{"database":"EGA","file_versions":[],"scores":null,"additional":{"omics_type":["Genomics"],"study_type":["Other"],"full_dataset_link":["https://ega-archive.org/studies/EGAS00001004410"],"host":["EGA"],"description":["EGA study EGAS00001004410"],"dataset_title":["RNA-seq of high grade serous ovarian tumours","WGS of high grade serous ovarian tumours and matched blood normals"],"category":["restricted"],"repository":["EGA"],"name_synonyms":["grade 3/4, malignant ovarian serous tumour, serous ovarian cancer., high grade"],"description_synonyms":["Formol, dp53, WIT-2, ran, EWS-WT1, Personal, KL receptor activity, Immunogold-Silver Techniques, domestic cat, Domestic Cats, Methanal, Parafilm, bbl, GRP1, Grp1, SCO5, DGS, SCO1, 2-amino-3-mercaptopropanoic acid, Gsfsow3, 2210418N07, bacterial catalase-peroxidase activity, DmelCG9999, Multicase, C, thymus nucleic acid, BCC7, CT21282, M, N, PTPSTEP, beta-Tub6D, Tissue, dmp53, Oxomethane, T, 1422/04, W, haem catalase activity, Immunogold-Silver Technic, Dp53, sample, Immunolabeling Technique, CT, Bs, ran-1, CG17117, RG7MT1, Histological Labeling, p50/tubulin, GPH, AI315345, CG10873, equilase activity, subdivided, Ct, Immunogold Technique, A330009E03Rik, xran, PBT, Immunolabeling Technic, Stickstoff, Felis domestica, Immunolabeling Technics, Methionin, simple tissue, bfy, Technics, Hmet, desoxyribose nucleic acid, (2R)-2-amino-3-sulfanylpropanoic acid, HTH, Hth, forked, HGF/SF receptor, ACGNAT, pbt, divided, CG11628, nephroblastoma, CG3401, beta3Tub, beta3TUB, Immunogold Silver Techniques, Records as Topic, Striatum-enriched protein-tyrosine phosphatase, hCMT1c, Controls, septate, c-Met, study protocol, Felis sylvestris catus, dRanGAP, CG1106, DTB3, nitrogen, Identification Systems, ds DNA, Personal Identification System, bhy, WT1, wt1, DNA, DROCATHPO, CG31325, bs36h11.y1, krk1, beta[[3]]-Tub, Immunogold-Silver, DmelCG17117, l(1)VE614, 2-amino-4-(methylsulfanyl)butanoic acid, DNS, GRP1/cytohesin 1, (Deoxyribonucleotide)n, AWT1, L-Zystein, dran, 143391_i_at, GUD, beta3 TU, LFS1, WAGR, l(3)05745, ara24, CG11633, CrAT, Sd-RanGAP, Sd-RanGap, manganese catalase activity, Deoxyribonucleic Acid, Documents, anon-EST:Liang-2.13, RCCP2, Technique, Immunogold Silver Technics, xwt1, F15E12_6, anatomical systems, xWT1, Academic, scatter factor receptor, E-920, Double Stranded, Deoxyribonucleic acid, Hcys, kf, DmelCG6871, 2-amino-4-(methylthio)butanoic acid, Quality Controls, Formalin, CYSTEINE, FREE CYSTEINE, (Deoxyribonucleotide)m, beta[[3]]-tubulin, wt-1, (2R)-2-amino-3-mercaptopropanoic acid, metionina, proto-oncogene c-Kit, DMCATHPO, Dmbeta3, whole blood, heme catalase activity, Immunogold Technic, Laboratory., DNAn+1, prac, beta3t, ran10A, Immunohistocytochemistry, stepk, Personal Identification Systems, Stainings, Faces, KIT ligand receptor activity, p53/tubulin, Felis domesticus, Met, MET, ATCMPG1, ATCMPG2, XKrk1, Immunolabeling, CS1, CG33336, Immunocytochemistry, Peripheral Blood, RanGap1, tyrosine-protein kinase Met, D-p53, WT33, Dm-P53, (R)-2-amino-3-mercaptopropanoic acid, CG6871, azote, beta3, CD117, Record, dtl, 2-Amino-3-mercaptopropionic acid, DmelCG11628, Reticuloendothelial System, Tub, plan specification, Oxomethylene, C-Kit, betatub60D, Ssm, Desoxyribonukleinsaeure, Immunogold-Silver Technics, xkl-1, Immunolabeling Techniques, E920, biopsy, 5730455C01Rik, E 920, Hgfr, Blood, 5730555F13Rik, Domestic Cat, Cs-1, Imaging, Xkl-1, clefted, Technic, betaTub3, Tp53, Cut, Techniques, ranGap, ranGAP, Gsfsco1, DMP53, l(1)7Ba, HGFR, l(1)7Bb, Immunogold-Silver Technique, Dmp53, Cystein, cytopathology, AAF30287, Gsfsco5, SOW3, 1323/07, rangap, MUB3_18, cisteina, Formaldehyd, SD, Records as Topics, DmP53, Domestic, MUB3.18, Travel Documents, CG11387, B3t, DmelCG3401, DmelCG1106, l(2)k08110, Pathologies, Sd, Double-Stranded DNA, deoxyribonucleic acids, DNAn, Sl, Racemethionine, Immunogold Technics, catalase-peroxidase activity, proto-oncogene c-Met, CT28175, PRO, 2-Amino-4-(methylthio)butyric acid, Tr-kit, Labeling and Staining, Double-Stranded, 2.3.1.7, 