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30,948 results for “Profile”
Supplemental data for "Transcriptomic Profiling of the Bovine Endosalpinx and Endometrium to Identify Putative Embryokines"
<p>Supplemental data for paper describing expression of genes encoding for cell-signaling ligands in the oviduct and endometrium of cows. </p>
BSSE_QGF_61757 L010-L016 (Single-cell mRNA profiling reveals the hierarchical response of miRNA targets to miRNA induction)
<p>Fastq files from sequencing of sample BSSE_QGF_61757 L010 to L016</p> <p>Publication: https://doi.org/10.15252/msb.20188266</p>
BSSE_QGF_61757 L001-L009 (Single-cell mRNA profiling reveals the hierarchical response of miRNA targets to miRNA induction)
<p>Fastq files from sequencing of sample BSSE_QGF_61757 L001 to L009</p> <p>Publication: https://doi.org/10.15252/msb.20188266</p>
BSSE_QGF_61756 (Single-cell mRNA profiling reveals the hierarchical response of miRNA targets to miRNA induction)
<p>Fastq files from sequencing of sample BSSE_QGF_61756</p> <p>Publication: https://doi.org/10.15252/msb.20188266</p>
BSSE_QGF_61759 (Single-cell mRNA profiling reveals the hierarchical response of miRNA targets to miRNA induction)
<p>Fastq files from sequencing of sample BSSE_QGF_61759</p> <p>Publication: https://doi.org/10.15252/msb.20188266</p>
BSSE_QGF_61758 (Single-cell mRNA profiling reveals the hierarchical response of miRNA targets to miRNA induction)
<p>Fastq files from sequencing of sample BSSE_QGF_61758</p> <p>Publication: https://doi.org/10.15252/msb.20188266</p>
Transcriptomic profiles of MCF7-derived tamoxifen resistant cell lines
<p>We report mRNA profiles of human breast cancer cell lines, MCF7 parental, and MCF7-derived tamoxifen-resistant cell lines MCF7-TR1 and MCF7-TR2.</p> <p>These cells have been previously described in </p> <p>Ines Barone, Lauren Brusco, Guowei Gu, Jennifer Selever, Amanda Beyer, Kyle R. Covington, Anna Tsimelzon, Tao Wang, Susan G. Hilsenbeck, Gary C. Chamness, Sebastiano Andò, and Suzanne A.W. Fuqua. Loss of Rho GDIα and Resistance to Tamoxifen via Effects on Estrogen Receptor α. J Natl Cancer Inst. 2011 Apr 6; 103(7): 538–552. PMID: 21447808</p>
Gradients 5 - Hyperpro Profiles
<p>This dataset was collected on the R/V Thompson during the Gradients V cruise which departed from San Diego, CA and ended in Honolulu, HI. A transect was performed on the 140 degree longitude line from roughly 16 degrees N to 4 degrees S before heading to Honolulu. The Satlantic (now Seabird) HyperPro is an in-situ free-fall profiling unit designed to measure the apparent optical properties of the ocean with concurrent measurements of temperature, salinity, chlorophyll and dissolved matter fluorescence, and optical backscattering (a proxy for total particle load). The unit is equipped with one up-looking and one down-looking hyperspectral (350-800nm) radiometer with 10 ± 0.3 nm resolution, a WET Labs ECO-Puck Triplet, and temperature, pressure, and conductivity sensors. It also incorporates a ship-mounted surface (air) hyperspectral radiometer. These data are collated from the vertical profiles. Note that lat/lon was pulled from the Station ID and may not exactly match the ship's cruise log. Time in UTC.</p>
Gradients 5 - LISST DEEP Profiles
<p>This dataset was collected on the R/V Thompson during the Gradients V cruise which departed from San Diego, CA and ended in Honolulu, HI. A transect was performed on the 140 degree longitude line from roughly 16 degrees N to 4 degrees S before heading to Honolulu. A Sequoia Scientific LISST-DEEP instrument was mounted to the R/V Thompson's rosette and ctd system and operated during CTD casts. The data presented here are blank-corrected using a deepwater background scattering calibration, and binned in 2-meter bins from 2 to 200m depths. The summed volume concentration of particles (in uL/L), the standard LISST output, is presented for 3 size ranges: 1.25-2 µm, 2-20 µm, and 20-100 µm. Note that data have not been processed to remove outliers. Time is in UTC.</p>
Unidirectional spin wave emission by travelling pair of magnetic field profiles
<p>This is the full data for this paper: https://arxiv.org/pdf/2307.12653.pdf</p> <p>G. P. anf J. W. K. would like to acknowledge the erasmus mundus MaMaSELF programm and the support from the National Science Center – Poland grant No. 2021/43/I/ST3/00550</p>
PARAGON 1 - KM2112 - LISST DEEP Profiles
