|
| Status |
Public on Oct 11, 2012 |
| Title |
C. brenneri adult females+males |
| Sample type |
SRA |
| |
|
| Source name |
whole animal
|
| Organism |
Caenorhabditis brenneri |
| Characteristics |
strain: PB2801
developmental stage: young adult
tissue: whole organism
gender: pooled male and female
|
| Growth protocol |
Animals were grown at 20˚C on E. coli strain OP50.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from synchronized animals, and 18-28 nt small RNAs were size selected.
Small RNAs were treated with Tobacco Acid Phosphatase, then ligated to 3’ and 5’ adapters and RT-PCR amplified.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Raw datasets are fastq files generated using Illumina software.
Small RNA sequences were parsed using a custom Python program, then mapped to corresponding nematode reference genomes (Wormbase release WS230) allowing 0 mismatch using Bowtie software.
Genome_build: WS230
Supplementary_files_format_and_content: tab-delimited text files include Sequence and read count
|
| |
|
| Submission date |
Oct 10, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Zhen Shi |
| Organization name |
Massachusetts General Hospital
|
| Department |
Molecular Biology
|
| Lab |
Gary Ruvkun
|
| Street address |
185 Cambridge Street
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02114 |
| Country |
USA |
| |
|
| Platform ID |
GPL16138 |
| Series (1) |
| GSE41461 |
Analysis of miRNA, piRNA and siRNA in Caenorhabditis species |
|
| Relations |
| SRA |
SRX193370 |
| BioSample |
SAMN01760786 |
