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Sample GSM34218 Query DataSets for GSM34218
Status Public on Jul 01, 2005
Title TGCT cell line NTera2/clone D1, treated 7 days with retinoic acid, differentiated
Sample type RNA
 
Channel 1
Source name TGCT cell line NTera2/clone D1, treated 7 days with retinoic acid, differentiated
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name Universal Human Reference RNA (Stratagene)
Organism Homo sapiens
Extracted molecule total RNA
 
 
Description Testicular germ cell tumor (embryonal carcinoma) cell line NTera2 (clone D1). Embryonal carcinoma cell lines, and especially NTera2, are generally pluripotent and share features with embryonic stem cells. Time point 7 days in a time series of 0, 3, and 7 days of culturing with retinoic acid which stimulates these cells to differentiation. Maintained at high cell density (>5 000 000 cells per 75 cm2 tissue culture flask) in Dulbecco Modified Eagles Medium (DMEM high glucose formulation; GIBCO LifeTechnologies, UK) supplemented with 10% fetal calf serum.
Keywords = cell line
Keywords = differentiation
Keywords = embryonal carcinoma
Keywords = embryonic stem cell
Keywords = NT2
Keywords = NTera2
Keywords = pluripotency
Keywords = pluripotent
Keywords = retinoic acid
Keywords = seminoma
Keywords = teratocarcinoma
Keywords = testicular germ cell tumor
Keywords = testicular neoplasm
Keywords = testis
Keywords = totipotency
 
Submission date Oct 31, 2004
Last update date Mar 09, 2006
Contact name Rolf I Skotheim
E-mail(s) rolf.i.skotheim@rr-research.no
Phone +47 2293 4000
Fax +47 2293 5767
URL http://www.radium.no/cancerprevention
Organization name Rikshospitalet-Radiumhospitalet Medical Center, Institute for Cancer Research
Department Department of Cancer Prevention
Street address
City Oslo
ZIP/Postal code N-0310
Country Norway
 
Platform ID GPL885
Series (1)
GSE1818 Testicular germ cell tumors and their histological subgroups

