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25,372 results for “Transcriptomics”
Tomopteris sp. Transcriptome data and associated annotations
<p>Transcriptome sequences for specimen RAD2-051, Tompteris sp. </p> <p>Files are:</p> <p>RAD2-051_ISOseq_clustered.hq.fasta --> Long read PacBio IsoSeq assembly of Tomopteris mRNA, from body segments</p> <p>RAD2-051_combinedAssembly_c0.95_EXPRfilt_nocontam.fasta --> Combined Trinity and IsoSeq assemblies to capture all expressed genes in dorsal cirri and body segments. Contaminants removed by expression count level filtering and manual removal of human, drosophila, and xenopus sequences (100% blastn hits).</p> <p>RAD2-051_combinedAssembly_c0.95_EXPRfilt_nocontam.fasta.transdecoder.pep --> translated proteins from the combined assembly file.</p> <p>RAD2-051.tsv --> InterProScan annotation for RAD2-051 proteins.</p> <p>RAD2-051.x.swissprot.BLASTXOUT-hssp.txt --> best BLASTX hits of RAD2-051 transcripts against the curated SwissProt database.</p> <p>RAD2-051_Tomopteris.sp.counts.CPMs.csv --> file with read counts in CPMs for mRNA quantification for samples from dorsal cirri and body segments. LA=Left antenna (dorsal cirrus); RA=Right antenna (dorsa cirrus); BD=body segment sample.</p> <p>RAD2-051.iproscan.goa --> a gene ontology annotation file for RAD2-051 annotations from interproscan. For use with topGO in R.</p> <p> </p> <p> </p> <p> </p> <p> </p>
The raw data of transcriptomes in whole brains when EcR-A was knocked down in pC1 neurons or not
<p class="MsoNormal">The establishment of neural circuits for female sexual receptivity is essential to reproduction, but the underlying mechanism of associated neurodevelopment is still not fully understood. Here we found that neuropeptide prothoracicotropic hormone (PTTH), hormone of the PG axis, regulates virgin female receptivity through ecdysone in <em>Drosophila melanogaster</em>. PTTH-positive PG neurons are doublesex-expressing neurons, they regulate virgin female receptivity before the metamorphosis during the 3<sup>rd</sup>-instar larval stage. Furthermore, the genetic knocking down of ecdysone receptor EcR-A in pC1 neurons regulates the morphological development of pC1 neurons and further the virgin female copulation rate. However, the activity of pC1 neurons did not change, suggesting the changes of synaptic connection between pC1 neurons and other neurons. Analysis of brain transcriptomes when EcR-A was knocked down in pC1 neurons reveals that additional genes are regulated downstream of EcR-A in pC1 neurons. Our work suggests a mechanism underlying how the neurodevelopment of neural circuits regulates virgin female receptivity in adults.</p>
Fig. 2 in Transcriptomic investigation of the biochemical function of 7-dehydro- cholesterol reductase 1 from the traditional Chinese medicinal plant Anemarrhena asphodeloides Bunge
Fig. 2. GO (A) and KEGG (B) analyses of unigenes.
Fig. 1 in Transcriptomic investigation of the biochemical function of 7-dehydro- cholesterol reductase 1 from the traditional Chinese medicinal plant Anemarrhena asphodeloides Bunge
Fig. 1. The proposed timosaponin biosynthetic pathway in A. asphodeloides Bunge.
Transcriptomics-guided identification of an algicidal protease of the marine bacterium Kordia algicida OT-1
<p>Transcriptomic comparison of active and inactive cultures of Kordia algicida OT-1 (sequencing and analysis performed by Novogene)</p>
Fig. 4 in Detection of candidate proteins in the indican biosynthetic pathway of Persicaria tinctoria (Polygonum tinctorium) using protein-protein interactions and transcriptome analyses
Fig. 4. Scheme of the hypothesized indican biosynthetic pathway.
Fig. 5 in Transcriptome analysis of Paris polyphylla var. yunnanensis illuminates the biosynthesis and accumulation of steroidal saponins in rhizomes and leaves
Fig. 5. KEGG enrichments of DEGs.
Fig. 9 in Comparative transcriptome analysis reveals the regulatory effects of acetylcholine on salt tolerance of Nicotiana benthamiana
Fig. 9. Differential expressed genes in response to CN, NaCl and NaCl + ACh.
Fig. 2 in Transcriptome profiling of two Dactylis glomerata L. cultivars with different tolerance in response to submergence stress
Fig. 2. Venn diagram of differentially expressed genes (DEGs).
Fig. 6 in Transcriptome sequencing of the apricot (Prunus armeniaca L.) and identification of differentially expressed genes involved in drought stress
Fig. 6. Relative expression of con (control) and tre (treat) genes by qRT-PCR (A) and RNA-Seq (B).
Fig. 2 in Transcriptome sequencing of the apricot (Prunus armeniaca L.) and identification of differentially expressed genes involved in drought stress
Fig. 2. Comparison of expression of differential unigenes identified between Treat and Control.
