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7,157 results for “Cell lines”
Supplementary files to An integrated RNA-proteomic landscape of drug induced senescence in a cancer cell line.
<p>Senescent cells are characterized by an arrest in proliferation. In addition to replicative senescence resulting from telomere exhaustion, sub-lethal genotoxic stress resulting from DNA damage, oncogene activation, mitochondrial dysfunction or reactive metabolites also elicits a senescence phenotype. Senescence is a controlled programme affecting a wide variety of biological processes with some core hallmarks of senescence as well as tissue specific changes. This study presents an integrative multi-omic analysis of proteomic and RNA-seq from proliferating and senescent osteosarcoma cells. This study demonstrates senescence induction in a widely used cell line which can be used as a model system for characterising cancer cell responses to sub-lethal doses of chemotherapeutic agents, and makes available both RNA-seq and proteomic data from proliferating and senescent cells in open access repositories to aid reuse by the community.</p>
Asymmetric mechanotransduction by hair cells of the zebrafish lateral line (Part 1/2)
<p>In the lateral line system, water motion is detected by neuromast organs, fundamental units that are arrayed on a fish's surface. Each neuromast contains hair cells, specialized mechanoreceptors that convert mechanical stimuli, in the form of water movement, into electrical signals. The orientation of hair cells' mechanosensitive structures ensures that the opening of mechanically-gated channels is maximal when deflected in a single direction. In each neuromast organ, hair cells have two opposing orientations, enabling bi-directional detection of water movement. Interestingly, Tmc2b and Tmc2a proteins, which constitute the mechanotransduction channels in neuromasts, distribute asymmetrically so that Tmc2a is expressed in hair cells of only one orientation. Here, using both<em> in vivo</em> recording of extracellular potentials and calcium imaging of neuromasts, we demonstrate that hair cells of one orientation have larger mechanosensitive responses. The associated afferent neuron processes that innervate neuromast hair cells faithfully preserve this functional difference. Moreover, Emx2, a transcription factor required for the formation of hair cells with opposing orientations, is necessary to establish this functional asymmetry within neuromasts. Remarkably, loss of Tmc2a does not impact hair cell orientation but abolishes the functional asymmetry as measured by recording extracellular potentials and calcium imaging. Overall, our work indicates that oppositely oriented hair cells within a neuromast employ different proteins to alter mechanotransduction to sense the direction of water motion.</p>
Asymmetric mechanotransduction by hair cells of the zebrafish lateral line (Part 2/2)
<p>In the lateral line system, water motion is detected by neuromast organs, fundamental units that are arrayed on a fish's surface. Each neuromast contains hair cells, specialized mechanoreceptors that convert mechanical stimuli, in the form of water movement, into electrical signals. The orientation of hair cells' mechanosensitive structures ensures that the opening of mechanically-gated channels is maximal when deflected in a single direction. In each neuromast organ, hair cells have two opposing orientations, enabling bi-directional detection of water movement. Interestingly, Tmc2b and Tmc2a proteins, which constitute the mechanotransduction channels in neuromasts, distribute asymmetrically so that Tmc2a is expressed in hair cells of only one orientation. Here, using both<em> in vivo</em> recording of extracellular potentials and calcium imaging of neuromasts, we demonstrate that hair cells of one orientation have larger mechanosensitive responses. The associated afferent neuron processes that innervate neuromast hair cells faithfully preserve this functional difference. Moreover, Emx2, a transcription factor required for the formation of hair cells with opposing orientations, is necessary to establish this functional asymmetry within neuromasts. Remarkably, loss of Tmc2a does not impact hair cell orientation but abolishes the functional asymmetry as measured by recording extracellular potentials and calcium imaging. Overall, our work indicates that oppositely oriented hair cells within a neuromast employ different proteins to alter mechanotransduction to sense the direction of water motion.</p>
Fig 2 in Soluble total antigen derived from Toxoplasma gondii RH strain prevents apoptosis, but induces anti-apoptosis in human monocyte cell line
Fig 2. This schematic overview suggests signaling pathways of apoptosis. Apoptosis is induced through either the extrinsic pathway or intrinsic pathway. Toxoplasma gondii can prevent cell apoptosis via inhibition of cytochrome c release from the mitochondria into the cytosol, inhibition of cas-3, -6, -7, and -9 via blocking the mitochondrial pathway, and blocking cas-8 by external pathways. The parasite may also suppress pro-apoptotic protein (Bax) and induce anti-apoptotic Bcl-2 proteins and is able to activate transcription factors STAT6 and STAT3-miR-17-92-Bim pathway to inhibit apoptosis. Some proteins of T. gondii such as ROP18 plays a role in Fas/ CD95-mediated apoptosis to inhibit this process. Similarly ROP16 phosphorylates STAT3 and STAT6 to inhibit cell death. Original (S. Nemati).
