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Status |
Public on Mar 14, 2019 |
Title |
BJ/hTERT LT/ST HDAC4 TM cells, rep1 |
Sample type |
RNA |
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Source name |
BJ/hTERT LT/ST HDAC4 TM
|
Organism |
Homo sapiens |
Characteristics |
cell type: human fibroblasts
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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).
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Label |
biotin
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Label protocol |
RNA samples were labeled according to the standard one-cycle amplification and labeling protocol (Affymetrix, Santa Clara, CA).
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Hybridization protocol |
Labeled cRNA was hybridized on Affymetrix Clariom S Human array
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Scan protocol |
Scanning was performed using a GeneChip Scanner 3000 7G (Affymetrix).
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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.
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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 |
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|
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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