|
| Status |
Public on Jun 30, 2019 |
| Title |
Hormad1_2 |
| Sample type |
SRA |
| |
|
| Source name |
Hormad1_testis
|
| Organism |
Mus musculus |
| Characteristics |
strain background: B6;129
gender: male
genotype/variation: Hormad1-/-
age: post natal 4 months 3 days
tissue/cell type: Testis
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 HiSeq 2500 |
| |
|
| 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 |
GPL17021 |
| Series (1) |
| GSE113293 |
Phenotyping spermatogenic defects by single-cell expression profiling |
|
| Relations |
| BioSample |
SAMN08943297 |
| SRA |
SRX3958706 |
