Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNA-seq of NP peptide stimulated F5 huCD2iCre Ikk2fx/fx CD8+ T cells

ABSTRACT: Cells were isolated from lymph nodes of F5 Rag1-/- Cre -ve and F5 Rag1-/- huCD2iCre Ikk2fx/fx mice and cultured for 24hrs with NP-68 peptide, necrostatin-1 and splenocytes from Rag1-/- mice. A pure population of CD8+ T cells was sorted by FACS and the RNA extracted.

INSTRUMENT(S): Illumina Genome Analyzer IIx, BD FACS Aria Cell Sorter

ORGANISM(S): Mus musculus

SUBMITTER: Scott Layzell

PROVIDER: E-MTAB-14348 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

RNA-seq of NP peptide stimulated F5 huCD2iCre Ikk2fx/fx CD8+ T cells

Project description:RNA-seq of NP peptide stimulated F5 huCD2iCre Ikk2fx/fx CD8+ T cells

| PRJEB78890 | ENA

Transcription profiling of mouse naive CD8+ T-cell differentiation during a primary immune response

Project description:Title: Gene Expression analysis of naive CD8+ T-cell differentiation during a primary immune response Description: C57BL/6 wild type mice are administered GK1.5 (depleting anti CD4 antibody) or isotope control by intraperitoneal injection at 3 and 1 day pre-infection, then every 36-48 hour post infection. 24 hours pre-infection, splenocytes from F5 RAG -/- mice are stained with CFSE and 10^7 splenocytes are transfered to recipient C57BL/6 mice by intravenous injection. 24 hours laters, recipient mice are infected with 10^7 PFU of a recombinant Vaccinia virus expressing NP366-74. At timepoints 0, 12, 24, 48, 72 and 96 splenocytes are obtained and FACS sorted to obtain CD8+ T-cells.

2005-09-29 | E-MIMR-38 | biostudies-arrayexpress

Naive and memory B6.2.16 CD8 T cell(11K A and B)

Project description:Naive B6.2.16 CD8 T cells (>85% pure) were isolated from the lymph nodes (LN) of female RAG1-deficient B6.2.16 mice. B6.2.16 CD8 T cell effectors were generated by culturing splenocytes from female RAG1-deficient B6.2.16 mice with HY peptide for 4 d and adoptively transferred into female RAG1-deficient mice. After 200 d, memory B6.2.16 CD8 T cells (>80% pure) were recovered from the spleens and LNs by magnetic bead sorting. Sample proRNA from naïve and memoryB6.2.16 CD8 T cells was isolated using Trizol(r) Reagent and used to make cRNA for hybridization according to Affymetrix protocols. Keywords: other

2004-08-05 | GSE1578 | GEO

Gene expression profiling of fucose-deficient Fx-/- mice cDC1-enriched splenocytes

Project description:Gene expression profiling of fucose-deficient Fx-/- mice cDC1-enriched splenocytes

| PRJNA688317 | ENA

The underlying pathway involved in inter-subspecific hybrid male sterility in rice

Project description:Asian cultivated rice (Oryza sativa L.) consists of two major subspecies, indica and japonica. Inter-subspecific hybrids between indica and japonica, usually accompanying hybrid sterility, exhibit much more vigorous heterosis than intra-subspecific hybrids. f5 locus, also called S24 or Sb, confers significant effects on hybrid male sterility and segregation distortion. BC14F2 plants with f5-i/i, f5-j/j and f5-i/j genotype respectively, were used to dissect the underlying pathway of f5-caused hybrid male sterility via comparative transcriptome analysis. 350, 421, and 480 differentially expressed genes (DEGs) were identified from f5-i/j vs. f5-j/j, f5-j/j vs. f5-i/i, and f5-i/j vs. f5-i/i respectively. 145 DEGs demonstrated simultaneously differential expression in both f5-i/j vs. f5-j/j and f5-i/j vs. f5-i/i. Enrichment analysis with MapMan and AgriGO indicated that protein and DNA metabolism, and cell control related processes were enriched in the 145 DEGs. Stress and cell control related processes were enriched in the DEGs of f5-i/j vs. f5-j/j and f5-i/j vs. f5-i/i, whereas, these two processes were not enriched in the DEGs of f5-j/j vs. f5-i/i. Biotic and abiotic stress resistance genes were suppressed, which may result in pollen cell more sensitive to various stresses. The down regulation of ascorbate peroxidase (APX) may break the dynamic homeostasis of ROS (reactive oxygen species) and cause oxidative stress, which can damage cellular components. The expression of most of the heat shock protein (HSP) genes, which can protect proteins and cells from been destroyed, were also decreased. Based on these results, a model was proposed to summarize the underlying process for f5-caused rice hybrid male sterility. These results provide significant clues to further dissecting the molecular mechanism of f5-caused intersubspecific reproductive barrier.

