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opencc-by-4.0Nov 2023View details →

Raw band intensity values for ATG3 WT or Mutants in vitro LC3 lipidation

Raw band intensity values used for the quantification of in vitro LC3 lipidation results (Fig4C) in Three-step docking by WIPI2, ATG16L1 and ATG3 delivers LC3 to the phagophore.

opencc-by-4.0Jan 2023View details →

Data for: 3D in vitro modeling of the exocrine pancreatic unit using tomographic volumetric bioprinting

Abstract <div> <div> Pancreatic ductal adenocarcinoma (PDAC) is the most frequent type of pancreatic cancer, one of the leading causes of cancer-related deaths worldwide. The first lesions associated with PDAC occur within the functional units of exocrine pancreas. The crosstalk between PDAC cells and stromal cells plays a key role in tumor progression. Thus, in vitro, fully human models of the pancreatic cancer microenvironment are needed to foster the development of new, more effective therapies. However, it is challenging to make these models anatomically and functionally relevant. Here, we used tomographic volumetric bioprinting, a novel method to fabricate three-dimensional cell-laden constructs, to produce a portion of the complex convoluted exocrine pancreas in vitro. Human fibroblast-laden gelatin methacrylate-based pancreatic models were processed to reassemble the tubuloacinar structures of the exocrine pancreas and, then human pancreatic ductal epithelial (HPDE) cells overexpressing the KRAS oncogene (HPDE-KRAS) were seeded in the acinar lumen to reproduce the pathological exocrine pancreatic tissue. The growth and organization of HPDE cells within the structure was evaluated and the formation of a thin epithelium which covered the acini inner surfaces in a physiological way inside the 3D model was successfully demonstrated. Interestingly, immunofluorescence assays revealed a significantly higher expressions of alpha smooth muscle actin (α-SMA) vs. actin in the fibroblasts co-cultured with cancerous than with wild-type HPDE cells. Moreover, α-SMA expression increased with time, and it was found to be higher in fibroblasts that laid closer to HPDE cells than in those laying deeper into the model. Increased levels of interleukin (IL)-6 were also quantified in supernatants from co-cultures of stromal and HPDE-KRAS cells. These findings correlate with inflamed tumor-associated fibroblast behavior, thus being relevant biomarkers to monitor the early progression of the disease and to target drug efficacy.   </div> <div> To our knowledge, this is the first demonstration of a 3D bioprinted portion of pancreas that recapitulates its true 3-dimensional microanatomy, and which shows tumor triggered inflammation.   </div> </div>   Contents This repository contains the raw data, materials list, protocols, and code necessary to reproduce the work in the namesake preprint.

opencc-by-4.0Jul 2024View details →

Mass spectrometry raw data for "Proteomics reveals substantial differences between in vitro matured abattoir-derived and in vivo matured oocytes in cattle"

In vitro production (IVP) of bovine embryos still has its limitations such as low blastocyst rate and lower embryo quality, resulting in lower pregnancy rates following the transfer of IVP embryos compared to in vivo produced embryos. Given these differences in developmental competence, RNA sequencing and microarray technology have been applied to describe the differences in transcriptional activity between in vitro and in vivo produced embryos. All but one of these studies solely utilized oocytes obtained from slaughterhouse material for the in vitro production of embryos, thereby introducing the possibility, that differences between IVP and in vivo embryos are in part attributable to differing sources of oocytes. The aim of the present study was therefore to compare the proteome of oocytes retrieved from slaughterhouse material, with and without a period of in vitro maturation and in vivo matured oocytes obtained from donor cattle following superovulation. For each group the protein pattern of four biological replicates containing ten oocytes each were analyzed via SWATHTM-MS.

