Sample information curated by ChIP-Atlas

Antigen

Antigen Class
ATAC-Seq
Antigen
ATAC-Seq

Cell type

Cell type Class
Gonad
Cell type
Sperm
NA
NA

Attributes by original data submitter

Sample

source_name
Sperm
strain background
CD1
tissue
sperm

Sequenced DNA Library

library_strategy
ATAC-seq
library_source
GENOMIC
library_selection
other
library_construction_protocol
After sperm cells were counted, the nuclei from 100,000 sperm were isolated with Lysis Buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3mM MgCl2) containing 0.1% NP40, 0.1% Tween-20, and 0.01% Digitonin. Purified sperm nuclei pellet was then resuspended in the transposase reaction mix containing 0.05% digitonin and incubated for 30 min at 37°C. Following incubation, sperm were treated with Proteinase K at 55°C for 2 hr, and gDNA was isolated by phenol:chloroform:isoamyl alcohol and EtOH precipitation. Library amplification was done with 2x KAPA HiFi mix and 1.25 µM indexed primers using the following PCR conditions: 72°C for 5 min; 98°C for 30 s; and 10-11 cycles at 98°C for 10 s, 63°C for 30 s, and 72°C for 1 min.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

mm10

Number of total reads
47601884
Reads aligned (%)
97.5
Duplicates removed (%)
6.3
Number of peaks
9754 (qval < 1E-05)

mm9

Number of total reads
47601884
Reads aligned (%)
97.4
Duplicates removed (%)
6.3
Number of peaks
9735 (qval < 1E-05)

Base call quality data from DBCLS SRA