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Sample GSM149982 Query DataSets for GSM149982
Status Public on May 07, 2007
Title NHGRI_MDA-MB-415_01-31-06Slide79T
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-415
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 2328 236 2348 255 1 1.0 0.0 0.1 0.0000 322.9 10.6 2328 236 2348 255 1 1.0 0.0 0.1 0.0000 375.0 10.2 0 0.0000 0.4146 0.0 99.0 0.5876 1.7018 2.4122 0.1380 1
20_RP11-64H23 0.2091 1 1 2 2328 256 2348 275 149076 691.8 454.9 38.5 1.0000 322.3 9.8 2328 256 2348 275 91581 248.1 158.9 21.3 1.0000 374.9 7.4 147 0.9363 1.1560 1.0 99.0 0.5876 1.7018 2.4122 0.1380 1
16_RP11-62A21 0.1672 1 1 3 2328 276 2348 295 91838 364.8 121.1 20.0 1.0000 325.8 10.2 2328 276 2348 295 67834 134.7 43.8 11.3 1.0000 375.4 7.8 133 0.8471 1.1229 1.0 99.0 0.5876 1.7018 2.4122 0.1380 1
12_RP11-61J01 0.1295 1 1 4 2329 296 2349 315 89072 249.6 96.6 12.5 1.0000 332.5 13.0 2329 296 2349 315 72044 94.6 33.8 7.9 1.0000 376.3 7.9 153 0.9745 1.0939 1.0 99.0 0.5876 1.7018 2.4122 0.1380 1
8_RP11-63J14 0.1750 1 1 5 2329 316 2349 335 134343 561.6 196.3 26.8 1.0000 340.0 14.5 2329 316 2349 335 87733 206.2 80.7 14.6 1.0000 382.6 10.9 149 0.9490 1.1290 1.0 99.0 0.5876 1.7018 2.4122 0.1380 1
4_RP11-55M17 0.1790 1 1 6 2329 336 2349 355 135541 576.5 236.0 28.7 1.0000 339.4 13.2 2329 336 2349 355 88170 211.1 87.6 14.2 1.0000 384.7 11.8 148 0.9427 1.1321 1.0 99.0 0.5876 1.7018 2.4122 0.1380 1
120_RP11-76C02 0.5357 1 1 7 2329 356 2349 375 140410 766.2 330.2 37.7 1.0000 339.4 13.6 2329 356 2349 375 76807 219.1 102.4 14.5 1.0000 385.7 12.2 127 0.8089 1.4496 1.0 99.0 0.5876 1.7018 2.4122 0.1380 1
116_RP11-78F05 0.1274 1 1 8 2330 376 2350 395 92197 392.9 156.2 18.9 1.0000 344.7 14.4 2330 376 2350 395 66742 149.1 63.9 11.6 1.0000 384.8 9.1 125 0.7962 1.0923 1.0 99.0 0.5876 1.7018 2.4122 0.1380 1
112_RP11-75G10 0.2139 1 1 9 2330 396 2350 415 178332 790.4 221.1 40.4 1.0000 345.5 12.5 2330 396 2350 415 105128 282.5 69.3 19.9 1.0000 387.1 11.0 157 1.0000 1.1598 1.0 99.0 0.5876 1.7018 2.4122 0.1380 1
108_Rp11-71N03 0.5940 1 1 10 2330 416 2350 435 122742 437.3 89.3 21.7 1.0000 349.5 13.3 2330 416 2350 435 79172 120.1 31.1 8.8 1.0000 387.4 10.3 156 0.9936 1.5094 1.0 99.0 0.5876 1.7018 2.4122 0.1380 1
104_RP11-71I11 0.1340 1 1 11 2330 436 2350 455 105787 355.7 98.4 16.9 1.0000 354.3 14.6 2330 436 2350 455 77769 134.4 37.2 11.7 1.0000 387.6 7.1 149 0.9490 1.0973 1.0 99.0 0.5876 1.7018 2.4122 0.1380 1
100_RP11-68P19 0.6425 1 1 12 2331 455 2351 474 228775 1100.0 229.5 53.3 1.0000 357.2 14.0 2331 455 2351 474 107614 292.1 60.3 22.5 1.0000 393.3 9.4 157 1.0000 1.5610 1.0 99.0 0.5876 1.7018 2.4122 0.1380 1
216_RP11-89P09 0.6097 1 1 13 2331 475 2351 494 189135 832.1 187.8 33.1 1.0000 372.5 20.1 2331 475 2351 494 97934 226.1 59.7 15.9 1.0000 397.7 11.0 157 1.0000 1.5259 1.0 99.0 0.5876 1.7018 2.4122 0.1380 1
212_RP11-89M16 0.0178 1 1 14 2331 495 2351 514 158574 638.8 144.3 27.4 1.0000 371.2 17.8 2331 495 2351 514 103434 261.6 62.9 19.7 1.0000 397.3 9.7 157 1.0000 1.0124 1.0 99.0 0.5876 1.7018 2.4122 0.1380 1
208_RP11-92A09 0.5818 1 1 15 2331 515 2351 534 87468 340.2 113.3 16.6 1.0000 359.5 13.8 2331 515 2351 534 60930 94.2 43.9 7.7 1.0000 393.2 8.3 125 0.7962 1.4967 1.0 99.0 0.5876 1.7018 2.4122 0.1380 1
204_RP11-91J19 0.1264 1 1 16 2332 535 2352 554 121950 565.0 139.7 25.9 1.0000 365.9 15.7 2332 535 2352 554 79826 214.6 59.5 17.6 1.0000 394.8 8.3 131 0.8344 1.0916 1.0 99.0 0.5876 1.7018 2.4122 0.1380 1
200_RP11-91I20 0.1400 1 1 17 2332 555 2352 574 109444 474.8 148.2 22.0 1.0000 367.1 15.4 2332 555 2352 574 74189 178.6 63.1 15.4 1.0000 392.1 7.3 130 0.8280 1.1019 1.0 99.0 0.5876 1.7018 2.4122 0.1380 1
196_RP11-88J18 0.5049 1 1 18 2332 575 2352 594 124122 536.8 232.8 26.0 1.0000 362.6 14.1 2332 575 2352 594 74904 156.8 72.0 14.6 1.0000 386.0 5.8 138 0.8790 1.4190 1.0 99.0 0.5876 1.7018 2.4122 0.1380 1
312_RP11-105A04 0.1482 1 1 19 2332 595 2352 614 98517 448.5 187.9 21.4 1.0000 365.7 14.6 2332 595 2352 614 67525 167.8 74.6 13.8 1.0000 390.3 8.1 121 0.7707 1.1082 1.0 99.0 0.5876 1.7018 2.4122 0.1380 1
308_RP11-100J23 0.6906 1 1 20 2333 615 2353 634 136789 666.8 305.1 33.3 1.0000 361.7 13.1 2333 615 2353 634 75010 171.3 90.4 13.5 1.0000 392.7 9.0 133 0.8471 1.6139 1.0 99.0 0.5876 1.7018 2.4122 0.1380 1

Total number of rows: 5760

Table truncated, full table size 1143 Kbytes.




Supplementary file Size Download File type/resource
GSM149982.txt.gz 318.9 Kb (ftp)(http) TXT

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