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Curated Sample Data


Antigen Class
TFs and others
Antigen
Cp190
Cell type Class
Pupae
Cell type
White prepupae

Cell type information


NA
NA

Attributes by Original Data Submitter


source_name
White prepupa (Oregon-Modencode)
cell line/tissue
White prepupa (Oregon-Modencode)
chip antibody
anti-CP190 antibodies obtained by A. Golovnin (Golovnin et al (2012) J. Cell Sci. 125, 2064–2074)

Metadata from Sequence Read Archive

Library Description


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

Platform Information


instrument_model
Illumina NovaSeq 6000

External Database Query

Logs in read processing pipeline


dm3

Number of total reads
0
Reads aligned (%)
0.0
Duplicates removed (%)
47.8
Number of peaks
4581 (qval < 1E-05)

dm6

Number of total reads
0
Reads aligned (%)
0.0
Duplicates removed (%)
48.1
Number of peaks
4802 (qval < 1E-05)

Sequence Quality Data from DBCLS SRA