|
| Status |
Public on Feb 10, 2021 |
| Title |
PV |
| Sample type |
SRA |
| |
|
| Source name |
Micro dissected ventricular-subventricular zone
|
| Organism |
Mus musculus |
| Characteristics |
strain: CD1-elite (Charles River)
tissue: Ventricular-subventricular zone (brain)
age: Postnatal day 35
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
The V-SVZs were microdissected and mechanically dissociated into single nuclei using a tissue douncer. Cell debris were removed using ultacentrifugation on a sucrose cushion. The nuclei were washed, filtered and counted.
Genomic mRNA libraries were prepared according to 10x Genomics 3’ version 2 chemistry & Illumina protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Reads were aligned using CellRanger 2.1.0-2.3.0 (AV, AD, PD samples); 3.0.2-v3.2.0 (PV sample) (10x Genomics) using standard parameters
Seurat version 3 was used to analyze data
Low-quality cells were filtered out of the dataset: percentage mitochondrial genes >10%, nCount <5th or >95th percentiles, nFeatures <5th percentile
Genome_build: GRCm38
Supplementary_files_format_and_content: Seurat 3 Data Object rds file of all biological samples and technical replicates
Supplementary_files_format_and_content: CellRanger filtered output: sparse UMI matrix mtx file with features (rows) and cells (columns)
Supplementary_files_format_and_content: Cell Ranger filtered output: cell barcodes in tsv file
Supplementary_files_format_and_content: Cell Ranger filtered output: features/genes in tsv file
|
| |
|
| Submission date |
Jan 26, 2021 |
| Last update date |
Feb 11, 2021 |
| Contact name |
Stephanie A Redmond |
| E-mail(s) |
stephanie.redmond@ucsf.edu
|
| Organization name |
University of California San Francisco
|
| Department |
Neurosurgery
|
| Lab |
Arturo Alvarez-Buylla
|
| Street address |
35 Medical Center Way, 933D Box 0525
|
| City |
San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94143 |
| Country |
USA |
| |
|
| Platform ID |
GPL21103 |
| Series (2) |
| GSE165551 |
Single cell analysis of the ventricular-subventricular zone reveals signatures of dorsal and ventral adult neurogenic lineages. [single nucleus sequencing] |
| GSE165555 |
Single cell analysis of the ventricular-subventricular zone reveals signatures of dorsal and ventral adult neurogenic lineages. |
|
| Relations |
| BioSample |
SAMN17577414 |
| SRA |
SRX9940564 |
