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Sample GSM149985 Query DataSets for GSM149985
Status Public on May 07, 2007
Title NHGRI_MDA-MB-436_01-31-06Slide83T
Sample type genomic
 
Channel 1
Source name HMEC
Organism Homo sapiens
Characteristics Human Mammary Epithelial cells
Extracted molecule genomic DNA
Extraction protocol DNA was extracted with Phenol/Chloroform/ Isoamyl alcohol method according to manufacturer protocol (Invitrogen#15593-031) and the DNA is further purified by ethanol precipitation.
Label Cy3
Label protocol 600 nanogram of genomic DNA was labeld with random hexamers in the presence of Cy3 dUTPs using the Bioprime DNA labeling system from Invitrogen( cat#18094-011)
 
Channel 2
Source name MDA-MB-436
Organism Homo sapiens
Characteristics Human Breast cell line
Extracted molecule genomic DNA
Extraction protocol DNA was extracted with Phenol/Chloroform/ Isoamyl alcohoil method according to manifecturer protocol (Invitro#15593-031) and the DNA is further purified by the Alcohol precipitation.
Label Cy5
Label protocol 600 nanogram of genomic DNA was labeld with random hexamers in the presence of Cy5 dUTPs using the Bioprime DNA labeling system from Invitrogen( cat#18094-011)
 
 
Hybridization protocol The test and reference labeled DNAs were mixed with 75 microgram of Cot I DNA and precipitated with alcohol. The pellet is resuspended in35 micro liter of hybridization solution (50% Formamide, 10% Dextran sulfate, 4% SDS and 2xSSC). The hybridization is performed under a cover slip in a humid chamber at 37 degree for 48 hours.
Scan protocol Agilent Scanner
Description Human Breast cell line
Data processing IPLab/DeArray
 
Submission date Dec 13, 2006
Last update date May 07, 2007
Contact name Christopher Pan
E-mail(s) cpan@mail.nih.gov
Organization name NIH
Department NHGRI
Street address Rm 5228, Bldg 50, South Dr.
City Bethesda
State/province MD
ZIP/Postal code 20892
Country USA
 
Platform ID GPL4615
Series (1)
GSE6567 Chromosome 8 BAC Array CGH and Expression Studies Identify Amplification and Overexpression of TRMT12 in Breast Cancer

Data table header descriptions
ID_REF
VALUE log-ratio (log2 of calRatio with low quality (rQuality < 0.5) removed. (float)
PenAt Pen Position. It is always numbered from left-to-right, and top-to-bottom. (serpentine, start from top-left)(Integer)
RowAt Within each sub-array (pen), row offset (start from 1 at top-most) to the spot of interest(Integer)
ColumnAt Within each sub-array (pen), column offset (start from 1 at left-most) to the spot of interest(Integer)
SR_top Bonding box location in Red channel image coordinates - (top, left, bottom, right) (SR -- Sample in Red channel, or Ch1)(Integer)
SR_left see above(Integer)
SR_bottom see above(Integer)
SR_right see above(Integer)
SR_T. Int. Total Intensity - Sum of all pixel gray-levels within the target area. No data trimming is performed here.(Integer)
SR_Mean Mean Signal Intensity - Average gray-levels within the target area, after trimming top and bottom 5% (background subtracted)(float)
SR_S.Dev Std. Dev. Of intensity - Std. Dev. Of signal intensity. Derived along with mean intensity(float)
SR_SNR Signal-to-Noise Ratio. It is roughly the ratio of mean signal intensity to the local background std. Dev.(float)
SR_iQuality The measurement quality. Summarized from Area, Background, Consistency, and Saturation. From 0 (bad) to 1 (good)(float)
SR_bkMean Mean background Intensity (float)
SR_bkDev Std. Dev. Of background intensity(float)
SG_top Bonding box location in Red channel image coordinates - (top, left, bottom, right) (SG -- Sample in Green channel, or Ch2)(Integer)
SG_left see above(Integer)
SG_bottom see above(Integer)
SG_right see above(Integer)
SG_T. Int. Total Intensity - Sum of all pixel gray-levels within the target area. No data trimming is performed here.(Integer)
SG_Mean Mean Signal Intensity - Average gray-levels within the target area, after trimming top and bottom 5% (background subtracted)(float)
SG_S.Dev Std. Dev. Of intensity - Std. Dev. Of signal intensity. Derived along with mean intensity(float)
SG_SNR Signal-to-Noise Ratio. It is roughly the ratio of mean signal intensity to the local background variation.(float)
SG_iQuality The measurement quality. Summarized from Area, Background, Consistency, and Saturation. From 0 (bad) to 1 (good)(float)
SG_bkMean Mean background Intensity (float)
SG_bkDev Std. Dev. Of background intensity(float)
unionArea Union Area - the detected target area. All calculations are based on this region(Integer)
propArea Proportional area relatively to the mask size.(float)
calRatio Calibrated Red-to-Green ratio, (or normalized Ch1/Ch2 ratio)(float)
rQuality Ratio measurement quality (including all intensity measurement quality, plus the signal-to-noise-ratio requirement).(float)
confLevel Confidence Level, typically set at 99%(float)
lowerLimit Lower Limit of confidence interval for cal. Ratio(float)
upperLimit Upper Limit of confidence interval for cal. Ratio(float)
M Magnitude parameter for channel compensation(float)
CV Coefficient of variation of the intensity(float)
Flag User flagged. 0 - deleted spot by user, 1 - good spot(Integer)

