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Sample GSM3040911 Query DataSets for GSM3040911
Status Public on Mar 19, 2018
Title library 10X_P7_13
Sample type SRA
 
Source name Mammary
Organism Mus musculus
Characteristics tissue: Mammary
age: 3 months
strain: C57BL/6 NIA
Extracted molecule total RNA
Extraction protocol 10x Genomics single cell protocol
10x Genomics single cell protocol
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Description Single cell
Data processing Sequences from the NovaSeq were demultiplexed using CellRanger version 2.0.1, with bcl2fastq 2.19.0.316. Reads were aligned using to a copy of the mm10 genome augmented with ERCC sequences using CellRanger and STAR version 2.5.2b
cellranger mkfastq --localmem 60
cellranger count --localmem 240 --nosecondary --cells=3000 --transcriptome=MM10-Plus
Genome_build: mm10
Supplementary_files_format_and_content: output of 10X CellRanger: gene lists, barcode lists and UMI count files in mtx format
 
Submission date Mar 14, 2018
Last update date May 14, 2019
Contact name Angela Oliveira Pisco
E-mail(s) angela.pisco@czbiohub.org
Organization name CZ Biohub
Department Data Sciences
Street address 499 Illinois St
City San Francisco
State/province CA
ZIP/Postal code 94103
Country USA
 
Platform ID GPL24247
Series (2)
GSE109774 Tabula Muris: Transcriptomic characterization of 20 organs and tissues from Mus musculus at single cell resolution
GSE132042 Tabula Muris
Relations
BioSample SAMN08712875
SRA SRX3791784

Supplementary file Size Download File type/resource
GSM3040911_Mammary-10X_P7_13.tar.gz 13.3 Mb (ftp)(http) TAR
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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