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| Status |
Public on Oct 04, 2023 |
| Title |
sin-3(tm1276)_rep1 |
| Sample type |
SRA |
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| Source name |
germline
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| Organism |
Caenorhabditis elegans |
| Characteristics |
tissue: germline
genotype: sin-3(tm1276)
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| Extracted molecule |
total RNA |
| Extraction protocol |
Gonad dissections and extractions were performed as in Herbette et al, Cells. 2020 ,doi: 10.3390/cells9092049. Briefly, gonads of 5 to 7 young adults at the L4 stage + 12 h were dissected in dissection buffer (Egg Buffer1.1 × (HEPES pH 7.3 25 mM, NaCl 118 mM, KCL 48 mM, CaCl2 2 mM, 2 mM MgCl2), 0.5 mM Levamisole, 0.1% Tween 20) on slides. Extruded gonads were cut at the elbow and the distal part recovered using a drawn capillary and transferred to 30 µL of ×B extraction buffer (Kit Picopure, Life Technology, # 12204-01, Carlsbad, MA, USA), frozen in liquid nitrogen and stored at −80 °C. For RNA preparation tubes were thawed, the volume of XB extraction buffer adjusted to 100 μL, and RNA purified using the PicoPure kit (Life Technology, # 12204-01) according to the manufacturer’s instructions. Elution was in 13 μL of nuclease-free water. The integrity of RNA was evaluated using Tape Station 4200 (Agilent, Santa Clara, CA, USA), and the concentration of RNA measured using DropSense 96 (Unchained Labs, Pleasanton, CA, USA).
Librairies were generated using the Stranded Total RNA Prep Ligation with Ribo-Zero Plus kit (Illumina) and sequenced using the Illumina Hiseq 4000 technology (1x50 bases)
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Description |
sin3tm_vs_wt.csv
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| 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)
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| Submission date |
Mar 16, 2023 |
| Last update date |
Oct 04, 2023 |
| Contact name |
Cecile Bedet |
| E-mail(s) |
[email protected]
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| Organization name |
ENS de Lyon
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| Department |
Bilogie
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| Lab |
LBMC, CNRS UMR5239
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| Street address |
46 allée d'Italie
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| City |
Lyon |
| ZIP/Postal code |
69007 |
| Country |
France |
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| Platform ID |
GPL22765 |
| Series (2) |
| GSE227498 |
SIN3 acts in distinct complexes to regulate the germline transcriptional program in C. elegans [sin-3(tm1276)] |
| GSE227499 |
SIN3 acts in distinct complexes to regulate the germline transcriptional program in C. elegans |
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| Relations |
| BioSample |
SAMN33782575 |
| SRA |
SRX19693377 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7101448_CLBT19.tsv.gz |
140.1 Kb |
(ftp)(http) |
TSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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