Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Unclassified
Antigen
Unclassified

Cell type

Cell type Class
Blood
Cell type
SEM
Primary Tissue
Blood
Tissue Diagnosis
Leukemia

Attributes by original data submitter

Sample

source_name
Leukemia cell line (SEM)
cell line
Leukemia cell line; SEM
cell type
Paediatric pro B-cell line derived from ALL with t(4;11)(q21;q23) translocation

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIP-seq: Fixed cells were lysed in 1% SDS lysis buffer. Samples were sonicated and protein-DNA complexes were isolated with antibody. Nascent RNA-seq: 108 4sU-treated cells were lysed in 10ml Trizol. RNA was extracted using chloroform and precipitated with EtOH. 4sU RNA was biotinylated with 1mg/ml Biotin-HPDP and nascent RNA was enriched for using streptavidin-coated beads. Libraries were prepared according to Illumina's protocol accompanying the DNA Library Prep Master Mix Set (Part# E6040) or Ultra RNA Library Prep Master Mix Set (Part# E7530).

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg38

Number of total reads
34072527
Reads aligned (%)
99.0
Duplicates removed (%)
1.8
Number of peaks
1031 (qval < 1E-05)

hg19

Number of total reads
34072527
Reads aligned (%)
97.9
Duplicates removed (%)
2.1
Number of peaks
784 (qval < 1E-05)

Base call quality data from DBCLS SRA