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| Status |
Public on Jul 30, 2024 |
| Title |
SIG_9060 |
| Sample type |
SRA |
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| Source name |
infected_f_blood
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| Organism |
Homo sapiens |
| Characteristics |
status: infected
Sex: f
tissue: blood
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| Treatment protocol |
Blood samples from patients and controls were collected and stored in PAX tubes. Project SIG-2019
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| Extracted molecule |
total RNA |
| Extraction protocol |
Whole blood RNA was extracted from PAX gene tubes as described in the manufacturer’s protocol (QIAGEN PreAnalytiX)
Quality and integrity of total RNA was controlled on Agilent Technologies 2100 Bioanalyzer (Agilent Technologies; Waldbronn, Germany). Library construction: Globin mRNA was depleted from total RNA using GLOBINclear Kit, human (ThermoFisher, Invitrogen). Subsequently, a strand-specific RNA sequencing library was generated using NEBNext® Ultra II Directional RNA Library Prep Kit (New England Biolabs) according to manufacturer’s protocols.
The library was sequenced on Illumina HiSeq 4000 using HiSeq 3000/4000 SBS Kit (300 cycles) with an average of 40 million reads per RNA sample
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Data processing |
Reads were quality checked with package FastQC (version 0.11.4, reference see link below), then trimmed using Trimgalore (version 0.4.4, reference see link below) with default settings.
Trimmed reads were mapped to human genome annotation hg38 (ENSMBL hg38 release 91) using STAR (version 2.5.2b, (Dobin and Gingeras, 2015)) with default settings.
Mapped reads were counted using RsubRead (version 1.32.4, (Liao et al., 2019)). Reads for beta-globin were set to 1000. Raw counts were then normalized using DESeq2 (version 1.16.1, (Love et al., 2014)).
Sex was validated by gene expression for Y-specific genes and corrected if different from recorded sex.
Genome_build: ENSMBL hg38 release 91
Supplementary_files_format_and_content: txt matrix with log2 normalized values per sample.
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| Submission date |
Aug 03, 2020 |
| Last update date |
Jul 30, 2024 |
| Contact name |
Klaus Schughart |
| E-mail(s) |
[email protected]
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| Phone |
+49-159-0483-7911
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| Organization name |
University Münster
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| Department |
Virology
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| Street address |
Von-Esmarch-Str 56
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| City |
Münster |
| ZIP/Postal code |
48149 |
| Country |
Germany |
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| Platform ID |
GPL20301 |
| Series (1) |
| GSE155635 |
RNAseq analysis of blood from influenza infected patients and healthy controls-SIG2019 |
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| Relations |
| Reanalyzed by |
GSE272879 |
| BioSample |
SAMN15716899 |
| SRA |
SRX8875539 |
| 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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