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Sample GSM149978 Query DataSets for GSM149978
Status Public on May 07, 2007
Title NHGRI_SKBR3_01-31-06Slide75T
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 SKBR3
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 2333 255 2353 274 1 1.0 0.0 0.1 0.0000 320.0 10.0 2333 255 2353 274 1 1.0 0.0 0.1 0.0000 368.7 7.2 0 0.0000 0.4968 0.0 99.0 0.1754 7.3884 2.0127 0.3232 1
20_RP11-64H23 -0.5920 1 1 2 2333 275 2353 294 82740 232.6 125.9 11.9 1.0000 322.7 10.5 2333 275 2353 294 81179 174.2 80.5 14.3 1.0000 370.6 6.8 149 0.8613 0.6634 1.0 99.0 0.1754 7.3884 2.0127 0.3232 1
16_RP11-62A21 -0.6795 1 1 3 2333 295 2353 314 64027 171.8 68.8 8.4 1.0000 324.5 12.0 2333 295 2353 314 65795 136.7 52.1 10.9 1.0000 373.3 7.4 129 0.7457 0.6244 1.0 99.0 0.1754 7.3884 2.0127 0.3232 1
12_RP11-61J01 -0.4608 1 1 4 2333 315 2353 334 69447 179.6 65.9 9.2 1.0000 323.6 10.2 2333 315 2353 334 68180 122.8 41.8 10.1 1.0000 371.2 6.6 138 0.7977 0.7266 1.0 99.0 0.1754 7.3884 2.0127 0.3232 1
8_RP11-63J14 1.4294 1 1 5 2333 335 2353 354 177545 830.6 456.0 44.0 1.0000 322.3 9.1 2333 335 2353 354 81676 153.2 72.3 11.2 1.0000 377.1 9.2 154 0.8902 2.6934 1.0 99.0 0.1754 7.3884 2.0127 0.3232 1
4_RP11-55M17 1.0253 1 1 6 2334 355 2354 374 125266 616.1 265.1 26.0 1.0000 340.1 17.0 2334 355 2354 374 70098 150.4 59.2 9.4 1.0000 384.7 12.3 131 0.7572 2.0354 1.0 99.0 0.1754 7.3884 2.0127 0.3232 1
120_RP11-76C02 -0.6638 1 1 7 2334 375 2354 394 78080 179.9 56.3 8.1 1.0000 340.6 15.0 2334 375 2354 394 79042 141.6 47.7 9.2 1.0000 385.3 11.5 150 0.8671 0.6312 1.0 99.0 0.1754 7.3884 2.0127 0.3232 1
116_RP11-78F05 0.0384 1 1 8 2334 395 2354 414 106238 359.6 134.1 17.9 1.0000 334.8 11.4 2334 395 2354 414 85607 174.0 53.3 12.0 1.0000 385.5 10.3 153 0.8844 1.0270 1.0 99.0 0.1754 7.3884 2.0127 0.3232 1
112_RP11-75G10 -0.8409 1 1 9 2334 415 2354 434 90979 267.8 96.4 13.3 1.0000 334.7 11.5 2334 415 2354 434 94754 238.3 87.0 17.0 1.0000 389.2 9.7 151 0.8728 0.5583 1.0 99.0 0.1754 7.3884 2.0127 0.3232 1
108_Rp11-71N03 -1.1025 1 1 10 2334 435 2354 454 85665 165.5 47.3 7.6 1.0000 341.4 14.3 2334 435 2354 454 95822 176.6 42.9 12.2 1.0000 390.4 10.3 169 0.9769 0.4657 1.0 99.0 0.1754 7.3884 2.0127 0.3232 1
104_RP11-71I11 1.5260 1 1 11 2334 455 2354 474 251634 1142.3 418.6 53.7 1.0000 337.9 13.4 2334 455 2354 474 99783 197.1 55.1 14.0 1.0000 389.9 9.7 170 0.9827 2.8799 1.0 99.0 0.1754 7.3884 2.0127 0.3232 1
100_RP11-68P19 -0.6962 1 1 12 2334 475 2354 494 117705 389.5 162.7 18.5 1.0000 337.1 13.1 2334 475 2354 494 113838 313.6 128.8 22.5 1.0000 389.1 9.6 162 0.9364 0.6172 1.0 99.0 0.1754 7.3884 2.0127 0.3232 1
216_RP11-89P09 1.0117 1 1 13 2335 494 2355 513 281310 1366.9 566.0 68.1 1.0000 338.0 11.3 2335 494 2355 513 120475 336.8 115.1 24.1 1.0000 393.3 9.6 165 0.9538 2.0163 1.0 99.0 0.1754 7.3884 2.0127 0.3232 1
212_RP11-89M16 -0.7440 1 1 14 2335 514 2355 533 124251 381.0 153.0 19.5 1.0000 337.2 10.3 2335 514 2355 533 123961 317.0 112.0 18.3 1.0000 399.5 14.0 173 1.0000 0.5971 1.0 99.0 0.1754 7.3884 2.0127 0.3232 1
208_RP11-92A09 -0.0514 1 1 15 2335 534 2355 553 92832 229.6 94.3 9.2 1.0000 358.0 18.8 2335 534 2355 553 81206 118.2 38.8 7.7 1.0000 395.8 11.5 158 0.9133 0.9650 1.0 99.0 0.1754 7.3884 2.0127 0.3232 1
204_RP11-91J19 -0.5984 1 1 16 2335 554 2355 573 132992 482.0 162.5 19.3 1.0000 359.7 18.7 2335 554 2355 573 119786 362.6 107.4 24.7 1.0000 395.5 10.6 158 0.9133 0.6605 1.0 99.0 0.1754 7.3884 2.0127 0.3232 1
200_RP11-91I20 -0.0894 1 1 17 2335 574 2355 593 129954 499.2 181.7 22.5 1.0000 355.8 14.7 2335 574 2355 593 100657 263.9 84.0 19.7 1.0000 398.3 8.7 152 0.8786 0.9399 1.0 99.0 0.1754 7.3884 2.0127 0.3232 1
196_RP11-88J18 2.9768 1 1 18 2335 594 2355 613 449046 2417.1 1200.0 92.6 1.0000 372.0 20.2 2335 594 2355 613 88842 152.6 56.7 11.0 1.0000 399.3 9.5 161 0.9306 7.8723 1.0 99.0 0.1754 7.3884 2.0127 0.3232 1
312_RP11-105A04 -0.7817 1 1 19 2335 614 2355 633 94946 248.8 85.8 9.5 1.0000 380.0 20.2 2335 614 2355 633 93517 212.5 62.9 13.2 1.0000 406.8 12.4 151 0.8728 0.5817 1.0 99.0 0.1754 7.3884 2.0127 0.3232 1
308_RP11-100J23 -0.2591 1 1 20 2336 634 2356 653 130470 505.0 151.6 20.5 1.0000 382.5 18.3 2336 634 2356 653 104044 300.3 76.6 18.7 1.0000 407.5 12.5 147 0.8497 0.8356 1.0 99.0 0.1754 7.3884 2.0127 0.3232 1

Total number of rows: 5760

Table truncated, full table size 1154 Kbytes.




Supplementary file Size Download File type/resource
GSM149978.txt.gz 337.8 Kb (ftp)(http) TXT

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