|
| Status |
Public on May 23, 2024 |
| Title |
control_E14_1 |
| 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 |
SAMN37538199 |
| SRA |
SRX21883934 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7804884_control_E14_1.Rds.gz |
26.9 Mb |
(ftp)(http) |
RDS |
| GSM7804884_control_E14_1_aligned_fiducials.jpg.gz |
1.0 Mb |
(ftp)(http) |
JPG |
| GSM7804884_control_E14_1_barcodes.tsv.gz |
4.8 Kb |
(ftp)(http) |
TSV |
| GSM7804884_control_E14_1_detected_tissue_image.jpg.gz |
745.7 Kb |
(ftp)(http) |
JPG |
| GSM7804884_control_E14_1_features.tsv.gz |
164.2 Kb |
(ftp)(http) |
TSV |
| GSM7804884_control_E14_1_matrix.mtx.gz |
17.1 Mb |
(ftp)(http) |
MTX |
| GSM7804884_control_E14_1_scalefactors_json.json.gz |
181 b |
(ftp)(http) |
JSON |
| GSM7804884_control_E14_1_spatial_enrichment.csv.gz |
781.8 Kb |
(ftp)(http) |
CSV |
| GSM7804884_control_E14_1_tissue_hires_image.png.gz |
2.6 Mb |
(ftp)(http) |
PNG |
| GSM7804884_control_E14_1_tissue_lowres_image.png.gz |
276.8 Kb |
(ftp)(http) |
PNG |
| GSM7804884_control_E14_1_tissue_positions.csv.gz |
62.6 Kb |
(ftp)(http) |
CSV |
| GSM7804884_control_E14_1_web_summary.html.gz |
1.9 Mb |
(ftp)(http) |
HTML |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
