Sample information curated by ChIP-Atlas

Antigen

Antigen Class
No description
Antigen
NA

Cell type

Cell type Class
No description
Cell type
NA
NA
NA

Attributes by original data submitter

Sample

gap_accession
phs000791
submitter handle
NIDA_RoadmapEpigenomics_UCSF
biospecimen repository
NIDA_RoadmapEpigenomics_UCSF
study name
Integrated Epigenetic Maps of Human Embryonic, Extraembryonic and Adult Cells
study design
Control Set
biospecimen repository sample id
PF006-DNA
submitted sample id
PF006-DNA
submitted subject id
H1
gap_sample_id
1461269
gap_subject_id
1129088
sex
male
body site
Embryo ICM
histological type
Embryonic stem cell
analyte type
DNA
is tumor
No
gap_consent_code
1
gap_consent_short_name
HMB

Sequenced DNA Library

library_name
HS1032
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Refer to document 'REMC ChIP and Library Construction Protocol' from the Farnham Lab at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)

Sequencing Platform

instrument_model
Illumina Genome Analyzer II

hg38

Number of total reads
26961548
Reads aligned (%)
44.2
Duplicates removed (%)
3.4
Number of peaks
590 (qval < 1E-05)

hg19

Number of total reads
26961548
Reads aligned (%)
43.8
Duplicates removed (%)
4.0
Number of peaks
559 (qval < 1E-05)

Base call quality data from DBCLS SRA