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Sample GSM618994 Query DataSets for GSM618994
Status Public on Jan 01, 2021
Title thigh; stromal pellet; F83
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; F83, 10 ug labeled aRNA
Organism Homo sapiens
Characteristics age: 83 years
organism part: thigh
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/2008-04/79731.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 1925 3686 60 50 1865 3636 2001 3803 59 50 1941 3753 0 0 198 359 4 4 100 100 100 100 null null .513 1.95 1.934 null null null 52 389 null 1 80 1880 6250 101 109 131 139 0 3433 47 3387 1.816 3542 3496 .551 1.801 .861 .849
2 2043 3948 60 50 1983 3898 2166 4140 59 50 2106 4090 0 0 347 566 5 5 100 100 100 100 null null .509 1.966 1.942 null null null 52 279 null 1 80 2030 6250 101 109 146 154 0 3678 47 3631 1.831 3856 3810 .546 1.809 .873 .855
3 6346 16733 60 51 6286 16682 8371 21610 61 55 8311 21559 0 0 3179 8060 15 29 93 97 91 96 null null .377 2.654 2.594 null null null 69 287 null 1 90 2170 6240 99 108 159 168 0 15587 48 15539 2.472 20129 20082 .405 2.416 1.306 1.273
4 2026 3957 60 51 1966 3906 2123 4074 61 54 2063 4023 0 0 307 475 14 28 100 100 100 100 null null .503 1.987 1.95 null null null 52 302 null 1 80 2330 6250 101 109 176 184 0 3686 48 3638 1.851 3795 3747 .54 1.816 .888 .861
5 734 286 60 51 674 235 834 323 60 51 774 272 0 0 201 76 5 4 100 99 100 99 null null 2.868 .349 .351 null null null 69 273 null 1 90 2490 6240 99 108 191 200 0 266 48 219 .325 301 253 3.079 .327 -1.622 -1.611
6 6109 20573 61 51 6048 20522 7107 23729 60 51 7046 23678 0 0 1794 5739 5 5 100 100 100 100 null null .295 3.393 3.36 null null null 80 209 null 1 100 2640 6250 100 110 206 216 0 19164 48 19116 3.161 22103 22056 .316 3.13 1.66 1.646
7 206 166 60 51 146 115 221 175 61 51 161 124 0 0 37 32 13 4 100 100 100 100 null null 1.27 .788 .77 null null null 69 249 null 1 90 2790 6240 99 108 221 230 0 155 48 107 .734 163 116 1.363 .717 -.447 -.479
8 6844 18447 61 52 6783 18395 8345 21904 60 52 8284 21852 0 0 2638 6452 5 5 100 100 100 100 null null .369 2.712 2.638 null null null 69 260 null 1 90 2930 6240 99 108 235 244 0 17183 48 17135 2.526 20403 20355 .396 2.457 1.337 1.297
9 372 1909 60 52 312 1857 409 2149 60 51 349 2097 0 0 80 474 5 5 100 100 100 100 null null .168 5.952 6.009 null null null 69 278 null 1 90 3090 6240 99 108 251 260 0 1778 48 1730 5.544 2002 1953 .18 5.597 2.471 2.485
10 128 123 60 51 68 72 132 128 60 51 72 77 0 0 18 18 5 5 100 100 100 100 null null .944 1.059 1.069 null null null 69 278 null .99 90 3240 6240 99 108 266 275 0 115 48 67 .986 119 72 1.014 .996 -.02 -.006
11 3638 4350 60 52 3578 4298 4221 5069 60 51 4161 5017 0 0 986 1169 5 5 100 100 100 100 null null .832 1.201 1.206 null null null 69 263 null 1 90 3390 6240 99 108 281 290 0 4052 48 4004 1.119 4722 4673 .894 1.123 .162 .168
12 456 354 60 52 396 302 484 374 60 51 424 322 0 0 76 57 5 4 100 100 100 100 null null 1.311 .763 .759 null null null 69 262 null 1 90 3540 6240 99 108 296 305 0 330 48 281 .71 348 300 1.408 .707 -.493 -.499
13 2176 1809 60 53 2116 1756 2402 1989 158 105 2342 1936 0 0 487 367 954 489 99 100 77 96 null null 1.205 .83 .827 null null null 69 276 null 1 90 3690 6240 99 108 311 320 0 1685 49 1636 .773 1853 1803 1.294 .77 -.371 -.377
14 1253 1927 61 53 1192 1874 1278 1987 627 379 1217 1934 0 0 123 207 3130 1802 0 87 0 0 null null .636 1.572 1.589 null null null 52 284 null 1 80 3850 6240 100 108 328 336 0 1795 49 1746 1.464 1851 1802 .683 1.48 .55 .566
15 65 51 60 52 5 -1 66 52 60 52 6 0 0 0 5 5 4 5 61 16 25 3 null null null null null null null null 69 252 null .1 90 4000 6250 100 109 342 351 -50 48 48 -1 null 48 0 null null null null
16 5060 7105 61 53 4999 7052 5211 7367 61 53 5150 7314 0 0 454 743 5 5 100 100 100 100 null null .709 1.411 1.42 null null null 52 301 null 1 80 4150 6240 100 108 358 366 0 6618 49 6569 1.314 6862 6813 .761 1.323 .394 .404
17 1375 1456 60 53 1315 1403 1395 1479 61 53 1335 1426 0 0 131 128 5 6 100 100 100 100 null null .937 1.067 1.068 null null null 52 320 null 1 80 4300 6240 100 108 373 381 0 1356 49 1307 .994 1378 1328 1.006 .995 -.009 -.007
18 63 48 61 52 2 -4 63 49 61 53 2 -3 0 0 5 3 5 7 41 0 7 0 null null null null null null null null 69 234 null .75 90 4450 6250 100 109 387 396 -50 45 48 -4 null 46 -3 null null null null
19 2795 3964 61 53 2734 3911 3279 4567 61 53 3218 4514 0 0 1049 1342 4 5 99 100 97 100 null null .699 1.431 1.403 null null null 69 260 null 1 90 4590 6230 98 107 401 410 0 3692 49 3643 1.333 4254 4205 .75 1.307 .414 .386
20 2743 24555 63 54 2680 24501 3448 30802 62 57 3385 30748 0 0 1197 10284 7 30 91 100 90 100 null null .109 9.142 9.084 null null null 69 278 null 1 90 4740 6230 98 107 416 425 0 22873 50 22822 8.516 28692 28641 .117 8.461 3.09 3.081

Total number of rows: 44544

Table truncated, full table size 9337 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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