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Sample GSM318497 Query DataSets for GSM318497
Status Public on Apr 13, 2010
Title Male human kidney sample No.67 tubulointerstitial fraction
Sample type RNA
 
Source name Human kidney sample No.67
Organism Homo sapiens
Characteristics Diseased tubulointerstitium
Male
Treatment protocol Kidney tissue was obtained in the operating room immediately after removal from the patient. Tissue was placed into RNALater right after removal from the body and was kept at 4C. 1mmx1mm biopsy tissues were placed under Olympus model SZX12 stereomicroscope using 90 x magnification. The biopsy tissue was manually microdissected at 4C in RNALater for glomerular and tubular compartment using 2 fine tip (1mm) forceps. Dissected tissue was homogenized using Powergen125 (Fisher) homogenizer and stored at -80C.
Extracted molecule total RNA
Extraction protocol RNA was prepared using RNAeasy mini columns (Qiagen, Valencia, CA) according to manufacturer’s instruction. RNA quality and quantity was determined using Lab-on-Chip Total RNA PicoKit, Agilent BioAnalyzer. Only samples without evidence of degradation were further used.
Label biotin
Label protocol Biotinylated cRNA were prepared according to the standard Affymetrix Two-Cycle target preparation protocol from 10 ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
 
Hybridization protocol Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HG133A 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
Scan protocol GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
Description Gene expression data from diseased male tubuli
Data processing The data were analyzed with ArrayAssist software using gcRMA as normalization method.
 
Submission date Sep 05, 2008
Last update date Apr 13, 2010
Contact name Han Si
E-mail(s) hsi@aecom.yu.edu
Organization name AECOM
Department Medicine/Nephrology
Lab Susztak, Katalin MD, PhD
Street address 1300 Morris Park
City Bronx
State/province NY
ZIP/Postal code 10461
Country USA
 
Platform ID GPL571
Series (1)
GSE12682 Expression data from Human Kidney (HK) samples

Data table header descriptions
ID_REF
VALUE gcRMA signal

Data table
ID_REF VALUE
1007_s_at 528.5243
1053_at 12.172862
117_at 6.052899
121_at 1264.3793
1255_g_at 4.4153013
1294_at 51.684746
1316_at 10.590028
1320_at 5.160496
1405_i_at 46.998074
1431_at 5.491145
1438_at 4.186159
1487_at 196.56851
1494_f_at 4.7590923
1598_g_at 153.06487
160020_at 6.331846
1729_at 187.19698
177_at 43.7109
1773_at 3.8881087
179_at 3.8041353
1861_at 11.610735

Total number of rows: 22277

Table truncated, full table size 446 Kbytes.




Supplementary file Size Download File type/resource
GSM318497.CEL.gz 2.1 Mb (ftp)(http) CEL
Processed data included within Sample table

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