Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
SMC1A

Cell type

Cell type Class
Digestive tract
Cell type
DKO
NA
NA

Attributes by original data submitter

Sample

source_name
DKO_SMC1_ChIPSeq
cell line
DKO
tissue source
Colon
cell type
Colorectal carcinoma cell line
chip antibody
SMC1 (Bethyl #A300-005A)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cultured cells were fixed with 1% formaldehyde for 15 min and quenched with 0.125 M glycine. Chromatin was isolated by the addition of lysis buffer, followed by disruption with a Dounce homogenizer. Lysates were sonicated and the DNA sheared to an average length of 300-500 bp. Genomic DNA (Input) was prepared by treating aliquots of chromatin with RNase, proteinase K and heat for de-crosslinking, followed by ethanol precipitation. Pellets were resuspended and the resulting DNA was quantified on a NanoDrop spectrophotometer. Extrapolation to the original chromatin volume allowed quantitation of the total chromatin yield. An aliquot of chromatin (30 ug) was precleared with G (for Pol2-Ser2 and Pol2-Ser5) or A (for CTCF, RAD21, SMC1, and H3K27) agarose beads (Invitrogen). Genomic DNA regions of interest were isolated using 4 ug of antibody against each of the protein. Complexes were washed, eluted from the beads with SDS buffer, and subjected to RNase and proteinase K treatment. Crosslinks were reversed by incubation overnight at 65 C, and ChIP DNA was purified by phenol-chloroform extraction and ethanol precipitation. Illumina sequencing libraries were prepared from the ChIP and Input DNAs by the standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation. After a final PCR amplification step, the resulting DNA libraries were quantified and sequenced on Illumina's NextSeq 500 (75 nt reads, single end).

Sequencing Platform

instrument_model
NextSeq 500

hg19

Number of total reads
57517115
Reads aligned (%)
83.6
Duplicates removed (%)
12.8
Number of peaks
32011 (qval < 1E-05)

hg38

Number of total reads
57517115
Reads aligned (%)
85.3
Duplicates removed (%)
11.6
Number of peaks
31820 (qval < 1E-05)

Base call quality data from DBCLS SRA