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Sample GSM3102984 Query DataSets for GSM3102984
Status Public on Jun 30, 2019
Title Secondary Spermatocyte
Sample type SRA
 
Source name WT_Secondary Spermatocyte
Organism Mus musculus
Characteristics strain background: C57BL/6
gender: male
genotype/variation: Wild-type
age: post natal 2 months 21 days
tissue/cell type: Secondary Spermatocyte
dissociation method: Mechanical
Extracted molecule total RNA
Extraction protocol Whole testes were dissociated using two different methods, enzymatic and mechanical. Single-cell suspensions were either FACS sorted for enriching different germ cell subpopulations or directly paired to Drop-seq protocol to generate single-cell RNA sequencing libriaries.
Library preparations were perforemd with Drop-seq protocol (Macosko et al. Cell 2015)
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina MiSeq
 
Description FACS sorted with Hoescht (Lima et al. JoVE, 2017)
Data processing Base calls were performed with bcl2fastq.
Sequenced reads were tagged with molecular(UMI) and cell barcodes. Then reads with low quality scores were removed and the adaptor sequences were trimmed. 
Reads were aligned to Mus_musculus.GRCm38.76 genome with STAR (v. 2.5.3a) with default configuration.
STAR aligned reads were merged with tagged SAM file to recover cell/molecular barcode information. Then the reads were annotated with exon and other annotation tags.
Digital gene expression matrix was extracted by counting the number of unique UMIs per gene within individual cell from exon-tagged bam files.
Additional step of bead synthesis error correction was performe by collapsing UMI counts when the first 11 bases of cell barcodes were the identical.
Genome_build: mm10
Supplementary_files_format_and_content: Digital Gene Expression(DGE) matrix of gene counts for each cell. Columns are cells and rows are genes.
 
Submission date Apr 17, 2018
Last update date Apr 29, 2022
Contact name Donald F. Conrad
E-mail(s) conradon@ohsu.edu
Organization name Oregon Health & Science University
Department Division of Genetics; Oregon National Primate Research Center
Street address 505 NW 185th Ave
City Beaverton
State/province OR
ZIP/Postal code 97006
Country USA
 
Platform ID GPL16417
Series (1)
GSE113293 Phenotyping spermatogenic defects by single-cell expression profiling
Relations
BioSample SAMN08943317
SRA SRX3958686

Supplementary file Size Download File type/resource
GSM3102984_SPCIImat.txt.gz 303.4 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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