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Sample GSM5866569 Query DataSets for GSM5866569
Status Public on Feb 09, 2022
Title WT_2558_S2
Sample type SRA
 
Source name colon
Organism Mus musculus
Characteristics sample preparation: inDrop scRNA-seq
genotype: WT
tissue: colon
Growth protocol primary cells
Extracted molecule total RNA
Extraction protocol Human epithelial cell suspensions were obtained by EDTA chelation and cold protease dissociation. Cells were encapsulated using the inDrop platform (1CellBio), and RNA was extracted according to the protocol of Klein et al., 2015. MARIS libraries are generated according to Chen et al., 2021.
CEL-Seq linear amplification of using standard structure (single index) (Klein et al., 2015) or TruDrop library structure (dual index) (Southard-Smith et al., 2020)
RNA-Seq was performed on Novaseq6000 with a 2 x 150 paired-end kit standard run (for dual index)
RNA-Seq was performed on NextSeq500 with a 2 x 75 paired-end kit using custom read lengths (for single index)
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Description single index
Data processing After sequencing, reads were filtered, sorted by their barcode of origin and aligned to the reference transcriptome using DROPEST pipeline (https://github.com/hms-dbmi/dropEst). Mapped reads were quantified into UMI-filtered counts per gene, and barcodes that correspond to cells were retrieved based on previously established methods
Barcodes were filtered (Liu et al., 2018), resulting in the processed data table.
NextSeq: Technical read: read1 - 3' end - the oligo barcodes are TruDrop which is positioned exactly as in (Klein et al., 2015) Biological read: read2 -UMI/cell barcode
NovaSeq:Technical read: read1 - UMI/cell barcode - the oligo barcodes are TruDrop which is positioned exactly as in (Southard-Smith et al., 2020) Biological read: read2 - 3' end
Genome_build: Mouse: GRCm38.85
Supplementary_files_format_and_content: Delimited tables, with cells and genes, as columns and rows, filtered
 
Submission date Feb 07, 2022
Last update date Feb 10, 2022
Contact name Ken Lau
E-mail(s) ken.s.lau@vanderbilt.edu
Phone 6159366859
Organization name Vanderbilt University
Department Cell and Developmental Biology
Street address 2215 Garland Ave. MRBIV10475
City Nashville
State/province TN
ZIP/Postal code 37232
Country USA
 
Platform ID GPL19057
Series (1)
GSE196256 Mouse Mist1 and Lrig1 apc tumors
Relations
BioSample SAMN25703478
SRA SRX14071718

Supplementary file Size Download File type/resource
GSM5866569_WT_2558_S2epi_nonepi.h5ad.gz 13.3 Mb (ftp)(http) H5AD
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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