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Sample GSM621338 Query DataSets for GSM621338
Status Public on Nov 11, 2010
Title E0-4_rbCBP
Sample type genomic
 
Channel 1
Source name E0-4_rbCBP
Organism Drosophila melanogaster
Characteristics developmental stage: E0-4h
antibody: rbCBP
antibody provider: Mannervik Lab
antibody lot/batch#: N/A
antibody catalog#: N/A
fly: iso1 (y; bw cn sp)
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).
Extracted molecule genomic DNA
Extraction protocol Drosophila samples are crushed in presence of 1.8% of formaldehyde for 15 minutes. 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 reference samples. 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. Amplification of the DNA is done by linker-mediated PCR and used for labeling.
Label biotin
Label protocol Affymetrix Labeling Protocol (TdT labeling)
 
Channel 2
Source name input
Organism Drosophila melanogaster
Characteristics antibody: none
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).
Extracted molecule genomic DNA
Extraction protocol Drosophila samples are crushed in presence of 1.8% of formaldehyde for 15 minutes. 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 reference samples. 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. Amplification of the DNA is done by linker-mediated PCR and used for labeling.
Label biotin
Label protocol Affymetrix Labeling Protocol (TdT labeling)
 
 
Hybridization protocol Affymetrix Hybridization Protocol - Hybridizations were performed at the Functional Genomics Facility (FGF) at the University of Chicago.
Scan protocol Affymetrix Protocol - Scans were performed at the Functional Genomics Facility (FGF) at the University of Chicago.
Description input CEL file: extracted_0-4h_Input.CEL
input CEL file: extracted_E-0-4h_Input-0-4h_Ctl1.CEL
Data processing .CEL files generated by the scanner are used as Input files in the MAT software to generate the signal files that are used by CisGenome to identify peaks.
.bed were generated with MAT then converted to gff format. .wig files are genereted by CisGenome from MAT .bar files.
 
Submission date Nov 10, 2010
Last update date Feb 02, 2015
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 GPL6629
Series (2)
GSE23537 modENCODE_White Lab: genome-wide ChIP-chip and ChIP-Seq data
GSE25259 modENCODE_White Lab: genome-wide ChIP-chip data
Relations
Named Annotation GSM621338_extracted_MAT_rbCBP_E-0-4h.Dm_tiling2_MR_v01_dm3.NR.bpmap_matscore.bar.txt_IGB.wig.gz

Supplementary file Size Download File type/resource
GSM621338_extracted_E-0-4h_0-4h-cbp_Test3.CEL.gz 35.6 Mb (ftp)(http) CEL
GSM621338_extracted_E-0-4h_cbp-1_Test1.CEL.gz 34.8 Mb (ftp)(http) CEL
GSM621338_extracted_E-0-4h_cbp-2_Test2.CEL.gz 35.5 Mb (ftp)(http) CEL
GSM621338_extracted_MAT_rbCBP_E-0-4h.Dm_tiling2_MR_v01_dm3.NR.bpmap_matscore.bar.txt_IGB.wig.gz 19.2 Mb (ftp)(http) WIG
GSM621338_extracted_MAT_rbCBP_E-0-4h.bed_dcc.gff.gz 14.6 Kb (ftp)(http) GFF
Processed data provided as supplementary file

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