Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Unclassified
Antigen
Unclassified

Cell type

Cell type Class
Blood
Cell type
CLL
Tissue
blood
Lineage
mesoderm
Description
chronic lymphocytic leukemia cell, T-cell lymphocyte

Attributes by original data submitter

Sample

source_name
Human Peripheral Blood
tissue
Human Peripheral Blood
tumor type
Chronic lymphocytic leukemia
tumor classification
IGHV Mutated CLL

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
For hMeDIP and MeDIP seq, genomic DNA was extracted using DNA extraction kit, Total RNA for RNA seq was extracted using RNA extraction kit and then quality was asses using Bioanalyser. For ChIP seq chromatin was extracted, sponicated and specific antibody was used to pulldown the ChIP DNA. Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3' end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg38

Number of total reads
56400283
Reads aligned (%)
99.4
Duplicates removed (%)
4.5
Number of peaks
46127 (qval < 1E-05)

hg19

Number of total reads
56400283
Reads aligned (%)
98.9
Duplicates removed (%)
5.3
Number of peaks
45844 (qval < 1E-05)

Base call quality data from DBCLS SRA