Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
SUPT5H

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
HCT116
cell line/genotype
HCT116
spike in
mouse M12
growth conditions
McCoy's 10% FCS 0.1%DMSO
antibody
rabbit anti Spt5 (Glover-Cutter et al NSMB 15:71-78, 2008)
experiment
Chromatin IP against Spt5

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
cross-linked Chromatin was sonicated with a Bioruptor 1-2 mg of cross-linked extract was immunoprecipitated, and prepared for illumina library construction by repair with Klenow, T4 DNA polymerase and T4 polynucleotide kinase, A-tailing with Klenow exo-, ligation to branched adaptors, gel purification of ~200bp fragments, and amplification (18cycles) with Illumina Tru-seq primers using Phusion DNA polymerase.

Sequencing Platform

instrument_model
Illumina HiSeq 4000

hg19

Number of total reads
39956550
Reads aligned (%)
78.8
Duplicates removed (%)
12.5
Number of peaks
17220 (qval < 1E-05)

hg38

Number of total reads
39956550
Reads aligned (%)
79.5
Duplicates removed (%)
12.0
Number of peaks
17178 (qval < 1E-05)

Base call quality data from DBCLS SRA