The optimal period for oocyte retrieval after the administration of recombinant human chorionic gonadotropin in in vitro fertilization

This is the dataset of the study called "The optimal period for oocyte retrieval after the administration of recombinant human chorionic gonadotropin in in vitro fertilization". Abstract Background Our objective was to investigate the existence of an optimal period for oocyte retrieval in regards to the clinical pregnancy occurrence after the administration of recombinant human chorionic gonadotropin (rhCG) (Ovitrelle®). Methods We studied the digital records of 3362 middle eastern couples who underwent in vitro fertilization (IVF) treatment between 2019 and 2021. Results Through statistical testing, we found that there is a significant positive correlation between the oocyte retrieval period and the clinical pregnancy occurrence up to the 37th hour, where retrieval at the 37th hour was found to provide the most optimal outcome, especially in the case of gonadotropin-releasing hormone agonist (GnRHa) long protocol. Conclusions This cohort study recommends retrieval at hour 37 after ovulation triggering under the described conditions.

Dataset for Evaluation of a novel microfluidic chip-like device for purifying bovine frozen-thawed semen for in vitro fertilization

VetCountTM Harvester (MotilityCount ApS, Copenhagen, Denmark) is a novel sperm purification device. It consists of two chambers separated by a 10 μM microporous membrane. Untreated semen is applied in one chamber, sperm collection medium in the other. Motile sperm cells are selected by actively swimming through the membrane pores into the medium containing chamber. After 30 min incubation, the sperm collection medium can be aspirated and the purified sperm is ready for further use. In a first experiment we assessed sperm quality and recovery of frozen-thawed semen from six different bulls (n = 6) prior to and after purification with the VetCountTM Harvester or BoviPureTM gradient centrifugation, a commercial available standard technique. In a second approach, a competitive fertilization assay was performed. Ten straws per bull were pooled, split in two subsamples, and simultaneously purified either with the VetCountTM Harvester or BoviPureTM gradient centrifugation. Following purification, sperm cells from each treatment group were fluorescently labeled with either MitoTrackerTM Red FM or MitoTrackerTM Green FM. In vitro matured oocytes were inseminated with equal numbers of red and green labeled sperm. Eighteen hours after fertilization, fluorescence microscopy was used to determine the origin of the fertilizing spermatozoon.

opencc-by-4.0Dec 2019View details →

Plant regeneration in leaf culture of Centaurium erythraea Rafn. Part 3: de novo transcriptome assembly and validation of housekeeping genes for studies of in vitro morphogenesis

Six centaury transcriptomes (embryogenic calli, globular somatic embryos, cotyledonary somatic embryos, adventitious buds, leaves and roots of in vitro grown plants) were sequenced and de novo assembled using <a href="https://github.com/trinityrnaseq/trinityrnaseq/wiki">Trinity</a> . <a href="https://zenodo.org/api/files/a0546879-e382-4cf9-8185-f188d1a0c5f0/CE_Assembly.tar.gz">CE_Assembly.tar.gz</a> - Centaury referent transcriptome comprises of 160.839 Trinity transcripts grouped in 105.726 Trinity genes. <a href="https://zenodo.org/api/files/a0546879-e382-4cf9-8185-f188d1a0c5f0/CE_Assembly_fpkm.tar.gz">CE_Assembly_fpkm.tar.gz</a> - fpkm normalized read counts of the assembled transcripts in the six sequenced centaury tissues. <a href="https://zenodo.org/api/files/a0546879-e382-4cf9-8185-f188d1a0c5f0/nt.db_CE_assembly.tar.gz">nt.db_CE_assembly.tar.gz</a> - annotation of assembled transcripts by mapping them against NCBI nucleotide (NT) database using BLASTn . The obtained results were filtered with E-value E ≤ 10-3. <a href="https://zenodo.org/api/files/a0546879-e382-4cf9-8185-f188d1a0c5f0/swissprot.db_CE_assembly.tar.gz">swissprot.db_CE_assembly.tar.gz</a> - annotation of assembled transcripts by mapping them against NCBI nucleotide (<a href="https://zenodo.org/api/files/a0546879-e382-4cf9-8185-f188d1a0c5f0/swissprot.db_CE_assembly.tar.gz">s</a>wissprot) database using BLASTx . The obtained results were filtered with E-value E ≤ 10-3. <a href="https://zenodo.org/api/files/a0546879-e382-4cf9-8185-f188d1a0c5f0/pfam30.db_CE_assembly.tar.gz">pfam30.db_CE_assembly.tar.gz</a> - annotation of assembled transcripts by mapping them against Pfam30 domain database using hmmer3. The obtained results were filtered with independent E-value E ≤ 10-3.