Data table header descriptions
ID_REF
FLAG Boolean for measurement quality. 1=Feature with inadequate measurements, 0=Feature with good quality measurements
VALUE same as UNF_VALUE but with flagged values removed
Log2_NormalTestisCenteredRatio For features with FLAG=0: Log2(SampleRATIO/MedianRATIO of the three Normal testis samples); gives an indication of up- and downregulation in the sample relative to the mRNA level in normal testis
RATIO For features with FLAG=0: CH1_ProcessedSignal / CH2_ProcessedSignal
PositionX X-coordinate, pixel position, of feature centroid on the original scan (tif-image)
PositionY Y-coordinate, pixel position, of feature centroid on the original scan (tif-image)
CH1_SurrogateUsed The CH1 surrogate value used
CH2_SurrogateUsed The CH2 surrogate value used
CH1_ProcessedSignal The propagated CH1 feature signal, used further for computation of ratios and log2ratios
CH2_ProcessedSignal The propagated CH2 feature signal, used further for computation of ratios and log2ratios
CH1_ProcessedSigError Standard error of propagated CH1 feature signal
CH2_ProcessedSigError Standard error of propagated CH2 feature signal
CH1_AREA Total number of pixels used to compute CH1 feature statistics
CH2_AREA Total number of pixels used to compute CH2 feature statistics
CH1_MEAN Raw mean signal of feature in CH1
CH2_MEAN Raw mean signal of feature in CH2
CH1_MEDIAN Raw median signal of feature in CH1
CH2_MEDIAN Raw median signal of feature in CH2
CH1_SD Standard deviation of all inlier pixels per CH1 feature
CH2_SD Standard deviation of all inlier pixels per CH2 feature
CH1_BKD_AREA Total number of pixels used to compute local CH1 background statistics per spot
CH2_BKD_AREA Total number of pixels used to compute local CH2 background statistics per spot
CH1_BKD_MEAN Mean local background CH1 signal (local to corresponding feature)
CH2_BKD_MEAN Mean local background CH2 signal (local to corresponding feature)
CH1_BKD_MEDIAN Median local background CH1 signal (local to corresponding feature)
CH2_BKD_MEDIAN Median local background CH2 signal (local to corresponding feature)
CH1_BKD_SD Standard deviation of all inlier pixels per local CH1 background of each feature
CH2_BKD_SD Standard deviation of all inlier pixels per local CH2 background of each feature
CH1_NumSatPix Total number of CH1 saturated pixels per feature
CH2_NumSatPix Total number of CH2 saturated pixels per feature
CH1_IsSaturated Boolean flag indicating if a feature is saturated for CH1 or not. 1=Saturated (>50% of the pixels above the saturation threshold), 0=NotSaturated
CH2_IsSaturated Boolean flag indicating if a feature is saturated for CH2 or not. 1=Saturated (>50% of the pixels above the saturation threshold), 0=NotSaturated
CH1_IsFeatNonUnifOL Boolean flag indicating if a feature is a NonUniformity Outlier or not for CH1. 1=The feature is non-uniform in that the pixel noise of feature exceeds a threshold established for a "uniform" feature, 0=Uniform feature
CH2_IsFeatNonUnifOL Boolean flag indicating if a feature is a NonUniformity Outlier or not for CH2. 1=The feature is non-uniform in that the pixel noise of feature exceeds a threshold established for a "uniform" feature, 0=Uniform feature
CH1_IsBGNonUnifOL Boolean flag indicating if a feature is a Background NonUniformity Outlier or not for CH1. 1=The background is non-uniform in that the pixel noise of feature background exceeds a threshold established for a "uniform" background, 0=Uniform background
CH2_IsBGNonUnifOL Boolean flag indicating if a feature is a Background NonUniformity Outlier or not for CH2. 1=The background is non-uniform in that the pixel noise of feature background exceeds a threshold established for a "uniform" background, 0=Uniform background
CH1_IsFeatPopnOL Boolean flag indicating if a feature is a Population Outlier or not for CH1. Probes with replicate features on the microarray were examined using population statistics. 1=IsPopulationOutlier, 0=IsNotPopulationOutlier
CH2_IsFeatPopnOL Boolean flag indicating if a feature is a Population Outlier or not for CH2. Probes with replicate features on the microarray were examined using population statistics. 1=IsPopulationOutlier, 0=IsNotPopulationOutlier
CH1_BGSubSignal The net CH1 signal following the subtraction of the CH1 background from the raw mean CH1 signal
CH2_BGSubSignal The net CH2 signal following the subtraction of the CH2 background from the raw mean CH2 signal
CH1_BGSubSigError Propagated standard error as computed on net CH1 background subtracted signal
CH2_BGSubSigError Propagated standard error as computed on net CH2 background subtracted signal
CH1_IsWellAboveBG Boolean flag indicating if CH1 for a feature is WellAbove Background or not. 1=WellAboveBackground, 0=NotWellAboveBackground
CH2_IsWellAboveBG Boolean flag indicating if CH2 for a feature is WellAbove Background or not. 1=WellAboveBackground, 0=NotWellAboveBackground
IsNormalization A boolean flag which indicates if a feature is used to measure dye bias. 1=Feature used, 2=Feature not used.
CH1_DyeNormSignal The CH1 dye normalized signal
CH2_DyeNormSignal The CH2 dye normalized signal
CH1_DyeNormError The standard error associated with the CH1 dye normalized signal
CH2_DyeNormError The standard error associated with the CH2 dye normalized signal
DyeNormCorrelation Dye normalized CH1 and CH2 pixel correlation
UNF_VALUE Expression level (mRNA abundance) relative to the common universal human reference RNA. Log2(CH1_ProcessedSignal/CH2_Processed signal)

