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| Status |
Public on Jan 30, 2023 |
| Title |
Whole blood, COVID positive, rep 87 |
| Sample type |
SRA |
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| Source name |
Whole blood
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| Organism |
Homo sapiens |
| Characteristics |
tissue: Whole blood
disease state: COVID positive
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from whole blood samples stored and stabilized in PAXgene RNA tubes according to the manufacturer's guidelines (PreAnalytiX)
Libraries were prepared with 300ng of total RNA per sample using the Illumina Stranded Total RNA Prep with Ribo-Zero Plus (RZP) as per manufacturer instructions (Illumina, CA, USA).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
RNASeq-DE workflow (v1.0.0), available online at https://github.com/Sydney-Informatics-Hub/RNASeq-DE
3’ adapter and polyA tails were trimmed from raw sequence reads with BBDuk (v37.89)
Quality checked, trimmed reads were aligned as pairs to the human reference genome, GRCh38 primary assembly and gene set release 106 (obtained from Ensembl) with STAR, setting –sjdbOverhand to 149
Sequencing batch level binary alignment (BAM) files were merged and indexed with SAMtools (v1.10) to obtain sample level BAMs.
HTSeq-count (v0.12.4) with -s reverse was used to obtain feature level raw counts.
Assembly: GRCh38
Supplementary files format and content: HTSeq-count output, containing raw counts per sample
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| Submission date |
Nov 14, 2022 |
| Last update date |
Feb 01, 2023 |
| Contact name |
Tracy Chew |
| Organization name |
University of Sydney
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| Department |
Sydney Informatics Hub
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| Street address |
Merewether Building (H04) City Rd & Butlin Ave
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| City |
Darlington |
| State/province |
NSW |
| ZIP/Postal code |
2008 |
| Country |
Australia |
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| Platform ID |
GPL24676 |
| Series (1) |
| GSE217948 |
COVID-19 patient samples collected by the PREDICT-19 consortium |
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| Relations |
| BioSample |
SAMN31714351 |
| SRA |
SRX18257583 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6730948_nCWES052d6.counts.txt.gz |
210.8 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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