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 cell line
cell line
S2
chip antibody
none (input)
treatment
GST RNAi

Metadata from Sequence Read Archive

Library Description


library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIP DNA; cells were crosslinked in growth medium using 1% formaldehyde for 60 minutes in icewater. Fixation was quenched by addition of glycine to a final concentration of 125 mM. After washing, cells were resuspended in RIPA buffer and sonciated using a Covaris S220 (PIP 100 W, DF 20%, 200 CB for 30 min) to generate 180-bp chromatin fragments. Chromatin was precleared using a protein A/protein G-sepharose mixture for 1 hr at 4°C. 200 µl chromatin was incubated with appropriate amounts of antibodies in a total volume of 500 µl RIPA buffer at 4°C over night. After washing and crosslink revearsal, immunprecipitated nucleic acids were purified on GFX columns (GE Healthcare). Input DNA; cells were crosslinked in growth medium using 1% formaldehyde for 60 minutes in icewater. Fixation was quenched by addition of glycine to a final concentration of 125 mM. After washing, cells were resuspended in RIPA buffer and sonciated using a Covaris S220 (PIP 100 W, DF 20%, 200 CB for 30 min) to generate 180-bp chromatin fragments. After crosslink revearsal, nucleic acids were purified on GFX columns (GE Healthcare). The Diagenode MicroPlex library kit was used to prepare libraries from 1-2ng of either input or DIP DNA quantified using the Qubit® dsDNA HS Assay kit (Life Technologies Q32851)

Platform Information


instrument_model
Illumina HiSeq 1500

External Database Query

Logs in read processing pipeline


Number of total reads
26926875
Reads aligned (%)
96.6
Duplicates removed (%)
13.8
Number of peaks
3396 (qval < 1E-05)

Sequence Quality Data from DBCLS SRA