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Sample GSM4363333 Query DataSets for GSM4363333
Status Public on Aug 24, 2020
Title 323_colon1 [re-analysis]
Sample type SRA
 
Source name colon/K562
Organisms Homo sapiens; Mus musculus
Characteristics mouse strain: C57Bl6
human 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
 
Description 323-AS-1_S1
reanalysis of GSM3131535
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
Barcodes were filtered (Liu et al., 2018), resulting in the processed data table. Bcd code can be converted to sequence barcodes within the inDrops pipeline. An example is at https://www.dropbox.com/s/tm9ciucqwgunwip/20190419_2969_AS-1-GCCAAT_pickle_bcd.txt?dl=0
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.
NextSeq:Technical read: read2 - UMI/cell barcode - the oligo barcodes are inDrop Version 2 which is positioned exactly as in (Klein et al. 2015) Biological read: read1 - 3' end
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 Feb 27, 2020
Last update date Aug 29, 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 (2)
GSE145830 Ileal single-cell analysis in the context of inflammation focused on tuft cells
GSE146042 WT colonic scRNA-seq experiment [re-analysis]
Relations
Reanalysis of GSM3131535
BioSample SAMN14237453
SRA SRX7814261

Supplementary file Size Download File type/resource
GSM4363333_counts_323_1.csv.gz 3.3 Mb (ftp)(http) CSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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