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Sample GSM618861 Query DataSets for GSM618861
Status Public on Jan 01, 2021
Title perirenal (retroperitoneal); tissue; M58
Sample type RNA
 
Channel 1
Source name Stratagene Human Universal Reference, 10 ug labeled aRNA
Organism Homo sapiens
Characteristics reference: Stratagene Human Universal Reference
Extracted molecule total RNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name perirenal (retroperitoneal); tissue; M58, 10 ug labeled aRNA
Organism Homo sapiens
Characteristics age: 58 years
organism part: perirenal (retroperitoneal)
sample fraction: tissue
Sex: Male
Extracted molecule total RNA
Extraction protocol Adipose Tissue Samples; Specimen Collection Adipose tissue specimens were collected either from the Stanford Tissue Bank, Stanford Dermatology Clinic, Stanford Surgical Pathology or directly from the surgeon at the time of surgery. All surgeries were performed at Stanford Hospital and Clinics. When necessary a trained pathologist dissected the desired adipose specimen from the organ/limb/skin to which it was attached. Samples acquired by Stanford Tissue Bank or Surgical Pathology may have been stored at 4C for up to several hours but were always processed on the same day as the surgery was performed. All samples are considered normal human tissues and were originally collected under the IRB Study of Messenger RNA Expression in Normal Human Tissues ID: 76363, which did not require patient consent as very little patient information (age, gender, procedure) was provided. Subsequently it was determined that our sample collection does not meet the definitions of human subject research under Stanfords Human Research Protection Program and therefore an IRB protocol was no longer required.
Tissue Fractionation - Clemons; Tissue Fractionation Adipose tissue samples were thoroughly rinsed with 70% ethanol to minimize risk of microbial contamination of cell cultures. Tissues were then rinsed with Hanks Balanced Salt Solution (HBSS) and transferred to a clean dish. At this time 1-4 g of tissue were removed and stored at -80C. Additionally a thin slice of each tissue was placed in 10% formalin for paraffin embedding. The remainder of each tissue sample was minced using surgical scissors. Tissue pieces were transferred to 50 ml conical tubes (up to 25 ml tissue per tube), and an equivalent volume of collagenase solution* was added to the tube. Tissue was again minced with scissors until no large pieces remained. Tubes were shaken to mix and incubated at 37C for 30 min to 4 hours, until pieces of tissue were no longer visible. Shin/calf adipose tissue in general took the longest and abdominal and thigh lipoaspirate the shortest time to digest. Digested tissues were then passed through a 180-micron nylon net filter and centrifuged at 100g for 5 minutes to pellet stromal-vascular cells. A 16-gauge needle attached to a 20 ml syringe was passed through the top visible lipid/adipocyte layer and the entire bottom layer containing buffer, cell pellet and blood cells was aspirated from the bottom and transferred to a new conical, tube. This cell suspension (stromal-vascular fraction) was thoroughly mixed by pipetting and divided equally into 2 conical tubes. One of these was set aside for cell culture (see Cell Culture) and the other was centrifuged at 400g for 7 minutes. Buffer was carefully aspirated with a pipette to avoid losing pelleted cells and 15 ml Trizol was added. The remaining lipid/adipocyte layer was washed 