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36 results for “SMRT”
Optimized SMRT-UMI protocol produces highly accurate sequence datasets from diverse populations – application to HIV-1 quasispecies
<p>Pathogen diversity resulting in quasispecies can enable persistence and adaptation to host defenses and therapies. However, accurate quasispecies characterization can be impeded by errors introduced during sample handling and sequencing which can require extensive optimizations to overcome. We present complete laboratory and bioinformatics workflows to overcome many of these hurdles. The Pacific Biosciences single molecule real-time platform was used to sequence PCR amplicons derived from cDNA templates tagged with universal molecular identifiers (SMRT-UMI). Optimized laboratory protocols were developed through extensive testing of different sample preparation conditions to minimize between-template recombination during PCR and the use of UMI allowed accurate template quantitation as well as removal of point mutations introduced during PCR and sequencing to produce a highly accurate consensus sequence from each template. Handling of the large datasets produced from SMRT-UMI sequencing was facilitated by a novel bioinformatic pipeline, Probabilistic Offspring Resolver for Primer IDs (PORPIDpipeline), that automatically filters and parses reads by sample, identifies and discards reads with UMIs likely created from PCR and sequencing errors, generates consensus sequences, checks for contamination within the dataset, and removes any sequence with evidence of PCR recombination or early cycle PCR errors, resulting in highly accurate sequence datasets. The optimized SMRT-UMI sequencing method presented here represents a highly adaptable and established starting point for accurate sequencing of diverse pathogens. These methods are illustrated through characterization of human immunodeficiency virus (HIV) quasispecies.</p>
SMRT PacBio Sequel sequencing of 12 Silene herbarium specimens
<p>The folder includes reads sequenced with SMRT PacBio Sequel from twelve Silene herbarium specimens. Both demultiplexed and non demultiplexed reads are included. The demultiplexed reads are in folder called "demultiplexed.zip", in files starting with "Barcodenumber_speciesnamesamplingyear.fastq". The barcode number and sequence can be found below, in the description. The non demultiplexed reads are in file called "ps_248_001.ccsreads.fastq.gz".</p> <p>#NebNext Barcodes<br> #Adapter('Barcode 1 (forward)',<br> # start_sequence=('BC01', 'CGTGAT'),<br> # end_sequence=('BC01_rev', 'ATCACG')),<br> #Adapter('Barcode 2 (forward)',<br> # start_sequence=('BC02', 'ACATCG'),<br> # end_sequence=('BC02_rev', 'CGATGT')),<br> #Adapter('Barcode 3 (forward)',<br> # start_sequence=('BC03', 'GCCTAA'),<br> # end_sequence=('BC03_rev', 'TTAGGC')),<br> #Adapter('Barcode 4 (forward)',<br> # start_sequence=('BC04', 'TGGTCA'),<br> # end_sequence=('BC04_rev', 'TGACCA')),<br> #Adapter('Barcode 5 (forward)',<br> # start_sequence=('BC05', 'CACTGT'),<br> # end_sequence=('BC05_rev', 'ACAGTG')),<br> #Adapter('Barcode 6 (forward)',<br> # start_sequence=('BC06', 'ATTGGC'),<br> # end_sequence=('BC06_rev', 'GCCAAT')),<br> #Adapter('Barcode 7 (forward)',<br> # start_sequence=('BC07', 'GATCTG'),<br> # end_sequence=('BC07_rev', 'CAGATC')),<br> #Adapter('Barcode 8 (forward)',<br> # start_sequence=('BC08', 'TCAAGT'),<br> # end_sequence=('BC08_rev', 'ACTTGA')),<br> #Adapter('Barcode 9 (forward)',<br> # start_sequence=('BC09', 'CTGATC'),<br> # end_sequence=('BC09_rev', 'GATCAG')),<br> #Adapter('Barcode 10 (forward)',<br> # start_sequence=('BC10', 'AAGCTA'),<br> # end_sequence=('BC10_rev', 'TAGCTT')),<br> #Adapter('Barcode 11 (forward)',<br> # start_sequence=('BC11', 'GTAGCC'),<br> # end_sequence=('BC11_rev', 'GGCTAC')),<br> #Adapter('Barcode 12 (forward)',<br> # start_sequence=('BC12', 'TACAAG'),<br> # end_sequence=('BC12_rev', 'CTTGTA')),]</p> <p> </p>
Optimized SMRT-UMI protocol produces highly accurate sequence datasets from diverse populations – application to HIV-1 quasispecies
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SMRT sequencing data on four hypersuppressive Saccharomyces cereviciae mitochondrial DNAs
<p>Hypersuppressive mitochondrial DNAs are thought to be linear tandem repeats of the base unit of specific ORI regions on the mitochondrial genome. Here we confirm the linear tandem repeats using SMRT sequencing technology on four hypersuppressive clones. Mitochondrial DNA from four <em>Saccharomyces cervisiae</em> hypersuppressive mutants and a wild-type control was enriched and sequenced using SMRT sequencing technology.</p>
SMRT sequencing data on four hypersuppressive Saccharomyces cereviciae mitochondrial DNAs
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Znf687 recruits Brd4-Smrt complex to regulate gfi1aa expression during neutrophil development
GEO Series GSE235609. Danio rerio. 4 samples. Type: Expression profiling by high throughput sequencing.
