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Sample GSM3131535 Query DataSets for GSM3131535
Status Public on Oct 23, 2018
Title Replicate 1
Sample type SRA
 
Source name colon/K562
Organisms Homo sapiens; Mus musculus
Characteristics treatment: none
cell type: epithelial enrichment
strain: C57Bl6
cell line: K562
Growth protocol primary cells/cell line mix
Extracted molecule total RNA
Extraction protocol Mouse epithelial cell suspensions were obtained by EDTA extraction and Collagenase/DNAse dissociation. Viable cells were enriched with MACS. K562 cells were spiked in. 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 of RNA/cDNA followed by index primer-based amplification
RNA-Seq was performed on NextSeq500 with a 2 x 75 paired-end kit using custom read lengths
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Data processing After sequencing, reads were filtered, sorted by their barcode of origin and aligned to the reference transcriptome using inDrops pipeline (https://github.com/indrops/indrops). Mapped reads were quantified into UMI-filtered counts per gene, and barcodes that correspond to cells were retrieved based on previously established methods
Human and mouse genes were separated and then human and mouse cells were deconvolved to observe doublet rate.
Mouse cells were selected for further analysis, and barcodes with number of unique UMIs greater than a threshold (Klein et al., 2015) were selected, resulting in the processed data table.
Genome_build: Human: GRCh38.85, Mouse: GRCm38.85 (mixed database)
Supplementary_files_format_and_content: Delimited tables, with cells and genes, as columns and rows
 
Submission date May 04, 2018
Last update date Feb 27, 2020
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 GPL19415
Series (1)
GSE114044 Colonic single-cell RNA-seq experiment
Relations
Reanalyzed by GSM4363333
BioSample SAMN09070528
SRA SRX4042028

Supplementary file Size Download File type/resource
GSM3131535_colon_bio1.csv.gz 2.7 Mb (ftp)(http) CSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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