SRX067456
GSM733705: Bernstein HMEC H3K4me1

Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3K4me1

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
ENCDO830BUW,ENCDO344AAA
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: H3K4me1
antibody
H3K4me1
antibody targetdescription
Histone H3 (mono methyl K4). Is associated with enhancers, and downstream of transcription starts.
antibody vendorname
abcam
antibody vendorid
ab8895
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
GSM733705: Bernstein_HMEC_H3K4me1
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
50790210
Reads aligned (%)
74.4
Duplicates removed (%)
7.1
Number of peaks
62432 (qval < 1E-05)

hg19

Number of total reads
50790210
Reads aligned (%)
74.0
Duplicates removed (%)
7.7
Number of peaks
62065 (qval < 1E-05)

Base call quality data from DBCLS SRA