Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
Cap-D3

Cell type

Cell type Class
Cell line
Cell type
S2R+
Source
Oregon R
Developmental Stage
late embryonic stage

Attributes by original data submitter

Sample

source_name
S2R+ cells
cell type
embryonic
strain
Oregon R
chip antibody
YZ384 (Longworth lab)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
See protocol using Mnase digestion published in Schuster et. al. PLOS Genetics (2013). 10 units of micrococcal nuclease were used to digest DNA in each sample. Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

dm3

Number of total reads
29453199
Reads aligned (%)
98.2
Duplicates removed (%)
24.8
Number of peaks
3736 (qval < 1E-05)

dm6

Number of total reads
29453199
Reads aligned (%)
97.4
Duplicates removed (%)
26.0
Number of peaks
3545 (qval < 1E-05)

Base call quality data from DBCLS SRA