Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3K27me1

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
HCT116
transfection
siUXT
antibody
H3K27me1

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
For RNASeq 10ug total RNA was used, and mRNA purification was performed using oligo-dT magnic beads(NEBNext PolyA mRAN magnetic isolation module # E7490). mRNA was fragmented and reverse transcript into 200-400bp dscDNA for library construction(NEB # E7525 # E6111). For ChIPSeq chromatin was fragmented into single nucleosome by micrococcal nuclease, and H3K27me1(Millipore Cat. 17-643),H3K27me2(Active Motif Cat. 61435),H3K27me3(Millipore Cat. 17-622 ) ChIP grade antibody were used for ChIP. ChIPed DNA was eluted in TE buffer. Rubicon ThruPLEX DNA-seq 48D kit was used for RNASeq and ChIPSeq library construction. Brifely, about 100ng dscDNA was used as initiation for end repair and prepared for adaptor ligation. After adaptor ligation, PCR amplification with 15 cycles for each library and gel selection was used for library size selection and purification. For ChIPSeq library construction, 10ng-20ng ChIP eluted DNA was used as initiation and after adaptor ligation, PCR with 15-18 cycles was used to amplify library. Size selection of ChIPSeq library by electrophoresis gel.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg38

Number of total reads
8411550
Reads aligned (%)
88.0
Duplicates removed (%)
18.8
Number of peaks
200 (qval < 1E-05)

hg19

Number of total reads
8411550
Reads aligned (%)
86.7
Duplicates removed (%)
19.3
Number of peaks
175 (qval < 1E-05)

Base call quality data from DBCLS SRA