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Series GSE103011 Query DataSets for GSE103011
Status Public on Nov 27, 2017
Title Identification of genes expressed in a mesenchymal subset regulating prostate organogenesis using tissue and single cell transcriptomics
Organism Rattus norvegicus
Experiment type Expression profiling by high throughput sequencing
Summary Prostate organogenesis involves epithelial growth in response to inductive signalling from specialised subsets of mesenchyme. To identify regulators and morphogens active in mesenchyme, we performed transcriptomic analysis using Tag-seq, RNA-seq, and single cell RNA-seq and defined new mesenchymal subsets and markers. We documented transcript expression using Tag-seq and RNA-seq in female rat Ventral Mesenchymal Pad (VMP) as well as adjacent urethra comprised of smooth muscle and peri-urethral mesenchyme. Transcripts enriched in VMP were identified in Tag-seq data from microdissected tissue, and RNA-seq data derived from cell populations and single cells. We identified 400 transcripts as enriched or specific to the VMP using bio-informatic comparisons of Tag-seq and RNA-seq data. Comparison with single cell RNA-seq identified transcripts yielded 45 transcriptscommon to both approaches. Cell subset analysis showed that VMP and adjacent mesenchyme were composed of distinct cell types and that each tissue was comprised of two subgroups. Markers for these subgroups were highly subset specific. Thirteen transcripts were validated by qPCR to confirm cell specific expression in microdissected tissues, as well as expression in neonatal prostate. Immunohistochemical staining demonstrated that Ebf3 and Meis2 showed a restricted expression pattern in VMP condensed mesenchyme. Taken together, we demonstrate that the VMP shows limited cellular heterogeneity and that our high-resolution transcriptomic analysis identified new mesenchymal subset markers associated with prostate organogenesis.
Overall design Tag-sequencing, RNA-sequencing and single-cell RNA-sequencing on 2 female inductive mesenchymal tissues of the developing prostate/urogenital tract.
Contributor(s) Nash CE, Thomson AA
Citation(s) 29180763
Submission date Aug 23, 2017
Last update date May 15, 2019
Contact name Claire Elizabeth Nash
Organization name Research Institute of McGill University Health Centre
Department Urology
Lab Dr A Thomson
Street address 1001 Decarie Blvd
City Montréal
State/province QC
ZIP/Postal code H3G 1A4
Country Canada
Platforms (2)
GPL10669 Illumina Genome Analyzer IIx (Rattus norvegicus)
GPL14844 Illumina HiSeq 2000 (Rattus norvegicus)
Samples (119)
GSM2752505 VMP_Tag_seq
GSM2752506 SU_Tag_seq
GSM2778522 VMP_RNA-sequencing
BioProject PRJNA399753
SRA SRP116037

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Supplementary file Size Download File type/resource
GSE103011_Counts_RNAseq.csv.gz 157.8 Kb (ftp)(http) CSV
GSE103011_Counts_SU_scRNAseq.csv.gz 757.4 Kb (ftp)(http) CSV
GSE103011_Counts_VMP_scRNAseq.csv.gz 542.9 Kb (ftp)(http) CSV
GSE103011_VMP_SU_Tag_counts.csv.gz 143.9 Kb (ftp)(http) CSV
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