Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
SOX17

Cell type

Cell type Class
Gonad
Cell type
Tcam-2
NA
NA

Attributes by original data submitter

Sample

source_name
Human testicular germ cell tumour cell line
cell line
TCam-2
cell type
Seminoma-like cells
chip antibody
Anti-SOX17

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
For chromatin preparation of cell lines, 1 x 10e7 cells / immunoprecipitation were fixed for 30 minutes (min) at room temperature (RT) using Diagenode Crosslink Gold (Diagenode, Liège, Belgium). After two washing steps with PBS (Thermo Fisher Scientific) cells were additionally fixed for 10 min in 1% formaldehyde (Applichem, Darmstadt, Germany) and then processed according to the SimpleChIP® Plus Enzymatic Chromatin IP Kit (Cell Signaling Technology, Leiden, Netherlands). ChIP-seq libraries were generated using the MicroPlex Library Preparation Kit v2 (Diagenode).

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg19

Number of total reads
32023406
Reads aligned (%)
78.5
Duplicates removed (%)
10.5
Number of peaks
30983 (qval < 1E-05)

hg38

Number of total reads
32023406
Reads aligned (%)
80.2
Duplicates removed (%)
9.3
Number of peaks
31288 (qval < 1E-05)

Base call quality data from DBCLS SRA