opencc-by-4.0Apr 2020View details →

An inflamed human alveolar model for testing the efficiency of anti-inflammatory drugs in vitro

The data set accompanies the study where we developed an inflamed human alveolar epithelium model and to test the resolution lipopolysaccharide (LPS)-induced inflammation in vitro with a corticosteroid, methylprednisolone (MP). A specific focus of the study was in macrophage phenotype shifts in response to these stimuli. The data set includes: - Pro-inflammatory marker (interleukin (IL)-8, tumor necrosis factor α (TNFα), IL1β) secretion data, analysed via ELISA,  and cell viability (analysed via lactate dehydrogenase assay) of both monocultures (human monocyte-derived macrophages) and of the multicellular human alveolar model, composed of macrophages, dendritic cells, and epithelial cells.  - Barrier permeability data of the multicellular model, assessed via labeled-dextran permeability assay.  All the above-stated data is joined in the file: DraslerB_Frontiers 2020_Inflammatory model. Sample codes are explained int he first tabs.  - Pro-inflammatory marker gene expression data of the multicellular model, assessed via real time RT-qPCR. The data prepared for analysis and analysed is joined to the above-mentioned folder, whereas the direct PCR runs are joined in the file: DraslerB_Frontiers 2020_Inflammatory model_PCR runs.   - Confocal laser scanning microscopy raw files (lsm) of the multicellular model can be opened with an open source software Fiji, based on ImageJ.

opencc-by-4.0Mar 2024View details →

Amino Acids Modulate Liquid-Liquid Phase Separation in vitro and in vivo by Regulating Protein-Protein Interactions

The metadata, plots and microscopy images for the manuscript "Amino Acids Modulate Liquid-Liquid Phase Separation in vitro and in vivo by Regulating Protein-Protein Interactions".

opencc-by-4.0Mar 2024View details →

Early deficits in an in vitro striatal microcircuit model carrying the Parkinson's GBA-N370S mutation

ABSTRACT Understanding medium spiny neuron (MSN) physiology is essential to understand motor impairments in Parkinson’s disease (PD) given the architecture of the basal ganglia. Here, we developed a custom three-chambered microfluidic platform and established a cortico-striato-nigral microcircuit partially recapitulating the striatal presynaptic landscape in vitro using induced pluripotent stem cell (iPSC)-derived neurons. We found that, cortical glutamatergic projections facilitated MSN synaptic activity, and dopaminergic transmission enhanced maturation of MSNs in vitro. Replacement of wild-type iPSC-derived dopamine neurons (iPSC-DaNs) in the striatal microcircuit with those carrying the PD-related GBA-N370S mutation led to a depolarisation of resting membrane potential and an increase in rheobase in iPSC-MSNs, as well as a reduction in both voltage-gated sodium and potassium currents. Such deficits were resolved in late microcircuit cultures, and could be reversed in younger cultures with antagonism of protein kinase A activity in iPSC-MSNs. Taken together, our results highlight the unique utility of modelling striatal neurons in a modular physiological circuit to reveal mechanistic insights into GBA1 mutations in PD. FILE DESCRIPTIONS Source Data.xlsx: Tabular datasets plotted on main figures 1, 3, 4, 5 and 6. Supplementary Data.xlsx: Tabular datasets plotted on supplementary figures 1, 2, 3, 4, 5, 6, 7, 9, 10, 11, and 12. Key Resources Table.xlsx: Table containing key resources (primary and secondary antibodies, cell lines and software) used in this study. List of Primers.xlsx: Primers used in RT-qPCR.

