 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on May 20, 2015 |
| Title |
EV |
| Sample type |
SRA |
| |
|
| Source name |
germline
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
strain: N2
RNAi: L4440 plasmid in HT115
age: Young adult
|
| Growth protocol |
RNAi feeding was started in L1 staged worms at 24C; germlines were dissected from their F1 young adult progeny
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was collected from young adult hermpahrodite germlines. Mouth-pipetting with a pulled capillary needle was used to isolate the gonad at the dorsal-to-ventral bend. Germlines were dissected in egg buffer and immediately dispensed into Trizol on ice. 400-500 total dissected germlines were collected for each replicate, resulting in total RNA ranging from 1.5 to 4 ug per replicate sample.
Using a TruSeq RNAv2 kit (Illumina), mRNA was polyA-selected, fragmented and used to create adapter-ligated cDNA for sequencing. One hundred base pair sequences were obtained on an Illumina HiSeq2500 and processed as single end reads
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
EV
|
| Data processing |
Base calling was done using Illumina Casava software
Reads were aligned using TopHat (v. 2.0.8b) using -G, -M arguments
samtools (v.0.1.18) used for indexing
HTSeq (v.0.5.4p3) used to generate read counts per gene using '-m union' argument
DESeq (v.1.1.2.1) was used to normalize gene counts across samples; 'method="blind"' was used for dispersion estimation. Fold change between the average of the four control replicates and the average of the four test replicates was used to calculate the significance using a negative binomial distribution.
Genome_build: WBcel215, Ensembl release 70
Supplementary_files_format_and_content: There are 3 included tab delimited text files: the first ('Raw read counts for EV…') include the raw read counts output from HTSeq for EV, P granule ('QUAD') and CSR-1. The other two ('CSR1 RNAi…' and 'P granule RNAi…') include base mean, fold change, log2fold change, p value, and adj p value calculations output from DESeq.
|
| |
|
| Submission date |
Apr 16, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Dustin Lynn Updike |
| E-mail(s) |
dupdike@mdibl.org
|
| Phone |
2082889880
|
| Organization name |
Mount Desert Island Biological Laboratory
|
| Lab |
Updike Lab
|
| Street address |
159 Old Bar Harbor Rd.
|
| City |
Salisbury Cove |
| State/province |
ME |
| ZIP/Postal code |
04672 |
| Country |
USA |
| |
|
| Platform ID |
GPL18245 |
| Series (1) |
| GSE67954 |
CSR-1 and P granules suppress sperm-specific transcription in the C. elegans germline |
|
| Relations |
| BioSample |
SAMN03487377 |
| SRA |
SRX997493 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
