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Sample GSM149965 Query DataSets for GSM149965
Status Public on May 07, 2007
Title NHGRI_HCC1419_HB7-21
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 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)
 
 
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 1 283 190 296 203 1 1.0 0.0 0.1 0.0000 318.5 14.2 283 190 296 203 1 1.0 0.0 0.0 0.0000 305.4 18.4 0 0.0000 1.3885 0.0 99.0 0.4499 2.2227 0.7202 0.1947 1
HEEBO-001-CTRL1A12 1 1 2 283 204 296 217 1 1.0 0.0 0.1 0.0000 324.1 15.2 283 204 296 217 1 1.0 0.0 0.0 0.0000 305.0 17.1 0 0.0000 1.3885 0.0 99.0 0.4499 2.2227 0.7202 0.1947 1
HEEBO-001-CTRL1E24 -1.2430 1 1 3 283 217 296 230 145933 1706.5 972.6 112.7 1.0000 320.4 12.7 283 217 296 230 426050 5607.7 4098.2 253.7 1.0000 309.7 17.2 72 1.0000 0.4225 1.0 99.0 0.4499 2.2227 0.7202 0.1947 1
HEEBO-001-CTRL1E12 0.8287 1 1 4 283 231 296 244 186272 2266.4 1181.5 164.7 1.0000 320.8 11.0 283 231 296 244 150166 1771.8 991.1 82.9 1.0000 313.9 16.3 72 1.0000 1.7761 1.0 99.0 0.4499 2.2227 0.7202 0.1947 1
HEEBO-001-CTRL1I24 0.0014 1 1 5 283 244 296 257 64738 583.2 268.4 49.3 1.0000 315.9 8.5 283 244 296 257 81054 808.9 448.3 36.2 1.0000 316.8 17.5 72 1.0000 1.0010 1.0 99.0 0.4499 2.2227 0.7202 0.1947 1
HEEBO-001-CTRL1I12 0.5281 1 1 6 283 258 296 271 1076663 14634.9 9556.9 1024.5 1.0000 318.7 11.7 283 258 296 271 1037067 14092.0 9653.2 686.8 1.0000 311.7 15.2 72 1.0000 1.4420 1.0 99.0 0.4499 2.2227 0.7202 0.1947 1
HEEBO-001-CTRL1M24 0.8774 1 1 7 283 271 296 284 213344 2634.6 1361.4 148.7 1.0000 328.5 15.7 283 271 296 284 165995 1991.4 1213.5 83.1 1.0000 314.1 19.6 72 1.0000 1.8370 1.0 99.0 0.4499 2.2227 0.7202 0.1947 1
HEEBO-001-CTRL1M12 -0.2746 1 1 8 283 285 296 298 1685834 23087.5 16177.0 1471.5 1.0000 326.8 13.4 283 285 296 298 2814619 38776.3 24786.6 1554.1 1.0000 315.7 20.8 72 1.0000 0.8267 1.0 99.0 0.4499 2.2227 0.7202 0.1947 1
HEEBO-002-CTRL2A24 0.7391 1 1 9 283 298 296 311 889296 12023.8 9222.8 784.4 1.0000 327.6 12.9 283 298 296 311 742939 10002.5 9635.0 390.2 0.6837 316.1 21.6 72 1.0000 1.6691 1.0 99.0 0.4499 2.2227 0.7202 0.1947 1
HEEBO-002-CTRL2A12 -1.4375 1 1 10 283 312 296 325 129925 2035.1 1226.4 121.2 1.0000 327.1 14.6 283 312 296 325 438263 7653.9 4853.7 316.8 1.0000 314.5 19.8 55 0.7639 0.3692 1.0 99.0 0.4499 2.2227 0.7202 0.1947 1
HEEBO-002-CTRL2E24 -0.4737 1 1 11 283 325 296 338 1083966 14942.4 13005.7 962.5 1.0000 324.8 13.2 283 325 296 338 2068134 28812.5 26474.6 1137.5 0.9057 316.1 21.2 71 0.9861 0.7201 1.0 99.0 0.4499 2.2227 0.7202 0.1947 1
HEEBO-002-CTRL2E12 -0.4189 1 1 12 283 339 296 352 64645 579.9 245.3 39.6 1.0000 317.9 12.1 283 339 296 352 99691 1076.5 486.8 47.8 1.0000 308.1 17.8 72 1.0000 0.7480 1.0 99.0 0.4499 2.2227 0.7202 0.1947 1
HEEBO-002-CTRL2I24 -0.4580 1 1 13 283 352 296 365 83225 895.0 603.2 73.6 1.0000 311.1 8.9 283 352 296 365 139117 1707.0 1278.8 77.1 1.0000 309.2 17.3 69 0.9583 0.7280 1.0 99.0 0.4499 2.2227 0.7202 0.1947 1
HEEBO-002-CTRL2I12 0.3208 1 1 14 283 366 296 379 173483 2242.6 1504.6 208.2 1.0000 308.6 7.0 283 366 296 379 190547 2493.0 1896.2 110.2 1.0000 309.1 17.9 68 0.9444 1.2490 1.0 99.0 0.4499 2.2227 0.7202 0.1947 1
HEEBO-002-CTRL2M24 -0.2564 1 1 15 283 379 296 392 77950 769.3 400.2 62.3 1.0000 313.4 9.2 283 379 296 392 114088 1275.8 847.5 59.6 1.0000 308.7 16.4 72 1.0000 0.8372 1.0 99.0 0.4499 2.2227 0.7202 0.1947 1
HEEBO-002-CTRL2M12 -0.1087 1 1 16 283 393 296 406 232123 2908.8 1231.8 210.9 1.0000 315.2 11.1 283 393 296 406 335639 4354.9 2247.1 219.4 1.0000 306.7 14.2 72 1.0000 0.9274 1.0 99.0 0.4499 2.2227 0.7202 0.1947 1
HEEBO-003-CTRL3A24 -0.6967 1 1 17 283 407 296 420 62507 580.8 296.4 32.2 1.0000 325.1 16.1 283 407 296 420 111543 1307.0 628.3 60.4 1.0000 309.5 16.7 69 0.9583 0.6170 1.0 99.0 0.4499 2.2227 0.7202 0.1947 1
HEEBO-003-CTRL3A12 -0.9434 1 1 18 283 420 296 433 43940 328.1 202.5 22.4 1.0000 318.1 12.1 283 420 296 433 80269 876.0 731.1 41.6 1.0000 304.4 15.9 68 0.9444 0.5200 1.0 99.0 0.4499 2.2227 0.7202 0.1947 1
HEEBO-003-CTRL3E24 -0.6268 1 1 19 283 434 296 447 26206 88.9 45.8 5.9 1.0000 314.3 12.5 283 434 296 447 31893 190.6 107.8 9.4 1.0000 300.0 14.7 65 0.9028 0.6476 1.0 99.0 0.4499 2.2227 0.7202 0.1947 1
HEEBO-003-CTRL3E12 -0.3644 1 1 20 283 447 296 460 37391 237.2 115.0 19.5 1.0000 304.7 8.9 283 447 296 460 50041 423.9 251.7 20.4 1.0000 301.3 15.4 69 0.9583 0.7768 1.0 99.0 0.4499 2.2227 0.7202 0.1947 1

Total number of rows: 49152

Table truncated, full table size 10096 Kbytes.




Supplementary file Size Download File type/resource
GSM149965.txt.gz 3.9 Mb (ftp)(http) TXT

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