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Alternative splicing induced by bacterial pore-forming toxins sharpens CIRBP-mediated cell response to Listeria infection

ABSTRACT: We investigated wether host cell gene expression response to a bacterial infection can involve changes at alternative splicing level. To identify these events, we have analyzed the long read sequencing data to identify which transcript isoforms were altered in a human epithelial colon adenocarcinoma cell line (LoVo ATCC CCL-229) along a 0- to 10-h time-course of infection by Listeria monocytogenes strain LL195. This set is linked to a previous short-read set referenced on ENA (https://www.ebi.ac.uk/ena/browser/view/PRJEB26593).

ORGANISM(S): Homo sapiens

PROVIDER: GSE225417 | GEO | 2023/10/17

REPOSITORIES: GEO

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Alternative splicing induced by bacterial pore-forming toxins sharpens CIRBP-mediated cell response to Listeria infection

Project description:We aimed at identifying the targets of the protein Cold-Inducible RNA-Binding Protein in a human epithelial colon adenocarcinoma cell line (LoVo ATCC CCL-229) in cells infected by Listeria monocytogenes strain LL195 compared to non-infected cells. This set is linked to a previous one referenced on ENA (https://www.ebi.ac.uk/ena/browser/view/PRJEB26593)

2023-10-17 | GSE225516 | GEO

RNA-Seq CAGE (Cap Analysis of Gene Expression) analysis of mice cells in RIKEN FANTOM5 project

Project description:This experiment captures the expression data reported by the RIKEN FANTOM5 project ( http://fantom.gsc.riken.jp/5/ ), focusing on mice cell data which was deposited in the seqence read archive (SRA) under study accession DRP001032 (https://www.ebi.ac.uk/ena/data/view/DRP001031 ) . The samples in this experiment can also be found on a dedicated page of the FANTOM website: http://fantom.gsc.riken.jp/5/sstar/Browse_samples. Since this is CAGE analsyis, gene expression data is reported by FANTOM5 in TPMs (tags per milliion) for gene promoters. This is in conjunction with E-MTAB-3577 (http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-3577/)

2015-05-14 | E-MTAB-3578 | biostudies-arrayexpress

RNA-Seq CAGE (Cap Analysis of Gene Expression) analysis of mice tissue in RIKEN FANTOM5 project

Project description:This experiment captures the expression data reported by the RIKEN FANTOM5 project ( http://fantom.gsc.riken.jp/5/ ), focusing on mice tissue data which was deposited in the sequence read archive (SRA) under study accession DRP001032 (https://www.ebi.ac.uk/ena/data/view/DRP001031 ) . The samples in this experiment can also be found on a dedicated page of the FANTOM website: http://fantom.gsc.riken.jp/5/sstar/Browse_samples. Since this is CAGE analysis, gene expression data is reported by FANTOM5 in TPMs (tags per milliion) for gene promoters. This is in conjunction with E-MTAB-3578 (http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-3578/)

2015-05-14 | E-MTAB-3579 | biostudies-arrayexpress

Expression data from LoVo colon cancer lines +/- constitutive LIN28B expression

Project description:We sought to elucidate the molecular mechanisms whereby LIN28B functions by comparing the gene expression profile of cells constitutively expressing LIN28B to empty vector controls. Accordingly, we performed microarray analysis on total RNA isolated from empty vector LoVo and LIN28B-expressing LoVo colon cancer cell lines. Constitutive LIN28B expression was achieved in the LoVo (ATCC #CCL-229) colon cancer cell line via retroviral transduction of MSCV-PIG-LIN28B. Contol = empty vector MSCV-PIG.

2010-12-29 | E-GEOD-26334 | biostudies-arrayexpress

RNA-Seq CAGE (Cap Analysis of Gene Expression) analysis of human tissues in RIKEN FANTOM5 project

Project description:This experiment captures the expression data reported by the RIKEN FANTOM5 project ( http://fantom.gsc.riken.jp/5/ ), focusing on tissue/organism part data which was deposited in the seqence read archive (SRA) under study accssion DRP001031 ( https://www.ebi.ac.uk/ena/data/view/DRP001031 ) . The samples in this experiment can also be found on a dedicated page of the FANTOM website: http://fantom.gsc.riken.jp/5/sstar/Browse_samples . Since this is CAGE analsyis, gene expression data is reported by FANTOM5 in TPMs (tags per milliion) for gene promoters.

