Sample information curated by ChIP-Atlas

Antigen

Antigen Class
ATAC-Seq
Antigen
ATAC-Seq

Cell type

Cell type Class
Larvae
Cell type
Germline cells
NA
NA

Attributes by original data submitter

Sample

source_name
Sorted L1 PGCs
developmental stage
Starved L1

Sequenced DNA Library

library_strategy
ATAC-seq
library_source
GENOMIC
library_selection
other
library_construction_protocol
Worm were dissociated with pronase solution. Cell suspensions were subjected to FACS to isolated PGL-1::GFP marked primordial germ cells (PGCs) Library construction was performed as described in Buenrostro et al. 2015. In brief, 30,000 sorted PGCs were used for ATAC-seq library construction. The transposition reaction was performed with a 50l reaction mixture (25l TD, 2.5l TDE, 22.5 l nuclease-free H2O. Illumina, Nextera DNA library preparation Kit FC-121-1030) at 37C for 30 min. Transposed DNA was purified using Qiagen MinElute kit and saved in -20C. qPCR was used to determine appropriate PCR cycle number for PCR amplification as detailed in Buenrostro et al. 6-7 cycles of PCR amplification were used. Final cDNA libraries (150bp to 700bp) were selected using Agencourt AMPure beads (Beckman-Coulter A63880).

Sequencing Platform

instrument_model
Illumina HiSeq 2500

ce11

Number of total reads
41403819
Reads aligned (%)
92.6
Duplicates removed (%)
73.0
Number of peaks
8394 (qval < 1E-05)

ce10

Number of total reads
41403819
Reads aligned (%)
92.6
Duplicates removed (%)
73.0
Number of peaks
8388 (qval < 1E-05)

Base call quality data from DBCLS SRA