Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
PAX5

Cell type

Cell type Class
Gonad
Cell type
Testis
MeSH Description
The male gonad containing two functional parts: the SEMINIFEROUS TUBULES for the production and transport of male germ cells (SPERMATOGENESIS) and the interstitial compartment containing LEYDIG CELLS that produce ANDROGENS.

Attributes by original data submitter

Sample

source_name
Fetal testis
cell type
2nd trimester human fetal testis
antibody
anti-PAX5 (sc-1974, Santa Cruz Biotechnology);

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were lysed with 1% SDS Lysis Buffer (on ice, 5 min) and then centrifuged (2,000 rpm, 10 min). Remove supernatant as described above and resuspend samples in 0.1% SDS buffer with PIC (1ml 0.1%SDS buffer for every 100ul nuclear pellet). Samples were then sonicated with glass beads for 12 times (30 s pulses with 30 s break interval) using the Bioruptor water bath sonicator (Diagenode). Libraries were prepared according to Illumina's instructions by Stanford genomic core facility

Sequencing Platform

instrument_model
Illumina Genome Analyzer

hg19

Number of total reads
45191381
Reads aligned (%)
32.4
Duplicates removed (%)
58.7
Number of peaks
4131 (qval < 1E-05)

hg38

Number of total reads
45191381
Reads aligned (%)
33.5
Duplicates removed (%)
57.9
Number of peaks
4280 (qval < 1E-05)

Base call quality data from DBCLS SRA