1-2 times depending on the amount of visible blood cells: 25 ml HBSS was added to the adipocytes, and gently inverted to mix. Adipocytes were centrifuged at 100g and excess buffer along with contaminating cells was aspirated from the bottom using a needle and syringe as described above. An equal volume of Trizol was added to the washed adipocytes. The stromal-vascular pellet sample and the adipocyte sample were stored in Trizol at -80C. Collagenase Solution: For stock solution 1000 U/ml Sigma Type II Collagenase (Cat# C6885) was dissolved in HBSS and centrifuged at 1000g for 20 minutes. Resulting liquid fraction was filtered (.22 micron) and stored at -20C and pelleted crystals were discarded. For working solution 1000 U/ml collagenase stock solution was diluted 3x in HBSS containing 5mM CaCl2
Amplification 1 ug of each total RNA sample was amplified using Ambion Amino Allyl MessageAmp II-96 Kit (Cat# 1821) according to manufacturers protocol
Label Cy5
Label protocol not provided
 
 
Hybridization protocol not provided
Scan protocol Model: GenePix 4000A
Description Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79626.gif
Data processing VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)
 
Submission date Nov 08, 2010
Last update date Jan 01, 2021
Contact name Heather Clemons
E-mail(s) hjeanc@gmail.com
Phone (650) 723-0005
Organization name Stanford School of Medicine
Department Dept of Biochemistry
Street address Beckman Center
City Stanford
State/province CA
ZIP/Postal code 94305
Country USA
 
Platform ID GPL11179
Series (1)
GSE25194 Expression profiles of human adipose tissue, adipocytes and stromal-vascular pellet cells from multiple body sites

Data table header descriptions
ID_REF ID_REF
CH1I_MEAN Mean feature pixel intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale
CH2I_MEAN Mean feature pixel intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale
CH1B_MEDIAN The median feature background intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale; Channel: Cy3 Channel; Background
CH2B_MEDIAN The median feature background intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Channel: Cy5 channel; Background
CH1D_MEAN The mean feature pixel intensity at wavelength 532 nm with the median background subtracted.; Type: integer; Scale: linear_scale; Channel: Cy3 Channel
CH2D_MEAN .The mean feature pixel intensity at wavelength 635 nm with the median background subtracted.; Type: integer; Scale: linear_scale; Channel: Cy5 channel
CH1I_MEDIAN Median feature pixel intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale
CH2I_MEDIAN Median feature pixel intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale
CH1B_MEAN The mean feature background intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale; Background
CH2B_MEAN The mean feature background intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Background
CH1D_MEDIAN The median feature pixel intensity at wavelength 532 nm with the median background subtracted.; Type: integer; Scale: linear_scale
CH2D_MEDIAN The median feature pixel intensity at wavelength 635 nm with the median background subtracted.; Type: integer; Scale: linear_scale
CH1_PER_SAT The percentage of feature pixels at wavelength 532 nm that are saturated.; Type: integer; Scale: linear_scale
CH2_PER_SAT The percentage of feature pixels at wavelength 635 nm that are saturated.; Type: integer; Scale: linear_scale
CH1I_SD The standard deviation of the feature intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale; Channel: Cy3 Channel
