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Sample GSM149987 Query DataSets for GSM149987
Status Public on May 07, 2007
Title NHGRI_HCC38_02-06-06Slide88T
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 -1.2389 1 1 1 2304 270 2324 289 29941 79.6 68.9 3.1 1.0000 354.3 13.7 2304 270 2324 289 31243 73.4 53.5 5.7 1.0000 379.4 7.5 69 0.3920 0.4237 0.5 99.0 0.4560 2.1930 2.5600 0.1921 1
20_RP11-64H23 -0.5351 1 1 2 2304 290 2324 309 231560 1000.9 356.7 39.3 1.0000 353.2 13.8 2304 290 2324 309 161656 566.5 170.5 42.9 1.0000 378.8 8.2 171 0.9716 0.6901 1.0 99.0 0.4560 2.1930 2.5600 0.1921 1
16_RP11-62A21 -0.1538 1 1 3 2304 310 2324 329 204746 856.4 285.5 34.8 1.0000 355.1 12.1 2304 310 2324 329 126584 372.2 115.9 28.7 1.0000 376.8 7.8 169 0.9602 0.8989 1.0 99.0 0.4560 2.1930 2.5600 0.1921 1
12_RP11-61J01 0.1063 1 1 4 2305 330 2325 349 185337 711.8 233.6 27.5 1.0000 359.5 14.6 2305 330 2325 349 109781 258.3 72.7 19.9 1.0000 376.3 7.8 173 0.9830 1.0765 1.0 99.0 0.4560 2.1930 2.5600 0.1921 1
8_RP11-63J14 0.1981 1 1 5 2305 350 2325 369 337915 1611.0 650.2 64.1 1.0000 353.6 13.1 2305 350 2325 369 159209 548.6 184.0 42.2 1.0000 377.1 7.9 172 0.9773 1.1472 1.0 99.0 0.4560 2.1930 2.5600 0.1921 1
4_RP11-55M17 0.4474 1 1 6 2305 370 2325 389 370826 1802.3 786.0 71.5 1.0000 353.7 13.3 2305 370 2325 389 153707 516.3 201.1 40.4 1.0000 377.4 7.5 172 0.9773 1.3636 1.0 99.0 0.4560 2.1930 2.5600 0.1921 1
120_RP11-76C02 -0.5389 1 1 7 2305 390 2325 409 193187 1077.3 444.2 41.3 1.0000 364.4 14.9 2305 390 2325 409 132628 611.4 246.7 48.1 1.0000 378.4 7.4 134 0.7614 0.6883 1.0 99.0 0.4560 2.1930 2.5600 0.1921 1
116_RP11-78F05 -0.2391 1 1 8 2306 410 2326 429 207230 857.9 286.5 32.6 1.0000 361.1 15.3 2306 410 2326 429 131347 395.5 121.5 31.7 1.0000 377.1 6.9 170 0.9659 0.8473 1.0 99.0 0.4560 2.1930 2.5600 0.1921 1
112_RP11-75G10 0.0287 1 1 9 2306 430 2326 449 260600 1118.1 368.5 43.1 1.0000 362.6 14.6 2306 430 2326 449 142168 428.1 125.6 30.8 1.0000 379.6 9.3 176 1.0000 1.0201 1.0 99.0 0.4560 2.1930 2.5600 0.1921 1
108_Rp11-71N03 -0.6686 1 1 10 2306 450 2326 469 136786 438.9 129.3 16.6 1.0000 361.0 15.6 2306 450 2326 469 110808 272.5 78.2 21.0 1.0000 375.5 7.9 171 0.9716 0.6291 1.0 99.0 0.4560 2.1930 2.5600 0.1921 1
104_RP11-71I11 0.4369 1 1 11 2306 470 2326 489 259518 1192.7 345.0 44.6 1.0000 361.3 16.0 2306 470 2326 489 120419 344.2 93.5 27.0 1.0000 376.9 7.4 167 0.9489 1.3537 1.0 99.0 0.4560 2.1930 2.5600 0.1921 1
100_RP11-68P19 -0.5992 1 1 12 2307 490 2327 509 229964 966.3 277.7 34.9 1.0000 370.7 17.5 2307 490 2327 509 163377 571.9 145.6 44.2 1.0000 378.0 7.8 172 0.9773 0.6601 1.0 99.0 0.4560 2.1930 2.5600 0.1921 1
216_RP11-89P09 0.3279 1 1 13 2307 510 2327 529 362155 1692.3 607.0 65.1 1.0000 365.4 14.7 2307 510 2327 529 159716 526.7 179.2 39.6 1.0000 380.8 8.3 176 1.0000 1.2552 1.0 99.0 0.4560 2.1930 2.5600 0.1921 1
212_RP11-89M16 -0.7152 1 1 14 2307 530 2327 549 209716 829.7 187.1 31.7 1.0000 361.9 15.0 2307 530 2327 549 160477 532.1 112.1 41.0 1.0000 379.7 7.8 176 1.0000 0.6091 1.0 99.0 0.4560 2.1930 2.5600 0.1921 1
208_RP11-92A09 0.0771 1 1 15 2307 550 2327 569 110797 365.9 134.7 14.1 1.0000 363.0 14.6 2307 550 2327 569 77808 135.5 54.4 11.4 1.0000 376.4 5.8 152 0.8636 1.0549 1.0 99.0 0.4560 2.1930 2.5600 0.1921 1
204_RP11-91J19 -0.3494 1 1 16 2308 570 2328 589 161851 663.1 194.4 25.0 1.0000 367.8 15.7 2308 570 2328 589 111353 330.0 104.0 25.8 1.0000 379.2 7.5 157 0.8920 0.7849 1.0 99.0 0.4560 2.1930 2.5600 0.1921 1
200_RP11-91I20 -0.1748 1 1 17 2308 590 2328 609 170411 672.8 251.2 26.0 1.0000 366.3 14.6 2308 590 2328 609 111196 296.7 108.1 22.8 1.0000 381.4 7.8 164 0.9318 0.8859 1.0 99.0 0.4560 2.1930 2.5600 0.1921 1
196_RP11-88J18 0.3410 1 1 18 2308 610 2328 629 181770 788.6 318.4 29.3 1.0000 369.2 16.3 2308 610 2328 629 98057 243.2 100.5 18.7 1.0000 381.4 7.9 157 0.8920 1.2666 1.0 99.0 0.4560 2.1930 2.5600 0.1921 1
312_RP11-105A04 -0.6193 1 1 19 2308 630 2328 649 121445 452.8 158.3 16.7 1.0000 373.4 16.7 2308 630 2328 649 96141 271.7 116.5 20.6 1.0000 382.4 8.1 147 0.8352 0.6510 1.0 99.0 0.4560 2.1930 2.5600 0.1921 1
308_RP11-100J23 -0.9376 1 1 20 2309 650 2329 669 112030 438.6 145.3 16.6 1.0000 373.2 15.5 2309 650 2329 669 98115 328.1 109.7 24.1 1.0000 382.9 8.9 138 0.7841 0.5221 1.0 99.0 0.4560 2.1930 2.5600 0.1921 1

Total number of rows: 5760

Table truncated, full table size 1147 Kbytes.




Supplementary file Size Download File type/resource
GSM149987.txt.gz 330.9 Kb (ftp)(http) TXT

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