Sample information curated by ChIP-Atlas

Antigen

Antigen Class
No description
Antigen
NA

Cell type

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

Attributes by original data submitter

Sample

ENA first public
2013-08-01
ENA last update
2018-03-08
External Id
SAMEA2064706
INSDC center alias
University of Helsinki
INSDC center name
University of Helsinki
INSDC first public
2013-08-01T17:01:25Z
INSDC last update
2018-03-08T16:22:39Z
INSDC status
public
Submitter Id
E-MTAB-1648:IgG_E2f_Myb_HA
broker name
ArrayExpress
cell line
S2
common name
fruit fly
genetic modification
transfection
genotype
transfected with HA tagged E2f ORF
sample name
E-MTAB-1648:IgG_E2f_Myb_HA
specimen with known storage state
fresh specimen

Sequenced DNA Library

library_name
IgG_E2f_Myb_HA
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Chromatin immunoprecipitation (ChIP)-assays were done as in Tuupanen et al.Nature Genetics 41, 885, 2009. ChIP-seq was performed essentially as described in (Tuupanen et al.Nature Genetics 41, 885, 2009) with the following modifications. ChIP for Myc and Max: S2 cells were formaldehyde crosslinked, sonicated and immunoprecipitated with the following set of antibodies (Santa Cruz Biotechnology, Inc.): Myc: dN-20 and d1-717, sc-15832 and sc-28207. Max: d1-160, sc-28209. IgG controls sc-2027 and sc-2028. ChIP for E2f and Myb: S2 cells were transiently transfected with plasmids (backbone pRmHa-1) containing metallothionein promoter driven Cterminally His-streptavidin binding peptide-3xV5 tagged Drosophila open reading frames. Expression of the genes was induced 24 hr after transfection by 0.5 mM CuSO4, and the incubation continued for 48 hr until formaldehyde crosslinking was done. Immunoprecipitations were made with 7.5 mg of monoclonal anti-V5 antibody (46-1157; Invitrogen) or IgG control antibody (sc-2025; Santa Cruz Biotechnology, Inc.) Chromatin immunoprecipitation (ChIP)-seq libraries were prepaired as in Tuupanen et al.Nature Genetics 41, 885, 2009. Library preparations were done by repairing the immunoprecipitated DNA using Klenow and T4 DNA polymerase and T4 polynucleotide kinase (MBI Fermentas, Vilnius, Latvia), and ligating the Illumina sequencing adapters according to manufacturers instructions.

Sequencing Platform

instrument_model
Illumina Genome Analyzer II

dm6

Number of total reads
884951
Reads aligned (%)
89.0
Duplicates removed (%)
19.0
Number of peaks
260 (qval < 1E-05)

dm3

Number of total reads
884951
Reads aligned (%)
91.0
Duplicates removed (%)
18.0
Number of peaks
365 (qval < 1E-05)

Base call quality data from DBCLS SRA