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
cell type
S2 cells
chip antibody
none

Metadata from Sequence Read Archive

Library Description


library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
10^8 cells with and without treatment were harvested. Chromatin was sonicated with Tip sonicator (Omni Sonic Ruptor 250 Watt Ultrasonic Homogenizer) for 7 cycles (1 min on (duty cycle 30%, output 20%)) 1 min off) in 2 ml of Lysis buffer 3. The anti-EcR monoclonal antibody (DDA2.7) developed by C. Thummel in D. Hogness laboratory was obtained from the Developmental Studies Hybridoma Bank developed under the auspices of the NICHD and maintained by The University of Iowa, Department of Biology, Iowa City, IA 52242. 1 ml of chromatin was incubated with 3 μl of antibody (135 μg/ml) overnight. Chromatin and 25 μl of blocked Dynabeads Protein G (Invitrogen, cat. no. 10004D) were combined and incubated at 4° C for additional 2 hrs. 3 ng of material was used for library generation. Library was constructed following instructions of NEBNext® DNA Library Prep Reagent Set for Illumina® (NEB; cat. no. E6000L). Library amplifcation was done using KAPA Library Amp Real Time (KAPA biosystems: cat.no. KK2701).

Platform Information


instrument_model
Illumina HiSeq 2000

External Database Query

Logs in read processing pipeline


Number of total reads
30030493
Reads aligned (%)
93.9
Duplicates removed (%)
48.4
Number of peaks
4868 (qval < 1E-05)

Sequence Quality Data from DBCLS SRA