|
| Status |
Public on Dec 21, 2020 |
| Title |
PD sample 3 |
| Sample type |
SRA |
| |
|
| Source name |
Blood
|
| Organism |
Homo sapiens |
| Characteristics |
disease: Parkinson's Disease
|
| Growth protocol |
Peripheral blood mononuclear cells (PBMCs) were prepared by centrifugation. Peripheral blood was layered (density=1.077) and centrifuged at 950g for 30 min. After isolation on a Ficoll-Histopaque layer (Sigma, Italy), cell viability was assayed by a trypan blue exclusion test and the cells were used for RNA extraction.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Samples were homogenized and total RNA was isolated by Trizol® reagent (Life Science Technologies, Italy) following the manufacturer’s specifications. RNAs were quantified using a Nanodrop ND-100 Spectrophotometer (Nanodrop Technologies, Wilmington, USA) and a 2100 Bioanalyzer (Agilent RNA 6000 Nano Kit, Waldbronn, Germany); RNAs with a 260:280 ratio of ≥1.5 and an RNA integrity number of ≥8 were subjected to deep sequencing.
Sequencing libraries were prepared by the Illumina TruSeq Stranded Total RNA kit (Illumina) using 500-ng total RNA (Illumina) and by the Lexogen SENSE Total RNA-Seq Library Prep Kit using 500-ng total RNA (Lexogen). Qualities of sequencing libraries were assessed with 4200 TapeStation with the DNA1000 reagent kit. RNA processing has been carried out using Illumina NextSeq 500 Sequencing.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
PD3
|
| Data processing |
FastQ files were generated via llumina bcl2fastq2 Version 2.17.1.14
Gene and transcript intensities were computed using STAR/RSEM software using Gencode Release m24 (GRCm38) as a reference, using the “-strandness forward” option. Differential expression analysis for mRNA and lncRNA was performed using R package DESeq2
Genome_build: HG19
Supplementary_files_format_and_content: couts,FPKM,TPM
|
| |
|
| Submission date |
Nov 10, 2020 |
| Last update date |
Dec 21, 2020 |
| Contact name |
Maria Garofalo |
| E-mail(s) |
maria.garofalo01@universitadipavia.it
|
| Organization name |
IRCCS Mondino Foundation
|
| Lab |
Genomic and Post Genomic Unit
|
| Street address |
Via Mondino 2
|
| City |
Pavia |
| ZIP/Postal code |
27100 |
| Country |
Italy |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE161199 |
Alzheimer’s, Parkinson’s disease and Amyotrophic Lateral Sclerosis gene expression patterns divergence reveals different grade of RNA metabolism involvement |
|
| Relations |
| BioSample |
SAMN16727481 |
| SRA |
SRX9470335 |
