Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3K4me2

Cell type

Cell type Class
Digestive tract
Cell type
Colonic adenoma
NA
NA

Attributes by original data submitter

Sample

source_name
Primary colonic adenoma, snap-frozen tissue
tissue
Primary colonic adenoma
chip antibody
H3K4me2 (Millipore, catalog# 07-030, lot# 2019745)
patient
2

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIPseq: Lysates were clarified from micrococcal nuclease digested or sonicated or and histone-DNA or CNOT3-DNA complexed were isolated with antibody. RNAseq: Total RNA was extracted with TRIzol reagent (Invitrogen) and the RNeasy Mini Kit (Qiagen). RNA was treated with the Turbo DNA-free kit (Ambion) to remove genomic DNA. For ChIPseq:ThruPLEX-FD kits (Rubicon Genomics) was used and 50 bp single-end reads were sequenced on a HiSeq2000 instrument (Illumina). For RNAseq: TruSeq RNA Sample Preparation Kit (Illumina) was used according to the manufacturer's instructions and 75 bp single-end reads were sequenced on an Illumina NextSeq 500 instrument.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg38

Number of total reads
114749301
Reads aligned (%)
92.7
Duplicates removed (%)
18.0
Number of peaks
1474 (qval < 1E-05)

hg19

Number of total reads
114749301
Reads aligned (%)
92.2
Duplicates removed (%)
19.1
Number of peaks
1277 (qval < 1E-05)

Base call quality data from DBCLS SRA