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Sample GSM8686962 Query DataSets for GSM8686962
Status Public on Jan 15, 2025
Title Slide1A_IntactMouseProstate_C57BL6_rep1
Sample type SRA
 
Source name prostate
Organism Mus musculus
Characteristics tissue: prostate
cell type: mixed
treatment: Intact
Treatment protocol Mice were orchiectomized and prostates harvested 15 or 20 days later. Upon removal of adhering fats, dissected whole prostates were placed in histocassettes sandwiched between sponges (Fisher) and fixed in 10% Formaldehyde for 4 hours and paraffin embedded within 24 hrs. Cryosections 5 to 7µm and 5um paraffin sections for FFPE were performed by ULAM-IVAC (University of Michigan ILAB Core).
Growth protocol Male C57BL/6 mice 10 to 18 weeks old were either purchased from The Jackson Laboratory, or bred in-house from purchased mice
Extracted molecule total RNA
Extraction protocol Slides in quadruplet on mice FFPE samples from two timepoints for a total of eight sections on two slides. Tissue sections of each sample type were analyzed for RNA integrity prior to placement on Spatial Tissue Optimization slides. Optimization was performed only for samples with RIN greater than or equal to 7. Spatial gene expression slides specific for either cryosections or FFPE sections were used (10X Genomics, Pleasanton, CA) and were submitted to the Advanced Genomics Core, (AGC, University of Michigan ILAB Core) for tissue optimization / permeabilization and Library Construction. Tissue was processed and placed the according to the manufacturer's instructions(CG000408 Visium Spatial Gene Expression for FFPE –Tissue Preparation Guide and CG000407 Visium Spatial Gene Expression for FFPE User Guide). Samples were stained lightly with H&E on the Spatial Gene Expression slides using a standard protocol CG000409 Visium Spatial Gene Expression for FFPE –Deparaffinization, H&E Staining, Imaging & Decrosslinkingand images scanned at high resolution and then probed with the Visium Mouse Transcriptome Probe Set (Visium Mouse Transcriptome Probe Set v1.0).
Visium sequencing depth for probe set assay was 100m reads/sample. All sequencing was performed at the University of Michigan Advanced Sequencing core on the NovaSeq6000 with 300 cycles and paired end 150. Each sequenced library was demultiplexed to FASTQ files and aligned to reads to the mm10 mouse transcriptomewith tr the Spatial Space Ranger 1.3
 
Library strategy OTHER
Library source transcriptomic
Library selection other
Instrument model Illumina NovaSeq 6000
 
Description Library name: Slide 1A
Data processing Raw Sequencing data were processed using the 10x genomics space ranger pipeline to generate FastQs
Sequences were aligned to mm10 genome to gene expression count using Space Ranger default settings
Gene expression levels of Refseq coding genes were quantifed using Space Ranger default settings
Assembly: mm10
Supplementary files format and content: filtered_feature_bc_matrix.h5: filtered count matrix
Supplementary files format and content: scalefactors_json.json : scalefactors in json format
Supplementary files format and content: tissue_hires_image.png : hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png : low-res image of tissue
Supplementary files format and content: tissue_positions_list.csv : list of spatial barcodes and coordinates specifying spots
Library strategy: Spatial Transcriptomics
 
Submission date Dec 17, 2024
Last update date Jan 15, 2025
Contact name Arul M Chinnaiyan
Organization name University of Michigan
Street address 1500 E. Medical Center Dr
City Ann Arbor
State/province Michigan
ZIP/Postal code 48109
Country USA
 
Platform ID GPL24247
Series (1)
GSE284571 Cellular cartography reveals mouse prostate organization and determinants of castration resistance [Spatial Transcriptomics]
Relations
BioSample SAMN45883944
SRA SRX27116255

Supplementary file Size Download File type/resource
GSM8686962_slide1A_filtered_feature_bc_matrix.h5 15.3 Mb (ftp)(http) H5
GSM8686962_slide1A_scalefactors_json.json.gz 169 b (ftp)(http) JSON
GSM8686962_slide1A_tissue_hires_image.png.gz 3.8 Mb (ftp)(http) PNG
GSM8686962_slide1A_tissue_lowres_image.png.gz 360.6 Kb (ftp)(http) PNG
GSM8686962_slide1A_tissue_positions_list.csv.gz 64.6 Kb (ftp)(http) CSV
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