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Sample GSM466850 Query DataSets for GSM466850
Status Public on Nov 10, 2009
Title mir-124 12 hrs SS (5-12-08)
Sample type RNA
 
Channel 1
Source name universal reference
Organism Homo sapiens
Characteristics reference: universal reference
Extracted molecule total RNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name mir-124 12 hrs SS (5-12-08) (aRNA)
Organism Homo sapiens
Characteristics cell line: HEK293T
Extracted molecule total RNA
Extraction protocol not provided
Label Cy5
Label protocol not provided
 
 
Hybridization protocol not provided
Scan protocol GenePix
Description Simple annotation: RNA coimmunoprecipitation, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2008-07/80597.gif
Measurement: concentration(absolute) 60 nM
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 Oct 30, 2009
Last update date Nov 06, 2009
Contact name Patrick O Brown
E-mail(s) pbrown@cmgm.stanford.edu
Organization name Stanford university school of medicine
Department Department of biochemistry
Street address Beckman Center b439
City Stanford
State/province CA
ZIP/Postal code 94305
Country USA
 
Platform ID GPL9497
Series (2)
GSE18835 mRNA abundance in HEK293T cells mock or miR-124 transfected
GSE18889 Concordant Regulation of Translation and mRNA Abundance for Hundreds of Targets of a Human microRNA

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 31 33 31 32 0 1 31 32 31 33 0 0 0 0 2 2 2 2 13 20 1 2 1 0 null null null .966 1 2.258 80 420 1.449 .25 100 1630 6950 166 176 150 160 -50 53 51 2 null 51 0 null null null null
2 31 33 31 33 0 0 31 32 31 33 0 -1 0 0 2 2 2 2 10 11 0 1 0 -1 null null null .908 1 2.229 80 273 1.455 .25 100 1780 6950 166 176 165 175 -50 53 53 0 null 51 -2 null null null null
3 31 32 31 33 0 -1 31 33 31 33 0 0 0 0 2 2 2 2 15 7 2 0 -1 0 null null null .981 1 2.009 80 273 1.707 .28 100 1930 6950 166 176 180 190 -50 51 53 -2 null 53 0 null null null null
4 31 33 31 33 0 0 31 33 31 33 0 0 0 0 2 2 2 2 10 12 1 6 0 0 null null null 1.127 1 2.399 80 287 1.411 .19 100 2080 6950 166 176 195 205 -50 53 53 0 null 53 0 null null null null
5 31 33 31 33 0 0 31 33 31 33 0 0 0 0 2 2 2 3 10 11 0 0 0 0 null null null 1.221 1 2.097 80 287 1.579 .3 100 2240 6950 166 176 211 221 -50 53 53 0 null 53 0 null null null null
6 31 33 31 33 0 0 31 33 31 34 0 0 0 0 2 2 2 2 12 23 2 3 0 0 null null null 1.156 1 1.934 80 274 1.821 .24 100 2390 6950 166 176 226 236 -50 53 53 0 null 53 0 null null null null
7 31 34 31 33 0 1 31 33 31 34 0 0 0 0 2 3 2 2 10 21 1 7 1 0 null null null 1.162 1 2.129 80 297 1.992 .19 100 2540 6940 165 175 241 251 -50 54 53 2 null 53 0 null null null null
8 31 34 31 34 0 0 31 34 31 34 0 0 0 0 2 3 2 2 13 18 3 6 0 0 null null null 1.182 1 2.048 80 296 1.429 .23 100 2690 6940 165 175 256 266 -50 54 54 0 null 54 0 null null null null
9 32 34 31 34 1 0 32 34 31 34 1 0 0 0 2 2 2 2 18 13 6 3 1 1 null null null 1.113 1 2.301 80 296 1.265 .38 100 2840 6940 165 175 271 281 -50 54 54 0 null 54 0 null null null null
10 31 34 31 34 0 0 31 34 32 34 0 0 0 0 2 3 2 2 16 17 1 3 0 0 null null null 1.494 1.667 2.143 80 302 1.868 .24 100 2990 6940 165 175 286 296 -50 54 54 0 null 54 0 null null null null
11 32 35 32 35 0 0 32 35 32 34 0 0 0 0 2 2 2 3 6 3 1 0 0 0 null null null 1.233 1 1.908 80 296 1.876 .26 100 3140 6940 165 175 301 311 -50 56 56 0 null 56 0 null null null null
12 32 35 32 35 0 0 31 35 32 35 -1 0 0 0 2 2 2 2 7 18 2 1 0 -1 null null null 1.282 1.333 2.05 80 285 1.269 .31 100 3290 6940 165 175 316 326 -50 56 56 0 null 56 0 null null null null
13 32 35 32 35 0 0 32 34 32 35 0 -1 0 0 2 3 2 2 18 13 1 2 0 -1 null null null 1.192 1 2.195 80 273 1.645 .34 100 3440 6940 165 175 331 341 -50 56 56 0 null 54 -2 null null null null
14 32 35 32 35 0 0 32 35 32 35 0 0 0 0 2 2 2 3 12 7 2 0 0 0 null null null .972 1 2.274 80 287 1.345 .3 100 3590 6940 165 175 346 356 -50 56 56 0 null 56 0 null null null null
15 33 35 32 35 1 0 33 35 32 35 1 0 0 0 2 3 2 3 15 6 5 1 1 1 null null null 1.157 1 2.197 80 287 2.03 .26 100 3750 6940 165 175 362 372 -50 56 56 0 null 56 0 null null null null
16 32 35 32 35 0 0 32 35 32 35 0 0 0 0 2 2 2 3 12 11 5 0 0 0 null null null 1.087 1 1.967 80 273 1.581 .26 100 3900 6940 165 175 377 387 -50 56 56 0 null 56 0 null null null null
17 32 35 32 35 0 0 32 35 32 35 0 0 0 0 2 3 2 2 13 18 1 6 0 0 null null null 1.111 1 2.016 80 273 2.253 .28 100 4050 6940 165 175 392 402 -50 56 56 0 null 56 0 null null null null
18 33 36 33 35 0 1 33 35 33 35 0 0 0 0 2 3 2 3 10 10 3 2 1 0 null null null 1.028 1 2.255 80 273 1.717 .26 100 4200 6940 165 175 407 417 -50 58 56 2 null 56 0 null null null null
19 33 36 33 35 0 1 33 36 33 36 0 1 0 0 2 2 2 2 10 28 0 7 1 1 null null null 1.163 1.5 2.275 80 273 1.311 .29 100 4350 6940 165 175 422 432 -50 58 56 2 null 58 2 null null null null
20 33 36 33 36 0 0 33 35 33 36 0 -1 0 0 2 2 2 3 13 8 2 0 0 -1 null null null .949 1 1.986 80 280 1.391 .3 100 4500 6940 165 175 437 447 -50 58 58 0 null 56 -2 null null null null

Total number of rows: 44544

Table truncated, full table size 9641 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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