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Sample GSM149998 Query DataSets for GSM149998
Status Public on May 07, 2007
Title NHGRI_MDA-MB-415_02-06-06Slide33T
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-415
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 0.9367 1 1 1 2354 204 2374 224 48828 38.8 10.9 7 1 286.7 3.9 2354 204 2374 224 49186 29.6 12.5 2.3 1 298.3 9.4 150 0.8772 1.9141 0.6 99 0.4823 2.0734 0.6838 0.181 1
20_RP11-64H23 0.7088 1 1 2 2354 224 2374 244 61309 72.8 18.7 12.8 1 287.9 4.1 2354 224 2374 244 61747 65.1 23.6 5 1 298.1 9.9 170 0.9942 1.6345 1 99 0.4823 2.0734 0.6838 0.181 1
16_RP11-62A21 1.1342 1 1 3 2354 244 2374 264 48619 49.7 14.6 9.5 1 285.6 3.5 2354 244 2374 264 48068 33.1 12.3 2.7 1 298.4 8.7 145 0.848 2.1949 1 99 0.4823 2.0734 0.6838 0.181 1
12_RP11-61J01 1 1 4 2353 264 2373 284 46695 31.7 8.6 6.1 1 285.9 3.4 2353 264 2373 284 47647 25 8.7 2.1 1 299.1 8.8 147 0.8596 1.8552 0.4 99 0.4823 2.0734 0.6838 0.181 1
8_RP11-63J14 0.5269 1 1 5 2353 284 2373 304 62671 79.2 20.3 14.7 1 287.3 3.7 2353 284 2373 304 64998 80.4 27.7 6.5 1 299.7 9 171 1 1.4408 1 99 0.4823 2.0734 0.6838 0.181 1
4_RP11-55M17 0.4839 1 1 6 2353 304 2373 324 59273 67.1 25.3 11.1 1 290 4.6 2353 304 2373 324 61733 70.2 29.8 5.6 1 301.7 9.3 166 0.9708 1.3985 1 99 0.4823 2.0734 0.6838 0.181 1
120_RP11-76C02 0.9590 1 1 7 2353 324 2373 344 67597 107.4 26.2 18.9 1 288 4.2 2353 324 2373 344 64974 80.8 21.5 6.9 1 299.2 8.1 171 1 1.9439 1 99 0.4823 2.0734 0.6838 0.181 1
116_RP11-78F05 0.6407 1 1 8 2353 344 2373 364 47324 58.3 21.8 10.6 1 287.2 3.9 2353 344 2373 364 48329 54.7 18.2 4.9 1 298.1 7.2 137 0.8012 1.5591 1 99 0.4823 2.0734 0.6838 0.181 1
112_RP11-75G10 1.2770 1 1 9 2353 364 2373 384 43339 45.6 15.5 8.3 1 287.8 3.9 2353 364 2373 384 42595 27.5 12.4 2.3 1 300.1 8.6 130 0.7602 2.4233 0.8 99 0.4823 2.0734 0.6838 0.181 1
108_Rp11-71N03 1.2332 1 1 10 2353 384 2373 404 60947 68.6 15 12.6 1 287.8 3.8 2353 384 2373 404 58853 42.7 12.8 3.3 1 301.5 9.7 171 1 2.3509 1 99 0.4823 2.0734 0.6838 0.181 1
104_RP11-71I11 0.8478 1 1 11 2353 404 2373 424 58880 56.5 11.9 10.4 1 287.8 3.8 2353 404 2373 424 59377 45.9 12.8 3.8 1 301.3 8.5 171 1 1.7998 1 99 0.4823 2.0734 0.6838 0.181 1
100_RP11-68P19 1.0041 1 1 12 2353 424 2373 444 74726 161.3 36.4 29.4 1 288.8 3.9 2353 424 2373 444 69585 117.6 29.7 9.7 1 301.6 8.6 166 0.9708 2.0057 1 99 0.4823 2.0734 0.6838 0.181 1
216_RP11-89P09 1.0676 1 1 13 2353 444 2373 464 60320 107.7 33.8 20.4 1 289.1 3.6 2353 444 2373 464 57390 75.2 26.5 6.4 1 302.4 8.2 152 0.8889 2.096 1 99 0.4823 2.0734 0.6838 0.181 1
212_RP11-89M16 0.3443 1 1 14 2352 464 2372 484 64885 89.2 18.8 15.4 1 290.3 4.3 2352 464 2372 484 69186 102.7 25.6 8.8 1 301.9 8.1 171 1 1.2695 1 99 0.4823 2.0734 0.6838 0.181 1
208_RP11-92A09 1 1 15 2352 484 2372 504 39565 31.5 9.7 5.4 1 290.1 4.3 2352 484 2372 504 41222 33.3 12.6 2.8 1 301.9 8.3 123 0.7193 1.3862 0.4 99 0.4823 2.0734 0.6838 0.181 1
204_RP11-91J19 0.8990 1 1 16 2352 504 2372 524 48496 100.6 32.8 17.1 1 290.5 4.4 2352 504 2372 524 47082 78.9 25.9 6.9 1 300.8 7.7 124 0.7251 1.8648 1 99 0.4823 2.0734 0.6838 0.181 1
200_RP11-91I20 0.6096 1 1 17 2352 524 2372 544 43881 63.5 20.5 11.9 1 290.4 3.7 2352 524 2372 544 44860 60.8 20.9 5.3 1 300.9 7.7 124 0.7251 1.5258 1 99 0.4823 2.0734 0.6838 0.181 1
196_RP11-88J18 0.9305 1 1 18 2352 544 2372 564 44157 73.9 30.3 13.4 1 291 3.9 2352 544 2372 564 43358 56.7 24.7 4.6 1 301.6 9.1 121 0.7076 1.9059 1 99 0.4823 2.0734 0.6838 0.181 1
312_RP11-105A04 0.6038 1 1 19 2352 564 2372 584 44627 42.5 16.3 7.7 1 293 4 2352 564 2372 584 45614 40.9 16.7 3.5 1 302 8.3 133 0.7778 1.5197 0.9 99 0.4823 2.0734 0.6838 0.181 1
308_RP11-100J23 0.8011 1 1 20 2352 584 2372 604 49662 96.3 37.4 17.8 1 291.7 3.7 2352 584 2372 604 49252 80.8 32.5 6.6 1 304 8.9 128 0.7485 1.7424 1 99 0.4823 2.0734 0.6838 0.181 1

Total number of rows: 5760

Table truncated, full table size 993 Kbytes.




Supplementary file Size Download File type/resource
GSM149998.txt.gz 278.2 Kb (ftp)(http) TXT

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