<p>These Simons Collaboration on Ocean Processes and Ecology (SCOPE) data products were produced by the University of Hawaiʻi at Mānoa with support from the Simons Foundation.</p> <p>This dataset was collected on the R/V Kilo Moana, which departed and returned to Honolulu, HI, with most of the cruise spent following an anticyclonic eddy northeast of the Hawaiian islands. A Sequoia Scientific LISST-100X instrument performed yo-yo profiles to 200m depth. The data presented here are blank-corrected using a deepwater background scattering calibration, and binned in 2-meter bins from 2 to 200m depths. Note that data have not been processed to remove outliers. Time stamp is in UTC.</p>
Lipidomic profiling of SPNS1-KO lysosomes
<p>Lysosomes degrade macromolecules and recycle their nutrient content to support cell function and survival. Yet, the machineries involved in lysosomal recycling of many nutrients remain to be discovered, with a notable example being choline, an essential metabolite liberated via phospholipid degradation. Here, we engineered metabolic dependency on lysosome-derived choline in pancreatic cancer cells to perform an endolysosome-focused CRISPR-Cas9 screen for genes mediating lysosomal choline recycling. We identified the orphan lysosomal transmembrane protein SPNS1 as critical for cell survival under choline limitation. SPNS1 loss leads to intralysosomal accumulation of lysophosphatidylcholine (LPC) and lysophosphatidylethanolamine (LPE). Mechanistically, we reveal that SPNS1 is a proton gradient-dependent transporter of LPC species from the lysosome for their re-esterification into phosphatidylcholine in the cytosol. Finally, we establish that LPC efflux by SPNS1 is required for cell survival under choline limitation. Collectively, our work defines a lysosomal phospholipid salvage pathway that is essential under nutrient limitation, and more broadly, provides a robust platform to deorphan lysosomal gene function.</p>
PARAGON 2 - KM2209 - Hyperpro Profiles
<p>These Simons Collaboration on Ocean Processes and Ecology (SCOPE) data products were produced by the University of Hawaiʻi at Mānoa with support from the Simons Foundation.</p> <p>This dataset was collected on the R/V Kilo Moana during the PARAGON 2 cruise which departed from and returned to Honolulu, HI. The cruise track was Lagrangian, following free-floating arrays deployed in a chlorophyll bloom feature. The Satlantic (now Seabird) HyperPro is an in-situ free-fall profiling unit designed to measure the apparent optical properties of the ocean with concurrent measurements of temperature, salinity, chlorophyll and dissolved matter fluorescence, and optical backscattering (a proxy for total particle load). The unit is equipped with one up-looking and one down-looking hyperspectral (350-800nm) radiometer with 10 ± 0.3 nm resolution, a WET Labs ECO-Puck Triplet, and temperature, pressure, and conductivity sensors. It also incorporates a ship-mounted surface (air) hyperspectral radiometer. These data are collated from the vertical profiles. Note that lat/lon was hand recorded at time of deployment and may not exactly match the ship's cruise log. Time stamp is in UTC.</p>
PARAGON 1 - KM2112 - Hyperpro Profiles
<p>These Simons Collaboration on Ocean Processes and Ecology (SCOPE) data products were produced by the University of Hawaiʻi at Mānoa with support from the Simons Foundation.</p> <p>This dataset was collected on the R/V Kilo Moana, which departed and returned to Honolulu, HI, with most of the cruise spent following an anticyclonic eddy northeast of the Hawaiian islands. The Satlantic (now Seabird) HyperPro is an in-situ free-fall profiling unit designed to measure the apparent optical properties of the ocean with concurrent measurements of temperature, salinity, chlorophyll and dissolved matter fluorescence. The unit is equipped with one up-looking and one down-looking hyperspectral (350-800nm) radiometer with 10 ± 0.3 nm resolution, a WET Labs ECO-Puck Triplet, and temperature, pressure, and conductivity sensors. It also incorporates a ship-mounted surface (air) hyperspectral radiometer. These data are collated from the vertical profiles. Note that lat/lon was hand recorded at time of deployment and may not exactly match the ship's cruise log. Time stamp is in UTC.</p>
Clinical subtyping of cancer from plasma based on comprehensive epigenomic profiling
