|
Status |
Public on Dec 31, 2018 |
Title |
A6 |
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 |
SAMN05420535 |
SRA |
SRX1962064 |