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Transcriptome profiling of cytoplasmic fraction of naïve CD8 T cells from Nxf1 mutant and control mice [Lymphocytes]

ABSTRACT: Transcriptome profiling of cytoplasmic fraction of naïve CD8 T cells from Nxf1 mutant and control mice [Lymphocytes]

PROVIDER: PRJNA592455 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR10559866.fastq.gz	Fastqsanger.gz
	SRR10559867.fastq.gz	Fastqsanger.gz
	SRR10559868.fastq.gz	Fastqsanger.gz
	SRR10559869.fastq.gz	Fastqsanger.gz
	SRR10559870.fastq.gz	Fastqsanger.gz

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Transcriptome profiling of cytoplasmic fraction of naïve CD8 T cells from Nxf1 mutant and control mice [Lymphocytes]

Project description:Purpose: Nxf1 is thought to be an essential nuclear exporter of messenger RNA (mRNA) in eukaryotic cells. Whether perturbations in the Nxf1 pathway affect mammalian physiology is not known. The aim of this study is to determine the impact of a Nxf1 mutation in the representation of mRNA transcripts in the cytoplasm of naïve CD8 T cells. Methods: For Naïve CD8 T cell isolation, splenocyte suspensions were submitted to red blood cell lysis, stained first with biotinylated CD8 antibodies and then labelled with anti-Biotin microbeads. CD8+ T cells were magnetically enriched by positive selection on MACS separation columns, stained with fluorescently-labelled antibodies before being FACS-sorted as CD8+ CD44low CD62L+. Sorted Naïve T cells were fractionated with Norgen cytoplasmic and nuclear fractionation RNA purification kit. Only cytoplasmic fractions were used for subsequent RNAseq.

2020-03-04 | GSE141158 | GEO

Knockdown of SR protein family in P19 cells and RNA-seq of cytoplasmic and whole cell polyA+ RNA

Project description:Our data suggest that all SR proteins contribute to mRNA export via NXF1. To identify endogenous export targets we depleted all seven SR proteins individually from P19 WT cells prepared cytoplasmic fractions. We sequenced the cytoplasmic fraction and as a control whole celll RNA from the identical sample. Knockdown of seven SR Proteins plus control, total RNA and cytoplasmic RNA, polyA+ enriched, 2 biological replicates per condition, 2 technical replicates per condition

2016-03-07 | E-GEOD-69733 | biostudies-arrayexpress

Knockdown of SR protein family in P19 cells and RNA-seq of cytoplasmic and whole cell polyA+ RNA

2016-03-07 | GSE69733 | GEO

Transcriptome profiling of purified mouse platelets from Nxf1 mutant and control mice [Platelet]

Project description:Purpose: Nxf1 is thought to be an essential nuclear exporter of messenger RNA (mRNA) in eukaryotic cells. Whether perturbations in the Nxf1 pathway affect mammalian physiology is not known. The aim of this study is to determine the impact of a Nxf1 mutation in the representation of mRNA transcripts in platelets. Methods: Platelets were purified from individual males. Blood was obtained by cardiac puncture into 0.1 volume of Aster Jandl citrate-based anticoagulant. Mouse platelet rich fraction was obtained by centrifugation of the murine blood at 125 g for 8 min at room temperature, followed by centrifugation of the supernatant buffy coat at 125 g for 8 min. Mouse platelets were washed by two sequential centrifugations at 860 g for 5 min in 140 mM NaCl, 5 mM KCl, 12 mM trisodium citrate, 10 mM glucose, and 12.5 mM sucrose, pH 6.0.The platelet pellet was resuspended in 10 mM Hepes, 140 Mm NaCl, 3 mM KCl, 0.5 mM MgCl2, 10 mM glucose, and 0.5 mM NaHCO3, pH 7.4. The purity of each platelet suspension was assessed by flow cytometry and suspensions for which more than 98% of total events were CD41+ platelets were pooled together. RNA was purified with Norgen cytoplasmic and nuclear fractionation RNA purification kit.

