|
| Status |
Public on Feb 05, 2024 |
| Title |
ChIP-seq_ES_BJ_H3K4me3 |
| Sample type |
SRA |
| |
|
| Source name |
ES_BJE2
|
| Organism |
Mus musculus |
| Characteristics |
cell line: ES_BJE2
cell type: ES cells
genotype: C57BL/6 x JF1
chip antibody: H3K4me3 (Diagenode 030-050)
|
| Growth protocol |
ES cell lines were maintained in gelatin-coated dishes with ESGRO complete plus medium (Millipore, SF001-500P) containing LIF, BMP4, and a GSK3-β inhibitor. ES-derived neural precursor cells were generated using in vitro corticogenesis as described in Montibus et al 2021 (PMID: 32405722).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChiP-seq experiments on native chromatin were performed on ESC and NPC for the B6xJF1 genetic backgrounds as previously in Le Boiteux et al., 2021 (PMID: 33720519).
Library preparation (TruSeq® ChIP Sample Preparation) and sequencing on a HiSeq 2500 instrument (Illumina) were performed by MGX, according to the manufacturer’s recommendations
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
ChIP-seq were mapped on the mouse genome (mm39 masked for JF1 SNPs)using Bowtie2 .
Alignments filtering was realized with samtools (view -q 20).
peaks were called using MACS1.4.2. (--nomodel --shiftsize 73 --pvalue 1e-5 ) and the coverage was computed using bamCoverage (--normalizeUsing RPKM --extendReads 200 --ignoreDuplicates --binSize 20).
Assembly: mm39
Supplementary files format and content: bigWig
|
| |
|
| Submission date |
Sep 27, 2023 |
| Last update date |
Feb 05, 2024 |
| Contact name |
franck court |
| Organization name |
GReD CNRS
|
| Street address |
28 Place Henri Dunant
|
| City |
Clermont-Ferrand |
| ZIP/Postal code |
63000 |
| Country |
France |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE244144 |
Biallelic non-productive enhancer-promoter interaction precedes imprinted expression of KcnK9 during mouse neural commitment [ChIP-seq] |
| GSE244147 |
Biallelic non-productive enhancer-promoter interaction precedes imprinted expression of KcnK9 during mouse neural commitment |
|
| Relations |
| BioSample |
SAMN37560889 |
| SRA |
SRX21902974 |
