EGAGenomicsOtherhttps://ega-archive.org/studies/EGAS00001003893EGAEGA study EGAS00001003893Transcriptome sequencing of Gingivo-buccal Cancer : ICGC-India Project_2020EGArestrictedOCSC, Carcinoma, Squamous Cell Carcinoma of the Mouth, Transcriptome, Materials, Squamous Cell Carcinoma of the Nasal Cavity, determination, Transcriptome Profile, Expression Profiles, Squamous Cell Carcinoma of the Head and Neck, Gene Expression Profile, Gene, Head And Neck, Profiles, Squamous Cell Carcinoma, Squamous Cell Carcinoma of the Larynx, Cistrons, Hypopharyngeal Squamous Cell Carcinoma, Gene Expression, oral squamous cell carcinoma, Expression Signatures, Gene Expression Signatures, chemical analysis, Oral Squamous Cell Carcinoma, Genetic Materials, Gene Expression Signature, HNSCC, methylation, Expression Profile, Genetic Material, Transcriptome Profiles, Oropharyngeal Squamous Cell Carcinoma, Methylations., Genetic, Profile, Laryngeal Squamous Cell Carcinoma, Oral Tongue Squamous Cell Carcinoma, Head And Neck Squamous Cell Carcinomas, Oral Squamous Cell Carcinomas, Signatures, Oral Cavity Squamous Cell Carcinoma, Expression Signature, Material, Gene Expression Profiles, Squamous Cell Carcinoma of Larynx, Transcriptomes, Cistron, Head and Neck Squamous Cell Carcinoma, assay, Signature, Squamous Cell of Head and NeckORAL NEOPL, neoplasm of tongue, Ribonucleic, DmelCG9412, malignant neoplasm of fixed part of tongue, RNA Sequence Determination, Oral Neoplasm, multiple endocrine neoplasia syndrome, Sequence Determination, tumor of the tongue, RNA Sequence, Gene Expression Profile, Head And Neck, ribosomal RNA, malignant neoplasm of dorsal tongue, Profiles, Xkl-1, Squamous Cell Carcinoma, Tumor, Case Fatality Rates, Death Rates, KL receptor activity, Gsfsco1, oral squamous cell carcinoma, tumour of the tongue, SCO5, malignant neoplasm of mobile part of tongue, SCO1, Excess Mortalities, Analysis, malignant tumour of lingual tonsil, Gsfsow3, Gsfsco5, Non Polyadenylated, RNA Gene Products, SOW3, treatment, average, malignant neoplasm of tip and lateral border of tongue, thymus nucleic acid, Prognoses, TONGUE NEOPL, Analyses, Crude Mortality Rates, Determination, tumour of tongue, Tissue, cg9412, Ribosomal RNA, Head And Neck Squamous Cell Carcinomas, W, Oral Squamous Cell Carcinomas, Boys, malignant neoplasm of mobile part of tongue NOS, malignant neoplasm of base of tongue, malignant neoplasm of dorsal surface of tongue, Sequence Determinations, Signatures, malignant neoplasm of other sites of tongue, tongue tumor, HHT1., malignant neoplasm, Expression Signature, ELL1, CFR Case Fatality Rate, Ell1, disease management, tumor of tongue, Therapies, Transcriptomes, Bs, Malignancies, Double-Stranded DNA, NEOPL TONGUE, deoxyribonucleic acids, Age-Specific Death Rate, DNAn, Squamous Cell of Head and Neck, Sl, Tongue Cancers, Tumors, single-organism behavior, Therapy, DNA Libraries, Tongue, Carcinoma, Multiple endocrine neoplasms, total RNA extract, DmelCG10120, malignant neoplasm of ventral tongue surface, Process, ribose nucleic acid, malignant tumour of mobile part of tongue, Expression Profiles, RIBA, ribonucleic acids, Crude Death, Tr-kit, malignant neoplasm of tongue, Double-Stranded, Gene Libraries, familial endocrine, Acceptance Processes, Crude Mortality, Determinations, NEOPL ORAL, (Deoxyribonucleotide)n+m, malignant tumor of mobile part of tongue, Gene Expression, PBT, Acceptance Process, malignant tumor of anterior two-thirds of tongue, Mortality, Benign, malignant neoplasm of border of tongue, Expression Signatures, Ribonukleinsaeure, 15S, Oral Squamous Cell Carcinoma, kl1-A, pentosenucleic acids, NOS, simple tissue, Ribonucleic acids, malignant neoplasm of tip and/or lateral border of tongue, KIT, CG9412, multiple endocrine adenomatosis, desoxyribose nucleic acid, Expression Profile, END, Transcriptome Profiles, tyrosine-protein kinase Kit, Oropharyngeal Squamous Cell Carcinoma, Acid, pbt, tongue neoplasm, Factors, death rate, ribosomal protein, Prognostic, Laryngeal Squamous Cell Carcinoma, Cancer of the Tongue, Adenomatosis, common, Benign Neoplasms, Mortalities, malignant tumor of base of tongue, kit, Treatments, Malignant Neoplasms, Endocrine neoplasia, Mortality Rate, Crude Death Rate, multiple, Patient, C19orf17, Republic of India, ds DNA, anon-WO0118547.278, malignant tumour of anterior two-thirds of tongue, DNA, Rin, RIN, multiple endocrine neoplasia syndrome(s), Mortality Determinant, other neoplasm, rasp, Mdh-NADP, Prognostic Factor, krk1, OCSC, malignant neoplasm of junctional zone of tongue, DNS, (Deoxyribonucleotide)n, Transcriptome Profile, Processes, Mortality