2020-03-04 | GSE141159 | GEO

Transcriptome profiling of purified red blood cells from Nxf1 mutant and control mice [Erythrocytes]

Project description:Purpose: Nxf1 is thought to be an essential nuclear exporter of messenger RNA (mRNA) in eukaryotic cells. Whether perturbations in the Nxf1 pathway affect mammalian physiology is not known. The aim of this study is to determine the impact of a Nxf1 mutation in the representation of mRNA transcripts in erythrocytes. Methods: Red blood cells were obtained from cardiac puncture, mixed with 100µl Aster Jandl citrate-based anticoagulant and subsequently diluted in 2 ml of phosphate buffer saline (PBS) with 2mM EDTA. This suspension was layered with 1.5 ml Ficoll-paque PLUS (GE Healthcare) and centrifuged at 400g for 30 minutes at room temperature with minimal acceleration and brake. The red blood cell containing pellet was washed twice with PBS 2mM EDTA and lysed for RNA extraction. The purity of each sample was checked by flow cytometry to assess the relative contamination of Ter199+ red blood cells with CD41+ platelets, CD45+ lymphocytes and DRAQ5+ (Thermo Fisher Scientific) nucleated cells. Red blood cell suspensions used for RNAseq were > 99.8% pure. RNA was extracted with Qiagen RNA extraction kit.

2020-03-04 | GSE141160 | GEO

PANAD/C7orf25 interacts with NXF1 to promote CDK6 mRNA nuclear export and G1/S transition

Project description:Nuclear export factor 1 (NXF1) exerts mRNA transporter activity via binding to adaptors. We aimed to identify new NXF1 adaptors, and found that the R122/E125/G133/D139 amino acid residues of C7orf25 interacted with the Q20/K22/K23 residues in the RBD domain of NXF1, which disrupted the intramolecular interaction between the RBD and NTF2L domains of NXF1, consequently enhancing the binding of NXF1 to target mRNAs and promoting mRNA nuclear export. Furthermore, C7orf25 accelerated the G1/S transition and promoted tumor cell growth via interacting with NXF1 to promote nuclear export of CDK6 mRNA. The levels of C7orf25, NXF1, and CDK6 proteins were elevated in human hepatocellular carcinomas, and high C7orf25 levels were associated with worse survival. These findings identify C7orf25, which we named PANAD (Proliferation-Associated NXF1 Adaptor), as a novel NXF1-interacting adaptor and disclose the crucial roles of PANAD/C7orf25 in mRNA nuclear export and tumor growth, which provides potential target for cancer therapy.

2025-06-27 | GSE300612 | GEO

Profiling of Alu cDNA in the cytoplasmic fraction of human RPE cells

Project description:Profiling of Alu cDNA in the cytoplasmic fraction of human RPE cells

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SUM159 cells treated with H3B-8800 or DMSO, Cytoplasmic fraction RNA-seq

Project description:SUM159 cells treated with H3B-8800 or DMSO, Cytoplasmic fraction RNA-seq

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The mRNA export receptor NXF1 coordinates transcriptional dynamics, alternative polyadenylation and mRNA export

Project description:Alternative polyadenylation (APA) produces mRNA isoforms with different 3’UTR lengths. Previous studied indicated that 3’ end processing and mRNA nuclear export are intertwined in gene regulation. Here, we show that mRNA export factors generally facilitate usage of distal cleavage and polyadenylation sites (PASs), leading to expression of long 3’UTR isoforms. By focusing on the export receptor NXF1, which exhibits the most potent effect on APA in this study, we reveal a number of gene features that impact NXF1-dependent APA, including 3’UTR size, gene size and AT content. Surprisingly, downregulation of NXF1 results in accumulation of RNAP II at the 3’ end of genes, correlating with its role in APA regulation. Moreover, we show that NXF1 cooperates with CFI-68 to facilitate nuclear export of long 3’UTR isoform with UGUA motifs. Together, our work reveals several important roles of NXF1 in coordinating RNAPII distribution, 3’ end processing, and mRNA export of long 3’UTR transcripts, implicating NXF1 as the nexus of gene expression regulation.

2019-01-14 | GSE117701 | GEO

Single cell analysis of circulating B lymphocytes and myocardial B lymphocytes in naïve C57/B6 mice

Project description:Single cell analysis of circulating B lymphocytes and myocardial B lymphocytes in naïve C57/B6 mice

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