Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNAseq of duodenal tissue from C57BL/6 mice both susceptible and resistant to Heligmosomoides polygyrus

ABSTRACT: Purpose: Identify genes implicated in resistance to H. polygyrus Method: RNA was extracted from duodenal tissue from C57BL/6 mice during primary and secondary H. polygyrus. Total RNA libraries were created using the Encore® Complete RNA-Seq Library Systems kit (NuGEN), following manufacturer’s instructions. Total RNA libraries were sequenced using the Illumina® HiSeq 2500. The raw Illumina reads were analysed as follows. First, the data quality was analysed using FastQC. Then the low quality bases were trimmed using Trimmomatic. The read pairs which passed the trimming quality filters were then aligned to mm10 (Ensembl version 75) using Tophat2. Counts were determined using htseq_count. Normalisation and statistical analysis was performed using edgeR. Differential gene analysis was calculated from naïve control group (A). Statistically significant genes with FDR < 0.05 are reported. Results: Following analysis, we identified many transcripts significantly different from the naïve control following primary and secondary H. polygyrus infection. Conclusions: The intestinal transcriptome of both primary and secondary infected mice differ significantly, identifying qualitative and quantitative differences between susceptible (primary infected) and resistant (secondary infected) mice.

ORGANISM(S): Mus musculus

PROVIDER: GSE102789 | GEO | 2017/10/11

SECONDARY ACCESSION(S): PRJNA398683

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Gene expression analysis of ex-Foxp3 Th2 cells during Heligmosomoides polygyrus infection

Project description:Gene expression of Treg cells that have lost Foxp3 expression and acquired Il4 expression following adoptive transfer into T-cell deficient mice (HpTR-IL-4gfp+), cmpared to conventional Treg cells isolated from H. polygyrus-infected wild-type mice (HpTR) and Th2 cells generated from naïve T cells following adoptive transfer into H. polygyrus-infected T-cell deficient mice (nT-IL-4gfp+). Immunity to intestinal helminth infections requires the rapid activation of T helper 2 (Th2) cells. However, simultaneous expansion of regulatory CD4+Foxp3+ T (Treg) cells impedes protective responses, resulting in chronic infections. The ratio between regulatory and effector T cells can therefore determine the outcome of infection. The re-differentiation of Treg into T helper (Th) cells has been identified in hyper-inflammatory diseases. In this study, we asked whether ex-Treg Th2 cells develop and contribute to type 2 immunity. Using multi-gene reporter and fate-reporter systems we demonstrate that a significant proportion of Th2 cells derive from Foxp3+ cells following Heligmosomoides polygyrus infection and airway allergy. Ex-Foxp3 Th2 cells exhibit characteristic Th2 effector functions and provide immunity to H. polygyrus. Through selective deletion of Il4ra on Foxp3+ cells, we further demonstrate IL-4 is required for the development of ex-Foxp3 Th2 cells. Collectively, our findings indicate that converting Treg cells into Th2 cells could concomitantly enhance Th2 cells and limit Treg-mediated suppression.

2017-05-04 | GSE98518 | GEO

Gene expression of SARS-CoV-2-infected Vero E6 cells with remdesivir treatment

Project description:RNA sequencing was performed on control and SARS-CoV-2 infected Vero E6 cells, with or without remdesivir treatment to study the biological changes after SARS-CoV-2 infection and to evaluate the effectiveness of remdesivir on the gene expression level. 500,000 Vero E6 cells were seeded in 6-well plates. The following day, the cell medium was replaced with fresh medium supplemented with either DMSO or 1 µM remdesivir, and cells were either mock-infected or infected with SARS-CoV-2 USA-WA1/2020 (MOI=0.3), with three replicates per experimental condition. Cells were harvested 24 hours after infection, and total RNA was extracted using the Qiagen® RNeasy® Plus Mini Kit. The quality of the extracted RNA was assessed with the Agilent® 2100 Bioanalyzer. Libraries were prepared from total RNA following ribosome RNA depletion using standard protocol according to Illumina®. Total RNA sequencing was then performed on the Illumina® NextSeq system; 150bp paired-end runs were performed and 100 million raw reads per sample were generated.

2021-02-02 | GSE165955 | GEO

Expression data from primary and secondary CD4 T cell effectors responding towards influenza A virus infection

Project description:How secondary CD4 T cell effectors, derived from resting memory cells, differ from primary cells, derived from naïve precursors, and how such differences impact recall responses to pathogens is unknown. We used microarrays to detail the global programme of gene expression underlying differences between primary and secondary CD4 T cell effectors purified from the spleen, dLN, and lung on day 7 following A/PR8/34 influenza infection. Congenic naïve or in vivo influenza primed memory HNT TCR trangenic CD4 T cells were sort purifed from the spleens, dLNs, and lungs of infected mice on day 7 post infection for RNA extraction and hybridization on Affymetrix microarrays. We sought to obtain only CD4 T cell populations that had entered into the immune response by also sorting and collecting only those cells that had divided at least 5 times by CFSE analysis.

