Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
RARA

Cell type

Cell type Class
Blood
Cell type
TSU-1621MT
NA
NA

Attributes by original data submitter

Sample

source_name
TSU-1621-MT_ChIP RAR alpha
cell line
TSU-1621-MT
antibody target
RAR
chip antibody vendor
Diagenode

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Chromatin was sonicated and used for ChIP seq using specific antibodies. RNA was extracted using qiagen RNeasy kit according to manufacturer instructions and total RNA was treated using Ribo-zero to remove rRNA according to manufacturer instructions. ChIP seq and RNA-seq libraries were prepared according to Illumina's standard protocol.

Sequencing Platform

instrument_model
Illumina Genome Analyzer IIx

hg19

Number of total reads
21070685
Reads aligned (%)
30.0
Duplicates removed (%)
66.8
Number of peaks
15957 (qval < 1E-05)

hg38

Number of total reads
21070685
Reads aligned (%)
31.3
Duplicates removed (%)
65.7
Number of peaks
16062 (qval < 1E-05)

Base call quality data from DBCLS SRA