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| Status |
Public on Mar 01, 2014 |
| Title |
C3 |
| Sample type |
SRA |
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| Source name |
eye imaginal disk
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| Organism |
Drosophila melanogaster |
| Characteristics |
treatment: Overexpression
phenotype: Normal eyes
genotype: GMR-Gal4; UAS-eGFP
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was recovered from surgically-isolated GMR expression domains (GFP+) from 25 to 30 third instar eye discs using a RNeasy kit (Qiagen). For each genotype, total RNA extraction was conducted in triplicate.
TruSeq RNA Sample Preparation (Low Throughput (LT) Protocol) Part# 15015050, Rev A, November 2010
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer IIx |
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| Description |
wt
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| Data processing |
Data was processed with CASAVA version 1.7.0
Sequence reads in fastq format were mapped to dm3 using tophat-1.0.14. Flybase transcripts (v5.29) were quantified and compared between control and each overexpression condition using cuffdiff v1.0.2.
Genome_build: dm3
Supplementary_files_format_and_content: The file FPKM.txt includes the FPKM values for each gene from each sample as determined by cufflinks. The file cuffdiff_ratio_data.txt includes the log2 ratios, and p-values for each gene for each replicate set of overexpressed variants relative to control as determined by cuffdiff. Also listed are the BH adjusted p-values, gene annotations. There is also a value called Amean, a very general abundance ranking factor, which is the average of the “A” values from each comparison where A is equal to the log2 of the geometric mean of the averaged FPKM values for both treatment and control.
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| Submission date |
Jan 31, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Chris W Seidel |
| E-mail(s) |
seidel@phageT4.org
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| Phone |
816 926 9054
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| Organization name |
Stowers Institute
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| Department |
Genomics
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| Lab |
Seidel
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| Street address |
1000 E 50th St
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| City |
Kansas City |
| State/province |
MO |
| ZIP/Postal code |
64110 |
| Country |
USA |
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| Platform ID |
GPL11203 |
| Series (2) |
| GSE54600 |
Global transcriptional Analysis of Yap/Yki Orthologs in Drosophila melanogaster by RNA Seq |
| GSE54603 |
Functional Evolution of the Yap/Yorkie Proto-oncogene and Elucidation of its Core Transcriptional Program |
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| Relations |
| Reanalyzed by |
GSM3285194 |
| SRA |
SRX457517 |
| BioSample |
SAMN02614601 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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