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| Status |
Public on May 01, 2020 |
| Title |
HC2 RV |
| Sample type |
SRA |
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| Source name |
heart right ventricle
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| Organism |
Homo sapiens |
| Characteristics |
cell type: Mesenchymal Stromal Cells
subject: HC2
tissue: heart right ventricle
Sex: Male
age (years): 57
country of origin: Italy
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| Treatment protocol |
No treatment applied.
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| Growth protocol |
C-MSC were obtained by collagenase digestion from ventricular tissues, expanded and mantained in culture medium.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using TRIzol reagent (Thermo Fisher Scientific), following manufacturer's instructions, precipitated through ammonium acetate/ethanol method, and treated with DNAse (Turbo-DNAse; Thermo Fisher Scientific) to remove genomic DNA contamination.
Poly(A)+ RNA enrichment followed the Dynabeads™ mRNA DIRECT Micro Kit protocol (Thermo Fisher Scientific). Libraries were prepared and pooled together (6 samples per sequencing run) using multiplex library RNA Barcoding reagents and Total RNA-Seq Kit v2 (Thermo Fisher Scientific).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Ion Torrent S5 |
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| Data processing |
We mapped all reads to the Human genome version HG38/GRCh38.96, downloaded from the Ensembl database, using a 2-steps approach. First, we aligned reads against the whole genome, by STAR (v.2.7.0f); then, the unmapped reads were locally mapped by Bowtie2 (version 2.3.5). We set the default parameters for both tools, except for --chimSegmentMin 18, --chimScoreMin 12 (STAR) and --local --very-sensitive-local, -q, --mm (Bowtie2).
Gene expression quantification was performed by the featuresCount tool (v. 1.6.4), taking into account genes annotated in the GRCh38.96 release.
We filtered out genes with less than 10 counts in at least 6 samples.
Genome_build: HG38/GRCh38.96
Supplementary_files_format_and_content: Tab-delimited text file includes raw counts for each sample. The header of the files reports gene name, sample identifiers.
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| Submission date |
Dec 17, 2019 |
| Last update date |
May 01, 2020 |
| Contact name |
Gualtiero Ivanoe Colombo |
| E-mail(s) |
gualtiero.colombo@cardiologicomonzino.it
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| Phone |
+39 0258002464
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| Organization name |
Centro Cardiologico Monzino IRCCS
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| Lab |
Immunology and Functional Genomics
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| Street address |
Via Carlo Parea, 4
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| City |
Milano |
| ZIP/Postal code |
20138 |
| Country |
Italy |
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| Platform ID |
GPL23934 |
| Series (1) |
| GSE142205 |
Cardiac mesenchymal stromal cells from right and left ventricles display different biological properties. |
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| Relations |
| BioSample |
SAMN13615217 |
| SRA |
SRX7397645 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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