 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Jul 30, 2024 |
| Title |
SIG 2077 |
| Sample type |
SRA |
| |
|
| Source name |
blood
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: blood
treatment: infected
gender: f
|
| Treatment protocol |
Blood samples from patients and controls were collected and stored in PAX tubes.
|
| 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 NovaSeq S4 6000 SBS Kit (300 cycles) with an average of 80M PE reads (40M in each direction).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Reads were quality checked with package FastQC (version 0.11.9), then trimmed using Trimgalore (version 0.6.7) with default settings.
Trimmed reads were mapped to human genome annotation hg38 (ENSMBL hg38 release 91) using STAR (version 2.7.9a) with default settings.
Mapped reads were counted using RsubRead (version 2.8.1). Reads for beta-globin were set to 1000. Raw counts were then normalized using DESeq2 (version 1.26.0).
Assembly: ENSMBL hg38 release 91
Supplementary files format and content: txt matrix with log2 normalized values per sample.
|
| |
|
| Submission date |
Sep 12, 2022 |
| Last update date |
Jul 30, 2024 |
| Contact name |
Klaus Schughart |
| E-mail(s) |
[email protected]
|
| Phone |
+49-159-0483-7911
|
| Organization name |
University Münster
|
| Department |
Virology
|
| Street address |
Von-Esmarch-Str 56
|
| City |
Münster |
| ZIP/Postal code |
48149 |
| Country |
Germany |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE213168 |
RNAseq analysis of blood from influenza infected patients and healthy controls, project SIG_2022 |
|
| Relations |
| BioSample |
SAMN30809680 |
| SRA |
SRX17535244 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
