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Bulk RNA sequencing of ABCA3 mutant, and gene-corrected patient iPSC-derived iAEC2s

ABSTRACT: Bulk RNA sequencing of ABCA3 mutant, and gene-corrected patient iPSC-derived iAEC2s

PROVIDER: PRJNA844380 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR19509911.fastq.gz	Fastqsanger.gz
	SRR19509911_1.fastq.gz	Fastqsanger.gz
	SRR19509911_2.fastq.gz	Fastqsanger.gz
	SRR19509912.fastq.gz	Fastqsanger.gz
	SRR19509912_1.fastq.gz	Fastqsanger.gz

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Bulk RNA sequencing of ABCA3 mutant, and gene-corrected patient iPSC-derived iAEC2s

Project description:We performed transcriptomic profiling of patient induced pluripotent stem cell (iPSC)-derived iAEC2s containing E690K and W308R ABCA3 mutations as well as their syngeneic, gene-corrected iAEC2s (total of four iPSC-derived iAEC2 lines). We first reprogrammed iPSCs from 2 patients with two homozyguos ABCA3 mutations (E690K and W308R ABCA3 mutations). Next we utilized TALENs gene-editing technique previously published in Jacob et al. (2017) to monoallelically target the endogenous SFTPC locus with the tdTomato reporter, allowing for sorting and isolation of SFTPCtdTomato positive iAEC2s. Finally, we used CRISPR-Cas9 footprint-free gene-correction to generate syngeneic patient iPSCs which were dfferentiated into the corresponding iAEC2s for syngeneic comparisons. Following tripplicate differentiations of all 4 patient iPSC lines, we sorted the SFTPCtdTomato+ iAEC2s on day 43-44 of differentiation for transcriptomic analyses.

2023-06-01 | GSE205318 | GEO

Bulk RNA sequencing of wildtype and ABCA3 mutant human iPSC-derived mutant containing the ABCA3:GFP fusion reporter

Project description:We performed transcriptomic profiling of induced pluripotent stem cell (iPSC)-derived iAEC2s containing wildtype, E690K homozygous ABCA3 mutantion, and W308R homozygous ABCA3 mutation. We first performed CRISPR-Cas9 gene editing on a wildtype human iPSC line (BU3) to engineer a GFP reporter bi-allelically targeted at the stop codon of the endigenous ABCA3 locus, thus generating an ABCA3:GFP fusion reporter line (as previous published iin Sun. et al, 2021). Next we utilized CRISPR-Cas9 gene-mutagenesis to introduce two homozygous ABCA3 mutations (E690K and W308R), resulting in two, new ABCA3 mutant iPSC lines containg the ABCA3:GFP fusion reporter, totally a total of 3 ABCA3:GFP fusion iPSC lines (wildtype, E690K-AG, W308R-AG). Following triplicate distal lung directed differentiations of all 3 ABCA3:GFP fusion iPSC lines we sorted the ABCA3:GFP positive iAEC2s on day 43 for transcriptomic analyses.

2023-06-01 | GSE205319 | GEO

Bulk RNA sequencing of wildtype and ABCA3 mutant human iPSC-derived mutant containing the ABCA3:GFP fusion reporter

Project description:Bulk RNA sequencing of wildtype and ABCA3 mutant human iPSC-derived mutant containing the ABCA3:GFP fusion reporter

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RNA-seq of retinal organoids derived from RPGR patient-, control- and mutation-corrected-iPSC at different developmental stages

Project description:Retinitis pigmentosa (RP) is an irreversible and inherited retinopathy. RPGR mutations are the most common causes of this disease. It remains challenging to decipher the mechanism of RPGR mutation because of the lack of appropriate study models. The substitution of patient-specific diseased retina without ethical restrictions is desired and iPSC-derived 3D retina is the best choice. In our experiment, we generated iPSCs from one RP patient with 2-bp frameshift mutation in the exon14 of RPGR gene, which were differentiated into retinal organoids. Also we generated iPSCs from a normal control and differentiated those control-iPSCs into healthy retinal organoids. Samples of patient- and control-retinal organoids at W0, W7, W13 (two replicates), W18 (two replicates) and W22 (two replicates for patient) were collected for RNA-seq. Corrected-iPSC were derived from CRISPR/Cas9-mediated gene correction. Then we collected the corrected-iPSC derived retinal organoids at W0, W7, W13 (two replicates), W18 (two replicates) and W22 (two replicates) for RNA-seq. Through the RNA-seq data, we demonstrate that patient-specific iPSC-dervied 3D retinae can recapitulate disease progress of Retinitis Pigmentosa through presenting defects in photoreceptors' gene profile. CRISPR/Cas9-mediated gene correction can rescue photoreceptor gene profile. Those transcriptome are consistent with the phenotype and function.

2020-02-01 | E-MTAB-6490 | biostudies-arrayexpress

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Project description:We perform transcriptomic profiling of cells derived from human induced pluripotent stem cells (iPSCs) using distal lung directed differentiation protocol previously described to generate alveolar type II epithelial-like cells (iAEC2s). We use the BU3 ABCA3:GFP iPSC line containing a GFP knock-in fluorescent reporter for the canonical AEC2 gene, ABCA3, to sort out pure populations of GFP positive and negative cells on day 31 of distal lung differentiation for bulk RNA sequencing analysis. We find canonical AEC2s transcripts as well as lamellar body-associated transcripts to be enriched in the ABCA3:GFP positive population suggestive of enrichment of AEC2 program. In contrast, we find non-lung endodermal lineages to be enriched in the ABCA3:GFP negative cells. Combined, these findings indicate the reliability of the ABCA3:GFP reporter in enriching iAEC2s in our in vitro distal lung directed differentiation protocol.

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Project description:Purpose: A proof of concept study examining the disease modelling capabilities of patient iPSC derived kidney organoids. Methods: A proband was diagnosed by genome sequencing with compound heterozygous IFT140 mutations. A one-step reprogramming/gene-editing protocol of proband fibroblasts was used to derive both uncorrected patient and isogenic gene-corrected induced pluripotent stem cells (iPSC) which were differentiated to kidney organoids. Organoids were examined by immunofluorescence. Additionally, epithelial cells magnetically sorted from whole kidney organoids underwent transcriptional profiling and spheroid culture. Results: Differential expression analysis of organoid epithelial cell fractions demonstrated apicobasal polarity, cell-cell junction and dynein motor assembly downregulation in patient organoids. Defective ciliary morphology and spheroid culture were rescued in gene corrected organoids. Conclusions: This study validates patient iPSC-derived kidney organoids as a novel, faithful and patient-specific model to further the study of inherited renal disease in regenerated, human, in vitro tissue.

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Project description:We generated iPSc from skin fibroblasts of two MPSIIIB patients (P1 and P2). MPSIIIB-associated cell defects were prominent in undifferentiated iPSc, in neural stem cells and in their neuronal progeny. We explored alterations of metabolic pathways in MPSIIIB neural cells by performing gene expression profiling of patient versus control neural stem cells. Exon array transcriptome analysis showed 295 transcripts with increased expression level and 1275 transcripts with decreased expression level in patient versus control neural precursors. Total RNA was extracted from proliferating neurosphere cultures derived from two control (C1 and C3) and three patient (P1.1, P1.3, and P2.3) iPSc clones. We considered a minimal fold change of 1.5 fold and a corrected P value lower than 0.05.

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