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| Status |
Public on Aug 07, 2023 |
| Title |
Skin - Gut axis, spatialRNAseq 3 |
| Sample type |
SRA |
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| Source name |
whole colon
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| Organism |
Mus musculus |
| Characteristics |
tissue: whole colon
cell type: section of the large intestine
strain: C57BL/6 back ground mouse
treatment: N/A
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| 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)
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| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| 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
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| Submission date |
Mar 21, 2023 |
| Last update date |
Aug 07, 2023 |
| Contact name |
Tatsuya Dokoshi |
| E-mail(s) |
ta1983@hotmail.com
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| Organization name |
Univeristy of California, San Diego
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| Department |
Department of Dermatology
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| Street address |
9500 Gilman
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| City |
San Diego |
| State/province |
California |
| ZIP/Postal code |
92093 |
| Country |
USA |
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| Platform ID |
GPL24247 |
| Series (1) |
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| Relations |
| BioSample |
SAMN33845201 |
| SRA |
SRX19741528 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7109547_filtered_feature_bc_matrix_k14_control.tar.gz |
28.4 Mb |
(ftp)(http) |
TAR |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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