GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM635816 Query DataSets for GSM635816
Status Public on Dec 10, 2011
Title Baseline (0 months) - Progressive CADI score (Project 2) [KT609_2_16_09]
Sample type RNA
Source name Kidney transplant biopsy
Organism Homo sapiens
Characteristics tissue: Kidney transplant biopsy
i-ifta grade: 0
total i score: 0
cadi score: 4
time point: 00 months
Treatment protocol Tacrolimus-Mycophenolate mofetil
Extracted molecule total RNA
Extraction protocol each kidney allograft biopsy (n=120), a separate biopsy core was placed in RNAlater (Ambion Inc, Austin, TX, USA) and stored at –20°C until RNA extraction. Total RNA was extracted from each biopsy using TRIzol Reagent (Invitrogen, Carlsbad, CA, USA).
Label biotin
Label protocol biotin labeling using the OvationTM Biotin System (NuGEN Technologies, San Carlos, CA, USA)
Hybridization protocol The cDNA fragments of all 120 biopsies were hybridized onto Affymetrix GeneChip® Human Genome U133 Plus 2.0 Arrays comprising more than 54,000 probe sets, covering more than 47,000 transcripts and variants, including 38,500 well-characterized human genes (Affymetrix Inc., Santa Clara, CA, USA).
Scan protocol The microarrays were scanned using GeneChip Scanner 3000 (Affymetrix Inc., Santa Clara, CA, USA).
Description Baseline (0 months) - Progressive CADI score (Project 2)
Data processing For processing and normalization of the scanned images, dChip 2006 software was used, with perfect match [PM]/mismatch [MM] difference modeling and invariant set normalization
Submission date Dec 07, 2010
Last update date Dec 10, 2011
Contact name Maarten Naesens
Organization name Stanford University
Street address Pasteur Drive
City Stanford
ZIP/Postal code 94305
Country USA
Platform ID GPL570
Series (1)
GSE25902 Innate and adaptive immune responses associate with progressive histological damage of renal allografts

Data table header descriptions
VALUE log 2 dCHIP signal

Data table
AFFX-BioB-5_at 9.17
AFFX-BioB-M_at 9.97
AFFX-BioB-3_at 10.13
AFFX-BioC-5_at 10.31
AFFX-BioC-3_at 10.61
AFFX-BioDn-5_at 12.2
AFFX-BioDn-3_at 13.09
AFFX-CreX-5_at 13.61
AFFX-CreX-3_at 13.95
AFFX-DapX-5_at 4.27
AFFX-DapX-M_at 4.55
AFFX-DapX-3_at 5.02
AFFX-LysX-5_at 4.04
AFFX-LysX-M_at 5.69
AFFX-LysX-3_at 5.3
AFFX-PheX-5_at 4.09
AFFX-PheX-M_at 3.92
AFFX-PheX-3_at 5.07
AFFX-ThrX-5_at 5.36
AFFX-ThrX-M_at 3.95

Total number of rows: 54675

Table truncated, full table size 840 Kbytes.

Supplementary file Size Download File type/resource
GSM635816.CEL.gz 8.0 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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