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Sample GSM570048 Query DataSets for GSM570048
Status Public on Aug 11, 2010
Title kni_INPUT_3
Sample type SRA
Source name E8-16h
Organism Drosophila melanogaster
Characteristics developmental stage: E8-16h
fraction: input
Treatment protocol No Treatment
Growth protocol 1. the iso1 (y; bw cn sp) flies or the transgenic flies are cultivated in cages with apple juice agar plates covered with yeast powder. and the egg laying is performed for the desired amount of time to correspond to the proper stage. The biological material is collected using a filter mesh and a brush and rinsed extensively with Embryonic Wash Buffer (EWB). The material is then used freshly for cross-linking.
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 26, 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)
GSE23147 modENCODE_White Lab: genome-wide ChIP data of kni from E8-16h on Illumina Genome Analyzer.
GSE23537 modENCODE_White Lab: genome-wide ChIP-chip and ChIP-Seq data
SRA SRX025483
BioSample SAMN00100807

Supplementary data files not provided
SRA Run SelectorHelp
Processed data not applicable for this record
Raw data are available in SRA

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