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| Status |
Public on Jun 01, 2015 |
| Title |
3_8 |
| Sample type |
SRA |
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| Source name |
stage 8 follicles sample 3
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| Organism |
Drosophila melanogaster |
| Characteristics |
strain: Oregon R
gender: female
age: 6-14 days old
developmental stage: adult
subregion: stage 8
tissue: follicle
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| Treatment protocol |
EcR mutant flies were shifted to the restrictive temperature 2 days after eclosion.
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| Growth protocol |
Fertilized adult females 4-14 days of age were employed to ensure that follicle production has reached steady state. Females were kept at a controlled density in fresh vials, at 25°C and provided with a optimal nutrition 36hr prior to analysis. Under these conditions, follicle progression in the ovary is stable and reproducible.
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Ovarian follicles of the indicated stage and genotype were dissected under a dissecting microscope at room temperature in Grace's medium and transferred to iced tripure (Roche/Boehringer Mannheim cat: 11667157001) to avoid RNA degradation. Samples of 100 follicles were homogenized. 600μl of fresh tripure was added, mixed, and allowed to stand at room temperature for 5-10 min. After adding 180μl chloroform, samples were vortexed 2 x 45 secs, and incubated at room temperature for 10 minutes. Samples were then centrifuged for 15 min at 12,000 rpm at 4°C, and the aqueous layer was moved to a fresh tube. RNA was precipitated by adding 400μl of isopropanol, vortexing for 15 seconds, and incubating at room temperature for 15 min, and centrifuging at 12,000 rpm for 15 min at 4°C. After washing the pellet with 75% EtOH, the RNA was dried in air dry for 5 minutes, resuspended in 50μl nuclease free H2O, and stored at -80°C.
cDNA libraries were constructed from poly(A)-selected RNA using Illumina TruSeq RNA Library Prep Kit v2
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
basecalling: CASAVA v1.8.2
reads aligned to genome using Bowtie2 v 2.0.6
identified reads hitting transcripts using TopHat v 2.0.7 with -G --no novel juncs and Refseq dm3-iGenomes.gtf
calculated transcript fpkm values and gene fpkm values using Cufflinks version 2.02 -G with dm3-iGenomes.gtf
Genome_build: Refseq annotation file: dm3 (Release 5) and dm3-iGenomes.gtf
Supplementary_files_format_and_content: Cufflinks output file (.xlsx)
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| Submission date |
Feb 06, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Allan C Spradling |
| E-mail(s) |
spradling@ciwemb.edu
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| Phone |
410 246-3015
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| Organization name |
Carnegie Institution/HHMI
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| Department |
Embryology
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| Street address |
3520 San Martin Dr.
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| City |
Baltimore |
| State/province |
MD |
| ZIP/Postal code |
21218 |
| Country |
USA |
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| Platform ID |
GPL13304 |
| Series (1) |
| GSE65567 |
Drosophila ovarian stage 8 and 10 follicle gene expression |
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| Relations |
| Reanalyzed by |
GSM3287766 |
| BioSample |
SAMN03332432 |
| SRA |
SRX868568 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1603396_3_8R1genes.xlsx |
1.6 Mb |
(ftp)(http) |
XLSX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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