|
Status |
Public on Apr 24, 2024 |
Title |
PXGL, siScr, Rep2 |
Sample type |
SRA |
|
|
Source name |
H9
|
Organism |
Homo sapiens |
Characteristics |
hesc status: PXGL cell line: H9 cell type: human embryonic stem cell genotype: siScr
|
Extracted molecule |
total RNA |
Extraction protocol |
RNA was extracted using RNeasy mini kit (QIAGEN) following the manufacturer's recommendation. Libraries were prepared using the Illumina Stranded Total RNA Prep Ligation with Ribo-Zero Plus kit according to the manufacturer’s recommendation
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NovaSeq 6000 |
|
|
Data processing |
Reads were trimmed using trim_galore (v0.6.5) with a minimum length of 50 bp. Reads were then mapped to the human genome (hg38) using bowtie 2 (version?) (Langmead and Salzberg 2012) with the following parameters: --local --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -L 10 -X 700. Reads were then deduplicated using MarkDuplicates from picard (v2.23.5) with the following options: --CREATE_INDEX=true --VALIDATION_STRINGENCY=SILENT --REMOVE_DUPLICATES=true --ASSUME_SORTED=true. Read counts were quantified for each gene with htseq-count from htseq (v0.13.5) (Anders et al., 2015) using the following options: --stranded reverse -a 10 -t exon -i gene_id -m intersection-nonempty. The annotation file used: Homo_sapiens.GRCh38.90.gtf. Assembly: hg38 Supplementary files format and content: Tab-delimited text file includes raw counts for each sample
|
|
|
Submission date |
Oct 31, 2023 |
Last update date |
Apr 24, 2024 |
Contact name |
Claire Rougeulle |
E-mail(s) |
claire.rougeulle@u-paris.fr
|
Organization name |
Université Paris Cité, CNRS
|
Department |
Epigenetics and Cell Fate
|
Street address |
35 rue Helene Brion
|
City |
Paris |
ZIP/Postal code |
75013 |
Country |
France |
|
|
Platform ID |
GPL24676 |
Series (2) |
GSE246642 |
XIST dampens X chromosome activity in a SPEN-dependent manner during early human development [RNA-seq] |
GSE246643 |
XIST dampens X chromosome activity in a SPEN-dependent manner during early human development |
|
Relations |
BioSample |
SAMN38051381 |
SRA |
SRX22319165 |