|
| Status |
Public on Mar 31, 2019 |
| Title |
293T |
| Sample type |
RNA |
| |
|
| Source name |
Immortalized cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: 293T
cell type: Epithelial
tissue origin: Embryonic Kidney
|
| Treatment protocol |
-
|
| Growth protocol |
Cells were grown to approx. 90% confluency on 10 cm dishes prior extraction. Maintenance of adherent immortalized cell lines was carried out by culture with Dulbecco´s Modified Eagle Medium (DMEM) supplemented with 10% Fetal Calf Serum (FCS), penicillin/streptomycin (100 U/ml), non-essential amino acids (1X), and L-glutamine (2mM) at 37C and 5% CO2. Suspension cell line Jurkat was cultured with Roswell Park Memorial Institute (RPMI) 1640 medium plus 25 mM HEPES with the same supplements and conditions as adherent cell lines.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted as instructed in the RNeasy Midi kit (Qiagen, Hilden, Germany) guidelines.
|
| Label |
Cy3
|
| Label protocol |
Synthesis of Cy3-labeled cRNA was performed with the ‘Quick Amp Labeling kit, one color’ (#5190-0442, Agilent Technologies) according to the manufacturer’s recommendations.
|
| |
|
| Hybridization protocol |
cRNA fragmentation, hybridization and washing steps were carried-out exactly as recommended in the ‘One-Color Microarray-Based Gene Expression Analysis Protocol V5.7’.
|
| Scan protocol |
Slides were scanned on the Agilent Micro Array Scanner G2565CA (pixel resolution 5 µm, bit depth 20).
|
| Description |
M4709
|
| Data processing |
Data extraction was performed with the ‘Feature Extraction Software V10.7.3.1’ by using the recommended default extraction protocol file ‘GE1_107_Sep09.xml’. Measurements of on-chip replicates were averaged using the geometric mean of processed intensity values of the green channel, ‘gProcessedSignal’ (gPS) to retrieve one resulting value per unique non-control probe. Single Features were excluded from averaging, if they i) were manually flagged, ii) were identified as Outliers by the Feature Extraction Software, iii) lay outside the interval of ‘1.42 x interquartile range‘ regarding the normalized gPS distribution of the respective on-chip replicate population, or, iv) showed a coefficient of variation of pixel intensities per Feature that exceeded 0.5. Averaged gPS values were normalized by global linear scaling. For this, all gPS values of one sample were multiplied by an array-specific scaling factor. This factor was calculated by dividing a ‘reference 75th Percentile value’ (set as 1500 for the whole series) by the 75th Percentile value of the particular Microarray to be scaled (‘Array i’ in the formula shown below). Accordingly, normalized gPS values for all samples (microarray data sets) were calculated by the following formula: normalized gPSArray i = gPSArray i x (1500 / 75th PercentileArray i) A lower intensity threshold (surrogate value) was defined based on intensity distribution of negative control features. This value was fixed at 15 normalized gPS units. All of those measurements that fell below this intensity cutoff were substituted by the respective surrogate value of 15. Finally, normalized signal intensities were log-transformed for visualization (base 10).
Log-transformed normalized processed signal intensities. Measurements of control features have been removed.
|
| |
|
| Submission date |
Sep 19, 2017 |
| Last update date |
Mar 31, 2019 |
| Contact name |
Rui Costa |
| Phone |
+49(0)5115323899
|
| Organization name |
Medizinische Hochschule Hannover
|
| Department |
Gastroenterology Hepatology and Endocrinology
|
| Lab |
von Hahn
|
| Street address |
Carl Neuberg Strasse 1
|
| City |
Hannover |
| State/province |
Niedersachsen |
| ZIP/Postal code |
30625 |
| Country |
Germany |
| |
|
| Platform ID |
GPL13497 |
| Series (1) |
| GSE104008 |
Characterization of the Filovirus-Resistant Cell Line SH-SY5Y Reveals Redundant Role of Cell Surface Entry Factors |
|
