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Status |
Public on Jan 15, 2025 |
Title |
Slide3B_CastratedD15_MouseProstate_C57BL6_rep2 |
Sample type |
SRA |
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Source name |
prostate
|
Organism |
Mus musculus |
Characteristics |
tissue: prostate cell type: mixed treatment: Castracted D15
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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).
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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
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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
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Library strategy |
OTHER |
Library source |
transcriptomic |
Library selection |
other |
Instrument model |
Illumina NovaSeq 6000 |
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|
Description |
Library name: Slide 3B
|
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
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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] |
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Relations |
BioSample |
SAMN45883939 |
SRA |
SRX27116260 |