|
| Status |
Public on May 13, 2024 |
| Title |
LN2 |
| Sample type |
SRA |
| |
|
| Source name |
Sentinel Lymph Node
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Sentinel Lymph Node
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Sentinel lymph nodes biopsies were embedded in OCT and flash frozen in liquid nitrogen prior to sectioning and mounting on 10x genomics visium slides
Libraries were constructed using the Visium Spatial 3' v1 protocol
Libraries sequenced using paired-end, dual indexed following 10x Genomics protocol
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Spatial transcriptomics processed using the 10x Genomics Visium protocol
|
| Data processing |
Sequencing was demultiplexed, the barcodes were identified and the genes were counted using the spaceranger 2.1 pipeline (https://www.10xgenomics.com/support/software/space-ranger/latest/analysis/inputs/fastqs-generating-fastqs)
Assembly: GRCh38-3.0.0
Supplementary files format and content: tab seperated values and matrix files
Supplementary files format and content: jpg image file of analyzed tissue
Library strategy: Spatial transcriptomics
|
| |
|
| Submission date |
Jan 18, 2024 |
| Last update date |
May 13, 2024 |
| Contact name |
Brent Hanks |
| E-mail(s) |
brent.hanks@duke.edu
|
| Organization name |
Duke University
|
| Department |
Medicine
|
| Street address |
308 Research Dr
|
| City |
Durham |
| State/province |
North Carolina |
| ZIP/Postal code |
27710 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE253588 |
A Lactate-induced SREBF2-dependent genetic program drives an immunotolerant dendritic cell population during cancer progression [Spatial transcriptomics] |
| GSE253593 |
A Lactate-induced SREBF2-dependent genetic program drives an immunotolerant dendritic cell population during cancer progression |
|
| Relations |
| BioSample |
SAMN39487069 |
| SRA |
SRX23293468 |
