Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3K4me3

Cell type

Cell type Class
Uterus
Cell type
HeLa
Primary Tissue
Cervix
Tissue Diagnosis
Adenocarcinoma

Attributes by original data submitter

Sample

source_name
Hela
cell line
HeLa
cell stage
G2M
drug treatment
RO-3306
chip antibody
H3K4me3(homemade)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
For ChIP-seq, HeLa cells were crosslinked with 1% paraformaldehyde for 10 minutes and were quenched by glycine for 5 minutes at room temperature. Fixed chromatin was sonicated with a Misionix sonicator 3000 and immunoprecipitated with a specific antibody. ChIP-sequencing libraries were prepared with Illumina’s Tru-seq DNA sample prep kit using standard protocols. Nascent RNA-seq libraries were prepared with Illumina’s Ribo-Zero Gold and TruSeq RNA sample Prep Kit using standard protocols.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg38

Number of total reads
34248707
Reads aligned (%)
97.7
Duplicates removed (%)
16.9
Number of peaks
21355 (qval < 1E-05)

hg19

Number of total reads
34248707
Reads aligned (%)
97.3
Duplicates removed (%)
17.7
Number of peaks
21423 (qval < 1E-05)

Base call quality data from DBCLS SRA