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| Status |
Public on Apr 15, 2021 |
| Title |
SARS-CoV-2 titration - 640 - rep1 |
| Sample type |
SRA |
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| Source name |
Saliva
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| Organism |
Homo sapiens |
| Characteristics |
technology: COV-ID
virus added: SARS-CoV-2
experiment: titration
viral concentration: 640
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| 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.
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| Growth protocol |
Saliva was harvested from human donors
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| 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 ∞).
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| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
processed data file:
titration.count.table.tsv
200901.FGC2160.ACACGTGT-TGCGTTCT.gz
210414.RWT.Bonasio.sample05
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| 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
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| Submission date |
Apr 15, 2021 |
| Last update date |
Feb 04, 2022 |
| Contact name |
Roberto Bonasio |
| Organization name |
University of Pennsylvania
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| Department |
Cell and Developmental Biology
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| Lab |
Bonasio
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| Street address |
3400 Civic Center Blvd - SCTR 9-111
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| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19104 |
| Country |
USA |
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| 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 |
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| Relations |
| BioSample |
SAMN18746791 |
| SRA |
SRX10605611 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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