Raw gel images accompanying the publication: Koralewska et al, NAR 2024, Short 2'-O-methyl/LNA oligomers as highly-selective inhibitors of miRNA production in vitro and in vivo, DOI 10.1093/nar/gkae284

A set of raw gel images used in the article: Koralewska et al. Short 2’-O-methyl/LNA oligomers as highly-selective inhibitors of miRNA production in vitro and in vivo, NAR 2024,  DOI 10.1093/nar/gkae284.

opencc-by-4.0Feb 2022View details →

Ash (Fraxinus excelsior L.) in vitro survival data for the UKs Living Ash Project

In-vitro propagation and survival data sets (including nursery survival) of the ash plants generated i.e. Fraxinus excelsior L., plus the PCR primers used and conditions applied. Surveyed from a range of ash seed material taken from across the UK, and held at the UK ash collection hosted by the Earth Trust in Oxfordshire, UK. A more detailed analysis of this data is currently expected to be be published in the Annals of Forest Science, and which has already provisionally accepted this work for publication, subject to the underlying data being made available i.e. here The data deposited here represents the underlying data that will be presented in graphical form in the forthcoming paper by Fenning et al., plus the associated metadata and statistical analyses, along with the original .jpg of the photos used.

opencc-by-4.0Apr 2022View details →

Semi-automated Quantitative Morphometric Analysis of E18 Rat Hippocampal Neurons from 0.5 to 6 Days In Vitro

This is the dataset presented in "Semi-automated quantitatve evaluation of neuron developmental morphology in vitro using the change-point test" by AS Liao, W Cui, VS Webster-Wood, and YJ Zhang (submitted to Neuroinformatics 2022).

opencc-by-4.0Apr 2024View details →

Validation data for a Microwave Exposure Prototype for In Vitro Growth Inhibition of Plasmodium falciparum

The dataset presented in this article revolves around the validation of an innovative irradiation device designed for in vitro malaria tests. The motivation stems from the escalating need for new malaria treatments due to the high mortality rates, the absence of an effective vaccine, and rising antimalarial drug resistance. The theoretical background for generating this data is based on prior studies indicating that microwave exposure can non-thermally kill malaria parasites by interacting with hemozoin crystals within infected erythrocytes, a process in which healthy cells remain unaffected, probably due to the absence of these crystals. This dataset aims to provide a thorough validation of the device's biological and electrical efficacy, by providing models to simulate various parameters such as the magnetic and electric field strength, and experimentally validate the biological effects on parasite viability under controlled microwave exposure. This contribution is pivotal for advancing research in electromagnetic therapy as a potential treatment for malaria, providing a foundational dataset for future experimental and theoretical work.

opencc-by-4.0Jun 2024View details →

"The pathway of hyaluronic acid (HA) and its receptors (CD44, RHAMM) in the regulation of Rho GTPases and their effectors in an in vitro colorectal cancer model" ("Szlak kwasu hialuronowego (HA) i jego receptorów (CD44, RHAMM) w regulacji GTPaz Rho i ich efektorów w modelu raka jelita grubego in vitro"); NCN Miniatura 2022/06/X/NZ3/00848

Results from Screening for "The pathway of hyaluronic acid (HA) and its receptors (CD44, RHAMM) in the regulation of Rho GTPases and their effectors in an in vitro colorectal cancer model" the project Miniatura (2022/06/X/NZ3/00848) funded by Polish National Science Centre (NCN) Wyniki skriningu w projekcie "Szlak kwasu hialuronowego (HA) i jego receptorów (CD44, RHAMM) w regulacji GTPaz Rho i ich efektorów w modelu raka jelita grubego in vitro", Miniatura (2022/06/X/NZ3/00848) finansowanym przez Narodowe Centrum Nauki (NCN)

A new in vitro blood flow model for the realistic evaluation of antimicrobial surfaces

Dataset to the publication A new in vitro blood flow model for the realistic evaluation of antimicrobial surfaces Juliane Valtin, Stephan Behrens, André Ruland, Florian Schmieder, Frank Sonntag, Lars D. Renner, Manfred F. Maitz, Carsten Werner Adv. Healthcare Mater. 2023, 2301300. <a href="https://doi.org/10.1002/adhm.202301300">https://doi.org/10.1002/adhm.202301300</a>

opencc-by-4.0Jul 2021View details →

Dataset related to article "New in silico models to predict in vitro micronucleus induction as marker of genotoxicity"

The .txt file contains the dataset of the in silico model for genotoxicity as induction of micronuclei. The .doc file contains the descriptors of the models and the structural alerts.