Sample information curated by ChIP-Atlas

Antigen

Antigen Class
RNA polymerase
Antigen
RNA polymerase II

Cell type

Cell type Class
Blood
Cell type
GM19239
Tissue
blood
Lineage
mesoderm
Description
B-lymphocyte, 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
GM19239
cell line
GM19239
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
204235178
Reads aligned (%)
98.2
Duplicates removed (%)
54.1
Number of peaks
16654 (qval < 1E-05)

hg19

Number of total reads
204235178
Reads aligned (%)
97.2
Duplicates removed (%)
55.6
Number of peaks
17200 (qval < 1E-05)

Base call quality data from DBCLS SRA