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Sample GSM835 Query DataSets for GSM835
Status Public on May 21, 2002
Title HS-5_06
Sample type RNA
 
Channel 1
Source name HS-5 RNA
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name Universal human reference RNA
Organism Homo sapiens
Extracted molecule total RNA
 
 
Description Target Source: human bone marrow stromal cells, HS-5
Description: human bone marrow stromal cells cultured in RPMI medium 1640 containing 10% fetal calf serum.
Values are ratio of HS-5 to Universal RNA.

HS-5 cells were plated in T75 flasks at 3,000,000 cells/flask. They were cultured for 3 days and harvested by trypsinization followed by pelleting of the cells. All RNA isolation was accomplished with Qiagen RNeasy Mini Kit reagents. As a control RNA, Human Universal RNA (Stratagene, La Jolla, CA) which is a mixture of RNA from 10 control cell lines approximating the expression profile of the majority of human genes was used. The RNA (30 µg) was annealed with 5 µg oligo dT12-18, and reverse-transcribed into cDNA with Superscript II reverse transcriptase for 2h at 42°C in the presence of 0.5 mM dGTP, 0.5 mM dCTP, 0.5 mM dATP, 0.3 mM dTTP, 0.2 mM amino-allyl dUTP. After hydrolysis of RNA in 0.2 M NaOH, Tris was removed from the reaction with a Microcon-30 concentrator. The cDNA from HS-5 RNA and Human Universal RNA was covalently coupled separately with Cy5 and Cy3 monoreactive fluors, respectively, in 50 mM sodium bicarbonate, pH 9.0, followed by quenching with 2.7 M hydroxylamine. The Cy5 and Cy3 labelled cDNAs were combined and purified with a QIAquick PCR purification kit and suspended in 36 µl of 3X SSC and 0.8 mg/ml of poly-A for hybridization to the microarray.
Fluorescent array images were collected for both Cy3 and Cy5 with a GenePix 4000A fluorescent scanner and image intensity data were extracted and analyzed with GenePix Pro 3.0 analysis software. After background correction and removal of flagged values, log base 2 expression ratios were mean centered and linear transformed to obtain the log and linear values given in the data table.
 
Submission date Feb 08, 2002
Last update date Mar 15, 2006
Contact name Mineo Iwata
E-mail(s) miwata@fhcrc.org
Phone 206-667-4545
Fax 206-667-5978
URL http://parma.fhcrc.org/MIwata
Organization name Fred Hutchinson Cancer Research Institute
Department Clinical Research
Lab Torok-Storb
Street address 1100 Fairview Ave. N. D1-100
City Seattle
State/province WA
ZIP/Postal code 98109
Country USA
 
Platform ID GPL44
Series (2)
GSE463 Profiling of human bone marrow stromal cell lines HS-5 and HS-27a
GSE3472 Bone marrow microenvironment: interaction of monocytes and stromal cells

Data table header descriptions
ID_REF
VALUE same as UNF_VALUE but with flagged values removed
LINEARIZED_VALUE Linear transform of the normalized log of ratio
CH_1 Signal at 635nm - background at 635nm (HS-5)
CH_2 Signal at 532nm - background at 532nm (reference)
FLAGS Quality measure of individual spots (negative value indicates substandard signal)
UNF_VALUE Normalized log base 2 of ratio of medians of HS-5 to universal human reference RNA

Data table
ID_REF VALUE LINEARIZED_VALUE CH_1 CH_2 FLAGS UNF_VALUE
1 -0.804986179 0.572367564 762 1630 0 -0.804986179
2 0.493013821 1.407381858 907 789 0 0.493013821
3 0.536013821 1.449960724 624 527 0 0.536013821
4 -0.436986179 0.738676108 739 1225 0 -0.436986179
5 0.082013821 1.058494535 2791 3228 0 0.082013821
6 -1.006986179 0.497584628 165 406 0 -1.006986179
7 -0.748986179 0.595021549 417 858 0 -0.748986179
8 -0.440986179 0.7366309 83 138 0 -0.440986179
9 0.850013821 1.802518194 240 163 0 0.850013821
10 -0.544986179 0.685397969 692 1236 0 -0.544986179
11 #VALUE! 4 -4 -50 No number for Log Ratio
12 -0.000986179 0.999316667 129 158 0 -0.000986179
13 -0.500986179 0.706623591 2070 3586 0 -0.500986179
14 1.258013821 2.391662506 1164 596 0 1.258013821
15 0.734591354 9 15 -50 -0.444986179
16 #VALUE! -4 2 -50 No number for Log Ratio
17 -0.231986179 0.851461865 73 105 0 -0.231986179
18 -0.894986179 0.537752347 454 1034 0 -0.894986179
19 -2.929986179 0.131215843 12 112 0 -2.929986179
20 -0.439986179 0.737141671 59 98 0 -0.439986179

Total number of rows: 17582

Table truncated, full table size 889 Kbytes.




Supplementary data files not provided

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