Curated Sample Data


Genome
hg19
Antigen Class
Histone
Antigen
H3K4me2
Cell type Class
Blood
Cell type
RS4-11

Cell type information


Primary Tissue
Blood
Tissue Diagnosis
Leukemia Acute Lymphocytic

Attributes by Original Data Submitter


source_name
RS4;11_Dex_1hr
cell line
RS4;11
cell type
acute lymphoblastic leukemia cell line
treated with
10 nM dexamethasone for 1 hour
chip antibody
H3K4me2 (Millipore, 07-030)

Metadata from Sequence Read Archive

Library Description


library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Histone modification ChIP and DHS were performed on MNase-digested and DNase-digested native chromatin, respectively. Transcription factor ChIP was performed on sonicated nuclei isolated from cells treated with EGS and formaldehyde cross-linking agents. 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 (3' to 5' 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 7-9 cycles and library fragments of ~270 bp for histone modification libraries, ~75 bp for DHS libraries, and ~320 bp for transcription factor libraries (insert plus adaptor and PCR primer sequences) were size selected using PippinPrep (Sage Science) 2% agarose gels. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the HiSeq2000 following the manufacturer's protocols.

Platform Information


instrument_model
Illumina HiSeq 2000

External Database Query

Logs in read processing pipeline


Number of total reads
40247322
Reads aligned (%)
99.3
Duplicates removed (%)
26.0
Number of peaks
91100 (qval < 1E-05)

Sequence Quality Data from DBCLS SRA