|
| Status |
Public on Mar 14, 2019 |
| Title |
BJ/hTERT LT/ST HRAS cells, rep2 |
| Sample type |
RNA |
| |
|
| Source name |
BJ/hTERT LT/ST HRAS
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: human fibroblasts
|
| Growth protocol |
BJ/TERT cells were cultured in Earle’s salts minimal essential medium (EMEM) (Euroclone) completed with nonessential amino acids (HyClone). Media was supplemented with 10% fetal bovine serum (FBS), L-glutamine (2mM), penicillin (100U/ml), and streptomycin (100µg/ml) (Lonza)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using Direct-zol RNA mini prep (Zymo Research). RNA samples concentration and purity (assessed as 260/280 nm and 260/230 nm ratios) were evaluated by NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies; Wilmington, DE), while RNA integrity was assessed by using the Agilent 2100 Bioanalyzer (Agilent Technologies; Waldbrunn, Germany).
|
| Label |
biotin
|
| Label protocol |
RNA samples were labeled according to the standard one-cycle amplification and labeling protocol (Affymetrix, Santa Clara, CA).
|
| |
|
| Hybridization protocol |
Labeled cRNA was hybridized on Affymetrix Clariom S Human array
|
| Scan protocol |
Scanning was performed using a GeneChip Scanner 3000 7G (Affymetrix).
|
| Data processing |
Data processing was performed with BioConductor packages (http://www.bioconductor.org/). Robust Multi-Array Average (RMA) normalization was applied. Normalized intensity values for all probes on the Affymetrix chip are presented in the Matrix table. Data analysis was performed using the moderated t-test as implemented in the limma package. P values were adjusted for multiple testing using the False Discovery Rate method.
|
| |
|
| Submission date |
Sep 17, 2018 |
| Last update date |
Mar 14, 2019 |
| Contact name |
raffaella picco |
| E-mail(s) |
raf.picco@uniud.it
|
| Organization name |
university of Udine
|
| Department |
department of medical and biological sciences
|
| Lab |
bioinformatics
|
| Street address |
piazzale kolbe 4
|
| City |
udine |
| ZIP/Postal code |
33100 |
| Country |
Italy |
| |
|
| Platform ID |
GPL23159 |
| Series (1) |
| GSE120040 |
Unscheduled HDAC4 repressive activity in human fibroblasts triggers TP53-dependent senescence and favours cell transformation |
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