Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
CTCF

Cell type

Cell type Class
Larvae
Cell type
Eye-antennal discs
NA
NA

Attributes by original data submitter

Sample

source_name
Eye-Antennal disc
genotype
CantonS
sample type
CTCF Immunoprecipitated
Stage
Wandering third instar larvae
tissue
Eye-Antennal disc
chip antibody
CTCF

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ATAC-Seq - Nuclei were extracted from 10 eye-antennal discs . FAIRE-Seq - 150 Head complexes were first dissected, fixed and lysed. 200 eye-antennal discs were the uncrosslinked and sonicated, phenol chloroform extraction was used for DNA purification. ChIP-Seq - 750 Head complexes were first fixed, 1000 eye-antennal discs were then dissected and sonicated. Sonicated chromatin was then immunoprecipitated and purified using magnetic beads ATAC-Seq libraries were prepared using a simple PCR reaction with adapters based against the transpon sequence. FAIRE-Seq and ChIP-Seq libraries were prepared using standard Illumina Protocols.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

dm3

Number of total reads
14181487
Reads aligned (%)
48.1
Duplicates removed (%)
34.5
Number of peaks
6540 (qval < 1E-05)

dm6

Number of total reads
14181487
Reads aligned (%)
47.2
Duplicates removed (%)
35.5
Number of peaks
6815 (qval < 1E-05)

Base call quality data from DBCLS SRA