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1,350 results for “iPSC”
ATAC-seq Bioanalyzer profiles from iPSC-derived macrophages
<p>Agilent Bioanalyzer profiles for the iPSC-derived macrophage ATAC-seq samples. </p>
CRISPR-Cas12a-integrated transgenes in genomic safe harbors retain high expression in human hematopoietic iPSC-derived lineages and primary cells
<p>We identified and characterized potential integration safe harbor sites (SHS) in human cells. Using the CRISPR-MAD7 system, we integrated transgenes at these genomic sites in iPSC, primary T and NK cells, and Jurkat cell line, and demonstrated efficient and stable expression at these loci. Subsequently, we validated the differentiation capabilities of engineered iPSC towards CD34+ hematopoietic stem and progenitor cells (HSPC), lymphoid progenitors (LPC), and natural killer (NK) cells, and showed that transgene expression was retained in these lineages. </p>
2D Monolayer Cardiomyocytes of Healthy control individual differentiated from iPSC
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scRNA-seq dataset of iPSC-derived pancreatic islet cells
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Transcriptome profiling of derived-hepatocyte progenitors from human iPSCs with nanoCAGE - part 1 - sequencing data (FASTQ files)
<p>This repository contains raw sequencing data (FASTQ files) produced from Illumina MiSeq run IDs "170630_M00528_0292_000000000-B9JY8" (aka "NC_LIMMS") and "180221_M00528_0334_000000000-B6PJM" (aka "NC_LIMMS2") . Sequencing libraries were prepared following the latest version of the nanoCAGE protocol (Poulain et al., Methods Mol Biol. 2017;1543:57-109. doi: 10.1007/978-1-4939-6716-2_4). They respectively contain a mix of 24 ("NC_LIMMS") and 18 ("NC_LIMMS2") samples tagged by specific barcode sequences at the 5'-ends (see tables below). The tagmentation step included in the protocol was performed using an equimolar mix of 12 Nextera XT N-series index primers (N701 to N712), therefore "NNNNNNNN" was indicated as index sequence on the Illumina Sample Sheet for the demultiplexing (see tables below). Libraries were sequenced paired-end on Illumina MiSeq system with the MiSeq Reagent Kit v3 (150 cycles: 58 cycles used for READ1, 8 cycles used for the Index, and 84 cycles used for READ2). Genomic alignments (BED files) of paired-end reads on human genome assemblies hg19 and hg38 using the MOIRAI pipeline (Hasegawa et al. BMC Bioinformatics 2014 May 16;15:144. doi: 10.1186/1471-2105-15-144) were deposited at Zenodo under the following Digital Object Identifier: 10.5281/zenodo.1017276.</p> <p> </p> <p><em><strong>"170630_M00528_0292_000000000-B9JY8" ("NC_LIMMS") :</strong></em></p> <p><strong>ID Sample_name Barcode_number Barcode_sequence Index_sequence</strong></p> <p>1 iPSC_control_rep1 4 ACAGAT NNNNNNNN</p> <p>2 iPSC_control_rep2 24 ATCGTG NNNNNNNN</p> <p>3 iPSC_control_rep3 31 CACGAT NNNNNNNN</p> <p>4 S3P1_OK_rep1 36 CACTGA NNNNNNNN</p> <p>5 S3P1_OK_rep2 46 CTGACG NNNNNNNN</p> <p>6 S3P1_OK_rep3 63 GAGTGA NNNNNNNN</p> <p>7 S4P1_OK_rep1 79 GTATAC NNNNNNNN</p> <p>8 S4P1_OK_rep2 92 TCGAGC NNNNNNNN</p> <p>9 S4P1_OK_rep3 9 ACATGA NNNNNNNN</p> <p>10 S4P2_OK_rep1 21 ATCATA NNNNNNNN</p> <p>11 S4P2_OK_rep2 33 CACGTG NNNNNNNN</p> <p>12 S4P2_OK_rep3 45 CGATGA NNNNNNNN</p> <p>13 S1P1_rep1 57 GAGATA NNNNNNNN</p> <p>14 