|
| Status |
Public on Jun 15, 2021 |
| Title |
LK0949 cell line grown with CAF in 2D |
| Sample type |
RNA |
| |
|
| Source name |
cell co-culture with CAF
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: HNSCC cell line (tongue)
age: 62
|
| Treatment protocol |
Tumor cells were separated from CAFs by magnetic activated cell sorting (MACS).
Gene expression data from HNSCC cell lines grown with or without CAFs in 2D
|
| Growth protocol |
Tumor cells and CAFs were co-cultured in 2D in cell culture flasks. Tumor cell and CAF numbers were adjusted to that an approximate ratio of 3:1 was achieved by the end of co-culture
|
| 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 Terminal La-beling User Manual for use with the Ambion® WT Expression Kit (Affymetrix). The starting amount of total RNA was 100 ng. 15 µg of cRNA was used for single-stranded cDNA-synthesis (sscDNA).
|
| |
|
| Hybridization protocol |
Hybridization was done according to the GeneChip® WT Hy-bridization User Manual for use with the Ambion® WT Expression Kit (Affymetrix). A total of 5.5 µg of sscDNA was fragmented and hybridized on a Human Exon 1.0 ST Array.
|
| Scan protocol |
Hybridized arrays were scanned with an Affymetrix GeneChip® 3000 fluorescent scanner.
|
| Description |
Gene expression data; RMA expression value derived from TAC software
|
| 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 RMA summarization method.
|
| |
|
| Submission date |
Jun 14, 2021 |
| Last update date |
Jun 15, 2021 |
| Contact name |
Emilia Wiechec |
| E-mail(s) |
[email protected]
|
| Organization name |
Linköping University
|
| Department |
Biomedical and Clinical Sciences
|
| Street address |
Sandbäcksgatan 7
|
| City |
Linköping |
| ZIP/Postal code |
58183 |
| Country |
Sweden |
| |
|
| Platform ID |
GPL5175 |
| Series (1) |
| GSE178153 |
Expression data of HNSCC cell lines grown without and with patient-matched CAFs in 2D |
|
