Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
cg

Cell type

Cell type Class
Larvae
Cell type
CNS and imaginal discs
NA
NA

Attributes by original data submitter

Sample

source_name
3rd instar brains and imaginal discs
genotype/variation
ry- wild type
developmental stage
3rd instar larva
tissue
CNS and imaginal discs
chip antibody
antiCg (custom-made)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Fixed brains and imaginal discs were dissected from 10 third instar larvae, and sonicated chromatin incubated with anti ChIP was performed with 1:100 dilutions of anti-Cg [custom made], anti-Ph (a kind gift from Donna Arndt-Jovin) antibodies and 1:200 dilutions of anti-H3K27me3 (Millipore, 17-622) antibodies. Input ChIP DNA (30 ng) is blunt-ended and phosphorylated. A single 'A' nucleotide is added to the 3' ends of the fragments in preparation for ligation to an adapter that has a single-base 'T' overhang. The ligation products are purified and accurately size-selected by agarose gel electrophoresis. Size-selected DNA is purified and PCR-amplified to enrich for fragments that have adapters on both ends. The final purified product is then quantitated before cluster generation. http://ethanomics.wordpress.com/chip-seq-library-construction-using-the-illumina-truseq-adapters/.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

dm3

Number of total reads
9795504
Reads aligned (%)
59.1
Duplicates removed (%)
13.8
Number of peaks
9987 (qval < 1E-05)

dm6

Number of total reads
9795504
Reads aligned (%)
58.3
Duplicates removed (%)
14.8
Number of peaks
9965 (qval < 1E-05)

Base call quality data from DBCLS SRA