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Sample GSM149970 Query DataSets for GSM149970
Status Public on May 07, 2007
Title NHGRI_MCF10A_DyeSwap_HB7-27
Sample type RNA
 
Channel 1
Source name MCF10A
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 1 291 191 304 204 1 1.0 0.0 0.1 0.0000 273.3 9.0 291 191 304 204 1 1.0 0.0 0.2 0.0000 292.8 3.4 0 0.0000 0.5588 0.0 99.0 0.5599 1.7859 1.7897 0.1491 1
HEEBO-001-CTRL1A12 1 1 2 291 205 304 218 1 1.0 0.0 0.1 0.0000 273.9 10.4 291 205 304 218 1 1.0 0.0 0.2 0.0000 293.1 3.4 0 0.0000 0.5588 0.0 99.0 0.5599 1.7859 1.7897 0.1491 1
HEEBO-001-CTRL1E24 0.6160 1 1 3 291 218 304 231 655802 7433.8 6165.1 472.9 1.0000 281.5 12.8 291 218 304 231 255414 2710.2 1942.6 495.9 1.0000 294.6 4.0 85 0.9659 1.5326 1.0 99.0 0.5599 1.7859 1.7897 0.1491 1
HEEBO-001-CTRL1E12 -0.1562 1 1 4 291 232 304 245 151024 1500.6 971.2 121.0 1.0000 276.1 8.3 291 232 304 245 104478 934.3 542.5 165.6 1.0000 294.8 4.2 85 0.9659 0.8974 1.0 99.0 0.5599 1.7859 1.7897 0.1491 1
HEEBO-001-CTRL1I24 -0.2564 1 1 5 291 245 304 258 74487 598.3 294.6 46.5 1.0000 278.0 9.0 291 245 304 258 59089 399.3 174.4 66.0 1.0000 295.8 4.8 85 0.9659 0.8372 1.0 99.0 0.5599 1.7859 1.7897 0.1491 1
HEEBO-001-CTRL1I12 -0.7926 1 1 6 291 259 304 272 735140 8368.1 5926.9 586.6 1.0000 280.6 10.9 291 259 304 272 713686 8099.0 4946.9 1135.9 1.0000 297.3 6.1 85 0.9659 0.5773 1.0 99.0 0.5599 1.7859 1.7897 0.1491 1
HEEBO-001-CTRL1M24 -0.1981 1 1 7 291 272 304 285 164748 1659.3 1012.5 115.6 1.0000 278.9 11.0 291 272 304 285 115638 1063.7 597.4 155.5 1.0000 296.8 5.7 85 0.9659 0.8717 1.0 99.0 0.5599 1.7859 1.7897 0.1491 1
HEEBO-001-CTRL1M12 -0.5984 1 1 8 291 286 304 299 3102006 36218.2 26313.5 2504.9 1.0000 276.0 11.2 291 286 304 299 2629428 30638.2 22269.2 5476.9 1.0000 296.2 4.2 85 0.9659 0.6605 1.0 99.0 0.5599 1.7859 1.7897 0.1491 1
HEEBO-002-CTRL2A24 -0.7757 1 1 9 291 299 304 312 532598 5982.2 5532.4 349.9 0.8759 283.7 14.4 291 299 304 312 511605 5722.4 4807.0 912.8 1.0000 296.5 5.0 85 0.9659 0.5841 1.0 99.0 0.5599 1.7859 1.7897 0.1491 1
HEEBO-002-CTRL2A12 0.6113 1 1 10 291 313 304 326 682408 7743.4 6947.2 489.7 1.0000 285.0 12.9 291 313 304 326 265725 2832.3 2437.5 585.6 1.0000 293.9 3.1 85 0.9659 1.5276 1.0 99.0 0.5599 1.7859 1.7897 0.1491 1
HEEBO-002-CTRL2E24 -0.6634 1 1 11 291 326 304 339 2138085 24883.1 23785.6 2097.7 0.7205 270.8 7.5 291 326 304 339 1896667 22019.3 19484.2 4167.0 1.0000 294.5 3.7 85 0.9659 0.6314 1.0 99.0 0.5599 1.7859 1.7897 0.1491 1
HEEBO-002-CTRL2E12 -0.1897 1 1 12 291 340 304 353 115234 1083.6 420.2 86.1 1.0000 272.1 8.6 291 340 304 353 83706 690.6 295.5 134.0 1.0000 294.2 3.5 85 0.9659 0.8768 1.0 99.0 0.5599 1.7859 1.7897 0.1491 1
HEEBO-002-CTRL2I24 -0.4110 1 1 13 291 353 304 366 145089 1455.3 1130.3 117.4 1.0000 271.9 8.3 291 353 304 366 115689 1081.3 727.2 184.1 1.0000 296.0 4.5 84 0.9545 0.7521 1.0 99.0 0.5599 1.7859 1.7897 0.1491 1
HEEBO-002-CTRL2I12 -0.7651 1 1 14 291 367 304 380 154274 1580.9 1237.6 109.7 1.0000 277.8 11.1 291 367 304 380 149113 1501.2 1121.9 248.4 1.0000 295.3 4.7 83 0.9432 0.5884 1.0 99.0 0.5599 1.7859 1.7897 0.1491 1
HEEBO-002-CTRL2M24 0.5169 1 1 15 291 380 304 393 151835 1530.3 1242.1 108.3 1.0000 277.3 10.7 291 380 304 393 74839 597.6 398.6 108.5 1.0000 293.4 4.0 84 0.9545 1.4309 1.0 99.0 0.5599 1.7859 1.7897 0.1491 1
HEEBO-002-CTRL2M12 0.0658 1 1 16 291 394 304 407 463608 5181.0 3919.7 385.0 1.0000 273.3 9.8 291 394 304 407 260040 2765.9 1767.9 508.3 1.0000 293.4 4.0 85 0.9659 1.0467 1.0 99.0 0.5599 1.7859 1.7897 0.1491 1
HEEBO-003-CTRL3A24 -0.4272 1 1 17 291 407 304 420 83544 827.0 583.7 61.8 1.0000 272.3 9.7 291 407 304 420 69713 621.4 384.3 107.6 1.0000 295.9 4.4 76 0.8636 0.7437 1.0 99.0 0.5599 1.7859 1.7897 0.1491 1
HEEBO-003-CTRL3A12 0.4870 1 1 18 291 420 304 433 147698 1777.5 1529.7 133.0 1.0000 273.8 9.7 291 420 304 433 72151 708.7 554.8 137.5 1.0000 293.4 3.5 72 0.8182 1.4015 1.0 99.0 0.5599 1.7859 1.7897 0.1491 1
HEEBO-003-CTRL3E24 -0.0271 1 1 19 291 434 304 447 37508 217.5 170.7 16.2 1.0000 276.0 9.8 291 434 304 447 31700 123.8 74.0 23.4 1.0000 293.3 3.8 76 0.8636 0.9814 1.0 99.0 0.5599 1.7859 1.7897 0.1491 1
HEEBO-003-CTRL3E12 -0.3855 1 1 20 291 447 304 460 41810 346.7 230.9 31.0 1.0000 268.2 6.4 291 447 304 460 37245 253.1 163.3 44.6 1.0000 294.6 4.3 68 0.7727 0.7655 1.0 99.0 0.5599 1.7859 1.7897 0.1491 1

Total number of rows: 49152

Table truncated, full table size 10078 Kbytes.




Supplementary file Size Download File type/resource
GSM149970.txt.gz 3.9 Mb (ftp)(http) TXT

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