Sample information curated by ChIP-Atlas

Antigen

Antigen Class
ATAC-Seq
Antigen
ATAC-Seq

Cell type

Cell type Class
Pupae
Cell type
Pupal legs
NA
NA

Attributes by original data submitter

Sample

source_name
second (T2) pupal legs
strain
ebony[4],white ocelli[1], rough[1]
age
20-28 h after puparium formation
tissue
second (T2) pupal legs

Sequenced DNA Library

library_strategy
ATAC-seq
library_source
GENOMIC
library_selection
other
library_construction_protocol
Leg cells were lysed in 50 µl Lysis Buffer (10 mM Tris-HCl, pH = 7.5; 10 mM NaCl; 3 mM MgCl2; 0.1 % IGEPAL). Nuclei were collected by centrifugation at 500 g for 5 min. Approximately 60,000 nuclei were suspended in 50 µl Tagmentation Mix [25 µl Buffer (20 mM Tris-CH3COO-, pH = 7.6; 10 mM MgCl2; 20 % Dimethylformamide); 2.5 µl Tn5 Transposase; 22.5 µl H2O] and incubated at 37 °C for 30 min. After addition of 3 µl 2 M NaAC, pH = 5.2 DNA was purified using a QIAGEN MinElute Kit. PCR amplification for library preparation was done for 15 cycles with NEBNext High Fidelity Kit; primers were used according to Buenrostro et al. (2013) DOI:10.1038/NMETH.2688

Sequencing Platform

instrument_model
Illumina HiSeq 2500

dm6

Number of total reads
39843406
Reads aligned (%)
76.2
Duplicates removed (%)
21.5
Number of peaks
18925 (qval < 1E-05)

dm3

Number of total reads
39843406
Reads aligned (%)
76.5
Duplicates removed (%)
20.4
Number of peaks
18439 (qval < 1E-05)

Base call quality data from DBCLS SRA