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Sample GSM149979 Query DataSets for GSM149979
Status Public on May 07, 2007
Title NHGRI_HCC38_01-31-06Slide76T
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 HCC38
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 2314 231 2334 250 1 1.0 0.0 0.0 0.0000 336.6 11.2 2314 231 2334 250 1 1.0 0.0 0.1 0.0000 375.5 8.6 0 0.0000 0.2571 0.0 99.0 0.4575 2.1858 3.8899 0.1915 1
20_RP11-64H23 -0.8127 1 1 2 2314 251 2334 270 145960 582.6 240.1 27.5 1.0000 341.2 11.6 2314 251 2334 270 101269 263.1 95.4 22.3 1.0000 377.9 8.0 158 0.9576 0.5693 1.0 99.0 0.4575 2.1858 3.8899 0.1915 1
16_RP11-62A21 -0.3160 1 1 3 2314 271 2334 290 153574 652.2 255.6 30.4 1.0000 345.0 12.1 2314 271 2334 290 90710 208.7 70.6 17.6 1.0000 380.3 8.2 154 0.9333 0.8033 1.0 99.0 0.4575 2.1858 3.8899 0.1915 1
12_RP11-61J01 0.0377 1 1 4 2314 291 2334 310 162110 638.6 184.4 28.4 1.0000 349.9 13.8 2314 291 2334 310 88040 159.9 47.3 14.0 1.0000 376.9 7.4 164 0.9939 1.0265 1.0 99.0 0.4575 2.1858 3.8899 0.1915 1
8_RP11-63J14 0.1568 1 1 5 2314 311 2334 330 270798 1292.1 442.5 59.5 1.0000 349.1 12.5 2314 311 2334 330 111119 298.0 91.8 26.5 1.0000 375.5 7.2 165 1.0000 1.1148 1.0 99.0 0.4575 2.1858 3.8899 0.1915 1
4_RP11-55M17 0.2804 1 1 6 2315 331 2335 350 273851 1315.6 621.7 57.5 1.0000 354.2 14.5 2315 331 2335 350 107496 278.5 114.9 24.5 1.0000 377.0 7.4 164 0.9939 1.2145 1.0 99.0 0.4575 2.1858 3.8899 0.1915 1
120_RP11-76C02 -0.6144 1 1 7 2315 351 2335 370 196069 891.9 315.8 39.0 1.0000 356.9 14.4 2315 351 2335 370 114441 351.0 122.2 30.0 1.0000 377.9 7.9 157 0.9515 0.6532 1.0 99.0 0.4575 2.1858 3.8899 0.1915 1
116_RP11-78F05 -0.3237 1 1 8 2315 371 2335 390 189536 804.1 257.9 37.4 1.0000 351.6 12.1 2315 371 2335 390 104011 258.7 74.8 23.0 1.0000 375.5 7.2 164 0.9939 0.7990 1.0 99.0 0.4575 2.1858 3.8899 0.1915 1
112_RP11-75G10 -0.0660 1 1 9 2315 391 2335 410 249820 1158.6 363.7 52.9 1.0000 355.5 12.8 2315 391 2335 410 113437 311.8 86.6 27.0 1.0000 375.7 7.7 165 1.0000 0.9553 1.0 99.0 0.4575 2.1858 3.8899 0.1915 1
108_Rp11-71N03 -0.8973 1 1 10 2315 411 2335 430 128354 419.8 85.4 18.2 1.0000 358.1 14.8 2315 411 2335 430 95097 201.0 34.8 17.7 1.0000 375.3 7.4 165 1.0000 0.5369 1.0 99.0 0.4575 2.1858 3.8899 0.1915 1
104_RP11-71I11 0.2366 1 1 11 2315 431 2335 450 215321 991.6 280.2 41.0 1.0000 362.6 16.4 2315 431 2335 450 94580 216.4 48.2 19.3 1.0000 378.5 7.1 159 0.9636 1.1782 1.0 99.0 0.4575 2.1858 3.8899 0.1915 1
100_RP11-68P19 -0.6719 1 1 12 2315 451 2335 470 204531 875.0 287.6 36.3 1.0000 364.6 16.4 2315 451 2335 470 122295 358.4 121.4 29.6 1.0000 382.8 8.5 165 1.0000 0.6277 1.0 99.0 0.4575 2.1858 3.8899 0.1915 1
216_RP11-89P09 0.3128 1 1 13 2316 471 2336 490 317896 1557.0 431.4 61.5 1.0000 369.7 18.1 2316 471 2336 490 116146 322.2 91.5 27.3 1.0000 381.7 8.0 165 1.0000 1.2421 1.0 99.0 0.4575 2.1858 3.8899 0.1915 1
212_RP11-89M16 -0.7964 1 1 14 2316 491 2336 510 207235 891.4 261.2 37.5 1.0000 364.6 15.8 2316 491 2336 510 128455 398.0 102.8 33.7 1.0000 380.5 8.0 165 1.0000 0.5758 1.0 99.0 0.4575 2.1858 3.8899 0.1915 1
208_RP11-92A09 -0.2944 1 1 15 2316 511 2336 530 97815 345.5 115.2 15.6 1.0000 363.3 13.3 2316 511 2336 530 67256 108.9 44.6 9.4 1.0000 378.4 7.7 138 0.8364 0.8154 1.0 99.0 0.4575 2.1858 3.8899 0.1915 1
204_RP11-91J19 -0.5076 1 1 16 2316 531 2336 550 150389 849.4 235.7 38.8 1.0000 363.5 12.8 2316 531 2336 550 85758 310.4 88.4 26.5 1.0000 381.2 7.9 124 0.7515 0.7034 1.0 99.0 0.4575 2.1858 3.8899 0.1915 1
200_RP11-91I20 -0.2396 1 1 17 2316 551 2336 570 136803 709.4 298.3 30.5 1.0000 367.8 15.1 2316 551 2336 570 76009 215.3 101.8 17.7 1.0000 383.2 8.5 127 0.7697 0.8470 1.0 99.0 0.4575 2.1858 3.8899 0.1915 1
196_RP11-88J18 0.3358 1 1 18 2316 571 2336 590 159570 867.1 359.3 35.3 1.0000 369.8 17.0 2316 571 2336 590 72298 176.6 76.3 14.5 1.0000 383.8 8.6 129 0.7818 1.2621 1.0 99.0 0.4575 2.1858 3.8899 0.1915 1
312_RP11-105A04 -0.6014 1 1 19 2316 591 2336 610 118917 503.4 237.2 21.4 1.0000 371.0 15.5 2316 591 2336 610 78841 196.3 96.1 17.1 1.0000 383.4 7.5 136 0.8242 0.6591 1.0 99.0 0.4575 2.1858 3.8899 0.1915 1
308_RP11-100J23 -1.0227 1 1 20 2317 611 2337 630 97813 424.1 173.5 17.7 1.0000 371.2 16.1 2317 611 2337 630 74465 221.5 103.3 18.7 1.0000 383.9 8.1 123 0.7455 0.4922 1.0 99.0 0.4575 2.1858 3.8899 0.1915 1

Total number of rows: 5760

Table truncated, full table size 1143 Kbytes.




Supplementary file Size Download File type/resource
GSM149979.txt.gz 321.7 Kb (ftp)(http) TXT

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