CH2I_SD The standard deviation of the feature pixel intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Channel: Cy5 channel
CH1B_SD The standard deviation of the feature background intensity at wavelength 532 nm.; Type: float; Scale: linear_scale; Channel: Cy3 Channel; Background
CH2B_SD The standard deviation of the feature background intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Channel: Cy5 channel; Background
PERGTBCH1I_1SD The percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, at wavelength 532 nm.; Type: integer; Scale: linear_scale
PERGTBCH2I_1SD The percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, at wavelength 635 nm.; Type: integer; Scale: linear_scale
PERGTBCH1I_2SD The percentage of feature pixels with intensities more than two standard deviations above the background pixel intensity, at wavelength 532 nm.; Type: integer; Scale: linear_scale
PERGTBCH2I_2SD The percentage of feature pixels with intensities more than two standard deviations above the background pixel intensity, at wavelength 532 nm.; Type: integer; Scale: linear_scale
SUM_MEAN The sum of the arithmetic mean intensities for each wavelength, with the median background subtracted.; Type: integer; Scale: linear_scale
SUM_MEDIAN The sum of the median intensities for each wavelength, with the median background subtracted.; Type: integer; Scale: linear_scale
RAT1_MEAN Ratio of the arithmetic mean intensities of each spot for each wavelength, with the median background subtracted. Channel 1/Channel 2 ratio, (CH1I_MEAN - CH1B_MEDIAN)/(CH2I_MEAN - CH2B_MEDIAN) or Green/Red ratio.; Type: float; Scale: linear_scale
RAT2_MEAN The ratio of the arithmetic mean intensities of each feature for each wavelength, with the median background subtracted.; Type: float; Scale: linear_scale
RAT2_MEDIAN The ratio of the median intensities of each feature for each wavelength, with the median background subtracted.; Type: float; Scale: linear_scale
PIX_RAT2_MEAN The geometric mean of the pixel-by-pixel ratios of pixel intensities, with the median background subtracted.; Type: float; Scale: linear_scale
PIX_RAT2_MEDIAN The median of pixel-by-pixel ratios of pixel intensities, with the median background subtracted.; Type: float; Scale: linear_scale
RAT2_SD The geometric standard deviation of the pixel intensity ratios.; Type: float; Scale: linear_scale
TOT_SPIX The total number of feature pixels.; Type: integer; Scale: linear_scale
TOT_BPIX The total number of background pixels.; Type: integer; Scale: linear_scale
REGR The regression ratio of every pixel in a 2-feature-diameter circle around the center of the feature.; Type: float; Scale: linear_scale
CORR The correlation between channel1 (Cy3) & Channel 2 (Cy5) pixels within the spot, and is a useful quality control parameter. Generally, high values imply better fit & good spot quality.; Type: float; Scale: linear_scale
DIAMETER The diameter in um of the feature-indicator.; Type: integer; Scale: linear_scale
X_COORD X-coordinate of the center of the spot-indicator associated with the spot, where (0,0) is the top left of the image.; Type: integer; Scale: linear_scale
Y_COORD Y-coordinate of the center of the spot-indicator associated with the spot, where (0,0) is the top left of the image.; Type: integer; Scale: linear_scale
TOP Box top: int(((centerX - radius) - Xoffset) / pixelSize).; Type: integer; Scale: linear_scale
BOT Box bottom: int(((centerX + radius) - Xoffset) / pixelSize).; Type: integer; Scale: linear_scale
