|
| Status |
Public on Jun 15, 2021 |
| Title |
LK0902 cell line grown with CAF in 3D |
| Sample type |
RNA |
| |
|
| Source name |
cell co-culture with CAF
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: HNSCC cell line (tongue)
age: 68
|
| Treatment protocol |
Tumor cells were separated from CAFs by magnetic activated cell sorting (MACS).
|
| Growth protocol |
Tumor cells and CAFs were co-cultured in 3D. To achieve spheroids of tumor cells or co-cultures of tumor cells and CAFs, 15,000 tumor cells or 10,000 tumor cells with 5,000 CAFs were seeded into each well of ultra-low at-tachment (ULA) 96-well round-bottomed plates (Corning, Amsterdam, The Netherlands) and were thereafter cultured in standard culture conditions
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extraction was performed using the RNeasy Mini Kit according to the manufacturer's instructions.
|
| Label |
biotin
|
| Label protocol |
Labeling was done according to the GeneChip® WT Plus Reagent Kit manufacturer’s instructions The starting amount of total RNA was 150 ng. 15 µg of cRNA was used for single-stranded cDNA-synthesis (sscDNA).
|
| |
|
| Hybridization protocol |
Hybridization was done according to the GeneChip® WT Plus Reagent Kit manufacturer's instructions. A total of 5.5 µg of sscDNA was fragmented and hybridized on a Human Transcriptome 2.0 Array.
|
| Scan protocol |
Hybridized arrays were scanned with an Affymetrix GeneChip® 3000 fluorescent scanner.
|
| Description |
Gene expression data; SST-RMA expression value derived from TAC software
Gene expression data from HNSCC cell lines grown with or without CAFs in 3D
|
| Data processing |
Raw intensity CEL files generated by the GeneChip Command Console were imported into Transcriptome Analysis Console (TAC) and CHP files were generated for gene level analysis using the SST-RMA summarization method.
|
| |
|
| Submission date |
Jun 14, 2021 |
| Last update date |
Jun 15, 2021 |
| Contact name |
Emilia Wiechec |
| E-mail(s) |
emilia.wiechec@liu.se
|
| Organization name |
Linköping University
|
| Department |
Biomedical and Clinical Sciences
|
| Street address |
Sandbäcksgatan 7
|
| City |
Linköping |
| ZIP/Postal code |
58183 |
| Country |
Sweden |
| |
|
| Platform ID |
GPL17586 |
| Series (1) |
| GSE178154 |
Expression data of HNSCC cell lines grown without and with patient-matched CAFs in 3D |
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