Curated Sample Data


Genome
dm3
Antigen Class
Input control
Antigen
Input control
Cell type Class
Cell line
Cell type
Kc167

Cell type information


Source
e/se
Developmental Stage
dorsal closure stage

Attributes by Original Data Submitter


source_name
Kc cell line
cell line
Kc
chip antibody
none (input)
RNAi
SXL construct 1
days of treatment
3

Metadata from Sequence Read Archive

Library Description


library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIP DNA; 40 million cells were re-suspended in ice-cold homogenization buffer and fixed with 1% formaldehyde for 10 minutes at room temperature. After quenching with 125 mM glycine (final) the cells were collected and washed three-times with ice-cold RIPA buffer. Fixed nuclei were sonicated in RIPA buffer with a Covaris sonifier (PIP: 140, DF 20%, CB: 200) for 30 minutes. 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; 40 million cells were re-suspended in ice-cold homogenization buffer and fixed with 1% formaldehyde for 10 minutes at room temperature. After quenching with 125 mM glycine (final) the cells were collected and washed three-times with ice-cold RIPA buffer. Fixed nuclei were sonicated in RIPA buffer with a Covaris sonifier (PIP: 140, DF 20%, CB: 200) for 30 minutes. 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
39459749
Reads aligned (%)
96.6
Duplicates removed (%)
50.4
Number of peaks
11390 (qval < 1E-05)

Sequence Quality Data from DBCLS SRA