Dataset Information

A Multistep Workflow to Evaluate Newly Generated iPSCs and Their Ability to Generate Different Cell Types.

ABSTRACT: Induced pluripotent stem cells (iPSCs) derived from human somatic cells have created new opportunities to generate disease-relevant cells. Thus, as the use of patient-derived stem cells has become more widespread, having a workflow to monitor each line is critical. This ensures iPSCs pass a suite of quality-control measures, promoting reproducibility across experiments and between labs. With this in mind, we established a multistep workflow to assess our newly generated iPSCs. Our workflow tests four benchmarks: cell growth, genomic stability, pluripotency, and the ability to form the three germline layers. We also outline a simple test for assessing cell growth and highlight the need to compare different growth media. Genomic integrity in the human iPSCs is analyzed by G-band karyotyping and a qPCR-based test for the detection of common karyotypic abnormalities. Finally, we confirm that the iPSC lines can differentiate into a given cell type, using a trilineage assay, and later confirm that each iPSC can be differentiated into one cell type of interest, with a focus on the generation of cortical neurons. Taken together, we present a multistep quality-control workflow to evaluate newly generated iPSCs and detail the findings on these lines as they are tested within the workflow.

SUBMITTER: Chen CX

PROVIDER: S-EPMC8293472 | biostudies-literature | 2021 Jul

REPOSITORIES: biostudies-literature

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Publications

A Multistep Workflow to Evaluate Newly Generated iPSCs and Their Ability to Generate Different Cell Types.

Chen Carol X-Q CX Abdian Narges N Maussion Gilles G Thomas Rhalena A RA Demirova Iveta I Cai Eddie E Tabatabaei Mahdieh M Beitel Lenore K LK Karamchandani Jason J Fon Edward A EA Durcan Thomas M TM

Methods and protocols 20210719 3

Induced pluripotent stem cells (iPSCs) derived from human somatic cells have created new opportunities to generate disease-relevant cells. Thus, as the use of patient-derived stem cells has become more widespread, having a workflow to monitor each line is critical. This ensures iPSCs pass a suite of quality-control measures, promoting reproducibility across experiments and between labs. With this in mind, we established a multistep workflow to assess our newly generated iPSCs. Our workflow tests ...[more]

PMID: 34287353

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Project description:BackgroundThe decline of pollinating insects in agricultural landscapes proceeds due to intensive land use and the associated loss of habitat and food sources. The feeding of those insects depends on the spatial and temporal distribution of nectar and pollen as food resource. Hence, to protect insect biodiversity, a spatio-temporal assessment of food quantity of their habitats is necessary. Therefore, sufficient data on traits of floral resources are required.New informationAs floral resources' traits of plants are important to quantify food availability, we present two databases, the FloRes Database (Floral Resources Database) and the raw database, from where FloRes was derived. Both databases contain the plant traits: (1) flowering period, (2) floral-unit density per day, (3) nectar volume per floral unit per day, (4) sugar content per floral unit, (5) sugar concentration in nectar, (6) pollen mass or volume per floral unit and per day, (7) protein content of pollen and (8) corolla depth. All traits were sampled from literature and online databases. The raw database consists of 702 specified plant species, 138 unspecified species 37 species (spec., sp), 22 species pluralis (spp) and, for 79, only the genus was identified) and two species complexes (agg.). Those 842 taxa belong to 488 genera and 102 families. Finally, only 27 taxa have a complete set of traits, too few for a sufficient assessment of spatio-temporal availability of floral food-resources.As information on floral resources is scattered throughout many publications with different units, we also present our multistep workflow implemented in five consecutive R-scripts. The multistep workflow standardises the trait units of the raw database to comparable entities with identical units and aggregates them on a reasonable taxonomic level into the second application database, the FloRes Database. Finally, the FloRes Database contains aggregated information of traits for 42 taxa and, when corolla depth is excluded, for 72 taxa.This is the first attempt to gather these eight traits from different literature sources into one database with a multistep workflow. The publication of the multistep workflow enables the users to extend the FloRes Database on their own demands with other literature data or newly-gathered data to improve quantification of food resources. Especially, the combination of pollen, nectar and the open flowers per square metre is, as far as we know, a novelty.The FloRes Database can be used to evaluate the quantity of food-resource habitats available for pollinators, for example, to compare seed mixtures of agri-environmental measures, such as flower strips, considering flower phenology on a daily basis.

Dataset Information

A Multistep Workflow to Evaluate Newly Generated iPSCs and Their Ability to Generate Different Cell Types.

Publications

A Multistep Workflow to Evaluate Newly Generated iPSCs and Their Ability to Generate Different Cell Types.

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