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Sample GSM308533 Query DataSets for GSM308533
Status Public on Jun 30, 2009
Title bioCnot3
Sample type genomic
 
Channel 1
Source name bioCnot3 ChIP DNA from ES cells (3 repeats)
Organism Mus musculus
Characteristics J1 ES cells
Growth protocol Normal J1 ES growth condition
Extracted molecule genomic DNA
Extraction protocol bioChIP (biotin-mediated ChIP) was performed as described previously (Kim et al., 2008).
Label biotin
Label protocol Each ChIP was amplified using ligation-mediated PCR (LM-PCR). Labeling was according to standard Affymetrix protocols.
 
Channel 2
Source name Mock biotin ChIP DNA from ES cells expression BirA (4 repeats)
Organism Mus musculus
Characteristics Reference for bioChIP
J1 ES cells
Growth protocol Normal J1 ES growth condition
Extracted molecule genomic DNA
Extraction protocol bioChIP (biotin-mediated ChIP) was performed as described previously (Kim et al., 2008).
Label biotin
Label protocol Each ChIP was amplified using ligation-mediated PCR (LM-PCR). Labeling was according to standard Affymetrix protocols.
 
 
Hybridization protocol According to standard Affymetrix protocols.
Scan protocol According to standard Affymetrix protocols.
Description IP samples:
bioCnot3_1.CEL
bioCnot3_2.CEL
bioCnot3_3.CEL
Control samples:
BirA_1.CEL
BirA_2.CEL
BirA_3.CEL
BirA_4.CEL
Data processing MAT (Johnson et al., 2006) was used to process the raw CEL files with the following settings; Bandwith = 300, MaxGap = 300, MinProbe = 10. BAR and BED files were generated by using Mm_PromPR_v02-1_NCBIv33.bpmap and genomic coordinates in BED files were converted to new coordinates based on mouse genome assembly mm8.
 
Submission date Jul 29, 2008
Last update date Jan 04, 2012
Contact name guang hu
E-mail(s) ghu@rics.bwh.harvard.edu
Phone 617-525-4513
Organization name Brigham and Women's Hospital, Harvard Medical School
Department Genetics
Lab Stephen J. Elledge
Street address NRB 160, 77 Ave. Louis Pasteur
City Boston
State/province MA
ZIP/Postal code 02115
Country USA
 
Platform ID GPL5811
Series (1)
GSE12283 Chip-chip from mouse embryonic stem (mES) cells with bioTrim28, and bioCnot3

Supplementary file Size Download File type/resource
GSM308533_BirA_1.CEL 44.8 Mb (ftp)(http) CEL
GSM308533_BirA_2.CEL 44.8 Mb (ftp)(http) CEL
GSM308533_BirA_3.CEL 44.8 Mb (ftp)(http) CEL
GSM308533_BirA_4.CEL 44.8 Mb (ftp)(http) CEL
GSM308533_bioCnot3.bar 31.7 Mb (ftp)(http) BAR
GSM308533_bioCnot3.bed 70.7 Kb (ftp)(http) BED
GSM308533_bioCnot3_1.CEL 44.8 Mb (ftp)(http) CEL
GSM308533_bioCnot3_2.CEL 44.9 Mb (ftp)(http) CEL
GSM308533_bioCnot3_3.CEL 44.8 Mb (ftp)(http) CEL
Processed data provided as supplementary file

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