|
| Status |
Public on Nov 22, 2024 |
| Title |
H2AK119Ub ChIP-seq of mESC TSA-treated rep1 |
| Sample type |
SRA |
| |
|
| Source name |
cell line
|
| Organism |
Mus musculus |
| Characteristics |
tissue: cell line
cell line: E14tg2a
cell type: mESC wt
genotype: Wild type
treatment: 100 ng/ml TSA
|
| Treatment protocol |
DMSO: 0.01% DMSO for 4 hours; TSA: 100 ng/ml TSA for 4 hours; REC: 4 hours TSA (100 ng/ml) followed by 24 hours of recovery
|
| Growth protocol |
ESC were grown in FBS+LIF media with standard conditions.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin was fixed with 1% formaldehyde for 10 min at RT. To each 12 million mouse cells 1 million HEK cells were added for spike-in calibration. Nuclei were isolated with three different lysis buffers as in Lee et al., 2006 and sonicated in the lysis buffer 3 until the chromatin was disrupted to the size between 200 and 500bp. For detailed protocol see adjoning paper.
Libraries were prepared using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina according to manufacturer's instructions.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
DNBSEQ-G400 |
| |
|
| Data processing |
Data were mapped using bowtie2 against mm10 and hg19 and duplicates reads were discarded. Unique mouse and human reads were discarded and a donwsampling factor for spike-in normalisation was calulated as in Fursova et al. (2019) and bigwigs were produced directly from deduplicated bam files. For detailed protocol see the Method section of the adjoining paper.
Assembly: mm10
Supplementary files format and content: Processed files are given as a spike-in normalised mouse bigwig file of the two merged replicates. Peak files correspond to high-confidence peaks present in both replicates.
|
| |
|
| Submission date |
Oct 28, 2024 |
| Last update date |
Nov 22, 2024 |
| Contact name |
Marco Di Stefano |
| E-mail(s) |
[email protected]
|
| Organization name |
Institut de Génétique Humaine - CNRS / University of Edinburgh
|
| Lab |
Giacomo Cavalli lab
|
| Street address |
141 rue de la Cardonille
|
| City |
Montpellier |
| ZIP/Postal code |
34396 |
| Country |
France |
| |
|
| Platform ID |
GPL28457 |
| Series (2) |
| GSE280487 |
A histone hyperacetylation pulse induces cellular memory of gene expression and 3-dimensional genome folding [ChIP-seq] |
| GSE281151 |
Transient histone deacetylase inhibition induces cellular memory of gene expression and three-dimensional genome folding |
|
| Relations |
| BioSample |
SAMN41564098 |
| SRA |
SRX24722309 |
