Find research datasets worth reusing

opencc-by-4.0Aug 2022View details →

Datasets for 'Label-free imaging of 3D pluripotent stem cell differentiation dynamics on chip'

Here we publish the datasets associated with our publication ‘Label-free imaging of 3D pluripotent stem cell differentiation dynamics on chip’. 3D cultures of human induced pluripotent stem cells (hiPSCs) were imaged while undergoing definitive endoderm (DE) differentiation. Data were acquired either on the live 3D cultures at various time points during the 3 days DE differentiation, or after fixation and immunostaining, with the 3D cultures being fixed at regular 24 h intervals during differentiation, as to form a timeline. Images were recorded with a standard confocal microscope using a xy-resolution of 0.25 μm/px and a z-resolution of 1 μm/plane.

opencc-by-4.0Sep 2022View details →

ETV6 represses Tumor Necrosis Factor During Stress Hematopoiesis to Regulate Mouse Stem Cell Function

At the root of the blood system lies a heterogenous population of hematopoietic stem and progenitor cells (HSPCs), which reside in the bone marrow (BM) and give rise to diverse blood lineages. Maintaining this pool of self-renewing HSPCs is critical to uphold hematopoiesis during period of stress such as bleeding or infection1. ETS Variant Transcription Factor 6 (ETV6) is a transcriptional repressor that is highly expressed in HSPCs2 where it is essential for development and maintenance of the adult hematopoiesis 3. In 2015, our group4 and others5-7  identified germline pathogenic ETV6 variants in families with predisposition to B-acute lymphoblastic leukemia (B-ALL) and thrombocytopenia, defining a new genetic syndrome known as Thrombocytopenia 5 (T5). Subsequently, we performed targeted germline ETV6 sequencing of remission blood samples from over 4,000 children with B-ALL and identified germline ETV6 variants in ~1% of cases7. In vitro studies revealed that ETV6 variant proteins exhibit impaired repressor activity, reduced DNA binding, and aberrant subcellular localization4,5,7,8. Overall, these studies indicated that T5-associated germline ETV6 variants negatively impact the repressor activity of ETV6. In support of this notion, transcriptional profiling of peripheral blood cells from T5 patients has revealed upregulation of interferon response genes9. Nevertheless, little remains known about the mechanisms by which ETV6 regulates the HSPC compartment and how T5-associated ETV6 variants contribute to disease.   To address these questions, we used CRISPR-Cas9 gene editing to generate a novel mouse model harboring a pathogenic heterozygous germline Etv6 variant, R355X, the murine equivalent to the human T5-associated variant R359X10. Through the comprehensive study of this model, we describe a novel role for ETV6 during aging and regenerative hematopoiesis and show that the heterozygous Etv6R355X variant impairs HSC function in vitro and in vivo. Using genomic approaches to interrogate mouse and human HSCs, we identify new ETV6 targets, including the gene encoding Tumor Necrosis Factor (TNF) and genes involved in TNF signaling. Further, we show increased TNF production and cell cycling in Etv6R355X/+ mouse HSPCs post-BM transplantation. Finally, we demonstrate that genetic ablation of Tnf restores the long-term potential of Etv6R355X/+ cells in serial replating assays in vitro. Together, these findings provide novel insights into the pathways regulated by ETV6 and demonstrate how a pathogenic variant impacts ETV6 function in the context of hematopoietic stress. All bulk RNAseq, Cut&Run, ATACseq, and Hi-C data has been submitted to in the Gene Expression Omnibus (accession number GSE213597) and Sequence Read Archive (BioProject number PRJNA880871). Due to the journal’s limitation on submitted supplementary data  as an Excel file, all post-analysis supplemental data files are deposited in Dryad data repository to be made available with this manuscript.

opencc-by-4.0Oct 2022View details →

High-resolution hard X-ray tomography and histology of a rat jaw for stem cell-mediated distraction osteogenesis

Histology and microtomography of a rat jaw after distraction. These datasets appear in "Combining high-resolution hard X-ray tomography and histology for stem cell-mediated distraction osteogenesis" Applied Sciences 12(12) (2022) 6268. Micromography (hdr/img files) has pixel size of 10.0228 µm. Histology (.tif file) has pixel size of 0.243094 µm. Slice to volume registration scripts can be found at https://github.com/grodgers1/SliceToVolume.

