Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
NRF1

Cell type

Cell type Class
Blood
Cell type
NAMALWA
Primary Tissue
Blood
Tissue Diagnosis
Malignant Lymphoma - Burkitts Type

Attributes by original data submitter

Sample

source_name
Namalwa B lymphoblasts
cell type
Namalwa B lymphoblasts
chip antibody
anti-NRF1 [in house antibody]

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody for ChIP-seq. RNA was harvested using Trizol reagent and mRNA isolated with polydT dynabeads. Strand-specific protocol was used with 5 ug of mRNA for the construction of the library. Libraries were prepared according to Illumina's instructions. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for a controlled (qPCR estimated) cycles and library fragments of ~220 bp were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer (GA), GAIIx, or Hiseq2000) following the manufacturer's protocols.

Sequencing Platform

instrument_model
Illumina Genome Analyzer IIx

hg19

Number of total reads
12620990
Reads aligned (%)
66.6
Duplicates removed (%)
20.6
Number of peaks
9202 (qval < 1E-05)

hg38

Number of total reads
12620990
Reads aligned (%)
67.6
Duplicates removed (%)
20.4
Number of peaks
8995 (qval < 1E-05)

Base call quality data from DBCLS SRA