|
| Status |
Public on Aug 04, 2024 |
| Title |
Spatial_Transciptomics_Mouse_627_LUNG |
| Sample type |
SRA |
| |
|
| Source name |
Lung
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Lung
genotype: BALB/c
treatment: 1x10^5 4T1 cells were resuspended in PBS and injected in the mammary fat pad of 8-week- old murine model.
|
| Treatment protocol |
1x105 4T1 cells were resuspended in PBS and injected in the mammary fat pad of 8-week- old BALB/c mice. After 28 days from the inoculum, mice were sacrificed, and tumors and lungs were collected for histopathologicand spatial transcriptomical analyses. Four micrometer-thick FFPE sections were sliced and mounted on a Visium glass slide before undergoing HE staining.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Tissues underwent decrosslinking and enzymatic permeabilization for the preparation of RNA libraries, followed by the addition of Illumina indexes (i5 and i7) required for sequencing, as outlined in the Visium Spatial Gene Expression for FFPE protocol (10x Genomics Visium, CG000407).
Right-hand side (RHS) and left-hand side (LHS) probes specific to mouse samples from the Mouse Transcriptome Probe Kit (10x PN 2000457 and 2000458) were applied to the Visium slide according to the manufacturer's guidelines. The slide was then incubated at around 50 °C in a Thermocycler for approximately 18 hours.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 2000 |
| |
|
| Description |
Visium Spatial Gene expression for FFPE tissue Sequencing
|
| Data processing |
The raw sequencing data was processed using the 10x Genomics Space Ranger pipeline to produce FASTQ files.
The sequences were mapped to the mm10 genome for gene expression counting using Space Ranger's default parameters.
The gene expression levels of RefSeq coding genes were quantified using Space Ranger's default settings.
Assembly: mm10
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
Supplementary files format and content: aligned_fiducials.jpg.gz: aligned fiducilas 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_lowers_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
|
| |
|
| Submission date |
Jul 30, 2024 |
| Last update date |
Aug 04, 2024 |
| Contact name |
Claudio Tripodo |
| E-mail(s) |
[email protected]
|
| Organization name |
Univerisity of Palermo
|
| Department |
PROMISE
|
| Lab |
Tumor immunology Unit
|
| Street address |
Corso Tukory 211
|
| City |
Palermo |
| ZIP/Postal code |
90134 |
| Country |
Italy |
| |
|
| Platform ID |
GPL30172 |
| Series (1) |
| GSE273439 |
Extraction of a Stromal Metastatic Gene Signature in Breast Cancer via Spatial Profiling |
|
| Relations |
| BioSample |
SAMN42920113 |
| SRA |
SRX25515153 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8428409_01.9_627_LUNG_V11Y03-083_B_aligned_fiducials.jpg.gz |
656.6 Kb |
(ftp)(http) |
JPG |
| GSM8428409_02.9_627_LUNG_V11Y03-083_B.tif.gz |
47.1 Mb |
(ftp)(http) |
TIFF |
| GSM8428409_03.9_627_LUNG_V11Y03-083_B_scalefactors_json.json.gz |
183 b |
(ftp)(http) |
JSON |
| GSM8428409_04.9_627_LUNG_V11Y03-083_B_tissue_hires_image.png.gz |
1.6 Mb |
(ftp)(http) |
PNG |
| GSM8428409_05.9_627_LUNG_V11Y03-083_B_tissue_lowres_image.png.gz |
168.9 Kb |
(ftp)(http) |
PNG |
| GSM8428409_06.9_627_LUNG_V11Y03-083_B_tissue_positions_list.csv.gz |
58.9 Kb |
(ftp)(http) |
CSV |
| GSM8428409_07.9_627_LUNG_V11Y03-083_B_barcodes.tsv.gz |
9.8 Kb |
(ftp)(http) |
TSV |
| GSM8428409_08.9_627_LUNG_V11Y03-083_B_features.tsv.gz |
164.2 Kb |
(ftp)(http) |
TSV |
| GSM8428409_09.9_627_LUNG_V11Y03-083_B_matrix.mtx.gz |
17.4 Mb |
(ftp)(http) |
MTX |
SRA Run Selector |
| Raw data are available in SRA |
