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Sample GSM149989 Query DataSets for GSM149989
Status Public on May 07, 2007
Title NHGRI_BT-474_02-06-06Slide90T
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 BT-474
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 -1.6506 1 1 1 2324 205 2344 225 29266 187.4 162.0 8.6 0.9781 344.7 11.9 2324 205 2344 225 31204 190.5 174.6 16.1 0.9158 376.9 7.5 55 0.2973 0.3185 0.9 99.0 0.5502 1.8175 3.0889 0.1530 1
20_RP11-64H23 -0.3944 1 1 2 2324 225 2344 245 331085 1453.5 538.1 55.8 1.0000 365.6 18.6 2324 225 2344 245 181857 618.5 199.5 50.0 1.0000 380.7 8.4 182 0.9838 0.7608 1.0 99.0 0.5502 1.8175 3.0889 0.1530 1
16_RP11-62A21 -0.3564 1 1 3 2324 245 2344 265 261259 1124.9 460.0 48.9 1.0000 359.5 14.0 2324 245 2344 265 148884 466.2 175.6 37.5 1.0000 379.7 8.4 176 0.9514 0.7811 1.0 99.0 0.5502 1.8175 3.0889 0.1530 1
12_RP11-61J01 0.2377 1 1 4 2324 265 2344 285 288480 1260.0 511.5 52.0 1.0000 360.7 16.0 2324 265 2344 285 128850 346.0 124.0 25.3 1.0000 377.9 10.2 178 0.9622 1.1791 1.0 99.0 0.5502 1.8175 3.0889 0.1530 1
8_RP11-63J14 0.2083 1 1 5 2324 285 2344 305 561756 2717.9 1230.8 102.0 1.0000 368.7 19.4 2324 285 2344 305 207470 761.6 317.7 55.6 1.0000 378.4 10.2 182 0.9838 1.1553 1.0 99.0 0.5502 1.8175 3.0889 0.1530 1
4_RP11-55M17 0.3698 1 1 6 2323 305 2343 325 540157 2637.4 1221.1 108.5 1.0000 363.4 16.1 2323 305 2343 325 186540 660.8 271.4 52.6 1.0000 375.6 8.6 180 0.9730 1.2922 1.0 99.0 0.5502 1.8175 3.0889 0.1530 1
120_RP11-76C02 0.4912 1 1 7 2323 325 2343 345 546098 3011.4 1329.9 123.5 1.0000 359.5 16.2 2323 325 2343 345 172754 693.6 288.8 50.0 1.0000 372.8 10.5 162 0.8757 1.4056 1.0 99.0 0.5502 1.8175 3.0889 0.1530 1
116_RP11-78F05 -0.4020 1 1 8 2323 345 2343 365 236444 1147.1 482.0 48.3 1.0000 358.9 15.2 2323 345 2343 365 135661 490.7 211.9 35.4 1.0000 373.4 10.4 157 0.8486 0.7568 1.0 99.0 0.5502 1.8175 3.0889 0.1530 1
112_RP11-75G10 0.1222 1 1 9 2323 365 2343 385 356416 1569.9 597.9 68.2 1.0000 356.6 14.1 2323 365 2343 385 154847 467.0 147.7 41.3 1.0000 370.1 6.7 185 1.0000 1.0884 1.0 99.0 0.5502 1.8175 3.0889 0.1530 1
108_Rp11-71N03 0.3242 1 1 10 2323 385 2343 405 295331 1248.8 413.9 54.1 1.0000 356.2 14.2 2323 385 2343 405 127384 322.9 106.0 26.2 1.0000 369.4 8.3 184 0.9946 1.2520 1.0 99.0 0.5502 1.8175 3.0889 0.1530 1
104_RP11-71I11 -0.0565 1 1 11 2323 405 2343 425 269411 1098.1 478.2 47.4 1.0000 358.2 14.3 2323 405 2343 425 136890 369.7 150.9 29.9 1.0000 370.3 8.4 185 1.0000 0.9616 1.0 99.0 0.5502 1.8175 3.0889 0.1530 1
100_RP11-68P19 0.4245 1 1 12 2323 425 2343 445 397730 1811.4 813.9 77.5 1.0000 362.0 14.7 2323 425 2343 445 148590 436.9 179.8 31.6 1.0000 375.0 10.4 183 0.9892 1.3421 1.0 99.0 0.5502 1.8175 3.0889 0.1530 1
216_RP11-89P09 0.3608 1 1 13 2323 445 2343 465 468799 2167.7 1082.9 84.8 1.0000 366.3 17.9 2323 445 2343 465 170478 546.5 244.4 38.8 1.0000 375.0 10.8 185 1.0000 1.2841 1.0 99.0 0.5502 1.8175 3.0889 0.1530 1
212_RP11-89M16 -0.4436 1 1 14 2323 465 2343 485 311878 1315.3 458.9 51.6 1.0000 370.6 17.8 2323 465 2343 485 176970 579.1 171.2 42.7 1.0000 377.5 10.0 185 1.0000 0.7353 1.0 99.0 0.5502 1.8175 3.0889 0.1530 1
208_RP11-92A09 -0.0707 1 1 15 2323 485 2343 505 105985 389.1 158.1 16.7 1.0000 362.5 14.6 2323 485 2343 505 71257 132.3 50.5 11.6 1.0000 373.1 6.9 141 0.7622 0.9522 1.0 99.0 0.5502 1.8175 3.0889 0.1530 1
204_RP11-91J19 -0.5748 1 1 16 2322 505 2342 525 179243 785.1 286.5 33.5 1.0000 363.9 14.8 2322 505 2342 525 116938 378.5 135.9 35.5 1.0000 371.1 5.5 156 0.8432 0.6714 1.0 99.0 0.5502 1.8175 3.0889 0.1530 1
200_RP11-91I20 -0.0726 1 1 17 2322 525 2342 545 213552 944.9 393.1 37.6 1.0000 373.3 17.3 2322 525 2342 545 112823 321.7 137.8 27.3 1.0000 374.8 7.5 162 0.8757 0.9509 1.0 99.0 0.5502 1.8175 3.0889 0.1530 1
196_RP11-88J18 0.3294 1 1 18 2322 545 2342 565 230697 1115.1 563.5 45.4 1.0000 373.3 16.5 2322 545 2342 565 102777 287.3 147.7 24.1 1.0000 375.8 7.7 155 0.8378 1.2565 1.0 99.0 0.5502 1.8175 3.0889 0.1530 1
312_RP11-105A04 -0.3232 1 1 19 2322 565 2342 585 163418 754.2 359.0 27.7 1.0000 372.9 20.2 2322 565 2342 585 99285 305.5 150.4 20.2 1.0000 379.3 12.1 145 0.7838 0.7993 1.0 99.0 0.5502 1.8175 3.0889 0.1530 1
308_RP11-100J23 0.4028 1 1 20 2322 585 2342 605 249416 1274.1 552.9 45.5 1.0000 377.7 21.3 2322 585 2342 605 104418 312.0 129.8 19.3 1.0000 379.5 13.3 151 0.8162 1.3221 1.0 99.0 0.5502 1.8175 3.0889 0.1530 1

Total number of rows: 5760

Table truncated, full table size 1147 Kbytes.




Supplementary file Size Download File type/resource
GSM149989.txt.gz 322.7 Kb (ftp)(http) TXT

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