NYU Medical Center ICU cohort lower airway RNA-seq
Year: 2026
Type: dataset
Abstract: Critically ill COVID-19 subjects were enrolled from March 3rd, 2020 to July 21st, 2022. Patients with laboratory-confirmed SARS-CoV-2 infection were recruited upon admission to the intensive care unit. Research bio-specimens collected included peripheral blood and lower airway respiratory samples (obtained via endotracheal suctioning or bronchoalveolar lavage) obtained via endotracheal suctioning or bronchoalveolar lavage. RNA was isolated using ZymoBIOMIC DNA/RNA Miniprep Kit (Zymo cat #R2002) per the manufacturer’s instructions. RNA library prep was performed on a Beckman-Coulter Biomek FXp workstation using the Trio RNA-Seq Library Preparation Kit (Tecan, Cat# 0506-A01). RNA obtained from lower airway samples went for RNA sequencing. Samples were added in an equimolar manner to two sequencing pools, quantified using the KAPA Library Quantification Kit (Illumina). RNA quantity and integrity were tested with a BioAnalyzer 2100 (Agilent). The Nugen Ovation Trio Low Input RNA method was used for library preparation with 3 ng RNA/sample. Samples were sequenced using 2x Illumina NovaSeq 6000 S4 200 cycle Flowcells using PE100 sequencing after six cycles. Trimmomatic (v0.3665) was used to remove adaptor sequences (leading and trailing values at 3 and minimum length at 36) and removed rRNA reads from the metatranscriptome using SortMeRNA (v.4.2.0).Human genome reads were mapped using Bowtie2 (v2.3.4.166). Transcriptomic reads were analyzed using Rsubread v2.10.5.
Source: Figshare
Language: English
Subfield: Infectious Diseases
Field: Medicine
Domain: Health Sciences
Open Access status: green
OpenAlex ID: W7167937364