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Series GSE129798 Query DataSets for GSE129798
Status Public on Nov 04, 2019
Title Single cell profiling reveals sex, lineage and regional diversity in adult mouse kidney
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary To obtain new insight into the mammalian kidney, anatomy-guided, single cell RNA sequencing was performed on the adult male and female mouse kidney. Key observations were followed up through a variety of secondary studies including genetic lineage tracing. The data document novel cell diversity, unexpected origins to key cell types, and significant sex differences centered on proximal tubules segments of the nephron and principal cells of the collecting system. A searchable database integrating these data will facilitate an understanding of gene to cell relationships in the normal and diseased mammalian kidney.
Overall design With regard to generating the scRNASeq dataset, single cell dissociation was optimized for micro-dissected kidney zones [cortex, outer medulla and inner medulla ] of two adult male and female C57BL6/J mice. Single cell suspensions were processed through the 10X Genomics Chromium platform with Illumina Hi-Seq sequencing of barcoded single-cell libraries. Gene/barcode matrices were merged and further processed using the Seurat R package to perform unsupervised clustering. Profiles were annotated by matching enriched gene sets with kidney cell-type specific markers. Key observations were followed up through a variety of secondary studies including genetic lineage tracing.
Web link
Contributor(s) Ransick A, Lindstrom NO, McMahon AP, Kim AD, Liu J
Citation(s) 31689386
Submission date Apr 15, 2019
Last update date Nov 15, 2019
Contact name Andrew P McMahon
Phone 323-442-7847
Organization name University of Southern California
Department Stem Cell Biol & Regen Med
Lab Andrew McMahon
Street address 1425 San Pablo St, BCC 312
City Los Angeles
State/province California
ZIP/Postal code 90033
Country USA
Platforms (1)
GPL21103 Illumina HiSeq 4000 (Mus musculus)
Samples (12)
GSM3722255 Mouse adult, female 1, cortex
GSM3722256 Mouse adult, female 1, outer medulla
GSM3722257 Mouse adult, female 1, inner medulla
BioProject PRJNA532850
SRA SRP192559

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Supplementary file Size Download File type/resource
GSE129798_Mouse_Adult_DGE.tar.gz 141.1 Mb (ftp)(http) TAR
GSE129798_Mouse_Adult_DGE_final.tar.gz 138.4 Mb (ftp)(http) TAR
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Raw data are available in SRA
Processed data are available on Series record

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