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Sample GSM149964 Query DataSets for GSM149964
Status Public on May 07, 2007
Title NHGRI_MDA436_HB7-20
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 MDA436
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 1 272 188 285 201 1 1.0 0.0 0.1 0.0000 302.0 5.0 272 188 285 201 1 1.0 0.0 0.1 0.0000 307.1 12.9 0 0.0000 1.1969 0.0 99.0 0.4930 2.0285 0.8355 0.1765 1
HEEBO-001-CTRL1A12 1 1 2 272 202 285 215 1 1.0 0.0 0.1 0.0000 300.6 4.7 272 202 285 215 1 1.0 0.0 0.0 0.0000 311.7 15.4 0 0.0000 1.1969 0.0 99.0 0.4930 2.0285 0.8355 0.1765 1
HEEBO-001-CTRL1E24 1.5215 1 1 3 272 215 285 228 1200771 12885.5 8146.5 1231.4 1.0000 309.8 8.7 272 215 285 228 517637 5372.2 3931.8 240.2 1.0000 316.1 16.7 91 1.0000 2.8709 1.0 99.0 0.4930 2.0285 0.8355 0.1765 1
HEEBO-001-CTRL1E12 1.6185 1 1 4 272 229 285 242 429510 4408.8 2346.9 416.7 1.0000 311.1 8.8 272 229 285 242 184912 1718.5 976.3 80.8 1.0000 313.5 15.2 91 1.0000 3.0706 1.0 99.0 0.4930 2.0285 0.8355 0.1765 1
HEEBO-001-CTRL1I24 0.1871 1 1 5 272 242 285 255 75859 534.7 249.2 56.3 1.0000 308.2 7.5 272 242 285 255 78818 562.1 289.3 26.3 1.0000 313.7 15.4 90 0.9890 1.1385 1.0 99.0 0.4930 2.0285 0.8355 0.1765 1
HEEBO-001-CTRL1I12 -3.1923 1 1 6 272 256 285 269 128215 1117.3 706.0 117.9 1.0000 307.3 7.5 272 256 285 269 1128247 12224.2 9090.0 632.8 1.0000 311.9 12.4 90 0.9890 0.1094 1.0 99.0 0.4930 2.0285 0.8355 0.1765 1
HEEBO-001-CTRL1M24 1.5165 1 1 7 272 270 285 283 411581 4269.7 2465.8 564.6 1.0000 303.5 4.8 272 270 285 283 188611 1786.3 1109.2 85.8 1.0000 309.4 14.6 90 0.9890 2.8609 1.0 99.0 0.4930 2.0285 0.8355 0.1765 1
HEEBO-001-CTRL1M12 0.3486 1 1 8 272 283 285 296 3468915 38236.3 25868.7 3890.6 1.0000 307.2 7.9 272 283 285 296 3263151 35942.8 26794.8 1450.1 1.0000 314.4 19.9 90 0.9890 1.2733 1.0 99.0 0.4930 2.0285 0.8355 0.1765 1
HEEBO-002-CTRL2A24 -3.1443 1 1 9 272 297 285 310 101175 926.1 702.6 91.4 1.0000 307.8 8.3 272 297 285 310 829409 9799.5 8711.2 384.2 1.0000 315.3 20.7 82 0.9011 0.1131 1.0 99.0 0.4930 2.0285 0.8355 0.1765 1
HEEBO-002-CTRL2A12 1.4078 1 1 10 272 310 285 323 1094300 11989.7 10125.6 1243.2 1.0000 305.8 7.7 272 310 285 323 508979 5408.5 4629.5 263.5 1.0000 310.3 14.2 89 0.9780 2.6533 1.0 99.0 0.4930 2.0285 0.8355 0.1765 1
HEEBO-002-CTRL2E24 0.3178 1 1 11 272 324 285 337 2599854 28584.3 26033.1 3487.5 0.9463 302.9 5.8 272 324 285 337 2498301 27449.1 26145.2 1393.6 0.7375 309.8 12.9 90 0.9890 1.2464 1.0 99.0 0.4930 2.0285 0.8355 0.1765 1
HEEBO-002-CTRL2E12 0.0761 1 1 12 272 337 285 350 100643 815.0 378.3 96.4 1.0000 303.3 6.1 272 337 285 350 111133 925.3 421.4 47.7 1.0000 309.5 12.5 90 0.9890 1.0542 1.0 99.0 0.4930 2.0285 0.8355 0.1765 1
HEEBO-002-CTRL2I24 -0.0068 1 1 13 272 351 285 364 135527 1501.3 1030.4 169.7 1.0000 305.7 6.7 272 351 285 364 158280 1805.3 1323.4 101.4 1.0000 305.1 9.8 75 0.8242 0.9953 1.0 99.0 0.4930 2.0285 0.8355 0.1765 1
HEEBO-002-CTRL2I12 -0.7452 1 1 14 272 364 285 377 131772 1284.6 979.6 144.0 1.0000 303.0 6.8 272 364 285 377 239178 2577.1 1936.1 149.0 1.0000 304.6 8.9 83 0.9121 0.5966 1.0 99.0 0.4930 2.0285 0.8355 0.1765 1
HEEBO-002-CTRL2M24 0.4012 1 1 15 272 378 285 391 132264 1200.6 772.5 139.5 1.0000 302.4 6.3 272 378 285 391 122916 1088.1 748.2 54.0 1.0000 308.6 13.6 88 0.9670 1.3206 1.0 99.0 0.4930 2.0285 0.8355 0.1765 1
HEEBO-002-CTRL2M12 0.3080 1 1 16 272 391 285 404 433627 4461.9 2430.7 573.2 1.0000 303.3 5.2 272 391 285 404 422033 4313.8 2576.3 166.6 1.0000 324.0 21.2 91 1.0000 1.2380 1.0 99.0 0.4930 2.0285 0.8355 0.1765 1
HEEBO-003-CTRL3A24 0.4321 1 1 17 272 405 285 418 128663 1231.1 692.6 164.5 1.0000 300.6 4.7 272 405 285 418 119159 1092.2 662.0 43.8 1.0000 326.4 20.0 84 0.9231 1.3492 1.0 99.0 0.4930 2.0285 0.8355 0.1765 1
HEEBO-003-CTRL3A12 -0.1168 1 1 18 272 419 285 432 76603 795.0 587.9 112.3 1.0000 299.4 4.0 272 419 285 432 94541 1031.7 775.2 43.5 1.0000 318.9 18.5 70 0.7692 0.9222 1.0 99.0 0.4930 2.0285 0.8355 0.1765 1
HEEBO-003-CTRL3E24 0.2723 1 1 19 272 432 285 445 32722 158.5 82.8 20.9 1.0000 302.4 4.9 272 432 285 445 33533 157.1 85.3 6.9 1.0000 315.2 17.4 71 0.7802 1.2077 1.0 99.0 0.4930 2.0285 0.8355 0.1765 1
HEEBO-003-CTRL3E12 -0.1097 1 1 20 272 446 285 459 45039 340.5 217.1 42.3 1.0000 302.9 5.6 272 446 285 459 52835 439.8 253.5 20.1 1.0000 315.0 16.1 70 0.7692 0.9268 1.0 99.0 0.4930 2.0285 0.8355 0.1765 1

Total number of rows: 49152

Table truncated, full table size 10138 Kbytes.




Supplementary file Size Download File type/resource
GSM149964.txt.gz 3.9 Mb (ftp)(http) TXT

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