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Sample GSM149971 Query DataSets for GSM149971
Status Public on May 07, 2007
Title NHGRI_MDA436_DyeSwap_HB7-27
Sample type RNA
 
Channel 1
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)
 
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 1 296 191 309 204 1 1.0 0.0 0.1 0.0000 282.3 12.7 296 191 309 204 1 1.0 0.0 0.2 0.0000 293.5 4.6 0 0.0000 0.3050 0.0 99.0 0.4305 2.3230 3.2782 0.2031 1
HEEBO-001-CTRL1A12 1 1 2 296 205 309 218 8176 36.7 47.6 2.0 1.0000 290.3 16.1 296 205 309 218 8110 30.1 20.7 5.4 1.0000 294.3 4.3 25 0.3049 0.3720 0.2 99.0 0.4305 2.3230 3.2782 0.2031 1
HEEBO-001-CTRL1E24 1.2404 1 1 3 296 218 309 231 1534174 18879.9 14458.9 965.5 1.0000 297.2 17.1 296 218 309 231 218786 2437.6 1662.3 362.3 1.0000 297.2 5.7 80 0.9756 2.3627 1.0 99.0 0.4305 2.3230 3.2782 0.2031 1
HEEBO-001-CTRL1E12 1.3662 1 1 4 296 232 309 245 569824 6816.8 3722.1 315.7 1.0000 306.0 19.4 296 232 309 245 89033 806.7 420.0 82.2 1.0000 306.3 9.2 80 0.9756 2.5779 1.0 99.0 0.4305 2.3230 3.2782 0.2031 1
HEEBO-001-CTRL1I24 -0.3162 1 1 5 296 246 309 259 88146 774.7 291.4 42.7 1.0000 300.3 15.4 296 246 309 259 48904 294.2 109.0 37.5 1.0000 302.2 7.0 82 1.0000 0.8032 1.0 99.0 0.4305 2.3230 3.2782 0.2031 1
HEEBO-001-CTRL1I12 -3.6565 1 1 6 296 259 309 272 169409 1765.2 985.0 91.8 1.0000 300.8 16.7 296 259 309 272 581588 6790.3 3566.7 877.1 1.0000 302.3 6.9 82 1.0000 0.0793 1.0 99.0 0.4305 2.3230 3.2782 0.2031 1
HEEBO-001-CTRL1M24 1.1134 1 1 7 296 273 309 286 526881 6132.2 4177.5 348.0 1.0000 293.2 14.8 296 273 309 286 95554 864.6 439.2 109.5 1.0000 300.7 7.1 82 1.0000 2.1636 1.0 99.0 0.4305 2.3230 3.2782 0.2031 1
HEEBO-001-CTRL1M12 -0.9529 1 1 8 296 286 309 299 3439011 41644.2 23230.4 2082.0 1.0000 295.0 17.6 296 286 309 299 2040953 24589.1 16504.9 2908.4 1.0000 300.6 7.7 82 1.0000 0.5166 1.0 99.0 0.4305 2.3230 3.2782 0.2031 1
HEEBO-002-CTRL2A24 -3.4297 1 1 9 296 300 309 313 136295 1366.9 965.1 70.5 1.0000 295.3 16.9 296 300 309 313 393163 4494.7 3699.6 580.2 1.0000 300.0 6.9 82 1.0000 0.0928 1.0 99.0 0.4305 2.3230 3.2782 0.2031 1
HEEBO-002-CTRL2A12 1.2455 1 1 10 296 313 309 326 1614863 19397.5 17069.7 955.6 1.0000 295.9 17.9 296 313 309 326 229023 2495.6 1983.5 371.8 1.0000 297.4 5.7 82 1.0000 2.3710 1.0 99.0 0.4305 2.3230 3.2782 0.2031 1
HEEBO-002-CTRL2E24 -0.9582 1 1 11 296 327 309 340 2387256 28820.1 26957.2 1292.1 0.8232 292.8 20.1 296 327 309 340 1424913 17082.1 15252.5 3046.2 1.0000 294.9 4.4 82 1.0000 0.5147 1.0 99.0 0.4305 2.3230 3.2782 0.2031 1
HEEBO-002-CTRL2E12 -0.0900 1 1 12 296 341 309 354 145051 1472.3 703.3 65.6 1.0000 296.6 20.3 296 341 309 354 63087 478.1 198.3 102.6 1.0000 291.3 3.0 82 1.0000 0.9395 1.0 99.0 0.4305 2.3230 3.2782 0.2031 1
HEEBO-002-CTRL2I24 -0.4767 1 1 13 296 354 309 367 190623 2034.8 1655.6 117.7 1.0000 289.8 14.4 296 354 309 367 94872 863.7 671.9 159.3 1.0000 293.2 4.1 82 1.0000 0.7186 1.0 99.0 0.4305 2.3230 3.2782 0.2031 1
HEEBO-002-CTRL2I12 -0.9986 1 1 14 296 368 309 381 174202 1834.4 1517.7 108.6 1.0000 290.1 13.9 296 368 309 381 115697 1117.9 844.8 214.6 1.0000 293.0 3.8 82 1.0000 0.5005 1.0 99.0 0.4305 2.3230 3.2782 0.2031 1
HEEBO-002-CTRL2M24 -0.1971 1 1 15 296 381 309 394 150309 1549.7 1235.8 105.4 1.0000 283.3 11.2 296 381 309 394 68390 541.9 357.3 101.5 1.0000 292.1 4.0 82 1.0000 0.8723 1.0 99.0 0.4305 2.3230 3.2782 0.2031 1
HEEBO-002-CTRL2M12 0.2964 1 1 16 296 395 309 408 547120 6390.7 4542.4 464.2 1.0000 281.5 9.9 296 395 309 408 154320 1587.4 1038.2 256.9 1.0000 294.5 5.1 82 1.0000 1.2281 1.0 99.0 0.4305 2.3230 3.2782 0.2031 1
HEEBO-003-CTRL3A24 0.2036 1 1 17 296 409 309 422 150526 1644.7 1219.8 109.6 1.0000 285.1 11.6 296 409 309 422 57019 435.7 288.7 70.8 1.0000 295.3 5.0 78 0.9512 1.1516 1.0 99.0 0.4305 2.3230 3.2782 0.2031 1
HEEBO-003-CTRL3A12 -0.6500 1 1 18 296 422 309 435 95790 957.6 784.2 59.6 1.0000 286.4 12.9 296 422 309 435 58111 458.3 347.0 74.2 1.0000 296.3 5.1 77 0.9390 0.6373 1.0 99.0 0.4305 2.3230 3.2782 0.2031 1
HEEBO-003-CTRL3E24 -0.2593 1 1 19 296 436 309 449 41633 257.4 129.5 18.0 1.0000 283.3 10.6 296 436 309 449 29499 94.0 47.4 19.7 1.0000 289.1 3.2 77 0.9390 0.8355 1.0 99.0 0.4305 2.3230 3.2782 0.2031 1
HEEBO-003-CTRL3E12 -0.4456 1 1 20 296 449 309 462 59735 448.0 265.2 32.7 1.0000 280.5 9.8 296 449 309 462 38966 186.1 100.7 37.8 1.0000 289.1 3.4 82 1.0000 0.7343 1.0 99.0 0.4305 2.3230 3.2782 0.2031 1

Total number of rows: 49152

Table truncated, full table size 10072 Kbytes.




Supplementary file Size Download File type/resource
GSM149971.txt.gz 3.9 Mb (ftp)(http) TXT

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