Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
RAD21

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
HCT-116 cell line
genotype
Rad21Degron
cell type
colon carcinoma cell line
chip antibody
Abcam, ab992

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Promoter Capture HiC-Seq: we used the same protocol at Montefiori et al., (Elife, 2018 Jul 10; 7) BS-seq: Genomic DNA was isolated from 3×106 cells using Qiagen DNeasy blood and tissue kit (Cat #: 69506). The bisulfite conversion was performed using the EZ DNA Methylation-Gold™ Kit (Cat #: D5005) from Zymo Research. Whole-genome bisulfite sequencing libraries were prepared from 50 ng converted DNA using Illumina TruSeq® DNA Methylation Kit (Cat #: EGMK91324), which was performed following the manufacturer's protocol. Promoter Capture HiC-seq: DNA was isolated and prepared for paired-end Illumina sequencing following the genomic DNA protocol. 100 cycles of sequencing data were acquired on the HiSeq 3000 (Illumina). BS-seq: standard RNA-Seq library preparation was performed following the genomic DNA protocol with 20% PhiX. 50 cycles of sequencing data were acquired on HiSeq 3000 (Illumina)

Sequencing Platform

instrument_model
Illumina HiSeq 3000

hg19

Number of total reads
31400648
Reads aligned (%)
87.7
Duplicates removed (%)
9.9
Number of peaks
1140 (qval < 1E-05)

hg38

Number of total reads
31400648
Reads aligned (%)
90.1
Duplicates removed (%)
8.3
Number of peaks
922 (qval < 1E-05)

Base call quality data from DBCLS SRA