Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
Cp190

Cell type

Cell type Class
Embryo
Cell type
0-14h embryos
NA
NA

Attributes by original data submitter

Sample

source_name
0-14 hour old embryos
strain
CTCF[0]
tissue
whole embryo
age
0-14 hour old
genotype
CTCF[0]
replicate
3
chip antibody
Cp190 rabbit polyclonal (Kaushal et al. 2021)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
About 400 0-14 hour old embryos per biological replicate (three biological replicates prepared per genotype) were dechorionated, dounced in 5 ml crosslinking solution (50 mM Hepes pH 7.9, 1 mM EDTA, 0.5 mM EGTA, 100 mM NaCl, 1.8% formaldehyde), and fixed for 15 minutes. Nuclei were sonicated in RIPA buffer in a Covaris S220 sonicator as described in Kaushal et al. 2021. 60 third instar larval central nervous systems per biological replicate (two biological replicates per genotype) were dissected in PBS and chromatin was prepared as in Kaushal et al. 2021. NEBNext Ultra II DNA Library Prep kit for Illumina

Sequencing Platform

instrument_model
Illumina HiSeq 4000

dm6

Number of total reads
32082984
Reads aligned (%)
95.7
Duplicates removed (%)
10.5
Number of peaks
3874 (qval < 1E-05)

dm3

Number of total reads
32082984
Reads aligned (%)
96.4
Duplicates removed (%)
10.2
Number of peaks
4818 (qval < 1E-05)

Base call quality data from DBCLS SRA