Data table
ID_REF FLAG VALUE Log2_NormalTestisCenteredRatio RATIO PositionX PositionY CH1_SurrogateUsed CH2_SurrogateUsed CH1_ProcessedSignal CH2_ProcessedSignal CH1_ProcessedSigError CH2_ProcessedSigError CH1_AREA CH2_AREA CH1_MEAN CH2_MEAN CH1_MEDIAN CH2_MEDIAN CH1_SD CH2_SD CH1_BKD_AREA CH2_BKD_AREA CH1_BKD_MEAN CH2_BKD_MEAN CH1_BKD_MEDIAN CH2_BKD_MEDIAN CH1_BKD_SD CH2_BKD_SD CH1_NumSatPix CH2_NumSatPix CH1_IsSaturated CH2_IsSaturated CH1_IsFeatNonUnifOL CH2_IsFeatNonUnifOL CH1_IsBGNonUnifOL CH2_IsBGNonUnifOL CH1_IsFeatPopnOL CH2_IsFeatPopnOL CH1_BGSubSignal CH2_BGSubSignal CH1_BGSubSigError CH2_BGSubSigError CH1_IsWellAboveBG CH2_IsWellAboveBG IsNormalization CH1_DyeNormSignal CH2_DyeNormSignal CH1_DyeNormError CH2_DyeNormError DyeNormCorrelation UNF_VALUE
1 0 1.71994196 -0.834255072 3.294231538 37.236 34.764 0 0 1391.77 422.487 31.242 12.3484 61 61 1005.23 376.902 982 363 156.302 70.984 252 252 42.6984 67.119 43 66 3.49449 9.21164 0 0 0 0 0 0 0 0 0 0 891.565 311.59 20.0136 9.10707 1 1 0 1391.77 422.487 31.242 12.3484 0.745678 1.71994196
2 1 58.6239 33.5872 0 11.0606 14.5037 11.0606 2.40571 1.59587 54 54 120.167 72 120 71 8.79483 9.90521 267 267 41.8539 67.6966 42 66 3.74733 10.3161 0 0 0 0 0 0 0 0 0 0 7.34679 6.11038 1.2186 1.48845 0 0 0 14.5037 6.55135 2.40571 1.59587 0.111335 0.39099134
3 0 0.199526038 -0.308515783 1.14832104 79.7214 34.4979 0 0 162.848 141.814 5.98578 5.58043 57 57 217.035 171.123 215 168 28.8072 30.8314 275 275 42.0509 68.0364 42 67 4.03872 9.95421 0 0 0 0 0 0 0 0 0 0 104.018 104.893 3.82337 4.1276 1 1 1 162.848 141.814 5.98578 5.58043 0.488247 0.199526038
4 0 0.144655913 -0.681819445 1.105466965 100.966 34.5385 0 0 51043.5 46173.7 506.557 501.682 60 60 32851.8 34078.3 32268.5 33330.5 2516.58 2862.55 266 266 43.2068 67.1992 43 67 4.15348 9.17676 0 0 0 0 0 0 0 0 0 0 32737.6 34013 324.889 369.555 1 1 1 51043.5 46173.7 506.557 501.682 0.943454 0.144655913
5 0 -0.225756263 -0.504983719 0.855146639 122.416 35.658 0 0 1393.47 1629.51 26.9625 24.1088 57 57 1015.26 1254.86 1017 1253 131.697 132.848 262 262 42.6718 66.8359 43 66 4.28924 8.29345 0 0 0 0 0 0 0 0 0 0 901.625 1189.83 17.4457 17.6036 1 1 1 1393.47 1629.51 26.9625 24.1088 0.760696 -0.225756263
7 0 2.437653416 -0.601736149 5.417598264 164.558 34.1707 0 0 1078.27 199.031 24.0183 6.55638 57 57 810.421 209.228 793 207 117.404 35.8818 280 280 41.2643 65.8143 41 66 3.682 9.11738 0 0 0 0 0 0 0 0 0 0 698.191 145.221 15.5521 4.78379 1 1 0 1078.27 199.031 24.0183 6.55638 0.568058 2.437653416
8 0 -0.116943008 0.231066432 0.922139545 185.899 34.3105 0 0 2209.64 2396.21 28.744 34.3955 57 57 1529.25 1832 1550 1845 139.073 191.379 266 266 42.1165 67.4098 42 66 3.73529 9.31631 0 0 0 0 0 0 0 0 0 0 1416.16 1766.4 18.4221 25.3552 1 1 1 2209.64 2396.21 28.744 34.3955 0.696856 -0.116943008
9 0 1.555143923 1.188985951 2.93863041 206.976 35.3588 0 0 4430.72 1507.75 100.984 29.9074 61 61 2942.93 1183.33 2870 1142 503.499 172.789 258 258 43.4496 69.2984 43 68 4.67789 10.766 0 0 0 0 0 0 0 0 0 0 2828.52 1115.84 64.4671 22.1335 1 1 1 4430.72 1507.75 100.984 29.9074 0.935917 1.555143923
11 0 0.287533506 -0.241028898 1.220551785 249.269 35.3889 0 0 594.366 486.965 15.1389 12.498 59 59 496.966 424.102 501 411 75.0028 70.1035 248 248 42.5282 69.3145 42 69 3.67054 10.7194 0 0 0 0 0 0 0 0 0 0 383.472 356.594 9.76731 9.15205 1 1 1 594.366 486.965 15.1389 12.498 0.706869 0.287533506
