NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM618947 Query DataSets for GSM618947
Status Public on Jan 01, 2021
Title arm (upper); tissue; F48
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 arm (upper); tissue; F48, 10 ug labeled aRNA
Organism Homo sapiens
Characteristics age: 48 years
organism part: arm (upper)
sample fraction: tissue
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/2008-02/78538.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 2372 3984 65 74 2307 3910 2494 4263 65 74 2429 4189 0 0 468 845 8 7 100 100 100 100 6217 6618 .59 1.695 1.725 1.68 1.72 .26 52 414 1.67 1 80 1810 6600 124 132 93 101 0 3227 60 3167 1.373 3453 3393 .728 1.397 .457 .482
2 2490 4428 66 74 2424 4354 2572 4582 66 74 2506 4508 0 0 413 603 6 7 100 100 100 100 6778 7014 .557 1.796 1.799 2.01 1.82 1.7 52 333 1.77 .99 80 1960 6600 124 132 108 116 0 3586 60 3527 1.455 3711 3651 .687 1.457 .541 .543
3 18695 21634 67 73 18628 21561 20406 23378 66 74 20339 23305 0 0 4387 4398 7 8 100 100 100 100 40189 43644 .864 1.157 1.146 1.28 1.16 .95 52 333 1.15 .99 80 2110 6600 124 132 123 131 0 17522 59 17463 .937 18935 18876 1.067 .928 -.093 -.108
4 2606 4657 66 72 2540 4585 2607 4651 66 72 2541 4579 0 0 159 186 7 7 100 100 100 100 7125 7120 .554 1.805 1.802 1.8 1.85 .09 52 333 1.79 1 80 2260 6600 124 132 138 146 0 3772 58 3714 1.462 3767 3709 .684 1.46 .548 .546
5 1002 325 66 73 936 252 1053 331 66 72 987 258 0 0 198 35 7 7 100 100 100 100 1188 1245 3.714 .269 .261 .3 .26 .26 52 308 .32 .99 80 2410 6600 124 132 153 161 0 263 59 204 .218 268 209 4.586 .212 -2.197 -2.24
6 5982 34844 68 75 5914 34769 6722 37803 68 75 6654 37728 0 0 2042 8444 7 9 99 100 97 100 40683 44382 .17 5.879 5.67 6.35 5.88 5.22 69 264 5.75 .99 90 2560 6600 123 132 167 176 0 28222 61 28161 4.762 30618 30558 .21 4.592 2.251 2.199
7 276 302 66 73 210 229 285 309 66 73 219 236 0 0 37 26 7 7 100 100 100 100 439 455 .917 1.09 1.078 1.14 1.09 .38 52 316 1.09 1 80 2710 6600 124 132 183 191 0 245 59 185 .883 250 191 1.132 .873 -.179 -.196
8 18373 19803 66 76 18307 19727 20717 21571 67 76 20651 21495 0 0 5332 4324 8 8 100 100 100 100 38034 42146 .928 1.078 1.041 1.15 1.05 .48 52 334 1.07 .99 80 2860 6600 124 132 198 206 0 16039 62 15978 .873 17471 17410 1.146 .843 -.196 -.246
9 349 1466 68 77 281 1389 386 1659 69 77 318 1582 0 0 113 544 8 9 96 98 94 98 1670 1900 .202 4.943 4.975 5.07 5 2.82 52 334 4.15 1 80 3010 6590 123 131 213 221 0 1187 62 1125 4.004 1344 1281 .25 4.029 2.001 2.011
10 161 350 73 77 88 273 166 365 73 78 93 288 0 0 25 54 9 9 98 100 96 100 361 381 .322 3.102 3.097 3.35 3.13 1.21 52 316 2.12 .99 80 3160 6600 124 132 228 236 0 283 62 221 2.513 296 233 .398 2.508 1.329 1.327
11 3130 9253 74 75 3056 9178 3460 9764 74 75 3386 9689 0 0 940 1494 9 8 100 100 100 100 12234 13075 .333 3.003 2.861 3.38 2.86 2.45 52 320 2.92 .99 80 3320 6600 124 132 244 252 0 7494 61 7434 2.432 7908 7848 .411 2.318 1.282 1.213
12 472 646 71 74 401 572 531 714 71 73 460 640 0 0 148 186 7 7 97 100 97 100 973 1100 .701 1.426 1.391 1.9 1.43 2.21 69 304 1.36 .99 90 3460 6590 122 131 257 266 0 523 60 463 1.155 578 518 .866 1.127 .208 .172
13 1758 2666 71 74 1687 2592 2160 3132 71 73 2089 3058 0 0 801 1051 8 7 94 99 90 96 4279 5147 .651 1.536 1.464 2.94 1.47 5.63 69 281 1.51 .99 90 3620 6600 123 132 273 282 0 2159 60 2099 1.244 2537 2477 .804 1.186 .316 .246
14 1107 3887 71 73 1036 3814 1200 3968 71 73 1129 3895 0 0 293 433 6 7 98 100 98 100 4850 5024 .272 3.681 3.45 4.7 3.57 5.02 52 316 3.44 .99 80 3770 6600 124 132 289 297 0 3148 59 3089 2.982 3214 3155 .335 2.794 1.576 1.482
15 82 60 72 74 10 -14 82 59 72 74 10 -15 0 0 7 5 7 7 75 0 35 0 -4 -5 null null null 0 0 0 52 306 .73 .94 80 3930 6600 124 132 305 313 -50 49 60 -11 null 48 -12 null null null null
16 5296 6411 72 75 5224 6336 5420 6630 72 75 5348 6555 0 0 473 923 7 7 100 100 100 100 11560 11903 .824 1.213 1.226 1.2 1.23 .15 52 317 1.23 .99 80 4070 6590 123 131 319 327 0 5193 61 5132 .982 5370 5309 1.018 .993 -.026 -.011
17 1434 3062 71 75 1363 2987 1481 3305 72 78 1410 3230 0 0 172 682 7 43 100 100 100 100 4350 4640 .456 2.191 2.291 2.16 2.33 .39 37 354 2.15 .99 70 4210 6580 122 129 333 340 0 2480 61 2419 1.775 2677 2616 .563 1.855 .828 .892
18 76 59 72 75 4 -16 76 59 73 78 4 -16 0 0 6 6 7 45 31 0 4 0 -12 -12 null null null .2 .2 0 52 326 .8 .82 80 4380 6600 124 132 350 358 -50 48 61 -13 null 48 -13 null null null null
19 2921 4867 73 76 2848 4791 2982 4858 73 76 2909 4782 0 0 444 308 6 7 100 100 100 100 7639 7691 .594 1.682 1.644 2 1.67 2.47 52 318 1.65 1 80 4520 6590 123 131 364 372 0 3942 62 3880 1.363 3935 3873 .734 1.331 .446 .413
20 3717 23226 74 77 3643 23149 4472 27653 74 76 4398 27576 0 0 1482 8065 7 7 99 100 97 100 26792 31974 .157 6.354 6.27 6.53 6.67 3.07 69 283 6.26 .99 90 4670 6590 122 131 378 387 0 18812 62 18749 5.147 22397 22335 .194 5.078 2.364 2.344

Total number of rows: 44544

Table truncated, full table size 9152 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap