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Sample GSM149999 Query DataSets for GSM149999
Status Public on May 07, 2007
Title NHGRI_MDA-MB-435S_02-06-06Slide34T
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 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)
 
Channel 2
Source name MDA-MB-435S
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 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)
 
 
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 0.5661 1 1 1 2334 212 2354 232 60730 67.5 22.5 12.6 1 285.6 3.6 2334 212 2354 232 58669 46.2 19.6 3.8 1 294.9 8.9 172 0.9885 1.4805 1 99 0.5705 1.7528 0.9877 0.1448 1
20_RP11-64H23 0.4603 1 1 2 2334 232 2354 252 59470 117.6 50.7 21.2 1 287 3.8 2334 232 2354 252 56514 86.5 47.5 7.1 1 297.9 8.9 147 0.8448 1.3758 1 99 0.5705 1.7528 0.9877 0.1448 1
16_RP11-62A21 0.8399 1 1 3 2334 252 2354 272 45259 75.6 19.3 14.2 1 286.5 3.5 2334 252 2354 272 42514 42.7 16.6 3.8 1 297.4 7.7 125 0.7184 1.7899 1 99 0.5705 1.7528 0.9877 0.1448 1
12_RP11-61J01 0.7615 1 1 4 2334 273 2354 293 58051 52.5 14.3 9.9 1 287 3.4 2334 273 2354 293 56608 31.4 12.4 2.5 1 299.7 9.3 171 0.9828 1.6952 1 99 0.5705 1.7528 0.9877 0.1448 1
8_RP11-63J14 0.4279 1 1 5 2334 293 2354 313 61511 106 44.5 18 1 290.9 4.3 2334 293 2354 313 58863 79.8 34.4 6.3 1 300 9.6 155 0.8908 1.3453 1 99 0.5705 1.7528 0.9877 0.1448 1
4_RP11-55M17 0.6335 1 1 6 2334 313 2354 333 64494 119.7 46.5 21.5 1 288.4 3.8 2334 313 2354 333 59922 78.2 36.6 6.2 1 301.1 9.6 158 0.908 1.5513 1 99 0.5705 1.7528 0.9877 0.1448 1
120_RP11-76C02 0.6284 1 1 7 2334 333 2354 353 71781 134.4 22 23.8 1 287.9 4 2334 333 2354 353 66018 88 22.9 7 1 300.3 9.3 170 0.977 1.5458 1 99 0.5705 1.7528 0.9877 0.1448 1
116_RP11-78F05 0.6329 1 1 8 2334 353 2354 373 55727 86.1 31.9 15.7 1 287.9 3.8 2334 353 2354 373 52854 56.2 21.4 4.7 1 298.5 8.7 149 0.8563 1.5507 1 99 0.5705 1.7528 0.9877 0.1448 1
112_RP11-75G10 0.5413 1 1 9 2334 374 2354 394 50319 79.8 27.4 15.4 1 287.5 3.3 2334 374 2354 394 48647 55.5 20.9 4.7 1 299.5 8.5 137 0.7874 1.4553 1 99 0.5705 1.7528 0.9877 0.1448 1
108_Rp11-71N03 0.8367 1 1 10 2334 394 2354 414 61612 83.2 20.4 14.2 1 288 4.2 2334 394 2354 414 57555 47.1 13.7 4 1 299.6 8.3 166 0.954 1.786 1 99 0.5705 1.7528 0.9877 0.1448 1
104_RP11-71I11 0.5437 1 1 11 2334 414 2354 434 57588 77.6 17.4 12.8 1 289.2 4.6 2334 414 2354 434 55503 53.9 13.5 4.5 1 299.6 8.5 157 0.9023 1.4577 1 99 0.5705 1.7528 0.9877 0.1448 1
100_RP11-68P19 0.6058 1 1 12 2334 434 2354 454 84428 207.2 46.3 35.7 1 289.5 4.2 2334 434 2354 454 74344 137.8 35.3 11.5 1 299.5 8.6 170 0.977 1.5218 1 99 0.5705 1.7528 0.9877 0.1448 1
216_RP11-89P09 0.6146 1 1 13 2334 454 2354 474 67411 125.2 38.1 22.1 1 290.9 4 2334 454 2354 474 61999 82.8 22.5 6.9 1 299.9 8.6 162 0.931 1.5311 1 99 0.5705 1.7528 0.9877 0.1448 1
212_RP11-89M16 0.2101 1 1 14 2334 475 2354 495 61207 118.4 37.8 19.9 1 292.4 4.4 2334 475 2354 495 60256 103.6 32.7 8.9 1 300.8 8.1 149 0.8563 1.1568 1 99 0.5705 1.7528 0.9877 0.1448 1
208_RP11-92A09 -0.0042 1 1 15 2334 495 2354 515 36250 45.5 16.9 8.3 1 290.1 3.8 2334 495 2354 515 37584 46.2 15.3 3.7 1 301.8 9.4 108 0.6207 0.9971 1 99 0.5705 1.7528 0.9877 0.1448 1
204_RP11-91J19 0.3116 1 1 16 2334 515 2354 535 42477 113.9 38.8 20.4 1 290.7 3.9 2334 515 2354 535 41338 92.9 27.2 8 1 300.8 8.1 105 0.6034 1.2411 1 99 0.5705 1.7528 0.9877 0.1448 1
200_RP11-91I20 0.2562 1 1 17 2334 535 2354 555 41754 94.8 32.7 16.2 1 291.8 4.2 2334 535 2354 555 41296 80.4 23.5 6.7 1 302 8.6 108 0.6207 1.1943 1 99 0.5705 1.7528 0.9877 0.1448 1
196_RP11-88J18 0.2987 1 1 18 2334 555 2354 575 41618 78.5 28.3 13.2 1 293.1 4.4 2334 555 2354 575 41234 64.7 19.2 5.3 1 303.5 9 112 0.6437 1.23 1 99 0.5705 1.7528 0.9877 0.1448 1
312_RP11-105A04 0.1412 1 1 19 2334 576 2354 596 33638 65.9 23.3 11.6 1 292 4 2334 576 2354 596 34252 60.5 22 5 1 303.9 8.9 94 0.5402 1.1028 1 99 0.5705 1.7528 0.9877 0.1448 1
308_RP11-100J23 0.3639 1 1 20 2334 596 2354 616 33770 125.1 54.2 22.7 1 291.8 3.8 2334 596 2354 616 32697 98.4 40.5 7.9 1 305.2 9.3 81 0.4655 1.2869 1 99 0.5705 1.7528 0.9877 0.1448 1

Total number of rows: 5760

Table truncated, full table size 1003 Kbytes.




Supplementary file Size Download File type/resource
GSM149999.txt.gz 278.8 Kb (ftp)(http) TXT

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