13 0 0.157432837 0.316077963 1.11530078 291.694 35.414 0 0 403.711 361.975 8.80279 8.60462 56 56 376.518 328.857 377.5 335.5 42.7768 46.5842 260 260 43.1269 67.5769 43 67 4.15659 9.67372 0 0 0 0 0 0 0 0 0 0 262.425 263.087 5.7221 6.25392 1 1 1 403.711 361.975 8.80279 8.60462 0.463469 0.157432837
14 0 2.568491669 -0.527359419 5.931889275 312.986 34.0626 0 0 1107.46 186.696 21.8369 6.15251 59 59 831.119 202.169 803 198 108.621 34.0953 254 254 42.8701 67.7913 43 67 3.85852 10.5531 0 0 0 0 0 0 0 0 0 0 717.283 136.185 14.1433 4.48794 1 1 0 1107.46 186.696 21.8369 6.15251 0.413715 2.568491669
15 0 0.282280119 0.134658 1.216115386 333.644 35.8492 0 0 5574.15 4583.57 63.8717 61.4802 58 58 3660.41 3469.67 3683 3430.5 309.465 347.671 258 258 43.1589 67.6822 43 66 3.64819 10.0202 0 0 0 0 0 0 0 0 0 0 3546.29 3403.8 40.6353 45.6557 1 1 1 5574.15 4583.57 63.8717 61.4802 0.868681 0.282280119
16 0 -0.154612302 -0.2050072 0.898373762 355.01 35.3959 0 0 659.153 733.718 14.4738 11.7741 59 59 535.644 606.525 527 598 71.1828 66.5752 266 266 42.5038 67.1053 42 66 3.82864 9.06976 0 0 0 0 0 0 0 0 0 0 422.174 541.227 9.27018 8.68517 1 1 1 659.153 733.718 14.4738 11.7741 0.726576 -0.154612302
17 0 0.117882103 -1.200663583 1.085140691 376.435 35.4189 0 0 149.4 137.678 5.08346 4.20419 54 54 208.5 166.704 207 162 23.7477 22.4857 277 277 42.296 66.4729 42 64 3.99534 9.78224 0 0 0 0 0 0 0 0 0 0 95.238 102.038 3.24056 3.11586 1 1 1 149.4 137.678 5.08346 4.20419 0.424392 0.117882103
21 0 2.572097677 -0.648799075 5.946734545 460.708 35.1671 0 0 1069.99 179.929 16.6234 5.47984 57 57 806.596 195 810 192 81.3142 29.855 261 261 42.2107 65.636 42 65 3.92693 9.16692 0 0 0 0 0 0 0 0 0 0 693.42 131.171 10.7731 3.99489 1 1 0 1069.99 179.929 16.6234 5.47984 0.209078 2.572097677
23 0 0.704388623 1.861743 1.629453998 503.054 35.3637 0 0 5508.19 3380.39 64.647 37.5807 60 60 3618.12 2574.72 3484.5 2563 318.64 216.076 262 262 42.1145 66.7252 42 66 3.93947 9.99391 0 0 0 0 0 0 0 0 0 0 3505.04 2509.8 41.1369 27.9021 1 1 1 5508.19 3380.39 64.647 37.5807 0.854348 0.704388623
25 0 -0.702031567 -0.658638759 0.614705984 546.015 35.5388 0 0 893.469 1453.49 10.2064 14.1636 56 56 691.125 1131.41 692 1133.5 49.2559 77.4127 285 285 43.5298 69.193 44 67 4.28763 11.8286 0 0 0 0 0 0 0 0 0 0 576.629 1064.02 6.587 10.3684 1 1 1 893.469 1453.49 10.2064 14.1636 0.54861 -0.702031567
26 0 -1.639557118 0.160825499 0.320954987 566.519 35.4452 0 0 235.191 732.785 6.76987 12.8531 60 60 266.433 601.683 264 596 33.9628 72.2992 254 254 42.8661 69.9173 43 68 4.22184 10.9276 0 0 0 0 0 0 0 0 0 0 152.601 533.573 4.39257 9.35893 1 1 1 235.191 732.785 6.76987 12.8531 0.457878 -1.639557118
28 0 2.437675064 -1.444905493 5.417679558 609.201 35.0325 0 0 1225.75 226.25 25.9235 8.36714 62 62 905.081 229.484 888 226.5 131.765 48.0477 267 267 42.7828 65.7191 43 65 4.11736 8.29483 0 0 0 0 0 0 0 0 0 0 791.332 165.572 16.736 6.12314 1 1 0 1225.75 226.25 25.9235 8.36714 0.605181 2.437675064
29 0 0.321446793 -2.375087582 1.249583053 630.388 35.9714 0 0 128.121 102.531 5.46907 3.25065 58 58 194.103 141.276 197.5 137.5 26.2275 18.0601 262 262 42.271 66.3359 42 66 3.82158 8.81927 0 0 0 0 0 0 0 0 0 0 80.8665 76.747 3.45193 2.4332 1 1 1 128.121 102.531 5.46907 3.25065 0.225388 0.321446793

Total number of rows: 19061

Table truncated, full table size 5548 Kbytes.




Supplementary file Size Download File type/resource
GSM34218.tif.gz 20.4 Mb (ftp)(http) TIFF

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