Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

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
testicular cells
strain
FVB/N
Sex
male
age
adult (10-16 weeks)
tissue/cells
testes
chip antibody
IgG from rabbit serum (Sigma)
treatment
pooled from all treatments

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
The ChIP assay was carried out according to the protocol of a ChIP kit from Upstate Biotechnology (Lake Placid, NY) using protein A-sepharose beads (Amersham). Standard crosslinking procedure was used. For each IP reaction 48-50 µg of chromatin sonicated to 100-500 bp fragments and 5 µg of anti-SPEN polyclonal antibodies, or IgG from rabbit serum (Sigma) as a negative control were used. Immunoprecipitated DNA was additionally digested by RNase A (in a final concentration 70 μg/ml, 30 minutes, 37°C) before Proteinase K treatment and organic solvents extraction. Glycogen (70 μg/ml) was added at the precipitation step. DNA was dissolved in H2O. In each experimental point five to six ChIP replicates were collected and combined in one sample before DNA sequencing. Sequencing libraries were generated using KAPA library preparation kit (for Illumina) KK8201. Template amplification and cluster generation were performed using the TruSeq SBS Kit.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

mm10

Number of total reads
48535239
Reads aligned (%)
92.4
Duplicates removed (%)
16.9
Number of peaks
666 (qval < 1E-05)

mm9

Number of total reads
48535239
Reads aligned (%)
92.1
Duplicates removed (%)
16.8
Number of peaks
746 (qval < 1E-05)

Base call quality data from DBCLS SRA