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Sample GSM318490 Query DataSets for GSM318490
Status Public on Apr 13, 2010
Title Female human kidney sample No.76 tubulointerstitial fraction
Sample type RNA
 
Source name Human kidney sample No.76
Organism Homo sapiens
Characteristics Healthy tubulointerstitium
Female
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 healthy female 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 363.34076
1053_at 8.898986
117_at 6.20137
121_at 1378.3086
1255_g_at 4.19694
1294_at 22.142887
1316_at 19.42779
1320_at 5.231161
1405_i_at 8.393269
1431_at 5.688722
1438_at 4.1933017
1487_at 239.58522
1494_f_at 4.7535996
1598_g_at 279.0366
160020_at 6.599722
1729_at 162.55206
177_at 80.3841
1773_at 3.860411
179_at 3.7471185
1861_at 15.411246

Total number of rows: 22277

Table truncated, full table size 446 Kbytes.




Supplementary file Size Download File type/resource
GSM318490.CEL.gz 2.2 Mb (ftp)(http) CEL
Processed data included within Sample table

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