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Hypoxia-induced translational profiles of murine fetal liver derived macrophages (FLDM)

ABSTRACT: We report changes in total and translated poly(A) RNA in mouse fetal liver derived macrophages after exposure to hypoxia. We employed translating ribosome affinity purification (TRAP) to isolate polysomal RNA from mouse fetal liver derived macrophages after exposure to hypoxia.

ORGANISM(S): Mus musculus

PROVIDER: GSE196966 | GEO | 2023/09/07

REPOSITORIES: GEO

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Hypoxia-induced translational profiles of murine bone marrow derived macrophages (BMDM)

Project description:We report changes in total and translated poly(A) RNA in mouse bone marrow derived macrophages after exposure to hypoxia. We employed translating ribosome affinity purification (TRAP) to isolate polysomal RNA from mouse bone marrow derived macrophages after exposure to hypoxia

2023-09-07 | GSE196517 | GEO

Development of a new macrophage-specific TRAP mouse (MacTRAP) and the definition of the renal macrophage translational signature

Project description:We generated a new macrophage-specific mouse line for the application of Translating Ribosome Affinity Purification (MacTRAP). MacTRAP mice express an eGFP-tagged ribosomal protein (L10a) under the control of the macrophage-specific c-fms promoter (driver of Csf1r). The TRAP line was characterized and expression of the transgene confirmed in kidney and other tissues. Validation included testing the responsiveness of the transgene under pro-inflammatory challenge in the kidney. Using TRAP, we successfully extracted macrophage-specific polysomal RNA from MacTRAP kidneys and conducted RNA-Seq following bioinformatic analyses to establish a comprehensive in vivo gene expression and pathway signature of resident renal macrophages, which may be of use to investigators studying the gene expression profile of these cells. Overall, this new in vivo tool may be of great value for the study of macrophage biology in different organs and various models of injury and disease.

2020-05-13 | GSE136265 | GEO

Translational activation of developmental mRNAs during neonatal mouse testis development

Project description:The sequence of gene regulatory events that drive neonatal germ cell development in the mammalian testis is not yet clear. We assessed changes in mRNA utilization in the neonatal testis at 1 and 4 dpp, times when the testis contains quiescent gonocytes (1 dpp) and proliferating spermatogonia (4 dpp). There are not thought to be major changes in the nature or number of somatic cells over that interval. We used microarrays to detail the global expression levels of mRNA distribution between non-translating mRNAs and efficiently translating mRNAs during testis development at 1 dpp and 4 dpp Extracts of mouse testes from 1 dpp and 4 dpp CD-1 mice were fractionated over a sucrose gradient in triplicate. Gradients were fractionated using an ISCO gradient fractionation system equipped with a UA-6 detector. The position of the 80S peak defined the boundary between translating and non-translating mRNAs. Pooled non-polysomal (non-translating; fractions 1-3) and heavy polysomal (efficiently translating, fractions 7-13) RNAs were isolated from sucrose gradient fractions for hybridization on Affymetrix 420 2.0 microarrays.

2013-07-27 | E-GEOD-49283 | biostudies-arrayexpress

High-resolution mapping of ribosome footprints from Arabidopsis thaliana

Project description:Post-transcriptional gene regulation plays a significant role in the response to oxygen deprivation. Here, we utilized advances in next-generation sequencing technology to examine changes in transcriptional control, mRNA loading on to polysome, and regulation of ribosome activity during mRNA translation in 7-day-old Arabidopsis seedlings subjected to 2 hour hypoxia treatment. 14 samples, 2 conditions (2 hr hypoxia and 2 hr normoxia), 2 bioreplicates of 3 RNA pools (total mRNA, immunopurified (TRAP) polysomal mRNA, ribosome footprints), 1 bioreplicate of 1 RNA pool (immunopurified (TRAP)-ribosome footprints).

