Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
CDK8

Cell type

Cell type Class
Blood
Cell type
MM.1S
Primary Tissue
Blood
Tissue Diagnosis
Multiple Myeloma

Attributes by original data submitter

Sample

source_name
Multiple myeloma
cell line
MM1.S
chip antibody
CDK8
chip antibody
Santa Cruz
chip antibody
SC-1521
barcode removed
CAGATC

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 500 bp were immunoprecipitated using different antibodies. Purified immunoprecipitated DNA were prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 300bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
43719232
Reads aligned (%)
89.8
Duplicates removed (%)
6.8
Number of peaks
6556 (qval < 1E-05)

hg38

Number of total reads
43719232
Reads aligned (%)
91.5
Duplicates removed (%)
5.9
Number of peaks
6669 (qval < 1E-05)

Base call quality data from DBCLS SRA