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Series GSE98816 Query DataSets for GSE98816
Status Public on Dec 06, 2017
Title Single cell RNA-seq of mouse brain vascular transcriptomes
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary By analyzing thousands of vascular single cell transcriptomes from adult mouse brain, we provide molecular definitions of the principal vascular (endothelial and mural cells), and vascular-associated cell classes.
Overall design 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 10 to 19 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 followed by the SmartSeq2 methodology for the generation and sequencing of full length polyadenylated cDNAs
Contributor(s) Vanlandewijck M, He L, Mäe M, Andrae J, Betsholtz C
Citation(s) 29443965, 30129931
Submission date May 11, 2017
Last update date May 15, 2019
Contact name L. H.
Organization name Uppsala University
Street address Dag Hammarskjölds Väg 20
City Uppsala
ZIP/Postal code 751 85
Country Sweden
Platforms (1)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
Samples (3186)
GSM2612539 Brain single cell 1
GSM2612540 Brain single cell 2
GSM2612541 Brain single cell 3
BioProject PRJNA386336
SRA SRP106908

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Supplementary file Size Download File type/resource
GSE98816_Brain_samples_normalized_counts_matrix.txt.gz 17.5 Mb (ftp)(http) TXT
GSE98816_Brain_samples_raw_read_counts_matrix.txt.gz 16.8 Mb (ftp)(http) TXT
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Raw data are available in SRA
Processed data are available on Series record

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