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Sample GSM150000 Query DataSets for GSM150000
Status Public on May 07, 2007
Title NHGRI_HCC-1419_02-06-06Slide35T
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 HCC-1419
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 -0.1693 1 1 1 2335 266 2355 286 52714 45.3 12.8 9.6 1 282.1 3 2335 266 2355 286 60616 76.2 25.1 6.1 1 300.3 8.9 161 0.9817 0.8893 1 99 0.2815 3.5955 0.669 0.2692 1
20_RP11-64H23 -0.3620 1 1 2 2335 286 2355 306 59605 82 26.1 15.6 1 283.7 3.8 2335 286 2355 306 74944 157.5 50.3 12 1 302.2 9.9 163 0.9939 0.7781 1 99 0.2815 3.5955 0.669 0.2692 1
16_RP11-62A21 -0.0056 1 1 3 2335 306 2355 326 43358 45.1 12.1 8.7 1 283.4 3.7 2335 306 2355 326 48704 67.6 17.5 5.6 1 301.3 8.6 132 0.8049 0.9961 1 99 0.2815 3.5955 0.669 0.2692 1
12_RP11-61J01 0.7332 1 1 4 2335 326 2355 346 53447 59 18.2 13.8 1 281.4 2.2 2335 326 2355 346 55565 53.1 20.5 4.4 1 300.8 8.4 157 0.9573 1.6623 1 99 0.2815 3.5955 0.669 0.2692 1
8_RP11-63J14 -0.3491 1 1 5 2335 346 2355 366 57677 69.2 19.8 13.5 1 282.5 3.6 2335 346 2355 366 71025 131.8 46.4 10.4 1 301.3 9.3 164 1 0.7851 1 99 0.2815 3.5955 0.669 0.2692 1
4_RP11-55M17 -0.2524 1 1 6 2335 366 2355 386 57769 72.8 22.7 13.1 1 283.8 4.2 2335 366 2355 386 69619 129.6 51.8 10.7 1 300.2 8.4 162 0.9878 0.8395 1 99 0.2815 3.5955 0.669 0.2692 1
120_RP11-76C02 -0.8664 1 1 7 2335 386 2355 406 53781 44.5 8 9.1 1 283.5 3.3 2335 386 2355 406 69448 121.2 24 9.6 1 302.2 9.2 164 1 0.5485 1 99 0.2815 3.5955 0.669 0.2692 1
116_RP11-78F05 -0.2505 1 1 8 2335 406 2355 426 47376 46.9 16.4 10.2 1 282.1 2.8 2335 406 2355 426 55405 83.4 31.7 7.1 1 301.4 7.9 144 0.878 0.8406 1 99 0.2815 3.5955 0.669 0.2692 1
112_RP11-75G10 0.6532 1 1 9 2335 426 2355 446 48162 74.5 23.6 16.1 1 282.2 2.8 2335 426 2355 446 50300 70.8 24.2 6 1 301.7 7.9 135 0.8232 1.5726 1 99 0.2815 3.5955 0.669 0.2692 1
108_Rp11-71N03 -0.5688 1 1 10 2335 446 2355 466 48680 30.5 7.8 6.3 1 283.6 3.2 2335 446 2355 466 57418 67.6 18 5.5 1 302.8 8.8 155 0.9451 0.6742 1 99 0.2815 3.5955 0.669 0.2692 1
104_RP11-71I11 0.0012 1 1 11 2335 466 2355 486 51578 50.6 10.5 10.2 1 284.3 3.4 2335 466 2355 486 58253 75.5 16.8 6.1 1 302.7 8.8 154 0.939 1.0008 1 99 0.2815 3.5955 0.669 0.2692 1
100_RP11-68P19 -1.0312 1 1 12 2335 487 2355 507 54586 58.4 15.1 12.5 1 284.9 2.9 2335 487 2355 507 76457 178.4 46.7 15.1 1 302.4 8 159 0.9695 0.4893 1 99 0.2815 3.5955 0.669 0.2692 1
216_RP11-89P09 1.1560 1 1 13 2335 507 2355 527 68448 145.5 38.8 31.4 1 285 2.8 2335 507 2355 527 63636 97.6 22.3 8.4 1 302.6 7.8 159 0.9695 2.2284 1 99 0.2815 3.5955 0.669 0.2692 1
212_RP11-89M16 -0.3129 1 1 14 2335 527 2355 547 57734 66.8 14.6 14.4 1 285.3 2.8 2335 527 2355 547 69987 124 31.6 10.6 1 302.8 7.8 164 1 0.805 1 99 0.2815 3.5955 0.669 0.2692 1
208_RP11-92A09 -0.4626 1 1 15 2336 547 2356 567 34978 26.3 8.1 5.5 1 286 3 2336 547 2356 567 40212 54.2 16.8 4.7 1 304.8 7.5 112 0.6829 0.7257 0.7 99 0.2815 3.5955 0.669 0.2692 1
204_RP11-91J19 -0.0948 1 1 16 2336 567 2356 587 41736 67.1 21.2 13.6 1 286.6 3.3 2336 567 2356 587 48612 107.1 31.1 9.3 1 304.8 7.6 118 0.7195 0.9364 1 99 0.2815 3.5955 0.669 0.2692 1
200_RP11-91I20 -0.3969 1 1 17 2336 587 2356 607 34935 34 10.1 6.2 1 286.5 4 2336 587 2356 607 40546 66.9 18.8 5.6 1 305.1 8.2 109 0.6646 0.7595 1 99 0.2815 3.5955 0.669 0.2692 1
196_RP11-88J18 1.4367 1 1 18 2336 607 2356 627 41950 109.3 45.5 20.4 1 286.5 3.9 2336 607 2356 627 38627 60.3 23.1 5.1 1 304.1 7.9 106 0.6463 2.707 1 99 0.2815 3.5955 0.669 0.2692 1
312_RP11-105A04 -0.4262 1 1 19 2336 627 2356 647 38414 29.7 11.5 5.5 1 287.8 4 2336 627 2356 647 44046 59.6 21.4 5.1 1 304.4 7.8 121 0.7378 0.7442 0.8 99 0.2815 3.5955 0.669 0.2692 1
308_RP11-100J23 -1.1443 1 1 20 2336 647 2356 667 35643 28.4 9.4 5.6 1 287 3.5 2336 647 2356 667 45104 93.8 35.2 7.9 1 305.3 8.2 113 0.689 0.4524 1 99 0.2815 3.5955 0.669 0.2692 1

Total number of rows: 5760

Table truncated, full table size 993 Kbytes.




Supplementary file Size Download File type/resource
GSM150000.txt.gz 279.8 Kb (ftp)(http) TXT

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