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Sample GSM5036548 Query DataSets for GSM5036548
Status Public on Feb 10, 2021
Title AV
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 total 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
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.
BioSample SAMN17577416
SRA SRX9940562

Supplementary file Size Download File type/resource
GSM5036548_AV_CellRanger_outs_barcodes.tsv.gz 34.8 Kb (ftp)(http) TSV
GSM5036548_AV_CellRanger_outs_genes.tsv.gz 375.8 Kb (ftp)(http) TSV
GSM5036548_AV_CellRanger_outs_matrix.mtx.gz 52.1 Mb (ftp)(http) MTX
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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