NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM4227185 Query DataSets for GSM4227185
Status Public on Dec 21, 2019
Title Ptger4 epithelial knock-out-3 (V2)
Sample type SRA
 
Source name Ptger4 knock-out crypt cells
Organism Mus musculus
Characteristics genotype: Ptger4 knock-out crypt cells
strain: C57BL6
age: 10 weeks
tissue: Small intestine, freshly isolated crypts
Treatment protocol No treatment of mice. No treatement of cells.
Growth protocol Standard mouse housing conditions, freshly isolated cells
Extracted molecule polyA RNA
Extraction protocol Crypt isolation from the small intestine with EDTA and dissociation with trypsin
Drop-seq protocol
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model HiSeq X Ten
 
Description V2
Data processing Drop-seq preprocessing was performed using DropSeq tools (https://anaconda.org/bioconda/dropseq_tools).
The alignment was peformed using STAR (2.6)
Bead synthesis error was detected using DetectBeadSynthesisErrors in DropSeq tools.
Read counts per cell were generated using BAMTagHistogram in DropSeq tools.
Visualization was done using ggplot2 R package.
Genome_build: mm10
Supplementary_files_format_and_content: Gzipped text file which includes gene-by-cell count matrix
 
Submission date Dec 20, 2019
Last update date Dec 22, 2019
Contact name Richard Flavell
E-mail(s) richard.flavell@yale.edu
Organization name Yale University
Department Department of Immunobiology
Street address 300 Cedar Street, TAC S-569
City New Haven
State/province CT
ZIP/Postal code 06511
Country USA
 
Platform ID GPL21273
Series (2)
GSE142418 Single cell RNA sequencing of cells isolated from the intestinal crypts of mice bearing epithelial cell-specific Ptger4 ablation (Drop-seq)
GSE142431 Paracrine orchestration of intestinal tumorigenesis by a confined mesenchymal niche
Relations
BioSample SAMN13649580
SRA SRX7421138

Supplementary file Size Download File type/resource
GSM4227185_V2_gene_exon_tagged_dge.txt.gz 1.8 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