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Sample GSM619052 Query DataSets for GSM619052
Status Public on Jan 01, 2021
Title omentum (colon); adipocyte; F59_redo
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 omentum (colon); adipocyte; F59_redo, 10 ug labeled aRNA
Organism Homo sapiens
Characteristics age: 59 years
organism part: omentum (colon)
sample fraction: adipocyte
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/2008-06/80286.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
1 383 357 33 44 350 313 401 370 33 44 368 326 0 0 58 68 2 4 100 100 100 100 663 694 1.118 .894 .886 .88 .91 .11 52 420 .94 1 80 2040 6040 13 21 76 84 0 327 40 287 .819 339 299 1.221 .811 -.288 -.302
2 413 391 33 44 380 347 440 406 33 44 407 362 0 0 69 61 2 4 100 100 100 100 727 769 1.095 .913 .889 .91 .9 .11 52 330 .95 1 80 2190 6050 14 22 91 99 0 358 40 318 .836 372 332 1.196 .815 -.258 -.296
3 5176 5876 34 45 5142 5831 5624 6387 34 45 5590 6342 0 0 1323 1320 7 9 100 100 100 100 10973 11932 .882 1.134 1.135 1.21 1.14 .49 52 361 1.13 1 80 2340 6040 13 21 106 114 0 5381 41 5340 1.039 5849 5808 .963 1.039 .055 .055
4 426 404 34 45 392 359 442 416 34 45 408 371 0 0 50 58 7 9 100 100 100 100 751 779 1.092 .916 .909 .91 .93 .1 52 342 .95 1 80 2490 6040 13 21 121 129 0 370 41 329 .839 381 340 1.192 .833 -.254 -.264
5 165 78 33 45 132 33 166 79 33 45 133 34 0 0 10 9 2 5 100 100 100 100 165 167 4 .25 .256 .24 .25 .06 52 303 .49 .99 80 2640 6040 13 21 136 144 0 71 41 30 .229 72 31 4.368 .234 -2.127 -2.095
6 2647 4533 34 45 2613 4488 2880 4860 33 45 2846 4815 0 0 671 994 2 4 100 100 100 100 7101 7661 .582 1.718 1.692 1.82 1.72 .51 80 261 1.7 1 100 2790 6040 12 22 150 160 0 4151 41 4110 1.573 4451 4410 .636 1.549 .653 .632
7 64 62 34 46 30 16 64 62 33 45 30 16 0 0 4 5 2 4 100 100 100 90 46 46 1.875 .533 .533 .53 .5 .18 52 284 .99 .98 80 2940 6040 13 21 166 174 0 57 42 15 .488 57 15 2.047 .488 -1.034 -1.034
8 5064 5739 34 46 5030 5693 5564 6339 34 45 5530 6293 0 0 1331 1488 2 4 100 100 100 100 10723 11823 .884 1.132 1.138 1.16 1.14 .3 69 244 1.14 1 90 3090 6040 12 21 180 189 0 5256 42 5214 1.037 5805 5763 .965 1.042 .052 .06
9 86 117 34 45 52 72 92 123 34 45 58 78 0 0 17 27 2 4 99 97 99 97 124 136 .722 1.385 1.345 1.38 1.35 .37 69 234 1.37 1 90 3250 6040 12 21 196 205 0 107 41 66 1.268 113 71 .789 1.232 .343 .301
10 54 56 34 45 20 11 55 57 34 45 21 12 0 0 4 6 2 4 100 88 100 75 31 33 1.818 .55 .571 .6 .6 .26 52 276 1.06 .97 80 3390 6040 13 21 211 219 0 51 41 10 .504 52 11 1.985 .523 -.989 -.934
11 1175 1343 35 46 1140 1297 1195 1360 34 46 1160 1314 0 0 96 76 2 4 100 100 100 100 2437 2474 .879 1.138 1.133 1.13 1.14 .07 52 274 1.14 1 80 3540 6050 14 22 226 234 0 1230 42 1188 1.042 1245 1203 .96 1.037 .059 .053
12 138 131 34 46 104 85 145 137 34 45 111 91 0 0 26 22 2 4 100 100 100 100 189 202 1.224 .817 .82 .88 .83 .47 69 271 .95 .99 90 3690 6040 12 21 240 249 0 120 42 78 .748 125 83 1.336 .751 -.418 -.414
13 426 462 35 46 391 416 429 469 34 46 394 423 0 0 56 52 2 4 100 100 100 100 807 817 .94 1.064 1.074 1.07 1.08 .12 52 323 1.08 1 80 3840 6040 13 21 256 264 0 423 42 381 .974 430 387 1.026 .983 -.037 -.024
14 310 252 35 46 275 206 329 272 34 46 294 226 0 0 51 51 2 5 100 100 100 100 481 520 1.335 .749 .769 .73 .76 .12 69 298 .83 1 90 4000 6040 12 21 271 280 0 231 42 189 .686 249 207 1.458 .704 -.544 -.506
15 36 44 35 46 1 -2 36 44 35 46 1 -2 0 0 2 4 2 4 30 6 6 0 -1 -1 null null null 1.56 1 1.84 69 221 1.23 .44 90 4160 6050 13 22 287 296 -50 40 42 -2 null 40 -2 null null null null
16 1346 1563 35 47 1311 1516 1344 1615 35 46 1309 1568 0 0 120 234 2 4 100 100 100 100 2827 2877 .865 1.156 1.198 1.14 1.19 .12 52 290 1.17 1 80 4300 6040 13 21 302 310 0 1431 43 1388 1.059 1479 1436 .944 1.097 .083 .134
17 439 318 35 47 404 271 443 326 35 46 408 279 0 0 28 44 2 4 100 100 100 100 675 687 1.491 .671 .684 .66 .68 .1 52 314 .73 .99 80 4460 6040 13 21 318 326 0 291 43 248 .614 299 256 1.628 .626 -.703 -.675
18 35 44 35 46 0 -2 35 45 35 46 0 -1 0 0 2 4 2 4 14 7 0 0 -2 -1 null null null 2.17 2 1.26 69 247 -1 -1 90 4610 6050 13 22 332 341 -50 40 42 -2 null 41 -1 null null null null
19 671 451 35 47 636 404 709 469 35 47 674 422 0 0 123 71 2 4 100 100 100 100 1040 1096 1.574 .635 .626 .71 .63 .64 69 222 .67 1 90 4750 6050 13 22 346 355 0 413 43 370 .582 430 386 1.719 .573 -.782 -.802
20 2687 7685 35 47 2652 7638 2851 8148 35 47 2816 8101 0 0 521 1233 2 4 100 100 100 100 10290 10917 .347 2.88 2.877 2.97 2.94 .65 69 223 2.85 1 90 4900 6050 13 22 361 370 0 7038 43 6995 2.638 7462 7419 .379 2.635 1.399 1.398

Total number of rows: 44544

Table truncated, full table size 8736 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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