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Sample GSM7865475 Query DataSets for GSM7865475
Status Public on May 20, 2024
Title L1 24h SARS
Sample type SRA
 
Source name Lung
Organism Homo sapiens
Characteristics tissue: Lung
treatment: SARS
Treatment protocol Precision-Cut Lung slices (PCLS) were infected with 500K or 50K pfu for 24.48 or 72h (n=3 slices per condition)
Growth protocol Culture in DMEM 1%PS, 10% FCS
Extracted molecule total RNA
Extraction protocol PCLSs were enzymatically and mechanically dissociated. Single cell suspension was used for the 10X encapsulation. Cells were counted and the targeted cell number for loading was 8000 cells per sample.
10X encapsulation and library construction were done using Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 per the manufacturer’s instruction. Multi-seq library preparation was done as previously described. Libraries were mixed at an approximate 10:1 molar ratio of gene expression to LMO barcodes for sequencing. The sequencing was done on the Illumina NovaSeq 6000 using 10X Genomics recommended sequencing parameters.
 
Library strategy RNA-Seq
Library source transcriptomic single cell
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Description 10x Genomics
Data processing Sequencer-generated bcl data (Gene expression and Lipid Hashtag) was demultiplexed into individual fastq libraries using the mkfastq command on the Cellranger 3.0.2 suite of tools (https://support.10xgenomics.com)
Raw gene-expression fastqs were aligned to the GRCh38 reference genome annotated with Ensembl v85, and Lipid Hashtag fastqs were processed to count the incidences of each expected index per cell.
Feature-barcode matrices were read into Seurat 4.0.1 and poorly captured genes (in < 3 cells) were dropped from the analyses.
Matrices were further filtered to remove events with greater than 20% mitochondrial content, events with greater than 50% ribosomal content, or events with fewer than 100 total genes.
Data quality control and nornalization
Assembly: GRCh38 reference genome
Supplementary files format and content: HDF5 feature barcode matrix format
 
Submission date Oct 25, 2023
Last update date May 20, 2024
Contact name Bushra Samad
E-mail(s) Bushra.Samad@ucsf.edu
Organization name USCF Immunoprofiler
Street address 505 Parnassus Ave
City San Francisco
State/province CA
ZIP/Postal code 94143
Country USA
 
Platform ID GPL24676
Series (1)
GSE246242 Immediate myeloid depot for SARS-CoV-2 in the human lung
Relations
BioSample SAMN37984842
SRA SRX22226500

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA

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