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Sample GSM618868 Query DataSets for GSM618868
Status Public on Jan 01, 2021
Title heel; tissue; M77
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 heel; tissue; M77, 10 ug labeled aRNA
Organism Homo sapiens
Characteristics age: 77 years
organism part: heel
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 4000B
Description Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79641.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
1 851 1071 48 67 803 1004 963 1230 48 67 915 1163 0 0 282 366 4 6 100 100 100 100 1807 2078 .8 1.25 1.271 1.32 1.28 .54 52 431 1.26 .99 80 1730 6290 93 101 82 90 0 1342 84 1258 1.567 1541 1457 .638 1.593 .648 .671
2 959 1261 48 66 911 1195 1118 1464 49 69 1070 1398 0 0 326 438 20 25 97 100 97 100 2106 2468 .762 1.312 1.307 1.34 1.32 .36 37 363 1.32 1 70 1870 6280 92 99 96 103 0 1580 83 1497 1.644 1834 1752 .608 1.637 .717 .711
3 6889 14872 48 67 6841 14805 7416 16044 50 69 7368 15977 0 0 1086 2305 20 25 100 100 100 100 21646 23345 .462 2.164 2.168 2.18 2.22 .3 37 360 2.16 .99 70 2030 6290 93 100 112 119 0 18634 84 18550 2.712 20102 20018 .369 2.717 1.439 1.442
4 1023 1287 48 66 975 1221 1067 1365 48 66 1019 1299 0 0 123 191 3 6 100 100 100 100 2196 2318 .799 1.252 1.275 1.24 1.28 .12 52 354 1.26 1 80 2190 6290 93 101 128 136 0 1613 83 1530 1.569 1710 1628 .637 1.597 .65 .676
5 345 119 48 66 297 53 402 126 48 65 354 60 0 0 125 25 3 6 95 92 95 89 350 414 5.604 .178 .169 .17 .18 .04 37 349 .35 .99 70 2320 6280 92 99 141 148 0 149 83 66 .224 158 75 4.472 .212 -2.161 -2.235
6 4665 16475 49 66 4616 16409 4857 17113 49 66 4808 17047 0 0 565 2195 4 6 100 100 100 100 21025 21855 .281 3.555 3.546 3.57 3.57 .46 52 361 3.53 .99 80 2490 6290 93 101 158 166 0 20642 83 20560 4.454 21442 21359 .225 4.442 2.155 2.151
7 127 101 48 66 79 35 132 103 48 66 84 37 0 0 17 9 4 6 100 100 100 100 114 121 2.257 .443 .44 .45 .44 .11 52 334 .81 .99 80 2640 6290 93 101 173 181 0 127 83 44 .555 129 46 1.801 .552 -.849 -.858
8 5836 11278 49 66 5787 11212 7047 13367 48 66 6998 13301 0 0 2249 4250 4 10 100 100 100 100 16999 20299 .516 1.937 1.901 3 1.96 3.85 37 334 1.92 1 70 2780 6280 92 99 187 194 0 14131 83 14048 2.428 16748 16666 .412 2.381 1.279 1.252
9 196 276 48 65 148 211 214 297 48 66 166 232 0 0 37 51 4 10 100 100 100 100 359 398 .701 1.426 1.398 1.43 1.43 .21 52 330 1.4 .99 80 2940 6290 93 101 203 211 0 346 81 264 1.786 372 291 .56 1.751 .837 .808
10 98 152 48 66 50 86 103 157 48 66 55 91 0 0 15 25 3 6 100 100 100 100 136 146 .581 1.72 1.655 1.77 1.75 .61 52 334 1.54 .99 80 3090 6290 93 101 218 226 0 190 83 108 2.155 197 114 .464 2.073 1.108 1.052
11 2285 6373 49 65 2236 6308 2642 7313 49 66 2593 7248 0 0 761 1926 5 8 100 100 100 100 8544 9841 .354 2.821 2.795 3.32 2.86 2.07 37 347 2.77 1 70 3230 6280 92 99 232 239 0 7985 81 7904 3.535 9163 9081 .283 3.502 1.822 1.808
12 324 292 49 67 275 225 357 319 49 66 308 252 0 0 81 69 5 7 100 100 100 100 500 560 1.222 .818 .818 .81 .82 .13 52 367 .9 1 80 3390 6280 92 100 248 256 0 366 84 282 1.025 400 316 .975 1.025 .036 .036
13 1259 928 49 67 1210 861 1346 1014 49 67 1297 947 0 0 231 202 4 6 100 100 100 100 2071 2244 1.405 .712 .73 .69 .74 .08 52 343 .74 1 80 3550 6280 92 100 264 272 0 1163 84 1079 .892 1270 1187 1.122 .915 -.166 -.128
14 662 1553 49 67 613 1486 802 1878 49 67 753 1811 0 0 256 598 6 10 95 100 92 100 2099 2564 .413 2.424 2.405 2.98 2.44 1.98 37 344 2.33 1 70 3680 6280 92 99 277 284 0 1946 84 1862 3.037 2353 2269 .329 3.013 1.603 1.591
15 55 55 49 68 6 -13 56 54 49 68 7 -14 0 0 5 5 6 10 65 0 17 0 -7 -7 null null null 0 0 0 52 340 1 .92 80 3860 6290 93 101 295 303 -50 69 85 -16 null 68 -18 null null null null
16 2722 3376 50 68 2672 3308 3038 3738 49 68 2988 3670 0 0 521 693 3 6 100 100 100 100 5980 6658 .808 1.238 1.228 1.23 1.23 .13 52 348 1.24 1 80 4000 6280 92 100 309 317 0 4230 85 4145 1.551 4684 4598 .645 1.539 .633 .622
17 876 1266 50 69 826 1197 956 1403 50 69 906 1334 0 0 196 310 3 7 100 100 100 100 2023 2240 .69 1.449 1.472 1.43 1.49 .16 37 372 1.45 1 70 4150 6280 92 99 324 331 0 1586 86 1500 1.816 1758 1671 .551 1.845 .861 .884
18 53 58 50 69 3 -11 53 58 50 69 3 -11 0 0 4 6 3 6 46 0 23 0 -8 -8 null null null 0 0 0 52 333 1.12 .84 80 4310 6290 93 101 340 348 -50 73 86 -14 null 73 -14 null null null null
19 1299 1386 51 71 1248 1315 1493 1609 51 70 1442 1538 0 0 359 436 4 6 100 100 100 100 2563 2980 .949 1.054 1.067 1.03 1.09 .24 69 292 1.07 .99 90 4450 6270 90 99 353 362 0 1737 89 1648 1.32 2016 1927 .757 1.336 .401 .418
20 1979 17940 52 72 1927 17868 2317 20892 52 71 2265 20820 0 0 565 4966 4 6 100 100 100 100 19795 23085 .108 9.272 9.192 9.46 10 1.51 52 322 9.04 1 80 4600 6280 92 100 369 377 0 22478 90 22388 11.618 26177 26087 .086 11.517 3.538 3.526

Total number of rows: 44544

Table truncated, full table size 8945 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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