Mus musculus
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA391308 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Purified CD11b+, Alveolar macrophage and HDM induced inflammatory DCs from WT and mTOR{delta} APC mice were profiled by RNA-seq to understand mTOR-dependent gene expression
2020-06-20 | GSE100316 | GEO
Project description:mTOR activation has been known to affect protein synthesis. To identify molecular signatures in transcriptome that could enhance protein synthesis, RNA-seq and quantitative proteomics studies were conducted using WT and TSC1 null MEFs. In this study, we found that the activation of mTOR leads to genome-wide 3'UTR shortening in mRNAs by alternative polyadenylation and activates ubiquitin-mediated proteolysis. The accession number for the RNA-seq data in this study is SRP056624.
2015-06-16 | PXD002006 | Pride
Project description:Characterization of Human Lung Airway APC Subsets
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Project description:Antigen presenting cells (APC) are a heterogenous population, comprised of macrophages/monocytes (CD14+ cells), classical dendritic cells (CD141+DC and CD1c+ DC) and pDC. Upon stimulation, APC migrate from peripheral organs to lymph nodes, where they drive T cell specific lineage fate, that is towards immune activation or suppression. APC in human tissues remain poorly defined. Through our previous published data we have charactised APC within adult skin and blood. Here we extend these findings, by increasing the sample for skin CD14+ DC and CD1c+ DC and performing gene array analysis of adult spleen CD14+ DC, CD141+DC and CD1c+ DC. Once, we were confident we could clearly distinguish our populations (CD14+ cell, CD141+ DC and CD1c+ DC) of interest from other cells, we sorted FACS purified the cells and prepared them for gene array analysis. Through generating subset specific gene signatures and comparing CMAP scores we confirmed we had identified equivalent APC subsets across human adult skin and spleen.
2016-12-19 | GSE85305 | GEO
Project description:We used RNA-seq to determine the effects of AraC and arabinose on RNA levels genome-wide in S. enterica. Wild-type or delta araC mutant cells were grown in both the presence and absence of 0.2% L-arabinose. RNA-Seq libraries from two independent biological replicate samples were sequenced for (i) wild-type cells with no treatment, (ii) wild-type cells treated with arabinose, (iii) delta araC cells with no treatment, (iv) delta araC cells treated with arabinose. Comparisons were made between (i) and (ii) [analysis file name: Salmonella RNA-seq processed WT without arabinose vs WT with arabinose.xls], between (i) and (iii) [analysis file name: Salmonella RNA-Seq proessed no arabinose WT vs no arabinose delta araC.xls], and between (ii) and (iv) [analysis file name: Salmonella RNA-Seq processed arabinose WT vs arabinose delta araC.xls]. All analysis files are available from https://www.ebi.ac.uk/arrayexpress/files/E-MTAB-1901/E-MTAB-1901.additional.1.zip
2013-10-04 | E-MTAB-1901 | biostudies-arrayexpress
Project description:Purpose: we used next generation sequencing to analyze gene expression profiles of lung and spleen tissues wild-type KrasLA2(WT-KrasLA2) and miR-301a knockout KrasLA2 (miR301aKO-KrasLA2) mice. The goals of this study are to compare the different gene expression profiles of lung tumorigenesis between WT-KrasLA2 and miR301aKO-KrasLA2 mice. Methods: WT-KrasLA2 and miR301aKO-KrasLA2 mice were sacrificed at 9 weeks and lung and spleen tissue were obtained and total RNA was extracted. mRNA profiles were generated by deep sequencing spleen tissue in single, lung tissue from WT and miR-301a KO mice in single, lung tissue from WT-KrasLA2 and miR301aKO-KrasLA2 mice in duplicate using High-seq 2000 Illumina sequencing platform. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRT–PCR validation was performed using TaqMan and SYBR Green assays Results: After quality filtering of raw sequencing data, we obtained 47,865,482 (95%) out of 50,579,239 tags of lung, 34,855,916 (96%) out of 36,426,771 tags of spleen from WT-KrasLA2 mice, and 44,632,009 (95%) out of 46,771,631 tags of lung, 44,306,242 (94%) out of 47,032,715 tags of spleen from miR301aKO-KrasLA2 mice. We then mapped these tags to the mouse genome. We identified 1,641 DEGs (1,166 upregulated and 475 downregulated) in lung between WT-KrasLA2 and miR301aKO-KrasLA2 mice with a fold change more than 2.0 (up-regulation) or less than 0.5 (down-regulation). Conclusions: We identified 1166 up-regulation and 475 down-regulation differentially expressed genes (DEGs) between WT-KrasLA2 and miR301aKO-KrasLA2 mice. Immune system response and cell cycle were major pathways involved in the protection role of miR-301a deletion in lung tumorigenesis. Runx3 activation is an early event identified in miR301aKO-KrasLA2 mice compared to WT-KrasLA2 mice.
