel Dorsal vessel specific pattern CNS Ventral nerve cord Polarized VNC Perinuclear VNC Polarized CNS Brain Blastoderm nuclei Amnioserosa Localized Subcellular localization patterns Perinuclear localization Perinuclear polarized Perinuclear around fat body nuclei Perinuclear around CNS nuclei Membrane associated Foci Small Foci Small Foci in fat body Small Foci in dorsal vessel |
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 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 |
Probe TP53INP-ex Links: Permalink
Genes: TP53INP
Embryo
| Area | Images | Terms |
|---|---|---|
| stage 1-3 |
|
Stage 1-3 Expressed Ubiquitous Maternal |
| stage 4-5 |
|
Stage 4-5 Expressed Zygotic Yolk nuclei All yolk nuclei Ubiquitous |
| stage 6-7 |
|
Stage 6-7 Expressed Zygotic Yolk Nuclei All yolk nuclei Ubiquitous |
| stage 8-9 |
|
Stage 8-9 Expressed Zygotic Yolk nuclei All yolk nuclei Blastoderm nuclei Subset blastoderm nuclei Expression in ectoderm Expression in amnioserosa Ubiquitous Localized Embryonic localization patterns Ventral localization Dorsal localization |
| stage 10-17 |
|
Stage 10-17 Expressed Zygotic Yolk nuclei Sensory system Segmented pattern PNS Muscles-embryo Visceral mesoderm Specific visceral mesoderm pattern Head Head epidermis Ectoderm CNS Ventral nerve cord Brain Amnioserosa Ubiquitous |
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 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 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 Maternal Localized Subcellular localization patterns Cytoplasmic foci |
| stage 4-5 |
|
Stage 4-5 Expressed Ubiquitous Maternal Degraded Degraded partially stage 4 |
| stage 6-7 |
|
Stage 6-7 Expressed Weak expression (>41ms exp) Ubiquitous Degraded Degraded partially stage 7 Degraded partially stage 6 |
| stage 8-9 |
|
Stage 8-9 Expressed Zygotic Blastoderm nuclei Subset blastoderm nuclei Expression in ectoderm Ubiquitous Localized Embryonic localization patterns Ventral localization Dorsal localization |
| stage 10-17 |
|
Stage 10-17 Expressed Zygotic Head Head epidermis Ectoderm CNS Ventral nerve cord Polarized VNC Brain Localized Subcellular localization patterns Basal enrichment Basal (outside) in CNS Basal (outside) 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 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 Expression in ectoderm Localized Embryonic localization patterns Dorsal localization |
| stage 8-9 |
|
Stage 8-9 Expressed Zygotic Blastoderm nuclei Subset blastoderm nuclei Expression in ectoderm Expression in API Localized Embryonic localization patterns Dorsal localization |
| stage 10-17 |
|
Stage 10-17 Expressed Zygotic Midgut Hindgut Head Head epidermis Foregut Ectoderm Polarized Ectoderm Dorsal vessel |
Larva
| Area | Images | Terms |
|---|
Adult
| Area | Images | Terms |
|---|
Comments
| -performed via HCR-FISH using 3 probe sets targeting the RF 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 Ubiquitous Maternal Degraded Degraded partially stage 3 Degradation maternal transcripts |
| stage 4-5 |
|
Stage 4-5 Expressed Zygotic Zygotic starting stage 5 Pole cell nuclei Blastoderm nuclei Subset blastoderm nuclei Ventral blastoderm nuclei All blastoderm nuclei Transiently widespread Ubiquitous Localized Subcellular localization patterns Nuclei-associated localization Perinuclear localization Perinuclear subset of nuclei Perinuclear around blastoderm nuclei Intranuclear accumulation Accumulation in subset nuclei Exclusionary patterns Yolk plasm exclusion Basal localization Apical localization |
| stage 6-7 |
|
Stage 6-7 Expressed Zygotic 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 Ubiquitous 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 Basal localization Basal enrichment Embryonic localization patterns Ventral localization Dorsal localization |
| stage 8-9 |
|
Stage 8-9 Expressed Zygotic Blastoderm nuclei Subset blastoderm nuclei Single stripe Expression in ectoderm Anterior blastoderm nuclei Ubiquitous Localized Subcellular localization patterns Cytoplasmic foci Embryonic localization patterns Ventral localization Dorsal localization Anterior localization |
| stage 10-17 |
|
