Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
zfh1

Cell type

Cell type Class
Embryo
Cell type
Embryos
NA
NA

Attributes by original data submitter

Sample

Alias
E-MTAB-7422:Zfh1ChIP_IP_6-8h_zfh1EF_chrA
Broker name
ArrayExpress
Description
Protocols: Canton S wild-type Drosophila melanogaster were grown in population cages at 25 degr. Staged 2 hr collections of embryos were made on apple-agar plates and aged at 25 degr until the required stage of development. Embryos were dechorionated using 50% bleach and formaldehyde fixed in 10 ml cross-linking solution (50 mM Hepes, 1 mM EDTA, 0.5 mM EGTA, 100 mM NaCl, 1.8 % formaldehyde, pH 8.0) and 30ml n-heptane on a shaker table at RT for 15 minutes. The reaction was terminated with 125 mM glycine, 0.1% Triton X-100 in PBS. After washing out the fix, the embryos were blotted dry, snap frozen in liquid nitrogen, and stored at -80 degr. A small number of embryos from each collection was set aside for staging. Sandmann T, Jakobsen JS, Furlong EEM. ChIP-on-chip protocol for genome-wide analysis of transcription factor binding in Drosophila melanogaster embryos. Nat Protoc. 2006;1(6):2839-55. Libraries were prepared by using Illumina ChIP-Seq sample prep kit (part#11257047). ChIP-DNA was first end-repaired, added 3’-dA overhang and ligated with adapter. Adapter-modified DNA was then size-selected by electrophoresis, purified by gel purification (Qiagen part#28704), and enriched by PCR (and purified by using Qiagen Minielute PCR purification kit, part #28004). Size, purity and concentration of the library samples were examined by Agilent DNA 1000 kit with an Agilent Technologies 2100 Bioanalyzer.
ENA checklist
ERC000011
INSDC center alias
Genome Biology Unit, European Molecular Biology Laboratory
INSDC center name
Genome Biology Unit, European Molecular Biology Laboratory
INSDC first public
2019-07-01T04:02:36Z
INSDC last update
2018-11-26T08:57:35Z
INSDC status
public
SRA accession
ERS2913281
Sample Name
ERS2913281
Title
Zfh1ChIP_IP_6-8h_zfh1EF_chrA
age
6-8
developmental stage
embryo
genotype
wild type genotype
organism
Drosophila melanogaster
organism part
whole organism
sex
mixed
strain
Canton S

Sequenced DNA Library

library_name
Zfh1ChIP_IP_6-8h_zfh1EF_chrA_s
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Canton S wild-type Drosophila melanogaster were grown in population cages at 25 degr. Staged 2 hr collections of embryos were made on apple-agar plates and aged at 25 degr until the required stage of development. Embryos were dechorionated using 50% bleach and formaldehyde fixed in 10 ml cross-linking solution (50 mM Hepes, 1 mM EDTA, 0.5 mM EGTA, 100 mM NaCl, 1.8 % formaldehyde, pH 8.0) and 30ml n-heptane on a shaker table at RT for 15 minutes. The reaction was terminated with 125 mM glycine, 0.1% Triton X-100 in PBS. After washing out the fix, the embryos were blotted dry, snap frozen in liquid nitrogen, and stored at -80 degr. A small number of embryos from each collection was set aside for staging. Sandmann T, Jakobsen JS, Furlong EEM. ChIP-on-chip protocol for genome-wide analysis of transcription factor binding in Drosophila melanogaster embryos. Nat Protoc. 2006;1(6):2839-55. Libraries were prepared by using Illumina ChIP-Seq sample prep kit (part#11257047). ChIP-DNA was first end-repaired, added 3'-dA overhang and ligated with adapter. Adapter-modified DNA was then size-selected by electrophoresis, purified by gel purification (Qiagen part#28704), and enriched by PCR (and purified by using Qiagen Minielute PCR purification kit, part #28004). Size, purity and concentration of the library samples were examined by Agilent DNA 1000 kit with an Agilent Technologies 2100 Bioanalyzer.

Sequencing Platform

instrument_model
Illumina Genome Analyzer IIx

dm3

Number of total reads
33445463
Reads aligned (%)
37.8
Duplicates removed (%)
60.8
Number of peaks
14977 (qval < 1E-05)

dm6

Number of total reads
33445463
Reads aligned (%)
35.5
Duplicates removed (%)
63.1
Number of peaks
13325 (qval < 1E-05)

Base call quality data from DBCLS SRA