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Sample GSM618869 Query DataSets for GSM618869
Status Public on Jan 01, 2021
Title pelvic; adipocyte; F51b_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 pelvic; adipocyte; F51b_redo, 10 ug labeled aRNA
Organism Homo sapiens
Characteristics age: 51 years
organism part: pelvic
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/2008-06/80302.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
1 598 371 34 36 564 335 600 378 34 36 566 342 0 0 35 46 3 4 100 100 100 100 899 908 1.684 .594 .604 .58 .6 .07 52 417 .63 1 80 1680 6240 33 41 40 48 0 496 48 447 .793 505 457 1.26 .807 -.334 -.309
2 633 391 35 36 598 355 659 409 34 36 624 373 0 0 82 75 7 6 100 100 100 100 953 997 1.685 .594 .598 .58 .61 .08 52 329 .63 1 80 1830 6240 33 41 55 63 0 522 48 474 .793 546 498 1.261 .798 -.335 -.325
3 5430 5144 35 37 5395 5107 6102 5508 35 38 6067 5471 0 0 1561 1247 8 10 100 100 100 100 10502 11538 1.056 .947 .902 1.22 .93 1.9 69 275 .95 1 90 1990 6240 32 41 70 79 0 6871 49 6821 1.264 7357 7308 .791 1.204 .338 .268
4 617 370 35 37 582 333 632 383 34 37 597 346 0 0 84 71 2 8 100 100 100 100 915 943 1.748 .572 .58 .56 .58 .08 52 319 .61 1 80 2130 6230 32 40 85 93 0 494 49 445 .764 512 462 1.308 .774 -.388 -.369
5 209 69 35 37 174 32 214 69 35 37 179 32 0 0 21 10 4 4 100 100 100 98 206 211 5.438 .184 .179 .18 .19 .05 52 323 .35 .99 80 2280 6230 32 40 100 108 0 92 49 43 .246 92 43 4.071 .239 -2.025 -2.066
6 2518 20276 35 38 2483 20238 2727 21818 35 37 2692 21780 0 0 580 5175 3 4 100 100 100 100 22721 24472 .123 8.151 8.091 8.26 8.33 2.08 80 266 8.1 1 100 2440 6230 31 41 115 125 0 27083 51 27032 10.887 29142 29092 .092 10.807 3.445 3.434
7 71 56 35 38 36 18 72 57 35 37 37 19 0 0 6 7 2 4 100 100 100 94 54 56 2 .5 .514 .51 .52 .21 52 307 .81 .98 80 2580 6230 32 40 130 138 0 75 51 24 .668 76 25 1.497 .686 -.582 -.544
8 6450 6021 35 38 6415 5983 6465 6043 35 37 6430 6005 0 0 368 433 2 4 100 100 100 100 12398 12435 1.072 .933 .934 .92 .93 .04 52 281 .94 1 80 2750 6240 33 41 147 155 0 8042 51 7992 1.246 8072 8021 .803 1.247 .317 .319
9 98 116 35 37 63 79 103 116 35 37 68 79 0 0 15 19 3 4 100 100 100 100 142 147 .797 1.254 1.162 1.36 1.27 .62 69 244 1.17 .99 90 2880 6230 31 40 159 168 0 155 49 106 1.675 155 106 .597 1.552 .744 .634
10 55 55 35 37 20 18 57 55 35 37 22 18 0 0 7 9 4 4 97 94 93 86 38 40 1.111 .9 .818 .89 .9 .32 69 297 .98 .99 90 3030 6220 30 39 174 183 0 73 49 24 1.202 73 24 .832 1.093 .266 .128
11 1326 1575 36 38 1290 1537 1348 1589 35 38 1312 1551 0 0 102 117 3 4 100 100 100 100 2827 2863 .839 1.191 1.182 1.19 1.19 .11 52 307 1.19 1 80 3190 6230 32 40 191 199 0 2104 51 2053 1.591 2122 2072 .628 1.579 .67 .659
12 160 146 36 39 124 107 160 147 35 38 124 108 0 0 10 14 3 4 100 100 100 100 231 232 1.159 .863 .871 .86 .88 .11 52 306 .92 1 80 3340 6230 32 40 206 214 0 195 52 143 1.153 196 144 .868 1.163 .205 .218
13 562 646 36 39 526 607 563 657 35 38 527 618 0 0 47 94 3 4 100 100 100 100 1133 1145 .867 1.154 1.173 1.14 1.18 .14 52 339 1.17 1 80 3490 6220 31 39 221 229 0 863 52 811 1.541 878 825 .649 1.566 .624 .647
14 363 626 36 38 327 588 363 632 36 38 327 594 0 0 18 50 3 4 100 100 100 100 915 921 .556 1.798 1.817 1.79 1.82 .15 52 326 1.74 1 80 3640 6230 32 40 236 244 0 836 51 785 2.402 844 793 .416 2.426 1.264 1.279
15 36 39 36 38 0 1 37 39 35 38 1 1 0 0 2 6 3 4 19 17 0 1 1 2 null null 1 2.97 1.52 7.78 69 272 1.06 .24 90 3800 6220 30 39 251 260 -50 52 51 1 null 52 1 null 1.336 null .418
16 1790 1736 36 39 1754 1697 1808 1734 36 39 1772 1695 0 0 123 146 2 4 100 100 100 100 3451 3467 1.034 .968 .957 .96 .97 .07 52 323 .98 1 80 3940 6220 31 39 266 274 0 2319 52 2267 1.292 2316 2264 .774 1.278 .37 .354
17 503 668 36 39 467 629 505 671 36 39 469 632 0 0 25 55 2 4 100 100 100 100 1096 1101 .742 1.347 1.348 1.34 1.37 .11 52 334 1.34 1 80 4100 6230 32 40 282 290 0 892 52 840 1.799 896 844 .556 1.8 .847 .848
18 35 38 36 39 -1 -1 36 38 36 39 0 -1 0 0 2 3 2 4 9 9 3 0 -2 -1 null null null 1.44 1 1.66 69 269 1.06 .64 90 4250 6220 30 39 296 305 -50 51 52 -1 null 51 -1 null null null null
19 865 705 36 39 829 666 920 718 36 39 884 679 0 0 196 117 2 4 100 100 100 100 1495 1563 1.245 .803 .768 .91 .79 .65 69 236 .81 1 90 4390 6220 30 39 310 319 0 942 52 890 1.073 959 907 .932 1.026 .102 .037
20 2545 8123 37 40 2508 8083 3016 9406 36 40 2979 9366 0 0 1036 3052 3 5 97 100 94 100 10591 12345 .31 3.223 3.144 4.47 3.23 5.92 69 240 3.19 1 90 4530 6220 30 39 324 333 0 10850 53 10797 4.305 12564 12510 .232 4.199 2.106 2.07

Total number of rows: 44544

Table truncated, full table size 8751 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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