<p><em><strong>Fragment bed files part 1.</strong></em></p> <p> </p> <p>While circulating tumor DNA (ctDNA) assays are increasingly used to inform clinical decisions in cancer care, they have limited ability to identify the transcriptional programs that govern cancer phenotypes and their dynamic changes during the course of disease. To address these limitations, we developed a method for comprehensive epigenomic profiling of cancer from 1mL of patient plasma. Using an immunoprecipitation-based approach targeting histone modifications and DNA methylation, we measured 1,268 epigenomic profiles in plasma from 433 individuals with one of 15 cancers. Our assay provided a robust proxy for transcriptional activity, allowing us to infer the expression levels of diagnostic markers and drug targets, measure the activity of therapeutically targetable transcription factors, and detect epigenetic mechanisms of resistance. This proof-of-concept study in advanced cancers shows how plasma epigenomic profiling could unlock clinically actionable information that is currently accessible only via direct tissue sampling. </p> <div class="notranslate"> </div>
Clinical subtyping of cancer from plasma based on comprehensive epigenomic profiling
<p><strong><em>Fragment bed files part 2.</em></strong></p> <p>While circulating tumor DNA (ctDNA) assays are increasingly used to inform clinical decisions in cancer care, they have limited ability to identify the transcriptional programs that govern cancer phenotypes and their dynamic changes during the course of disease. To address these limitations, we developed a method for comprehensive epigenomic profiling of cancer from 1mL of patient plasma. Using an immunoprecipitation-based approach targeting histone modifications and DNA methylation, we measured 1,268 epigenomic profiles in plasma from 433 individuals with one of 15 cancers. Our assay provided a robust proxy for transcriptional activity, allowing us to infer the expression levels of diagnostic markers and drug targets, measure the activity of therapeutically targetable transcription factors, and detect epigenetic mechanisms of resistance. This proof-of-concept study in advanced cancers shows how plasma epigenomic profiling could unlock clinically actionable information that is currently accessible only via direct tissue sampling. </p> <p> </p>
Clinical subtyping of cancer from plasma based on comprehensive epigenomic profiling
<p><strong><em>Peak bed files.</em></strong></p> <p> </p> <p>While circulating tumor DNA (ctDNA) assays are increasingly used to inform clinical decisions in cancer care, they have limited ability to identify the transcriptional programs that govern cancer phenotypes and their dynamic changes during the course of disease. To address these limitations, we developed a method for comprehensive epigenomic profiling of cancer from 1mL of patient plasma. Using an immunoprecipitation-based approach targeting histone modifications and DNA methylation, we measured 1,268 epigenomic profiles in plasma from 433 individuals with one of 15 cancers. Our assay provided a robust proxy for transcriptional activity, allowing us to infer the expression levels of diagnostic markers and drug targets, measure the activity of therapeutically targetable transcription factors, and detect epigenetic mechanisms of resistance. This proof-of-concept study in advanced cancers shows how plasma epigenomic profiling could unlock clinically actionable information that is currently accessible only via direct tissue sampling. </p>
Germplasm diversity of sunflower volatile terpenoid profiles across vegetative and reproductive organs
<p>Cultivated sunflower (<em>Helianthus</em> <em>annuus</em>) is the fourth most important oilseed crop globally and is known to have experienced multiple genetic bottlenecks during domestication and improvement. Homogenization of crop germplasm may limit breeding efforts to improve pest and pathogen resistance or optimize other biotic interactions like pollinator attraction. Such interactions are often strongly influenced by plant phytochemistry, especially volatile compounds like terpenoids. Here we use solid-phase microextraction gas chromatography mass spectrometry (SPME GC-MS) to evaluate volatile phytochemistry across leaves, involucral bracts, disc florets, and ray floret petals in a collection of twelve inbred lines selected to represent a cross-section of sunflower germplasm diversity. Results indicate considerable