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Sample GSM533939 Query DataSets for GSM533939
Status Public on May 24, 2010
Title renal allograft biopsy, (U of A/Chicago) 126A4AGX7
Sample type RNA
 
Source name renal allograft biopsy
Organism Homo sapiens
Characteristics failed=1/non failed=0: 0
time of biopsy post transplant (days): 42
time from biopsy to failure/censoring (days): 1167
rejection/non rejection: nonrej
sample included in the main analysis- the first biopsy per patient from the 105 late (> 1 year) patients: 0
Treatment protocol The immunosuppressive treatment of the patients before the biopsy was based on individual treatment regiments; the treatment after the biopsy was adjusted based on the histopathological diagnosis.
Growth protocol All human renal allograft biopsies taken for clinical indication during the period specified above were included. Tissue was immediately placed in RNA later.
Extracted molecule total RNA
Extraction protocol Following homogenization of the tissue in 0.5ml of Trizol reagent (Invitrogen, Carlsbad, CA), total RNA was extracted and purified using the Rneasy Micro Kit (Quiagen, Ontario, Canada) (average yield 4ug/core, (RNA integrity number >7).
Label biotin
Label protocol RNA (1-2ug) was labeled using GeneChip HT One-Cycle Target Labeling and Control kit. Quality of labeled cRNA was assessed on an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA) before hybridization to HGU133Plus2.0. GeneChip (Affymetrix, Santa Clara, CA).
 
Hybridization protocol Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HGU133 Plus 2.0 Human Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
Scan protocol GeneChips were scanned using Gene Array Scanner (Affymetrix) and processed with GeneChip Operating Software Version 1.4.0 (Affynetrix).
Description Samples with the same initial numbers in the sample names are replicates from the same patient. For the main analysis, only the earliest biopsy per patient was used, and only in those patients with a biopsy taken > 1 year post-transplant
Data processing Microarray data files were preprocessed using robust multi-chip averaging (RMA) implemented in Bioconductor.
 
Submission date Apr 17, 2010
Last update date Jul 15, 2011
Contact name Jeff Reeve
E-mail(s) jreeve@ualberta.ca
Organization name University of Alberta
Lab Halloran
Street address 250 HMRC University of Alberta
City Edmonton
State/province Alberta
ZIP/Postal code T6G 2S2
Country Canada
 
Platform ID GPL570
Series (1)
GSE21374 Expression data from human renal allograft biopsies
Relations
Reanalyzed by GSM761727

Data table header descriptions
ID_REF
VALUE log2-RMA signal

Data table
ID_REF VALUE
1007_s_at 9.793265572
1053_at 6.203782673
117_at 5.699795749
121_at 10.79496959
1255_g_at 3.019438972
1294_at 7.802959918
1316_at 5.436446785
1320_at 5.168858032
1405_i_at 4.658466095
1431_at 7.201685767
1438_at 6.290477158
1487_at 8.848731414
1494_f_at 5.854803116
1552256_a_at 7.13247065
1552257_a_at 7.221309148
1552258_at 4.338982024
1552261_at 6.714650973
1552263_at 4.66360925
1552264_a_at 6.94384001
1552266_at 3.70918766

Total number of rows: 54675

Table truncated, full table size 1212 Kbytes.




Supplementary file Size Download File type/resource
GSM533939.CEL.gz 4.8 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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