|
| Status |
Public on Dec 31, 2018 |
| Title |
A5 |
| Sample type |
SRA |
| |
|
| Source name |
400nM β-amyloid, HAOEC
|
| Organism |
Homo sapiens |
| Characteristics |
treatment: HAOEC cells treated with 400nM β-amyloid
cell line: HAOEC
|
| Treatment protocol |
Cells were stimulated or not with 400nM β-amyloid in EGM-2 medium containing 0.5% FBS, 0.5 ng/ml VEGF, 1 μg/ml ascorbic acid and 0.1% Heparin for 24 hours
|
| Growth protocol |
HAOEC cells were grown in EGM-2 (Lonza) complete containing 2& FBS
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extraction by TRIZOL method
The TruSeq™ RNA Sample preparation kit (Illumina) was used to generate poly-A selected, indexed cDNA libraries, according to the manufacturer’s instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Reads have been aligned using STAR (version 2.3.0e_r291) on hg19 reference with default parameters. Samples A4 and A5 have been merged with their specific re-runs at BAM level using samtools merge software (version 1.2-17-ge91985a)
Gene-level counts have been calculated using Rsubread package (version 1.16.1) for R statistical program using the ensmbl Gene annotation file for hg19 in GTF format.
Counts have been tested for gene-level differential expression using limma-voom package (version 3.22.7) for R with a TMM normalization and taking account for quality weights.
Design has been built to test condition-related differences in Amyloid in respect to control samples.
Genome_build: hg19
Supplementary_files_format_and_content: [.txt] Tab-delimited file containing the matrix output by Rsubread. Columns correspond to samples, rows correspond to single genes
|
| |
|
| Submission date |
Jul 20, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Fabio Martelli |
| E-mail(s) |
fabio.martelli@grupposandonato.it
|
| Phone |
+390252774533
|
| Organization name |
IRCCS-Policlinico San Donato
|
| Lab |
Molecular Cardiology
|
| Street address |
via morandi 30
|
| City |
Milan |
| ZIP/Postal code |
20097 |
| Country |
Italy |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE84620 |
Transcriptomic changes mediated by β-amyloid in human aortic endothelial cells (HAOEC) |
|
| Relations |
| BioSample |
SAMN05420533 |
| SRA |
SRX1962062 |
