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Sample GSM619007 Query DataSets for GSM619007
Status Public on Jan 01, 2021
Title thigh; stromal pellet; MU
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 thigh; stromal pellet; MU, 10 ug labeled aRNA
Organism Homo sapiens
Characteristics age: unknown
organism part: thigh
sample fraction: stromal pellet
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/2008-04/79690.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 1797 2723 66 58 1731 2665 1828 2759 66 58 1762 2701 0 0 148 196 7 6 100 100 100 100 4396 4463 .65 1.54 1.533 1.53 1.56 .1 52 429 1.49 1 80 1810 6130 60 68 53 61 0 2527 54 2473 1.429 2560 2507 .7 1.423 .515 .509
2 1881 2747 67 57 1814 2690 1898 2911 67 57 1831 2854 0 0 108 552 6 6 100 100 100 100 4504 4685 .674 1.483 1.559 1.47 1.59 .3 52 355 1.47 .99 80 1960 6120 59 67 68 76 0 2549 53 2496 1.376 2702 2649 .727 1.447 .461 .533
3 13544 16219 68 57 13476 16162 15715 19854 68 57 15647 19797 0 0 4533 6318 6 6 100 100 100 100 29638 35444 .834 1.199 1.265 1.32 1.28 1.29 69 284 1.21 .99 90 2110 6130 59 68 82 91 0 15052 53 14999 1.113 18425 18373 .898 1.174 .154 .232
4 1881 2775 67 57 1814 2718 1863 2907 66 57 1796 2850 0 0 102 483 6 6 100 100 100 100 4532 4646 .667 1.498 1.587 1.49 1.59 .26 52 317 1.49 .99 80 2260 6120 59 67 98 106 0 2575 53 2522 1.391 2698 2645 .719 1.473 .476 .558
5 695 242 67 57 628 185 741 267 67 58 674 210 0 0 139 63 6 6 100 100 100 97 813 884 3.395 .295 .312 .28 .31 .07 69 274 .36 .99 90 2410 6120 58 67 112 121 0 225 53 172 .273 248 195 3.658 .289 -1.871 -1.79
6 5358 32925 68 61 5290 32864 6102 37113 68 61 6034 37052 0 0 1858 10824 6 8 99 100 99 100 38154 43086 .161 6.212 6.141 6.97 6.25 3.96 69 262 6.07 1 90 2550 6120 58 67 126 135 0 30556 57 30499 5.765 34443 34386 .173 5.699 2.527 2.511
7 215 155 68 60 147 95 221 159 67 59 153 99 0 0 27 27 6 8 100 100 100 97 242 252 1.547 .646 .647 .63 .65 .15 69 283 .73 .99 90 2710 6120 58 67 142 151 0 144 56 88 .6 148 92 1.667 .601 -.738 -.736
8 14316 17420 68 60 14248 17360 15850 20569 68 59 15782 20509 0 0 3617 5754 6 7 100 100 100 100 31608 36291 .821 1.218 1.3 1.2 1.3 .29 69 263 1.24 .99 90 2860 6120 58 67 157 166 0 16167 56 16111 1.131 19089 19033 .884 1.206 .177 .27
9 368 1555 67 59 301 1496 384 1667 67 59 317 1608 0 0 65 351 6 6 100 100 100 100 1797 1925 .201 4.97 5.073 4.97 5.26 .94 69 280 4.19 1 90 3010 6120 58 67 172 181 0 1443 55 1388 4.612 1547 1492 .217 4.708 2.206 2.235
10 158 217 67 58 91 159 158 217 66 59 91 159 0 0 13 18 6 6 100 100 100 100 250 250 .572 1.747 1.747 1.76 1.75 .24 52 330 1.35 1 80 3160 6120 59 67 188 196 0 201 54 148 1.622 201 148 .617 1.622 .697 .697
11 3905 7645 67 58 3838 7587 4086 7997 66 59 4019 7939 0 0 574 1101 6 8 100 100 100 100 11425 11958 .506 1.977 1.975 1.98 2 .16 52 338 1.95 1 80 3310 6120 59 67 203 211 0 7095 54 7041 1.835 7422 7368 .545 1.833 .875 .874
12 540 524 67 60 473 464 542 528 66 59 475 468 0 0 48 39 6 6 100 100 100 100 937 943 1.019 .981 .985 .98 .99 .09 52 353 .96 1 80 3460 6120 59 67 218 226 0 486 56 431 .91 490 434 1.098 .914 -.135 -.129
13 2265 1707 67 60 2198 1647 2267 1714 67 59 2200 1654 0 0 102 84 7 6 100 100 100 100 3845 3854 1.335 .749 .752 .74 .75 .03 52 338 .74 1 80 3620 6120 59 67 234 242 0 1584 56 1528 .695 1591 1535 1.438 .698 -.524 -.519
14 1335 1753 67 60 1268 1693 1318 1757 67 60 1251 1697 0 0 56 61 7 6 100 100 100 100 2961 2948 .749 1.335 1.357 1.33 1.35 .06 52 311 1.29 1 80 3770 6120 59 67 249 257 0 1627 56 1571 1.239 1631 1575 .807 1.259 .309 .332
15 77 59 67 60 10 -1 80 60 67 59 13 0 0 0 10 7 6 6 62 13 51 3 9 13 null null null .56 .5 .51 69 248 .75 .1 90 3910 6130 59 68 262 271 -50 55 56 -1 null 56 0 null null null null
16 5302 5264 68 60 5234 5204 5813 6116 67 60 5745 6056 0 0 1250 1834 6 7 100 100 100 100 10438 11801 1.006 .994 1.054 .94 1.06 .26 69 312 1.01 .99 90 4070 6110 57 66 278 287 0 4885 56 4830 .923 5676 5620 1.084 .978 -.116 -.032
17 1557 1485 67 60 1490 1425 1581 1505 67 60 1514 1445 0 0 133 127 6 7 100 100 100 100 2915 2959 1.046 .956 .954 .95 .96 .06 52 314 .93 1 80 4220 6120 59 67 294 302 0 1378 56 1322 .888 1397 1341 1.127 .886 -.172 -.175
18 73 53 68 59 5 -6 73 53 68 59 5 -6 0 0 7 6 7 7 36 3 14 1 -1 -1 null null null .35 .25 .39 69 260 .72 .79 90 4360 6130 59 68 307 316 -50 49 55 -6 null 49 -6 null null null null
19 2826 4614 68 60 2758 4554 2845 4792 68 60 2777 4732 0 0 213 687 6 7 100 100 100 100 7312 7509 .606 1.651 1.704 1.64 1.72 .22 69 281 1.65 1 90 4520 6110 57 66 323 332 0 4282 56 4226 1.532 4447 4392 .653 1.581 .616 .661
20 7975 27161 68 60 7907 27101 8356 29988 68 60 8288 29928 0 0 1087 6198 6 6 100 100 100 100 35008 38216 .292 3.427 3.611 3.38 3.7 .66 69 244 3.45 .99 90 4670 6110 57 66 338 347 0 25207 56 25151 3.181 27830 27775 .314 3.351 1.669 1.745

Total number of rows: 44544

Table truncated, full table size 9096 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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