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| Status |
Public on Aug 24, 2021 |
| Title |
H3_mESC |
| Sample type |
SRA |
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| Source name |
H3_mESC
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| Organism |
Mus musculus |
| Characteristics |
cell type: embryonic stem cells
cell line: E14Tg2A
chip antibody: H3 (Abcam, Ab1791)
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| Growth protocol |
E14Tg2A ESCs were cultured feeder-free on 15-cm plates coated with 0.1% gelatin. Coating was achieved by covering the plates with gelatin 15 minutes at 37 °C. After removing any remaining gelatin, ESCs were cultured with Glasgow minimum essential medium (Sigma) supplemented with β-mercaptoethanol, sodium pyruvate, penicillin–streptomycin, non-essential amino acids, GlutaMAX, 20% fetal bovine serum (Hyclone), and leukemia inhibitory factor (LIF).
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were grown in 15-cm plates until 70% confluency and crosslinked in 1% formaldehyde in growth medium for 10 minutes at room temperature (RT) in a shaker. To stop the fixation glycine was added to a final concentration of 0.125 M and incubated for 5 minutes at RT. Cells were then washed twice with ice cold PBS and harvested by gently scrapping on ice in PBS plus protease inhibitors. Cells from two 15-cm plates were pooled together and centrifuged at 3,400 x g, 4ºC, 5 minutes.
Libraries were prepared according to Illumina instructions.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
ChIP-seq experiment
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| Data processing |
ChIP-seq analysis: Alignment: Sequence reads of the samples without were mapped to the mouse genome (mm10) using BOWTIE (PubMed ID 19261174) with the option -m 1. ChIPseq profiles were produced by SeqCode (http://ldicrocelab.crg.eu/) using buildChIPprofile function, in BedGraph format.
Genome_build: mm10
Supplementary_files_format_and_content: Files *.bdg.gz (BedGraph, genome-wide ChIP-seq)
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| Submission date |
May 15, 2020 |
| Last update date |
Aug 24, 2021 |
| Contact name |
Mar Gonzalez-Ramirez |
| E-mail(s) |
mar.bellvisgonzalez@gmail.com
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| Organization name |
Center for Genomic Regulation (CRG)
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| Street address |
C/ Dr Aiguader 88
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| City |
Barcelona |
| ZIP/Postal code |
08003 |
| Country |
Spain |
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| Platform ID |
GPL13112 |
| Series (1) |
| GSE150633 |
Differential contribution to gene expression prediction of histone modifications at enhancers or promoters |
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| Relations |
| BioSample |
SAMN14931271 |
| SRA |
SRX8346882 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4555158_H3_mESC_34279.bedgraph.gz |
122.2 Mb |
(ftp)(http) |
BEDGRAPH |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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