Curated Sample Data


Genome
hg19
Antigen Class
Histone
Antigen
H3K4me2
Cell type Class
Blood
Cell type
Acute myeloid leukemia

Cell type information


NA
NA

Attributes by Original Data Submitter


source_name
AML blast cells from blood
sample id
AML 11
gender
male
chip antibody
H3K4me2 (07-030 Upstate)

Metadata from Sequence Read Archive

Library Description


library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
cells were fixed with 1% formaldehyde for 10 min. After fixation, nuclei were isolated, the nuclear DNA was digested by micrococcal nuclease to 150-200 bp DNA fragments, the DNA fragments with attached proteins were resuspended in SDS-containing lysis buffer, and immunoprecipitated by antibodies against various histone modifications. For Illumina Hi-Seq 2500 sequencing we used New England BioLabs NEBNext ChIP-Seq library preparation reagent set for Illumina and and constructed library as described in the E6240 instruction manual. For SOLiD sequencing we used Applied Biosystems SOLiD 4 System and constructed library as described in the SOLiD 4 System Library Preparation Guide.

Platform Information


instrument_model
Illumina HiSeq 2500

External Database Query

Logs in read processing pipeline


Number of total reads
33955356
Reads aligned (%)
100.0
Duplicates removed (%)
17.1
Number of peaks
52061 (qval < 1E-05)

Sequence Quality Data from DBCLS SRA