opencc-by-4.0Jun 2024View details →

Single-cell proteo-transcriptomic profiling reveals altered characteristics of stem and progenitor cells in patients receiving cytoreductive hydroxyurea in early-phase chronic myeloid leukemia

This repository contains CITE-seq data generated from CML stem and progenitor cells before and after hydroxyurea treatment using the BD Rhapsody Single-Cell Analysis System.  File descriptions: 1. RSEC-adjusted UMI count files generated using the BD Rhapsody Targeted Analysis Pipeline (v. 1.10.1): <ul> <li>CartridgeS1_RSEC_MolsPerCell.csv</li> </ul> 2. RSEC-adjusted UMI counts for cells remaining after cell quality filtering using SeqGeq software (genes expressed vs library size): <ul> <li>CartridgeS1_RSEC_MolsPerCell_postQC.csv</li> </ul> 3. Sample tag (sample of origin) calls for each putative cell, outputted by the BD Rhapsody Targeted Analysis Pipeline (v. 1.10.1).  <ul> <li>CartridgeS1_Sample_Tag_Calls.csv</li> </ul>

opencc-by-4.0Jul 2018View details →

Data: In vivo fate of free and encapsulated iron oxide nanoparticles after injection of labelled stem cells

This data set is composed of magnetic resonance images (MRI) that are supporting the article entitled In vivo fate of free and encapsulated iron oxide nanoparticles after injection of labelled stem cells by the same authors. Nanoparticle contrast agents are used to label stem cells and monitor their bio-distribution in pre-clinical models of disease. Due to the impact on the interpretation of imaging results, understanding the in vivo fate of the particles is important. The bio-distribution after intra-cardiac injection of labelled cells with superparamagnetic iron oxide nanoparticles was monitored longitudinally by MRI.

opencc-by-4.0Nov 2011View details →

Text-fig. 2: Microscopic photo of the wood from Kučlín (specimen No. G 4723, NM, transverse section) shoving growth ring boundary with markedly rounded tracheids and abundant axial parenchyma (dark cells) present both in late- and earlywood (scale bar = 100 µm). in Silicified Stem From The Late Eocene Fossil Locality Of Kučlín (Czech Republic): Overview And New Remarks

Text-fig. 2: Microscopic photo of the wood from Kučlín (specimen No. G 4723, NM, transverse section) shoving growth ring boundary with markedly rounded tracheids and abundant axial parenchyma (dark cells) present both in late- and earlywood (scale bar = 100 µm).

opencc-by-4.0Aug 2024View details →

A pro-inflammatory stem cell niche drives myelofibrosis through a targetable galectin-1 axis

Myeloproliferative neoplasms are stem cell-driven cancers associated with a large burden of morbidity and mortality. The majority of <a>patients p</a>resent with early-stage disease, but a substantial proportion progress to myelofibrosis and/or secondary leukemia, advanced cancers with a poor prognosis and high symptom burden. Currently, it remains difficult to predict progression, and therapies that reliably prevent or reverse fibrosis are lacking. A major bottleneck to the discovery of disease-modifying therapies has been an incomplete understanding of the interplay between perturbed cellular and molecular states. Several cell types have individually been implicated, but a comprehensive analysis of myelofibrotic bone marrow is lacking. We therefore mapped the crosstalk between bone marrow cell types in myelofibrotic bone marrow. We found that inflammation and fibrosis are orchestrated by a ‘quartet’ of immune and stromal cell lineages – with basophils and mast cells creating a TNF signaling hub, communicating with megakaryocytes, mesenchymal stromal cells and pro-inflammatory fibroblasts. We identified the b-galactoside binding protein galectin-1 as a striking biomarker of progression to myelofibrosis and poor survival in multiple patient cohorts, and as a promising therapeutic target, with reduced myeloproliferation and fibrosis <a>in vitro</a> and in vivo and improved survival following galectin-1 inhibition. In human bone marrow organoids, TNF increased galectin-1 expression, suggesting a feedback loop wherein the pro-inflammatory MPN clone creates a self-reinforcing niche, fueling progression to advanced disease. This study provides a valuable resource for studying hematopoietic cell-niche interactions, with broad relevance for cancer-associated inflammation and disorders of tissue fibrosis.

