Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR15861649_1.fastq.gz | Fastqsanger.gz | |||
| SRR15861649_2.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:To establish the role of Chd4 on controlling gene expression programs in the beta cell, we generated a tamoxifen-inducible, beta-cell-specific knockout mouse model; control (MIP-CreERT; Chd4flox/+;R26RtdTomato) and Chd4Db (MIP-CreERT; Chd4flox/flox;R26RtdTomato.
2023-05-31 | GSE217444 | GEO
Project description:The Mycoplasma Immunoglobulin Binding/Protease (MIB-MIP) system is a candidate virulence factor present in multiple pathogenic species of the Mollicutes, including the fast-growing species Mycoplasma feriruminatoris. The MIB-MIP system cleaves the heavy chain of host immunoglobulins, hence affecting antigen-antibody interactions and potentially facilitating immune evasion. In this work, using -omics technologies and 5’RACE, we show that the four copies of the M. feriruminatoris MIB-MIP system have different expression levels and are transcribed as operons controlled by four different promoters. Individual MIB-MIP gene pairs of M. feriruminatoris and other Mollicutes were introduced in an engineered M. feriruminatoris strain devoid of MIB-MIP genes and were tested for their functionality using newly developed oriC-based plasmids. The two proteins are functionally expressed at the surface of M. feriruminatoris, which confirms the possibility to display large membrane-associated proteins in this bacterium. However, functional expression of heterologous MIB-MIP systems introduced in this engineered strain from phylogenetically distant porcine Mollicutes like Mesomycoplasma hyorhinis or Mesomycoplasma hyopneumoniae could not be achieved. Finally, since M. feriruminatoris is a candidate for biomedical applications such as drug delivery, we confirmed its safety in vivo in domestic goats, which are the closest livestock relatives to its native host the Alpine ibex.
2024-06-28 | PXD053286 | Pride
Project description:We studied the differential gene expression in the gastric cell line AGS infected with wild type (WT) or arginase gene mutant (rocF) Helicobacter pylori (Hp). We found that the presence of the gene regulates the inflammatory responses in terms of IL8 and MIP-1B. We conclude that arginase may be involved in regulating inflammatory responses which improves the chances of survival against the human immune response.
2013-06-15 | GSE39919 | GEO
Project description:To establish the role of Chd4 on controlling gene expression programs in the beta cell, we generated a tamoxifen-inducible, beta-cell-specific knockout mouse model; control (MIP-CreERT; Chd4flox/+;R26RtdTomato) and Chd4Db (MIP-CreERT; Chd4flox/flox;R26RtdTomato.
2023-05-31 | GSE217445 | GEO
Project description:This SuperSeries is composed of the following subset Series: GSE14740: FFPE study using MIP copy number platform - kidney GSE14741: FFPE study using MIP copy number platform - bladder/colorectal/kidney/liver GSE14742: FFPE study using MIP copy number platform - colorectal GSE14743: FFPE study using MIP copy number platform - breast cancer I GSE14744: FFPE study using MIP copy number platform - breast cancer II GSE14745: FFPE study using MIP copy number platform - liver Refer to individual Series, GSE14856_quartets.txt contains list of matched samples
2010-05-06 | E-GEOD-14856 | biostudies-arrayexpress
Project description:Background: Mirror-image pain (MIP), which develops from the healthy body region contralateral to the actual injured site, is a mysterious pain phenomenon accompanying many chronic pain conditions, including complex regional pain syndrome (CRPS). However, the pathogenesis of MIP still remained largely unknown. The purpose of this study is to perform an expression profiling to identify genes related with MIP in an animal model of CRPS-I. Methods: We established a rat chronic post-ischemic pain (CPIP) model to mimic human CRPS-I. RNA-sequencing (RNA-Seq), bioinformatics, qPCR, immunostaining and animal behavioral assays were used to screen potential genes in contralateral dorsal root ganglia (DRG) that may be involved in MIP. Results: The CPIP model rats developed robust and persistent MIP in contralateral hind paws. Bilateral DRG neurons did not exhibit obvious neuronal damage. RNA-Seq of contralateral DRG from CPIP model rats identified a total 527 differentially expressed genes (DEGs) vs. control rats. The expression changes of several representative DEGs were verified by qPCR. Bioinformatics analysis indicated that immune system process, innate immune response and cell adhesion were among the mostly enriched biological processes, which are all important processes involved in pain sensitization, neuroinflammation and chronic pain. We further identified DEGs potentially involved in pain mechanisms or enriched in small- to medium-sized sensory neurons or TRPV1-lineage nociceptors. By comparing with published datasets summarizing genes enriched in pain mechanisms, we sorted out a core set of genes which might contribute to nociception and pain mechanism in MIP. Conclusions: We provided by far the first study to profile gene expression changes and pathway analysis of contralateral DRG for investigating MIP mechanisms. This work may provide novel insights into understanding the mysterious mechanisms underlying MIP.
2021-09-15 | GSE174299 | GEO
Project description:Primary outcome(s): cancer-related gene alteration, gene expression, microsatellite instability, BRAF mutant allele frequency
| 2646701 | ecrin-mdr-crc
Project description:Melioidosis, caused by the Gram-negative bacterium Burkholderia pseudomallei, is a disease endemic to South-East Asia and Northern Australia. Clinical presentation is highly variable, ranging from asymptomatic to fatal septicaemia, and thus the outcome of infection can depend on the host immune responses. The aim of this study was to characterise the macrophage immune response to B. pseudomallei in the presence of novel inhibitors targeting the virulence factor, Macrophage Infectivity Potentiator (Mip) protein. To do this. murine macrophage J774A.1 cells were infected with B. pseudomallei K96243 in the presence and absence of two small-molecule inhibitors designed to target the Mip protein. Global transcriptional profiling of macrophages infected with B. pseudomallei was analysed by RNA-Seq four hours post-infection. In the presence of Mip inhibitors, we found a significant reduction in the expression of pro-inflammatory cytokines highlighting the potential to utilize Mip inhibitors to dampen potentially harmful pro-inflammatory responses resulting from B. pseudomallei infection in macrophages. We then performed gene expression profiling analysis using data obtained from RNA-seq of J774A.1 macrophages infected with Burkholderia pseudomallei in the presence of two Mip inhibitors or vehicle control 4 hours post-infection
2024-03-06 | GSE244127 | GEO
Project description:The classification of haematolymphoid neoplasms has important clinical implications, yet current methods to determine cell lineage on formalin-fixed paraffin-embedded (FFPE) tissues are unsatisfactory, especially for neoplasms of NK- and T-cell lineages. Herein, we performed copy number analysis using the MIP platform on 86 cases, including T-, NK- and B-cell lymphomas, malignant cell lines and normal lymphocyte subsets. We demonstrate that the loss of T- and B-cell receptor gene loci correlates with cell lineage. The overall sensitivity of the assay in our cohort was 91% and 78%, while the specificity was 84% and 93%, for the corresponding antigen receptors in T- and B-cell samples, respectively. Fluorescence in situ hybridization showed no detectable translocation or deletion of the TCRA locus in samples showing loss of TCRA. Compared to PCR-based gene arrangement assay for lineage assignment, the MIP assay showed good reliability on FFPE samples, including cases more than 10 years old. In conclusion, the detection of the loss of the antigen receptor gene loci using the MIP array is a novel genetic marker of lymphoid cell lineage and a potentially valuable tool in the diagnosis and classification of lymphoid neoplasms especially of T- and NK-cell origin.
2019-02-19 | GSE111052 | GEO