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Sample GSM149993 Query DataSets for GSM149993
Status Public on May 07, 2007
Title NHGRI_MDA-MB-436_02-06-06Slide95T
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 1 1 1 2286 248 2306 268 1 1.0 0.0 0.1 0.0000 315.2 10.1 2286 248 2306 268 1 1.0 0.0 0.1 0.0000 373.0 7.6 0 0.0000 0.6082 0.0 99.0 0.5323 1.8787 1.6442 0.1603 1
20_RP11-64H23 -0.1329 1 1 2 2286 268 2306 288 105547 497.4 274.8 33.9 1.0000 314.5 8.6 2286 268 2306 288 91829 331.7 153.1 28.2 1.0000 374.7 8.1 130 0.8442 0.9120 1.0 99.0 0.5323 1.8787 1.6442 0.1603 1
16_RP11-62A21 -0.2704 1 1 3 2286 288 2306 308 78783 310.5 105.4 21.3 1.0000 314.8 8.4 2286 288 2306 308 75823 227.7 65.0 20.3 1.0000 374.0 7.4 126 0.8182 0.8291 1.0 99.0 0.5323 1.8787 1.6442 0.1603 1
12_RP11-61J01 -0.3761 1 1 4 2286 309 2306 329 75096 228.6 79.4 15.9 1.0000 315.6 8.0 2286 309 2306 329 76509 180.4 54.3 16.2 1.0000 374.0 7.3 138 0.8961 0.7705 1.0 99.0 0.5323 1.8787 1.6442 0.1603 1
8_RP11-63J14 -0.1981 1 1 5 2286 329 2306 349 123308 545.7 181.8 38.2 1.0000 316.6 7.9 2286 329 2306 349 108179 380.8 112.0 33.2 1.0000 375.7 7.7 143 0.9286 0.8717 1.0 99.0 0.5323 1.8787 1.6442 0.1603 1
4_RP11-55M17 -0.2617 1 1 6 2287 349 2307 369 119236 525.3 226.2 34.1 1.0000 320.3 9.8 2287 349 2307 369 107103 383.1 139.5 33.6 1.0000 376.5 7.6 141 0.9156 0.8341 1.0 99.0 0.5323 1.8787 1.6442 0.1603 1
120_RP11-76C02 0.7274 1 1 7 2287 369 2307 389 221769 1120.0 324.4 72.3 1.0000 320.1 9.9 2287 369 2307 389 121310 411.4 107.1 36.2 1.0000 376.3 7.6 154 1.0000 1.6556 1.0 99.0 0.5323 1.8787 1.6442 0.1603 1
116_RP11-78F05 0.2471 1 1 8 2287 390 2307 410 113298 492.6 192.4 29.6 1.0000 322.5 11.7 2287 390 2307 410 87412 252.5 90.9 21.9 1.0000 376.4 7.8 139 0.9026 1.1868 1.0 99.0 0.5323 1.8787 1.6442 0.1603 1
112_RP11-75G10 -0.2685 1 1 9 2287 410 2307 430 111310 423.0 129.1 26.1 1.0000 324.1 11.0 2287 410 2307 430 102409 309.9 79.4 27.9 1.0000 377.4 7.2 149 0.9675 0.8302 1.0 99.0 0.5323 1.8787 1.6442 0.1603 1
108_Rp11-71N03 0.5288 1 1 10 2287 430 2307 450 128249 535.9 139.5 31.7 1.0000 324.8 12.0 2287 430 2307 450 89854 225.9 47.9 20.2 1.0000 377.1 7.3 149 0.9675 1.4427 1.0 99.0 0.5323 1.8787 1.6442 0.1603 1
104_RP11-71I11 0.1393 1 1 11 2287 450 2307 470 113591 469.2 148.8 28.8 1.0000 325.1 11.2 2287 450 2307 470 91128 259.1 69.3 22.7 1.0000 378.2 7.6 143 0.9286 1.1014 1.0 99.0 0.5323 1.8787 1.6442 0.1603 1
100_RP11-68P19 0.7854 1 1 12 2288 471 2308 491 250803 1305.5 402.7 89.6 1.0000 323.1 8.4 2288 471 2308 491 129221 460.6 123.3 41.8 1.0000 378.5 7.0 154 1.0000 1.7236 1.0 99.0 0.5323 1.8787 1.6442 0.1603 1
216_RP11-89P09 0.3984 1 1 13 2288 491 2308 511 169218 772.9 250.0 51.1 1.0000 325.9 9.4 2288 491 2308 511 113221 356.7 106.9 32.6 1.0000 378.5 6.9 154 1.0000 1.3180 1.0 99.0 0.5323 1.8787 1.6442 0.1603 1
212_RP11-89M16 0.0256 1 1 14 2288 511 2308 531 141963 592.8 141.9 37.5 1.0000 329.1 10.4 2288 511 2308 531 113009 354.2 73.3 31.9 1.0000 379.6 7.2 154 1.0000 1.0179 1.0 99.0 0.5323 1.8787 1.6442 0.1603 1
208_RP11-92A09 -0.0184 1 1 15 2288 531 2308 551 67197 209.0 70.0 12.1 1.0000 332.9 12.6 2288 531 2308 551 62980 128.7 42.1 11.2 1.0000 379.2 7.8 124 0.8052 0.9873 1.0 99.0 0.5323 1.8787 1.6442 0.1603 1
204_RP11-91J19 0.2091 1 1 16 2288 552 2308 572 93333 464.7 149.9 28.2 1.0000 333.0 11.4 2288 552 2308 572 73245 244.5 65.3 20.3 1.0000 381.5 8.5 117 0.7597 1.1560 1.0 99.0 0.5323 1.8787 1.6442 0.1603 1
200_RP11-91I20 -0.0950 1 1 17 2288 572 2308 592 80333 363.5 135.3 21.7 1.0000 335.1 11.8 2288 572 2308 592 71071 236.1 83.6 19.6 1.0000 381.9 8.6 115 0.7468 0.9363 1.0 99.0 0.5323 1.8787 1.6442 0.1603 1
196_RP11-88J18 0.8898 1 1 18 2288 592 2308 612 128196 742.5 259.1 44.6 1.0000 334.8 11.6 2288 592 2308 612 74273 243.7 90.9 20.7 1.0000 380.4 8.2 119 0.7727 1.8529 1.0 99.0 0.5323 1.8787 1.6442 0.1603 1
312_RP11-105A04 -0.2713 1 1 19 2289 612 2309 632 67978 300.8 146.9 18.4 1.0000 334.5 11.2 2289 612 2309 632 64360 220.8 106.4 20.0 1.0000 380.7 7.1 107 0.6948 0.8286 1.0 99.0 0.5323 1.8787 1.6442 0.1603 1
308_RP11-100J23 0.6551 1 1 20 2289 633 2309 653 107552 722.7 262.3 39.4 1.0000 342.2 14.0 2289 633 2309 653 66648 279.1 115.1 24.2 1.0000 380.8 7.8 101 0.6558 1.5747 1.0 99.0 0.5323 1.8787 1.6442 0.1603 1

Total number of rows: 5760

Table truncated, full table size 1142 Kbytes.




Supplementary file Size Download File type/resource
GSM149993.txt.gz 319.0 Kb (ftp)(http) TXT

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