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RNA-SEQ analysis of single cells extracted from the renal vesicles of P4 Crym-EGFP transgenic mice

ABSTRACT: We used micro-dissection with FACS sorting techniques to isolate renal vesicle single cell types from post natal day (P4) kidneys. A subset of these single cell populations is analysed individually via Fluidigm single cell analysis. This analysis will determine the transcriptional profile of each cell type, identify compartment specific transcripts, compartment specific transcript isoforms and cell-type specific long-noncoding RNAs. In addition the unbiased nature of RNA-SEQ will potentially identify novel transcripts that have not been annotated in the database.

ORGANISM(S): Mus musculus

PROVIDER: GSE59130 | GEO | 2014/08/01

SECONDARY ACCESSION(S): PRJNA254484

REPOSITORIES: GEO

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RNA-SEQ analysis of single cells extracted from the renal vesicles of Crym-EGFP transgenic post natal day 4 (P4) mice.

Project description:We used micro-dissection with FACS sorting techniques to isolate renal vesicle single cell types from post natal (P4) kidneys. A subset of these single cell populations is analysed individually via Fluidigm single cell analysis. This analysis will determine the transcriptional profile of each cell type, identify compartment specific transcripts, compartment specific transcript isoforms and cell-type specific long-noncoding RNAs. In addition the unbiased nature of RNA-SEQ will potentially identify novel transcripts that have not been annotated in the database. Kidneys are harvested from Tg(Crym-EGFP)GF82Gsat mice. Single cells are extracted from P4 renal vesicles using micro-dissection with FACS sorting techniques. A subset of these cells is analyzed individually via Fluidigm single cell analysis. The long term goal is to generate a transcriptional atlas of the developing kidney.

2014-08-01 | E-GEOD-59130 | biostudies-arrayexpress

RNA-SEQ analysis of single cells extracted from the metanephric mesenchyme of E11.5 Crym-EGFP transgenic mice

Project description:We used micro-dissection with FACS sorting techniques to isolate single cells from the metanephric mesenchyme of the Embryonic day 11.5 (E11.5) developing kidney. A subset of these single cell populations is analysed individually via Fluidigm single cell analysis. This analysis will determine the transcriptional profile of each cell type, identify compartment specific transcripts, compartment specific transcript isoforms and cell-type specific long-noncoding RNAs. In addition the unbiased nature of RNA-SEQ will potentially identify novel transcripts that have not been annotated in the database.

2014-08-01 | GSE59129 | GEO

RNA-SEQ analysis of single cells extracted from the metanephric mesenchyme of Embryonic day 11.5 (E11.5) Crym-EGFP transgenic mice.

Project description:We used micro-dissection with FACS sorting techniques to isolate single cells from the metanephric mesenchyme of the E11.5 developing kidney. A subset of these single cell populations is analysed individually via Fluidigm single cell analysis. This analysis will determine the transcriptional profile of each cell type, identify compartment specific transcripts, compartment specific transcript isoforms and cell-type specific long-noncoding RNAs. In addition the unbiased nature of RNA-SEQ will potentially identify novel transcripts that have not been annotated in the database. Kidneys are harvested from Tg(Crym-EGFP)GF82Gsat mice. Single cells are extracted from E11.5 metanephric mesenchyme using manual micro-dissection techniques. A subset of these cells is analyzed individually via Fluidigm single cell analysis. The long term goal is to generate a transcriptional atlas of the developing kidney.

2014-08-01 | E-GEOD-59129 | biostudies-arrayexpress

RNA-SEQ analysis of single cells extracted from E12.5 embryonic kidneys.

Project description:We used micro-dissection and trypsinization techniques to isolate single cells from the E12.5 total kidney. A subset of these single cell populations is analysed individually via Fluidigm single cell analysis. This analysis will determine the transcriptional profile of each cell type, identify compartment specific transcripts, compartment specific transcript isoforms and cell-type specific long-noncoding RNAs. In addition the unbiased nature of RNA-SEQ will potentially identify novel transcripts that have not been annotated in the database. E12.5 kidneys are dissected; the kidneys are made into a single cell suspension via trypsinization. A subset of these cells is analysed individually via Fluidigm C1 single cell analysis. The long term goal is to generate a single cell resolution transcriptional atlas of the developing kidney.

2014-08-01 | E-GEOD-59127 | biostudies-arrayexpress

RNA-SEQ analysis of single cells extracted from E12.5 embryonic kidneys.

