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Sample GSM7471996 Query DataSets for GSM7471996
Status Public on Jun 14, 2023
Title 4858-AS-1: S1 Un fixed test (CP on crypts)
Sample type SRA
 
Source name colon
Organism Mus musculus
Characteristics prep: inDrop scRNA-seq
genotype: WT
tissue: colon
Growth protocol primary cells, cell lines grown in standard conditions of C02 and DMEM
Extracted molecule total RNA
Extraction protocol Mouse 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.
CEL-Seq linear amplification 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 single cell
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
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 limited to the number denoted in the accompanying manuscript (Deronisha et al., 2023)
NextSeq: Technical read: Read 2 -UMI/Cell barcodes are positioned exactly as in (Klein et al., 2015) Biological read: read1 -transcript
NovaSeq:Technical read: Read1 - UMI/cell barcodes are positioned exactly as in (Southard-Smith et al., 2020) Biological read: read2 - transcript
Assembly: Mouse: GRCm38.85; Human: GRCh38.p7
Supplementary files format and content: Delimited tables, with cells and genes, as columns and rows
 
Submission date Jun 09, 2023
Last update date Aug 06, 2023
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 GPL24247
Series (1)
GSE234620 A contamination focused approach for optimizing the single-cell RNA-seq experiment
Relations
BioSample SAMN35688831
SRA SRX20650197

Supplementary file Size Download File type/resource
GSM7471996_4858-AS-1_cut.h5ad.gz 75.7 Mb (ftp)(http) H5AD
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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