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Sample GSM149968 Query DataSets for GSM149968
Status Public on May 07, 2007
Title NHGRI_BT474_DyeSwap_HB7-24
Sample type RNA
 
Channel 1
Source name BT474
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 1 282 209 295 222 1 1.0 0.0 0.1 0.0000 291.2 10.7 282 209 295 222 1 1.0 0.0 0.1 0.0000 298.3 5.7 0 0.0000 0.2828 0.0 99.0 0.4039 2.4760 3.5364 0.2146 1
HEEBO-001-CTRL1A12 1 1 2 282 223 295 236 1 1.0 0.0 0.1 0.0000 293.1 10.8 282 223 295 236 1 1.0 0.0 0.2 0.0000 297.6 5.2 0 0.0000 0.2828 0.0 99.0 0.4039 2.4760 3.5364 0.2146 1
HEEBO-001-CTRL1E24 -1.3944 1 1 3 282 236 295 249 381195 4713.6 3130.5 247.9 1.0000 302.1 14.9 282 236 295 249 288846 3503.5 2124.7 579.3 1.0000 297.1 4.5 76 0.9157 0.3804 1.0 99.0 0.4039 2.4760 3.5364 0.2146 1
HEEBO-001-CTRL1E12 1.6087 1 1 4 282 250 295 263 960125 12336.6 9095.9 707.3 1.0000 296.6 12.8 282 250 295 263 109327 1143.8 649.7 216.3 1.0000 294.7 3.4 76 0.9157 3.0498 1.0 99.0 0.4039 2.4760 3.5364 0.2146 1
HEEBO-001-CTRL1I24 -0.1733 1 1 5 282 263 295 276 115253 1240.6 655.7 71.1 1.0000 296.1 12.8 282 263 295 276 52040 395.6 167.2 60.7 1.0000 298.3 5.1 75 0.9036 0.8868 1.0 99.0 0.4039 2.4760 3.5364 0.2146 1
HEEBO-001-CTRL1I12 -0.3836 1 1 6 282 277 295 290 1759985 22855.5 15283.6 1253.2 1.0000 302.2 13.9 282 277 295 290 663591 8431.6 5554.2 1181.9 1.0000 299.8 5.9 76 0.9157 0.7665 1.0 99.0 0.4039 2.4760 3.5364 0.2146 1
HEEBO-001-CTRL1M24 1.7111 1 1 7 282 291 295 304 964374 11753.6 8536.2 606.2 1.0000 301.0 15.3 282 291 295 304 105250 1015.1 655.3 121.3 1.0000 300.5 7.3 80 0.9639 3.2741 1.0 99.0 0.4039 2.4760 3.5364 0.2146 1
HEEBO-001-CTRL1M12 -1.4856 1 1 8 282 304 295 317 2942712 35149.1 27550.4 1524.5 1.0000 305.2 19.8 282 304 295 317 2334828 27829.4 20977.0 3380.9 1.0000 301.1 7.2 83 1.0000 0.3571 1.0 99.0 0.4039 2.4760 3.5364 0.2146 1
HEEBO-002-CTRL2A24 -0.5305 1 1 9 282 318 295 331 1177588 13879.3 15445.3 609.7 0.0000 308.5 19.4 282 318 295 331 495360 5669.1 5484.2 812.4 0.6631 299.1 5.7 83 1.0000 0.6923 1.0 99.0 0.4039 2.4760 3.5364 0.2146 1
HEEBO-002-CTRL2A12 -1.4434 1 1 10 282 331 295 344 321947 4053.8 3455.7 212.8 1.0000 296.8 14.9 282 331 295 344 252879 3117.6 2677.7 441.3 1.0000 299.7 5.8 74 0.8916 0.3677 1.0 99.0 0.4039 2.4760 3.5364 0.2146 1
HEEBO-002-CTRL2E24 -1.2243 1 1 11 282 345 295 358 2373407 29747.4 27007.0 1529.6 0.9606 295.7 15.4 282 345 295 358 1576187 19652.8 18291.1 2830.1 0.8464 298.9 5.6 79 0.9518 0.4280 1.0 99.0 0.4039 2.4760 3.5364 0.2146 1
HEEBO-002-CTRL2E12 -0.2243 1 1 12 282 358 295 371 157548 1777.1 859.5 98.2 1.0000 295.9 13.7 282 358 295 371 67254 587.0 269.9 84.5 1.0000 297.9 5.6 76 0.9157 0.8560 1.0 99.0 0.4039 2.4760 3.5364 0.2146 1
HEEBO-002-CTRL2I24 -0.0508 1 1 13 282 372 295 385 272497 3292.1 2648.3 189.5 1.0000 293.3 12.7 282 372 295 385 95703 964.3 723.0 162.8 1.0000 295.0 4.3 76 0.9157 0.9654 1.0 99.0 0.4039 2.4760 3.5364 0.2146 1
HEEBO-002-CTRL2I12 0.2715 1 1 14 282 385 295 398 482385 6053.3 5214.1 345.2 1.0000 293.9 12.9 282 385 295 398 130180 1418.0 1068.0 236.0 1.0000 294.9 4.4 76 0.9157 1.2071 1.0 99.0 0.4039 2.4760 3.5364 0.2146 1
HEEBO-002-CTRL2M24 -1.1584 1 1 15 282 399 295 412 91343 910.6 527.2 54.7 1.0000 291.3 11.7 282 399 295 412 65941 574.8 337.8 112.0 1.0000 292.8 3.1 76 0.9157 0.4480 1.0 99.0 0.4039 2.4760 3.5364 0.2146 1
HEEBO-002-CTRL2M12 -0.1498 1 1 16 282 412 295 425 588328 7547.9 5127.5 406.7 1.0000 296.5 14.3 282 412 295 425 199889 2367.7 1394.4 314.3 1.0000 297.5 6.3 75 0.9036 0.9014 1.0 99.0 0.4039 2.4760 3.5364 0.2146 1
HEEBO-003-CTRL3A24 -0.5335 1 1 17 282 426 295 439 129084 1452.0 994.2 82.1 1.0000 292.4 13.1 282 426 295 439 65921 594.3 386.0 84.9 1.0000 296.5 5.7 74 0.8916 0.6909 1.0 99.0 0.4039 2.4760 3.5364 0.2146 1
HEEBO-003-CTRL3A12 -1.3789 1 1 18 282 440 295 453 79961 853.6 715.6 49.8 1.0000 288.7 12.4 282 440 295 453 64559 627.8 473.0 98.2 1.0000 294.5 4.9 70 0.8434 0.3845 1.0 99.0 0.4039 2.4760 3.5364 0.2146 1
HEEBO-003-CTRL3E24 -0.5127 1 1 19 282 453 295 466 46305 373.7 306.7 22.0 1.0000 287.8 12.1 282 453 295 466 30961 150.8 84.9 26.7 1.0000 291.5 3.9 70 0.8434 0.7009 1.0 99.0 0.4039 2.4760 3.5364 0.2146 1
HEEBO-003-CTRL3E12 -0.2226 1 1 20 282 467 295 480 74997 714.1 509.5 43.2 1.0000 285.9 11.5 282 467 295 480 39532 235.6 149.0 41.7 1.0000 291.5 3.9 75 0.9036 0.8570 1.0 99.0 0.4039 2.4760 3.5364 0.2146 1

Total number of rows: 49152

Table truncated, full table size 10141 Kbytes.




Supplementary file Size Download File type/resource
GSM149968.txt.gz 3.9 Mb (ftp)(http) TXT

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