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| Status |
Public on Dec 07, 2023 |
| Title |
R7-dependent transcription in the developing Drosophila retina |
| Organism |
Drosophila melanogaster |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Color vision in Drosophila is mediated by photoreceptors R7 and R8, which express various combinations of opsins Rh3, Rh4, Rh5 and Rh6 depending on their cellular identity. Most ommatidia are classified as either “pale” or “yellow” subtypes with pale ommatidia coordinately expressing Rh3 and Rh5—in R7 and R8 cells respectively—while yellow express Rh4 and Rh6. Subtype identity is established initially in R7 photoreceptors via a stochastic mechanism then transmitted to the R8 via an inductive signal to ensure paired opsin expression. To identify factors that may be involved in this process, we used RNA-Seq to detect genes that are differentially expressed in sevenless mutant retinas at 40 hours after puparium formation. Since loss of sevenless prevents R7 recruitment and specification, we reasoned that this approach would allow us to identify genes that are enriched in R7 cells during this critical time point. Furthermore, since it has previously been established that in the absence of R7 most R8s will adopt the yellow Rh6-expressing identity, this gives us the opportunity to identify genes which may inductive mechanism occurring in R8 cells.
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| Overall design |
Replicate samples (four per genotype) were prepared from dissected 40 hour apf female pupal retinas from w[1118] control or w[*] sev[14] animals. Normalized count data from RNA-Seq was used to identify differentially espressed transcripts.
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| Contributor(s) |
Aldrich JC, Vanderlinden LA, Jacobsen TL, Wood C, Saba LM, Britt SG |
| Citation(s) |
39149333 |
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| Submission date |
Dec 08, 2022 |
| Last update date |
Sep 12, 2024 |
| Contact name |
John Calvin Aldrich |
| E-mail(s) |
john.aldrich@austin.utexas.edu
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| Organization name |
University of Texas at Austin, Dell Medical School
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| Department |
Neurology
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| Street address |
1601 Trinity St. Bldg B
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| City |
Austin |
| State/province |
TX |
| ZIP/Postal code |
78712 |
| Country |
USA |
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| Platforms (1) |
| GPL16479 |
Illumina MiSeq (Drosophila melanogaster) |
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| Samples (8)
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| GSM6806734 |
retina, 40 hr apf, w[1118], rep 4 |
| GSM6806735 |
retina, 40 hr apf, w[*] sev[14], rep 1 |
| GSM6806736 |
retina, 40 hr apf, w[*] sev[14], rep 2 |
| GSM6806737 |
retina, 40 hr apf, w[*] sev[14], rep 3 |
| GSM6806738 |
retina, 40 hr apf, w[*] sev[14], rep 4 |
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| Relations |
| BioProject |
PRJNA910186 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE220550_normalized_counts_results.csv.gz |
872.5 Kb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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