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Sample GSM7109548 Query DataSets for GSM7109548
Status Public on Aug 07, 2023
Title Skin - Gut axis, spatialRNAseq 4
Sample type SRA
 
Source name whole colon
Organism Mus musculus
Characteristics tissue: whole colon
cell type: section of the large intestine
strain: C57BL/6 back ground mouse
treatment: 2.5% DSS for 7 days
Extracted molecule total RNA
Extraction protocol Colonic tissues from untreated and DSS-treated mice from WT and K14/HYAL1 mouse were cleaned from adipose tissue and cut longitudinally; the luminal content was removed by washing it in cold phosphate buffered saline (PBS). Starting from the most proximal portion (i.e., Cecum) and with the luminal side facing upward, the colon was rolled resulting in a roll with the proximal colon in the center and the distal colon in the outer portion of the roll. The roll was placed in a histology plastic cassette and snap frozen for 1 min in a bath of liquid nitrogen-cooled isopentane. The frozen tissue was then embedded in Optimal Cutting Temperature compound (OCT, Sakura Tissue-TEK) on dry ice and stored at −80 °C. OCT blocks were cut with a pre-cooled cryostat at 10um thickness, and sections were transferred to fit the 6.5mm2 oligo-barcoded capture areas on the Visium 10x Genomics slide. Before performing the complete protocol, Visium Spatial Tissue Optimization (10x Genomics) was performed according to manufacturer’s instructions, and the fluorescent footprint was imaged using a Metafer Slide Scanning Platform (Metasystems). 9 minutes was selected as optimal permeabilization time.
The experimental slide with colonic tissue was fixed and stained with hematoxylin and eosin (H&E) and imaged using a Keyence BZX-700 Fluorescent Microscopy (Keyence) at 2X magnification. Sequence libraries were then processed according to manufacturer’s instructions (10x Genomics, Visium Spatial Transcriptomic)
 
Library strategy OTHER
Library source transcriptomic
Library selection other
Instrument model Illumina NovaSeq 6000
 
Data processing The demultiplexing, barcoded processing, gene counting and aggregation were made using the space Ranger software v2.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files
Library strategy: spatialRNA-seq
 
Submission date Mar 21, 2023
Last update date Aug 07, 2023
Contact name Tatsuya Dokoshi
E-mail(s) ta1983@hotmail.com
Organization name Univeristy of California, San Diego
Department Department of Dermatology
Street address 9500 Gilman
City San Diego
State/province California
ZIP/Postal code 92093
Country USA
 
Platform ID GPL24247
Series (1)
GSE227836 Skin - Gut axis
Relations
BioSample SAMN33845200
SRA SRX19741529

Supplementary file Size Download File type/resource
GSM7109548_filtered_feature_bc_matrix_K14_DSS.tar.gz 23.2 Mb (ftp)(http) TAR
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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