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GEO help: Mouse over screen elements for information. |
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| Status |
Public on May 21, 2024 |
| Title |
d21, bleo, 1 |
| Sample type |
SRA |
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| Source name |
Lung
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| Organism |
Mus musculus |
| Characteristics |
tissue: Lung
treatment: Bleomycin
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| Treatment protocol |
The left lung lobe was inflated with 0.4-0.5 mL 37°C low-melt agarose via the trachea.
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Agarose-inflated mouse lungs were cryosectioned at 10 µm.
Sequencing libraries were prepared using Visium Spatial Gene Expression Slide & Reagent Kit (Cat. No. 1000184; 10X Genomics) with Dual Index Kit TT Set A (Cat. No. 1000215; 10X Genomics) according to the Visium Spatial Gene Expression User Guide (Rev C).
Spatial Transcriptomics
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
Day 7
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| Data processing |
FastQ files were processed using the Space Ranger 1.2.2 (10x Genomics) pipeline.
Manual alignment to the fiducial frame and identification of tissue-covered spots was performed using Loupe Browser (v.6, 10X Genomics)
Data filtering, processing, and analyses were performed in R (v.4.0.5) using the STUtility (v.1.1.1), Seurat (v.4.1.1), and semla (v. 1.1.6, under R v. 4.2.3 and Seurat v. 4.3.0.1) packages.
Assembly: mm10
Supplementary files format and content: aligned fiducials.jpg.gz: aligned fiducials of the tissue image
Supplementary files format and content: detected tissue image.jpg.gz: image of tissue and spots
Supplementary files format and content: scalefactors json.json.gz: scalefactors in json format
Supplementary files format and content: tissue hires image.png.gz: hi-res image of tissue
Supplementary files format and content: tissue lowres image.png.gz: low-res image of tissue
Supplementary files format and content: tissue positions list.csv.gz: list of spatial barcodes and the coordinates specifying spots
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expresion count data in Matrix Market Exchange Format
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| Submission date |
May 20, 2024 |
| Last update date |
Jun 03, 2024 |
| Contact name |
Benjamin Keith |
| E-mail(s) |
ben.keith@astrazeneca.com
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| Organization name |
AstraZeneca
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| Street address |
Pepparedsleden 1
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| City |
Mölndal |
| ZIP/Postal code |
43183 |
| Country |
Sweden |
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| Platform ID |
GPL24247 |
| Series (1) |
| GSE267904 |
Mapping spatially resolved transcriptomes in human and mouse pulmonary fibrosis |
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| Relations |
| BioSample |
SAMN41462532 |
| SRA |
SRX24612273 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8281399_V10A20-071-B1_aligned_fiducials.jpg.gz |
1.9 Mb |
(ftp)(http) |
JPG |
| GSM8281399_V10A20-071-B1_barcodes.tsv.gz |
25.1 Kb |
(ftp)(http) |
TSV |
| GSM8281399_V10A20-071-B1_detected_tissue_image.jpg.gz |
2.4 Mb |
(ftp)(http) |
JPG |
| GSM8281399_V10A20-071-B1_features.tsv.gz |
254.1 Kb |
(ftp)(http) |
TSV |
| GSM8281399_V10A20-071-B1_matrix.mtx.gz |
47.0 Mb |
(ftp)(http) |
MTX |
| GSM8281399_V10A20-071-B1_scalefactors_json.json.gz |
164 b |
(ftp)(http) |
JSON |
| GSM8281399_V10A20-071-B1_tissue_hires_image.png.gz |
13.5 Mb |
(ftp)(http) |
PNG |
| GSM8281399_V10A20-071-B1_tissue_lowres_image.png.gz |
1.3 Mb |
(ftp)(http) |
PNG |
| GSM8281399_V10A20-071-B1_tissue_positions_list.csv.gz |
65.7 Kb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
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