scHNSCC_207

Download processed single-cell RNA-seq data for this sample

Dataset Information

scHNDB ID

scHNSCC_207

Tissue Type

Tumor

Age

41

Gender

F

Position

Nasopharynx

Clinical Stage

II

Download Resources

Raw Data Files

Complete single-cell RNA sequencing data in standard 10X Genomics format

10X Raw Data Package

File: scHNSCC_207_10x_raw_package.zip

Format: ZIP

Description: Contains barcodes/features/matrix/metadata in standard 10X format

Zenodo download link pending upload.

10X format (4 files)

Files (typically included in the ZIP package above):

  • scHNSCC_207_barcodes.tsv.gz
  • scHNSCC_207_features.tsv.gz
  • scHNSCC_207_matrix.mtx.gz
  • scHNSCC_207_metadata.csv.gz

Use Read10X() / sc.read_10x_mtx() on the folder containing barcodes, features, and matrix.

Feature File

File: scHNSCC_207_features.tsv.gz

Format: TSV.GZ

Description: Gene features and annotations

Download

Matrix File

File: scHNSCC_207_matrix.mtx.gz

Format: MTX.GZ

Description: Sparse expression matrix

Download

Metadata File

File: scHNSCC_207_metadata.csv.gz

Format: CSV.GZ

Description: Cell-level metadata and annotations

Download

Usage Instructions

These files are compatible with standard single-cell analysis tools. To load the data:

In R (Seurat):

library(Seurat)
data <- Read10X(data.dir = "path/to/extracted/files")
seurat_obj <- CreateSeuratObject(counts = data)

In Python (Scanpy):

import scanpy as sc
adata = sc.read_10x_mtx('path/to/extracted/files')