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Sample GSM8162810 Query DataSets for GSM8162810
Status Public on Mar 24, 2024
Title B_big_v2
Sample type SRA
Source name big ducts
Organism Mus musculus
Characteristics tissue: pancreas
tissue: big ducts
cell type: Sox9:eGFP positive cells
Extracted molecule polyA RNA
Extraction protocol Whole pancreas ducts were isolated, seperated manually by size under a fluorescent stereoscope. Small, medium, and big ducts were further digested using 1mL of trypLE Express for 5-10min (depending on the size of the ducts) at 37ºC, vigorously shaking the digestion mix every 2-3 min. After digestion, tryPLE was neutralized by adding 10mL of blocking buffer, centrifuged, and washed twice. Sox9:eGFP positive cells were sorted from small, medoim and large ducts via FACS. Ten thousand sorted cells from each ductal fraction were pooled from 3 male mice in two independent experiments.
3’ mRNA library was prepared following 10xGenomics manufacturing instructions.
scRNA-seq, Sequencing was carried out as paired-end (PE77) using NovaSeq6000.
Library strategy RNA-Seq
Library source transcriptomic single cell
Library selection cDNA
Instrument model Illumina NovaSeq 6000
Description 10X Genomics
Data processing FASTQ files were aligned to mm10 using Cell Ranger V.5.0.1. Data quality control, filter, dimension reduction, clustering, and differential expression analysis was performed in Seurat V4.1.1. Briefly, cells were filtered with nFeature_RNA > 200, nFeature_RNA < 6000, < 5, and nCount_RNA < 50000. Sctransform was used to normalize the data and regress out potential sample batch effect. RunPCA, RunUMAP, FindNeighbors, and FindClusters (resolution of 0.6) were then sequentially applied to perform dimension reduction and cell clustering. FindAllMarkers were then called with min.pct=0.1 and logfc.threshold=0.25 to identify markers for each clusters.
Assembly: mm10
Supplementary files format and content: seurat objects containing gene expression matrix, cell clustering, and other metadata
Submission date Mar 22, 2024
Last update date Mar 25, 2024
Contact name Li Guo
Organization name Florida State University
Department College of Medicine
Lab Julia Wang lab
Street address Thrasher Medical Researcher Building, Suite 2300-D
City Tallahassee
ZIP/Postal code 32312
Country USA
Platform ID GPL24247
Series (1)
GSE262292 A single cell atlas of the murine pancreatic ductal tree identifies novel cell populations with potential implications in pancreas regeneration and exocrine pathogenesis.
BioSample SAMN40584259
SRA SRX24028816

Supplementary file Size Download File type/resource
GSM8162810_B_big_v2.rds.gz 124.1 Mb (ftp)(http) RDS
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Raw data are available in SRA

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