Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
so

Cell type

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

Attributes by original data submitter

Sample

source_name
eye-antennal imaginal disc
tissue
eye-antennal imaginal disc
developmental stage
wandering 3rd instar larva
genotype
w[1118]
chip antibody
guinea pig anti-So (from I. Rebay)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIP protocol (after Jemc and Rebay 2007): imaginal discs were fixed in formaldehyde and homogenized in lysis buffer. Resulting chromatin was sonicated, precleared, and incubated o/n with anti-So (negative control incubated w/o antibody). Chromatin was incubated with protein A beads, eluted, and crosslinks reversed at 65C, and DNA purified with PCR purification kit. Illumina libraries were generated according to the manufacturer’s sample preparation protocol. Briefly, ~10 ng of DNA was end-repaired using polynucleotide kinase and Klenow. The 5’ ends of the DNA fragments were phosphorylated and a single adenine base was added to the 3’ ends using Klenow exo-nuclease. Illumina Y-shaped index adaptors were ligated to the repaired ends, then the DNA fragments were PCR amplified for 21 cycles and fragments from 200-500 bp were isolated by gel purification. The libraries were quantified using the PicoGreen fluorescence assay and their size distributions determined by the Agilent 2100 Bioanalyzer. Libraries were sequenced on the Illumina Illumina Genome Analyzer IIx as 35-bp single-end reads, following the manufacturer's protocols.

Sequencing Platform

instrument_model
Illumina Genome Analyzer IIx

dm3

Number of total reads
12463004
Reads aligned (%)
7.9
Duplicates removed (%)
29.8
Number of peaks
2324 (qval < 1E-05)

dm6

Number of total reads
12463004
Reads aligned (%)
7.7
Duplicates removed (%)
29.9
Number of peaks
2430 (qval < 1E-05)

Base call quality data from DBCLS SRA