An investigation of Burkholderia cepacia complex methylomes via SMRT sequencing and mutant analysis
GEO Series GSE147038. Burkholderia cenocepacia H111. 4 samples. Type: Expression profiling by high throughput sequencing.
N6-Methyladenine DNA Methylation in Japonica and Indica Rice Genomes and Its Association with Gene Expression, Plant Development, and Stress Responses[SMRT sequencing Nipponbare]
GEO Series GSE108783. Oryza sativa. 1 samples. Type: Methylation profiling by high throughput sequencing.
Corepressors (NCoR and SMRT) as well as Coactivators are Recruited to Positively Regulated 1α,25-Dihydroxyvitamin D3-Responsive Genes
GEO Series GSE39277. Homo sapiens. 10 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Methylome of Salmonella enterica subsp. Enterica serovar Javiana str. CFSAN001992 by PacBio SMRT Sequencing
GEO Series GSE45178. Salmonella enterica subsp. enterica serovar Javiana str. CFSAN001992. 1 samples. Type: Methylation profiling by high throughput sequencing.
SMRT-Cappable-seq reveals complex operon variants in bacteria
GEO Series GSE117273. Escherichia coli. 6 samples. Type: Expression profiling by high throughput sequencing; Other.
The corepressors GPS2 and SMRT control enhancer and silencer function linked to eRNA transcription during inflammatory activation of macrophages
GEO Series GSE130383. Mus musculus. 247 samples. Type: Genome binding/occupancy profiling by high throughput sequencing; Other; Expression profiling by high throughput sequencing.
Distinct roles of the corepressors NCOR and SMRT in shaping the macrophage epigenome and transcriptome linked to metabolic and inflammatory pathways
GEO Series GSE291538. Mus musculus. 21 samples. Type: Expression profiling by high throughput sequencing.
DNA N6-adenine methylation in Arabidopsis thaliana [SMRT-seq]
GEO Series GSE107002. Arabidopsis thaliana. 1 samples. Type: Methylation profiling by high throughput sequencing.
H2A.X SMRT-ChIP
GEO Series GSE71940. Mus musculus. 8 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Corepressors NCOR1 and SMRT regulate metabolism via intestinal regulation of carbohydrate transport
GEO Series GSE268594. Mus musculus. 6 samples. Type: Expression profiling by high throughput sequencing.
N6-Methyladenine DNA Methylation in Japonica and Indica Rice Genomes and Its Association with Gene Expression, Plant Development, and Stress Responses [SMRT sequencing 93-11]
GEO Series GSE108780. Oryza sativa. 1 samples. Type: Methylation profiling by high throughput sequencing.
Small RNA (sRNA), mRNA and SMRT sequencing data from pre-meiotic and meiotic anthers of Lilium Maculatum
GEO Series GSE97978. Lilium maculatum. 15 samples. Type: Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing.
Robust bisulfite free SMRT Sequencing of mdC based on a novel hpTet3-enzyme
GEO Series GSE256446. Escherichia phage Lambda. 5 samples. Type: Methylation profiling by high throughput sequencing.
Genome-wide mapping of SMRT (silencing mediator of retinoid and thyroid hormone receptors) occupancy in mouse liver at different Zeitgeber times (ZTs).
GEO Series GSE51045. Mus musculus. 2 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
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DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.