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STRT RNAseq of human foreskin fibroblasts undergoing CRISPRa reprogramming

ABSTRACT: STRT RNAseq of human foreskin fibroblasts undergoing CRISPRa reprogramming

PROVIDER: PRJEB23472 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR2196050.fastq.gz	Fastqsanger.gz
	ERR2196060.fastq.gz	Fastqsanger.gz
	ERR2196070.fastq.gz	Fastqsanger.gz
	ERR2196080.fastq.gz	Fastqsanger.gz
	ERR2196051.fastq.gz	Fastqsanger.gz

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STRT RNAseq of human foreskin fibroblasts undergoing CRISPRa reprogramming

Project description:Comparison of human foreskin fibroblasts with different guide RNA compositions undergoing CRISPRa-mediated reprogramming. Cell samples have been collected at days 4, 8 and 12 of pluripotency induction. Each time point has three conditions with either (1) pluripotent reprogramming factor promoter targeting guides (OMKSL), (2) EEA-motif targeting guides (36bp), or reprorgamming factor promoter and EEA-motif targeting guides (OMKSL+36bp). Control samples have been collected from non-treated foreskin fibroblasts.

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Project description:In this study human neonatal foreskin fibroblasts (HFF1 and BJ) were lipofected with an equal mixture of human reprogramming factor-encoding mRNAs. The cells were lysed and total RNA was harvested 24 hours post-transfection. Gene regulation was evaluated with respect to corresponding mock-transfected, Lipofectamine-treated control fibroblasts. For comparison, wildtype (un-treated) HFF1 and BJ fibroblasts as well as undifferentiated HFF1- and BJ-derived induced pluripotent stem cells and human embryonic stem cells (generated and maintained in our laboratory (refer to GSE26575) were included in the analysis. Total RNA obtained from untreated human neonatal foreskin fibroblasts, reprogramming factor- and mock(Lipofectamine-treated)-transfected human neonatal fibroblasts, undifferentiated hESCs and iPSCs (derived from human neonatal foreskin fibroblasts).

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Project description:There is scant data on the mechanisms through which asymptomatic STIs (aSTIs) alter risk of HIV acquisition in the male genital tract. Foreskin removal lowers the risk of HIV acquisition, but molecular events leading to this protection are unclear. Here we show that an asymptomatic urethral infection with Chlamydia trachomatis significantly alters the foreskin epithelial proteome composition. We developed and optimised a shotgun liquid chromatography coupled tandem mass spectrometry based proteomics approach and applied this to foreskins collected at the time of medical male circumcision from 16 aSTI+ cis-gender men and 10 age-matched STI- controls. We used a novel bioinformatic metaproteomic pipeline to detect differentially expressed proteins. Gene enrichment ontology analysis revealed proteins associated with inflammatory and immune activation function in both inner and outer foreskin from men with an aSTI. Neutrophil activation/degranulation and viral-evasion proteins were significantly enriched in foreskins from men with aSTI whereas homotypic cell-cell adhesion proteins were enriched in foreskin tissue from men without an STI. Collectively, our data show that an asymptomatic urethral sexually transmitted infection result in profound alterations in epitheial tissue that potentially causes depletion of barrier integrity and function and that may encourage HIV susceptibilty.

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Project description:Purpose: To identify differential expressed genes upon CRISPRa activation. Methods: 293T cells were activated by different CRISPRa systems and then collected for RNA sequencing at 48 hpf (hours post CRISPRa activation).

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