LEFT Box left: int(((centerY - radius) - yoffset) / pixelSize).; Type: integer; Scale: linear_scale
RIGHT Box right: int(((centerY + radius) - yoffset) / pixelSize); Type: integer; Scale: linear_scale
FLAG The type of flag associated with a feature: -100 = user-flagged null spot; -50 = software-flagged null spot; 0 = spot valid.; Type: integer; Scale: linear_scale
CH2IN_MEAN Normalized value of mean Channel 2 (usually 635 nm) intensity (CH2I_MEAN/Normalization factor).; Type: integer; Scale: linear_scale; Channel: Cy5 channel
CH2BN_MEDIAN Normalized value of median Channel 2 (usually 635 nm) background (CH2B_MEDIAN/Normalization factor).; Type: integer; Scale: linear_scale; Channel: Cy5 channel; Background
CH2DN_MEAN Normalized value of mean Channel 2 (usually 635 nm) intensity with normalized background subtracted (CH2IN_MEAN - CH2BN_MEDIAN).; Type: integer; Scale: linear_scale; Channel: Cy5 channel
RAT2N_MEAN Type: float; Scale: linear_scale
CH2IN_MEDIAN Normalized value of median Channel 2 (usually 635 nm) intensity (CH2I_MEDIAN/Normalization factor).; Type: integer; Scale: linear_scale
CH2DN_MEDIAN Normalized value of median Channel 2 (usually 635 nm) intensity with normalized background subtracted (CH2IN_MEDIAN - CH2BN_MEDIAN).; Type: integer; Scale: linear_scale
RAT1N_MEAN Ratio of the means of Channel 1 (usually 532 nm) intensity to normalized Channel 2 (usually 635 nm) intensity with median background subtracted (CH1D_MEAN/CH2DN_MEAN). Channel 1/Channel 2 ratio normalized or Green/Red ratio normalized.; Type: float; Scale: linear_scale
RAT2N_MEDIAN Channel 2/Channel 1 ratio normalized, RAT2_MEDIAN/Normalization factor or Red/Green median ratio normalized.; Type: float; Scale: linear_scale
LOG_RAT2N_MEAN Log (base 2) of the ratio of the mean of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm) [log (base 2) (RAT2N_MEAN)].; Type: float; Scale: log_base_2
VALUE Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm) [log (base 2) (RAT2N_MEDIAN)].; Type: float; Scale: log_base_2

Data table
ID_REF CH1I_MEAN CH2I_MEAN CH1B_MEDIAN CH2B_MEDIAN CH1D_MEAN CH2D_MEAN CH1I_MEDIAN CH2I_MEDIAN CH1B_MEAN CH2B_MEAN CH1D_MEDIAN CH2D_MEDIAN CH1_PER_SAT CH2_PER_SAT CH1I_SD CH2I_SD CH1B_SD CH2B_SD PERGTBCH1I_1SD PERGTBCH2I_1SD PERGTBCH1I_2SD PERGTBCH2I_2SD SUM_MEAN SUM_MEDIAN RAT1_MEAN RAT2_MEAN RAT2_MEDIAN PIX_RAT2_MEAN PIX_RAT2_MEDIAN RAT2_SD TOT_SPIX TOT_BPIX REGR CORR DIAMETER X_COORD Y_COORD TOP BOT LEFT RIGHT FLAG CH2IN_MEAN CH2BN_MEDIAN CH2DN_MEAN RAT2N_MEAN CH2IN_MEDIAN CH2DN_MEDIAN RAT1N_MEAN RAT2N_MEDIAN LOG_RAT2N_MEAN VALUE
1 949 874 58 56 891 818 1075 957 58 56 1017 901 0 0 293 261 6 7 100 100 100 100 1709 1918 1.089 .918 .886 .92 .91 .21 52 442 .92 .99 80 1740 7480 148 156 50 58 0 1097 70 1027 1.152 1201 1131 .868 1.112 .205 .153
2 1158 1024 59 59 1099 965 1212 1097 73 69 1153 1038 0 0 169 198 60 48 100 100 100 100 2064 2191 1.139 .878 .9 .86 .89 .09 37 343 .89 1 70 1890 7470 147 154 65 72 0 1285 74 1211 1.102 1377 1303 .907 1.13 .14 .176
3 11798 10334 61 56 11737 10278 13329 11701 103 90 13268 11645 0 0 3703 3114 129 103 100 100 100 100 22015 24913 1.142 .876 .878 .88 .88 .08 37 337 .88 1 70 2030 7470 147 154 79 86 0 12971 70 12901 1.099 14687 14617 .91 1.102 .136 .14
4 1025 968 61 60 964 908 1115 1038 89 81 1054 978 0 0 255 186 115 91 100 100 100 100 1872 2032 1.062 .942 .928 .99 .93 .39 52 353 .94 .99 80 2190 7480 148 156 95 103 0 1215 75 1140 1.182 1303 1228 .846 1.165 .242 .22
