|
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 |