Sample information curated by ChIP-Atlas

Antigen

Antigen Class
ATAC-Seq
Antigen
ATAC-Seq

Cell type

Cell type Class
Adult
Cell type
Germline cells
NA
NA

Attributes by original data submitter

Sample

source_name
isolated germline nuclei
Stage
Day 1 Adult
strain
N2 - wild-type

Sequenced DNA Library

library_strategy
ATAC-seq
library_source
GENOMIC
library_selection
other
library_construction_protocol
Synchronized L1s of wild-type and mut-16(pk710) worms were plated on enriched peptone plates and cultured at 20°C and 25°C. One million animals per sample, in biological triplicates, were harvested as adults (~68hrs at 20°C and ~48hrs at 25°C). Germline nuclei were isolated as previously described (49). Nuclei were flash frozen in liquid nitrogen and stored at -80°C. For each sample, roughly 50,000 isolated germline nuclei were used. We prepared our ATAC-seq libraries as previously described (50). Library quality was assessed (Agilent BioAnalyzer Chip) and concentration was determined using the Qubit 1X dsDNA HS Assay kit (ThermoFisher Q32851). Libraries were sequenced on the Illumina NextSeq500 (PE 75-bp reads) platform. Three biological replicates were generated for wild-type (N2) and mut-16 mutants cultured at 20°C and 25°C.

Sequencing Platform

instrument_model
NextSeq 500

ce11

Number of total reads
30680231
Reads aligned (%)
96.8
Duplicates removed (%)
27.9
Number of peaks
476 (qval < 1E-05)

ce10

Number of total reads
30680231
Reads aligned (%)
96.8
Duplicates removed (%)
27.9
Number of peaks
471 (qval < 1E-05)

Base call quality data from DBCLS SRA