Curated Sample Data


Genome
dm3
Antigen Class
Histone
Antigen
H3
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
S2
RNAi treatment
ISWI RNAi
chip antibody
H3
chip antibody vendor
Abcam

Metadata from Sequence Read Archive

Library Description


library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
S2 cells were fixed in 1% formaldehyde for 15 min at 18°C. The reaction was stopped by adding glycine to a final concentration of 125 mM. After washing, cells were resuspended in SDS Lysis buffer (1% SDS, 10 mM EDTA, 50 mM Tris-HCl (pH 8.1), protease inhibitors) and incubated 10 min on ice. Chromatin was prepared by shearing with Bioruptor (Diagenode) at setting “high” for 20 cycles with 30 sec “On” and 30 sec “Off” to yield chromatin with a size ranging from 200-800 bp. The sonicated chromatin was diluted 10 fold in dilution buffer (0.01% SDS, 1.1% Triton X-100, 1.2 mM EDTA, 16.7 mM Tris-HCl (pH 8.1), 167 mM NaCl, protease inhibitors). Chromatin was immunoprecipitated by incubating with the appropriate antibodies overnight at 4°C. To collect the antibody/chromatin complexes the solution is incubated for 1 h at 4°C with 30 µl Protein G Plus/Protein A Agarose Suspension (Millipore). After washing one time with Low Salt Buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl (pH 8.1), 150 mM NaCl), one time with High Salt buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl (pH 8.1), 500 mM NaCl), one time with LiCl Buffer (0.25 M LiCl, 1% NP40, 1% deoxycholate, 1 mM EDTA, 10 mM Tris-HCl (pH 8.1)) and two times with TE Buffer (10 mM Tris-HCl, 1 mM EDTA (pH 8.0)) the crosslinks were reversed and DNA is recovered by illustra GFX columns (GE Healthcare) Sequencing libraries were prepared from 10 ng of immunoprecipitated DNA with the Illumina ChIPSeq DNA Sample Prep Kit according to Illuminas instructions. Cluster generation was performed using the Illumina cluster station, sequencing on the Genome Analyzer IIx followed a standard protocol. The fluorescent images were processed to sequences using the Genome Analyzer Pipeline Analysis software 1.8 (Illumina).

Platform Information


instrument_model
Illumina Genome Analyzer IIx

External Database Query

Logs in read processing pipeline


Number of total reads
34617023
Reads aligned (%)
37.4
Duplicates removed (%)
34.7
Number of peaks
3151 (qval < 1E-05)

Sequence Quality Data from DBCLS SRA