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Mammalia

ABSTRACT: tRIP of SF3B1 and PTBP1 in Matr3-knocked down cells

PROVIDER: PRJDB16289 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	DRR494392.fastq.gz	Fastqsanger.gz
	DRR494393.fastq.gz	Fastqsanger.gz
	DRR494394.fastq.gz	Fastqsanger.gz
	DRR494395_1.fastq.gz	Fastqsanger.gz
	DRR494395_2.fastq.gz	Fastqsanger.gz

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Mammalia

Project description:tRIP of MATR3

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Homo sapiens

Project description:RNA-seq of MATR3-knocked down HEK293 cells

| PRJDB17195 | ENA

Transcriptome profiling by high throughput sequencing of HeLa cells depleted of MATR3, PTBP1/2 individually or in combination by siRNA.

Project description:We performed RNA-seq experiments on three biological replicates of HeLa cells depleted of MATR3, PTBP1/2, controls, or combined depletion of MATR3/PTBP1/2. Cells were fractionated into cytoplasmic and nuclear RNA. Library preparation was done with the TruSeq stranded RNAseq library kit (Illumina) according to manufacturer’s recommendations; RNA was depleted of rRNA using the RiboZero kit (Epicentre). All libraries were sequenced on Illumina HiSeq2 machines in a single-end manner with a read length of 100 nt.

2018-05-01 | E-MTAB-6204 | biostudies-arrayexpress

4SU-iCLIP of PTBP1 from HEK293 cells with or without MATR3 depletion

Project description:The aim of the experiment was to compare binding of PTBP1 in presence and absence of MATR3. HEK293T cells were transfected with siRNA targeting MATR3 or control sequences and labelled with 4thio-uridine for 8 hours (100µM, crosslinking 2x400mJ/cm2 365nm UV light).

2018-05-01 | E-MTAB-6286 | biostudies-arrayexpress

Mus musculus

Project description:tRIP for PTBP1

| PRJDB5705 | ENA

4SU-iCLIP of MATR3 from HEK293 cells with or without PTBP1 depletion

Project description:The aim of the experiment was to compare binding of MATR3 in presence and absence of PTBP1. HEK293T cells were transfected with siRNA targeting PTBP1 and PTBP2 or control sequences and labelled with 4thio-uridine for 8 hours (100µM, crosslinking 2x400mJ/cm2 365nm UV light).

2018-05-01 | E-MTAB-6267 | biostudies-arrayexpress

Transcriptome 3' end profiling by high throughput sequencing of HeLa cells depleted of MATR3, PTBP1/2 individually or in combination.

Project description:We performed mRNA 3'end sequencing experiments on three biological replicates of HeLa cells depleted of MATR3, PTBP1/2, controls, or combined depletion of MATR3/PTBP1/2. Cells were fractionated into cytoplasmic and nuclear RNAn and only the nuclear RNA was used. Library preparation was done with the QuantSeq library kit (Lexogen) according to manufacturer’s recommendations. Replicates 1 and 2 were prepared with the QuantSeq forward library kit, replicates 3 and 4 with the QuantSeq reverse library kit. All libraries were sequenced on Illumina HiSeq2 machines in a single-end manner with a read length of 100 nt.

2018-05-01 | E-MTAB-6287 | biostudies-arrayexpress

An Xist-dependent protein assembly mediates Xist localization and gene silencing

Project description:Nuclear compartments play diverse roles in regulating gene expression, yet the molecular forces and components driving compartment formation are not well understood. Studying how the lncRNA Xist establishes the inactive-X-chromosome (Xi)-compartment, we found that the Xist RNA-binding-proteins PTBP1, MATR3, TDP43, and CELF1 form a condensate to create an Xi-domain that can be sustained in the absence of Xist. The E-repeat-sequence of Xist serves a multivalent binding-platform for these proteins. Without the E-repeat, Xist initially coats the X-chromosome during XCI onset but subsequently disperses across the nucleus with loss of gene silencing. Recruitment of PTBP1, MATR3, TDP-43 or CELF1 to E-Xist rescues these phenotypes, and requires both self-association of MATR3 and TDP-43 and a heterotypic PTBP1-MATR3-interaction. Together, our data reveal that Xist sequesters itself within the Xi-territory and perpetuates gene silencing by seeding a protein-condensate. Our findings uncover an unanticipated mechanism for epigenetic memory and elucidate the interplay between RNA and RNA-binding-proteins in creating compartments for gene regulation.

2020-09-03 | GSE137305 | GEO

Epigenetic checkpoint regulates anti-tumor immunity of CD4 T cell in Hepatocellular carcinoma

Project description:To investigated how Matr3 KO affected the function of CD4 T cells We then performed gene expression profiling analysis using data obtained from RNA-seq of Jurkat T cells knocked out of Matr3 or not.

2024-05-29 | GSE234457 | GEO

Epigenetic checkpoint regulates anti-tumor immunity of CD4 T cell in Hepatocellular carcinoma

Project description:To investigated how Matr3 KO affected the function of CD4 T cells We then performed gene expression profiling analysis using data obtained from Hi-C seq of Jurkat T cells knocked out of Matr3 or not.

2024-05-29 | GSE239507 | GEO

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