Curated Sample Data


Genome
hg19
Antigen Class
Histone
Antigen
H3K4me2
Cell type Class
Blood
Cell type
Granulocytes

Cell type information


MeSH Description
Leukocytes with abundant granules in the cytoplasm. They are divided into three groups according to the staining properties of the granules: neutrophilic, eosinophilic, and basophilic. Mature granulocytes are the NEUTROPHILS; EOSINOPHILS; and BASOPHILS.

Attributes by Original Data Submitter


source_name
Granulocyte from blood
sample id
Granulocyte 1
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
31151551
Reads aligned (%)
100.0
Duplicates removed (%)
19.7
Number of peaks
41365 (qval < 1E-05)

Sequence Quality Data from DBCLS SRA