5 460 122 62 62 398 60 496 126 62 62 434 64 0 0 92 17 7 7 100 100 100 98 458 498 6.633 .151 .147 .15 .15 .05 52 331 .28 .99 80 2350 7480 148 156 111 119 0 153 78 75 .189 158 80 5.285 .185 -2.402 -2.434
6 5204 14405 62 59 5142 14346 6186 16657 62 58 6124 16598 0 0 1982 5048 5 8 100 100 100 100 19488 22722 .358 2.79 2.71 3.89 2.78 5.2 69 262 2.77 .99 90 2500 7480 147 156 125 134 0 18081 74 18007 3.502 20908 20834 .286 3.402 1.808 1.766
7 167 112 62 62 105 50 180 111 62 61 118 49 0 0 33 17 6 8 98 96 96 96 155 167 2.1 .476 .415 .53 .45 .36 52 319 .66 .99 80 2640 7480 148 156 140 148 0 141 78 63 .598 139 62 1.673 .521 -.742 -.94
8 12530 10685 63 61 12467 10624 14720 12507 62 61 14657 12446 0 0 4344 3549 6 8 100 100 100 100 23091 27103 1.173 .852 .849 .91 .85 .46 52 325 .86 .99 80 2810 7480 148 156 157 165 0 13412 77 13335 1.07 15699 15622 .935 1.066 .097 .092
9 288 466 62 56 226 410 301 490 62 57 239 434 0 0 40 85 8 10 100 100 100 100 636 673 .551 1.814 1.816 1.79 1.82 .23 37 336 1.61 1 70 2940 7460 146 153 170 177 0 585 70 515 2.277 615 545 .439 2.279 1.187 1.189
10 127 136 61 60 66 76 128 139 61 60 67 79 0 0 15 21 8 10 100 98 98 96 142 146 .868 1.152 1.179 1.13 1.18 .34 52 345 1.06 .99 80 3100 7470 147 155 186 194 0 171 75 95 1.445 174 99 .692 1.48 .531 .566
11 2703 4391 61 59 2642 4332 3216 5236 61 59 3155 5177 0 0 1057 1729 5 8 100 100 100 98 6974 8332 .61 1.64 1.641 1.6 1.64 .48 52 333 1.63 1 80 3250 7470 147 155 201 209 0 5512 74 5437 2.058 6572 6498 .486 2.06 1.041 1.042
12 448 368 62 57 386 311 468 372 61 58 406 315 0 0 68 37 5 8 100 100 100 100 697 721 1.241 .806 .776 .85 .79 .34 52 333 .82 1 80 3400 7470 147 155 216 224 0 462 72 390 1.011 467 395 .989 .974 .016 -.038
13 1584 1136 61 60 1523 1076 1631 1166 61 60 1570 1106 0 0 190 124 10 10 100 100 100 100 2599 2676 1.415 .707 .704 .71 .71 .16 52 343 .72 .99 80 3550 7470 147 155 231 239 0 1426 75 1351 .887 1464 1388 1.128 .884 -.173 -.178
14 1056 1966 61 57 995 1909 1103 2097 62 57 1042 2040 0 0 148 360 10 10 100 100 100 100 2904 3082 .521 1.919 1.958 1.9 1.96 .29 52 339 1.86 .99 80 3710 7470 147 155 247 255 0 2468 72 2396 2.408 2632 2561 .415 2.457 1.268 1.297
15 69 46 61 57 8 -11 69 46 60 57 8 -11 0 0 8 8 5 7 65 2 40 0 -3 -3 null null null .53 .45 .3 52 285 .67 .92 80 3850 7490 149 157 261 269 -50 58 72 -14 null 58 -14 null null null null
16 3613 2491 60 59 3553 2432 4135 2706 62 60 4075 2647 0 0 1111 562 23 14 100 100 98 100 5985 6722 1.461 .684 .65 .92 .67 1.28 52 347 .68 .99 80 4000 7470 147 155 276 284 0 3127 74 3053 .859 3397 3322 1.164 .815 -.219 -.295
17 1103 1013 61 57 1042 956 1204 1098 63 58 1143 1041 0 0 247 209 24 15 100 100 100 100 1998 2184 1.09 .917 .911 1.02 .92 .74 52 336 .92 .99 80 4160 7470 147 155 292 300 0 1272 72 1200 1.152 1378 1307 .868 1.143 .204 .193
18 66 48 61 58 5 -10 65 49 60 58 4 -9 0 0 7 8 5 6 48 2 29 0 -5 -5 null null null 2.22 1.67 1.11 52 288 .73 .87 80 4300 7490 149 157 306 314 -50 60 73 -13 null 62 -11 null null null null
19 1655 3011 60 59 1595 2952 1669 3127 60 59 1609 3068 0 0 101 447 6 9 100 100 100 100 4547 4677 .54 1.851 1.907 1.83 1.92 .26 52 349 1.83 .99 80 4460 7460 146 154 322 330 0 3779 74 3705 2.323 3925 3851 .43 2.393 1.216 1.259
20 6374 15844 61 60 6313 15784 6902 17518 72 83 6841 17458 0 0 1387 4262 102 250 100 100 100 100 22097 24299 .4 2.5 2.552 2.42 2.56 .37 37 328 2.49 1 70 4600 7450 145 152 336 343 0 19887 75 19812 3.138 21988 21913 .319 3.203 1.65 1.68

Total number of rows: 44544

Table truncated, full table size 9058 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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