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Sample GSM3317832 Query DataSets for GSM3317832
Status Public on Aug 21, 2018
Title DMSO-treated Apc mutant organoids
Sample type SRA
Source name Apc mutant organoids
Organism Mus musculus
Characteristics strain: C57Bl
age: 3-4 months
tissue: intestinal organoid
Treatment protocol 300nM 4-OH-tam, 10uM DBZ
Growth protocol Intestinal organoids were grown according to Sato et al (Nature, 2009)
Extracted molecule total RNA
Extraction protocol The cells were loaded into Chromium Single Cell Chip v2 (10x Genomics, Pleasanton, CA) and gel beads in emulsion (GEM) generation was performed aiming at 3000 cell captures per sample
Subsequent cDNA purification, amplification (12 cycles) and library construction (sample index PCR 14 cycles) was performed as instructed
Sample libraries were sequenced on the Illumina NovaSeq 6000 system using S1 flow cell (Illumina) with following read lengths: 26bp (Read 1), 8bp (i7 Index), 0 bp (i5 Index) and 91bp (Read 2) resulting in 115 754 and 113 705 mean reads per cell for the sample vehicle and DBZ respectively
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
Data processing The Cell Ranger v 2.1.1 mkfastq and count pipelines (10x Genomics, Pleasanton, CA) were used to demultiplex and convert Chromium single-cell 3’ RNA-sequencing barcodes and read data to FASTQ files and to generate aligned reads and gene-cell matrices.
Reads were aligned to mouse reference genome mm10
We used the Seurat R package for QC, filtering and analysis of the data (Butler et al. Nature Biotechnology 2018)
Cells were filtered based on UMI counts and percentage of mitochondrial genes. Cells with more than 5% of mitochondrial genes were filtered out
The expression matrix was further filtered by removing genes with expression in less than 10 cells and cells with less than 800 expressed genes. The minimum expression threshold was set at 1
To be able to compare the two samples, we performed canonical correlation analysis (CCA) to identify shared correlation structures and aligned the dimensions using dynamic time warping
Genome_build: mm10
Supplementary_files_format_and_content: Filtered data was combined for CCA and further analysis, and saved as notch-combi.Robj
Submission date Aug 02, 2018
Last update date Aug 21, 2018
Contact name Jenny Hogstrom
Organization name University of Helsinki
Street address Haartmaninkatu 8
City Helsinki
ZIP/Postal code 00290
Country Finland
Platform ID GPL24247
Series (1)
GSE118055 Single cell changes in DBZ or DMSO treated cells derived from Apc-mutant organoid cultures
BioSample SAMN09761061
SRA SRX4502377

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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