NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM6859067 Query DataSets for GSM6859067
Status Public on Sep 27, 2023
Title Visium_Resistant sample of Tumor liver (Mouse 1)
Sample type SRA
 
Source name Liver containing metastases of CRC origin
Organism Mus musculus
Characteristics tissue: Liver containing metastases of CRC origin
condition: Resistant
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 SAMN32314985
SRA SRX18776187

Supplementary file Size Download File type/resource
GSM6859067_Sample4_barcodes.tsv.gz 7.4 Kb (ftp)(http) TSV
GSM6859067_Sample4_features.tsv.gz 284.1 Kb (ftp)(http) TSV
GSM6859067_Sample4_filtered_feature_bc_matrix.h5 7.6 Mb (ftp)(http) H5
GSM6859067_Sample4_matrix.mtx.gz 19.8 Mb (ftp)(http) MTX
GSM6859067_Sample4_spatial.tar.gz 14.2 Mb (ftp)(http) TAR
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap