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1,768 results for “beta cell”
Characterization of a loss-offunction NSF attachment protein beta mutation in monozygotic triplets affected with epilepsy and autism using cortical neurons from proband-derived and CRISPR-corrected induced pluripotent stem cell lines
<p>RNA-seq data of matured cortical neurons (8-weeks old) derived from the induced pluripoent stem cells (iPSC) of control parents (CtrlF and CtrlM) and corrected proband. There are three replicates (Rep1, Rep2, Rep3) for each sample with Forwad read (R1_001.fastq.gz)</p> <p>CtrlF: Control Father sample</p> <p>CtrlM: Control mother sample</p> <p>NDD_01_Corr_Het: Heterozygous correction of NAPB mutation (c.354+2T>G) in NDD_01 proband</p> <p>NDD_05_Corr_Hom: Homozygous correction of NAPB mutation (c.354+2T>G) in NDD_05 proband</p>
Supporting data for: Type 1 diabetes risk genes mediate pancreatic beta cell survival in response to proinflammatory cytokines
<p><strong>SUMMARY OF THE STUDY</strong></p> <p>We combined functional genomics and human genetics to investigate processes that affect type 1 diabetes (T1D) risk by mediating beta-cell survival in response to proinflammatory cytokines. We mapped 38,931 cytokine-responsive candidate <em>cis-</em>regulatory elements (cCREs) in beta-cells using ATAC-seq and snATAC-seq and linked them to target genes using co-accessibility and HiChIP. Using a genome-wide CRISPR screen in EndoC-βH1 cells we identified 867 genes affecting cytokine-induced survival, and genes promoting survival and up-regulated in cytokines were enriched at T1D risk loci. Using SNP-SELEX, we identified 2,229 variants in cytokine-responsive cCREs altering transcription factor (TF) binding, and variants altering binding of TFs regulating stress, inflammation and apoptosis were enriched for T1D risk. At the 16p13 locus, a fine-mapped T1D variant altering TF binding in a cytokine-induced cCRE interacted with <em>SOCS1</em>, which promoted survival in cytokine exposure. Our findings reveal processes and genes acting in beta-cells during inflammation that modulate T1D risk.</p> <p><strong>DESCRIPTION OF FILES:</strong></p> <ul> <li>Supplementary Data 1. List of islet cCREs annotated with cell type and cytokine response - also in GSE205853</li> <li>Supplementary Data 2. Coaccessible sites in untreated beta cells and promoter annotations - also in GSE205853</li> <li>Supplementary Data 3. Coaccessible sites in cytokine-treated beta cells and promoter annotations - also in GSE205853</li> <li>Supplementary Data 4. Coaccessible sites in cytokine treated and untreated beta cells and promoter annotations - also in GSE205853</li> <li>Supplementary Data 5. Chromatin interactions in EndoC-BH1 cells - also in GSE205853</li> <li>Supplementary Data 6. Variants selected for SNP-SELEX assay </li> <li>Supplementary Data 7. Variants with TF binding and allelic binding results from SNP-SELEX</li> <li>Supplementary Data 8. snATAC-seq barcodes and metadata - also in GSE205853</li> <li>Supplementary Data 9. CRISPR-KO screen results - also in GSE205853</li> <li>Supplementary Data 10. Bulk ATAC-seq count matrix - also in GSE205853</li> <li>Supplementary Data 11. Bulk RNA-seq count matrix - also in GSE205853</li> <li>Supplementary Data 12. Alpha cells snATAC-seq count matrix - also in GSE205853</li> <li>Supplementary Data 13. Acinar cells snATAC-seq count matrix - also in GSE205853</li> <li>Supplementary Data 14. Beta cells snATAC-seq count matrix - also in GSE205853</li> <li>Supplementary Data 15. Stellate cells snATAC-seq count matrix - also in GSE205853</li> <li>Supplementary Data 16. Endothelial cells snATAC-seq count matrix - also in GSE205853</li> <li>Supplementary Data 17. Delta cells snATAC-seq count matrix - also in GSE205853</li> <li>Supplementary Data 18. Luciferase assay rs10483809</li> <li>Supplementary Data 19. SOCS1 knockdown qPCR results</li> <li>Supplementary Data 20. SOCS1 knockdown Apotracker (flow-cytometry)results</li> </ul> <p><strong>Raw data deposited at GEO, accessions GSE205853 and GSE118725.</strong></p> <p><em>Please refer to publication and GEO for details on methods.</em></p>
Control T-cell receptor (TCR) alpha and beta chain nucleotide and amino acid sequences from human and mouse
