Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
Cp190

Cell type

Cell type Class
Cell line
Cell type
S2
Source
Oregon R
Developmental Stage
late embryonic stage

Attributes by original data submitter

Sample

source_name
S2 Schneider cells
cell line/tissue
S2 Schneider cells
expression of nuclear receptor
3xFLAG-EcR expression under Act5C promoter
isoform of nuclear receptor
D. melanogaster EcR-A isoform full length (1-849 aa)
treatment
0.3 uM 20-hydroxyecdysone (20E) for 1 hour
chip antibody
anti-CP190 antibodies obtained by A. Golovnin (Golovnin et al (2012) J. Cell Sci. 125, 2064–2074)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Crosslinking was performed with 1% formaldehyde for 10 min at RT and stopped by adding glycine. After washings, chromatin was lysed in SDS-containing buffer (50 mM HEPESKOH, pH 7.9; 140 mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% Na deoxycholate, 0.1% SDS) with protease inhibitors cocktail (Roche) and sheared to 500-bp fragments by sonication. Sonicated chromatin was centrifuged twice at 16 000 g for 20 min, and used in immunoprecipitation experiments. For one experiment, about 5 ug of antibodies and 8 uL of MabSelect sepharose (GE healthcare) were taken; BSA were added to a final concentration of 1%. The precipitated chromatin was sequentially washed twice with SDS-containing buffer and with TE buffer (20mM Tris-HCl, pH 8.0; 1mM EDTA). Precipitated chromatin complexes were eluted by sequential incubation in two portions of elution buffer (50mM Tris-HCl, pH 8.0; 1mM EDTA, 1% SDS), 30 min each, at room temperature. The eluted chromatin solution was supplemented with 5 M NaCl (16 uL per 500 uL sample) and incubated at 65°C for 16 h on a thermoshaker for de-crosslinking. De-crosslinked chromatin was subjected to proteinase treatment (3 uL of proteinase K and 5 uL of 0.5M EDTA per 500 uL sample) and incubated at 55°C for 4 h on thermoshaker. DNA was extracted with a phenol/chloroform mixture and precipitated with isopropanol. The precipitate was dissolved in TE buffer and subjected to library preparation. DNA libraries were prepared for sequencing using standard Illumina protocols

Sequencing Platform

instrument_model
Illumina NovaSeq 6000

dm6

Number of total reads
8913912
Reads aligned (%)
0.0
Duplicates removed (%)
23.3
Number of peaks
6106 (qval < 1E-05)

dm3

Number of total reads
8913912
Reads aligned (%)
0.0
Duplicates removed (%)
23.1
Number of peaks
6356 (qval < 1E-05)

Base call quality data from DBCLS SRA