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Sample GSM34236 Query DataSets for GSM34236
Status Public on Mar 16, 2005
Title Hypoxia day 1, replicate 2
Sample type RNA
 
Channel 1
Source name hypoxic lungs day 1
Organism Mus musculus
Extracted molecule total RNA
 
Channel 2
Source name control lungs day 1
Organism Mus musculus
Extracted molecule total RNA
 
 
Description Whole lungs of BALB/c (n=5) exposed to 1 day of 0.5 atm hypoxia and time-matched control mice (n=5) were pooled separately.
Total RNA isolation was accomplished with Qiagen RNeasy Midi Kit reagents. Total RNA (50 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 Hypoxic and Control groups was covalently coupled separately with Cy5 and Cy3 monoreactive fluors in 50 mM sodium bicarbonate, pH 9.0, followed by quenching with 2.7 M hydroxylamine. The Cy5 and Cy3 labeled 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 4.0 analysis software. After background correction and removal of flagged values, log base 2 expression ratios of median intensities were normalized using lowess method.
Keywords = hypoxia, pulmonary hypertension, vascular remodeling
 
Submission date Nov 01, 2004
Last update date Oct 19, 2022
Contact name Sina Gharib
E-mail(s) sagharib@uw.edu
Organization name University of Washington
Department Medicine
Street address 850 Republican St.
City Seattle
State/province WA
ZIP/Postal code 98109
Country USA
 
Platform ID GPL1674
Series (1)
GSE1909 Hypoxic pulmonary hypertension study

Data table header descriptions
ID_REF
VALUE Normalized log2 ratio of background subtracted medians defined by CH1/CH2. Note that this ratio is reversed when a dye switching replication is performed.
CH1_MEDIAN CH1 (F635) median fluorescence intensity
CH1_MEAN CH1 (F635) mean fluorescence intensity
CH1_SD CH1 (F635) fluorescence intensity standard deviation
CH1_BKD_MEDIAN
CH1_BKD_MEAN CH1 (F635) background mean fluorescence intensity
CH1_BKD_SD
CH2_MEDIAN CH2 (F532) median fluorescence intensity
CH2_MEAN CH2 (F532) mean fluorescence intensity
CH2_SD CH2 (F532) fluorescence intensity standard deviation
CH2_BKD_MEDIAN CH2 (F532) background median fluorescence intensity
CH2_BKD_MEAN CH2 (F532) background mean fluorescence intensity
CH2_BKD_SD CH2 (F532) background fluorescence intensity standard deviation
CH1_MEDIAN - CH1_BKD_MEDIAN Channel 1 median signal
CH2_MEDIAN - CH2_BKD_MEDIAN Channel 2 median signal
QUALITY_FLAG Denotes which features met our filtering criterion. A value of 0 means feature was accepted. A negative value of -50 means that the feature did not have at least 60% of its pixels greater than two standard deviations over the background intensity. A negative value of -100 means that manual inspection of spot revealed unacceptable quality (such as saturation, scratch, etc). Negatively flagged spots were not used in data normalization or VALUE calculation.

Data table
ID_REF VALUE CH1_MEDIAN CH1_MEAN CH1_SD CH1_BKD_MEDIAN CH1_BKD_MEAN CH1_BKD_SD CH2_MEDIAN CH2_MEAN CH2_SD CH2_BKD_MEDIAN CH2_BKD_MEAN CH2_BKD_SD CH1_MEDIAN - CH1_BKD_MEDIAN CH2_MEDIAN - CH2_BKD_MEDIAN QUALITY_FLAG
1 0.081609504 4247 4076 1229 71 77 56 2935 2814 695 102 105 25 4176 2833 0
2 -0.042307518 3034 3014 1500 77 80 23 2278 2058 1118 101 103 20 2957 2177 0
3 91 555 851 71 72 20 104 444 623 97 99 18 20 7 -50
4 -0.09779141 3027 2965 575 69 70 19 2339 2280 517 96 98 19 2958 2243 0
5 -0.716207034 308 304 79 67 69 22 448 432 97 99 100 21 241 349 0
6 -0.223381755 1001 992 238 68 70 27 946 926 220 98 100 21 933 848 0
7 -0.511213375 5071 5046 1503 67 73 43 5187 5105 1317 98 104 45 5004 5089 0
8 -0.137200945 1039 1006 259 67 71 40 932 900 174 97 103 47 972 835 0
9 -0.203982622 334 339 79 68 71 35 369 371 68 95 100 49 266 274 0
10 -0.257275137 329 340 94 66 72 50 376 376 80 95 99 47 263 281 0
11 -0.231582413 2838 2821 1093 65 70 40 2427 2473 853 96 99 20 2773 2331 0
12 0.312984902 1060 1052 268 68 72 26 734 731 158 99 101 23 992 635 0
13 -0.389230651 686 683 134 71 77 49 747 740 127 99 105 43 615 648 0
14 -0.452905685 291 299 112 71 77 48 370 359 117 98 105 45 220 272 0
15 -0.398114196 244 262 102 70 73 24 315 317 97 99 103 29 174 216 0
16 -0.300509111 213 260 135 71 74 24 271 300 128 99 101 23 142 172 0
17 0.059985117 2673 2619 618 70 78 57 1928 1887 405 99 103 42 2603 1829 0
18 -0.017318059 4327 4677 2042 71 78 56 3162 3293 1242 99 104 49 4256 3063 0
19 -0.103459241 749 732 380 72 77 35 683 692 352 99 105 45 677 584 0
20 -0.070739363 3385 3760 2850 67 80 76 2581 2696 2099 93 103 85 3318 2488 0

Total number of rows: 15388

Table truncated, full table size 1076 Kbytes.




Supplementary data files not provided
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