|
| Status |
Public on Sep 27, 2023 |
| Title |
Visium_Partial Responder sample of Tumor liver (Mouse 3) |
| Sample type |
SRA |
| |
|
| Source name |
Liver containing metastases of CRC origin
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Liver containing metastases of CRC origin
condition: Partial Responder
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Immediately after euthanizing the mice and perfusion of the liver with PBS containing 5 mM EDTA, small pieces of the liver containing metastasis from the mice were taken and shock-frozen in isopentane which was cooled down with liquid nitrogen. Afterwards, the samples were embedded in Killik, O.C.T. Compound embedding medium for cryostat (Bio-Optica/ 05-9801). The samples were stored at -80 °C.
Sections of previously prepared tissues were prepared using a cryostat (cooled to 16 °C) and placed on the visium slides. Methanol fixation and Hematoxilin & Eosin (H&E) staining was performed according to the manual provided by 10x Genomics under the name Methanol Fixation, H&E Staining & Imaging for Visium Spatial Protocols (10x Genomics/ CG000160 Rev A) using a Aperio ePathology digital scanner (Leica Biosystems) for image acquisition. Afterwards, the samples were processed for Visium analysis according to the manual: User Guide Visium Spatial Gene Expression Reagent Kits (10X Genomics/ CG000239 Rev F).
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
10x Visium
|
| Data processing |
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Space Ranger software v1.2.2 (https://support.10xgenomics.com/spatial-gene-expression/software/pipelines/latest/what-is-space-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files, matrix files, and spatial information (images and coordinates)
Library strategy: Spatial Transcriptomics
|
| |
|
| Submission date |
Dec 19, 2022 |
| Last update date |
Jan 04, 2024 |
| Contact name |
Stefano Beretta |
| E-mail(s) |
beretta.stefano1@hsr.it
|
| Organization name |
San Raffaele Telethon Institute for Gene Therapy
|
| Street address |
Via Olgettina, 60
|
| City |
Milan |
| ZIP/Postal code |
20132 |
| Country |
Italy |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE221359 |
In vivo macrophage engineering reshapes the tumor microenvironment leading to eradication of liver metastases [Visium] |
| GSE221360 |
In vivo macrophage engineering reshapes the tumor microenvironment leading to eradication of liver metastases |
|
| Relations |
| BioSample |
SAMN32314979 |
| SRA |
SRX18776193 |
