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SRX1589391: GSM2063993: Islet cell Sample 562; Mus musculus; RNA-Seq
1 ILLUMINA (Illumina HiSeq 2500) run: 3M spots, 147.7M bases, 101.9Mb downloads

Submitted by: NCBI (GEO)
Study: Use of the Fluidigm C1 platform for RNA sequencing of single mouse pancreatic islet cells
show Abstracthide Abstract
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. Overall design: Single-cell RNA sequencing of mouse C57BL/6 pancreatic islet cells
Sample: Islet cell Sample 562
SAMN04502154 • SRS1303801 • All experiments • All runs
Organism: Mus musculus
Library:
Instrument: Illumina HiSeq 2500
Strategy: RNA-Seq
Source: TRANSCRIPTOMIC
Selection: cDNA
Layout: SINGLE
Construction protocol: Single islet cells were captured with C1 Integrated Fluidic Circuit. Cell lysing, reverse transcription and cDNA amplification were performed on the C1 Single-Cell Auto Prep IFC, as specified by the manufacturer (Protocol #100-7168 E1). The SMARTer Ultra Low RNA Kit (Clontech) was used for cDNA synthesis from the single cells. Illumina NGS library was constructed with Nextera XT DNA Sample Prep kit (Illumina), according to the manufacturer’s recommendations (Protocol #100-7168 E1).
Experiment attributes:
GEO Accession: GSM2063993
Links:
Runs: 1 run, 3M spots, 147.7M bases, 101.9Mb
Run# of Spots# of BasesSizePublished
SRR31744422,953,720147.7M101.9Mb2016-02-21

ID:
2243845

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