NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM5039270 Query DataSets for GSM5039270
Status Public on Feb 10, 2021
Title mixed sample (non-demultiplexed); Male and Female
Sample type SRA
 
Source name Micro dissected ventricular-subventricular zone
Organism Mus musculus
Characteristics strain: hGFAP::GFP (FVB/N-Tg(GFAPGFP)14Mes/J, The Jackson Laboratory (003257))
tissue: Ventricular-subventricular zone (brain)
age: Postnatal day 35 and Postnatal day 29
mixed: mixed sample (non-demultiplexed)
Extracted molecule total RNA
Extraction protocol The V-SVZs were microdissected and mechanically dissociated into single cells after papain digestion. Cells from each sample were labeled with a MULTI-Seq barcode and combined together. Myelin was removed using Myelin Removal Beads (130-096-733, Miltenyi Biotec). The cells were incubated with TotalSeq antibodies against mouse VCAM1 and CD24 (Biolegend), washed, filtered and counted.
Genomic mRNA libraries were prepared according to 10x Genomics 3’ version 3 chemistry & Illumina protocols. MULTI-Seq & TotalSeq barcode libraries were prepared according to MULTI-Seq (McGinnis et al. 2019) and Illumina protocols.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Data processing Replicate 1 consists of the ‘G1; mRNA and ‘TGACCAAT’ barcode libraries. Replicate 2 consists of the ‘G2’ mRNA library and the ‘ACAGTGAT’ barcode libraries.
Reads were aligned using CellRanger 3.0.2-v3.2.0 (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
Cells with more than one detected MULTI-Seq barcode were considered doublets and removed from the analysis.
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 GPL24247
Series (2)
GSE165554 Single cell analysis of the ventricular-subventricular zone reveals signatures of dorsal and ventral adult neurogenic lineages. [single whole-cell]
GSE165555 Single cell analysis of the ventricular-subventricular zone reveals signatures of dorsal and ventral adult neurogenic lineages.
Relations
BioSample SAMN17577347
SRA SRX9940596

Supplementary file Size Download File type/resource
GSM5039270_G1_CellRanger_outs_barcodes.tsv.gz 86.1 Kb (ftp)(http) TSV
GSM5039270_G1_CellRanger_outs_features.tsv.gz 444.7 Kb (ftp)(http) TSV
GSM5039270_G1_CellRanger_outs_matrix.mtx.gz 215.6 Mb (ftp)(http) MTX
GSM5039270_G2_CellRanger_outs_barcodes.tsv.gz 81.3 Kb (ftp)(http) TSV
GSM5039270_G2_CellRanger_outs_features.tsv.gz 444.7 Kb (ftp)(http) TSV
GSM5039270_G2_CellRanger_outs_matrix.mtx.gz 236.0 Mb (ftp)(http) MTX
GSM5039270_scSeq.rds.gz 1.8 Gb (ftp)(http) RDS
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap