|
| Status |
Public on Nov 22, 2024 |
| Title |
Micro-C of control mouse ESCs (E-DMSO) |
| 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: 0.01% DMSO
|
| 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 |
Cell lysis, MNase digestion, ligation, biotin labeling and pulldown were preformed according to Dovetail Micro-C kit User Guide version 1.0.
Libraries were prepared as in the Dovetail Micro-C kit User Guide version 1.0, except that Dovetail reagents were replaced by reagents from the NEBNext Ultra II DNA Library Prep Kit for Illumina kit. For detailed protocol see adjoning paper.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
DNBSEQ-T7 |
| |
|
| Data processing |
Hi-C data was processed using the HiC-Pro v3.1.0 pipeline (https://github.com/nservant/HiC-Pro). In brief, raw sequencing reads were mapped independently to the reference genome using Bowtie2 in local alignment mode and non-informative reads were removed using the default options. See adjoning paper for the detailed pipeline.
Assembly: mm10
Supplementary files format and content: Each processed .mcool file represent pairwise information of the observed genome contacts (produced by the cooler package https://cooler.readthedocs.io/en/latest/index.html). Loop files represent coodrinates of focal contacts idenitied by mustache v1.0 (https://github.com/ay-lab/mustache) with default parameters on ICE-balanced .mcool maps at 1 kb and 4 kb resolutions. Redundant loops between different resolutions were filtered in 20 kb windows, and in case of overlap loop coordinates were retained at the finer resolution.
Library strategy: Micro-C
|
| |
|
| 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 |
GPL28330 |
| Series (2) |
| GSE280493 |
A histone hyperacetylation pulse induces cellular memory of gene expression and 3-dimensional genome folding [microC_1] |
| GSE281151 |
Transient histone deacetylase inhibition induces cellular memory of gene expression and three-dimensional genome folding |
|
| Relations |
| BioSample |
SAMN41231294 |
| SRA |
SRX24482690 |
