|
| Status |
Public on Oct 15, 2020 |
| Title |
Stellate cells treated with stellate cell conditioned medium rep1 |
| Sample type |
RNA |
| |
|
| Source name |
Primary Cell line
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Pancreas
|
| Treatment protocol |
Stellate cells were treated with conditioned medium (CM) from stellate cells or primary human PDAC cells (PACO) for 12 hours.
|
| Growth protocol |
Stellate cells were expanded in Stellate Cell Medium. Conditioned medium was CSC reduced.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were harvested directly by addition of Qiazol to the culture dishes. Total RNA was extracted using teh Qiagen RnEasy Mini Kit according to manufacturer's instructions.
|
| Label |
biotin
|
| Label protocol |
RNA (500 ng per sample) were labelled using the Illumina® TotalPrep™ RNA Amplification Kit according to the manufacturers' instructions.
|
| |
|
| Hybridization protocol |
cRNA was hybridized to human whole-genome Illumina HumanHT-12 V4.0 expression beadchip (Illumina, Inc.)
|
| Scan protocol |
BeadChips were scanned with an Illumina iScan system (Illumina Inc.) Scanning and feature extraction was performed using BeadScan and BeadStudio sofware (Illumina) with standard settings for the chips used.
|
| Data processing |
The analysis was done on the bead-level data using R following outlier removal (by taking only beads with an expression value > 20 before using the 2.5 MADs rule). The ProbeIDs expression values are the mean of the remaining beads. Finaly, quantile normalization was performed.
|
| |
|
| Submission date |
Jul 10, 2019 |
| Last update date |
Oct 12, 2020 |
| Contact name |
Elisa Espinet |
| Organization name |
German Cancer Research Center
|
| Street address |
Im Neuenheimer Feld 280
|
| City |
Heidelberg |
| ZIP/Postal code |
69120 |
| Country |
Germany |
| |
|
| Platform ID |
GPL10558 |
| Series (1) |
| GSE134093 |
Aggressive PDACs show hypomethylation of repetitive elements and the execution of an intrinsic IFN program linked to a ductal cell-of-origin. [Activation of stellate cells by tumor conditioned medium] |
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