2013-11-23 | E-GEOD-50597 | biostudies-arrayexpress

A translational profiling approach for the molecular characterization of CNS cell types

Project description:The cellular heterogeneity of the brain confounds efforts to elucidate the biological properties of distinct neuronal populations. Using Bacterial Artificial Chromosome (BAC) transgenic mice which express EGFP-tagged ribosomal protein L10a in defined cell populations, we have developed a methodology to affinity purify polysomal mRNAs from genetically defined cell populations in the brain. The utility of this approach is illustrated by the comparative analysis of four types of neurons, revealing hundreds of genes that distinguish these four cell populations. We find that even two morphologically indistinguishable, intermixed subclasses of medium spiny neuron display vastly different translational profiles and present examples of the physiological significance of such differences. This genetically targeted Translating Ribosome Affinity Purification (TRAP) methodology is a generalizable method useful for the identification of molecular changes in any genetically defined cell type in response to genetic alterations, disease, or pharmacological perturbations. This SuperSeries is composed of the SubSeries listed below.

2008-11-14 | GSE13394 | GEO

Genome-wide translational profiling of amygdala Crh-expressing

Project description:Here we translationally profiled the transcriptome of Crh-expressing neurons (Crh neurons) within the CeA following fear conditioning (FC) and fear extinction (EXT) in mice using translating ribosome affinity purification (TRAP) followed by RNA sequencing. A tone alone group (TA) was used as a control group.

2020-09-05 | GSE157021 | GEO

Comparison of translational profiles in Motor Neurons (CHAT), to all neurons (Snap25) in the spinal cord.

Project description:Translating ribosome affinity purification (TRAP) was performed on spinal cord dissections pooled from 3-4 mice 21 days post birth that were positive for the eGFP-L10A fusion ribosomal marker protein under the expression of either the Chat promoter (Tg(Chat-EGFP/Rpl10a)DW167Htz) or the Snap25 promoter (Tg(Snap25-EGFP/Rpl10a)JD362Jdd). RNA-sequencing was performed on both TRAP and pre-immunoprecipitation (PreIP) control RNA samples.

2017-06-20 | GSE93412 | GEO

Translational profiling of proximal tubule in fibrotic kidney

Project description:Injury to the proximal tubule plays a central role in the initiation and progression of kidney fibrosis, and rates of chronic kidney disease progresses approximately 50% faster in males compared to females. We applied Translating Ribosome Affinity Purification (TRAP) followed by RNA-sequencing to characterize the cell-specific proximal tubule transcriptional landscape during fibrosis in male vs. female mice.

2019-09-21 | GSE125015 | GEO

Ethanol induced transcriptional and translational changes in Aldh1l1-EGFP/Rpl10a cortical astrocyte cultures

Project description:The role astrocytes play in brain development and function has come under increased focus as the diversity of roles they are involved in has become apparent. We have previously shown ethanol exposed astrocytes alter neuronal neurite outgrowth in an in vitro co-culture system and that ethanol alters the astrocyte produced extracellular matrix (ECM) in vitro, with similar alterations in vivo. Here we utilize the translating ribosome affinity purification (TRAP) procedure in Aldh1l1-EGFP/Rpl10a transgenic mouse primary cortical astrocyte cultures to transcriptionally and translationally profile the astrocyte response to ethanol. We found large differences in the total RNA pool in comparison to the translating RNA pool while the ethanol response within each pool showed a large degree of overlap. Comparisons to published datasets indicate the in vitro model used here are most similar to PD1-PD7 in vivo cortical astrocytes and the ethanol regulated genes showed significant overlap with models of chronic ethanol exposure in astrocytes and a model of third-trimester ethanol exposure in the hippocampus and cerebellum. These findings will further our understanding of the effects of ethanol on astrocyte gene expression and protein translation and how these changes alter brain development.

2023-06-21 | GSE227891 | GEO

Translational profiling of zebrafish retina cells using translating ribosome affinity purification methods

Project description:Translating ribosome affinity purification (TRAP) methods allow cell-specific recovery of polyribosome-associated RNAs by genetic tagging of ribosomes in selected cell populations. In this study, we purified and analysed the polyribosome-associated RNA fraction of zebrafish embryo´s retinas at 22 hours post-fertilization. To this aim, we generated a transgenic strain in which the tagged ribosomes expression is restricted to the retina cells due to the activity of a specific promoter.

2021-12-29 | GSE192511 | GEO

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