<p>A dataset of pooled T-cell receptor (TCR) sequences for TCR alpha and beta chains of human and mouse.</p> <p>Sequences are obtained from various samples of healthy individuals/mice using our conventional protocols: see for example [Britanova et al "Dynamics of individual T cell repertoires: from cord blood to centenarians" The Journal of Immunology 2016] and [Izraelson et al. "Comparative analysis of murine T‐cell receptor repertoires." Immunology 2018].</p> <p>The sequences are stored as gzipped clonotype tables in VDJtools format, see [https://vdjtools-doc.readthedocs.io/en/master/input.html#vdjtools-format].</p> <p>This control dataset can be used as a proxy for a generative VDJ rearrangement model to estimate the expected frequency distribution of TCRs and check for enrichment of rare TCR clonotypes and groups of similar TCR sequences. For the implementation of the enrichment analysis, please see CalcDegreeStats routine from VDJtools software, see [https://vdjtools-doc.readthedocs.io/en/master/annotate.html#calcdegreestats].</p> <p>Files named "human.tra.strict.txt.gz", etc are pools of random/naive TCR clonotypes containing unique V/J/CDR3 nucleotide sequence combinations observed in data. The pools.zip file is used for TCR motif inference in VDJdb database [https://github.com/antigenomics/vdjdb-motifs], it contains human.tra.aa.txt, etc files that contain random/naive TCR clonotypes grouped by CDR3 amino acid sequence with the most frequent representative V and J.</p>
Generation of beta-like cell subtypes from differentiated human induced pluripotent stem cells in 3D spheroids
<p>This repository contains single-cell RNA-sequencing data files (raw FASTQ files generated from Illumina HiSeq sequencing) related to the article entitled "Generation of beta-like cell subtypes from differentiated human induced pluripotent stem cells in 3D spheroids" by Lisa Morisseau et al. (2023) published in the Molecular Omics journal (DOI: 10.1039/d3mo00050h).</p> <p> </p>
Aberrant development of pancreatic beta cells derived from human iPSCs with FOXA2 deficiency
<p><strong>Project manager(s)</strong><strong>: </strong>Essam M. Abdelalim</p> <p>Induced pluripotent stem cells (iPSCs) were generated from a patient with a heterozygous deletion of the short arm of chromosome 20 at bands p11.22 to p11.21 (~969 kb deletion), which contains only one gene, <em>FOXA2 </em>(<em>FOXA2<sup>+/-</sup></em>iPSCs) as well as healthy controls (Ctr1 iPSCs and Ctr2 iPSCs). <em>FOXA2<sup>+/-</sup></em>iPSCs were differentiated into different stages of beta cell development to understand the role of FOXA2 during pancreatic beta cell development as described in the article entitled "<strong>Aberrant development of pancreatic beta cells derived from human iPSCs with <em>FOXA2</em> deficiency" by Elsayed et al</strong>. The dataset represents RNA-seq data generated from pancreatic progenitors (PP2) and endocrine progenitors (EPs) derived from Ctr1 iPSCs, Ctr2 iPSCs, and three clones of <em>FOXA2<sup>+/-</sup></em>iPSCs. </p> <p>The file name is: Sample name _overall sample number_read direction_001 where:</p> <p>- PP2-Ctr 1: pancreatic progenitors (PP2) derived from Ctr1 iPSCs (healthy control 1)</p> <p>- PP2-Ctr 2: pancreatic progenitors (PP2) derived from Ctr2 iPSCs (healthy control 2)</p> <p>- PP2-FOX1, PP2-FOX2, and PP2-FOX3: pancreatic progenitors (PP2) derived from three different clones of patient-derived <em>FOXA2<sup>+/-</sup></em>iPSCs.</p> <p>- EP-Ctr1: endocrine progenitors (Eps) derived from Ctr1 iPSCs (healthy control 1)</p> <p>- EP-Ctr2: endocrine progenitors (Eps) derived from Ctr2 iPSCs (healthy control 2)</p> <p>- EP-FOX R1, EP-FOX R2, and EP-FOX R3: endocrine progenitors (EPs) derived from three different clones of patient-derived <em>FOXA2<sup>+/-</sup></em>iPSCs.</p> <p>- The RNA-Seq data were generated from two Ctr-iPSC lines and three FOXA2<sup>+/-</sup>iPSC lines.</p> <p>- Read direction: R1 (Forward), R2 (Reverse).</p>
Polysome profile glucose beta-cells
<p>Polysome profile analysis of human pancreatic beta-cells exposure to glucose</p> <p>A human pancreatic beta cell line (betaH2) was exposed to glucose after starvation.<br> Total RNA was collected for a bulk RNA-seq analysis. Three biological repeats were produced for each of the the low and high glucose conditions resulting in to 6 sequence (fastq) files.<br> Three different mRNA-ribosomal fractions were selected from a sucrose gradient corresponding to single ribosomes (monosomes), light ribosomes (2-4) and heavy ribosomes (5 and more).<br> Three biological repeats were produced for each fraction and for the two conditions (low and high glucose) resulting to 18 different (fastq) sequenced files.</p> <p>In total the study consists of 24 submitted fastq files, 6 corresponding to total RNA from two conditions (three replicates) and 18 corresponding to polysome profile, 3 fractions times two conditions times 3 replicates.</p> <p>All 24 *.fastq.gz files are available in the reads_PolysomeProfile_RNAseq_BetaCells.tar archive.</p> <p>In addition to the raw reads we provide the processed data:<br> The raw counts table ( countsTOTALS_CodingGenes.tsv) and the Transcripts Per Million table (TPMs) (polysomeProfile_TPM_proteinCoding.csv) files of the data produced from the polysome profile and RNA-seq experiments described in the experimental design that can be found in:<br> https://github.com/parisepigenetics/Translatome_Bcells_glucose</p>
Single and half-cell RNA-sequencing in Stentor coeruleus control and beta-tubulin knockdown cells
Open the record for dataset details and reuse information.
