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Sample GSM618864 Query DataSets for GSM618864
Status Public on Jan 01, 2021
Title perirenal (retroperitoneal); tissue; UU
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 perirenal (retroperitoneal); tissue; UU, 10 ug labeled aRNA
Organism Homo sapiens
Characteristics age: unknown
organism part: perirenal (retroperitoneal)
sample fraction: tissue
Sex: unknown
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 4000A
Description Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79763.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 GPL11178
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
1 959 1015 42 43 917 972 1072 1097 42 43 1030 1054 0 0 249 183 3 5 100 100 100 100 1889 2084 .943 1.06 1.023 1.34 1.04 1.51 32 452 1.05 .99 60 1900 6860 29 35 50 56 0 1063 45 1018 1.11 1149 1104 .901 1.072 .151 .1
2 855 924 43 42 812 882 1028 1104 42 41 985 1062 0 0 356 381 4 5 95 92 92 92 1694 2047 .921 1.086 1.078 1.17 1.09 .63 37 415 1.08 .99 70 2050 6840 26 33 64 71 0 968 44 924 1.137 1156 1112 .879 1.129 .186 .175
3 7448 8528 43 46 7405 8482 8677 9719 44 46 8634 9673 0 0 3032 3324 8 10 100 100 100 100 15887 18307 .873 1.145 1.12 1.25 1.15 .47 37 391 1.16 .99 70 2200 6850 27 34 79 86 0 8930 48 8882 1.199 10178 10129 .834 1.173 .262 .23
4 933 1080 43 43 890 1037 1086 1227 44 43 1043 1184 0 0 281 257 7 10 100 100 100 100 1927 2227 .858 1.165 1.135 1.3 1.18 .65 37 407 1.15 .99 70 2350 6850 27 34 94 101 0 1131 45 1086 1.22 1285 1240 .82 1.189 .287 .249
5 419 92 43 42 376 50 422 93 43 42 379 51 0 0 35 5 3 5 100 100 100 100 426 430 7.52 .133 .135 .13 .14 .02 32 381 .23 .99 60 2510 6860 29 35 111 117 0 96 44 52 .139 97 53 7.181 .141 -2.844 -2.827
6 3794 12706 43 45 3751 12661 4653 15049 44 46 4610 15004 0 0 1822 5489 9 9 100 100 99 99 16412 19614 .296 3.375 3.255 4.63 3.33 5.26 69 362 3.31 .99 90 2660 6850 26 35 124 133 0 13306 47 13258 3.535 15759 15712 .283 3.408 1.822 1.769
7 134 106 44 43 90 63 147 112 45 43 103 69 0 0 34 20 9 9 97 97 95 95 153 172 1.429 .7 .67 .79 .68 .37 37 385 .8 .99 70 2810 6840 26 33 140 147 0 111 45 66 .733 117 72 1.364 .702 -.448 -.511
8 8853 11169 44 45 8809 11124 9333 11197 45 45 9289 11152 0 0 1839 1163 8 8 100 100 100 100 19933 20441 .792 1.263 1.201 1.35 1.22 .55 32 381 1.24 .99 60 2960 6860 29 35 156 162 0 11696 47 11649 1.322 11725 11678 .756 1.257 .403 .33
9 209 469 44 45 165 424 243 550 44 45 199 505 0 0 70 177 8 7 92 92 92 92 589 704 .389 2.57 2.538 2.62 2.56 .56 37 409 2.24 1 70 3110 6840 26 33 170 177 0 491 47 444 2.691 576 529 .372 2.657 1.428 1.41
10 101 163 44 41 57 122 106 168 44 41 62 127 0 0 13 23 5 11 100 100 100 100 179 189 .467 2.14 2.048 2.19 2.13 .53 37 358 1.58 .99 70 3260 6870 29 36 185 192 0 171 43 128 2.241 176 133 .446 2.145 1.164 1.101
11 2681 6345 44 44 2637 6301 2928 6788 43 43 2884 6744 0 0 682 1277 3 5 100 100 100 100 8938 9628 .419 2.389 2.338 2.65 2.44 1.57 37 350 2.35 .99 70 3410 6870 29 36 200 207 0 6644 46 6598 2.502 7108 7062 .4 2.449 1.323 1.292
12 368 263 44 44 324 219 419 295 43 43 375 251 0 0 114 75 2 5 100 98 100 98 543 626 1.479 .676 .669 .82 .68 .93 52 340 .72 .99 80 3570 6870 29 37 216 224 0 275 46 229 .708 309 263 1.413 .701 -.499 -.513
13 1128 1039 44 41 1084 998 1344 1248 44 41 1300 1207 0 0 525 465 14 7 89 92 89 92 2082 2507 1.086 .921 .928 1.92 .93 5.59 37 386 .92 .99 70 3710 6860 28 35 230 237 0 1088 43 1045 .964 1307 1264 1.037 .972 -.053 -.041
14 787 3262 44 44 743 3218 957 3864 44 46 913 3820 0 0 343 1270 16 20 95 100 89 97 3961 4733 .231 4.331 4.184 4.91 4.35 2.21 37 391 4.12 .99 70 3860 6860 28 35 245 252 0 3416 46 3370 4.535 4046 4000 .22 4.381 2.181 2.131
15 47 43 43 44 4 -1 48 43 43 45 5 -1 0 0 4 4 7 20 37 0 2 0 3 4 null null null .72 .33 .87 52 377 -1 -1 80 4020 6860 28 36 261 269 -50 45 46 -1 null 45 -1 null null null null
16 3449 2490 43 43 3406 2447 4016 2875 45 44 3973 2832 0 0 1456 957 26 13 92 97 92 92 5853 6805 1.392 .718 .713 .93 .71 1.29 37 390 .72 .99 70 4170 6860 28 35 276 283 0 2608 45 2562 .752 3011 2966 1.329 .746 -.411 -.422
17 1262 1786 43 45 1219 1741 1404 2043 45 46 1361 1998 0 0 413 598 28 13 92 100 92 100 2960 3359 .7 1.428 1.468 3.19 1.47 6.64 37 338 1.41 .99 70 4330 6880 30 37 292 299 0 1870 47 1823 1.496 2139 2092 .669 1.537 .581 .62
18 43 39 43 43 0 -4 44 39 42 42 1 -4 0 0 3 4 2 4 29 2 8 0 -4 -3 null null null .96 .67 .76 52 355 .91 .17 80 4480 6860 28 36 307 315 -50 41 45 -4 null 41 -4 null null null null
19 1658 1933 43 43 1615 1890 1879 2096 43 43 1836 2053 0 0 620 586 6 5 100 100 100 100 3505 3889 .854 1.17 1.118 1.39 1.14 1.17 52 359 1.15 .99 80 4630 6870 29 37 322 330 0 2024 45 1979 1.226 2195 2150 .816 1.171 .293 .228
20 3405 19353 44 46 3361 19307 3779 21271 44 46 3735 21225 0 0 1004 5024 6 5 100 100 100 100 22668 24960 .174 5.744 5.683 6.68 5.88 3.97 37 358 5.67 .99 70 4780 6870 29 36 337 344 0 20266 48 20218 6.015 22275 22227 .166 5.951 2.589 2.573

Total number of rows: 44544

Table truncated, full table size 9029 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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