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Sample GSM4221119 Query DataSets for GSM4221119
Status Public on Mar 31, 2020
Title H007-TO
Sample type SRA
Source name Human colon tumor organoid
Organism Homo sapiens
Characteristics genotype: Mutation: APC mutant
culture condition: Standard colon organoid medium without Wnt-3A and R-spondin1
tissue: colon tumor organoid
Treatment protocol Normal and colorectal cancer organoid were cultured in a standard colon organoid medium, while APC mutant tumor organoids were cultured in a standard colon organoid medium without Wnt-3A and R-spondin1. Differentiated normal organoids have been cultured in a standard colon organoid medium without Wnt-3A for 4 days. Differentiated RSPO fusion tumor organoids have been cultured in a standard colon organoid medium with 5% Wnt-3A for 4 days.
Growth protocol Organoids were cultured in a standard colon organoid medium containing Wnt-3A, R-spondin1, Noggin, B27, A83-01, EGF, N-acetylcysteine, Gastrin and SB202190.
Extracted molecule total RNA
Extraction protocol Organoids with or without differentiation were dissociated into single cells using TrypLE and single cells were FACS-sorted based on standard parameters for forward scatter area versus forward scatter peak liner. Dead cells were removed based on DAPI staining. Single cells were encapsulated into Gel Beads. Libraries were constructed using a Chromium Single Cell 5' Library & Gel Bead Kit (10x genomics) according to the manufacturer's instructions.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
Description H007-TO
Data processing Sequence data was mapped to the human genome (GRCh38) using CellRanger (version 2.2.0). Unique molecular identifier (UMI) count matrices were imported into R (version 3.5.1) and were processed with R package Seurat (version 2.3.4).
We excluded cells with very low (< 500) and very high UMI counts (> 8000), as well as cells with a high percentage of counts assigned to mitochondrial (> 20%) or ribosomal genes (> 40%). Genes that had less than 5 total counts across a dataset, or were expressed in less than 3 individual cells, were also removed.
Log-normalized expression was obtained by NormalizeData function of the Seurat package.
Genome_build: GRCh38
Supplementary_files_format_and_content: UMI count data as well as Log-normalized expression data for each cell in a tab-delimited text format.
Submission date Dec 16, 2019
Last update date Apr 01, 2020
Contact name Suet Yi Leung
Organization name The University of Hong Kong
Department Department of Pathology
Street address Queen Mary Hospital, Pokfulam Road
City Hong Kong
ZIP/Postal code Nil
Country Hong Kong
Platform ID GPL24676
Series (1)
GSE142116 5' droplet-based single cell RNA sequencing of human colorectal cancer and normal organoids
BioSample SAMN13575687

Supplementary file Size Download File type/resource
GSM4221119_H007_TO_LogNormalized.txt.gz 157.2 Mb (ftp)(http) TXT
GSM4221119_H007_TO_count.txt.gz 15.0 Mb (ftp)(http) TXT
Processed data provided as supplementary file
Raw data not provided for this record

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