 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Jul 02, 2024 |
| Title |
Spatial Transcriptomics reveals that cells that experience intratumoral hypoxia retain hypoxia-associated transcriptional programs after invading into oxygenated tumor regions. |
| Organism |
Homo sapiens |
| Experiment type |
Other
|
| Summary |
To understand the role of hypoxia in metastatic progression, we sought to spatially map gene expression in hypoxic cells compared with cells that migrated to oxygenated tumor regions. We adapted the Visium spatial transcriptomics protocol to perform concurrent transcriptional profiling and fluorescent imaging of our hypoxia fate-mapping system.
|
| |
|
| Overall design |
Hypoxia fate-mapping MDA-MB-231 tumors (Godet et. al, 2019) were harvested 18 days post-implantation and immediately frozen in clear OCT. 10 μm tumor slices were placed within the fiducial frame of the Visium slide. The tissue was pre-fixed in cold methanol and imaged at 10X magnification using a Cytation5 in the RFP and GFP channels to acquire native fluorescence. The slide was immediately transferred to cold methanol with DAPI. DAPI staining was imaged at 10X using Cytation5.
|
| |
|
| Contributor(s) |
Godet I, Gilkes D |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| |
| Submission date |
Aug 07, 2023 |
| Last update date |
Jul 03, 2024 |
| Contact name |
Ines Godet |
| Organization name |
Johns Hopkins University
|
| Department |
Oncology
|
| Lab |
Gilkes
|
| Street address |
1650 Orleans Street, CRB1, room 128
|
| City |
Baltimore |
| State/province |
MD |
| ZIP/Postal code |
21231 |
| Country |
USA |
| |
|
| Platforms (1) |
| GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
|
| Samples (2) |
|
| Relations |
| BioProject |
PRJNA1002980 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE240212_RAW.tar |
110.1 Mb |
(http)(custom) |
TAR (of CSV, JPG, JSON, MTX, PNG, TSV) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
