|
| Status |
Public on Apr 24, 2024 |
| Title |
Primed, RAP input, Rep1 |
| Sample type |
SRA |
| |
|
| Source name |
H9
|
| Organism |
Homo sapiens |
| Characteristics |
hesc status: Primed
cell line: H9
cell type: human embryonic stem cell
fraction: RAP input
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was eluted by RNase H digestion, and crosslinking was reversed via proteinase K digestion at 65˚C for 1h. Finally, DNA was purified using the GeneJET Gel Extraction kit (Thermo Fisher Scientific).
Libraries were prepared using the TruSeq ChIP Library Preparation Kit from Illumina.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Reads were TM 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: RAP-seq
|
| |
|
| 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) |
| GSE246641 |
XIST dampens X chromosome activity in a SPEN-dependent manner during early human development [RAP-seq] |
| GSE246643 |
XIST dampens X chromosome activity in a SPEN-dependent manner during early human development |
|
| Relations |
| BioSample |
SAMN38051348 |
| SRA |
SRX22318804 |
