NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM5173930 Query DataSets for GSM5173930
Status Public on Jan 31, 2022
Title Main olfactory bulb replicate 1 slide 6
Sample type SRA
 
Source name Main olfactory bulb
Organism Mus musculus
Characteristics tissue: Main olfactory bulb
genotype: wild type
gender: male
Treatment protocol Male mice were euthanized according to our IACUC protocol. The anterior part of the brain containing the olfactory bulb was dissected and placed in a plastic mold filled with OCT (Sakura Finetek from VWR), The molds were then frozen with dry ice pre-chilled 2-methylbutane (Fisher Scientific). The samples were incubated in -80°C overnight prior to cryosectioning. 20 OB sections were obtained with equal spacing (130 μm) along the anterior-posterior axis. In total, two sets of 20 slides were obtained from different animals.
Extracted molecule polyA RNA
Extraction protocol The extraction and library protocol were performed as previously described (PMID: 33288904)
 
Library strategy OTHER
Library source transcriptomic
Library selection other
Instrument model Illumina NovaSeq 6000
 
Description OB1_slide6
Data processing Library strategy: Slide-seq V2
The data processing were performed as previously described (PMID: 33288904)
All the downstring analysis were processed with Seurat, the scripts can be found at https://github.com/Greerlab/OSN_2021_paper
Genome_build: mm10
Supplementary_files_format_and_content: Seruat object containing the raw and normalized count, PCA, UMAP, spatial coordinates
 
Submission date Mar 16, 2021
Last update date Jan 31, 2022
Contact name I-Hao Wang
Organization name UMMS
Department PMM
Street address 373 Plantation St. Suite 218
City Worcester
State/province Massachusetts
ZIP/Postal code 01605
Country USA
 
Platform ID GPL24247
Series (2)
GSE169012 Spatial transcriptome analysis (Slide-seq2) of mouse main olfactory bulb
GSE169021 Mouse olfactory sensory neurons, main olfactory epithelium and main olfactory bulb
Relations
BioSample SAMN18320380
SRA SRX10355490

Supplementary file Size Download File type/resource
GSM5173930_OB1_06_BeadLocationsForR.csv.gz 597.4 Kb (ftp)(http) CSV
GSM5173930_OB1_06_expression_matrix.mtx.gz 44.8 Mb (ftp)(http) MTX
GSM5173930_OB1_Slide6.rds.gz 440.1 Mb (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