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| Status |
Public on Jan 31, 2024 |
| Title |
LesionB |
| Sample type |
SRA |
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| Source name |
oral mucosa
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| Organism |
Homo sapiens |
| Characteristics |
tissue: tongue
diagnosis: Proliferative Verrucous Leukoplakia
histopathological diagnosis: corrugated orthohyperkeratosis
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
The OLK tissues were washed by phosphate-buffered saline (Gibco, USA), cut into tiny cubes (2mm3), and transferred to the C tube (Miltenyi Biotec, Germany). The tissue dissociation was performed by skin dissociation kits (Miltenyi Biotec, Germany), following the manufacturer’s instructions. After dissociation, single-cells were spun down at 400g for 5 min and resuspended with 1X Red Blood Cell Lysis (Abcam, USA) for 5 minutes to remove the blood cells. Then, dead cells removing using Dead Cell Removal kits (STEMCELL Technologies, Canada). Single-cells were spun down at 400g for 5 minutes and adjusted to 1 x 106/ml. The total time from biopsy to loading on the 10X platform was within 3 hours.
The cell suspension was loaded into Chromium microfluidic chips with 3’ v3, chemistry and barcoded with a 10× Chromium Controller (10X Genomics). RNA from the barcoded cells was subsequently reverse-transcribed and sequencing libraries constructed with reagents from a Chromium Single Cell 3’ v3 reagent kit (10X Genomics) according to the manufacturer’s instructions. Sequencing was performed with Illumina NovaSeq according to the manufacturer’s instructions (Illumina).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
We use fastp to perform basic statistics on the quality of the raw reads. Generally, celltanger count support FASTQ files from raw base call (BCL) files generated by Illumina sequencers as input file. 10x Genomics® not recommend additional processing of the sequence.
Raw reads were demultiplexed and mapped to the reference genome by 10X Genomics Cell Ranger pipeline (cellranger-5.0.1) using default parameters. All downstream single-cell analyses were performed using Cell Ranger and Seurat ( (Macosko et al., 2015; Satija et al., 2015) unless mentioned specifically. In brief, for each gene and each cell barcode (filtered by CellRanger), unique molecule identifiers were counted to construct digital expression matrices. Secondary filtration by Seurat : A gene with expression in more than 3 cells was considered as expressed, and each cell was required to have at least 200 expressed genes. And filter out some of the foreign cells.
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every cell
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| Submission date |
Feb 07, 2022 |
| Last update date |
Jan 31, 2024 |
| Contact name |
Liang Zhong |
| E-mail(s) |
zhongl035035@gmail.com
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| Organization name |
Sichuan University
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| Street address |
Renmin road
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| City |
Chengdu |
| State/province |
- |
| ZIP/Postal code |
610041 |
| Country |
China |
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| Platform ID |
GPL24676 |
| Series (1) |
| GSE196296 |
Single-cell Transcriptomics Dissects Premalignant Progression in Proliferative Verrucous Leukoplakia |
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| Relations |
| BioSample |
SAMN25715980 |
| SRA |
SRX14079084 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5870062_LesionB_barcodes.tsv.gz |
44.9 Kb |
(ftp)(http) |
TSV |
| GSM5870062_LesionB_features.tsv.gz |
297.6 Kb |
(ftp)(http) |
TSV |
| GSM5870062_LesionB_matrix.mtx.gz |
74.9 Mb |
(ftp)(http) |
MTX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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