Data table
ID_REF VALUE PenAt RowAt ColumnAt SR_top SR_left SR_bottom SR_right SR_T. Int. SR_Mean SR_S.Dev SR_SNR SR_iQuality SR_bkMean SR_bkDev SG_top SG_left SG_bottom SG_right SG_T. Int. SG_Mean SG_S.Dev SG_SNR SG_iQuality SG_bkMean SG_bkDev unionArea propArea calRatio rQuality confLevel lowerLimit upperLimit M CV Flag
24_RP11-64K14 -0.2739 1 1 1 2309 239 2329 259 95416 264.4 143.6 12.3 1.0000 328.3 13.8 2309 239 2329 259 91847 192.3 89.2 14.8 1.0000 378.2 8.5 161 0.9527 0.8271 1.0 99.0 0.4699 2.1282 1.6623 0.1863 1
20_RP11-64H23 -0.0212 1 1 2 2309 259 2329 279 161268 620.0 335.9 27.2 1.0000 334.3 15.8 2309 259 2329 279 128073 378.5 179.4 30.2 1.0000 379.3 7.8 169 1.0000 0.9854 1.0 99.0 0.4699 2.1282 1.6623 0.1863 1
16_RP11-62A21 -0.3889 1 1 3 2309 279 2329 299 107620 315.4 93.9 16.7 1.0000 325.1 9.3 2309 279 2329 299 106330 248.5 59.6 18.0 1.0000 384.4 9.8 168 0.9941 0.7637 1.0 99.0 0.4699 2.1282 1.6623 0.1863 1
12_RP11-61J01 -0.3208 1 1 4 2309 299 2329 319 96888 252.6 64.5 13.4 1.0000 324.1 9.3 2309 299 2329 319 96196 189.8 48.3 14.3 1.0000 382.8 9.0 168 0.9941 0.8006 1.0 99.0 0.4699 2.1282 1.6623 0.1863 1
8_RP11-63J14 -0.1283 1 1 5 2309 319 2329 339 154222 577.5 232.7 26.1 1.0000 340.5 14.9 2309 319 2329 339 128755 379.8 138.9 26.9 1.0000 386.6 10.2 168 0.9941 0.9149 1.0 99.0 0.4699 2.1282 1.6623 0.1863 1
4_RP11-55M17 -0.2247 1 1 6 2310 339 2330 359 154496 580.2 225.4 27.9 1.0000 339.4 12.8 2310 339 2330 359 133703 407.9 142.8 29.0 1.0000 388.0 10.1 168 0.9941 0.8558 1.0 99.0 0.4699 2.1282 1.6623 0.1863 1
120_RP11-76C02 1.0290 1 1 7 2310 359 2330 379 309927 1499.0 573.9 63.6 1.0000 345.8 16.9 2310 359 2330 379 139916 441.9 162.8 31.9 1.0000 390.9 9.8 168 0.9941 2.0406 1.0 99.0 0.4699 2.1282 1.6623 0.1863 1
116_RP11-78F05 0.3812 1 1 8 2310 379 2330 399 173576 699.5 270.0 33.3 1.0000 333.7 13.1 2310 379 2330 399 119524 323.1 118.7 24.4 1.0000 388.4 8.9 168 0.9941 1.3024 1.0 99.0 0.4699 2.1282 1.6623 0.1863 1
112_RP11-75G10 -0.4890 1 1 9 2310 399 2330 419 146009 529.6 183.7 25.5 1.0000 334.4 12.7 2310 399 2330 419 140760 447.2 144.3 36.4 1.0000 385.7 7.4 169 1.0000 0.7125 1.0 99.0 0.4699 2.1282 1.6623 0.1863 1
108_Rp11-71N03 0.7258 1 1 10 2310 419 2330 439 171098 668.9 210.7 29.7 1.0000 343.6 15.4 2310 419 2330 439 106427 243.3 71.9 19.9 1.0000 386.4 7.4 169 1.0000 1.6538 1.0 99.0 0.4699 2.1282 1.6623 0.1863 1