Fig 1 in Soluble total antigen derived from Toxoplasma gondii RH strain prevents apoptosis, but induces anti-apoptosis in human monocyte cell line
Fig 1. The comparison of the expression levels of Bcl-2 (A), Mcl-1 (B), Cas-7 (C), Cas-3 (D), and Bax (E) in THP-1 cell line regarding different concentrations of the soluble total antigen of Toxoplasma gondii (Nicolle et Manceaux, 1908) STAg. NS: not significant; * P value <0.05; ** P value <0.01; *** P value <0.001.
Study of Cabozantinib as 2nd Line Treatment in Subjects With Locally Advanced or Metastatic Renal Cell Carcinoma (RCC) With a Clear-Cell Component Who Progressed After 1st Line Treatment With Checkpoi
ClinicalTrials.gov study NCT03945773. IPD Sharing: YES. Countries: 7. Publications: 1.
A Study of Tislelizumab (BGB-A317) in Combination With Chemotherapy as First Line Treatment in Participants With Advanced Esophageal Squamous Cell Carcinoma
ClinicalTrials.gov study NCT03783442. IPD Sharing: YES. Countries: 16. Publications: 2.
Phase III Study Evaluating Efficacy and Safety of Canakinumab in Combination With Docetaxel in Adult Subjects With Non-small Cell Lung Cancers as a Second or Third Line Therapy
ClinicalTrials.gov study NCT03626545. IPD Sharing: YES. Countries: 26. Publications: 1.
Asymmetric mechanotransduction by hair cells of the zebrafish lateral line (Part 2/2)
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Asymmetric mechanotransduction by hair cells of the zebrafish lateral line (Part 1/2)
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Filtered and annotated SNV and indel variants in the PC3 and LNCaP human prostate cancer cell lines
<p>150bp paired-end reads (insert size 350bp) were obtained using the Illumina HiSeqX sequencer. Samtools v1.3.1 mpileup and bcftools were used to interrogate indexed BAM files, from whole-genome reads aligned to human reference genome GRCh38 build 82, and generate a VCF (Variant Call Format) file of single nucleotide variants (SNVs) and short indel variants. Variants private, or unique to a particular cell line, or shared by both were next identified. Variants (likely to be common germline variants) present in HapMap, 1000 genomes phase 3 (2,504 human genomes), and the National Heart Lung and Blood Institute’s Exome Sequencing Project (ESP) (bundled variant data file available at https://goo.gl/mEogvD) were excluded. Variant files (VCF) were filtered using SnpSift with the following parameters: 'QUAL \textgreater= 200 \&\& DP \textgreater= 30', where QUAL denotes minimum variance confidence and DP total depth threshold. Filtered variants were annotated using SnpEff v4.3g. Please see https://github.com/sciseim/PCaWGS for associated scripts.</p> <p> </p>
de novo genome assembly of the LNCaP human prostate cancer cell line
<p>Whole-genome sequencing reads from the LNCaP human prostate cancer cell line were used to generate a <em>de novo </em>assembly with SGA v0.10.15. Please see https://github.com/sciseim/PCaWGS for associated scripts. Library preparation was performed using a TruSeq Nano DNA kit (Illumina) with a target insert size of 350bp. Paired-end libraries (150bp) were sequenced using a HiSeqX sequencer (Illumina).</p>
de novo genome assembly of the PC3 human prostate cancer cell line
<p>Whole-genome sequencing reads from the PC3 human prostate cancer cell line were used to generate a <em>de novo </em>assembly with SGA v0.10.15. Please see https://github.com/sciseim/PCaWGS for associated scripts. Library preparation was performed using a TruSeq Nano DNA kit (Illumina) with a target insert size of 350bp. Paired-end libraries (150bp) were sequenced using a HiSeqX sequencer (Illumina).</p> <p> </p> <p> </p> <p> </p>
