SRX067463
GSM733712: Bernstein HMEC H3K4me3

Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3K4me3

Cell type

Cell type Class
Breast
Cell type
HMEC
Primary Tissue
Breast
Tissue Diagnosis
Normal

Attributes by original data submitter

Sample

source_name
HMEC
biomaterial_provider
Lonza
donor_id
ENCDO344AAA,ENCDO830BUW
biomaterial_type
primary cell
cell_type
mammary epithelial cell
lab
Broad
lab description
Bernstein - Broad Institute
datatype
ChipSeq
datatype description
Chromatin IP Sequencing
cell organism
human
cell description
mammary epithelial cells
cell karyotype
normal
cell lineage
ectoderm
cell sex
U
antibody antibodydescription
rabbit polyclonal. Antibody Target: H3K4me3
antibody
H3K4me3
antibody targetdescription
Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated.
antibody vendorname
1)abcam; 2)Millipore
antibody vendorid
ab8580; 07-473
treatment
None
treatment description
No special treatment or protocol applies
control
std
control description
Standard input signal for most experiments.
controlid
wgEncodeEH000093
labversion
Illumina_GA2e and Illumina_GA2x
replicate
1,2
softwareversion
ScriptureVPaperR3

Sequenced DNA Library

library_name
GSM733712: Bernstein_HMEC_H3K4me3
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP

Sequencing Platform

instrument_model
Illumina Genome Analyzer II

Where can I get the processing logs?

Read processing pipeline log

hg38

Number of total reads
49635576
Reads aligned (%)
60.5
Duplicates removed (%)
9.8
Number of peaks
31155 (qval < 1E-05)

hg19

Number of total reads
49635576
Reads aligned (%)
60.0
Duplicates removed (%)
10.7
Number of peaks
31553 (qval < 1E-05)

Base call quality data from DBCLS SRA