{"database":"EGA","file_versions":[],"scores":null,"additional":{"omics_type":["Genomics"],"study_type":["Other"],"full_dataset_link":["https://ega-archive.org/studies/EGAS00001002854"],"host":["EGA"],"description":["EGA study EGAS00001002854"],"dataset_title":["RNA-seq colorectal adenomas NKI-AvL TGO series NGS-ProToCol","Low-coverage Whole Genome Sequencing, colorectal adenomas NKI-AvL TGO series NGS-ProToCol","RNA-seq normal adjacent colon NKI-AvL TGO series NGS-ProToCol","RNA-seq colorectal carcinomas NKI-AvL TGO series NGS-ProToCol","Low-coverage Whole Genome Sequencing, normal adjacent colon NKI-AvL TGO series NGS-ProToCol","Low-coverage Whole Genome Sequencing, colorectal carcinomas NKI-AvL TGO series NGS-ProToCol"],"category":["restricted"],"repository":["EGA"],"name_synonyms":["Papillary Adenomas, average, acinar cell adenoma (morphologic abnormality), Follicular Adenoma, Microcystic Adenomas, Trabecular Adenomas, Adenomas, Adenoma, Basal Cell, acinar cell adenoma, Monomorphic Adenoma, adenoma, benign, study protocol, Microcystic Adenoma, Microcystic, Monomorphic Adenomas, plan specification, Papillary, method, Monomorphic, method used in an experiment., Papillary Adenoma, Trabecular, Basal Cell Adenoma, Follicular Adenomas, Trabecular Adenoma, Basal Cell Adenomas, Follicular"],"description_synonyms":["Forms, Colorectal Neoplasm, Ribonucleic, Antemortem Diagnosis, Materials, single-organism developmental process, RNA Sequence Determination, Adenomas, acetylglucosaminyltransferase-like protein, Sequence Determination, postnatal development, RNA Sequence, Mbp1, Gene Expression Profile, Mini Exon, growth and development, CG9842, Profiles, Tumor, Diagnosis, CG3629, Transcripts, Monomorphic Adenomas, Mutations, Alternative, Personal, Taenia Coli, Appendix, symptoms, CAN A1/PP2B, 2900074D19Rik, CG1455, Analysis, myd, Non Polyadenylated, Calna, Follicular, RNA Gene Products, Colorectal Tumors, Psychological, average, treatment, AI661365, CnnA14D, Art, ART, acinar cell adenoma (morphologic abnormality), Omental Appendix, thymus nucleic acid, Follicular Adenoma, Prognoses, Gene Expressions, like-acetylglucosaminyltransferase, Genomes, Analyses, Determination, Adenoma, developmental field, Tissue, RNA Splicing, Mbp-1, Colorectal Carcinomas, benign, Colorectal Tumor, Sequence Determinations, Microcystic Adenoma, Signatures, large intestine cancer, Ba, canA, Social, Transcript, malignant neoplasm, Expression Signature, CN, disease management, Therapies, Transcriptomes, Basal Cell Adenoma, Malignancies, Double-Stranded DNA, PP2B, deoxyribonucleic acids, Social Power, DNAn, Basal Cell Adenomas, INCURVATA 4, somatic mutation, Alternate Splicings, Diagnose, Cana1, colorectal (colon or rectal) cancer, Power, Tumors, Papillary Adenomas, Therapy, screening, Carcinoma, Prostates, DmelCG1455, dl, total RNA extract, Data Set, aberrant, ribose nucleic acid, gyltl1b-b, Tissue., Arts, Intervening Sequences, Expression Profiles, ribonucleic acids, future organ, Double-Stranded, Psychological Powers, Appendix Epiploica, Diagnoses, Determinations, Caln, (Deoxyribonucleotide)n+m, l(2)01092, Gene Expression, Splicing, DmelCG9842, Alternative RNA Splicings, Benign, Postmortem, Screenings, DmelCG3629, MDDGA6, Ribonukleinsaeure, Examinations and Diagnoses, mKIAA0609, Expression Signatures, BcDNA:LP01770, pentosenucleic acids, Genetic Materials, Ribonucleic acids, simple tissue, Colorectal Cancers, Postmortem Diagnosis, IVF, desoxyribose nucleic acid, KIAA0609, Expression Profile, Omental Appendices, Genetic Material, acetylglucosaminyltransferase-like 1A, Alternate Splicing, Transcriptome Profiles, Carcinomas, Diagnoses and Examination, fg, Acid, Postmortem Diagnoses, DLL, Factors, gyltl1b, acinar cell adenoma, Prognostic, susceptibility to, mdc1d, signs, Benign Neoplasms, Appendices, whole genome, study protocol, LARGE_HUMAN, cancer of large bowel, Treatments, E(Arp), En(Arp), Intervening, DmCanA1-100B, PP2B-14D, Malignant Neoplasms, Papillary, MDC1D, dll, Alternative Splicings, poly adenylated RNA, enr, Material, COLON, ds DNA, cancer of the large bowel, Follicular Adenomas, Trabecular Adenoma, Cistron, cancer of large intestine, DNA, AGRT, Powers, other