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Sample GSM5242325 Query DataSets for GSM5242325
Status Public on Apr 15, 2021
Title SARS-CoV-2 titration - 5 - rep2
Sample type SRA
 
Source name Saliva
Organism Homo sapiens
Characteristics technology: COV-ID
virus added: SARS-CoV-2
experiment: titration
viral concentration: 5
Treatment protocol Heat-inactivated SARS-CoV-2 (BEI Resources Cat. NR-52286) or H1N1 genomic RNA (Twist Biosciences Cat. 103001) was added to inactivated saliva prior to RT-LAMP.
Growth protocol Saliva was harvested from human donors
Extracted molecule total RNA
Extraction protocol We prepared 100x TCEP/EDTA buffer (250 mM TCEP, 100 mM EDTA, 1.15 N NaOH) 29. TCEP/EDTA buffer was added to human saliva at 1:100 volume, then samples were capped, vortexed to mix and heated in a thermocycler (95ºC 5 min, 4ºC hold) until ready to use for RT-LAMP.
1 μL of diluted LAMP material was used as a template for PCR using OneTaq DNA polymerase (NEB Cat. M0480L) with 100 nM each of custom dual-indexed Illumina P5 and P7 primers in either 10 or 25 μL reaction. PCR reactions were incubated as follows: (25 cycles of stage 1 [94ºC x 15 sec, 45ºC x 15 sec, 68ºC x 10 sec], 10 cycles of Stage 2 [ 94ºC x 15 sec, 68ºC x 10 sec], 68ºC x 1 min, 4ºC x ∞).
 
Library strategy OTHER
Library source transcriptomic
Library selection other
Instrument model Illumina NovaSeq 6000
 
Description processed data file:
titration.count.table.tsv
200901.FGC2160.ACACGTGT-AGCAATGG.gz
210414.RWT.Bonasio.sample20
Data processing library strategy: COV-ID
Reads were filtered for optical quality using FASTX-toolkit utility fastq_quality_filter (http://hannonlab.cshl.edu/fastx_toolkit/), then cutadapt45 was used to remove adapters and demultiplex LAMP barcodes.
Genome_build: Reads were aligned to a custom index containing SARS-CoV-2 genome (NC_045512.2), Influenza H1N1 coding sequences (NC_026431.1, NC_026432.1, NC_026433.1, NC_026434.1, NC_026435.1, NC_026436.1, NC_026437.1, NC_026438.1), STATH coding sequence (NM_003154.3), and custom N2 spike sequence.
Supplementary_files_format_and_content: Tab-delimited text files containing summaries of aligned raw reads to control sequences and viral genomes for each experiment
 
Submission date Apr 15, 2021
Last update date Feb 04, 2022
Contact name Roberto Bonasio
Organization name University of Pennsylvania
Department Cell and Developmental Biology
Lab Bonasio
Street address 3400 Civic Center Blvd - SCTR 9-111
City Philadelphia
State/province PA
ZIP/Postal code 19104
Country USA
 
Platform ID GPL24676
Series (1)
GSE172118 COV-ID: A LAMP sequencing approach for high-throughput co-detection of SARS-CoV-2 and influenza virus in human saliva
Relations
BioSample SAMN18746776
SRA SRX10605626

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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