Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
EcR

Cell type

Cell type Class
Cell line
Cell type
S2
Source
Oregon R
Developmental Stage
late embryonic stage

Attributes by original data submitter

Sample

source_name
S2 cells
cell type
S2 cells
agent
ecdysone
chip antibody
anti-EcR monoclonal antibody (DDA2.7) developed by C. Thummel in D. Hogness laboratory

Sequenced DNA Library

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).

Sequencing Platform

instrument_model
Illumina HiSeq 2000

dm6

Number of total reads
77605864
Reads aligned (%)
92.7
Duplicates removed (%)
53.9
Number of peaks
0 (qval < 1E-05)

dm3

Number of total reads
77605864
Reads aligned (%)
93.7
Duplicates removed (%)
50.5
Number of peaks
0 (qval < 1E-05)

Base call quality data from DBCLS SRA