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 without transfection
chip antibody
none
cell line
S2
treatment
no transfection
amount of dna used to make library
300 ng

Metadata from Sequence Read Archive

Library Description


library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Formaldehyde was added to a final concentration of 1 % to cross-link proteins to DNA. The fixation reaction was incubated on a shaker for 10 min at room temperature. The reaction was quenched by adding glycine to a final concentration of 125 mM and incubation for 5 min on a shaker at room temperature. Subsequently the cells were washed twice with ice-cold PBS. After centrifugation at 500 x g (1680 rpm) for 5 min at 4 °C the cell pellet was resuspended in 10 ml ice-cold cell lysis buffer (5 mM pH8.0 PIPES buffer, 85 mM Potassium chloride, 0.5% Nonidet P40 and protease inhibitors (cOmplete, EDTA-free, Roche, indianapolis, IN)) for 10 minutes at 4 °C. Nuclei were released by douncing with a Wheaton homogenizer (pestle B). The crude nuclear extract was collected by centrifugation at 500 x g (1680 rpm) for 5 min at 4 °C, resuspended in 2 ml ice–cold nuclear lysis buffer (50 mM pH8.1 Tris.HCl, 10 mM EDTA, 1 % SDS and protease inhibitors) and incubated for 20 minutes at 4 °C. After adding 1 ml ice-cold IP dilution buffer (0.01 % SDS, 1.1 % TritonX-100, 1.2 mM pH 8 EDTA.Na2, 16.7 mM pH8 Tris.HCl, 167 mM NaCl and protease inhibitors) and 0.3 g acid-washed glass beads (Sigma-Aldrich, St. Louis, MO) to the nuclear extract, the chromatin was sheared to 200-1000 bp using a Misonix Sonicator 3000 (Misonix, Inc. Farmingdale, NY). Sonication was performed on ice water with 8 pulses of 30 seconds and 30 second intervals. Thereafter the cell debris was removed by centrifugation at 16000 x g (13000 rpm) for 10 min at 4 °C. Aliquots of sonicated chromatin were stored at -80 °C. To assess chromatin quality, aliquots of the chromatin (100 μl) were treated with 40 µg proteinase K (Invitrogen, Carlsbad, CA) for 2 h at 50 °C after the DNA-protein complexes were de-crosslinked at 65°C overnight. After purification of the DNA by phenol-chloroform extraction and ethanol precipitation 3 μl aliquots were subjected to electrophoresis and the chromatin fractions with optimal size (200-1000 bp) range were subjected to immunoprecipitation experiments. Libraries were made using the Genomic DNA sample preparation kit (Illumina). Adapter-ligated DNA of 200 ± 25 bp range was excised from the gel before PCR amplification.

Platform Information


instrument_model
Illumina Genome Analyzer

External Database Query

Logs in read processing pipeline


Number of total reads
8125874
Reads aligned (%)
73.0
Duplicates removed (%)
8.3
Number of peaks
1631 (qval < 1E-05)

Sequence Quality Data from DBCLS SRA