2012-08-27 | E-GEOD-40230 | biostudies-arrayexpress

Gene expression of SARS-CoV-2-infected Vero E6 cells

Project description:We conducted a high-throughput drug repositioning screen using the LOPAC®1280 and the ReFRAME drug libraries to identify existing drugs that harbor antiviral activity against SARS-CoV-2, in a Vero E6 cell-based assay. We additionally performed RNA sequencing on control and SARS-CoV-2 infected Vero E6 cells to study the biological changes after SARS-CoV-2 infection and to elucidate the potential mechanisms underlying the positive hits identified from our high-throughput screen. Vero E6 cells were either mock-infected or infected with SARS-CoV-2 USA-WA1/2020 (MOI = 0.3) with three replicates. Cells were harvested 24 hours after infection, and total RNA was extracted using the Qiagen® RNeasy® Plus Mini Kit. The quality of the extracted RNA was assessed with the Agilent® 2100 Bioanalyzer. Libraries were prepared from total RNA following ribosome RNA depletion using standard protocol according to Illumina®. Total RNA sequencing was then performed on the Illumina® NextSeq system; 150bp paired-end runs were performed and 100 million raw reads per sample were generated.

2020-07-08 | GSE153940 | GEO

Comparing transcrional changes in Plasmodium yoelii infected to uninfected primary hepatocytes

Project description:GFP expressing Plasmodium yoelii (Py-GFP) infected, or naïve cultured primary hepatocytes were FACS sorted and re-suspended in TRIzol and RNA purified with RNAeasy kit (Qiagen).RNA was assessed for purity and quality using an Agilent 2100 Bioanalyzer and transcriptome analysis performed on Affymetrix GeneChip Mouse Transcriptome array 1.0. Data output was analyzed and visualized using Affymetrix Expression Console 4.0.

2019-05-10 | GSE130961 | GEO

Comparing transcrional changes in Plasmodium yoelii infected to uninfected primary hepatocytes

2021-10-18 | GSE186023 | GEO

Expression data from primary and secondary CD4 T cell effectors responding towards influenza A virus infection

2012-08-27 | GSE40230 | GEO

Antigen-specific memory and naïve CD4+ T cells following secondary Chlamydia trachomatis infection

Project description:Memory antigen-specific CD4+ T cells against Chlamydia trachomatis are necessary for protection against secondary genital tract infection. While it is known that naïve antigen-specific CD4+ T cells can traffic to the genital tract in an antigen-specific manner, these T cells are not protective during primary infection. Here, we sought to compare the differences between memory and naïve antigen-specific CD4+ T cells in the same mouse following secondary infection using transgenic CD4+ T cells (NR1 T cells). Using RNA sequencing, we found that there were subtle but distinct differences between these two T cell populations. Naïve NR1 T cells significantly upregulated cell cycle genes and were more proliferative than memory NR1 T cells in the draining lymph node. In contrast, memory NR1 T cells were more activated than naïve NR1 T cells and were enriched in the genital tract. Together, our data provide insight into the differences between memory and naïve antigen-specific CD4+ T cells during C. trachomatis infection.

2020-05-01 | GSE146265 | GEO

Comparative analysis of chicken Intestinal Intraepithelial lymphocytes (IEL) following Eimeria acervulina (EA), E. maxima (EM), or E. tenella (ET) infection

Project description:Relative expression levels of mRNAs in chicken IEL experimentally infected with EA, EM, or ET were measured at 1 to 6 days post-infection (dpi) following primary and secondary infections. One week-old chickens were uninfected (negative control) or were orally inoculated with sporulated oocysts of EA, EM, or ET. One week later, the infected chickens were challenged with an identical inoculum of the homologous parasite. Intestinal samples were collected daily from 5 birds in a treatment group at from 1 to 6 dpi following primary and secondary infections. Cecum, duodenum, and jejunum were collected from the birds challenged with E. acervulina, E. maxima, and E. tenella, respectively. Uninfected control samples and one of the 3 infection group samples were labeled with different fluorescent dyes and hybridized simultaneously on the same slide using a reference design with a dye swap protocol. Thirty seven-condition experiment, Non-infected control vs. Primary or secondary EA, EM, or ET infected IEL at 1 to 6. Biological replicates: 2 replicates with dye-switching from each infection groups. Two replicates per array.

2011-08-14 | E-GEOD-31213 | biostudies-arrayexpress

Comparative analysis of chicken Intestinal Intraepithelial lymphocytes (IEL) following Eimeria acervulina (EA), E. maxima (EM), or E. tenella (ET) infection

2011-08-15 | GSE31213 | GEO