Spatial Transcriptomic Experiment of Triple-Negative Breast Cancer PDX Model PIM001-P model treatment naive sample
<p>Spatial Transcriptomic Experiment of Triple-Negative Breast Cancer PDX Model PIM001-P model treatment naive sample</p> <p>10X Genomics Visium platform. </p> <p><strong>Library Preparation and Sequencing of PIM001P</strong></p> <p>Tissue sections of 10µm thickness were mounted onto the capture areas of the Visium Spatial Gene Expression slide and stained using hematoxylin and eosin. Tissue sections were permeabilized on a thermocycler for 24 minutes, as determined by the Tissue Optimization step. Poly-adenlyated mRNA is released and captured by surface-bound primers within each capture area. Reverse transcription, template switching, extension, and second strand synthesis are performed on the slide. Full-length, spatially barcoded cDNA transcripts are then denatured from the slide and amplified via PCR prior to library construction. Approximately 110 to 375 ng of amplified cDNA was carried forward into library construction. During library construction, cDNA is enzymatically fragmented to target amplicon size then undergoes end repair, A-tailing, adapter ligation, and then amplified using between 14 and 16 PCR cycles. The resulting libraries were quantitated using the Invitrogen Qubit 2.0 quantitation assay and fragment size assessed with the Agilent Bioanalyzer. A qPCR quantitation was performed on the libraries to determine the concentration of adapter ligated fragments using Applied Biosystems ViiA7 Real-Time PCR System and a KAPA Library Quant Kit (p/n KK4824). All samples were pooled equimolarly and re-quantitated by qPCR, and also re-assessed on the Bioanalyzer.</p> <p><strong>Sequencing: </strong></p> <p>150 pM of equimolarly pooled library was loaded onto the NovaSeq 6000 S4 flowcell and sequenced at the recommended 28-10-10-50 read configuration. PhiX Control v3 adapter-ligated library (Illumina p/n FC-110-3001) was spiked-in at 2% by weight to ensure balanced diversity and to monitor clustering and sequencing performance. A minimum of 300 million read pairs per sample was sequenced. FastQ file generation was executed using 10X Genomics’ Space Ranger mkfastq software.</p> <p> </p>
Time-course adaptive changes in hippocampal transcriptome and synaptic function induced by simulated microgravity associated with cognition
<p>Introduction: The investigation of cognitive function in microgravity, both short-term and long-term, remains largely descriptive. And the underlying mechanisms of the changes over time remain unclear. Methods: Behavioral tests, electrophysiological recording, and RNA sequencing were used to observe differences in behavior, synaptic plasticity, and gene expression. Results: Initially, we measured the performance of spatial cognition exposed to long-term simulated microgravity (SM). Both working memory and advanced cognitive abilities were enhanced. Somewhat surprisingly, the synaptic plasticity of the hippocampal CA3-CA1 synapse was impaired. To gain insight into the mechanism of changing regularity over time, transcriptome sequencing in the hippocampus was performed. The analysis identified 20 differentially expressed genes (DEGs) in the hippocampus after short-term modeling, 19 of which were up-regulated. Gene ontology (GO) analysis showed that these up-regulated genes were mainly enriched in synaptic-related processes, such as <em>Stxbp5l</em> and <em>Epha6</em>. This might be related to the enhancement of working memory performance under short-term SM exposure. Under exposure to long-term SM, 7 DEGs were identified in the hippocampus, all of which were up-regulated and related to oxidative stress and metabolism, such as <em>Depp1</em> and <em>Lrg1</em>. Compensatory effects occurred with increased modeling time. Discussion: To sum up, our current research indicates that the cognitive function under SM exposure is consistently maintained or potentially even being enhanced over both short and long durations. The underlying mechanisms are intricate and potentially linked to the differential expression of hippocampal-associated genes and alterations in synaptic function, with these effects being time-dependent. The present study will lay the experimental and theoretical foundation of the multi-level mechanism of cognitive function under space flight.</p>
Precision Therapy Based on Immune Microenvironment by Transcriptome Sequencing of Osteosarcoma, a Prospective, Multi-cohort Exploratory Clinical Study
ClinicalTrials.gov study NCT06776198. IPD Sharing: NO. Countries: 0. Publications: 1.
Transcriptome Sequencing Analysis of Whole Blood From Patients With Trigeminal Neuralgia
ClinicalTrials.gov study NCT04923399. IPD Sharing: Not stated. Countries: 0. Publications: 4.
Evaluating the Predictive Capability of Transcriptomic Profiling for Identifying the Primary Site of Metastatic Tumors
ClinicalTrials.gov study NCT07319949. IPD Sharing: NO. Countries: 0. Publications: 3.
Single-Cell and Spatial Transcriptomics Analysis of Steatotic Donor Liver Susceptibility to Post-Transplant Injury
ClinicalTrials.gov study NCT07362745. IPD Sharing: NO. Countries: 1. Publications: 0.
Transcriptomal and Molecular Characterization of Tumor Associated Monocytes/Macrophages in Human Cancers
ClinicalTrials.gov study NCT00979277. IPD Sharing: Not stated. Countries: 1. Publications: 2.
Dynamics of Androgen Receptor Genomics and Transcriptomics After Neoadjuvant Androgen Ablation
ClinicalTrials.gov study NCT03297385. IPD Sharing: Not stated. Countries: 0. Publications: 1.
Identification of an Immune Single Cell Transcriptomic Profile of Responder and Non-responder Hepatocellular Carcinoma Patients Treated With Immune-checkpoint Inhibitors
ClinicalTrials.gov study NCT07273708. IPD Sharing: UNDECIDED. Countries: 1. Publications: 0.
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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)
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.