Curated Sample Data


Genome
dm3
Antigen Class
Input control
Antigen
Input control
Cell type Class
Cell line
Cell type
S2R+

Cell type information


Source
Oregon R
Developmental Stage
late embryonic stage

Attributes by Original Data Submitter


source_name
S2R+ cells
cell type
embryonic
strain
Oregon R
chip antibody
Normal Rabbit IgG (Millipore 12-370)

Metadata from Sequence Read Archive

Library Description


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.

Platform Information


instrument_model
Illumina HiSeq 2500

External Database Query

Logs in read processing pipeline


Number of total reads
29957776
Reads aligned (%)
1.8
Duplicates removed (%)
95.9
Number of peaks
276 (qval < 1E-05)

Sequence Quality Data from DBCLS SRA