Curated Sample Data


Genome
dm3
Antigen Class
Input control
Antigen
Input control
Cell type Class
Cell line
Cell type
S2

Cell type information


Source
Oregon R
Developmental Stage
late embryonic stage

Attributes by Original Data Submitter


source_name
S2 cells
cell type
Stably transfected HA-tagged SIN3 220 cells
cell line
S2
chip antibody
none

Metadata from Sequence Read Archive

Library Description


library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Chromatin was prepared from cells which were treated with formaldehyde to chross-link protein and DNA. Fragmentation of chromatin to desired size was carried out by MNase treatment and sonication. Chromatin prepared was subjected to immunoprecipitation. Libraries were prepared according to a previously published protocol (Ford et al.,2014). 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 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, 5 cycles of PCR was carried out using Illumina universal primers to convert all adapter DNA fragments to double stranded DNA. Following the pre_PCR step fragments of approximately 270 - 420 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. Purified DNA was PCR amplified with Illumina primers for 12 more cycle cycles. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the HiSeq 2000 following the manufacturer's protocols.

Platform Information


instrument_model
Illumina HiSeq 2000

External Database Query

Logs in read processing pipeline


Number of total reads
22134084
Reads aligned (%)
94.6
Duplicates removed (%)
54.2
Number of peaks
4078 (qval < 1E-05)

Sequence Quality Data from DBCLS SRA