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Sample GSM34252 Query DataSets for GSM34252
Status Public on Mar 16, 2005
Title Hypoxia day 21, replicate 2
Sample type RNA
 
Channel 1
Source name hypoxic lungs day 21
Organism Mus musculus
Extracted molecule total RNA
 
Channel 2
Source name control lungs day 21
Organism Mus musculus
Extracted molecule total RNA
 
 
Description Whole lungs of BALB/c (n=5) exposed to 21 days 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 0.141341579 3224 2955 960 60 61 17 2622 2446 727 106 109 22 3164 2516 0
2 73 480 822 59 65 84 120 457 710 107 132 574 14 13 -50
3 61 375 636 59 64 83 110 369 539 105 129 568 2 5 -50
4 -0.030714952 1838 1760 481 58 60 18 1704 1660 403 103 105 22 1780 1601 0
5 -0.386144948 186 205 115 56 58 18 302 310 78 100 103 23 130 202 0
6 -0.158759084 553 542 149 55 57 15 634 615 172 101 103 21 498 533 0
7 -0.228795653 2739 2781 1044 55 57 15 2849 2783 951 104 106 21 2684 2745 0
8 0.243540196 556 547 168 56 59 17 514 510 154 102 105 21 500 412 0
9 -0.137503524 186 236 179 56 58 18 277 283 66 102 104 21 130 175 0
10 -0.169925001 268 373 253 55 57 15 361 365 92 101 103 22 213 260 0
11 -0.172812955 2146 2319 967 54 55 14 2164 2222 822 101 102 20 2092 2063 0
12 0.341358625 509 524 201 54 56 14 455 454 125 100 101 21 455 355 0
13 -0.242331268 297 310 101 54 58 21 403 412 112 100 104 25 243 303 0
14 -0.302387908 148 166 78 54 57 17 254 262 77 101 104 25 94 153 0
15 -0.536666944 116 120 41 53 55 15 236 223 67 102 104 23 63 134 0
16 -0.112700133 115 155 115 53 54 13 203 242 131 99 102 20 62 104 0
17 -0.274261661 1059 1027 325 54 57 17 1192 1190 334 100 102 21 1005 1092 0
18 -0.071397917 2041 2435 1213 54 56 14 1945 2209 1035 102 103 20 1987 1843 0
19 -0.221424494 372 362 125 56 59 20 476 456 140 104 105 22 316 372 0
20 0.292009124 3454 3397 1101 58 61 20 2520 2555 1018 104 107 21 3396 2416 0

Total number of rows: 15388

Table truncated, full table size 1077 Kbytes.




Supplementary data files not provided
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