|
Status |
Public on Dec 04, 2020 |
Title |
H3K4me3.FS.2 |
Sample type |
SRA |
|
|
Source name |
5ar1
|
Organism |
Mus musculus |
Characteristics |
histone mark: H3K4me3 cell line: 5ar1 condition: Formative replicate: Rep 2
|
Growth protocol |
ES cells were cultured in 2iL, FS cells were cultured in A3XR, AF cells were cultured in AF and AFX cells were cultured in AFX
|
Extracted molecule |
genomic DNA |
Extraction protocol |
Chromatin was cross-linked with 1% formaldehyde for 10 minutes at RT and quenched with 125 mM Glycine for 5 minutes at RT with rotation. After cell pellets were lysed, sonication was performed for 16 cycle on High setting, 30sec ON/30 sec OFF cycle by Bioruptor (Diagnode), 2x107 cells per 300 µl in Bioruptor tube (Diagnode). 10% inputs were collected for the later library construction. Chromatin was immunoprecipitated with 2 µg of each antibodies and 20 µl of Protein G Dynabeads (Invitrogen) were used against 3x106 cells. After the washes, DNA was eluted and each samples were treated with 2.5 µg/ml RNase A at 37˚C for 30 minutes followed by 87.5 µg/ml Proteinase K at 55˚C for 1 hour. DNA was purified with PCR clean-up kit (Qiagen). Libraries were prepared by NEXTflex Rapid DNA-Seq Kit 2.0 bundle with 96 HT barcodes (ParkinElmer).
|
|
|
Library strategy |
ChIP-Seq |
Library source |
genomic |
Library selection |
ChIP |
Instrument model |
Illumina HiSeq 4000 |
|
|
Data processing |
The quality of the data was assessed using FastQC and MultiQC The reads were aligned using bwa mem v0.7.10-r789 (default parameters) and BAM files sorted with samtools v1.9 MT, X, Y chromosomes and scaffolds were removed from BAM files Peaks were called using macs2 v2.2.6 (-f BAMPE -q 0.05) Genome browser tracks were created using deepTools bamCoverage v3.3.1 (--binSize 5 -of bigwig) Genome_build: GRCm38.p6 Supplementary_files_format_and_content: Bigwig tracks, created after removal of MT, X, Y chromosomes and scaffolds
|
|
|
Submission date |
Aug 14, 2020 |
Last update date |
Dec 05, 2020 |
Contact name |
Irina Mohorianu |
E-mail(s) |
data-submissions@stemcells.cam.ac.uk
|
Organization name |
University of Cambridge
|
Department |
Wellcome-MRC Cambridge Stem Cell Institute
|
Street address |
Puddicombe Way
|
City |
Cambridge |
ZIP/Postal code |
CB2 0AW |
Country |
United Kingdom |
|
|
Platform ID |
GPL21103 |
Series (2) |
GSE156261 |
Capture of mouse and human stem cells with features of formative pluripotency [ChIP-seq] |
GSE156589 |
Capture of mouse and human stem cells with features of formative pluripotency |
|
Relations |
BioSample |
SAMN15822325 |
SRA |
SRX8948727 |