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Sample GSM149973 Query DataSets for GSM149973
Status Public on May 07, 2007
Title NHGRI_SKBR3_DyeSwap_HB7-29
Sample type RNA
 
Channel 1
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)
 
Channel 2
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)
 
 
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 1 286 197 299 210 3258 34.7 16.0 2.0 0.0000 291.1 14.9 286 197 299 210 3313 31.9 8.8 4.4 0.0000 299.4 6.3 10 0.1163 0.3688 0.0 99.0 0.4482 2.2314 2.9435 0.1955 1
HEEBO-001-CTRL1A12 1 1 2 286 211 299 224 4582 121.9 56.2 6.2 0.0040 294.6 17.4 286 211 299 224 3668 34.7 15.4 4.9 0.0040 298.8 6.0 11 0.1279 1.1953 0.0 99.0 0.4482 2.2314 2.9435 0.1955 1
HEEBO-001-CTRL1E24 0.0259 1 1 3 286 224 299 237 620767 7185.5 5045.1 360.8 1.0000 293.7 17.5 286 224 299 237 223577 2397.7 1393.8 391.9 1.0000 296.0 4.9 83 0.9651 1.0181 1.0 99.0 0.4482 2.2314 2.9435 0.1955 1
HEEBO-001-CTRL1E12 0.7344 1 1 4 286 238 299 251 408715 4633.5 3237.5 276.3 1.0000 290.8 13.8 286 238 299 251 102984 946.2 520.3 158.1 1.0000 294.6 4.7 83 0.9651 1.6637 1.0 99.0 0.4482 2.2314 2.9435 0.1955 1
HEEBO-001-CTRL1I24 -0.3454 1 1 5 286 251 299 264 107658 1007.1 435.1 61.1 1.0000 290.0 13.5 286 251 299 264 60562 434.7 138.8 70.1 1.0000 295.0 5.0 83 0.9651 0.7871 1.0 99.0 0.4482 2.2314 2.9435 0.1955 1
HEEBO-001-CTRL1I12 -1.3670 1 1 6 286 265 299 278 568466 6565.0 4504.9 464.6 1.0000 284.0 10.5 286 265 299 278 501748 5752.7 3649.5 1041.2 1.0000 292.4 4.1 83 0.9651 0.3877 1.0 99.0 0.4482 2.2314 2.9435 0.1955 1
HEEBO-001-CTRL1M24 1.0725 1 1 7 286 278 299 291 480884 5502.8 3431.9 264.1 1.0000 291.0 18.6 286 278 299 291 98142 888.9 478.0 149.0 1.0000 293.5 4.7 83 0.9651 2.1031 1.0 99.0 0.4482 2.2314 2.9435 0.1955 1
HEEBO-001-CTRL1M12 -0.8342 1 1 8 286 292 299 305 3509217 41977.7 24132.7 1572.1 1.0000 302.0 25.0 286 292 299 305 2135728 25427.8 17444.2 2701.6 1.0000 303.8 8.6 83 0.9651 0.5609 1.0 99.0 0.4482 2.2314 2.9435 0.1955 1
HEEBO-002-CTRL2A24 -1.3737 1 1 9 286 305 299 318 448047 5094.5 4299.7 192.1 1.0000 303.6 24.8 286 305 299 318 397299 4484.9 3657.9 537.9 1.0000 301.8 7.5 83 0.9651 0.3859 1.0 99.0 0.4482 2.2314 2.9435 0.1955 1
HEEBO-002-CTRL2A12 -0.0165 1 1 10 286 319 299 332 696120 8085.1 7095.0 405.5 1.0000 301.9 17.5 286 319 299 332 255760 2778.6 2231.6 319.9 1.0000 302.9 7.9 83 0.9651 0.9886 1.0 99.0 0.4482 2.2314 2.9435 0.1955 1
HEEBO-002-CTRL2E24 -0.7981 1 1 11 286 332 299 345 2585094 30830.1 25644.9 1221.0 1.0000 315.6 23.4 286 332 299 345 1536728 18212.5 15822.5 2185.2 1.0000 302.3 7.5 83 0.9651 0.5751 1.0 99.0 0.4482 2.2314 2.9435 0.1955 1
HEEBO-002-CTRL2E12 -0.2971 1 1 12 286 346 299 359 155438 1577.1 708.3 93.7 1.0000 295.7 13.9 286 346 299 359 79594 658.3 207.2 81.3 1.0000 300.7 7.2 83 0.9651 0.8139 1.0 99.0 0.4482 2.2314 2.9435 0.1955 1
HEEBO-002-CTRL2I24 -0.2595 1 1 13 286 359 299 372 223740 2411.7 1774.0 164.9 1.0000 283.9 11.1 286 359 299 372 105886 980.7 578.2 163.1 1.0000 295.0 4.7 83 0.9651 0.8354 1.0 99.0 0.4482 2.2314 2.9435 0.1955 1
HEEBO-002-CTRL2I12 -0.2702 1 1 14 286 373 299 386 379733 4123.9 3190.8 233.2 1.0000 291.6 14.9 286 373 299 386 170645 1689.5 1175.3 257.2 1.0000 294.7 5.4 86 1.0000 0.8292 1.0 99.0 0.4482 2.2314 2.9435 0.1955 1
HEEBO-002-CTRL2M24 -0.9271 1 1 15 286 386 299 399 101833 932.9 629.2 52.5 1.0000 294.0 15.0 286 386 299 399 74933 602.6 397.2 79.5 1.0000 300.2 6.6 83 0.9651 0.5259 1.0 99.0 0.4482 2.2314 2.9435 0.1955 1
HEEBO-002-CTRL2M12 0.3390 1 1 16 286 400 299 413 590509 6822.1 5320.2 385.2 1.0000 292.5 15.0 286 400 299 413 176798 1832.2 1215.4 274.2 1.0000 297.8 5.6 83 0.9651 1.2649 1.0 99.0 0.4482 2.2314 2.9435 0.1955 1
HEEBO-003-CTRL3A24 -0.5181 1 1 17 286 414 299 427 123230 1194.0 800.4 70.0 1.0000 290.7 14.2 286 414 299 427 73024 580.9 401.1 83.3 1.0000 298.9 5.9 83 0.9651 0.6983 1.0 99.0 0.4482 2.2314 2.9435 0.1955 1
HEEBO-003-CTRL3A12 -1.3061 1 1 18 286 427 299 440 93139 884.4 683.6 47.3 1.0000 294.6 16.1 286 427 299 440 82540 743.0 576.8 78.9 1.0000 301.8 8.7 79 0.9186 0.4044 1.0 99.0 0.4482 2.2314 2.9435 0.1955 1
HEEBO-003-CTRL3E24 -0.3861 1 1 19 286 441 299 454 48950 327.2 177.2 22.1 1.0000 284.7 11.4 286 441 299 454 35521 145.3 71.9 18.5 1.0000 298.7 6.9 80 0.9302 0.7652 1.0 99.0 0.4482 2.2314 2.9435 0.1955 1
HEEBO-003-CTRL3E12 -0.5074 1 1 20 286 454 299 467 69697 555.3 280.6 39.0 1.0000 284.4 10.6 286 454 299 467 46748 268.2 134.1 43.2 1.0000 295.0 5.0 83 0.9651 0.7035 1.0 99.0 0.4482 2.2314 2.9435 0.1955 1

Total number of rows: 49152

Table truncated, full table size 10097 Kbytes.




Supplementary file Size Download File type/resource
GSM149973.txt.gz 3.9 Mb (ftp)(http) TXT

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