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Sample GSM6248650

Query DataSets for GSM6248650

Status

Public on Sep 11, 2024

Title

NPC_ST9

Sample type

SRA

Source name

Nasopharynx

Organism

Homo sapiens

Characteristics

tissue: Nasopharynx
disease state: Nasopharyngeal carcinoma

Extracted molecule

total RNA

Extraction protocol

Viable single cells were prepared from the PBMC and tumor of 10 nasopharyngeal carcinoma patients; formalin-fixed paraffin-embedded (FFPE) biopsy sections were prepared from 12 nasopharyngeal carcinoma patients
10X Genomics protocol CG000086 and CG000407

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina NovaSeq 6000

Data processing

BCR reads were aligned to human reference VDJ dataset (http://cf.10Xgenomics.com/supp/cell-vdj/refdata-cellranger-vdj-GRCh38-alts-ensembl-2.0.0.tar.gz) using CellRanger (“vdj” option; version 3.0.1; 10x Genomics).
Sequencing data in FASTQ files and manually aligned histological images were analysed with Space Ranger (version 1.3.0) and the probe set for alignment provided by 10X Genomics (Visium Human Transcriptome Probe Set v1.0 GRCh38-2020-A).
Assembly: hg38
Supplementary files format and content: BCR information were respectively represented by comma-separated text files including 20 samples.
Supplementary files format and content: 10X Genomics standard output format of spatial transcriptomics

Submission date

Jun 16, 2022

Last update date

Sep 11, 2024

Contact name

Dong-Mei Chi

E-mail(s)

chidm@sysucc.org.cn

Organization name

SYSUCC

Street address

651 Dongfeng Road East

City

GuangZhou

ZIP/Postal code

510000

Country

China

Platform ID

GPL24676

Series (1)

GSE206245

Single-Cell and Spatial Transcriptome Analyses Reveal Tertiary Lymphoid Structures Linked to Tumour Progression and Immunotherapy Response in Nasopharyngeal Carcinoma

Supplementary file	Size	Download	File type/resource
GSM6248650_NPC_ST9_aligned_fiducials.jpg.gz	1.7 Mb	(ftp)(http)	JPG
GSM6248650_NPC_ST9_barcodes.tsv.gz	14.7 Kb	(ftp)(http)	TSV
GSM6248650_NPC_ST9_detected_tissue_image.jpg.gz	2.1 Mb	(ftp)(http)	JPG
GSM6248650_NPC_ST9_features.tsv.gz	151.6 Kb	(ftp)(http)	TSV
GSM6248650_NPC_ST9_matrix.mtx.gz	15.0 Mb	(ftp)(http)	MTX
GSM6248650_NPC_ST9_scalefactors_json.json.gz	169 b	(ftp)(http)	JSON
GSM6248650_NPC_ST9_tissue_hires_image.png.gz	10.6 Mb	(ftp)(http)	PNG
GSM6248650_NPC_ST9_tissue_lowres_image.png.gz	917.3 Kb	(ftp)(http)	PNG
GSM6248650_NPC_ST9_tissue_positions_list.csv.gz	54.9 Kb	(ftp)(http)	CSV
Raw data not provided for this record
Processed data provided as supplementary file