|
| Status |
Public on Dec 01, 2014 |
| Title |
eye-antennal-imaginal-disc_eye-disc-Gal4_x_UAS-optix |
| Sample type |
SRA |
| |
|
| Source name |
eye-antennal discs
|
| Organism |
Drosophila melanogaster |
| Characteristics |
tissue: eye-antennal discs
developmental stage: third instar larvae
sample extraction method: Hand dissection
genotype: P{w[+mW.hs]=GawB}c701b, w[1118] x y[1] w[*]; P{w[+mC]=UAS-Optix.S}1
strain origin: Bloomington: 3735 X Bloomington: 26806
|
| Treatment protocol |
Wandering 3rd instar larvae were dissected in PBS to extract the tissues of interest
|
| Growth protocol |
All flies were raised at 25˚C on standards fly food
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted with the RNAqueous micro kit (Ambion)
RNA libraries were generated for sequencing using standard Illumina TruSeq protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
cleaning (fastX-clipper)
mapping to D. melanogaster genome using TopHat2.0.3 (default parameters)
quantification of gene expression measures with HT-Seq count (option -str=no) using D. melanogaster gene annotation release 5.45 from FlyBase
filtering (minimum of 1 read per million in 5 samples across the 72) of the raw counts
Normalization of the filtered raw counts using edgeR (version 2.4.6) and DESeq (version 1.6.1) variance-stabilizing transformation in R (version 2.14.0)
Genome_build: Drosophila melanogaster FlyBase version 5
Supplementary_files_format_and_content: RNAseq samples: HT-seq counts on Drosphila Flybase r5.45 annotation; VST normalized count on Drosphila FlyBase r5.45 annotation
|
| |
|
| Submission date |
Jul 03, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Delphine Potier |
| E-mail(s) |
[email protected]
|
| Organization name |
CIML
|
| Street address |
163 avenue de luminy
|
| City |
Marseille |
| ZIP/Postal code |
13009 |
| Country |
France |
| |
|
| Platform ID |
GPL13304 |
| Series (2) |
| GSE59059 |
Mapping gene regulatory networks in Drosophila eye development by large-scale transcriptome perturbations and motif inference. [RNA-seq] |
| GSE62558 |
Mapping gene regulatory networks in Drosophila eye development by large-scale transcriptome perturbations and motif inference |
|
| Relations |
| Reanalyzed by |
GSM3285757 |
| BioSample |
SAMN02902233 |
| SRA |
SRX645236 |
