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Sample GSM400172 Query DataSets for GSM400172
Status Public on May 12, 2009
Title bks_E-0-12h
Sample type genomic
 
Channel 1
Source name bks_E-0-12h
Organism Drosophila melanogaster
Characteristics antibody: bks
tissue: Embryos
time point: 0-12h
Treatment protocol No Treatment
Growth protocol 1. y; bw cn sp flies are cultivated in cages with apple juice agar plates covered with yeast powder. 2. For a 0-12 hours egg laying, new plates are added after a 2hours pre-egglaying at 9 pm and flies are allowed to lay eggs for 12 hours. 3. Embryos are collected at 8.45 am using a filter mesh and a brush. They are rinsed with EWB and cross-linked at 9 am in 1.8% formaldehyde at room temperature for 15 min.
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 bks_E-0-12h
Organism Drosophila melanogaster
Characteristics antibody: none
reference: input
Treatment protocol No Treatment
Growth protocol 1. y; bw cn sp flies are cultivated in cages with apple juice agar plates covered with yeast powder. 2. For a 0-12 hours egg laying, new plates are added after a 2hours pre-egglaying at 9 pm and flies are allowed to lay eggs for 12 hours. 3. Embryos are collected at 8.45 am using a filter mesh and a brush. They are rinsed with EWB and cross-linked at 9 am in 1.8% formaldehyde at room temperature for 15 min.
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 bks_E-0-12h
test: bks_1.CEL
test: bks_2.CEL
test: bks_3.CEL
reference: KW_Input_1.CEL
reference: KW_Input_2.CEL
reference: KW_Input_3.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 and .bar were generated with MAT.
 
Submission date May 05, 2009
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 (1)
GSE15958 ChIP-chip of bks in Drosophila embryos at E-0-12h time point.
Relations
Named Annotation GSM400172_MAT_bks_E-0-12h.bed.gz

Supplementary file Size Download File type/resource
GSM400172_KW_Input_1.CEL.gz 33.8 Mb (ftp)(http) CEL
GSM400172_KW_Input_2.CEL.gz 33.7 Mb (ftp)(http) CEL
GSM400172_KW_Input_3.CEL.gz 34.6 Mb (ftp)(http) CEL
GSM400172_MAT_bks_E-0-12h.Dm_tiling2_MR_v01_dm3.NR.bpmap_matscore.bar.gz 17.1 Mb (ftp)(http) BAR
GSM400172_MAT_bks_E-0-12h.bed.gz 166 b (ftp)(http) BED
GSM400172_bks_1.CEL.gz 33.4 Mb (ftp)(http) CEL
GSM400172_bks_2.CEL.gz 32.7 Mb (ftp)(http) CEL
GSM400172_bks_3.CEL.gz 34.1 Mb (ftp)(http) CEL
Processed data provided as supplementary file

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