Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

Cell type Class
Gonad
Cell type
Round spermatids
NA
NA

Attributes by original data submitter

Sample

source_name
Spermatogenic cells (round spermatids)
strain
Oncins France 1
chip antibody
none
developmental stage
round spermatids
tissue
testis

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
About 100 μg of mononucleosomes were used for each ChIP. ChIP experiments were carried out overnight at 4 °C, in LSDB 350 buffer (glycerol 20%, Hepes 50 mM, MgCl2 3 mM, KCl 350 mM, Na Butyrate 10 mM, Complete Protease Inhibitor Cocktail Tablets (Roche)), with 5 μg of antibodies (rabbit H4K8ac, rabbit antiH4K5ac, rabbit anti H4K8bu, rabbit anti H4K5bu) previously coupled to magnetic beads (Dynabeads protein G (Invitrogen)) for 4 h in 1X PBS, BSA 5 μg/μl. The beads were then washed five times in LSDB 350 buffer, and nucleosomes were eluted with the elution buffer (SDS 1%, 1X TE). DNA was purified from the nucleosomes, and the immunoprecipitated DNA was sequenced. The DNA corresponding to an aliquot of nucleosomes before immunoprecipitation (input) was also sequenced. ChIP-seq libraries were prepared following the Ovation Ultralow DR Multiplex System protocols (NuGEN Technologies INC, San Carlos, CA), followed by a size selection (200-700bp) step using SPRIselect beads (Beckman Coulter, Brea, CA).

Sequencing Platform

instrument_model
Illumina HiSeq 2500

mm10

Number of total reads
52492339
Reads aligned (%)
97.7
Duplicates removed (%)
10.2
Number of peaks
374 (qval < 1E-05)

mm9

Number of total reads
52492339
Reads aligned (%)
97.5
Duplicates removed (%)
10.1
Number of peaks
377 (qval < 1E-05)

Base call quality data from DBCLS SRA