104_RP11-71I11 0.1924 1 1 11 2310 439 2330 459 135564 467.2 152.7 21.0 1.0000 344.5 15.0 2310 439 2330 459 106217 246.0 77.8 18.3 1.0000 390.0 9.2 167 0.9882 1.1427 1.0 99.0 0.4699 2.1282 1.6623 0.1863 1
100_RP11-68P19 1.0119 1 1 12 2311 458 2331 478 324393 1566.9 475.9 66.0 1.0000 352.6 17.1 2311 458 2331 478 145461 467.4 114.4 35.3 1.0000 393.3 8.9 169 1.0000 2.0165 1.0 99.0 0.4699 2.1282 1.6623 0.1863 1
216_RP11-89P09 0.5246 1 1 13 2311 478 2331 498 254564 1140.8 351.3 39.7 1.0000 365.5 23.6 2311 478 2331 498 147652 477.1 133.0 34.3 1.0000 396.6 9.9 169 1.0000 1.4385 1.0 99.0 0.4699 2.1282 1.6623 0.1863 1
212_RP11-89M16 0.1431 1 1 14 2311 498 2331 518 208614 875.0 262.6 35.1 1.0000 359.4 18.8 2311 498 2331 518 147370 476.7 101.2 32.8 1.0000 395.3 10.8 169 1.0000 1.1043 1.0 99.0 0.4699 2.1282 1.6623 0.1863 1
208_RP11-92A09 0.3304 1 1 15 2311 518 2331 538 75977 230.9 57.3 10.0 1.0000 353.5 16.3 2311 518 2331 538 65144 110.5 30.8 7.9 1.0000 390.6 10.0 130 0.7692 1.2574 1.0 99.0 0.4699 2.1282 1.6623 0.1863 1
204_RP11-91J19 0.2328 1 1 16 2311 538 2331 558 131439 668.2 220.7 28.8 1.0000 358.6 16.4 2311 538 2331 558 94036 342.1 105.6 24.2 1.0000 392.5 10.2 128 0.7574 1.1751 1.0 99.0 0.4699 2.1282 1.6623 0.1863 1
200_RP11-91I20 0.0877 1 1 17 2311 558 2331 578 106850 500.3 183.0 23.5 1.0000 347.7 13.6 2311 558 2331 578 85368 283.2 116.4 20.6 1.0000 394.3 9.6 126 0.7456 1.0627 1.0 99.0 0.4699 2.1282 1.6623 0.1863 1
196_RP11-88J18 1.0010 1 1 18 2311 578 2331 598 125291 733.7 251.0 34.5 1.0000 346.4 13.5 2311 578 2331 598 71039 220.5 79.8 16.4 1.0000 391.9 9.2 116 0.6864 2.0014 1.0 99.0 0.4699 2.1282 1.6623 0.1863 1
312_RP11-105A04 -0.1854 1 1 19 2312 598 2332 618 85171 351.8 141.0 14.4 1.0000 358.0 18.1 2312 598 2332 618 75995 240.7 107.2 17.8 1.0000 392.6 9.3 120 0.7101 0.8794 1.0 99.0 0.4699 2.1282 1.6623 0.1863 1
308_RP11-100J23 0.6910 1 1 20 2312 618 2332 638 139947 766.1 269.9 30.2 1.0000 362.5 19.4 2312 618 2332 638 84052 285.5 102.9 22.1 1.0000 392.3 8.5 124 0.7337 1.6144 1.0 99.0 0.4699 2.1282 1.6623 0.1863 1

Total number of rows: 5760

Table truncated, full table size 1141 Kbytes.




Supplementary file Size Download File type/resource
GSM149985.txt.gz 316.7 Kb (ftp)(http) TXT

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