Project description:This SuperSeries is composed of the SubSeries listed below. This study aims to phenotype iPSC-derived trophoblast lines that contain homozygous null alleles for transcription factors expressed within the extra-embryonic lineage, with a focus on differentiation toward either primitive syncytium or extra-embryonic mesenchymal cells, depending on the TF being analyzed. Null alleles were generated using three distinct genetic engineering approaches: full protein coding region deletion (KO), critical exon deletion (CE), and insertion of a premature termination codon with frameshift (PTC+1). RNA-seq data was generated after 6 days of initiating differentiation from iPSCs. The study included the homozygous null alleles for the following transcription factors: GRHL1, POU2F3, EPAS1, FOSB, GCM1, PPARG, and ISL1, MEIS1, MXD1, MEIS2, RUNX1, MEF2C, NCOA3, and BHLHE40. Notably, the hypoxia-inducible factor EPAS1 was evaluated under both 20% oxygen and 3% (~ level present at peri-implantation) oxygen concentrations. This analysis provided insight into the differences between the various CRISPR-Cas9-based approaches and the impact of loss of function for these transcription factors in trophoblast lineage differentiation.

2025-02-01 | GSE288317 | GEO

Proteome profiling of human myoblastic RCMH cell line

Project description:The study aimed to comprehensively characterize human myoblastic cell line RCMH using using electron microscopic and proteomic approaches. Myoblastic cell lines can be useful to investigate the complex biochemical changes occuring under different conditions that reflect the physiological and pathophysiological mechanisms of muscle. So far, there are no suitable in vitro models of human muscle origin to study a variety of muscle related processes including responses to mechanical stress, EC-coupling and (ER-associated) myopathic disorders. Therefore, we characterized the human immortal myoblastic cell line RCMH and the results suggest RCMH as a suitable in vitro model for investigating human muscle related processes and disorders.

2016-07-20 | MSV000079948 | MassIVE

Integrated epigenetic and genetic programming of primary human T cells [WGBS]

Project description:Targeted epigenetic engineering of gene expression in cell therapies would allow programming of desirable phenotypes without many of the challenges and safety risks associated with double strand break-based genetic editing approaches. Here, we develop an all-RNA platform for efficient, durable, and multiplexed epigenetic programming in primary human T cells, stably turning endogenous genes off or on using CRISPRoff and CRISPRon epigenetic editors. We achieve epigenetic programming of diverse targeted genomic elements without the need for sustained expression of CRISPR systems. CRISPRoff-mediated gene silencing is maintained through numerous cell divisions, T cell stimulations, and in vivo adoptive transfer, avoiding cytotoxicity or chromosomal abnormalities inherent to multiplexed Cas9-mediated genome editing. Finally, we successfully combined genetic and epigenetic-engineering using orthogonal CRISPR Cas12a/dCas9 systems for targeted CAR knockin and CRISPRoff silencing of therapeutically relevant genes to improve preclinical CAR T cell-mediated in vivo tumor control and survival.

2025-09-08 | GSE306917 | GEO

Antibiotics and Immune Responses study

Project description:Antibiotics and Immune Responses study

| PRJNA814322 | ENA

Study 2- RNA-seq of male KOLF2.2J hiPSC-derived trophoblast cell lines homozygous null for seven different transcription factors

Project description:This study aims to phenotype iPSC-derived trophoblast lines that contain homozygous null alleles for transcription factors expressed within the extra-embryonic lineage, with a focus on differentiation toward either primitive syncytium or extra-embryonic mesenchymal cells, depending on the TF being analyzed. Null alleles were generated using three distinct genetic engineering approaches: full protein coding region deletion (KO), critical exon deletion (CE), and insertion of a premature termination codon with frameshift (PTC+1). RNA-seq data was generated after 6 days of initiating differentiation from iPSCs. The study included the homozygous null alleles for the following transcription factors: MEIS1, MXD1, MEIS2, RUNX1, MEF2C, NCOA3, and BHLHE40. This analysis provided insight into the differences between the various CRISPR-Cas9-based approaches and the impact of loss of function for these transcription factors in trophoblast lineage differentiation.

2025-02-03 | GSE288289 | GEO

Pan-genomic study of primary human retinoblastoma samples

Project description:Pan-genomic study of primary human retinoblastoma samples

| PRJNA253480 | ENA