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Sample GSM3308717 Query DataSets for GSM3308717
Status Public on Feb 28, 2019
Title Whole Epithelium-Normal
Sample type SRA
 
Source name Intestinal Epithelium
Organism Mus musculus
Characteristics cell type: All epithelial cells
treatment: None
strain: Crl:CD1(ICR)
Extracted molecule total RNA
Extraction protocol To isolate single cells, whole epithelial segments or crypts were washed in PBS prior to adding fresh prewarmed Trypsin (Corning, USA) and incubated at 37°C for 50 minutes, with mixing every 20 minutes. Tissues were filtered through a 40 mm mesh cell strainer on ice and pelleted by centrifugation at 4°C and washed twice with ice cold regular medium to remove debris. A manually estimated 4500 single cells per sample were then subjected to 10X Genomics single cell RNA sequencing following manufacturer’s recommendations. Illumina HiSeq 3000 was used for deep sequencing.
RNA libraries were prepared for sequencing using standard Illumina protocols
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 3000
 
Description C04
Data processing Cellranger 2.0 is run on the FASTQ files to generate matrix
Data is read into Seurat with 1 minimum cell and 200 minimum genes and subsequently converted in scater for quality control and filtering based on lirary size, feature size and percentage of mitochondrial genes. Furthermore, normalization steps are performed and then the normalized data is transported back to Seurat. In Seurat, data is scaled and dimesion reduction, cluster identification, PCA and tSNE are performed.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix in .mtx format generated by cellranger filtered_bc_matrices, barcodes.tsv, genes.tsv
Supplementary_files_format_and_content: *_processed.csv: Comma-separated files contain normalized expression data from combined whole epithelium, crypts and 170 FACS sorted cells with in-depth sequencing.
 
Submission date Jul 27, 2018
Last update date Feb 28, 2019
Contact name Bibaswan Ghoshal
E-mail(s) bibaswan.ghoshal@gmail.com
Organization name Lunenfeld Tanenbaum Research Institute
Street address 600 University Avenue
City Toronto
ZIP/Postal code M5G 1X5
Country Canada
 
Platform ID GPL21493
Series (2)
GSE117783 Single-Cell Transcriptomes of the Regenerating Intestine Reveal a Revival Stem Cell [part 1]
GSE123516 Single-Cell Transcriptomes of the Regenerating Intestine Reveal a Revival Stem Cell
Relations
BioSample SAMN09727300
SRA SRX4475873

Supplementary file Size Download File type/resource
GSM3308717_C04.mtx.gz 29.7 Mb (ftp)(http) MTX
GSM3308717_C04_barcodes.tsv.gz 18.4 Kb (ftp)(http) TSV
GSM3308717_C04_genes.tsv.gz 212.7 Kb (ftp)(http) TSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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