neoplasm, prostate, ATHB15, prostata, Prognostic Factor, Psychological Power, atypia, Colorectal Cancer, DNS, (Deoxyribonucleotide)n, Trabecular Adenomas, Professional Power, Transcriptome Profile, Neoplasms, Benign Neoplasm, number, adenoma, Gene, Prognostic Factors, 9930121L06Rik, CnA, Malignant, autosomal dominant, LARGE1, presence, Microcystic, Deoxyribonucleic acids, froggy, Gyltl1a, PpD33, Colorectal, colorectal cancer, method, organ field, Monomorphic, Deoxyribonucleic Acid, l(2)387, Pp2B-14DF, method used in an experiment, Mini-Exon, Alternative RNA Splicing, Gene Products, Mass, Screening, field, atypical, Antemortem, CNA, ICU4, CnnA21EF, Nested Transcripts, Microcystic Adenomas, Genetic, Malignancy, MDDGB6, Profile, posterior intestine, Double Stranded, Deoxyribonucleic acid, LARGE, Diagnoses and Examinations, Expressions, Sequencing, cancer of the large intestine, Non-Polyadenylated RNA, Neoplasias, BPFD#36, AW413465, D14, RNA Sequence Analyses, RNA Sequencing, Intron, (Deoxyribonucleotide)m, Expression, 2.7, Pp12-14D, Cancer, Sequence Analyses, Antemortem Diagnoses, RNA, findings, Transcriptome, Malignant Neoplasm, AI841391, DmPp2B-14D, RNA Sequence Determinations, Basal Cell, DNAn+1, Proteins, RNS, defective, Factor, Cistrons, Cell, Examination and Diagnoses, hindgut, Splicings, development, Sequences, RNA Splicings, CanA14D, read, count in organism, CNA1, Intervening Sequence, D33, MT, Mass Screenings, Sequence, male prostate, yeast nucleic acid, pMY4, Protein, Gene Expression Signatures, Trabecular, Neoplasm, Can, Professional, CRC, Gene Expression Signature, ds-DNA, Nested Transcript, large bowel cancer, ribonucleic acid, PP2B 21EF, primary cancer, CORONA, Nested, exonic region, Mini-Exons, Non Polyadenylated RNA, Colorectal Carcinoma, Monomorphic Adenoma, postnatal growth, Non-Polyadenylated, F5F19.21, Exon, INSDC_qualifier:unknown, Cancers, Ribonucleic Acid, Omental, malignant tumor, PpD14, Alternate, Protein Gene Products, plan specification, Gene Proteins, F5F19_21, Personal Power, PP2B 14D, colon cancer, Snm1l, like-glycosyltransferase, Therapeutic, Papillary Adenoma, Gene Expression Profiles, RNA Sequence Analysis, Power (Psychology), cardinality, Desoxyribonukleinsaeure, Alternative RNA, Treatment, Signature, growth, Neoplasia, glycosyltransferase-like protein LARGE1"],"additional_accession":[]},"is_claimable":false,"name":"Colorectal adenomas, carcinomas and adjacent normal NKI-AvL TGO series NGS-ProToCol","description":"Cancer is caused by changes in the genome of cells, resulting in aberrant transcripts and proteins. In order to understand why normal cells become cancer cells and how we can identify and destroy them, the CTMM-NGS-ProToCol project aimed to understand prostate and colorectal cancer through DNA and RNA molecular profiling, to further improve diagnosis, prognosis and treatment.The state-of-the-art within the field of genome sequencing makes it possible to identify all the modifications in our genome that encode for RNA and of the transcripts themselves. The latest development in RNA sequencing is that if one does not select for polyA RNA, but first removes rRNA from the total RNA and then performs ‘random’ RNA sequencing, 30-60% of the reads are intronic. Since about 40% of the genome consists of genes (and only 1.6% is exonic), deep RNA sequencing will cover not only the exons, but also a large portion of the introns and therefore much of the genome. The power of the combined sequencing of genome and transcriptome is the full view of copy number aberrations (CNA), exon mutations and the consequence and relevance of the mutations at the RNA level in the form of differential gene expression, alternative splicing, alternative promoter usage, novel transcripts, fusion transcripts, read-through transcripts and mutations. For the colorectal (tumor) tissue dataset, we applied molecular profiling to 30 colorectal adenomas, 30 colorectal carcinomas and 18 normal adjacent colon tissues.","dates":{"updated":"2024-07-23 11:10:03"},"accession":"EGAS00001002854","cross_references":{"TAXONOMY":["9606"],"EGA":["EGAD00001004094","EGAD00001004057","EGAD00001004093","EGAD00001004055","EGAD00001004056","EGAD00001004092","EGAC00001001051"]}}