Sample information curated by ChIP-Atlas

Antigen

Antigen Class
RNA polymerase
Antigen
RNA polymerase II

Cell type

Cell type Class
Blood
Cell type
GM19193
Tissue
blood
Lineage
mesoderm
Description
lymphoblastoid, International HapMap Project, Yoruba in Ibadan, Nigera, treatment: Epstein-Barr Virus transformed

Attributes by original data submitter

Sample

source_name
lymphoblastoid cell line
biomaterial_provider
GM19193
cell line
GM19193
cell type
lymphoblastoid cell line
population
YRI
ethnicity
Yoruba
country of origin
Nigeria
chip antibody
PolII (Santa Cruz sc-9001)
chip antibody manufacturer
Santa Cruz

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Chromatin was extracted using protocol described in Cain et al. 2011, except that for some samples chromatin was sheared with a Covaris S2 (settings: 40 min duty cycle 20%, intensity 8, 200 cycles/burst, 500 uL at a time in 12 x 24 mm tubes). Prepared Illumina sequencing libraries as described by the ENCODE Project Consortium (2011), starting with 20 uL of ChIP output or 4 ng of pooled input sample.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg38

Number of total reads
167057685
Reads aligned (%)
95.5
Duplicates removed (%)
50.8
Number of peaks
11955 (qval < 1E-05)

hg19

Number of total reads
167057685
Reads aligned (%)
94.6
Duplicates removed (%)
52.5
Number of peaks
12590 (qval < 1E-05)

Base call quality data from DBCLS SRA