Sample information curated by ChIP-Atlas

Antigen

Antigen Class
ATAC-Seq
Antigen
ATAC-Seq

Cell type

Cell type Class
Adult
Cell type
Testis
NA
NA

Attributes by original data submitter

Sample

source_name
testis
tissue
testis
developmental stage enriched
spermatogonia
time post heat shock
no heat shock
genotype
bam -/-
treatment
NA

Sequenced DNA Library

library_strategy
ATAC-seq
library_source
GENOMIC
library_selection
other
library_construction_protocol
No extraction was done prior to library construction. For each technical replicate, 10~20 pairs of testes from < 1 day old male flies were dissected in PBS on ice, and immediately digested for 8 minutes at room temperature in 0.5mg/ml of dispase (Worthington LS02109) and 0.5mg/ml of collagenase XI (Sigma C7657) dissolved in PBS with 0.3mM of CaCl2. Testis were washed once in cold PBS and broken open by pipetting 7 ~ 10 times in 50ul of cold PBS. Cells were spun down at 2000rpm for 1min, cold lysis buffer (Buenrostro et al. 2015) added, and the pellet gently resuspended by flicking the tube. After another 2000rpm 2min spin, 20ul of transposase mix from the Nextera Kit (Illumina, cat. no. FC-121-1030) was added and the pellet gently resuspended by flicking the tube. The reaction was incubated at 30oC for 25min with the tube flicked once during incubation. The DNA was purified using Qiagen MinElute column (Qiagen 28004) and the entire sample used for PCR with NEBNext (NEB M0541S) for a total of 8~9 amplification cycles.

Sequencing Platform

instrument_model
Illumina HiSeq 4000

dm6

Number of total reads
9501354
Reads aligned (%)
69.1
Duplicates removed (%)
19.9
Number of peaks
2431 (qval < 1E-05)

dm3

Number of total reads
9501354
Reads aligned (%)
69.4
Duplicates removed (%)
16.4
Number of peaks
2665 (qval < 1E-05)

Base call quality data from DBCLS SRA