Project description:We used micro-dissection and trypsinization techniques to isolate single cells from the Embryonic day 12.5 (E12.5) total kidney. A subset of these single cell populations is analysed individually via Fluidigm single cell analysis. This analysis will determine the transcriptional profile of each cell type, identify compartment specific transcripts, compartment specific transcript isoforms and cell-type specific long-noncoding RNAs. In addition the unbiased nature of RNA-SEQ will potentially identify novel transcripts that have not been annotated in the database.

2014-08-01 | GSE59127 | GEO

C1 single-cell RNA-seq of Adult ID4-EGFP mouse spermatoognia

Project description:To reveal distinct transcriptomes associated with spermatogonial stem cell renewal vs. initiation of differentiation, single-cell transcriptomes from Adult ID4-EGFP+ spermatogonia were subdivided into subpopulations that displayed distinct fates when assayed by transplantation, with ID4-EGFPbright cells highly enriched for SSCs, and ID4-EGFPdim cells enriched for progenitors. We used the Fluidigm C1 instrument to capture individual spermatogonia for SMART-Seq2 single-cell RNA-seq.

2018-11-06 | GSE108974 | GEO

C1 single-cell RNA-seq of immature (P6) ID4-EGFP mouse spermatoognia

Project description:To reveal distinct transcriptomes associated with spermatogonial stem cell renewal vs. initiation of differentiation, single-cell transcriptomes from P6 ID4-EGFP+ spermatogonia were subdivided into subpopulations that displayed distinct fates when assayed by transplantation, with ID4-EGFPbright cells highly enriched for SSCs, and ID4-EGFPdim cells enriched for progenitors. We used the Fluidigm C1 instrument to capture individual spermatogonia for SMART-Seq2 single-cell RNA-seq.

2018-11-06 | GSE108970 | GEO

Gene expression profiles of cap mesenchyme and renal vesicle isolated between P0-P4 from Crym-EGFP neonatal transgenic mice using FACS. (GUDMAP Series ID: 28)

Project description:The long term objective is to create an encyclopedia of the expression levels of all genes in multiple components of the developing kidney. The central thesis is straightforward. The combination of fluorescent activated cell sorting (FACS) plus microarray analysis offers a powerful, efficient and effective method for the creation of a global gene expression atlas of the developing kidney. Microarrays with essentially complete genome coverage can be used to quantitate expression levels of every gene in FACS isolated components of the developing kidney. The ensuing rapid read-out provides an expression atlas that is more sensitive, more economical and more complete than would be possible by in situ hybridizations alone.

2010-07-16 | GSE17139 | GEO

Single-cell polyadenylation sequencing (scPolyA-seq) reveals the dynamic of polyA site usage during cell cycles in tumor cell lines [C1]

Project description:Alternative polyadenylation (APA) plays an important role in post-transcriptional gene regulation. But how genes' APA usages are influenced by cell cycle remains largely unknown. Here we developed single cell polyadenylation sequencing (scPolyA-seq), a strand-specific approach for sequencing 3’ end of transcripts which can get very deep sequencing level around polyA site for each cell, to investigate the landscape of APA at single cell level, based on Fluidigm C1. We compared APA changes before and after thymidine double blocking (TdR) synchronization of HeLa cells. We then identify 6 gene clusters whose distal polyA site usages fluctuate during cell cycle.

2021-06-16 | GSE178264 | GEO

Use of the Fluidigm C1 platform for RNA sequencing of single mouse pancreatic islet cells

Project description:This study provides an assessment of the Fluidigm C1 platform for RNA sequencing of single mouse pancreatic islet cells. The system combines microfluidic technology and nanoliter-scale reactions. We sequenced 622 cells allowing identification of 341 islet cells with high-quality gene expression profiles. The cells clustered into populations of alpha-cells (5%), beta-cells (92%), delta-cells (1%) and PP-cells (2%). We identified cell-type specific transcription factors and pathways primarily involved in nutrient sensing and oxidation and cell signaling. Unexpectedly, 281 cells had to be removed from the analysis due to low viability (23%), low sequencing quality (13%) or contamination resulting in the detection of more than one islet hormone (64%). Collectively, we provide a resource for identification of high-quality gene expression datasets to help expand insights into genes and pathways characterizing islet cell types. We reveal limitations in the C1 Fluidigm cell capture process resulting in contaminated cells with altered gene expression patterns. This calls for caution when interpreting single-cell transcriptomics data using the C1 Fluidigm system. Single-cell RNA sequencing of mouse C57BL/6 pancreatic islet cells

2016-02-19 | E-GEOD-77980 | biostudies-arrayexpress

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