|
| Status |
Public on Feb 26, 2015 |
| Title |
CAGE_AdMateM_4d_testes_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
dissected testes and reproductive tracts
|
| Organism |
Drosophila melanogaster |
| Characteristics |
tissue: dissected testes and reproductive tracts
developmental stage: Adult
age: 4 days post eclosion
Sex: Male
read length: 36 nt
|
| Growth protocol |
Flies were grown on standard cornmeal medium at 25°C. Adults were aged 4 days for D. melanogaster and 5-8 days for D. pseudoobscura before dissection.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from dissected testes, ovaries and carcasses of D. melanogaster and D. pseudoobscura adults using the RNeasy procedure (Qiagen, Valencia, CA). See Chen ZX et al. Genome Res 2014, 24(7):1209-23.
The optimized CAGE library preparation protocol resulted in 27 nt tags that correspond to the 5’ ends of capped RNAs for sequencing on the Illumina platform. See Chen ZX et al. Genome Res 2014, 24(7):1209-23.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
CAGE |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Data processing |
We removed linkers and adapters from raw reads to extract the 27 nt CAGE tags. Tags were aligned to the D. melanogaster (release 5) and D. pseudoobscura (release 3) genomes with StatMap (http://www.statmap-bio.org/) to estimate tag density at the CAGE tag start sites (termed as CAGE sites). CAGE sites with >1 tag per million (TPM) were retained for further analysis. See Chen ZX et al. Genome Res 2014, 24(7):1209-23.
To compare orthologous transcription start sites (TSS) among CAGE sites in D. melanogaster and D. pseudoobscura, we used the AUG codons of 1:1 orthologs in the two species derived from OrthoDB version 6 (Waterhouse et al. Nucleic Acids Res. 2013, 41 (Database issue): D358–65.). We associated CAGE sites with the nearest downstream gene AUG codon within 5kb, and the CAGE sites with the highest TPM of the orthologous genes were classified as TSS of the genes.
Genome_build: Drosophila melanogaster Release 5, Drosophila pseudoobscura Release 3
Supplementary_files_format_and_content: BED files for CAGE sites corresponding to TSS of orthologous genes in D. melanogaster and D. pseudoobscura. Column 1: chromosome; Column 2: CAGE site start (0-based coordinates); Column 3: CAGE site end (1-based coordinates); Column 4: the orthoDB ID for protein-coding gene following the CAGE peak; Column 5: TPM (tags per million) for the CAGE site; Column 6: strand; Column 7: distance between the CAGE site and its nearest downstream gene AUG codon.
|
| |
|
| Submission date |
Feb 25, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Brian Oliver |
| E-mail(s) |
briano@nih.gov
|
| Phone |
301-204-9463
|
| Organization name |
NIDDK, NIH
|
| Department |
LBG
|
| Lab |
Developmental Genomics
|
| Street address |
50 South Drive
|
| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platform ID |
GPL11203 |
| Series (2) |
| GSE44612 |
Comparative Validation of the D. melanogaster Encyclopedia of DNA Elements Transcript Models |
| GSE66284 |
CAGE-Seq of gonads and carcasses from D. melanogaster and D. pseudoobscura |
|
| Relations |
| BioSample |
SAMN00116733 |
| SRA |
SRX144187 |
