GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM2175164 Query DataSets for GSM2175164
Status Public on Aug 08, 2016
Title Sample SC EMP preMac Mac e10.25
Sample type SRA
Source name whole_embryo EMPs_preMac_Mac, E10.25
Organism Mus musculus
Characteristics cell type: EMPs preMac Mac
tissue: whole embryo
tissue group: whole embryo
time: E10.25
Extracted molecule polyA RNA
Extraction protocol MARS-seq
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 1500
Description Single-cells mouse EMPs preMac Macs from whole embryo at day E10.25
Data processing After de-multiplexing, Cell barcode and RMT were extracted from Read 2 and stored in Read 1. Reads with a Phred<27 for any RMT base were removed from further analysis. Next, we removed contamination, by alignment against the e.coli genome and de-multiplexed the unmapped reads by pool barcode and cell barcode. Reads were aligned using Bowtie v 1.1.1 (parameters:“-m 1 -t --best --chunkmbs 64 –strata) to the Ensembl mouse mm10 + ERCC pseudo genome assembly. We used HTSeq-count (v 0.6.0) to quantify gene count levels based on the ensembl exon-model for mm10. Following UMI sequencing errors were filtered nad a gene expression matrix was generated.
Raw molecule counts were loaded into R and all cells with a mito-to-endogenous gene molecule count of 0.15, with less than 320 unique molecule counts or 150 unique genes were removed from further analysis. In addition we filtered for mitichondrial, ribosomal and predicted genes.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-separated text file
Submission date May 23, 2016
Last update date May 15, 2019
Contact name Christoph Bock
Organization name CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences
Street address Lazarettgasse 14
City Vienna
ZIP/Postal code 1090
Country Austria
Platform ID GPL18480
Series (2)
GSE81760 Differentiation and specification of resident tissue macrophages [MARS-seq]
GSE81774 Differentiation and specification of resident tissue macrophages
BioSample SAMN05163655
SRA SRX1793048

Supplementary file Size Download File type/resource
GSM2175164_processed_log_gene_expression.txt.gz 1.3 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