NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM6730948 Query DataSets for GSM6730948
Status Public on Jan 30, 2023
Title Whole blood, COVID positive, rep 87
Sample type SRA
 
Source name Whole blood
Organism Homo sapiens
Characteristics tissue: Whole blood
disease state: COVID positive
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).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
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
 
Submission date Nov 14, 2022
Last update date Feb 01, 2023
Contact name Tracy Chew
Organization name University of Sydney
Department Sydney Informatics Hub
Street address Merewether Building (H04) City Rd & Butlin Ave
City Darlington
State/province NSW
ZIP/Postal code 2008
Country Australia
 
Platform ID GPL24676
Series (1)
GSE217948 COVID-19 patient samples collected by the PREDICT-19 consortium
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 SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap