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| Status |
Public on Mar 27, 2012 |
| Title |
Period[0], CT40 |
| Sample type |
SRA |
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| Source name |
Adult Drosophila brain, per0, CT40
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| Organism |
Drosophila melanogaster |
| Characteristics |
background strain: Canton S
genotype: per0
developmental stage: adult
gender: female
tissue: brain
time point: CT40
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| Treatment protocol |
Brains were manually dissected in PBS at CT24, 28, 32, 36, 40, 44, 48, 52, 56, 60, 64, and 68.
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| Growth protocol |
3- to 5-day-old adult female flies were maintained on standard food and housed at 25 degrees in complete darkness.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was purified using the PicoPure kit from MDS. RNA amplification and rRNA depletion were performed using the RiboAmp kit from MDS (polyA) and the Ovation RNAseq kit from NuGEN (non-polyA). Fragmentation, cDNA synthesis, and adaptor ligation were performed using standard protocols.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
Per40
Amplified RNA
Amplification: Nugen (non-polyA)
Paired (2x100)
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| Data processing |
RUM (Grant et al. 2011) was used to align raw reads to the reference Drosophila genome and modENCODE transcriptome (Graveley et al. 2011). The following parameters were used: "-limitBowtieNU -limitNU 25".
*.cov.bedgraph files are coverage maps from uniquely-aligned reads.
*.bed files are coverage maps of uniquely-aligning, high-confidence gapped reads.
Genome Build:
Per_CT40.bed: Berkeley Drosophila Genome Project (BDGP) Release 5 (April 2006), and modENCODE gene models (Graveley et al. Nature 2011)
Per_CT40.cov.bedgraph: Berkeley Drosophila Genome Project (BDGP) Release 5 (April 2006), and modENCODE gene models (Graveley et al. Nature 2011)
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| Submission date |
Feb 27, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Michael Hughes |
| E-mail(s) |
michael.evan.hughes@gmail.com
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| Organization name |
UPenn
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| Street address |
421 Curie Bvd, Brb 835
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| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19104 |
| Country |
USA |
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| Platform ID |
GPL13304 |
| Series (1) |
| GSE36108 |
Deep sequencing the circadian and light-dependent transcriptome of Drosophila brain |
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| Relations |
| Reanalyzed by |
GSM3276676 |
| SRA |
SRX122606 |
| BioSample |
SAMN00792640 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM881240_Per_CT40.bed.gz |
582.9 Kb |
(ftp)(http) |
BED |
| GSM881240_Per_CT40.cov.bedgraph.gz |
49.5 Mb |
(ftp)(http) |
BEDGRAPH |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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