Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3K27me3

Cell type

Cell type Class
Blood
Cell type
CCRF-CEM
Primary Tissue
Blood
Tissue Diagnosis
Leukemia Acute Lymphocytic

Attributes by original data submitter

Sample

source_name
CCRF-CEM cell lines
cell type
CCRF-CEM Human T-cell lymphoblastic cell line
antibody
anti-H3K27me3 antibody (Active Motif Cat #39155)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Lysates were clarified from sonication which was performed to fragment chromatin to 200-700 bp size range using a Covaris E220 Focused-ultrasonicator. Immunoprecipitation was then performed on 5 million cells with H3K27me3 antibody Libraries were prepared according to Illumina's instructions. Briefly, DNA was end-repaired using End-It DNA End-Repair Kit (Epicenter Cat. No. ER0720) and 'A' Base was added to the 3' End of the DNA fragments. After Ligation of Adapters to the Ends of the DNA Fragments, adapter-modified DNA fragments were enriched by PCR. SPRI bead size selection was used to remove remaining primers and select a size-range of templates. The Libraries were sequenced with the Illumina NextSeq 500 platfom following the manufacturer's protocols.

Sequencing Platform

instrument_model
NextSeq 500

hg38

Number of total reads
24650677
Reads aligned (%)
98.3
Duplicates removed (%)
3.6
Number of peaks
402 (qval < 1E-05)

hg19

Number of total reads
24650677
Reads aligned (%)
97.6
Duplicates removed (%)
3.7
Number of peaks
314 (qval < 1E-05)

Base call quality data from DBCLS SRA