|
| Status |
Public on Apr 24, 2024 |
| Title |
PXGL, CRISPRi XIST Dox, Rep2 |
| Sample type |
SRA |
| |
|
| Source name |
H9
|
| Organism |
Homo sapiens |
| Characteristics |
hesc status: PXGL
cell line: H9
cell type: human embryonic stem cell
genotype: CRISPRi XIST Dox
|
| 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 |
SAMN38051390 |
| SRA |
SRX22319156 |