Genomic variant data for the Jurkat cell line
<p>Variant calling data from whole-genome sequencing of the Jurkat cell line. The data set includes output files from four variant calling tools (jurkat_raw_variant_caller_output.tar.gz), final variant calls after filtering and merging the calls from the separate tools (jurkat_final_variant_calls.tar.gz), and files with variant effect information (jurkat_variant_effects.tar.gz).</p>
Single-cell RNAseq of Day 49 midbrain organoids from healthy and alpha-synuclein triplication iPSC lines
<p>Unbiased single-cell RNAseq of Day 49 midbrain dopaminergic organoids (10x 3' v3) of the Patikas et al. publication.</p> <p> </p> <p>The mono-unt-celltypes.h5ad refers to the object shown at Fig 2A and contains 3 cell lines:</p> <ol> <li>KOLF2 ( Control cell line)</li> <li>SNCA-3x alpha Synuclein triplication Parkinson's Disease patient-derived iPSC line</li> <li>SNCA-corr (SNCA-3x isogenic control with the triplication mutation corrected)</li> </ol> <p>The all-celltypes.h5ad refers to the object shown at Fig 4 onwards and contains the 3 cell lines that are included in model-dataset.h5ad and 7 other single-cell RNAseq samples:</p> <ol> <li>SNCA-3x+KOLF2 (chimera organoid condition of SNCA-3x and KOLF2 of iPSCs grown together in a midbrain organoid)</li> <li>SNCA-corr+KOLF2 (chimera organoid condition of SNCA-corr and KOLF2 of iPSCs grown together in a midbrain organoid)</li> <li>5 paired rotenone conditions. For each condition (KOLF2, SNCA-3x, SNCA-corr, SNCA-3x+KOLF2, SNCA-corr+KOLF2) a paired condition with acute 24h rotenone treatment in an antioxidant-free medium.</li> </ol>
Neuroblastoma cell lines display heterogeneity in differentiation responses
<p>Underlying and extended data for the manuscript "Neuroblastoma cell lines display heterogeneity in differentiation responses", Ferguson et al (2024). Includes Underlying data for Figures 2A-C and Figures 3A-D, and Extended data - Table S1: qRT-PCR primer sequences, Table S2 - List of genes in clusters identified in [7] (Table S2 added after version 1).</p>
Automated bio-AFM generation of large mechanome data set and their analysis by machine learning to classify prostatic cell lines_Training base 100 PC3-GFP
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Metabolomics of KP mouse LUAD cell lines
<p>The goal of the experiment was to characterize the changes in metabolic pathway flux in these cells in response to HDAC and glutaminase inhibition. This dataset includes metabolomics of U-C13 glucose tracing (1h and 24h) and U-C13 glutamine (8h) of mouse LUAD cell lines with Kras overexpression and p53 knock-out (KP), carrying empty vector (EV) or overexpression of NRF2dNeh2 (NRF2) and treated with DMSO, Romidepsin or CB-839. 3 technical replicates were done per condition. The full methodology is described in the accompanying text file.</p>
Generation of KRAS knockout pancreatic cancer cell line PANC1
<p>We used CRISPR to inactivate mutant KRAS and STAT3 in PANC1 (KRASG12D) pancreatic cancer cell line. Gene expression analysis of KRAS intact vs. knockout cells identified sets of genes involved in protein synthesis, cell differentiation, and metabolic processes, while the expression of MAPK/ERK target genes remained unperturbed.</p>
RNA-sequencing of meningioma cell lines with miRNA constructs
<p>RNA-sequencing of meningioma cell lines with miRNA constructs.</p>
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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.