Stage 10-17 Expressed Zygotic Tracheal system Tracheal pits Sensory system Posterior spiracles Muscles-embryo Visceral mesoderm Hindgut Head Head epidermis Dorsal vessel CNS Ventral nerve cord Foci - VNC Axons Ubiquitous Localized Subcellular localization patterns Nuclei-associated localization Foci Small Foci Small Foci in PNS Small Foci in head Small Foci in ectoderm Small Foci in CNS |
Larva
| Area | Images | Terms |
|---|
Adult
| Area | Images | Terms |
|---|
Comments
| -performed via HCR-FISH using 3 probe sets targeting the RB transcript isoform |
| -neat and diverse expression patterns throughout development |
| -images are from two separate experiments under identical conditions for better coverage |
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 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 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 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 Ventral blastoderm nuclei Expression in ectoderm Dorsal blastoderm nuclei Localized Subcellular localization patterns Nuclei-associated localization Accumulation nuclear subregion Cytoplasmic foci Embryonic localization patterns Ventral localization Dorsal localization |
| stage 10-17 |
|
Stage 10-17 Expressed Zygotic Tracheal system Salivary glands Salivary glands - specific region CNS Ventral nerve cord Perinuclear VNC Brain Localized Subcellular localization patterns Perinuclear localization Perinuclear around tracheal nuclei Perinuclear around salivary gland nuclei Perinuclear around CNS nuclei Nuclei-associated localization Nuclear in salivary glands Foci Small Foci Small Foci in CNS Small Foci in Brain |
Larva
| Area | Images | Terms |
|---|
Adult
| Area | Images | Terms |
|---|
Comments
| -performed via HCR-FISH (3 probes) |
| -good marker of embryo tracheal system development |
| -transcript isoform targeted was trh-RD |
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! |
Embryo
| Area | Images | Terms |
|---|---|---|
| stage 1-3 |
|
Stage 1-3 Expressed Zygotic Zygotic starting stage 3 Ubiquitous Localized Subcellular localization patterns Nuclei associated localization Intranuclear accumulation Accumulation in subset nuclei Cytoplasmic foci |
| stage 4-5 |
|
Stage 4-5 Expressed Zygotic Pole cell nuclei Subset pole cell nuclei Blastoderm nuclei Subset blastoderm nuclei Posterior blastoderm nuclei Dorsal blastoderm nuclei Anterior blastoderm nuclei Localized Subcellular localization patterns Yolk cortex localization Yolk cortex enrichment Ventral localization Posterior localization Nuclei-associated localization Perinuclear localization Perinuclear subset of nuclei Perinuclear around blastoderm nuclei Exclusionary patterns Yolk plasm exclusion Yolk cortex exclusion Basal localization Apical localization Apical enrichment Anterior localization Embryonic localization patterns |
| stage 6-7 |
|
Stage 6-7 Expressed Zygotic Pole cell nuclei Subset pole cell nuclei Blastoderm nuclei Subset blastoderm nuclei Expression in ectoderm Expression in API Dorsal blastoderm nuclei Localized Yolk cortex localization Yolk cortex enrichment Subcellular localization patterns Nuclei-associated localization Perinuclear localization Perinuclear subset of nuclei Perinuclear around pole cell nuclei Perinuclear around blastoderm nuclei Intranuclear accumulation Accumulation in subset nuclei Exclusionary patterns Yolk plasm exclusion Yolk cortex exclusion Cytoplasmic foci Pole cell localization Pole cell enrichment Embryonic localization patterns Dorsal localization |
| stage 8-9 |
|
Stage 8-9 Expressed Zygotic Germ cell nuclei Subset pole cell nuclei Blastoderm nuclei Subset blastoderm nuclei Expression in ectoderm Expression in API Expression in amnioserosa Dorsal blastoderm nuclei Localized Yolk cortex localization Yolk cortex enrichment Subcellular localization patterns Perinuclear localization Perinuclear around pole cell nuclei Exclusionary patterns Yolk plasm exclusion Yolk cortex exclusion Cytoplasmic foci Basal localization Germ cell localization Germ cell enrichment Embryonic localization patterns Dorsal localization Degraded Degraded partially 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 transcript isoform |
| -neat expression patterns in early embryos and early germ band elongation stages; expression is no longer detectable after stage 9-10 (fits modENCODE RNA-seq data well) |