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Sample GSM618866 Query DataSets for GSM618866
Status Public on Jan 01, 2021
Title abdominal; stromal pellet; F50
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 abdominal; stromal pellet; F50, 10 ug labeled aRNA
Organism Homo sapiens
Characteristics age: 50 years
organism part: abdominal
sample fraction: stromal pellet
Sex: female
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/2008-04/79549.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 GPL11176
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 1499 1808 43 48 1456 1760 1620 1983 55 64 1577 1935 0 0 271 370 78 100 100 100 100 100 3216 3512 .827 1.209 1.227 1.2 1.25 .14 69 337 1.21 .99 90 1860 6160 100 109 173 182 0 1764 47 1717 1.179 1935 1888 .848 1.197 .238 .26
2 1730 2227 43 47 1687 2180 1795 2331 43 47 1752 2284 0 0 227 320 4 6 100 100 100 100 3867 4036 .774 1.292 1.304 1.28 1.32 .07 52 258 1.28 1 80 2010 6160 101 109 189 197 0 2173 46 2127 1.261 2274 2228 .793 1.272 .334 .347
3 10648 11699 44 49 10604 11650 13583 15026 65 59 13539 14977 0 0 5108 5659 212 86 90 96 88 94 22254 28516 .91 1.099 1.106 1.62 1.14 2.59 69 277 1.09 1 90 2150 6140 98 107 202 211 0 11414 48 11366 1.072 14660 14612 .933 1.079 .1 .11
4 1545 1916 44 49 1501 1867 1730 2164 65 59 1686 2115 0 0 408 506 212 86 99 100 97 100 3368 3801 .804 1.244 1.254 1.28 1.28 .34 69 278 1.24 .99 90 2300 6140 98 107 217 226 0 1869 48 1821 1.214 2111 2063 .824 1.224 .279 .291
5 560 194 44 49 516 145 617 208 45 49 573 159 0 0 127 41 14 9 100 100 100 100 661 732 3.559 .281 .277 .27 .28 .05 80 267 .35 1 100 2460 6140 98 108 233 243 0 189 48 141 .274 203 155 3.648 .271 -1.867 -1.885
6 7801 23763 44 49 7757 23714 8184 25352 47 50 8140 25303 0 0 1012 3757 29 6 100 100 100 100 31471 33443 .327 3.057 3.108 3.05 3.13 .29 80 214 3.05 1 100 2610 6150 99 109 248 258 0 23184 48 23136 2.983 24734 24686 .335 3.033 1.577 1.601
7 162 137 44 49 118 88 168 142 46 49 124 93 0 0 24 21 29 6 100 100 96 100 206 217 1.341 .746 .75 .75 .76 .17 80 221 .85 .99 100 2760 6150 99 109 263 273 0 134 48 86 .728 139 91 1.374 .732 -.459 -.451
8 12873 13748 44 50 12829 13698 13795 15154 48 51 13751 15104 0 0 1973 2933 66 20 100 100 100 100 26527 28855 .937 1.068 1.098 1.05 1.11 .13 69 244 1.07 .99 90 2910 6140 98 107 278 287 0 13413 49 13364 1.042 14785 14736 .96 1.072 .059 .1
9 226 820 44 50 182 770 248 928 44 50 204 878 0 0 60 242 4 5 97 100 97 100 952 1082 .236 4.231 4.304 4.4 4.35 1.09 69 223 3.58 .99 90 3050 6150 99 108 292 301 0 800 49 751 4.128 905 857 .242 4.199 2.045 2.07
10 92 119 44 50 48 69 97 131 44 50 53 81 0 0 19 31 4 5 97 94 93 93 117 134 .696 1.438 1.528 1.62 1.52 1.14 69 291 1.31 .97 90 3200 6130 97 106 307 316 0 116 49 67 1.402 128 79 .713 1.491 .488 .576
11 3180 4600 45 50 3135 4550 3425 5032 45 50 3380 4982 0 0 594 1000 5 5 100 100 100 100 7685 8362 .689 1.451 1.474 1.44 1.49 .16 69 267 1.45 1 90 3360 6140 98 107 323 332 0 4488 49 4439 1.416 4909 4861 .706 1.438 .502 .524
12 298 348 45 50 253 298 336 387 55 54 291 337 0 0 87 101 104 38 90 96 80 93 551 628 .849 1.178 1.158 1.21 1.2 .37 69 296 1.17 1 90 3500 6130 97 106 337 346 0 340 49 291 1.149 378 329 .87 1.13 .201 .176
13 1545 953 44 50 1501 903 1649 1043 44 50 1605 993 0 0 296 237 6 5 100 100 100 100 2404 2598 1.662 .602 .619 .58 .62 .09 69 323 .62 1 90 3660 6120 96 105 353 362 0 930 49 881 .587 1018 969 1.704 .604 -.769 -.728
14 698 814 43 49 655 765 825 959 43 49 782 910 0 0 269 309 6 5 94 100 93 100 1420 1692 .856 1.168 1.164 1.43 1.18 1.86 69 300 1.16 1 90 3800 6140 98 107 367 376 0 794 48 746 1.139 936 888 .878 1.135 .188 .183
15 50 48 44 48 6 0 51 49 43 48 7 1 0 0 5 5 4 4 77 23 39 7 6 8 null null .143 1.02 .58 2.06 69 276 .98 .26 90 3970 6140 98 107 384 393 -50 47 47 0 null 48 1 null .139 null -2.843
16 4001 3283 45 49 3956 3234 4316 3583 44 49 4271 3534 0 0 756 672 3 5 100 100 100 100 7190 7805 1.223 .817 .827 .81 .84 .11 69 251 .82 .99 90 4110 6130 97 106 398 407 0 3203 48 3155 .798 3496 3448 1.254 .807 -.326 -.309
17 946 812 45 49 901 763 1071 939 44 49 1026 890 0 0 299 263 4 5 99 100 99 100 1664 1916 1.181 .847 .867 .92 .87 .63 80 265 .86 .99 100 4260 6140 98 108 413 423 0 792 48 744 .826 916 868 1.21 .846 -.275 -.241
18 46 48 45 50 1 -2 45 48 44 49 0 -2 0 0 5 5 4 5 33 14 16 3 -1 -2 null null null 1.12 .5 1.55 69 265 1.04 .42 90 4430 6140 98 107 430 439 -50 47 49 -2 null 47 -2 null null null null
19 2569 2419 45 50 2524 2369 2676 2576 44 50 2631 2526 0 0 339 385 3 4 100 100 100 100 4893 5157 1.065 .939 .96 .93 .96 .09 69 279 .94 1 90 4560 6120 96 105 443 452 0 2360 49 2311 .916 2513 2464 1.092 .937 -.127 -.094
20 5250 16461 45 51 5205 16410 6555 20567 45 52 6510 20516 0 0 2441 7638 4 12 99 100 93 99 21615 27026 .317 3.153 3.151 3.9 3.23 4.21 69 314 3.12 1 90 4700 6120 96 105 457 466 0 16060 50 16010 3.076 20066 20016 .325 3.075 1.621 1.62

Total number of rows: 44544

Table truncated, full table size 9097 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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