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Sample GSM534164 Query DataSets for GSM534164
Status Public on May 24, 2010
Title renal allograft biopsy, (U of A/Chicago) 56A2AGX7
Sample type RNA
Source name renal allograft biopsy
Organism Homo sapiens
Characteristics failed=1/non failed=0: 0
time of biopsy post transplant (days): 26
time from biopsy to failure/censoring (days): 1302
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
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
Reanalyzed by GSM761734

Data table header descriptions
VALUE log2-RMA signal

Data table
1007_s_at 10.69963823
1053_at 6.606207491
117_at 6.671890287
121_at 11.16346632
1255_g_at 3.106218781
1294_at 7.764826157
1316_at 5.276637166
1320_at 5.142736211
1405_i_at 5.448180808
1431_at 3.500286901
1438_at 6.0334584
1487_at 8.305283395
1494_f_at 5.37977554
1552256_a_at 6.763228308
1552257_a_at 6.920729471
1552258_at 4.702654564
1552261_at 7.89748098
1552263_at 5.614570476
1552264_a_at 7.130173434
1552266_at 3.698502818

Total number of rows: 54675

Table truncated, full table size 1212 Kbytes.

Supplementary file Size Download File type/resource
GSM534164.CEL.gz 4.4 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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