Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3K4me3

Cell type

Cell type Class
Unclassified
Cell type
Unclassified
NA
NA

Attributes by original data submitter

Sample

source_name
WT mouse
p53 mutation status
WT
treatment
Untreated
antibody
H3K4me3 Abcam (ab8580)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
For ChIP-seq, cells were crosslinked with formaldehyde (1% final) for 10min at room temperature, and harvested for sonication. Nuclei were extracted and chromatin was sheared to an average size of 200bp using a Covaris S220 sonicator For RNA-seq, polyA+ RNA was isolated by two rounds of polyA selection using the Life Technologies mRNADirect kit per manufacturer's recommendations. Sequencing libraries for ChIP-seq were constructed using the NEBNext Ultra kit as per manufacturer's recommended instructions. Sequencing libraries for polyA+, stranded-RNA-seq were constructed using the NEBnext Ultra Directional RNAseq kit as per manufacturer's recommended instructions.

Sequencing Platform

instrument_model
NextSeq 500

mm10

Number of total reads
42567054
Reads aligned (%)
68.8
Duplicates removed (%)
39.9
Number of peaks
20392 (qval < 1E-05)

mm9

Number of total reads
42567054
Reads aligned (%)
68.7
Duplicates removed (%)
39.9
Number of peaks
20363 (qval < 1E-05)

Base call quality data from DBCLS SRA