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Status |
Public on Aug 21, 2018 |
Title |
DBZ-treated Apc mutant organoids |
Sample type |
SRA |
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Source name |
Apc mutant organoids
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Organism |
Mus musculus |
Characteristics |
strain: C57Bl age: 3-4 months tissue: intestinal organoid
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Treatment protocol |
300nM 4-OH-tam, 10uM DBZ
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Growth protocol |
Intestinal organoids were grown according to Sato et al (Nature, 2009)
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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
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NovaSeq 6000 |
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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
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Submission date |
Aug 02, 2018 |
Last update date |
Aug 21, 2018 |
Contact name |
Jenny Hogstrom |
E-mail(s) |
jenny.hogstrom@helsinki.fi
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Organization name |
University of Helsinki
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Street address |
Haartmaninkatu 8
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City |
Helsinki |
ZIP/Postal code |
00290 |
Country |
Finland |
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Platform ID |
GPL24247 |
Series (1) |
GSE118055 |
Single cell changes in DBZ or DMSO treated cells derived from Apc-mutant organoid cultures |
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Relations |
BioSample |
SAMN09761062 |
SRA |
SRX4502376 |
Supplementary data files not provided |
SRA Run Selector |
Raw data are available in SRA |
Processed data are available on Series record |
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