S1P1_rep2 69 GCTCTC NNNNNNNN</p> <p>15 S1P1_rep3 81 GTATGA NNNNNNNN</p> <p>16 S3P1_FAILED_rep1 93 TCGATA NNNNNNNN</p> <p>17 S3P1_FAILED_rep2 11 AGTAGC NNNNNNNN</p> <p>18 S3P1_FAILED_rep3 23 ATCGCA NNNNNNNN</p> <p>19 S4P1_FAILED_rep1 35 CACTCT NNNNNNNN</p> <p>20 S4P1_FAILED_rep2 47 CTGAGC NNNNNNNN</p> <p>21 S4P1_FAILED_rep3 59 GAGCGT NNNNNNNN</p> <p>22 S4P2_FAILED_rep1 71 GCTGCA NNNNNNNN</p> <p>23 S4P2_FAILED_rep2 83 TATAGC NNNNNNNN</p> <p>24 S4P2_FAILED_rep3 95 TCGCGT NNNNNNNN</p> <p> </p> <p><em><strong>"180221_M00528_0334_000000000-B6PJM" ("NC_LIMMS2"):</strong></em></p> <p><strong>ID Sample_name Barcode_number Barcode_sequence Index_sequence</strong></p> <p>25 PETRI_rep1 04 ACAGAT NNNNNNNN</p> <p>26 PETRI_rep2 24 ATCGTG NNNNNNNN</p> <p>27 PETRI_rep3 31 CACGAT NNNNNNNN</p> <p>28 BIOCHIP_E_rep1 6 CACTGA NNNNNNNN</p> <p>29 BIOCHIP_M_rep1 46 CTGACG NNNNNNNN</p> <p>30 BIOCHIP_S_rep1 63 GAGTGA NNNNNNNN</p> <p>31 BIOCHIP_E_rep2 79 GTATAC NNNNNNNN</p> <p>32 BIOCHIP_M_rep2 92 TCGAGC NNNNNNNN</p> <p>33 BIOCHIP_S_rep2 09 ACATGA NNNNNNNN</p> <p>34 BIOCHIP_E_rep3 21 ATCATA NNNNNNNN</p> <p>35 BIOCHIP_M_rep3 33 CACGTG NNNNNNNN</p> <p>36 BIOCHIP_S_rep3 45 CGATGA NNNNNNNN</p> <p>37 HEPATOCYTES_rep1 57 GAGATA NNNNNNNN</p> <p>38 HEPATOCYTES_rep2 69 GCTCTC NNNNNNNN</p> <p>39 iPSC_control_rep1-2 81 GTATGA NNNNNNNN</p> <p>40 BIOCHIP_E_rep2-2 93 TCGATA NNNNNNNN</p> <p>41 BIOCHIP_M_rep1-2 11 AGTAGC NNNNNNNN</p> <p>42 BIOCHIP_S_rep2-2 23 ATCGCA NNNNNNNN</p>
Sanger sequencing of target and off-target genomic regions for gene-edited iPSC clones with SETBP1 genetic variants
<p>This data set includes chromatograms generated using sanger sequencing of targeted regions of genomic DNA from clonal iPSC lines. The iPSC lines include clones generated using CRISPR/Cas9 homology directed repair to introduce genetic variants into <em>SETBP1,</em> and their wild-type controls. Additional files have been included in the data set to link chromatogram (ab1) files to specific iPSC clones for genomic regions across the variant in <em>SETBP1 (</em>SETBP1 clones genetic variant sanger sequencing.xslx)<em> </em>and top<em> </em>off-target sites (SETBP1 clones off-target sanger sequencing.xlsx). </p>
HD-MEA extracellular measurements of iPSC-derived cardiomyocytes
<p>Human iPSC-derived cardiomyocytes (short QT syndrome).</p> <p>Extracellular measurements obtained using high-density microelectrode arrays.</p> <p> </p> <p>Ethics statement: The generation of iPSCs was approved by the Ethics Committee of the University Medical Center Göttingen in Germany (approval number: 10/9/15) and carried out in accordance with the approved guidelines. Written informed consent was obtained from all participants or their legal representatives prior to participation in the study.</p> <p> </p>
HD-MEA intracellular-like measurements of iPSC-derived cardiomyocytes
<p>Human iPSC-derived cardiomyocytes (iCell Cardiomyocytes).</p> <p>Intracellular-like measurements obtained using high-density microelectrode arrays.</p>
Autologous iPSC-Derived Dopamine Neuron Transplantation for Parkinson's Disease
ClinicalTrials.gov study NCT06422208. IPD Sharing: NO. Countries: 1. Publications: 12.
Drug Repurposing for Mitochondrial Disorders Using iPSCs Derived Neural Cells
ClinicalTrials.gov study NCT06967831. IPD Sharing: UNDECIDED. Countries: 1. Publications: 6.
