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View article: Application of Pan-Viral Metagenomic Sequencing on United States Air Force Academy Wastewater to Uncover Potential Causes of Acute Gastroenteritis
Application of Pan-Viral Metagenomic Sequencing on United States Air Force Academy Wastewater to Uncover Potential Causes of Acute Gastroenteritis Open
Introduction Wastewater surveillance is an important technique to monitor public health and is being studied extensively for pandemic prevention, force health protection and readiness, and as a potential early warning system for chem-bio d…
View article: Evaluation of noninvasive biospecimens for transcriptome studies
Evaluation of noninvasive biospecimens for transcriptome studies Open
Transcriptome studies disentangle functional mechanisms of gene expression regulation and may elucidate the underlying biology of disease processes. However, the types of tissues currently collected typically assay a single post-mortem tim…
View article: Capture Sequencing Enables Sensitive Detection of Tick-Borne Agents in Human Blood
Capture Sequencing Enables Sensitive Detection of Tick-Borne Agents in Human Blood Open
Assay sensitivity can be a limiting factor in the use of PCR as a tool for the detection of tick-borne pathogens in blood. We evaluated the performance of Tick-borne disease Capture Sequencing Assay (TBDCapSeq), a capture sequencing assay …
View article: SARS-CoV-2 Sequence Analysis during COVID-19 Case Surge, Liberia, 2021
SARS-CoV-2 Sequence Analysis during COVID-19 Case Surge, Liberia, 2021 Open
In June 2021, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) cases surged in Liberia. SARS-CoV-2 sequences from patients hospitalized during March-July 2021 revealed the Delta variant was in Liberia in early March and was dom…
View article: An autoimmune disease risk variant: A trans master regulatory effect mediated by IRF1 under immune stimulation?
An autoimmune disease risk variant: A trans master regulatory effect mediated by IRF1 under immune stimulation? Open
Functional mechanisms remain unknown for most genetic loci associated to complex human traits and diseases. In this study, we first mapped trans -eQTLs in a data set of primary monocytes stimulated with LPS, and discovered that a risk vari…
View article: Development of a capture sequencing assay for enhanced detection and genotyping of tick-borne pathogens
Development of a capture sequencing assay for enhanced detection and genotyping of tick-borne pathogens Open
Inadequate sensitivity has been the primary limitation for implementing high-throughput sequencing for studies of tick-borne agents. Here we describe the development of TBDCapSeq, a sequencing assay that uses hybridization capture probes t…
View article: Tension promotes kinetochore–microtubule release by Aurora B kinase
Tension promotes kinetochore–microtubule release by Aurora B kinase Open
To ensure accurate chromosome segregation, interactions between kinetochores and microtubules are regulated by a combination of mechanics and biochemistry. Tension provides a signal to discriminate attachment errors from bi-oriented kineto…
View article: Transcriptome variation in human tissues revealed by long-read sequencing
Transcriptome variation in human tissues revealed by long-read sequencing Open
Summary Regulation of transcript structure generates transcript diversity and plays an important role in human disease. The advent of long-read sequencing technologies offers the opportunity to study the role of genetic variation in transc…
View article: A polyclonal allelic expression assay for detecting regulatory effects of transcript variants
A polyclonal allelic expression assay for detecting regulatory effects of transcript variants Open
We present an assay to experimentally test the regulatory effects of genetic variants within transcripts using CRISPR/Cas9 followed by targeted sequencing. We applied the assay to 32 premature stop-gained variants across the genome and in …
View article: Tension promotes kinetochore-microtubule release in response to Aurora B activity
Tension promotes kinetochore-microtubule release in response to Aurora B activity Open
Aurora B kinase regulates kinetochore-microtubule interactions to ensure accurate chromosome segregation in cell division. Tension provides a signal to discriminate attachment errors from bi-oriented kinetochores with sisters correctly att…
View article: An autoimmune disease risk variant has a<i>trans</i>master regulatory effect mediated by IRF1 under immune stimulation
An autoimmune disease risk variant has a<i>trans</i>master regulatory effect mediated by IRF1 under immune stimulation Open
Functional mechanisms remain unknown for most genetic loci associated to complex human traits and diseases. In this study, we first mapped trans -eQTLs in a data set of primary monocytes stimulated with LPS, and discovered that a risk vari…
View article: Additional file 1 of A polyclonal allelic expression assay for detecting regulatory effects of transcript variants
Additional file 1 of A polyclonal allelic expression assay for detecting regulatory effects of transcript variants Open
Additional file 1. Table S1. Information on the variants chosen for editing.
View article: Additional file 2 of A polyclonal allelic expression assay for detecting regulatory effects of transcript variants
Additional file 2 of A polyclonal allelic expression assay for detecting regulatory effects of transcript variants Open
Additional file 2. Table S2. Reference and alternate allele counts in cDNA and gDNA sequencing samples after editing variants.
View article: Additional file 3 of A polyclonal allelic expression assay for detecting regulatory effects of transcript variants
Additional file 3 of A polyclonal allelic expression assay for detecting regulatory effects of transcript variants Open
Additional file 3. Table S3. Effect sizes of edited variants which passed QC filtering steps.
View article: A polyclonal allelic expression assay for detecting regulatory effects of transcript variants
A polyclonal allelic expression assay for detecting regulatory effects of transcript variants Open
We present an assay to experimentally test regulatory effects of genetic variants within transcripts using CRISPR/Cas9 followed by targeted sequencing. We applied the assay to 35 premature stop-gained variants across the genome and in two …
View article: polyclonal_editing_fastq_files
polyclonal_editing_fastq_files Open
FASTQs from amplicon sequencing of cDNA and gDNA after CRISPR editing of putative regulatory and control variants. Files are contained in tarballs grouped by sequencing run. 20190312 is a rerun of the same samples from 20190308 to increase…
View article: Polyclonal Allelic Expression Assay Protocol v2
Polyclonal Allelic Expression Assay Protocol v2 Open
Polyclonal allelic expression assay for detecting the regulatory effects of genetic variants within transcripts using CRISPR/Cas9 genome editing and amplicon sequencing.
View article: Polyclonal Allelic Expression Assay Protocol v1
Polyclonal Allelic Expression Assay Protocol v1 Open
Polyclonal allelic expression assay for detecting the regulatory effects of genetic variants within transcripts using CRISPR/Cas9 genome editing and amplicon sequencing.
View article: polyclonal_editing_fastq_files
polyclonal_editing_fastq_files Open
FASTQs from amplicon sequencing of cDNA and gDNA after CRISPR editing of putative regulatory and control variants. Files are contained in tarballs grouped by sequencing run. 20190312 is a rerun of the same samples from 20190308 to increase…