 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Oct 04, 2023 |
| Title |
sin3_rep3 |
| Sample type |
SRA |
| |
|
| Source name |
germline
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
tissue: germline
genotype: sin-3(syb2172)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Gonads from 9-12 young adults were dissected in UltraPure water on microscope slides at 4°C to immobilize worms without use of anesthetic. RNA was isolated, reverse-transcribed, amplified and clean up following the Smart-seq2 protocol described by Serra et al. (Serra et al., 2018). Three independent biological replicates were performed for each strain
Librairies were generated using the SMART-Seq v4 UltraLow Input RNA kit (Clontech) followed by the Nextera XT DNA sample preparation Kit (Illumina) and sequenced using the Illumina Hiseq 4000 technology (1x50 bases)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
quality control, adapter trimming, quality filtering with fastp (Version 0.20.1)
mapping with RNA-STAR (Version 2.7.3a) on genome WS278
reads count was performed with htseq-count (Version 0.7.2)
differential expression was calculated with DESeq2 (Version 1.36.0) using a homemade R script (Rversion 4.2.2)
Assembly: WS278
Supplementary files format and content: raw read count table (.tsv)
Supplementary files format and content: diff expression file (.csv)
|
| |
|
| Submission date |
Mar 14, 2023 |
| Last update date |
Oct 04, 2023 |
| Contact name |
Cecile Bedet |
| E-mail(s) |
[email protected]
|
| Organization name |
ENS de Lyon
|
| Department |
Bilogie
|
| Lab |
LBMC, CNRS UMR5239
|
| Street address |
46 allée d'Italie
|
| City |
Lyon |
| ZIP/Postal code |
69007 |
| Country |
France |
| |
|
| Platform ID |
GPL22765 |
| Series (2) |
| GSE227368 |
SIN3 acts in distinct complexes to regulate the germline transcriptional program in C. elegans [sin-3(syb2172) and hda-3(ok1991)] |
| GSE227499 |
SIN3 acts in distinct complexes to regulate the germline transcriptional program in C. elegans |
|
| Relations |
| BioSample |
SAMN33761199 |
| SRA |
SRX19678018 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7099073_CLBT62.R1.tsv.gz |
131.6 Kb |
(ftp)(http) |
TSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
