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Sample GSM149966 Query DataSets for GSM149966
Status Public on May 07, 2007
Title NHGRI_SKBR3_HB7-22
Sample type RNA
 
Channel 1
Source name HMEC
Organism Homo sapiens
Characteristics Human Mammary Epithelial cells
Extracted molecule total RNA
Extraction protocol RNA was extracted with Trizol/Chloroform method according to manifecturer protocol and the RNA is further purified by the Qiagen RNAeazy columns
Label Cy3
Label protocol 15-25 microgram of total RNA was reverse transcribed with Anchor Oligo-dT and Fluoro dUTP (Cy3/Cy5), after NaOH RNA hydrolysis, the labeled cDNA is purified with Qiagen, QIAQuick PCR Purification Kit (Cat. # 28104)
 
Channel 2
Source name SKBR3
Organism Homo sapiens
Characteristics Human Breast cell line
Extracted molecule total RNA
Extraction protocol RNA was extracted with Trizol/Chloroform method according to manifecturer protocol and the RNA is further purified by the Qiagen RNAeazy columns
Label Cy5
Label protocol 15-25 microgram of total RNA was reverse transcribed with Anchor Oligo-dT and Fluoro dUTP (Cy3/Cy5), after NaOH RNA hydrolysis, the labeled cDNA is purified with Qiagen, QIAQuick PCR Purification Kit (Cat. # 28104)
 
