Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
RARA

Cell type

Cell type Class
Others
Cell type
Adenoid cystic carcinoma
NA
NA

Attributes by original data submitter

Sample

source_name
RAR ChIP on vehicle-treated ACC
xenograft
ACCx9
agent
vehicle
chip antibody
RAR (Santa Cruz, catalog# sc-773X, lot# B1715)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Frozen primagrafts were mechanically dissociated, formaldehyde cross-linked, and collected. ChIP was performed with 10 antibodies against c-myb (Bethyl, A304-136A), RAR (Santa Cruz, sc-773X), and H3K27ac (Abcam, ab4729). DNA was then de-cross-linked from pulled down proteins and purified by phenol:chloroform:isoamyl alcohol extraction. The NEBNext multiplex oligos for Illumina Kit (NEB) was used to make the samples suitable for multiplexing. The PCR reaction was run for 18 cycles. The indexed libraries were purified for 150 and 350 bp. The concentration of the isolated libraries was estimated with a high-sensitivity DNA chip from Agilent according to manufacturer’s protocol and libraries were mixed in equal quantities and sequenced on Illumina Hi-Seq2500. Index sequences from multiplexed primers were used to identify treatment group and reads were demultiplexed using a perl script.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg19

Number of total reads
29167321
Reads aligned (%)
89.4
Duplicates removed (%)
3.6
Number of peaks
1280 (qval < 1E-05)

hg38

Number of total reads
29167321
Reads aligned (%)
91.5
Duplicates removed (%)
2.1
Number of peaks
1223 (qval < 1E-05)

Base call quality data from DBCLS SRA