Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
sd

Cell type

Cell type Class
Larvae
Cell type
Imaginal wing disc
NA
NA

Attributes by original data submitter

Sample

source_name
wing discs
treatment
hand dissections
tissue
wing discs
genotype/variation
y w ubxflp/ y w; FRT82B M(3) ubiGFP/ FRT82B cicQ474X wts149
age
3rd instar-day9
chip antibody
anti-Sd

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Third instar larvae were dissected in cold PBS and imaginal disc complexes (anterior one third of the larvae after removing the fat body and salivary glands) were fixed in 1 ml fixation buffer (50 mM 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid [HEPES], pH 7.5; 1 mM ethylenediaminetetraacetic acid [EDTA]; 0.5 mM ethylene glycol tetraacetic acid [EGTA]; 100 mM NaCl; 2% formaldehyde) for 30 min at room temperature. Fixed disc complexes were washed 3x fast and 2x 20 minutes with PBST (PBS, pH 7.4; 0.1% Triton X-100; 0.1% Tween-20), and were stored at 4 C until enough discs were obtained. 100-500 wing discs were dissected away from the cuticle and resuspended in buffer A2 (15 mM HEPES, pH 7.5; 140 mM NaCl; 1 mM EDTA; 0.5 mM EGTA; 1% Triton X-100; 0.1% sodium deoxycholate; 0.1 % sodium dodecyl sulfate [SDS]; 0.5 % N-lauroylsarcosine; 1 Roche complete protease inhibitor cocktail, cat. no. 5056489001). Tubes were flash frozen in liquid nitrogen and stored at -80 C. Imaginal discs were pooled to reach 500 wt discs (or 100 mutant), and sonication was performed in a Bioruptor sonicator for 5 min (30 s on/off cycle at the high setting) in buffer A2. Following centrifugation (16,000 g; 10 min at 4 C), the supernatant containing soluble chromatin was transferred to fresh tubes, and used for ChIP-nexus. Library preparation was done as described in He, Johnston and Zeitlinger, 2015 Nature Biotechnology.

Sequencing Platform

instrument_model
NextSeq 500

dm3

Number of total reads
39140042
Reads aligned (%)
72.7
Duplicates removed (%)
11.3
Number of peaks
17057 (qval < 1E-05)

dm6

Number of total reads
39140042
Reads aligned (%)
71.8
Duplicates removed (%)
11.6
Number of peaks
18159 (qval < 1E-05)

Base call quality data from DBCLS SRA