|
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) |