Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Unclassified
Antigen
Unclassified

Cell type

Cell type Class
Cell line
Cell type
S2
Source
Oregon R
Developmental Stage
late embryonic stage

Attributes by original data submitter

Sample

source_name
Drosophila S2 cells
genotype/variation
PH-ML
cell type
S2 cells
cells derived from
Drosophila embryo
pull down
Streptavidin biotin-tagged PH pull down
source
S2 Cells obtained from Expression Systems

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
[ChIP-seq] Fixed cells were sonicated and PH-chromatin complexes were pulled down from clarified sonicated material Sequencing libraries were generated as described previously (Bowman et al., 2013). Briefly, ends of the immunoprecipetated DNA were repaired, followed by A-tailing, ligating to universal adapters, and amplification for 10 cycles with indexed primers. Excess adapters were removed by purification with Agencourt AMPureXP beads (Beckman Coulter). Fragment size was checked by Bioanalyzer using high sensitivity DNA chip, and an average size distribution of 300-500bp was observed. Libraries we multiplexed and sequenced on using Illumina HiSeq 2000 for 50bp single end reads. [RNA-seq] Total RNA was isolated using Qiagen RNA easy kit, ribosomal RNA was depleted by using ribozero gold kit and cDNA was prepared (and fragmented) by using Trueseq kit

Sequencing Platform

instrument_model
Illumina HiSeq 2000

dm6

Number of total reads
44707678
Reads aligned (%)
96.5
Duplicates removed (%)
26.1
Number of peaks
11162 (qval < 1E-05)

dm3

Number of total reads
44707678
Reads aligned (%)
97.1
Duplicates removed (%)
23.5
Number of peaks
12012 (qval < 1E-05)

Base call quality data from DBCLS SRA