NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM478747 Query DataSets for GSM478747
Status Public on May 18, 2010
Title Human Liver Total RNA, 6
Sample type mixed
 
Channel 1
Source name Human liver total RNA
Organism Homo sapiens
Characteristics tissue: liver
Extracted molecule total RNA
Extraction protocol Total or PolyA+ RNA was obtained from Clontech. After DNaseI (GE Healthcare) treatment to remove residual genomic DNA, 10 ug of RNA was incubated with random hexamers at 70C for 10 min, incubated at 15C for 30 min and reverse transcribed to single-stranded cDNA for 2 hours at 42C with Superscript II (Invitrogen). The cDNA was then directly used for second strand synthesis, after which the double-stranded cDNA (ds-cDNA) was purified using PCR purification columns (Qiagen) in combination with the nucleotide cleanup kit protocols.
Label biotin
Label protocol cDNA was fragmented by nuclease digestion in a solution containing 1X One-Phor-All buffer (GE Healthcare) and DNase I (GE Healthcare) at 37ーC until the average fragment size was approximately 70 bp. The fragmentation reaction was stopped by incubating at 95C for 10 min. Fragmented samples were biotinylated with GeneChip Labeling reagent (Affymetrix) using terminal deoxynucleotidyl transferase at 37C for 2 hours.
 
Channel 2
Source name Human genomic DNA
Organism Homo sapiens
Characteristics sample type: reference
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was obtained from Clontech.
Label biotin
Label protocol Genomic DNA was fragmented by nuclease digestion in a solution containing 1X One-Phor-All buffer (GE Healthcare) and DNase I (GE Healthcare) at 37C until the average fragment size was approximately 70 bp. The fragmentation reaction was stopped by incubating at 95C for 10 min. Fragmented samples were biotinylated with GeneChip Labeling reagent (Affymetrix) using terminal deoxynucleotidyl transferase at 37C for 2 hours.
 
 
Hybridization protocol Arrays were hybridized in a GeneChip Fluidics Station 450 using standard protocol “EukGE-WS2v5_450”.
Scan protocol Arrays were scanned in an Affymetrix 7G scanner.
Description HLT-F1
Data processing Raw data files were normalized with Affymetrix Tiling Analysis Software (TAS) v1.1. All samples were quantile normalized with a bandwidth of 70, using a genomic DNA hybridization as reference.
 
Submission date Dec 02, 2009
Last update date Apr 23, 2010
Contact name Harm van Bakel
E-mail(s) harm.vanbakel@mssm.edu
Organization name Mount Sinai School of Medicine
Department Genetics and Genomic Sciences
Lab Bakel Lab
Street address One Gustave L. Levy Place, Box 1498
City New York
State/province New York
ZIP/Postal code 10029
Country USA
 
Platform ID GPL4915
Series (1)
GSE19289 Most “dark matter” transcripts are associated with known genes

Supplementary file Size Download File type/resource
GSM478747_HLT-F1-vs-gDNA_ncbi36-bw70.bar.gz 33.8 Mb (ftp)(http) BAR
GSM478747_HLT-F1.CEL.gz 25.4 Mb (ftp)(http) CEL
GSM478747_hgDNA-F1.CEL.gz 29.8 Mb (ftp)(http) CEL
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap