Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
Trl

Cell type

Cell type Class
Larvae
Cell type
Salivary glands
NA
NA

Attributes by original data submitter

Sample

source_name
Or-R
genotype
wildtype
tissue
Imaginal discs and salivary glands
developmental stage
3rd instar stage
antibody
anti-GAF

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Lysates were prepared from sonicated nuclei and GAF-DNA complexes were isolated with antibody. The GAF antibodies were custom-made by this lab while anti-RNA Pol II antibodies were provided by the lab of Dr. John T. Lis. ChIP-seq libraries were prepared using the Illumina ChIP-seq Library preparation Kit following the manufacture’s instructions with minor modifications. Briefly 10ng of purified ChIP DNA was end repaired by conversion of overhangs to phosphorylated blunt ends. A’ bases were added to the 3’ends of the DNA fragments and Illumina adapters (1:30 dilution) were ligated to the ends of ChIP fragments. This fragment range corresponds to a ChIP fragment range of about 200 -300bp. Size selected fragments were PCR amplified for 12 cycles . Libraries were quantified and validated using Agilent Technologies 2100 Bioanalyser for size, concentration and purity. Q-PCR was repeated to confirm retention of relative enrichment.

Sequencing Platform

instrument_model
Illumina Genome Analyzer

dm3

Number of total reads
34101104
Reads aligned (%)
94.3
Duplicates removed (%)
45.4
Number of peaks
16305 (qval < 1E-05)

dm6

Number of total reads
34101104
Reads aligned (%)
94.2
Duplicates removed (%)
46.0
Number of peaks
16075 (qval < 1E-05)

Base call quality data from DBCLS SRA