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Sample GSM433909 Query DataSets for GSM433909
Status Public on Jul 28, 2009
Title HepG2_RCyP+
Sample type RNA
Source name BD SMARTTM RACE cDNA – HepG2
Organism Homo sapiens
Characteristics age: 15 years old caucasian male
tissue: HepG2 cell line
Growth protocol 11 tissues poly A+ RNA was purchased and 5 cell lines were grown as suggested by ATCC
Extracted molecule polyA RNA
Extraction protocol see Kapranov, et al Science 2002
Label biotin
Label protocol 2 micrograms of polyA+ RNA were converted into double-stranded cDNA essentially as described in Kapranov et al, Science. 2007 Jun 8;316(5830):1484-8.
Hybridization protocol 2 micrograms of double-stranded cDNA were labeled and hybridized to Affymetrix tiling arrays containing probes against non-repepetitive portions of human chromosomes 21 and 22 essentially as described in Kapranov et al, Science. 2007 Jun 8;316(5830):1484-8.
Scan protocol Arrays were scanned on Affymetrix GCS3000 scanner
Description includes cytoplasmic RNA
Single chip x 2 tech reps, each chromosome placed in separate file
Data processing See supplement materials of Djebali, S, et al (2009) Nature in press
Bar files generated with proprietary software (almost identical to Affymetrix TAS). Bandwidth = 0, Normalization target= 330
Submission date Jul 27, 2009
Last update date Jul 28, 2009
Contact name Chris Zaleski
Organization name Cold Spring Harbor Labs
Lab Gingeras
Street address 500 Sunnyside Blvd
City Woodbury
State/province NY
ZIP/Postal code 11797
Country USA
Platform ID GPL5715
Series (1)
GSE17358 Transcriptional termini of genes on chromosomes 21-22 (RNA mapping)

Supplementary file Size Download File type/resource
GSM433909_PI_20_AS_HepG2_RCyP+_C01_B1_T1.cel.gz 30.3 Mb (ftp)(http) CEL
GSM433909_PI_20_AS_HepG2_RCyP+_C01_B1_T2.cel.gz 30.8 Mb (ftp)(http) CEL 5.0 Mb (ftp)(http) BAR 5.1 Mb (ftp)(http) BAR
Processed data provided as supplementary file

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