 
Hybridization protocol The combined Cy3 and Cy5 labeled cDNAs in 30 ul DEPC H20 are denatured for 2 minutes. 15 ul 20X SSC, 5 ul 100% Formamide, 0.5 ul 10% SDS, and 4 ul DEPC H20 are added and the mixture hybridized on the array slide under a coverslip at 65 degre for 16 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 GPL4611
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
HEEBO-001-CTRL1A24 1 1 1 280 186 293 199 4491 22.7 6.7 3.6 0.1024 298.1 4.1 280 186 293 199 4619 6.3 36.2 0.2 0.1024 323.6 20.9 14 0.1867 4.3441 0.0 99.0 0.4420 2.2625 0.8300 0.1981 1
HEEBO-001-CTRL1A12 1 1 2 280 200 293 213 1 1.0 0.0 0.1 0.0000 300.5 5.0 280 200 293 213 1 1.0 0.0 0.0 0.0000 322.7 19.1 0 0.0000 1.2049 0.0 99.0 0.4420 2.2625 0.8300 0.1981 1
HEEBO-001-CTRL1E24 0.2404 1 1 3 280 213 293 226 430439 5437.4 3560.2 728.2 1.0000 301.8 5.7 280 213 293 226 440352 5546.1 4224.6 203.6 1.0000 325.2 19.6 75 1.0000 1.1813 1.0 99.0 0.4420 2.2625 0.8300 0.1981 1
HEEBO-001-CTRL1E12 1.3316 1 1 4 280 227 293 240 272765 3437.7 2238.6 537.2 1.0000 298.8 4.1 280 227 293 240 144065 1645.7 1018.5 56.9 1.0000 327.7 21.9 73 0.9733 2.5168 1.0 99.0 0.4420 2.2625 0.8300 0.1981 1
HEEBO-001-CTRL1I24 0.1496 1 1 5 280 240 293 253 62624 559.7 311.3 84.9 1.0000 298.2 4.4 280 240 293 253 68478 607.9 326.9 22.0 1.0000 330.1 20.2 73 0.9733 1.1093 1.0 99.0 0.4420 2.2625 0.8300 0.1981 1
HEEBO-001-CTRL1I12 -1.2079 1 1 6 280 254 293 267 382845 4804.6 3608.8 672.6 1.0000 300.0 5.2 280 254 293 267 1028773 13373.3 9516.5 396.0 1.0000 343.6 28.0 75 1.0000 0.4329 1.0 99.0 0.4420 2.2625 0.8300 0.1981 1
HEEBO-001-CTRL1M24 1.2395 1 1 7 280 267 293 280 306090 3780.7 2224.3 495.1 1.0000 300.5 5.9 280 267 293 280 170693 1929.3 1205.7 51.4 1.0000 346.6 32.4 75 1.0000 2.3611 1.0 99.0 0.4420 2.2625 0.8300 0.1981 1
HEEBO-001-CTRL1M12 0.2804 1 1 8 280 281 293 294 2830914 37445.3 27190.5 4856.4 1.0000 300.3 6.0 280 281 293 294 2811259 37148.0 27522.2 1087.0 1.0000 335.5 28.4 75 1.0000 1.2145 1.0 99.0 0.4420 2.2625 0.8300 0.1981 1
HEEBO-002-CTRL2A24 -1.0640 1 1 9 280 294 293 307 301522 3722.7 3345.5 535.0 1.0000 297.6 5.0 280 294 293 307 727757 9378.3 9547.1 340.5 0.4100 325.1 20.0 75 1.0000 0.4783 1.0 99.0 0.4420 2.2625 0.8300 0.1981 1
HEEBO-002-CTRL2A12 0.2129 1 1 10 280 308 293 321 421537 5475.3 4758.2 781.1 1.0000 299.2 5.0 280 308 293 321 439227 5691.9 5102.3 207.4 1.0000 325.0 19.9 73 0.9733 1.1590 1.0 99.0 0.4420 2.2625 0.8300 0.1981 1
HEEBO-002-CTRL2E24 0.3437 1 1 11 280 321 293 334 2182944 28806.7 26159.9 4141.1 0.9594 299.2 5.0 280 321 293 334 2075313 27350.1 27348.7 1095.7 0.5003 320.7 16.3 75 1.0000 1.2690 1.0 99.0 0.4420 2.2625 0.8300 0.1981 1
HEEBO-002-CTRL2E12 0.0830 1 1 12 280 335 293 348 84822 830.9 480.7 112.0 1.0000 300.1 5.6 280 335 293 348 95315 945.2 498.9 33.2 1.0000 325.7 21.3 75 1.0000 1.0592 1.0 99.0 0.4420 2.2625 0.8300 0.1981 1
HEEBO-002-CTRL2I24 0.1185 1 1 13 280 348 293 361 129466 1572.5 1173.0 173.4 1.0000 303.8 7.6 280 348 293 361 142893 1745.3 1359.8 59.1 1.0000 325.7 22.6 69 0.9200 1.0856 1.0 99.0 0.4420 2.2625 0.8300 0.1981 1
HEEBO-002-CTRL2I12 -0.1953 1 1 14 280 362 293 375 147873 1779.7 1470.7 198.6 1.0000 303.0 7.5 280 362 293 375 197121 2455.2 2021.8 87.8 1.0000 321.2 20.6 71 0.9467 0.8734 1.0 99.0 0.4420 2.2625 0.8300 0.1981 1
HEEBO-002-CTRL2M24 -0.7844 1 1 15 280 375 293 388 56274 511.5 314.9 56.7 1.0000 304.1 7.6 280 375 293 388 95566 1061.4 672.5 38.7 1.0000 323.6 19.8 69 0.9200 0.5806 1.0 99.0 0.4420 2.2625 0.8300 0.1981 1
HEEBO-002-CTRL2M12 0.3016 1 1 16 280 389 293 402 370141 4637.0 2988.3 666.7 1.0000 298.2 5.0 280 389 293 402 365023 4533.2 2980.1 142.7 1.0000 333.8 25.5 75 1.0000 1.2325 1.0 99.0 0.4420 2.2625 0.8300 0.1981 1
HEEBO-003-CTRL3A24 -0.6067 1 1 17 280 403 293 416 60311 616.6 398.2 87.4 1.0000 297.2 5.1 280 403 293 416 95893 1131.3 655.6 38.8 1.0000 321.6 22.2 66 0.8800 0.6567 1.0 99.0 0.4420 2.2625 0.8300 0.1981 1
HEEBO-003-CTRL3A12 -1.7452 1 1 18 280 416 293 429 34477 226.8 170.6 34.6 1.0000 295.6 4.4 280 416 293 429 81610 916.0 761.6 31.3 1.0000 320.5 22.4 66 0.8800 0.2983 1.0 99.0 0.4420 2.2625 0.8300 0.1981 1
HEEBO-003-CTRL3E24 0.0938 1 1 19 280 430 293 443 29852 184.9 112.8 29.0 1.0000 296.5 4.1 280 430 293 443 33107 208.8 119.3 7.1 1.0000 325.2 22.6 62 0.8267 1.0672 1.0 99.0 0.4420 2.2625 0.8300 0.1981 1
HEEBO-003-CTRL3E12 -0.2152 1 1 20 280 443 293 456 38214 280.3 175.0 38.8 1.0000 298.7 5.3 280 443 293 456 47353 392.1 247.3 13.3 1.0000 325.3 22.7 66 0.8800 0.8614 1.0 99.0 0.4420 2.2625 0.8300 0.1981 1

Total number of rows: 49152

Table truncated, full table size 10105 Kbytes.




Supplementary file Size Download File type/resource
GSM149966.txt.gz 3.9 Mb (ftp)(http) TXT

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