Spatial transcriptomic data of breast cancer
Fastq files from spatial transcriptomic of breast cancer coming from 8 Breast cancer sections. Sample preparation: frozen BC samples were chosen based on tissue structure and RNA quality (RIN > 8). The “Visium Spatial Tissue Optimization Slide and Reagent Kit” (10X Genomics; #PN-1000193) was then used to optimize permeabilization conditions for BC tissues. Briefly, sections were fixed, stained and then permeabilized at different time points to capture mRNA, and the reverse transcription was performed to generate fluorescently labeled cDNA. The permeabilization time that resulted in the highest fluorescence signal with the lowest background diffusion was chosen. The best permeabilization time for BC tissue was 18 min. Cryostat sections of 10 μm of thickness were cut and placed on Visium Spatial Gene Expression slides (10X Genomics, PN-1000184). The slide was incubated for 1 min at 37°C, then fixed with methanol for 30 min at -20°C followed by Hematoxylin and Eosin (H&E) staining and images were taken under a high-resolution microscope. After imaging, the coverslip was detached by holding the slide in water and the slide was mounted in a plastic slide cassette. The spatial gene expression process, including tissue permeabilization, second strand synthesis and cDNA amplification, was performed according to the manufacturer’s instructions (10X Genomics; #CG000239). cDNA quality was next assessed using Agilent High sensitivity DNA Kit (Agilent, #5067-4626). The spatial gene libraries were constructed using Visium Spatial Library Construction Kit (10X Genomics, PN-1000184).
- 07/03/2024
- 8 samples
- DAC: EGAC00001000581
- Technology: Illumina NovaSeq 6000
Data Access policy
Access to the sequence level data produced by the «U830 Stress and Cancer» laboratory at the Institut Curie is controlled by Fatima Mechta-Grigoriou, Principal Investigator (DAC). Access to data will be granted to qualified investigators for appropriate use after request to Fatima.Mechta-Grigoriou@curie.fr
Studies are experimental investigations of a particular phenomenon, e.g., case-control studies on a particular trait or cancer research projects reporting matching cancer normal genomes from patients.
| Study ID | Study Title | Study Type |
|---|---|---|
| EGAS50000000220 | Transcriptome Analysis |
This table displays only public information pertaining to the files in the dataset. If you wish to access this dataset, please submit a request. If you already have access to these data files, please consult the download documentation.
| ID | File Type | Size | Located in | |
|---|---|---|---|---|
| EGAF50000087515 | fastq.gz | 7.4 GB | ||
| EGAF50000087516 | fastq.gz | 3.4 GB | ||
| EGAF50000087517 | fastq.gz | 3.2 GB | ||
| EGAF50000087518 | fastq.gz | 5.6 GB | ||
| EGAF50000087519 | fastq.gz | 6.6 GB | ||
| EGAF50000087520 | fastq.gz | 3.0 GB | ||
| EGAF50000087521 | fastq.gz | 6.9 GB | ||
| EGAF50000087522 | fastq.gz | 15.1 GB | ||
| EGAF50000087523 | fastq.gz | 1.7 GB | ||
| EGAF50000087524 | fastq.gz | 3.4 GB | ||
| EGAF50000087525 | fastq.gz | 7.8 GB | ||
| EGAF50000087526 | fastq.gz | 16.4 GB | ||
| EGAF50000087529 | fastq.gz | 6.3 GB | ||
| EGAF50000087530 | fastq.gz | 13.6 GB | ||
| EGAF50000087531 | fastq.gz | 8.7 GB | ||
| EGAF50000087532 | fastq.gz | 19.0 GB | ||
| 16 Files (128.2 GB) | ||||