GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM2743165 Query DataSets for GSM2743165
Status Public on Nov 15, 2017
Title Colon/K562, replicate 2
Sample type SRA
Source name colon/K562
Organisms Homo sapiens; Mus musculus
Characteristics mouse strain/background: C57Bl6
mouse genotype/variation: WT
mouse cell type: Colonic epithelial cells
human cell line: K562
treatment: None
Treatment protocol None.
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
Description Epithelial enrichment
Data processing After sequencing, reads were filtered, sorted by their barcode of origin and aligned to the reference transcriptome using inDrops pipeline ( 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: *_colon_rnaseq.csv: Comma-delimited tables, with cells and genes, as columns and rows.
Submission date Aug 15, 2017
Last update date May 15, 2019
Contact name Ken Lau
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)
GSE102698 Colonic single-cell RNA-seq
BioSample SAMN07510117
SRA SRX3096215

Supplementary file Size Download File type/resource
GSM2743165_rep2_colon_rnaseq.csv.gz 1.9 Mb (ftp)(http) CSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap