Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3K4me3

Cell type

Cell type Class
Kidney
Cell type
293
Primary Tissue
Kidney
Tissue Diagnosis
Normal

Attributes by original data submitter

Sample

source_name
HEK293 Flp-in T-REx pcDNA5 Rpb1 Amr WT
cell line
HEK293
growth conditions
DMEM 10% FCS,+hygromycin+blasticidin+doxycycline+a-amanitin
antibody
rabbit anti H3K4me3 (Zhang et al EMBO J, 24: 2379, 2005 )

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 2000

hg38

Number of total reads
7895568
Reads aligned (%)
97.0
Duplicates removed (%)
3.1
Number of peaks
23842 (qval < 1E-05)

hg19

Number of total reads
7895568
Reads aligned (%)
96.5
Duplicates removed (%)
3.6
Number of peaks
23778 (qval < 1E-05)

Base call quality data from DBCLS SRA