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Sample GSM8281384 Query DataSets for GSM8281384
Status Public on May 21, 2024
Title d7, ctrl, 1
Sample type SRA
Source name Lung
Organism Mus musculus
Characteristics tissue: Lung
treatment: Control
Treatment protocol The left lung lobe was inflated with 0.4-0.5 mL 37°C low-melt agarose via the trachea.
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
Library strategy RNA-Seq
Library source transcriptomic single cell
Library selection cDNA
Instrument model Illumina NovaSeq 6000
Description Day 7
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. 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
Submission date May 20, 2024
Last update date Jun 03, 2024
Contact name Benjamin Keith
Organization name AstraZeneca
Street address Pepparedsleden 1
City Mölndal
ZIP/Postal code 43183
Country Sweden
Platform ID GPL24247
Series (1)
GSE267904 Mapping spatially resolved transcriptomes in human and mouse pulmonary fibrosis
BioSample SAMN41462547
SRA SRX24612258

Supplementary file Size Download File type/resource
GSM8281384_V10A20-072-A1_aligned_fiducials.jpg.gz 1.9 Mb (ftp)(http) JPG
GSM8281384_V10A20-072-A1_barcodes.tsv.gz 25.1 Kb (ftp)(http) TSV
GSM8281384_V10A20-072-A1_detected_tissue_image.jpg.gz 2.5 Mb (ftp)(http) JPG
GSM8281384_V10A20-072-A1_features.tsv.gz 254.1 Kb (ftp)(http) TSV
GSM8281384_V10A20-072-A1_matrix.mtx.gz 20.6 Mb (ftp)(http) MTX
GSM8281384_V10A20-072-A1_scalefactors_json.json.gz 162 b (ftp)(http) JSON
GSM8281384_V10A20-072-A1_tissue_hires_image.png.gz 12.9 Mb (ftp)(http) PNG
GSM8281384_V10A20-072-A1_tissue_lowres_image.png.gz 1.4 Mb (ftp)(http) PNG
GSM8281384_V10A20-072-A1_tissue_positions_list.csv.gz 66.0 Kb (ftp)(http) CSV
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Raw data are available in SRA

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