ArticleNature protocols2018
Mixed-species RNA-seq for elucidation of non-cell-autonomous control of gene transcription.
Article in Nature protocols, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
17 citing papers in PubMed, 27 citations in OpenAlex.
- Microglia in Health and Diseases: Integrative Hubs of the Central Nervous System (CNS).Cold Spring Harbor perspectives in biology · 2024Review
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- A comparison of basal and activity-dependent exon splicing in cortical-patterned neurons of human and mouse origin.Frontiers in molecular neuroscience · 2024Article
- Cooperative and competitive regulation of the astrocytic transcriptome by neurons and endothelial cells: Impact on astrocyte maturation.Journal of neurochemistry · 2023Article
- Article
- Functional roles of reactive astrocytes in neuroinflammation and neurodegeneration.Nature reviews. Neurology · 2023Review
- Sensory nerves enhance triple-negative breast cancer invasion and metastasis via the axon guidance molecule PlexinB3.NPJ breast cancer · 2022Article
- Loss-of-function variants in the schizophrenia risk gene SETD1A alter neuronal network activity in human neurons through the cAMP/PKA pathway.Cell reports · 2022Article
- Solving neurodegeneration: common mechanisms and strategies for new treatments.Molecular neurodegeneration · 2022Review
- Reactive astrocytes acquire neuroprotective as well as deleterious signatures in response to Tau and Aß pathology.Nature communications · 2022Article
- Cross-species RNA-seq for deciphering host-microbe interactions.Nature reviews. Genetics · 2021Review
- Mapping Astrocyte Transcriptional Signatures in Response to Neuroactive Compounds.International journal of molecular sciences · 2021Article
- Microglial identity and inflammatory responses are controlled by the combined effects of neurons and astrocytes.Cell reports · 2021Article
- Targeting mitochondrial dysfunction in amyotrophic lateral sclerosis: a systematic review and meta-analysis.Brain communications · 2019Article
- Complement 3Acta neuropathologica communications · 2019Article
- Article
Corrections and comments
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Authors and funding
7 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Transcriptomic changes induced in one cell type by another mediate many biological processes in the brain and elsewhere; however, achieving artifact-free physical separation of cell types to study them is challenging and generally allows for analysis of only a single cell type. We describe an approach using a co-culture of distinct cell types from different species that enables physical cell sorting to be replaced by in silico RNA sequencing (RNA-seq) read sorting, which is possible because of evolutionary divergence of messenger RNA (mRNA) sequences. As an exemplary experiment, we describe the co-culture of purified neurons, astrocytes, and microglia from different species (12-14 d). We describe how to use our Python tool, Sargasso, to separate the reads from conventional RNA-seq according to species and to eliminate any artifacts borne of imperfect genome annotation (10 h). We show how this procedure, which requires no special skills beyond those that might normally be expected of wet lab and bioinformatics researchers, enables the simultaneous transcriptomic profiling of different cell types, revealing the distinct influence of microglia on astrocytic and neuronal transcriptomes under inflammatory conditions.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.