Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcriptome sequencing in patients with tongue cancer

ABSTRACT: Transcriptome sequencing in patients with tongue cancer

PROVIDER: PRJNA602314 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR10916900_1.fastq.gz	Fastqsanger.gz
	SRR10916900_2.fastq.gz	Fastqsanger.gz
	SRR10916901_1.fastq.gz	Fastqsanger.gz
	SRR10916901_2.fastq.gz	Fastqsanger.gz
	SRR10916902_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 16

Similar Datasets

Transcriptome sequencing in patients with tongue cancer

Project description:Tongue cancer is one of the most common cancers, and its molecular etiology and pathogenesis remain unclear. This study aimed to uncover its pathogenesis and search for potential novel diagnostic and therapeutic targets for treating tongue cancer.

2020-04-22 | GSE143950 | GEO

Whole Transcriptome sequencing TSCC (tongue squamous cell carcinoma)

Project description:Of the multiple anatomical sites represented in oral cancer, squamous cell carcinoma of the tongue (TSCC) shows the highest incidence among younger age group. Chewing betel leaf, areca nut & slaked lime and smoking tobacco are common practises in India which have direct clinical implication in TSCC carcinogenesis. Here, for the first time we define the landscape of genomic alterations in TSCC from the Indian diaspora which would help to identify novel therapeutic targets for clinical intervention and define the genetic basis for TSCC. We performed high throughput sequencing of fifty four tongue samples using whole exome sequencing (n=47, 23 paired normal tumor and 1 unpaired) and transcriptome sequencing (n=17, 10 tumor and 5 normal). Mutation, copy number analysis were carried out using exome sequencing data and transcriptome analysis provided expressed genes and transcript fusions in tongue cancer patients. Further, integrated analysis were performed to identify biologically relevant alterations. Our preliminary analysis revealed presence of most frequently altered mutations in TSCC which includes mutations in TP53, NOTCH1, CDKN2A, USP6, KMT2D etc, consistent with literature. We observed high frequency of CG/T(GC/A) transversions in non-CpG islands, a signature associated with tobacco exposure. Somatic copy number analysis revealed copy number gain in known hallmarks such as CCND1, MYC, ORAOV1 genes along with copy number alteration in novel genes. Significant positive correlation was observed in the genes harbouring copy number gains and showing increased expression.

2018-05-31 | E-MTAB-4654 | biostudies-arrayexpress

Whole exome sequencing of TSCC (tongue squamous cell carcinoma)

2018-05-31 | E-MTAB-4653 | biostudies-arrayexpress

Integrated proteomics and phosphoproteomics revealed druggable kinases in neoadjuvant chemotherapy resistant tongue cancer

Project description:Tongue squamous cell carcinoma is characterised by poor prognosis and high metastatic events. Patients with unresectable tumors are benefiting from neoadjuvant chemotherapy (NACT) which surgical resection, and controls distant metastasis, and locoregional recurrence. However, resistance to NACT limit the success of the treatment regimen. In this study, we investigated the altered proteome and phosphoproteome of NACT resistant and sensitive cohort using Mass spectrometry-based proteomics. We carried out proteomic as well as phosphoproteomic analysis of treatment naïve tongue cancer patients whose response to NACT is recorded. Proteomic analysis revealed distinct protein expression between the responders and non-responders. The Phosphoproteomic analysis revealed kinases and the pathways associated with NACT resistance in tongue cancer.

2023-03-11 | PXD037356 | Pride

Whole Genome Sequencing of Tongue cancer samples and cell line

Project description:Whole genome sequencing (WGS) of tongue cancer samples and cell line was performed to identify the fusion gene translocation breakpoint. WGS raw data was aligned to human reference genome (GRCh38.p12) using BWA-MEM (v0.7.17). The BAM files generated were further analysed using SvABA (v1.1.3) tool to identify translocation breakpoints. The translocation breakpoints were annotated using custom scripts, using the reference GENCODE GTF (v30). The fusion breakpoints identified in the SvABA analysis were additionally confirmed using MANTA tool (v1.6.0).

2024-02-17 | E-MTAB-12534 | biostudies-arrayexpress

miR-762 overexpression effect on tongue cancer cells

Project description:Analysis of SCC-15 tongue cancer cells overexpressing miR-762. miR-762 is frequently upregulated in primary tongue cancer. Results provide insight into the role of miR-762 in the pathogenesis of tongue cancer. We used micorarrays to detailed the genes regulated by miR-762 in SCC-15 cells.

2018-11-09 | GSE122328 | GEO

miR-611 overexpression effect on tongue cancer cells

Project description:Analysis of SCC-15 tongue cancer cells overexpressing miR-611. miR-611 is frequently upregulated in primary tongue cancer. Results provide insight into the role of miR-611 in the pathogenesis of tongue cancer. We used micorarrays to detailed the genes regulated by miR-611 in SCC-15 cells.

2019-12-01 | GSE129118 | GEO

miR-585-5p overexpression effect on tongue cancer cells

Project description:Analysis of SCC-9 tongue cancer cells overexpressing miR-585-5p. miR-585-5p is frequently downregulated in primary tongue cancer. Results provide insight into the role of miR-585-5p in the pathogenesis of tongue cancer. We used micorarrays to detailed the genes regulated by miR-585-5p in SCC-9 cells.

2018-05-08 | GSE114093 | GEO

Human-derived proteome characterization of tongue coating in colorectal cancer

Project description:Tongue coating proteome data from healthy people, patients with colorectal hyperplastic polyps and colorectal cancer.

2024-09-07 | PXD055725 |

Whole Transcriptome sequencing TSCC (tongue squamous cell carcinoma)

Project description:Whole Transcriptome sequencing TSCC (tongue squamous cell carcinoma)

| PRJEB14202 | ENA