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Expression data from Soma dissected from single-cell rat Hippocampal neurons

ABSTRACT: To assess neuronal expression divergence between mice and rats, we used the Affymetrix array platform to assay the transcriptomes of micro-dissected individual soma and pool of dendrites of hippocampal neurons in dispersed primary cell cultures from rat and mouse. Using microdissected soma and dendrites from primary cultures of hippocampal neurons of two mouse strains (C57BL/6 and Balb/c) and one rat strain (Sprague-Dawley), we investigate via microarrays, subcellular localization of mRNAs in neurons

ORGANISM(S): Rattus norvegicus

SUBMITTER: Stephen Fisher

PROVIDER: E-GEOD-61085 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Expression data from Soma dissected from single-cell mouse Hippocampal neurons

Project description:To assess neuronal expression divergence between mice and rats, we used the Affymetrix array platform to assay the transcriptomes of micro-dissected individual soma and pool of dendrites of hippocampal neurons in dispersed primary cell cultures from rat and mouse. Using microdissected soma and dendrites from primary cultures of hippocampal neurons of two mouse strains (C57BL/6 and Balb/c) and one rat strain (Sprague-Dawley), we investigate via microarrays, subcellular localization of mRNAs in neurons

2014-10-14 | E-GEOD-61084 | biostudies-arrayexpress

Expression data from rat dissected dendrites

Project description:Using microdissected dendrites from primary cultures of hippocampal neurons of two mouse strains (C57BL/6 and Balb/c) and one rat strain (Sprague-Dawley), we investigate via microarrays, subcellular localization of mRNAs in dendrites of neurons to assay the evolutionary differences in subcellular dendritic transcripts localization. To assess neuronal dendrite expression divergence between mice and rats, we used the Affymetrix array platform to assay the transcriptomes of micro-dissected individual dendrites of hippocampal neurons in dispersed primary cell cultures from Sprague-Dawley rat (9 biological replicates), C57BL/6 mouse (14 biological replicates), and Balb/c mouse (5 biological replicates)

2014-10-14 | E-GEOD-61083 | biostudies-arrayexpress

Expression data from mouse dissected dendrites

2014-10-14 | E-GEOD-61082 | biostudies-arrayexpress

Expression data from rat adult and pups heart and hippocampal tissue.

Project description:To assess in order to assess potential disparities in gene expression due to developmental differences we performed a comparison between hippocampus and heart tissues from rat and mouse pup (one week old) and adult (10 week old) animals. Using heart and hippocampal tissue from mouse (C57BL/6) and rat (Sprague Dawley) we investigate via microarrays, gene expression divergence at the tissue level between a Brain and a Non-brain tissue. We also investigated any developement difference in gene expression between pups and adult animals. For the pups samples we used 3 biological replicates and for the adult samples we used 2 biological replicates with 2 technical replicates for each.

2014-10-14 | E-GEOD-61087 | biostudies-arrayexpress

Comprehensive catalog of dendritically localized mRNA isoforms from sub-cellular sequencing of single mouse neurons

Project description:To compare the RNAs present in dendrites and somas of individual neurons, we manually separated the dendrites and soma of primary mouse hippocampal neurons using a micropipette and performed RNA-sequencing on each subcellular fraction such that we obtained the subcellular transcriptomes of the same cell.

2019-01-07 | GSE115480 | GEO

Mouse and rat cells and tissues

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2014-10-14 | E-GEOD-61089 | biostudies-arrayexpress

Expression data from Soma dissected from single-cell rat Hippocampal neurons

2014-10-14 | GSE61085 | GEO

Expression data from Soma dissected from single-cell mouse Hippocampal neurons

2014-10-14 | GSE61084 | GEO

Dilution and amplification control study

Project description:Mouse adult female brainM-bM-^@M-^Ys cortex (C57BL/6, Charles River Laboratories, Inc.) was isolated and stored immediately at -80M-BM-0C. Subsequently, the mRNA (15M-BM-5g) was isolated using TRIzol Reagent and MicroFastTrack 2.0 Kit (Invitrogen). A Sample of 5M-BM-5g was assessed on Affymetrix Mouse 430.2 array. Aliquots from the leftovers of the same cortical mRNA were diluted to single-cell RNA levels (0.1, 1, and 10 pg) and independently aRNA amplified for a total of 2 and 4 rounds and assessed on Affymetrix Mouse 430.2 arrays. A Sample of 5M-BM-5g of mRNA was assessed on Affymetrix Mouse 430.2 array. Aliquots from the leftovers of the same cortical mRNA were diluted to single-cell RNA levels (0.1, 1, and 10 pg) and independently amplified, as described above, for a total of 2 and 4 rounds and assessed on Affymetrix Mouse 430.2 arrays.

2014-10-14 | E-GEOD-61081 | biostudies-arrayexpress

Subcellular Single Cell Sequencing: mRNA Diversity of Individual Glutamatergic and GABAergic Hippocampal Neurons and their Dendrites.

Project description:Neurons transport a variety of mRNAs to their dendritic and axonal compartments where they are locally translated. These processes are essential for the functional specialization of these cellular structures. To explore both the intercellular variability and intracellular dynamics of neuronal compartments we characterized the somatic and dendritic transcriptome of single neurons. We used Laser Capture Microdissection to isolate the dendrites and soma of individual neurons from primary hippocampal cultures, followed by scRNA-seq to profile the mRNA content of these compartments. In total, we sequence 276 dendrites and their respective somata, 227 somata without the dendrites, and 16 negative controls (LCM cuts of areas without cellular content). We observed less cell-type specific differences in the dendritic transcriptome than in the somatic transcriptome. However, the dendritic localization of a subset of mRNAs does vary in a cell-type specific manner. Furthermore, we observed that the relation between somatic and dendritic abundance varies according to gene and is strongly influenced by cellular function. This study provides a framework for the regulation of the dendritic transcriptome within and across individual neurons.

2021-01-15 | GSE157204 | GEO

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