opencc-by-4.0Oct 2024View details →

2D trajectories of human pluripotent stem cell colonies

This dataset is a part of the following manuscript submitted for publication in Life (MDPI): "Human Pluripotent Stem Cell Colony Migration is Related to Culture Environment and Morphological Phenotype" by Vitaly V. Gursky, Alina S. Chabina, Olga A. Krasnova, Anastasiya A. Kovaleva, Daria V. Kriger, Michail S. Zadorsky, Konstantin N. Kozlov, and Irina E. Neganova A trajectory in the csv file is an array of the 2D coordinates {{x1,y1}, {x2,y2}, ...} (in µm; centered at {x,y}={0,0}), which represent the migration history of the center of one cell colony. Trajectories were obtained from the time-lapse bright-field images, using the Manual Tracking tool in ImageJ (Fiji). The data were collected for colonies from three human pluripotent stem cell lines (human induced pluripotent stem cell line AD3, patient specific human induced pluripotent stem cell line HPCASRi002-A (CaSR), and human embryonic stem cell line H9), grown under two culture conditions (media/matrix = mTESR1/MG or E8/GT). The colonies were phenotyped according to their morphological characteristics associated with the pluripotency status ("good" and "bad" phenotype); cells with the "bad" phenotype showed signs of incipient differentiation. The time interval between adjacent coordinates is 15 min. The data were obtained under the financial supprot of the Russian Science Foundation, grant number 21-75-20132.

opencc-by-4.0Jul 2021View details →

Systematic Scoping Literature Review of Embryonic Stem Cells In Vitro Developmental Toxicity Tests: Included publications library

The publications included in the systematic scoping review conducted according to the protocol:<a href="https://zenodo.org/record/2528920">https://zenodo.org/record/2528920</a>

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Data for: Emergent dynamics of adult stem cell lineages from single nucleus and single cell RNA-Seq of Drosophila testes

Proper differentiation of sperm from germline stem cells, essential for production of the next generation, requires dramatic changes in gene expression that drive remodeling of almost all cellular components, from chromatin to organelles to cell shape itself. Here we provide a single nucleus and single cell RNA-seq resource covering all of spermatogenesis in Drosophila starting from in-depth analysis of adult testis single nucleus RNA-seq (snRNA-seq) data from the Fly Cell Atlas (FCA) study (Li et al., 2022). With over 44,000 nuclei and 6,000 cells analyzed, the data provide identification of rare cell types, mapping of intermediate steps in differentiation, and the potential to identify new factors impacting fertility or controlling differentiation of germline and supporting somatic cells. We justify assignment of key germline and somatic cell types using combinations of known markers, in situ hybridization, and analysis of extant protein traps. Comparison of single cell and single nucleus datasets proved particularly revealing of dynamic developmental transitions in germline differentiation. To complement the web-based portals for data analysis hosted by the FCA, we provide datasets compatible with commonly used software such as Seurat and Monocle. The foundation provided here will enable communities studying spermatogenesis to interrogate the datasets to identify candidate genes to test for function in vivo.

opencc-zeroJan 2023View details →

opencc-by-4.0Jan 2023View details →

RNA-seq - Definitive endoderm differentiation of human pluripotent stem cells in G1 phase

Backup copy of the processed RNA-seq data at http://ngs.sanger.ac.uk/production/endoderm/

dryad40/100

Patient-specific induced pluripotent stem cell properties implicate Ca2+-homeostasis in clinical arrhythmia associated with combined heterozygous RYR2 and SCN10A variants

