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| Status |
Public on Jun 05, 2020 |
| Title |
Superior Cervical Ganglia |
| Sample type |
SRA |
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| Source name |
primary murine SCG neurons
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| Organism |
Mus musculus |
| Characteristics |
tissue: Superior Cervical Ganglia
strain: Swiss-Webster
cell type: purified neurons
treatment: HSV-1 infected/~1/4 AAV1 transduced/~1/4 AAV8 transduced/~1/4 AAV-PhP.s transduced/~1/4 AAV-Rh10 transduced
gender: female
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| Treatment protocol |
Swiss-Webster mice were latently infected with 105 PFU HSV-1 syn 17+ via the ocular route, and after 60 days injected with one of 4 different AAV serotypes : 1, 8, PHP.S, and Rh10, each carrying a unique fluorescent protein transgene: mScarlet, mEGFP, DsRed.Express2, and TagBFP2 respectively under the CBh promoter. For each serotype three mice were independently injected with 1012 AAV genomes subcutaneously in the whisker pad (AAV1) or intravenously in the retro-orbital vein (AAV8, PHP.S, and Rh10).
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Three weeks after AAV treatment, TG and SCG from animals were collected and each tissue (TG or SCG) was pooled from all animals for neuron isolation via enzymatic tissue digest with papain and with collagenase/dispase, followed by density gradient centrifugation and enrichment using the Neuron Isolation Kit (Miltenyi BioTech.), which allows untouched neurons to flow through the column while non-neuronal cells remain bound. 3 animals from each AAV treatment except only 2 AAV8-mEGFP animals were used for cell preparations or analyses. Tissue and isolated neurons were maintained in ice cold Neurobasal A medium supplemented with 2% B27 supplement, 1% PenStrep, L-glutamine (500 μM) or PBS throughout the procedure except during the enzymatic tissue digestion steps. Cells were encapsulated, lysed and the mRNA captured/barcoded in the Genomics Core Facility at the FHCRC using the Chromium Single Cell 3’ Library and Gel Bead Kit v2 from 10X Genomics according to manufacturer instructions.
Libraries were prepared using the Chromium Single Cell 3’ Library and Gel Bead Kit v2 from 10X Genomics according to manufacturer instructions. 10X Genomics Single Cell 3’ expression libraries were sequenced on an Illumina HiSeq 2500 running in High-Output mode with a paired end (26 bp x 8 bp x 98 bp) sequencing strategy. The SCG and TG libraries were pooled and distributed over 4 sequencing lanes.
single cell RNA-seq
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
Sequencing reads were processed using Cell Ranger v 2.1 (10X Genomics) and cell by gene matrices further analyzed using Seurat v 2.3.4.
Reads were also filtered using bbduk to look for HSV and AAV
Analysis scripts available at https://github.com/proychou/HSV_10X
Genome_build: mm10
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| Submission date |
Jun 04, 2020 |
| Last update date |
Jun 05, 2020 |
| Contact name |
Pavitra Roychoudhury |
| E-mail(s) |
[email protected]
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| Phone |
2066677801
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| Organization name |
University of Washington
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| Street address |
1100 Fairview Ave N, PO Box 19024, E5-110
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| City |
Seattle |
| State/province |
Washington |
| ZIP/Postal code |
98109 |
| Country |
USA |
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| Platform ID |
GPL17021 |
| Series (1) |
| GSE151811 |
Herpes Simplex Virus 1 and Adeno Associated Virus distribution in neurons of the murine trigeminal and superior cervical ganglia |
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| Relations |
| BioSample |
SAMN15101283 |
| SRA |
SRX8471621 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4591238_SCG_barcodes.tsv.gz |
9.6 Kb |
(ftp)(http) |
TSV |
| GSM4591238_SCG_genes.tsv.gz |
212.7 Kb |
(ftp)(http) |
TSV |
| GSM4591238_SCG_matrix.mtx.gz |
35.5 Mb |
(ftp)(http) |
MTX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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