|
| Status |
Public on Dec 30, 2020 |
| Title |
HNSCC, untreated, patient 3 rep 2 |
| Sample type |
RNA |
| |
|
| Source name |
HNSCC
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: mesenchymal stromal cells
treatment: NONE
tissue: HNSCC
patient: 3
ChIP: 1
|
| Treatment protocol |
Cells were analyzed either resting either after 16 hours stimulation with IFNg and TNFa.
|
| Growth protocol |
Cells were kept in culture in DMEM medium supplemented with 10% FCS.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using RNeasy Micro Kit - QIAGEN following manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer
|
| Label |
Cy3
|
| Label protocol |
Labelling was performed with the one color (Cyanine 3-CTP) Low Input Quick Amp Labeling Kit (Agilent Technologies) accordinf to manufacturer protocol.
|
| |
|
| Hybridization protocol |
Hybridization was performed according to specifications in One-Color Microarray-Based Gene Expression Analysis Protocol
|
| Scan protocol |
The data was extracted using Agilent Feature Extraction Software version 10.7.3.1 with default parameters of protocol GE1_107_Sep09.
|
| Description |
H_3_2
|
| Data processing |
Data preprocessing was performed using R/Bioconductor (version 3.6) limma (version 3.34.9) package. Briefly, raw Feature Extractor data was loaded into R and further background corrected (method=”minimum”), normalized (method=”quantile”) and filtered to remove control probes.
|
| |
|
| Submission date |
Jan 01, 2020 |
| Last update date |
Dec 31, 2020 |
| Contact name |
Matteo Ramazzotti |
| E-mail(s) |
matteo.ramazzotti@unifi.it
|
| Organization name |
University of Florence
|
| Department |
Experimental and Clinical Biomedical Sciences
|
| Street address |
viale Morgagni 50
|
| City |
Firenze |
| ZIP/Postal code |
50134 |
| Country |
Italy |
| |
|
| Platform ID |
GPL17077 |
| Series (1) |
| GSE142816 |
Microarray gene expression analysis of HNSCC- and BM- derived mesenchymal stromal cells |
|
