NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM4008664 Query DataSets for GSM4008664
Status Public on Feb 10, 2020
Title Adult-Transverse-Colon2-2
Sample type SRA
 
Source name Microwell-seq analysis
Organism Homo sapiens
Characteristics age: None
Sex: Female
tissue: Intestine
Extracted molecule total RNA
Extraction protocol Tissue dissociation and single-cell lysate
Library preparations were performed with the Microwell-seq protocol
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model HiSeq X Ten
 
Data processing Base-calls were performed with Illumina bcl2fastq
Sequenced reads were trimmed for adaptor sequence.Then reads in bam files were tagged with the cell and molecular (UMI) barcode sequences using Drop-seq_tools-1.12. The reads quality under 10 were removed. Cellbarcode:In read1, the bases 1-6,22-27,43-48 merge (18bp); UMI:In read1, the bases 49-54 (6bp)
ScRNA-seq reads were aligned to the Homo_sapiens. GRCh38 assembly using STAR version (2.5.2a) with default configurations.
Next, merge the STAR alignment tagged bam SAM to recover cell /molecular barcodes and the reads are annotated with exon tags.
Last, we demultiplexed all cell barcodes taken into consideration for the analysis from the exon-tagged bam files to get a digital expression matrix based on UMI counts.The cellbarcode is tagged with XC, the UMI is tagged with XM, the gene is tagged with GE.
Genome_build: Homo_sapiens. GRCh38
Supplementary_files_format_and_content: tab-delimited text files of digital expression matrix (dge) based on raw UMI counts ,columns are cells, and rows are genes.
 
Submission date Aug 05, 2019
Last update date Aug 02, 2022
Contact name Guoji Guo
Organization name Center for Stem Cell and Regenerative Medicine
Department Zhejiang University School of Medicine
Street address Yuhangtang street 866
City Hanzhou
ZIP/Postal code 310058
Country China
 
Platform ID GPL20795
Series (1)
GSE134355 Construction of A Human Cell Landscape by Single-cell mRNA-seq
Relations
Reanalyzed by GSE210347
BioSample SAMN12429880
SRA SRX6640179

Supplementary file Size Download File type/resource
GSM4008664_Adult-Transverse-Colon2-2_dge.txt.gz 6.3 Mb (ftp)(http) TXT
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