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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Dec 06, 2017 |
| Title |
Brain single cell 175 |
| Sample type |
SRA |
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| Source name |
Brain
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: brain
age: adult mice 12 to 15 weeks old
genotype: Cldn5(BAC)eGFP
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| Extracted molecule |
total RNA |
| Extraction protocol |
We used four different transgenic mouse reporter lines with fluorescent expression in different populations of vascular cells, Cldn5(BAC)eGFP mice that strongly labels brain endothelial cells, mice doubly positive for Pdgfrb(BAC)eGFP and NG2dsRed, in which brain vascular mural cells express both markers whereas each single marker are expressed also in other, non-overlapping cell types, and Pdgfra-H2BGFP that we found labeled a perivascular population of cells distinct from mural cells and astrocytes, in addition to the known labeling of cells of the oligendendrocyte lineage. We chose to focus our efforts to adult mice 12 to 15 weeks old in order to primarily define fully differentiated and quiescent vascular cells and we chose a methodology based on fluorescence-activated cell sorting (FACS) into 384-well plates
Libraries for RNA-seq were prepared by using SMART-seq2 methodology
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
processed data column: Brain.EC3_H3
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| Data processing |
RNA-seq reads were mapped to the mouse reference genome (mm10) using STAR (version STAR_2.4.2a) and the count matrix shows the individual counts aligning to each gene per cell. In order to compare the gene expression counts between different cells, the total gene counts for each cell was normalized to 500,000.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include raw and normalized counts values for each sample
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| Submission date |
May 11, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
L. H. |
| Organization name |
Uppsala University
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| Street address |
Dag Hammarskjölds Väg 20
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| City |
Uppsala |
| ZIP/Postal code |
751 85 |
| Country |
Sweden |
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| Platform ID |
GPL13112 |
| Series (1) |
| GSE98816 |
Single cell RNA-seq of mouse brain vascular transcriptomes |
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| Relations |
| BioSample |
SAMN06929758 |
| SRA |
SRX2798817 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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