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| Status |
Public on Jun 29, 2022 |
| Title |
CAD_09 [EP00126] |
| Sample type |
SRA |
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| Source name |
Peripheral blood
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| Organism |
Homo sapiens |
| Characteristics |
tissue: Whole blood
group: coronary artery disease (CAD)
Sex: F
age: 62
sequencing batch: RunID_5
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using KingFisher Flex Purification system and MagMax for Stabilized Blood Tube RNA Isolation kit (Thermo Fisher Scientific), following manufacturer's instructions, and precipitated through ammonium acetate/ethanol method. α and β-globin mRNAs depletion were performed from precipitated total RNA using the GLOBINclearTM Human kit (Applied Biosystems)
Poly(A)+ RNA enrichment followed the Dynabeads mRNA Purification 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/GRCh38.99, 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 GRCh38.99 release.
Assembly: HG38/GRCh38.99
Supplementary files format and content: Tab-delimited text files include raw counts for each Sample. The header of the files reports gene name, sample identifiers.
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| Submission date |
May 10, 2022 |
| Last update date |
Jun 29, 2022 |
| 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) |
| GSE202625 |
Whole-blood transcriptional profiles early predict the presence of coronary atherosclerosis and high-risk plaque features at coronary CT angiography |
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| Relations |
| BioSample |
SAMN28175254 |
| SRA |
SRX15221334 |
| 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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