Figure 6 in Potential neuroprotective of trans-resveratrol a promising agent tempeh and soybean seed coats-derived against beta-amyloid neurotoxicity on primary culture of nerve cells induced by 2-methoxyethanol
Figure 6. Treatment Group with resveratrol standard after induced by Beta-Amyloid (10 x10).
Figure 3 in Potential neuroprotective of trans-resveratrol a promising agent tempeh and soybean seed coats-derived against beta-amyloid neurotoxicity on primary culture of nerve cells induced by 2-methoxyethanol
Figure 3. Treatment group: 2- ME + Resveratrol isolated from Tempeh (10 x10).
Figure 8 in Potential neuroprotective of trans-resveratrol a promising agent tempeh and soybean seed coats-derived against beta-amyloid neurotoxicity on primary culture of nerve cells induced by 2-methoxyethanol
Figure 8. Treatment Group with resveratrol tempeh + 2-ME after induced by Beta-Amyloid (10 x10).
Figure 5 in Potential neuroprotective of trans-resveratrol a promising agent tempeh and soybean seed coats-derived against beta-amyloid neurotoxicity on primary culture of nerve cells induced by 2-methoxyethanol
Figure 5. Treatment group: 2- ME (10 x10).
Figure 9. Treatment Group with 2 in Potential neuroprotective of trans-resveratrol a promising agent tempeh and soybean seed coats-derived against beta-amyloid neurotoxicity on primary culture of nerve cells induced by 2-methoxyethanol
Figure 9. Treatment Group with 2-ME after induced by Beta-Amyloid (10 x10).
Figure 2 in Potential neuroprotective of trans-resveratrol a promising agent tempeh and soybean seed coats-derived against beta-amyloid neurotoxicity on primary culture of nerve cells induced by 2-methoxyethanol
Figure 2. Treatment group: 2- ME + Resveratrol Standard (10 x10).
Figure 1 in Potential neuroprotective of trans-resveratrol a promising agent tempeh and soybean seed coats-derived against beta-amyloid neurotoxicity on primary culture of nerve cells induced by 2-methoxyethanol
Figure 1. Control Group (10 x10).
