Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
SUPT6H

Cell type

Cell type Class
Digestive tract
Cell type
HCT 116
Primary Tissue
Colon
Tissue Diagnosis
Carcinoma

Attributes by original data submitter

Sample

source_name
AS CDK12 HCT116 cells
treatment
DMSO
chip antibody
SPT6 (Novus Biologicals, NB100-2582)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIP was performed with SPT6 antibody. Immunoprecipitated DNA was dissolved in H2O and DNA concentration was measured by Qubit fluorometer (Thermo Fisher Scientific) and 3.5 ng of immunoprecipitated DNA was used for library preparation. ChIP-seq libraries were generated using the KAPA Biosystems Hyper Prep Kit (KK8502) with KAPA Pure Beads (KK8001), and NEBNext Multiplex Oligos for Illumina (Index Primers Set 1 (NEB, E7335S) with 15x PCR cycles for library amplification, as per manufacturer's instructions. Libraries were run on the fragment analyser (Advanced Analytical Technologies) to check the quality and were sequenced with 50 bp single-end reads on Illumina HiSeq 2500 (VBCF Vienna).

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg19

Number of total reads
31242680
Reads aligned (%)
51.4
Duplicates removed (%)
47.6
Number of peaks
2467 (qval < 1E-05)

hg38

Number of total reads
31242680
Reads aligned (%)
52.3
Duplicates removed (%)
46.9
Number of peaks
2411 (qval < 1E-05)

Base call quality data from DBCLS SRA