Sample information curated by ChIP-Atlas

Antigen

Antigen Class
No description
Antigen
NA

Cell type

Cell type Class
Embryo
Cell type
Embryos
NA
NA

Attributes by original data submitter

Sample

ENA first public
2019-07-01
ENA last update
2018-11-26
ENA-CHECKLIST
ERC000011
External Id
SAMEA5128894
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
Submitter Id
E-MTAB-7422:Zfh1ChIP_IP_4-6h_zfh1EF_chrA
age
4-6
broker name
ArrayExpress
common name
fruit fly
developmental stage
embryo
genotype
wild type genotype
organism part
whole organism
sample name
E-MTAB-7422:Zfh1ChIP_IP_4-6h_zfh1EF_chrA
sex
mixed
strain
Canton S

Sequenced DNA Library

library_name
Zfh1ChIP_IP_4-6h_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
21465971
Reads aligned (%)
36.6
Duplicates removed (%)
61.7
Number of peaks
10242 (qval < 1E-05)

dm6

Number of total reads
21465971
Reads aligned (%)
34.5
Duplicates removed (%)
63.7
Number of peaks
9672 (qval < 1E-05)

Base call quality data from DBCLS SRA