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| Status |
Public on Mar 17, 2016 |
| Title |
Ovary_RNAseq_w1118_0hr_R2 |
| Sample type |
SRA |
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| Source name |
ovary
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| Organism |
Drosophila melanogaster |
| Characteristics |
Stage: adult
tissue: ovary
genotype: w[1118]/w[1118]
hours at restrictive temperature: 0
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| Treatment protocol |
On the 5th day, 15-20 time matched flies were separated into 3 vials designated as t=0, t=12, and t=24hrs. Flies were maintained at 29°C for 0, 12, and 24hrs and dissected at 25°C.
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| Growth protocol |
15 males and 30 virgin females were used to set up 6-8 crosses in bottles. Parent flies were flipped to new bottles after 5 days. All flies were raised and maintained at 18°C. Experimental and control flies were collected within 24 hours of eclosion and aged 5 days.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Ovary and testis were dissected from age-matched adult flies of the genotypes w1118; tra2ts2/tra2ts1 (experimental) or w1118 (control for dsxF->dsxM experiments); for dsxM->dsxF experiments the genotypes were: y1 w*; P{w+mc=UAS-Tra.F}20J7; P{w+mc=tubP-GAL80ts}7/P{w+mc=tubP-GAL4}LL7 (experimental) or P{w+mc=tubP-GAL80ts}7/P{w+mc=tubP-GAL4}LL7 (control). All samples were raised at 18°C until 5 days after eclosion when adults were shifted to either 29°C (for tra2ts) or 30°C (for UAS-TraF) for 0, 12, or 24 hours. Total RNA was extracted from ovary and testis dissected at room temperature (placed on ice after 30 minutes) using TRIzol Reagent following manufacturer’s protocol (Ambion Life Technologies, Carlsbad, CA, USA). Egg chambers stage 10 and older were removed and discarded to enrich for younger-staged egg chambers in the ovaries. Purified RNA was treated with DNAse I following manufacturer's protocol (New England Biolabs, Ipswich, MA, USA) and purified again using phenol:chloroform extraction followed by ethanol precipitation. Duplicate RNA-seq libraries were constructed from 200 ng total RNA from independent dissection of each sample using the TruSeq RNA Sample Preparation v2 high-throughput (HT) protocol (Illumina, San Diego, CA, USA, 2011). Libraries were sequenced on the HiSeq 2000 machine following a 76 bp single-end protocol (Illumina, San Diego, CA, USA).
True-Seq v2 protocol starting with 200 ng of total RNA.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
replicate 2
EC80
G Wt0 R2
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| Data processing |
Reads passing the Illumina chastity filter were mapped to the D. melanogaster genome and assigned to gene models using Tophat 1.4.1 (Trapnell et al., 2009) and default settings except for the following; -G=true, minimum intron length was set to 42bp (-i 42), the maximum multihits was set to 1 (-g 1).
Transcript abundance was determined using HT-seq.
Genome_build: dm3, Flybase release 5 with no Uextra
Supplementary_files_format_and_content: Text files with raw counts; output from HT-seq.
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| Submission date |
Mar 16, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Brian Oliver |
| E-mail(s) |
briano@nih.gov
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| Phone |
301-204-9463
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| Organization name |
NIDDK, NIH
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| Department |
LBG
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| Lab |
Developmental Genomics
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| Street address |
50 South Drive
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| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
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| Platform ID |
GPL13304 |
| Series (1) |
| GSE79294 |
Identification of transcripts whose abundance changes in response to acute switches in DSX isoform in the ovary and testis |
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| Relations |
| Reanalyzed by |
GSM3278823 |
| BioSample |
SAMN04558397 |
| SRA |
SRX1637722 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2091025_Sample_EC80_htseq.txt.gz |
59.4 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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