Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
MED1

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
chip antibody
MED1 (Bethyl, A300-793A/2)

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 2500

hg19

Number of total reads
25888180
Reads aligned (%)
156.8
Duplicates removed (%)
14.0
Number of peaks
28332 (qval < 1E-05)

hg38

Number of total reads
25888180
Reads aligned (%)
158.0
Duplicates removed (%)
13.8
Number of peaks
28485 (qval < 1E-05)

Base call quality data from DBCLS SRA