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Sample GSM318496 Query DataSets for GSM318496
Status Public on Apr 13, 2010
Title Male human kidney sample No.65 tubulointerstitial fraction
Sample type RNA
Source name Human kidney sample No.65
Organism Homo sapiens
Characteristics Diseased tubulointerstitium
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
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
VALUE gcRMA signal

Data table
1007_s_at 378.42905
1053_at 19.699772
117_at 6.3598604
121_at 951.3719
1255_g_at 4.6315784
1294_at 38.115364
1316_at 21.57637
1320_at 5.9050384
1405_i_at 22.894047
1431_at 6.2777095
1438_at 4.3410454
1487_at 214.16678
1494_f_at 5.1766195
1598_g_at 87.70412
160020_at 6.4504967
1729_at 267.86227
177_at 29.719515
1773_at 3.992004
179_at 3.8605716
1861_at 11.840442

Total number of rows: 22277

Table truncated, full table size 446 Kbytes.

Supplementary file Size Download File type/resource
GSM318496.CEL.gz 2.1 Mb (ftp)(http) CEL
Processed data included within Sample table

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