Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

Cell type Class
Gonad
Cell type
Spermatocytes
MeSH Description
Male germ cells derived from SPERMATOGONIA. The euploid primary spermatocytes undergo MEIOSIS and give rise to the haploid secondary spermatocytes which in turn give rise to SPERMATIDS.

Attributes by original data submitter

Sample

source_name
mock ChIP from spermatocytes heat shocked at 43°C
strain
FVB/N
gender
male
tissue
testis
cell type
spermatocytes
developmental stage
adult
age
10-16 weeks
temperature
heatshock_43C
chip antibody
normal goat serum (negative control)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were fixed by adding of formaldehyde to a final concentration of 1% and incubated at room temperature for 10 minutes. Next 2.5 M glycine was added (1/20 volume) for 5 minutes. Cells were washed with ice-cold PBS and lysed following the manufacturer’s protocol. For analyses of HSF1 and HSF2 binding, the ChIP assay was carried out according to protocol for ChIP kit of Upstate Biotechnology (Lake Placid, NY) and protein A-sepharose (Amersham) was used. For 30µg of chromatin, sonicated to 100-500 bp fragments, 3 µg of rabbit anti-HSF1 (cat. no SPA-901, Enzo) or 5 µg of goat anti-HSF2 (cat. no AF5227, R&D Systems) polyclonal antibodies were used. Samples proceeded with normal goat serum served as negative controls. Sequencing libraries were generated using ChIP-Seq Sample Prep Kit (Illumina). Template amplification and cluster generation were performed using the cBot and TruSeq SR Cluster Kit v2 cBot-GA for cBot, and 80 nucleotides were sequenced with Illumina Genome Analyzer IIx using TruSeq SBS Kit v5 sequencing kits.

Sequencing Platform

instrument_model
Illumina Genome Analyzer IIx

mm10

Number of total reads
24049126
Reads aligned (%)
50.1
Duplicates removed (%)
89.0
Number of peaks
161 (qval < 1E-05)

mm9

Number of total reads
24049126
Reads aligned (%)
50.0
Duplicates removed (%)
89.2
Number of peaks
127 (qval < 1E-05)

Base call quality data from DBCLS SRA