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SRX5075381: GSM3484259: 2-month Dhh-Cre;Nf1 fl/fl nerve/DRG 10X Genomics single-cell RNA-Seq data set; Mus musculus; RNA-Seq
2 ILLUMINA (Illumina HiSeq 2500) runs: 247.8M spots, 45.1G bases, 27.9Gb downloads

Submitted by: NCBI (GEO)
Study: Cxcr3 expressing leukocytes are necessary for neurofibroma formation in mice
show Abstracthide Abstract
Plexiform neurofibroma is a major contributor to morbidity in Neurofibromatosis type I (NF1) patients. Macrophages and mast cells infiltrate neurofibroma, and data from mouse models implicate these leukocytes in neurofibroma development. Anti-inflammatory therapy targeting these cell populations has been suggested as a means to prevent neurofibroma development. Here, we compare gene expression in inflamed nerves from NF1 models which invariably form neurofibroma to those with inflammation driven by EGFR overexpression which rarely progresses to neurofibroma. We find that the chemokine Cxcl10 is uniquely up-regulated in NF1 mice that invariably develop neurofibroma. Global deletion of the CXCL10 receptor, Cxcr3, prevented neurofibroma development in these neurofibroma-prone mice. Cxcr3 expression localized to T cells and dendritic cells (DCs) in both inflamed nerves and neurofibromas. These data support a heretofore unappreciated role for T cells/DCs in neurofibroma initiation. Overall design: To identify cell populations associated with Cxcl10 expression, we utilized a single-cell RNA-Seq (scRNA-Seq) data set collected from 2-month Dhh-Cre;Nf1 fl/fl nerve/DRG using the 10x Genomics Chromium platform.
Sample: 2-month Dhh-Cre;Nf1 fl/fl nerve/DRG 10X Genomics single-cell RNA-Seq data set
SAMN10492204 • SRS4088994 • All experiments • All runs
Organism: Mus musculus
Library:
Instrument: Illumina HiSeq 2500
Strategy: RNA-Seq
Source: TRANSCRIPTOMIC
Selection: cDNA
Layout: PAIRED
Construction protocol: DRGs were cut into 1-2 mm3 pieces and dissociated in 20 mL L-15 medium (Mediatech) containing 0.5mg/mL collagenase type 1 (Worthington; Lakewood, NJ), and 2.5 mg/mL dispase protease type II (Cambrex; East Rutherford, NJ) at 37°C for 2 hours. Then, 30 mL DMEM medium containing 10% FBS was added to stop the reaction. Cells were centrifuged and supernatant was removed. Next, cells were resuspended in 5 mL DMED by trituration (30x) and filtered through 100um, 40um and 20um cell strainers sequentially. After straining, cells were centrifuged and resuspended in 1x PBS containing 0.1% BSA at 1000 cells/μL. We utilized the 10X Genomics Chromium Instrument and cDNA synthesis kit (10x Genomics) to generate a barcoded cDNA library for single cell RNA-sequencing from approximately 10,000 cells. cDNA library quality was determined using an Agilent Bioanalyzer. Using this library, we performed one full lane sequence on two paired-end 75bp Flow Cells using on an Illumina HiSeq2500. 10X Genomics Chromium v2 chemistry
Experiment attributes:
GEO Accession: GSM3484259
Links:
Runs: 2 runs, 247.8M spots, 45.1G bases, 27.9Gb
Run# of Spots# of BasesSizePublished
SRR8258197123,198,37922.4G13.9Gb2019-02-25
SRR8258196124,554,21122.7G14Gb2019-02-25

ID:
6845266

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