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Sample GSM149972 Query DataSets for GSM149972
Status Public on May 07, 2007
Title NHGRI_HCC1419_DyeSwap_HB7-28
Sample type RNA
 
Channel 1
Source name HCC1419
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 1 297 181 310 194 1 1.0 0.0 0.0 0.0000 352.4 31.1 297 181 310 194 1 1.0 0.0 0.1 0.0000 306.9 7.4 0 0.0000 0.3563 0.0 99.0 0.4246 2.3555 2.8063 0.2056 1
HEEBO-001-CTRL1A12 1 1 2 297 195 310 208 12625 95.5 69.2 2.3 1.0000 372.1 36.6 297 195 310 208 10078 54.1 15.3 4.4 1.0000 319.2 11.4 27 0.3293 0.6290 0.1 99.0 0.4246 2.3555 2.8063 0.2056 1
HEEBO-001-CTRL1E24 -1.6268 1 1 3 297 208 310 221 214076 2499.7 1688.8 72.5 1.0000 354.7 28.7 297 208 310 221 229434 2751.2 1655.7 277.8 1.0000 308.0 8.7 75 0.9146 0.3238 1.0 99.0 0.4246 2.3555 2.8063 0.2056 1
HEEBO-001-CTRL1E12 0.4795 1 1 4 297 222 310 235 286804 3359.8 1820.7 86.1 1.0000 364.9 34.0 297 222 310 235 89647 858.7 392.1 92.4 1.0000 305.6 7.9 77 0.9390 1.3943 1.0 99.0 0.4246 2.3555 2.8063 0.2056 1
HEEBO-001-CTRL1I24 -0.6421 1 1 5 297 235 310 248 70200 594.5 289.9 16.8 1.0000 354.1 29.9 297 235 310 248 47384 330.6 136.0 31.0 1.0000 309.7 9.5 74 0.9024 0.6408 1.0 99.0 0.4246 2.3555 2.8063 0.2056 1
HEEBO-001-CTRL1I12 0.3080 1 1 6 297 249 310 262 1883690 24093.9 13487.0 549.3 1.0000 369.6 39.5 297 249 310 262 557878 6935.3 3583.3 714.7 1.0000 309.9 8.4 77 0.9390 1.2380 1.0 99.0 0.4246 2.3555 2.8063 0.2056 1
HEEBO-001-CTRL1M24 0.5693 1 1 7 297 262 310 275 325194 3693.1 2217.5 85.1 1.0000 371.8 39.0 297 262 310 275 94743 886.9 468.6 149.1 1.0000 297.3 3.5 80 0.9756 1.4838 1.0 99.0 0.4246 2.3555 2.8063 0.2056 1
HEEBO-001-CTRL1M12 -1.1197 1 1 8 297 276 310 289 3096629 39837.9 22964.1 977.8 1.0000 378.1 36.0 297 276 310 289 2398260 30847.1 17980.8 4672.6 1.0000 299.1 4.5 77 0.9390 0.4602 1.0 99.0 0.4246 2.3555 2.8063 0.2056 1
HEEBO-002-CTRL2A24 0.2053 1 1 9 297 289 310 302 1240787 16195.1 15225.9 469.2 0.7992 348.7 28.7 297 289 310 302 398384 5005.5 4149.3 576.7 1.0000 306.3 7.2 75 0.9146 1.1529 1.0 99.0 0.4246 2.3555 2.8063 0.2056 1
HEEBO-002-CTRL2A12 -1.5696 1 1 10 297 303 310 316 238479 2865.4 2157.1 78.3 1.0000 357.3 31.2 297 303 310 316 247181 3030.4 2169.9 274.3 1.0000 309.9 9.9 74 0.9024 0.3369 1.0 99.0 0.4246 2.3555 2.8063 0.2056 1
HEEBO-002-CTRL2E24 -1.2099 1 1 11 297 316 310 329 2052199 25288.5 23507.4 634.6 0.8522 364.0 34.9 297 316 310 329 1692396 20844.2 18514.0 1767.8 1.0000 310.8 10.8 80 0.9756 0.4323 1.0 99.0 0.4246 2.3555 2.8063 0.2056 1
HEEBO-002-CTRL2E12 -0.8316 1 1 12 297 330 310 343 98841 939.0 351.6 28.5 1.0000 344.6 26.8 297 330 310 343 69560 595.5 231.6 62.1 1.0000 307.9 8.3 77 0.9390 0.5619 1.0 99.0 0.4246 2.3555 2.8063 0.2056 1
HEEBO-002-CTRL2I24 -0.8052 1 1 13 297 343 310 356 150296 1617.0 1069.8 54.3 1.0000 334.9 22.8 297 343 310 356 100983 1006.8 628.9 117.4 1.0000 304.7 7.1 77 0.9390 0.5723 1.0 99.0 0.4246 2.3555 2.8063 0.2056 1
HEEBO-002-CTRL2I12 0.1721 1 1 14 297 357 310 370 395535 4606.1 3754.8 137.5 1.0000 338.1 27.5 297 357 310 370 140963 1456.8 1031.6 163.0 1.0000 305.3 7.5 80 0.9756 1.1267 1.0 99.0 0.4246 2.3555 2.8063 0.2056 1
HEEBO-002-CTRL2M24 -1.0020 1 1 15 297 370 310 383 94605 848.0 679.4 21.7 1.0000 349.5 34.1 297 370 310 383 72157 605.2 388.9 57.8 1.0000 308.2 9.3 79 0.9634 0.4993 1.0 99.0 0.4246 2.3555 2.8063 0.2056 1
HEEBO-002-CTRL2M12 -0.3384 1 1 16 297 384 310 397 337558 4035.0 2730.7 107.6 1.0000 348.9 32.3 297 384 310 397 163593 1818.0 1090.4 185.1 1.0000 306.6 8.6 77 0.9390 0.7909 1.0 99.0 0.4246 2.3555 2.8063 0.2056 1
HEEBO-003-CTRL3A24 -0.9560 1 1 17 297 398 310 411 81650 752.7 463.7 25.4 1.0000 321.6 22.7 297 398 310 411 62433 520.3 331.5 65.0 1.0000 301.2 6.4 76 0.9268 0.5155 1.0 99.0 0.4246 2.3555 2.8063 0.2056 1
HEEBO-003-CTRL3A12 -1.6524 1 1 18 297 411 310 424 64383 544.4 383.6 19.8 1.0000 314.1 19.8 297 411 310 424 67975 609.7 464.1 82.4 1.0000 296.6 5.6 75 0.9146 0.3181 1.0 99.0 0.4246 2.3555 2.8063 0.2056 1
HEEBO-003-CTRL3E24 -0.1743 1 1 19 297 425 310 438 41929 250.9 137.6 10.4 1.0000 300.8 14.7 297 425 310 438 29933 100.9 49.8 17.8 1.0000 293.0 3.0 76 0.9268 0.8862 1.0 99.0 0.4246 2.3555 2.8063 0.2056 1
HEEBO-003-CTRL3E12 -0.8352 1 1 20 297 438 310 451 52780 381.8 222.9 15.6 1.0000 303.7 15.2 297 438 310 451 41577 242.7 126.7 33.9 1.0000 297.2 5.3 77 0.9390 0.5605 1.0 99.0 0.4246 2.3555 2.8063 0.2056 1

Total number of rows: 49152

Table truncated, full table size 10091 Kbytes.




Supplementary file Size Download File type/resource
GSM149972.txt.gz 3.9 Mb (ftp)(http) TXT

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