|
| Status |
Public on Dec 04, 2020 |
| Title |
H3K4me3.AFX.1 |
| Sample type |
SRA |
| |
|
| Source name |
AFX6
|
| Organism |
Mus musculus |
| Characteristics |
histone mark: H3K4me3
cell line: AFX6
condition: Primed
replicate: Rep 1
|
| 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 |
SAMN15822291 |
| SRA |
SRX8948722 |
