General Information

Title of Dataset
Single-nucleus and spatially resolved multi-omics uncover intracranial germinomas’ microenvironment and associated molecular features.

Author Contact Information 
  Name: Prof. Ng, Ho-Keung  
  Institution: The Chinese University of Hong Kong  
  Email: hkng@cuhk.edu.hk

Data Storage
The archive contains raw experimental data from 51 germinomas and is deposited in the China National Genomics Data Center under BioProjectID PRJCA045410. The accession number for single-nucleus RNA sequencing (snRNA-seq) and spatial transcriptomics (ST) data is HRA013006, while the accession number for imaging mass cytometry (IMC) data is OMIX011665. Alternatively, the raw data can be accessed at: https://www.surgery.cuhk.edu.hk/btc/hsbc/#OUR%20WORK.

Data Overview
This dataset includes raw data from 50 samples studied via snRNA-seq, 12 samples studied via ST (using Visium from 10X Genomics), and 29 samples studied via IMC. The approximate total file sizes are as follows:  
- snRNA-seq: 240 GB  
- ST: 99.4 GB  
- IMC: 1.1 GB  

The following sections describes the contents, including file names and corresponding case numbers under the China National Genomics Data Center, to facilitate evaluation prior to initiating a download. Probe barcodes and their corresponding case numbers for snRNA-seq are detailed in the file named "summary" available at: 
https://www.surgery.cuhk.edu.hk/btc/hsbc/#OUR%20WORK.

Dataset Contents and Structure
snRNA-seq Data (FASTQ Files)
The snRNA-seq data are provided in paired FASTQ files organized by case ranges. The following files contain raw sequencing reads for the specified cases:
• HRR2723124_f1.fastq.gz and HRR2723124_r1.fastq.gz: Contains snRNA-seq data for cases 1-4.
• HRR2723125_f1.fastq.gz and HRR2723125_r1.fastq.gz: Contains snRNA-seq data for cases 5-13.
• HRR2723126_f1.fastq.gz and HRR2723126_r1.fastq.gz: Contains snRNA-seq data for cases 14-20.
• HRR2723127_f1.fastq.gz and HRR2723127_r1.fastq.gz: Contains snRNA-seq data for cases 21-35.
• HRR2723128_f1.fastq.gz and HRR2723128_r1.fastq.gz: Contains snRNA-seq data for cases 36-50.


ST Data (FASTQ Files)
The ST data are provided in paired FASTQ files, each corresponding to a single case. The following files contain raw sequencing reads for specified cases: 
• HRR2723129_f1.fastq.gz and HRR2723129_r1.fastq.gz: Contains ST data for case 51.
• HRR2723130_f1.fastq.gz and HRR2723130_r1.fastq.gz: Contains ST data for case 5.
• HRR2723131_f1.fastq.gz and HRR2723131_r1.fastq.gz: Contains ST data for case 7.
• HRR2723132_f1.fastq.gz and HRR2723132_r1.fastq.gz: Contains ST data for case 8.
• HRR2723133_f1.fastq.gz and HRR2723133_r1.fastq.gz: Contains ST data for case 16.
• HRR2723134_f1.fastq.gz and HRR2723134_r1.fastq.gz: Contains ST data for case 17.
• HRR2723135_f1.fastq.gz and HRR2723135_r1.fastq.gz: Contains ST data for case 12.
• HRR2723136_f1.fastq.gz and HRR2723136_r1.fastq.gz: Contains ST data for case 19.
• HRR2723137_f1.fastq.gz and HRR2723137_r1.fastq.gz: Contains ST data for case 1.
• HRR2723138_f1.fastq.gz and HRR2723138_r1.fastq.gz: Contains ST data for case 2.
• HRR2723139_f1.fastq.gz and HRR2723139_r1.fastq.gz: Contains ST data for case 3.
• HRR2723140_f1.fastq.gz and HRR2723140_r1.fastq.gz: Contains ST data for case 4.



IMC Data
IMC data for 29 samples are included, and they are in text files. The file names in the China National Genomics Data Center under the accession number OMIX011665 corresponds to  specific cases.  

Notes
Additional Resources: For mapping probe barcodes to case numbers, consult the "summary" file at the alternative link.  
Contact: For inquiries or requests for subsets of data, contact the Principal Investigator at hkng@cuhk.edu.hk.