2015-02-28 | E-MTAB-3358 | biostudies-arrayexpress

RNA-seq of primary human macrophages infected with Yersinia enterocolitica strains

Project description:Pathogenic bacteria Yersinia enterocolitica injects virulence plasmid-encoded effectors through the type three secretion system into macrophages to modulate gene expression. Here we analyzed the effect on gene expression in primary human macrophages of Y. enterocolitica strains lacking effector YopP (1.5 h infection) or effectors YopP and YopM (1.5 h or 6 h infection) simultaneously using RNA-seq. This is part of a larger sequencing experiment for which other samples can be found in EMBL-EBI (www.ebi.ac.uk/arrayexpress) under accession number E-MTAB-10473 and European Nucleotide Archive (ENA) at http://www.ebi.ac.uk/ena/data/view/PRJEB10086.

2022-06-01 | E-MTAB-10602 | biostudies-arrayexpress

Expression data from xenograft tumors derived from LoVo colon cancer lines +/- constitutive LIN28B expression

Project description:We sought to elucidate functions of LIN28B and potential mechanisms whereby it may promote metastasis by comparing the gene expression profile of LIN28B metastases to primary tumors. Accordingly, we performed microarray analysis on total RNA isolated from empty vector tumors, LIN28B-LoVo tumors, and LIN28B-LoVo metastases Constitutive LIN28B expression was achieved in the LoVo (ATCC #CCL-229) colon cancer cell line via retroviral transduction of MSCV-PIG-LIN28B. xenografts were produced via injection of 1x106 cells subcutaneously into the rear flanks of nude mice. Microarrays were conducted on primary tumors from empty vector and LIN28B-expressing cells, as well as metastases derived from primary tumors constitutively expressing LIN28B. (Note: metastases did not occur with empty vector tumors)

2010-12-29 | E-GEOD-26335 | biostudies-arrayexpress

Genotyping by array of 1407 Heterogeneous Stock rats and the eight HS progenitors to study the genetic basis of complex traits.

Project description:These Heterogeneous Stock (HS) rats are derived from eight inbred progenitors through more than 60 generations of outbreeding. As a result they are fine-grained mosaics of the founder genomes, and well suited for high-resolution genetic mapping of complex traits. This experiment provides dense genotyping data for 1407 HS rats, 15 duplicates, and the 8 progenitors. From these data, each HS rat chromosome can be reconstructed as a mosaic of progenitor haplotypes. Together with phenotype and sequence data available elsewhere (DOI:10.1038/ng.2644), these data allowed fine-mapping of 160 complex traits, and identified causal genes at the QTLs. The sequences of the progenitors are available from ENA (study accession PRJEB3358, http://www.ebi.ac.uk/ena/data/view/PRJEB3358). A series of supporting data files are available from http://www.ebi.ac.uk/arrayexpress/files/E-MTAB-2332 , with an accompanying list (suppl_files_description.xlsx) describing each supporting file.

2014-02-28 | E-MTAB-2332 | biostudies-arrayexpress

ChIP-seq of Canis familiaris, Gallus gallus, Mus musculus, Homo sapiens, Monodelphis domestica to investigate CEBPA and HNF4a binding in five vertebrates

Project description:Five-vertebrate ChIP-seq reveals the evolutionary dynamics of trancription factor binding. The SRF files for this experiment can be found in the European Read Archive with study accession number ERP000054. The fastq files can be found in the raw archives and for some assays links to the ENA runs and ENA fastq files are provided.

2010-04-08 | E-TABM-722 | biostudies-arrayexpress

Allele-Specific Expression in Human Brain and Liver

Project description:Systematic survey of gene and isoform allele-specific expression in human brain and liver tissues, and description of optimised bioinformatic and statistical methods to accurately measure allele-specific expression. DNA-seq data for the same set of samples have been deposited at the European Nucleotide Archive under project accessino PRJEB5279 ( http://www.ebi.ac.uk/ena/data/view/PRJEB5279 ).

2014-05-01 | E-MTAB-2259 | biostudies-arrayexpress

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