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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Feb 23, 2023 |
| Title |
1202L |
| Sample type |
SRA |
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| Source name |
Skeletal Muscle
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| Organism |
Mus musculus |
| Characteristics |
tissue: Skeletal Muscle
days post_injury: 7
treatment: ITD1
slide serial_number: V11A06-373
Sex: Male
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| Extracted molecule |
total RNA |
| Extraction protocol |
Tissues were simultaneously flash frozen and OCT embedded according to 10x Genomics demonstrated protocol CG000240
Libraries were prepared according to manufacturer's protocol (10x Genomics demonstrated protocol CG000239). Briefly, 10um tissue sections were placed onto capture areas of visium slides and stained with hematoxylin and eosin, imaged, then permeabilized for 18 minutes (murine) or 24 minutes (canine). cDNAs were synthesized and amplified, followed by library construction.
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| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
10x Genomics Visium
Mus_ST_list_label_transfer.RDS
merged_filtered_599L_599R_600L_600R_1197L_1203L_1203R_1202L.RDS
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| Data processing |
Manual alignment of spatial barcodes to tissue location was performed using 10x Genomics Loupe Browser version 6
De-multiplexing, genome alignment (mm10-2020-A or CanFam3.1.97), and count matrix generation was performed using 10x Genomics Space Ranger version 1.3.0
Count matrices were imported into R using Seurat v4. Data normalization was performed using SCTransform, followed by principal component analysis (top 30 dimensions), FindNeighbors, FindClusters, and RunUMAP with default conditions.
Mouse datasets were integrated with annotated scRNA-Seq matrices publically available at GSE163376
Assembly: mm10-2020-A and CanFam3.1.97
Supplementary files format and content: Process data files are provided as (1) a list of Seurat Objects for each sample and (2) a single Seurat Object with all of the samples from the given species merged.
Library strategy: Spatial transcriptomics
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| Submission date |
Jun 08, 2022 |
| Last update date |
Feb 23, 2023 |
| Contact name |
Carlos Andres Aguilar |
| E-mail(s) |
caguilar@umich.edu
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| Phone |
734-764-8557
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| Organization name |
University of Michigan
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| Department |
Biomedical Engineering
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| Lab |
2100 Gerstacker Bldg
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| Street address |
2200 Bonisteel Blvd
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| City |
Ann Arbor |
| State/province |
MI |
| ZIP/Postal code |
48109 |
| Country |
USA |
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| Platform ID |
GPL24247 |
| Series (1) |
| GSE205707 |
Spatiotemporal mapping of immune and stem cell dysregulation after volumetric muscle loss |
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| Relations |
| BioSample |
SAMN28924140 |
| SRA |
SRX15640238 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6219593_Aguilar_5347-JL-S1-D_20220208_10X_V11A06-373.tif.gz |
1003.0 Mb |
(ftp)(http) |
TIFF |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
| Processed data provided as supplementary file |
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