Unknown,Transcriptomics,Genomics,Proteomics

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Single nuclei RNA-seq from adult mouse Hippocampus


ABSTRACT: We report RNA-seq of single nuclei isolated from the adult C57BL/6 male mouse Hippocampus region. Majority of the nuclei were isolated from 12 weeks old mice (4 different animal), with an additional set of nuclei from 3 months and 2 years old animals. In addition a set of GFP labeled nuclei driven by a VGAT promoter . Microdissections of dentate gyrus, CA1 and CA2/3 regions of the Hippocampus were placed into ice-cold RNA-later for fixation and stored at 4∘c overnight, then stored in -80∘c. Nuclei were isolated by sucrose gradient centrifugation and kept on ice until sorting using Fluorescence Activated Cell Sorting (FACS) into 96 well plates containing RNA lysis buffer. Single nucleus RNA was first purified then derived cDNA libraries were generated following a modified Smart-seq2 protocol. For VGAT nuclei: high titer AAV1/2 of pAAV-EF1a-DIO-EYFP-KASH-WPRE-hGH-polyA was injected into dorsal and/or ventral Hippocampus, animals were sacrificed two weeks after injections, and GFP labeled nuclei were sorted into plates and processed as described above.

ORGANISM(S): Mus musculus

SUBMITTER: Naomi Habib 

PROVIDER: E-GEOD-85721 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Div-Seq: Single-nucleus RNA-Seq reveals dynamics of rare adult newborn neurons.

Habib Naomi N   Li Yinqing Y   Heidenreich Matthias M   Swiech Lukasz L   Avraham-Davidi Inbal I   Trombetta John J JJ   Hession Cynthia C   Zhang Feng F   Regev Aviv A  

Science (New York, N.Y.) 20160728 6302


Single-cell RNA sequencing (RNA-Seq) provides rich information about cell types and states. However, it is difficult to capture rare dynamic processes, such as adult neurogenesis, because isolation of rare neurons from adult tissue is challenging and markers for each phase are limited. Here, we develop Div-Seq, which combines scalable single-nucleus RNA-Seq (sNuc-Seq) with pulse labeling of proliferating cells by 5-ethynyl-2'-deoxyuridine (EdU) to profile individual dividing cells. sNuc-Seq and  ...[more]

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