|
Status |
Public on Apr 24, 2024 |
Title |
PXGL, H2AK119Ub, KO, Rep2 |
Sample type |
SRA |
|
|
Source name |
H9
|
Organism |
Homo sapiens |
Characteristics |
hesc status: PXGL cell line: H9 cell type: human embryonic stem cell genotype: KO antibody: H2AK119Ub
|
Extracted molecule |
genomic DNA |
Extraction protocol |
Digested chromatin was treated with proteinase K and eluted using phenol chloroform extraction as described in Skene et al.,2017. High-throughput sequencing libraries were constructed using the TruSeq ChIP Library Preparation Kit according to the manufacturer’s recommendation. Paired-end sequencing was done on the Illumina NovaSeq 6000 with a read length of 100 bp.
|
|
|
Library strategy |
OTHER |
Library source |
genomic |
Library selection |
other |
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 (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. BigWig track files were generated with bamCoverage from deeptools (v3.5.0) using the following parameters: --normalizeUsing BPM --binSize 20 --smoothLength 40. normalizeUsing "BPM" --binSize 20 --smoothLength 40. Assembly: hg38 Supplementary files format and content: bigWig Library strategy: CUT&RUN
|
|
|
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) |
GSE246634 |
XIST dampens X chromosome activity in a SPEN-dependent manner during early human development [CUT&RUN] |
GSE246643 |
XIST dampens X chromosome activity in a SPEN-dependent manner during early human development |
|
Relations |
BioSample |
SAMN38050735 |
SRA |
SRX22318493 |