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| Status |
Public on Aug 19, 2021 |
| Title |
15-031_Mild_12_W.P.I. [3F2] |
| Sample type |
SRA |
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| Source name |
Peripheral blood
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| Organism |
Homo sapiens |
| Characteristics |
age: 25.1835616438356
Sex: Female
disease severity: Mild
rin: 8.5
tissue: Peripheral blood
subject_id: 15-031
timepoint: 12wpi
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extraction and genomic DNA elimination was carried out using the PAXgene® Blood RNA kit (762164, Qiagen, Feldbachstrasse, Germany) as per the manufacturer’s instructions
Total RNA was converted to strand-specific Illumina compatible sequencing libraries using the Nugen Universal Plus Total RNA-Seq library kit from Tecan (Mannedorf, Switzerland) as per the manufacturer’s instructions (MO1523 v2) using 12 cycles of PCR amplification for the final libraries. An Anydeplete probe mix targeting both human ribosomal and adult globin transcripts (HBA1, HBA2, HBB, HBD) was used to deplete these transcripts.
Total RNA-Seq 2x150 bp paired-end reads.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
P3F2
15-031_Female_Mild_12_W.P.I._Total RNA
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| Data processing |
Quality control with Trimmomatic version 0.38
Gene count matrix was generated with FeatureCounts version 1.5.0-p2 and Ensembl 101
Aligned to genome using HISAT2 version 2.1.0
Genome_build: GRCh38
Supplementary_files_format_and_content: FeatureCounts per gene counts
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| Submission date |
Aug 18, 2021 |
| Last update date |
Aug 19, 2021 |
| Contact name |
Feargal J Ryan |
| E-mail(s) |
feargal.ryan@sahmri.com
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| Organization name |
SAHMRI
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| Street address |
North Terrace
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| City |
Adelaide |
| State/province |
Adelaide |
| ZIP/Postal code |
5021 |
| Country |
Australia |
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| Platform ID |
GPL24676 |
| Series (1) |
| GSE169687 |
Long-term perturbation of the blood transcriptome months after SARS-CoV-2 infection. |
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| Relations |
| BioSample |
SAMN20848675 |
| SRA |
SRX11809457 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5527532_P3F2.featureCounts.txt.gz |
3.2 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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