Table 4 in Potential neuroprotective of trans-resveratrol a promising agent tempeh and soybean seed coats-derived against beta-amyloid neurotoxicity on primary culture of nerve cells induced by 2 - methoxyethanol
<p><b>Table 4.</b> Cytotoxic effect of various concentrations of Resveratrol and 2-Methoxyethanol Against Primary Neuron cell viability in MTT assay (570 nm).</p><table><tbody><tr><th><b>% Inhibition</b></th></tr></tbody><tbody><tr><th><b>Concentration of 2-Methoxyethanol</b></th><td><b>2-ME (10mM)</b></td><td><b>2-ME (10mM)</b></td><td><b>2-ME (10mM)</b></td></tr><tr><th><b>and Resveratrol</b></th><td><b>Resveratrol (Standard)</b></td><td><b>Resveratrol (Tempeh)</b></td><td><b>Resveratrol (Soybean Seed Coat)</b></td></tr><tr><th>IC50</th><td>(17.38 ± 0.99 µg/mL)</td><td>(31.14 ± 0.02 µg/mL)</td><td>(13.40 ± 0.30 µg/mL)</td></tr><tr><th>1.4 (µg/mL)</th><td>12.57</td><td>0</td><td>11.98</td></tr><tr><th>2.8 (µg/mL)</th><td>4.59</td><td>1.75</td><td>17.03</td></tr><tr><th>4.2 (µg/mL)</th><td>0</td><td>0</td><td>0</td></tr></tbody></table>
Table 3 in Potential neuroprotective of trans-resveratrol a promising agent tempeh and soybean seed coats-derived against beta-amyloid neurotoxicity on primary culture of nerve cells induced by 2 - methoxyethanol
<p><b>Table 3.</b> Cytotoxic effect of various concentrations of Resveratrol and 2-Methoxyethanol Against Primary Neuron cell viability in MTT assay (540 nm).</p><table><tbody><tr><th><b>% Inhibition</b></th></tr></tbody><tbody><tr><th><b>Concentration of 2-Methoxyethanol</b></th><td><b>2-ME (10mM)</b></td><td><b>2-ME (10mM)</b></td><td><b>2-ME (10mM)</b></td></tr><tr><th><b>and Resveratrol</b></th><td><b>Resveratrol (Standard)</b></td><td><b>Resveratrol (Tempeh)</b></td><td><b>Resveratrol (Soybean Seed Coat)</b></td></tr><tr><th>IC50</th><td>(17.64 ± 0.99 µg/mL)</td><td>(32.22 ± 1.18 µg/mL)</td><td>(17.43 ± 0.16 µg/mL)</td></tr><tr><th>1.4 (µg/mL)</th><td>11.8</td><td>0</td><td>7.95</td></tr><tr><th>2.8 (µg/mL)</th><td>5.27</td><td>0</td><td>14.41</td></tr><tr><th>4.2 (µg/mL)</th><td>0</td><td>0</td><td>0</td></tr></tbody></table>
Table 2 in Potential neuroprotective of trans-resveratrol a promising agent tempeh and soybean seed coats-derived against beta-amyloid neurotoxicity on primary culture of nerve cells induced by 2 - methoxyethanol
<p><b>Table 2.</b> Effect of Various concentrations of Resveratrol and 2-Methoxyethanol against Primary Neuron cell viability (570 nm).</p><table><tbody><tr><th><b>% Cell Viability</b></th></tr></tbody><tbody><tr><th><b>Concentration of 2-Methoxyethanol</b></th><td><b>2-ME (10mM)</b></td><td><b>2-ME (10mM)</b></td><td><b>2-ME (10mM)</b></td></tr><tr><th><b>and Resveratrol</b></th><td><b>Resveratrol (Standard)</b></td><td><b>Resveratrol (Tempeh)</b></td><td><b>Resveratrol (Soybean Seed Coat)</b></td></tr><tr><th>1.4 (µg/mL)</th><td>87.43</td><td>100</td><td>88.02</td></tr><tr><th>2.8 (µg/mL)</th><td>95.41</td><td>98.25</td><td>82.97</td></tr><tr><th>4.2 (µg/mL)</th><td>100</td><td>100</td><td>100</td></tr></tbody></table>
Table 1 in Potential neuroprotective of trans-resveratrol a promising agent tempeh and soybean seed coats-derived against beta-amyloid neurotoxicity on primary culture of nerve cells induced by 2 - methoxyethanol
<p><b>Table 1.</b> Effect of Various concentrations of Resveratrol and 2-Methoxyethanol against Primary Neuron cell viability (540 nm).</p><table><tbody><tr><th><b>% Cell Viability</b></th></tr></tbody><tbody><tr><th><b>Concentration of 2-Methoxyethanol</b></th><td><b>2-ME (10mM)</b></td><td><b>2-ME (10mM)</b></td><td><b>2-ME (10mM)</b></td></tr><tr><th><b>and Resveratrol</b></th><td><b>Resveratrol (Standard)</b></td><td><b>Resveratrol (Tempeh)</b></td><td><b>Resveratrol (Soybean Seed Coat)</b></td></tr><tr><th>1.4 (µg/mL)</th><td>88.2</td><td>100</td><td>92.05</td></tr><tr><th>2.8 (µg/mL)</th><td>94.73</td><td>100</td><td>85.59</td></tr><tr><th>4.2 (µg/mL)</th><td>100</td><td>100</td><td>100</td></tr></tbody></table>
Evaluation of 18 F-FP-DTBZ Pancreatic PET Scanning as a Tool to Measure Beta Cell Mass
ClinicalTrials.gov study NCT02236754. IPD Sharing: Not stated. Countries: 1. Publications: 2.
Beta Cell Restoration Through Fat Mitigation
ClinicalTrials.gov study NCT01763346. IPD Sharing: Not stated. Countries: 1. Publications: 11.
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