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Sample GSM570043 Query DataSets for GSM570043
Status Public on Aug 11, 2010
Title Trl_ChIPSeq_1 and 2
Sample type SRA
 
Source name E16-24h
Organism Drosophila melanogaster
Characteristics developmental stage: E16-24h
fraction: ChIP
antibody name: KW3-Trl-D2
manufacturer: White Lab/Aviva
lot/batch#: N/A
catalog#: N/A
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
E-mail(s) kpwhite@uchicago.edu
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)
GSE23146 modENCODE_White Lab: genome-wide ChIP data of Trl from E16-24h on Illumina Genome Analyzer.
GSE23537 modENCODE_White Lab: genome-wide ChIP-chip and ChIP-Seq data
Relations
SRA SRX025478
BioSample SAMN00100802

Supplementary file Size Download File type/resource
GSM570043_E16-24h_Trl_density.bedgraph.gz 22.1 Mb (ftp)(http) BEDGRAPH
GSM570043_E16-24h_Trl_peaks.bed.gz 74.1 Kb (ftp)(http) BED
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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