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| Status |
Public on Nov 01, 2023 |
| Title |
PBS 2_3 |
| Sample type |
SRA |
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| Source name |
Skin tissue section, PBS
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| Organism |
Mus musculus |
| Characteristics |
tissue: Skin
Sex: male
strain: C57BL/6J
treatment: PBS/ 0.1% DMSO
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| Treatment protocol |
Phosphate buffered saline (PBS), group and bleomycin group were injected subcutaneously with 0.1 mL PBS and (0.1 units) bleomycin (Sigma, B5507), Celastrol groups were injected celastrol (Sigma, C0869) intraperitoneally with 1mg/kg every day for 21 days
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| Growth protocol |
4 weeks old male C57BL/6 J mice were ordered from Jackson lab and the treatment was started from 6 weeks old.
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| Extracted molecule |
total RNA |
| Extraction protocol |
NA
Library was performed according to the manufacter’s instructions (Visium Spatial Gene Expression Reagents Kits for FFPE, User Guide CG000407, Rev C, 10x Genomics). Briefly, after decrosslinking, probes were hybridized, ligated and released, followed by extention and cDNA library prep which included an indexed primer.
scRNA-seq
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| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Space Ranger software v1.3.0 (https://support.10xgenomics.com/spatial-gene-expression/software/pipelines/latest/what-is-space-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files
Library strategy: Spatial Transcriptomics
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| Submission date |
May 01, 2023 |
| Last update date |
Nov 01, 2023 |
| Contact name |
Andrew Leask |
| E-mail(s) |
[email protected]
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| Organization name |
University of Saskatchewan
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| Department |
College of Dentistry
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| Lab |
Leask Lab
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| Street address |
105 Wiggins
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| City |
Saskatoon |
| State/province |
Saskatchewan |
| ZIP/Postal code |
S7N5E4 |
| Country |
Canada |
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| Platform ID |
GPL19057 |
| Series (2) |
| GSE226376 |
The Triptryium wilfordii derivative celastrol has anti-fibrotic effects in systemic sclerosis |
| GSE226760 |
The Triptryium wilfordii derivative celastrol has anti-fibrotic effects in systemic sclerosis [Spatial Transcriptomics] |
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| Relations |
| BioSample |
SAMN34494825 |
| SRA |
SRX20165694 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7267862_PBS_2_3.cloupe.gz |
417.0 Mb |
(ftp)(http) |
CLOUPE |
| GSM7267862_PBS_2_3.mri.tar.gz |
6.3 Mb |
(ftp)(http) |
TAR |
| GSM7267862_PBS_2_3_aligned_fiducials.jpg.gz |
1001.0 Kb |
(ftp)(http) |
JPG |
| GSM7267862_PBS_2_3_barcodes.tsv.gz |
2.4 Kb |
(ftp)(http) |
TSV |
| GSM7267862_PBS_2_3_detected_tissue_image.jpg.gz |
1.6 Mb |
(ftp)(http) |
JPG |
| GSM7267862_PBS_2_3_features.tsv.gz |
164.2 Kb |
(ftp)(http) |
TSV |
| GSM7267862_PBS_2_3_matrix.mtx.gz |
1.7 Mb |
(ftp)(http) |
MTX |
| GSM7267862_PBS_2_3_metrics_summary.csv.gz |
487 b |
(ftp)(http) |
CSV |
| GSM7267862_PBS_2_3_molecule_info.h5 |
10.8 Mb |
(ftp)(http) |
H5 |
| GSM7267862_PBS_2_3_probe_set.csv.gz |
726.4 Kb |
(ftp)(http) |
CSV |
| GSM7267862_PBS_2_3_scalefactors_json.json.gz |
168 b |
(ftp)(http) |
JSON |
| GSM7267862_PBS_2_3_spatial_enrichment.csv.gz |
568.7 Kb |
(ftp)(http) |
CSV |
| GSM7267862_PBS_2_3_tissue_hires_image.png.gz |
2.7 Mb |
(ftp)(http) |
PNG |
| GSM7267862_PBS_2_3_tissue_lowres_image.png.gz |
286.5 Kb |
(ftp)(http) |
PNG |
| GSM7267862_PBS_2_3_tissue_positions_list.csv.gz |
64.7 Kb |
(ftp)(http) |
CSV |
| GSM7267862_PBS_2_4_filtered_feature_bc_matrix.h5 |
875.1 Kb |
(ftp)(http) |
H5 |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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