Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
FOXA1

Cell type

Cell type Class
Uterus
Cell type
Ishikawa
Primary Tissue
Uterus
Tissue Diagnosis
Adenocarcinoma

Attributes by original data submitter

Sample

source_name
Ishikawa cell line, FOXA1-CHIP
cell line
Ishikawa
chip antibody
FoxA1 rabbit ab23738 (lot GR292351-2)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Libraries from ChIP samples were made with two different kits. With Illumina (San Diego, CA) TruSeq™ DNA Sample Preparation this modifications were used: ligation with of 1/10th the manufacturers recommended adapter amounts and agarose gel selection of DNA fragments in the 200-500 bp size range. For ThruPLEX (Rubicon Genomics, Ann Arbor, MI, USA. Supplied by Diagenode) library preparatiopn the manufacturer’s instructions were followed. ThruPLEX, Rubicon Genomics

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
65495297
Reads aligned (%)
65.4
Duplicates removed (%)
34.1
Number of peaks
48178 (qval < 1E-05)

hg38

Number of total reads
65495297
Reads aligned (%)
66.9
Duplicates removed (%)
32.8
Number of peaks
48376 (qval < 1E-05)

Base call quality data from DBCLS SRA