Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
FOXA1

Cell type

Cell type Class
Unclassified
Cell type
Unclassified
NA
NA

Attributes by original data submitter

Sample

source_name
Mice treated with ICI
tissue
human breast cancer cells from PDX mice
replicate number
first replicate
chip antibody
FoxA1 rabbit ab23738 (lot GR292351-2)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Tumors were frozen in liquid nitrogen. For ChIP the detailed protocol from Scmidt D. et al (Methods 2009) were followed, ie samples were pulverised and x-linked in PBS with 0,5% folmaldehyde for 10 minutes, then proceeded with Lysis buffers. Library construction: ThruPLEX (Rubicon Genomics, Ann Arbor, MI, USA) supplied by Diagenode. The manufacturer’s instructions were followed.

Sequencing Platform

instrument_model
NextSeq 500

hg19

Number of total reads
23482024
Reads aligned (%)
67.0
Duplicates removed (%)
12.8
Number of peaks
2572 (qval < 1E-05)

hg38

Number of total reads
23482024
Reads aligned (%)
67.3
Duplicates removed (%)
12.6
Number of peaks
2617 (qval < 1E-05)

Base call quality data from DBCLS SRA