2021-02-12 | GSE110483 | GEO

2019 Brecht et al. RAG1 vAbl BioID LC-MS/MS

Project description:To identify mechanisms that regulate V(D)J recombination, we used proximity-dependent biotin identification to analyze the interactomes of full length and truncated forms of RAG1 in pre-B cells. This revealed an association of RAG1 with numerous nucleolar proteins in a manner dependent on amino acids 216-383 and allowed identification of a motif required for nucleolar localization. Experiments in transformed pre-B cell lines and cultured primary pre-B cells reveal a strong correlation between disruption of nucleoli, reduced association of RAG1 with a nucleolar marker, and increases in V(D)J recombination activity. Mutation of the RAG1 nucleolar localization motif boosts recombination while removal of the first 215 amino acids of RAG1, which are required for efficient egress from nucleoli, reduces recombination activity. Our findings indicate that nucleolar sequestration of RAG1 is a negative regulatory mechanism in V(D)J recombination and identify regions of the RAG1 N-terminal region that control nucleolar association and egress.

2020-04-02 | PXD016221 | Pride

Gene expression of IKK1/2 deficient thymocytes

Project description:CD8SP TCRhi thymocytes were sorted from TNFR1-/- and TNFR1-/- CD4Cre+ IKK1fx/fx IKK2fx/fx R26REYFPfx/fx mice. RNA was produced from the sorted cells and sequencing performed. Samples 1,2 and 3 were from TNFR1-/- mice Samples 4, 5, 6 and 7 were from TNFR1-/- CD4Cre+ IKK1fx/fx IKK2fx/fx R26REYFPfx/fx mice

2017-07-05 | E-MTAB-4778 | biostudies-arrayexpress

Klebsiella pneumoniae strain:FX-CRKP046

Project description:FX-CRKP046

| PRJNA1090245 | ENA

Klebsiella pneumoniae strain:FX-CRKP067

Project description:FX-CRKP067

| PRJNA1089360 | ENA

Transcriptomic fingerprint of the type B trichothecene mycotoxins on the intestine

Project description:We employed whole genome gene expression analysis to characterize the intestinal exposure to 5 closely related food contaminants belonging to the type B trichocene mycotoxins groups The few data available on fusarenon-X (FX) do no support derivation of health-based guidance values for this mycotoxin, although preliminary results suggest higher toxicity compared to other regulated trichothecenes. Using histo-morphological analysis and whole-transcriptome profiling, the present study was designed to get a global view of intestinal alterations induced by FX. The well-described trichothecene deoxynivalenol (DON) served as a benchmark. FX exposure induced more severe intestinal histological alterations compared to DON. Intestinal inflammation was the hallmark of the molecular toxicity of DON, but also of FX. The dose-response analysis for FX revealed that benchmark doses for up-regulation of key-inflammatory genes expression were 4 to 45-fold higher than the previously reported ones for DON. Transcriptome analysis revealed that both mycotoxins down-regulated PPAR and LXR-RXR signaling pathways controlling lipid metabolism. Interestingly, several pathways including VDR/RXR activation, ephrin receptor signaling, and GNRH signaling were specific to FX and thus, discriminate the intestinal transcriptomic fingerprint of the two mycotoxins. Altogether, these results demonstrate that FX induces a more potent intestinal inflammation than DON. This study also reveals specific FX-targeted pathways, indicating that the toxicity of DON cannot serve as a benchmark for FX, and that toxicity evaluation of each trichothecene should be conducted separately.

2017-08-18 | GSE97821 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data