9130215G10Rik, CYS, Cys, AI195249, (Deoxyribonucleotide)n+m, 3t, Immunogold, Immunogold Techniques, catalase reaction, 3.1.3.48, kl1-A, BcDNA:GH10590, KIT, fixed, and GLY protein 2, GAT, Tub60D, Rasl2-8, HGF receptor, tyrosine-protein kinase Kit, beta-tub, and GLY protein 1, histopathology, Review, Step, DmelCG33336, hydrogen-peroxide:hydrogen-peroxide oxidoreductase activity, Control, Quality, kit, Felis silvestris catus, L-Cystein, hth1, Labelings, hth2, Patient, STEP, PBMCs, P53, Travel, p44, CG9999, Review of Reported Cases, 7N, U00145, betaTub, Cas1, Carnitine acetylase, p50, p53, Histological Labelings, SCF receptor activity, Deoxyribonucleic acids, RanGAP, cytohesin/GRP1, method, HGF, scfr, DmelCG1404, PBMC, method used in an experiment, Histological, F15E12.6, caperase activity, SCFR, study, Fdc, XWT1a, XWT1b, Staining, clone 2.13, D.m.BETA-60D, gel, l(2)SH2 0323, CatA, CATA, AUTS9, Cats, Trp53, Neural-specific protein-tyrosine phosphatase, DmelCG11387, Catl, Clients, betaTub60C, beta3-tubulin, cats, liquid, TRP53, AI838057, beta-Tub60D, WGS, Dm-HTH, DL-Methionine, Felis catus, BETA 60D, beta3-Tub, Client, Labeling, Carnitine acetyltransferase, gsp1, OK/SW-cl.81, Xp53, CG1404, TC4, tc4, Review Literature, FORMALIN, ds-DNA, beta[[3]] tubulin, Cat, CAT, l(2)SH0323, Zystein, XeWT1, optidase activity, CYH1, c-KIT, Cas-1, l(1)G0075, ARA24, 2-amino-3-sulfanylpropanoic acid, beta60C, L-2-Amino-3-mercaptopropionic acid, l(3)86Ca, cat, sample population, Methylene oxide, nitrogeno, requirements, Meis1, c-kit, Cat01, Gsp1, alpha-amino-gamma-methylmercaptobutyric acid, Par4, NPHS4, Scl, SF receptor, Ran"],"additional_accession":[]},"is_claimable":false,"name":"Scottish High Grade Serous Ovarian Cancer","description":"Scottish HGSOC samples were collected via local Bioresource facilities at Edinburgh, Glasgow, Dundee and Aberdeen and stored in liquid Nitrogen until required. HGSOC patients were determined from pathology records and were included in the study where there was matched tumour and whole blood samples. On receipt of tumour material the tumour was processed as follows: firstly, the tumour sample was divided into two for DNA and RNA extraction. Slivers of tissue were cut from the front and rear faces of the DNA sample, then fixed in formalin and embedded in paraffin wax. Sections from the front and rear tissues from all samples were examined by H&E staining supplemented by WT1/p53 immunohistochemistry if required. Following pathology review, samples were only included if they met the following criteria: they were confirmed as HGSOC and there was greater than 40% tumour cellularity throughout the tumour, determined using the H&E sections. Somatic DNA was extracted using the Qiagen DNeasy Blood and tissue kit (cat no 69504). The tissue was initially homogenised using a Qiagen Bioruptor, followed by the manufacturers recommended protocol (including RNase digestion step). Germline DNA was extracted from 1-3ml whole blood using the Qiagen FlexiGene kit (cat no 51206) following the manufacturers recommended protocol. The resulting DNA underwent quality control as follows: firstly, A260 and A280nm were measured on a Denovix DS-11 Fx to qualitatively illustrate A260/280nm and A260/230nm ratios as surrogate measures of DNA purity. A260/280 had to be 1.8 or greater and A260/230 had to be 2.0 or greater. Then, DNA was quantified using LifeTechnologies Qubit dsDNA BR kit (cat no Q32850) and we required a minimum of 50ul at 25ng/ul for WGS. Thirdly, DNA was diluted to 25ng/ul and a representative sample was loaded onto a 0.8% TAE gel, ran at 100v for 60mins and then imaged using a BioRad ChemiDoc imaging system to visualise the DNA quality. Only when all 4 quality control requirements were satisfied was the DNA sequenced. The DNA was sequenced at the Glasgow Precision Oncology Laboratories.","dates":{"updated":"2024-02-27 10:57:27"},"accession":"EGAS00001004410","cross_references":{"TAXONOMY":["9606"],"EGA":["EGAD00001009048","EGAD00001010135","EGAD00001010139","EGAD00001009049","EGAC00001001588"]}}