Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Unclassified
Antigen
Unclassified

Cell type

Cell type Class
Blood
Cell type
TEX
NA
NA

Attributes by original data submitter

Sample

source_name
TEX
cell type
TEX
transgene
HIST1H3H
mutation
WT
chip antigen
Input

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
For crosslinked ChIP, cells were crosslinked (1% formaldehyde, 10mins) and sonicated. Protein:DNA complexes were immunoprecipitated with specific antibodies pre-bound to protein A or goat anti-mouse IgG magnetic beads. Eluted DNA underwent crosslink reversal, and were purified using Qiagen PCR purification columns. For RNA extraction, 1 million TEX cells were pelleted, washed with PBS and resuspended in 350ul RLT buffer (Qiagen-RNAeasy mini kit) with beta-mercaptoethanol. The suspension was then stored at -80oC until frozen. Sample was thawed and RNA extraction was performed using Qiagen's RNAeasy mini kit as per the manufacturer's instructions. The eluted ChIP DNA undewent adaptor ligation based library construction for single-end 50bp Illumina sequencing on HiSeq 4000. RNA-seq library preparation was performed with ribosomal RNA (rRNA) depletion according to instructions from the manufacturer (Epicentre) to achieve greater coverage of mRNA and other long non-coding transcripts, paired-end sequencing (100 bp) was performed on the Illumina HiSeq 2500 or 4000 platform.

Sequencing Platform

instrument_model
Illumina HiSeq 4000

hg38

Number of total reads
42076944
Reads aligned (%)
93.9
Duplicates removed (%)
5.2
Number of peaks
1206 (qval < 1E-05)

hg19

Number of total reads
42076944
Reads aligned (%)
93.0
Duplicates removed (%)
6.3
Number of peaks
1322 (qval < 1E-05)

Base call quality data from DBCLS SRA