We illustrate the use of induced pluripotent stem cells (iPSCs) as platforms for investigating cardiomyocyte phenotypes in a human family pedigree exemplified by novel heterozygous RYR2-A1855D and SCN10A-Q1362H variants occurring alone and in combination. The proband, a four-month-old boy, presented with polymorphic ventricular tachycardia (PVT). Genetic tests revealed double novel heterozygous RYR2-A1855D and SCN10A-Q1362H variants inherited from his father (F) and mother (M) respectively. His father showed ventricular premature beats (VPB); his mother was asymptomatic. Molecular biological characterisations demonstrated greater TNNT2 mRNA expression in the iPSCs-induced cardiomyocytes (iPS-CMs) than in the iPSCs. cTNTs became progressively organised, but cytoplasmic RYR2 and SCN10A aggregations occurred in the iPS-CMs. Proband-specific iPS-CMs showed decreased RYR2 and SCN10A mRNA expression. The RYR2-A1855D variant resulted in premature spontaneous sarcoplasmic reticular (SR) Ca2+ transients (PCTs), Ca2+ oscillations (COs), and increased action potential durations (APDs). SCN10A-Q1362H did not confer any specific phenotype. However, the combined heterozygous RYR2-A1855D and SCN10A-Q1362H variants in the proband iPS-CMs resulted in accentuated Ca2+ homeostasis disorders, AP prolongation and susceptibility to early afterdepolarisations (EADs) at high stimulus frequencies. These findings attribute the clinical phenotype in the proband to effects of the heterozygous RYR2 variant exacerbated by heterozygous SCN10A modification.

opencc-zeroFeb 2023View details →

opencc-by-4.0Jun 2023View details →

Bulk RNA-seq dataset of human embryonic stem cells (hESCs) differentiation

The dataset consists of 31 bulk samples obtained from human embryonic stem cells undergoing undirected differentiation. The samples were collected at 16 time points on days 0 and 7-21 of differentiation. The file contains the raw read counts. More details can be found in: SPIRAL: Significant Process InfeRence ALgorithm for single cell RNA-sequencing and spatial transcriptomics\ Hadas Biran, Tamar Hashimshony, Tamar Lahav, Or Efrat, Yael Mandel-Gutfreund, and Zohar Yakhini  <a href="https://doi.org/10.1101/2022.05.24.493189">https://doi.org/10.1101/2022.05.24.493189</a>

opencc-by-4.0Jan 2022View details →

Figure 3 in The study of exposure times and dose-escalation of tick saliva on mouse embryonic stem cell proliferation

Figure 3. Effect of D. marginatus SGE (0-160 µg/ml) on mouse embryonic stem cell proliferation and viability. Values represent relative fold change of cell viability normalized to untreated negative control. The Geisser–Greenhouse correction and Dunnett´s test on multiple comparison were used. All experiments have the P value <0.05, on three different time laps. The results are mean ± standard deviation (SD) from a representative experiment carried out in triplicate and were seeded in equal amount in 3 different 96-well cultured plates.

opencc-by-4.0Jan 2022View details →

Figure 2 in The study of exposure times and dose-escalation of tick saliva on mouse embryonic stem cell proliferation

Figure 2. Effect of R. bursa SGE (0-160 µg/ml) on mouse embryonic stem cell proliferation and viability. Values represent relative fold change of cell viability normalized to untreated negative control. The Geisser–Greenhouse correction and Dunnett´s test on multiple comparison were used. The results are mean ± standard deviation (SD) from a representative experiment carried out in triplicate and were seeded in equal amount in 3 different 96-well cultured plates.

A Study of Oral Ixazomib Maintenance Therapy in Participants With Newly Diagnosed Multiple Myeloma (NDMM) Not Treated With Stem Cell Transplantation (SCT)

ClinicalTrials.gov study NCT02312258. IPD Sharing: YES. Countries: 35. Publications: 2.

Efficacy and Safety Study of CSJ148 in Stem Cell Transplant Patients

ClinicalTrials.gov study NCT02268526. IPD Sharing: YES. Countries: 6. Publications: 1.

A Study of the Efficacy and Safety of Hematopoietic Stem Cells Transduced With Lenti-D Lentiviral Vector for the Treatment of Cerebral Adrenoleukodystrophy (CALD)

ClinicalTrials.gov study NCT01896102. IPD Sharing: YES. Countries: 6. Publications: 3.

Vedolizumab in the Prophylaxis of Intestinal Acute Graft Versus Host Disease (aGVHD) in Participants Undergoing Allogeneic Hematopoietic Stem Cell (Allo-HSCT) Transplantation

ClinicalTrials.gov study NCT03657160. IPD Sharing: YES. Countries: 27. Publications: 1.

Activity, Safety and Pharmacokinetics in Pediatric Subjects With Moderate and Severe Chronic Graft vs. Host Disease After Allogeneic Stem Cell Transplant

ClinicalTrials.gov study NCT03774082. IPD Sharing: YES. Countries: 14. Publications: 1.