|
| Status |
Public on Jul 22, 2024 |
| Title |
Neonatal Esophagus WT P0_2 |
| Sample type |
SRA |
| |
|
| Source name |
esophagus
|
| Organism |
Mus musculus |
| Characteristics |
tissue: esophagus
developmental stage: P0
genotype: WT
treatment: not treated
|
| Treatment protocol |
N/A
|
| Growth protocol |
N/A
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Fresh frozen tissues were OCT embedded and 8um frozen sections were cut using cryostat
Spatial transcriptome sequencing libraries were prepared with 10x Genomics Visium Spatial Gene Expression Slides and Reagent Kit according to manufacture's instructions
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Fresh frozen spatial transcriptomic sequencing
|
| Data processing |
Raw sequencing data were processed by 10x Genomic using the 10x Genomic Space Ranger pipeline(version-2.0.0) to generate fastq files
Sequences were aligned to mm10 genome to gene expression count using Space Ranger default settings
Gene expression level of Refseq coding genes were quanitified using Space Ranger's default settings
Assembly: mm10
Supplementary files format and content: aligned_fiducials.jpg aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg image of tissue and spots
Supplementary files format and content: scalefactors_json.json scalefactors in json format
Supplementary files format and content: tissue_hires_image.png hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png low-res image of tissue
Supplementary files format and content: tissue_positions.csv 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 expression count data in Matrix Market Exchange Format
Library strategy: Spatial transcriptomics
|
| |
|
| Submission date |
Jul 09, 2024 |
| Last update date |
Jul 22, 2024 |
| Contact name |
Lana Kostic |
| Organization name |
A*STAR
|
| Department |
IMCB
|
| Lab |
Nick Barker
|
| Street address |
61 Biopolis Dr, Proteos
|
| City |
Singapore |
| ZIP/Postal code |
138673 |
| Country |
Singapore |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE271795 |
Lgr5 Marks Stem/Progenitor Cells Contributing to Epithelial and Muscle Development in the Mouse Esophagus |
|
| Relations |
| BioSample |
SAMN42382892 |
| SRA |
SRX25251510 |
