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| Status |
Public on Mar 24, 2024 |
| Title |
B_big |
| Sample type |
SRA |
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| Source name |
big ducts
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| Organism |
Mus musculus |
| Characteristics |
tissue: pancreas
tissue: big ducts
cell type: Sox9:eGFP positive cells
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| 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.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
10X Genomics
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| 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, percent.mt < 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
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| Submission date |
Mar 22, 2024 |
| Last update date |
Mar 25, 2024 |
| Contact name |
Li Guo |
| E-mail(s) |
lg23w@fsu.edu
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| Organization name |
Florida State University
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| Department |
College of Medicine
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| Lab |
Julia Wang lab
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| Street address |
Thrasher Medical Researcher Building, Suite 2300-D
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| City |
Tallahassee |
| ZIP/Postal code |
32312 |
| Country |
USA |
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| 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. |
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| Relations |
| BioSample |
SAMN40584260 |
| SRA |
SRX24028815 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8162809_B_big.rds.gz |
241.8 Mb |
(ftp)(http) |
RDS |
SRA Run Selector |
| Raw data are available in SRA |
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