compositional diversity of volatiles among lines, though substantial reduction in total volatile abundance relative to wild <em>H. annuus</em>. From leaves and bracts to disc florets and petals, we observe a strong increase in the proportion of monoterpenoids relative to sesquiterpenoids accompanying the transition to reproductive structures, with consistently over 85% monoterpenoids in disc florets and petals. This pattern is driven by substantially higher production of monoterpenoids (especially alpha-pinene and sabinene) in reproductive structures. Sesquiterpenoid production is roughly similar across organs, and in leaves varies among lines from 21–55% of volatiles, dominated by cadinene-type sesquiterpenoids. This work suggests that the compositional diversity of volatile terpenoids within cultivated germplasm may be sufficient for many breeding applications, though for breeding increased volatile production the use of wild <em>H. annuus</em> and other wild <em>Helianthus</em> germplasm may be necessary.</p>
Clinical subtyping of cancer from plasma based on comprehensive epigenomic profiling
<p><strong><em>Fragment bed files part 3.</em></strong></p> <p> </p> <p>While circulating tumor DNA (ctDNA) assays are increasingly used to inform clinical decisions in cancer care, they have limited ability to identify the transcriptional programs that govern cancer phenotypes and their dynamic changes during the course of disease. To address these limitations, we developed a method for comprehensive epigenomic profiling of cancer from 1mL of patient plasma. Using an immunoprecipitation-based approach targeting histone modifications and DNA methylation, we measured 1,268 epigenomic profiles in plasma from 433 individuals with one of 15 cancers. Our assay provided a robust proxy for transcriptional activity, allowing us to infer the expression levels of diagnostic markers and drug targets, measure the activity of therapeutically targetable transcription factors, and detect epigenetic mechanisms of resistance. This proof-of-concept study in advanced cancers shows how plasma epigenomic profiling could unlock clinically actionable information that is currently accessible only via direct tissue sampling. </p>
Proteomic profiling of survivors of SARS-CoV-2-induced ARDS
<p>Around 80% of patients who develop acute respiratory distress syndrome (ARDS) secondary to SARS-CoV-2 infection experience persistent lung dysfunction. The molecular factors that mediate pulmonary sequelae and recovery are unknown.<strong> </strong>In this context, we sought to comprehensively characterize the proteomic determinants of pulmonary diffusion impairment.<strong> </strong></p> <p>This was a prospective cohort study including eighty-seven SARS-CoV-2–induced ARDS survivors. A complete pulmonary function evaluation and chest computed tomography (CT) were performed 3 months after hospital discharge. Proteomic profiling (364 proteins) was performed in plasma samples using proximity extension assay (PEA) technology. Partial least squares-discriminant analysis (PLS-DA) and random forest (RF) methods were used to assess predictor importance.</p> <p>Thirty percent of patients presented moderate to severe impairment of lung diffusing capacity (D<sub>LCO</sub><60% predicted). In the univariate analysis, fifteen proteins showed high concentrations in patients with D<sub>LCO</sub><60% [false discovery rate (FDR)<0.05]. Pleiotrophin (PTN) displayed the highest differences: fold change=2.22 and FDR=0.001. Differentially detected proteins showed an inverse and independent dose–response relationship with D<sub>LCO</sub>. The multivariable approaches clustered proteins according to the severity of diffusion impairment. Clusters were composed of host mediators of cell proliferation and differentiation, tissue remodeling, angiogenesis, coagulation, inflammation, immune response and fibrosis signaling.</p> <p>In survivors of SARS-CoV-2–induced ARDS, lung diffusion impairment is associated with specific circulating factors implicated in multiple injury and repair mechanisms. The host protein signatures allow a better understanding of pulmonary sequelae and may constitute therapeutic targets and biomarkers. The long-term biological and clinical significance of these observations requires further investigation.</p>
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
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.