2018-01-17 | GSE109238 | GEO
Project description:Purpose: The goal of this study is to compare RNA-seq libraries of wildtype Caulobacter crescentus with two lon deletion strains (delta lon and delta lon clpX*). Methods: See Methods section of "Plasticity in AAA+ proteases reveals substrate specificity niches" for information regarding methods or contact lead correspondence. Briefly, Samples for RNAseq were extracted from wt and lon deletion strains grown to stationary phase. Conclusions: Our study represents the first detailed analysis of lon deletions (delta lon and delta lon clpX*) comparison to wt caulobacter transcriptomes, with biologic replicates, generated by RNA-seq technology in stationary phas
2022-02-12 | GSE166765 | GEO
Project description:To investigate the role of cytoplasmic helicases in the decay of Xrn1-sensitive lncRNAs, we performed RNA-Seq in WT, ecm32-delta, ski2-delta, slh1-delta, dbp1-delta and dhh1-delta yeast cells.
2023-07-27 | GSE235553 | GEO
Project description:To investigate the role of RAD21 in the transcriptional regulation of global gene expression at early stage of colorectal cancer developments, we peformed the genome-wide analysis to map genomic regions bound by Rad21 in normal small testinal crypts and tumors (adenomas) harvested from Apc Min/+ mice using ChIP-seq. ChIP-seq naalysis identified high confidence RAD21 binding sites unique to normal crypts or adenomas, as well as those common to both tissues. We further performed RNA-seq to profile the changes in gene expression from normal WT crypts to adenomas at the very early stage of adenomagenesis in the context of Rad21 heterozygous loss. mRNA profiles of normal small intestinal crypts (WT) and adenomas from Apc Min/+ and Apc Min/+:Rad21+/- double mutant mouse; Mapping of Rad21 genomic binding sites in normal intestinal crypts (WT) and Apc Min/+ adenomas
2014-10-31 | E-GEOD-59283 | biostudies-arrayexpress
Project description:To elucidate potential cell-based mechanisms by which deregulation of mTOR signaling in MVPC drives microvessel rarefaction and afore mentioned loss of tissue structure, we isolated eGFP positive MVPC lines by flow sorting and analyzed their transcriptomic signatures. Unbiased transcriptomic comparison was used to define mechanisms underlying the decreased stemness and angiogenic ability in Tsc2KD mTOR activated versus WT MVPC. Additionally, we identified a Tsc2KD line that exhibited pS6 expression similar to WT levels suggesting cell intrinsic adaptive regulation of mTOR. Bulk RNA seq was performed in triplicate using primary WT, Tsc2KD mTOR regulated and Tsc2KD mTOR activated (mTOR+) lines. Following normalization, hierarchical clustering analyses were presented as a heatmap depicting significant differences in gene expression between WT and Tsc2KD lines. Tsc2 KD was confirmed in bulk RNA sequencing analysis of the MVPC lines
2023-09-01 | GSE225656 | GEO