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Sample GSM3524295 Query DataSets for GSM3524295
Status Public on Nov 07, 2019
Title kidney biopsy 1000
Sample type RNA
 
Source name kidney biopsy
Organism Homo sapiens
Characteristics archetype cluster (1,2,3,4,5,6,7): 2
injpc1: 3.05241953831296
injpc2: -2.5517302264495
injpc3: 0.726341744244407
injaa (1,2,3,4,5,6): 1
in n=1526? (yes, no): yes
set (66 or 1679): 1679
in n=102? (yes, no): yes
mmdx (abmr, pabmr, mixed, tcmr, ptcmr, nr, na): TCMR
hprt (positive, negative): Negative
dsa (0,1): 0
rejaaclust (1,2,3,4,5,6): 2
in 1208? (1, 0): 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 kidney 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 Tissue was homogenization in 0.5ml of Trizol reagent (Invitrogen, Carlsbad, CA) and total RNA was extracted and purified using the Rneasy Micro Kit (Quiagen, Ontario, Canada) (average yield 8µg/core, (RNA integrity number >7).
Label biotin
Label protocol Total RNA (0.5µg) was labeled using GeneChip 3` IVT Express Labeling kit. Quality of labeled aRNA was assessed on an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA) before hybridization to GeneChip® PrimeView™ Human Gene Expression Array   
 
Hybridization protocol (Affymetrix, Santa Clara, CA).  Amplified RNA (10ug) was hybridized for 16 hr at 45C on  GeneChip® PrimeView™ Human Gene Expression Array . GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
Scan protocol GeneChips were scanned using Gene Array Scanner 3000 7G (Affymetrix) and processed with GeneChip® Command Console® Software (AGCC)(Affymetrix).
Description GPL13667
Data processing Microarray data files were preprocessed using robust multi-chip averaging (RMA) implemented in Bioconductor.
 
Submission date Dec 20, 2018
Last update date Aug 19, 2024
Contact name Jessica Chang
E-mail(s) jjchang@ualberta.ca
Organization name University of Alberta
Department Medicine
Lab ATAGC
Street address 250 Heritage Medical Research Centre
City Edmonton
ZIP/Postal code T6G 2S2
Country Canada
 
Platform ID GPL13667
Series (1)
GSE124203 Generating automated kidney transplant biopsy reports combining molecular measurements with ensembles of machine learning classifiers
Relations
Reanalyzed by GSM8465987

Data table header descriptions
ID_REF
VALUE log2-RMA signal

Data table
ID_REF VALUE
11715100_at 4.23
11715101_s_at 6.35
11715102_x_at 4.25
11715103_x_at 5.45
11715104_s_at 6.14
11715105_at 3.79
11715106_x_at 5.43
11715107_s_at 6.37
11715108_x_at 3.41
11715109_at 3.80
11715110_at 6.13
11715111_s_at 8.36
11715112_at 3.85
11715113_x_at 7.84
11715114_x_at 7.86
11715115_s_at 2.78
11715116_s_at 3.35
11715117_x_at 2.62
11715118_s_at 3.12
11715119_s_at 6.23

Total number of rows: 49293

Table truncated, full table size 894 Kbytes.




Supplementary file Size Download File type/resource
GSM3524295_kidney1000.CEL.gz 1.9 Mb (ftp)(http) CEL
Processed data included within Sample table

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