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Sample GSM569798 Query DataSets for GSM569798
Status Public on Aug 11, 2010
Title E16-24h_10T(Dfd-GFP)_ChIPSeq_1 and 2
Sample type SRA
Source name 10T-E16-24h
Organism Drosophila melanogaster
Characteristics developmental stage: 10T-E16-24h
fraction: ChIP
antibody name: NWG-GFP
manufacturer: White Lab/Chemicon
lot/batch#: N/A
catalog#: N/A
Treatment protocol No Treatment
Growth protocol 1. y w, VK37 flies are cultivated in cages with apple juice agar plates covered with yeast powder. 2. For a 0-4 hours egg laying for example, new plates are added after a 2hours pre-egglaying and flies are allowed to lay eggs for 4 hours. 3. Embryos are collected using a filter mesh and a brush. They are rinsed with EWB and cross-linked in 1.8% formaldehyde at room temperature for 15 min.
Extracted molecule genomic DNA
Extraction protocol Drosophila material is crushed in a glass homogenizer in presence of 1.8% of formaldehyde for 15 minutes at room temperature. After washing, the material is sonicated for 15 minutes to solubilize the chromatin. After centrifugation, the supernatant containing soluble chromatin is collected for IPs. Specific antibodies are added to the chromatin extract while one aliquot will be treated for DNA extraction corresponding to the Input reference sample. ChIP are carried overnight at room temperature. Protein A Sepharose beads are used to pull down the chromatin bound antibodies. After washes and finally elution, the DNA corresponding to the IPed material is extracted and purified. The DNA is directly used for Solexa library preparation. If used for hybridization on microarrays, the sample will undergo an LM-PCR amplification before labelling.
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer
Data processing Reads were aligned to the flybase BDGPv5 reference genome using Bowtie. Signal files were generated with the R package SPP. Peaks were called with MACS.
Submission date Jul 23, 2010
Last update date May 15, 2019
Contact name Kevin P. White
Organization name University of Chicago
Department Institute for Genomics and Systems Biology
Street address 900 E. 57th STR. 10th FL.
City Chicago
State/province IL
ZIP/Postal code 60615
Country USA
Platform ID GPL9058
Series (2)
GSE23126 modENCODE_White Lab: genome-wide ChIP data of GFP from 10T-E16-24h on Illumina Genome Analyzer.
GSE23537 modENCODE_White Lab: genome-wide ChIP-chip and ChIP-Seq data
SRA SRX025470
BioSample SAMN00100793
Named Annotation GSM569798_10T_E16-24h_GFP_peaks.bed.gz

Supplementary file Size Download File type/resource
GSM569798_10T_E16-24h_GFP_density.bedgraph.gz 20.9 Mb (ftp)(http) BEDGRAPH
GSM569798_10T_E16-24h_GFP_peaks.bed.gz 8.5 Kb (ftp)(http) BED
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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