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Sample GSM7804885 Query DataSets for GSM7804885
Status Public on May 23, 2024
Title control_E14_2
Sample type SRA
 
Source name diaphragm E14.5
Organism Mus musculus
Characteristics tissue: diaphragm E14.5
genotype: control
Extracted molecule total RNA
Extraction protocol Formaldehyde fixed parafin embedded, 5µm diaphragm sections by a microtome.
Spatial transcriptome sequencing libraries were prepared with 10xGenomics Visium Spatail Gene Expression Slides & Reagent kit according to manufacturer's construction
OTHER: Spatial Transcriptomics
 
Library strategy RNA-Seq
Library source transcriptomic single cell
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Description FFPE Spatial Transcriptome sequencing
Data processing Raw sequencing data were processed using the 10x Genomics Space Ranger pipeline to generate FAST files
Sequences were aligned to mm10 genome to gene expression count using Space Ranger's default settings
Gene expression level of Refseg coding genes were quantified using Space Ranger's default settings
Assembly: mm10
Supplementary files format and content: barcodes.tsv.oz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.qz: gene expresion count data in Matrix Market Exchange Format
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 lowes image.png.gz: low-res image of tissue
Supplementary files format and content: tissue positions list.csv.qz: list of spatial barcodes and the coordinates specifying spots
Supplementary files format and content: web_summary.html: 10X websummary of captured RNAs accross the tissue and QC metrics
Supplementary files format and content: spatial_enrichment.cvs: spatial enrichment of features
Supplementary files format and content: .Rds: Single seurat objects loaded to R environment or mulltiple samples integrated
 
Submission date Sep 25, 2023
Last update date May 23, 2024
Contact name Mehmet Mahsum Kaplan
Organization name Czech Academy of Sciences
Department Department of Developmental Biology
Street address Vídeňská 1083
City Prague
ZIP/Postal code 142 20
Country Czech Republic
 
Platform ID GPL24247
Series (1)
GSE244014 Spatial transcriptomics in embryonic mouse diaphragm muscle reveals regional gradients and subdomains of developmental gene expression
Relations
BioSample SAMN37538198
SRA SRX21883935

Supplementary file Size Download File type/resource
GSM7804885_control_E14_2.Rds.gz 37.8 Mb (ftp)(http) RDS
GSM7804885_control_E14_2_aligned_fiducials.jpg.gz 1.0 Mb (ftp)(http) JPG
GSM7804885_control_E14_2_barcodes.tsv.gz 5.0 Kb (ftp)(http) TSV
GSM7804885_control_E14_2_detected_tissue_image.jpg.gz 748.4 Kb (ftp)(http) JPG
GSM7804885_control_E14_2_features.tsv.gz 164.2 Kb (ftp)(http) TSV
GSM7804885_control_E14_2_matrix.mtx.gz 22.2 Mb (ftp)(http) MTX
GSM7804885_control_E14_2_scalefactors_json.json.gz 180 b (ftp)(http) JSON
GSM7804885_control_E14_2_spatial_enrichment.csv.gz 782.2 Kb (ftp)(http) CSV
GSM7804885_control_E14_2_tissue_hires_image.png.gz 2.7 Mb (ftp)(http) PNG
GSM7804885_control_E14_2_tissue_lowres_image.png.gz 296.6 Kb (ftp)(http) PNG
GSM7804885_control_E14_2_tissue_positions.csv.gz 62.1 Kb (ftp)(http) CSV
GSM7804885_control_E14_2_web_summary.html.gz 1.9 Mb (ftp)(http) HTML
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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