Generation of Cancer Antigen-Specific T-cells From Human Induced Pluripotent Stem Cells (iPSC) for Research and Potential FutureTherapy
ClinicalTrials.gov study NCT03407040. IPD Sharing: Not stated. Countries: 1. Publications: 3.
iPSC-based Drug Repurposing for ALS Medicine (iDReAM) Study
ClinicalTrials.gov study NCT04744532. IPD Sharing: YES. Countries: 1. Publications: 2.
Development of the Tool " iPSC " for the Functional Study of Mutations Responsible for Mental Retardation
ClinicalTrials.gov study NCT02980302. IPD Sharing: Not stated. Countries: 1. Publications: 26.
A study of gene expression, structure, and contractility of iPSC-Derived Cardiac Myocytes from a family with heart disease due to LMNA mutation
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Data from: Functional and mechanistic neurotoxicity profiling using human iPSC–derived neural 3D cultures
Neurological disorders affect millions of people worldwide and appear to be on the rise. While the reason for this increase remains unknown, environmental factors are a suspected contributor. Hence, there is an urgent need to develop more complex, biologically relevant, and predictive in vitro assays to screen larger sets of compounds with the potential for neurotoxicity. Here, we employed a human induced pluripotent stem cell (iPSC)-based 3D neural platform composed of mature cortical neurons and astrocytes as a model for this purpose. The iPSC-derived human 3D cortical neuron/astrocyte co-cultures (3D neural cultures) present spontaneous synchronized, readily detectable calcium oscillations. This advanced neural platform was optimized for high-throughput screening in 384-well plates and displays highly consistent, functional performance across different wells and plates. Characterization of oscillation profiles in 3D neural cultures was performed through multi-parametric analysis that included the calcium oscillation rate and peak width, amplitude, and waveform irregularities. Cellular and mitochondrial toxicity were assessed by high-content imaging. For assay characterization, we used a set of neuromodulators with known mechanisms of action. We then explored the neurotoxic profile of a library of 87 compounds that included pharmaceutical drugs, pesticides, flame retardants, and other chemicals. Our results demonstrated that 57% of the tested compounds exhibited effects in the assay. The compounds were then ranked according to their effective concentrations based on in vitro activity. Our results show that a human iPSC-derived 3D neural culture assay platform is a promising biologically-relevant tool to assess the neurotoxic potential of drugs and environmental toxicants.
Parkinsonism Sac domain mutation in Synaptojanin-1 affects ciliary properties in iPSC-derived dopaminergic neurons
<p>The tabular dataset for all graphs in Rafiq et al 2024 can be found in the ASAP data repository</p>
Human iPSC-derived liver co-culture spheroids to model liver fibrosis
<div> <p><span>The lack of adequate human <em>in vitro</em> models that recapitulate the cellular composition and response of the human liver to injury hampers the development of anti-fibrotic drugs. The goal of this study was to develop a human spheroid culture model to study liver fibrosis by using induced pluripotent stem cell (iPSC)-derived liver cells. iPSCs were independently differentiated towards hepatoblasts (iHepatoblasts), hepatic stellate cells (iHSCs), endothelial cells (iECs) and macrophages (iMΦ), before assembly into free floating spheroids by culturing cells in 96-well U-bottom plates and orbital shaking for up to 21 days to allow further maturation. Through transcriptome analysis, we show further maturation of iECs and iMΦ, the differentiation of the iHepatoblasts towards hepatocyte-like cells <span> </span>(iHeps) and the inactivation of the iHSCs by the end of the 3D culture. Moreover, these cultures display a similar expression of cell-specific marker genes (<em>CYP3A4</em>, <em>PDGFRβ</em>, <em>CD31</em> and <em>CD68</em>) and sensitivity to hepatotoxicity as spheroids made using freshly isolated primary human liver cells. Furthermore, we show the functionality of the iHeps and the iHSCs by mimicking liver fibrosis through iHep-induced iHSC activation, using acetaminophen.<span> </span><br>In conclusion, we have established a reproducible human iPSC-derived liver culture model that can be used to mimic fibrosis <em>in vitro</em> as a replacement of primary human liver derived 3D models. The model can be used to investigate pathways involved in fibrosis development and to identify new targets for chronic liver disease therapy.</span></p> </div>
2D cortical human neuron from ipsc - cultures and electrical activiy based on HD-MEA
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Dataset related to article "Neonicotinoid pesticides affect developing neurons in experi-mental mouse models and in human induced pluripotent stem cell (iPSC)-derived neural cultures and organoids"
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Neonicotinoid pesticides affect developing neurons in experi-mental mouse models and in human induced pluripotent stem cell (iPSC)-derived neural cultures and organoids
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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.