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IcIpsSexd

ABSTRACT: Ips sexdentatus, genomic and transcriptomic data

PROVIDER: PRJEB80998 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR13800532.fastq.gz	Fastqsanger.gz
	ERR13802668_1.fastq.gz	Fastqsanger.gz
	ERR13802668_2.fastq.gz	Fastqsanger.gz

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icIpsSexd

Project description:Ips sexdentatus

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Project description:This study compares transcriptomic profiles of human induced pluripotent stem cells (iPS cells) and human liver organoids (HLOs) using bulk RNA-seq. Three biological replicates were analyzed for each group. Processed expression values are provided as a gene-level TPM matrix, and differential expression results for iPS versus HLO are provided as a separate processed data table.

2026-07-15 | GSE333276 | GEO

How C/EBPa creates an elite cell state for reprogramming to pluripotency [array]

Project description:Mouse Bcell, upon ectopic expression of the transcription factor Cebpa for 18h, can be reprogrammed to iPS with extremely high efficiency. To understand the molecular control of this phenomena we performed multiple high throughtput functional genomic analysis. Transcriptomic by microarray in Bcell, Bcell+Cebpa18h, Bcell+Cebpa18h+OKSM1d, Bcell+Cebpa18h+OKSM2d, ES cells

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How C/EBPa creates an elite cell state for reprogramming to pluripotency [RNAseq]

Project description:Mouse Bcell, upon ectopic expression of the transcription factor Cebpa for 18h, can be reprogrammed to iPS with extremely high efficiency. To understand the molecular control of this phenomena we performed multiple high throughtput functionnal genomic analysis. Transcriptomic by RNAseqencing (polyA+, non stranded) in Bcell, Bcell+Cebpa18h, Bcell+Cebpa18h+OKSM1d, Bcell+Cebpa18h+OKSM2d, ES cells

2016-02-19 | E-GEOD-71217 | biostudies-arrayexpress

Genetic correction and analysis of induced pluripotent stem cells from a patient with gyrate atrophy

Project description:Gene-corrected patient-specific induced pluripotent stem (iPS) cells offer a novel approach to gene therapy. Yet it is unknown whether selective pressures during prolonged culture and multiple clonal events would introduce a mutational load incompatible with therapeutic use. Here we begin to assess whether the mutational load of gene-corrected iPS cells is compatible with use in the treatment of genetic causes of retinal degenerative disease. We isolated iPS cells free of transgene sequences from a patient with gyrate atrophy caused by a point mutation in the gene encoding ornithine-δ-aminotransferase (OAT) and used homologous recombination to correct the genetic defect. Cytogenetic analysis, array comparative genomic hybridization (aCGH), and exome sequencing were performed to assess the genomic integrity of an iPS cell line after three sequential clonal events: initial reprogramming, gene targeting, and subsequent removal of a selection cassette. No abnormalities were detected following standard G-band metaphase analysis. However, aCGH and exome sequencing identified two deletions, one amplification, and nine point mutations in protein-coding regions in the initial iPS cell clone. Except for the targeted correction of the single nucleotide in the OAT locus and a single synonymous base pair change, no additional mutations or copy number variation were identified in iPS cells following the two subsequent clonal events. These findings confirm that iPS cells themselves may carry a significant mutational load at initial isolation, but that the clonal events and prolonged cultured required for correction of a genetic defect can be accomplished without a substantial increase in mutational burden.

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Expression data from mouse protein iPS cells compared to mouse embryonic stem cells and mouse hepatocyte.

Project description:Increased genomic integrity an improved protein-based iPS cell method compared to current viral induced strategies We used microarrays to detail the global gene expression of protein-based iPS cells

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Copy number variation data from iPS cells with PTCHD1-AS deletions

Project description:iPS cell lines were generated from a male with ASD (proband or prb) and his unaffected mother (control or ctrl). Both individuals carry X-linked 167kb microdeletions that disrupt both PTCHD1 and PTCHD1-AS. We found that cells PTCHD1/PTCHD1-AS-null cells tended to have abnormal karyotypes. Copy number variation analyses were performed to examine genomic stability in control and proband iPS cell lines.

2019-05-18 | GSE83089 | GEO

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