Declines, Neoplasms, Benign Neoplasm, number, Excess, SCF receptor activity, men syndromes, Gene, Multiple endocrine neoplasia, Prognostic Factors, Crude Mortality Rate, OSCC cell, Malignant, mortality measurement, Oral Neoplasms, presence, malignant neoplasm of the tongue, Deoxyribonucleic acids, Age-Specific Death, Mortality Determinants, Crude, Rate, Determinant, Deoxyribonucleic Acid, scfr, Gene Products, Case Fatality, malignant tumour of base of tongue, HNSCC, tongue neoplasm (disease), Tongue Neoplasm, SCFR, Cancer of Tongue, Differential Mortality, Fdc, Excess Mortality, Oral Cancer, Malignancy, Oral, Nts, Profile, malignant tumor of posterior tongue, multiple endocrine neoplasia, Double Stranded, Deoxyribonucleic acid, cDNA Library, Age-Specific, Sequencing, Non-Polyadenylated RNA, OSCC, Neoplasias, men syndrome, malignant neoplasm of anterior 2/3 of tongue, RNA Sequence Analyses, ROC2, Roc2, Clients, Mortality Rates, mortality rate, Crude Death Rates, RNA Sequencing, (Deoxyribonucleotide)m, Behaviors, Age Specific Death Rate, Cancer, Sequence Analyses, proto-oncogene c-Kit, RNA, Squamous Cell Carcinoma of the Mouth, Tongue Cancer, Transcriptome, Malignant Neoplasm, Squamous Cell Carcinoma of the Nasal Cavity, Mortality Decline, Edg, RNA Sequence Determinations, DNAn+1, Multiple Endocrine Neoplasia, MDH, Squamous Cell Carcinoma of the Head and Neck, RNS, Factor, ME, Squamous Cell Carcinoma of the Larynx, Libraries, cDNA, Client, malignant tumour of posterior tongue, Hypopharyngeal Squamous Cell Carcinoma, Case Fatality Rate, count in organism, malignant neoplasm of tongue NOS, MT, survival, Oral Cancers, KIT ligand receptor activity, yeast nucleic acid, Gene Expression Signatures, Familial endocrine adenomatosis, Neoplasm, Tongue Neoplasms, DNA Library, Gene Expression Signature, MEN, Men, ds-DNA, 15S RNA, Me, malignant neoplasm of dorsum of tongue, tongue neoplasm malignant stage unspecified, Determinants, Death, membrane bound ribosome, Library, malignant neoplasm of anterior two-thirds of tongue, XKrk1, neoplasm of the tongue, free ribosome, Rates, Acceptance, ribonucleic acid, tip and lateral border, Ribosome, Death Rate, c-KIT, primary cancer, malignant neoplasm of dorsal tongue NOS, Non Polyadenylated RNA, malignant tumor of lingual tonsil, Non-Polyadenylated, Magnetic, mem, part unspecified, INSDC_qualifier:unknown, Oral Tongue Squamous Cell Carcinoma, patient, Cancers, men, Ribonucleic Acid, Age-Specific Death Rates, CD117, cDNA Libraries, malignant tumor, Differential, c-kit, Oral Cavity Squamous Cell Carcinoma, PPP1R68, Therapeutic, C-Kit, concentration, malignant neoplasm of fixed part of tongue NOS, Gene Expression Profiles, Ssm, Squamous Cell Carcinoma of Larynx, tongue tumour, RNA Sequence Analysis, cardinality, Decline, Desoxyribonukleinsaeure, xkl-1, Multiple endocrine adenomatosis, malignant neoplasm of ventral surface of tongue, Treatment, Head and Neck Squamous Cell Carcinoma, Signature, ORW1, Neoplasia, Differential Mortalities, CG10120falseTranscriptome sequencing of gingivo-buccal oral squamous cell carcinoma for integrative analysis: alterations in expression of genes attributable to methylation changesGingivo-buccal oral squamous cell carcinoma (OSCC-GB) is the most common cancer among men in India and is associated with high mortality. Although OSCC-GB is known to be quite different from tongue cancer in its genomic presentation and its clinical behavior, it is treated identically as tongue cancer. Predictive markers of prognosis and therapy that are specific to OSCC-GB are, therefore, required. To achieve this, we have carried out transcriptome (n=72) profiling of paired tumor-normal tissues collected from OSCC-GB patients from India. RNA sequencing was performed on tumor and paired adjacent normal samples from 72 OSCC-GB patients. From each patient, total RNA was extracted from tumor and normal tissue samples using AllPrep DNA/RNA Mini Kit (QIAGEN). The quality and concentration of isolated total RNA were checked using Agilent 2100 Bioanalyzer and NanoDrop 2000 (Thermo Fisher Scientific). The OD260/OD280 ratio was ≥ 2 and RNA Integrity Number (RIN) was ≥ 7.0 for all sequenced samples. Ribosomal RNA (rRNA) was removed from the RNA samples, using Ribo-Zero Magnetic Kit (Epicentre). Sequencing libraries were prepared from rRNA depleted samples using TrueSeq RNA Sample Preparation Kit (Illumina). Each triplex cDNA library pool was sequenced as 100bp paired-end on HiSeq-2000 or HiSeq-2500 (Illumina). Protocols suggested by the manufacturers were used for all assays.2021-03-24 14:30:11EGAS000010038939606EGAD00001006003EGAC00001000010