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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Dec 21, 2020 |
| Title |
CTRL sample 11 |
| Sample type |
SRA |
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| Source name |
Blood
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| Organism |
Homo sapiens |
| Characteristics |
disease: Helathy Control
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| 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.
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| 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.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
CTRL11
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| 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
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| Submission date |
Nov 10, 2020 |
| Last update date |
Dec 21, 2020 |
| Contact name |
Maria Garofalo |
| E-mail(s) |
maria.garofalo01@universitadipavia.it
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| Organization name |
IRCCS Mondino Foundation
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| Lab |
Genomic and Post Genomic Unit
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| Street address |
Via Mondino 2
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| City |
Pavia |
| ZIP/Postal code |
27100 |
| Country |
Italy |
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| 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 |
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| Relations |
| BioSample |
SAMN16727484 |
| SRA |
SRX9470332 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4891618_C11.gtf_annotated_genes.results.txt.gz |
1.9 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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