{"database":"EGA","file_versions":[],"scores":null,"additional":{"omics_type":["Genomics"],"study_type":["Transcriptome Analysis"],"full_dataset_link":["https://ega-archive.org/studies/EGAS00001006044"],"host":["EGA"],"description":["EGA study EGAS00001006044"],"dataset_title":["PPGL RNA-Seq dataset"],"repository":["EGA"],"category":["restricted"],"name_synonyms":["Gene Expression, Transcriptome, Expression Signature, Transcriptome Profile, Gene Expression Profiles, Transcriptome Profiles., Expression Signatures, Profile, Gene Expression Signatures, Expression Profiles, Transcriptomes, Gene Expression Profile, Gene, Gene Expression Signature, Profiles, Signature, Expression Profile, Signatures"],"description_synonyms":["Ribonucleic, DmelCG9412, AU023367, determination, PreP, fond, Xkl-1, CycEI, AA410010, Probes, Long Term, 1B1, anon-EST:Posey9, KL receptor activity, Gsfsco1, cDNA library construction, Ccne, Pop, SCO5, SCO1, Software Engineering, Polymerase Chain, Gsfsow3, Gsfsco5, CG18546, Effect, Non Polyadenylated, Computer Program, RNA Gene Products, SOW3, multicellular organismal biosynthetic process, single-organism biosynthetic process, me75, availability, Polyadenylated Messenger, Open, complementary DNA, Inverse Polymerase Chain Reaction, Computer Programs and Programming, nucleic acid library preparation, cg9412, W, D17Mit170, T1, mRNA-seq, PrEP, Reaction, Therapies, Bs, cDNA Probes, s, PI4K, l(2)01103, Nucleotide, Sl, Long-Term Effects, HtsF, Add, Therapy, DNA Libraries, ADD, Anchored Polymerase Chain Reaction, total RNA extract, ribose nucleic acid, Polyadenylated, RIBA, ribonucleic acids, Longterm Effect, Tr-kit, Gene Libraries, Tl3, Cyc E, br37, anon-WO03070958.3, Tl2, Dmel_CG9325, fragmented, Source Softwares, Software Tools, add, Programs, MP-1, PBT, Program, Computer Applications, htsRC, BG:DS07108.3, Ribonukleinsaeure, CG43443, Computer Applications Software, Computer Applications Softwares, kl1-A, pentosenucleic acids, Ligature, Ribonucleic acids, median, Softwares, CG9412, KIT, l(2)05206, END, nucleotides, PCR, Polyadenylated Messenger RNA, tyrosine-protein kinase Kit, Acid, pbt, Non Polyadenylated mRNA, HTS, Hts, Software Applications, protein_coding_transcript, l(2)k06121, Nested Polymerase Chain Reaction, GLI3FL, Source Software, AI854843, cracked, add-like, AI047692, mKIAA1104, kit, study protocol, Pdn, Treatments, Non-Polyadenylated mRNA, polymerase chain reaction, Applications, Adducin, l35Dd, Computer Software Applications., MP1, Complementary DNA, Rin, RIN, DNA, rasp, PEP, Poly(A) RNA, krk1, ADD-87, cycline, Effects, fractured, DmcyclinE, Ovhts, number, SCF receptor activity, IMAGE, Gene, HtsRC, Polymerase Chain Reactions, CG9325, cycE, Computer, Inverse, presence, Xt, l(2)br37, CYCLE, cdi7, method, Inverse PCR, cyclinE, scfr, Messenger, Add-hts, method used in an experiment, Gene Products, Cdi7, CDI7, anon-WO0118547.259, l(2)k14523, l(2)00634, Low, Ovhts-RC, SCFR, Application, Open Source Softwares, flow_cell, Fdc, HTS-R1, CYCE, Longterm, Nts, DmelCG3938, Software Application, CyclE, nucleic acid library construction, 3938, Open Source Software, messenger RNA, quantseq, HTS-RC, cDNA Library, CG7004, Long-Term, DmcycE, quant-seq, Computer Software Application, Non-Polyadenylated RNA, Ligations, l(2)k05007, template RNA, dm-cycE, Tools, ROC2, Roc2, Long-Term Effect, Anchored PCR, CG34197, HHT1, QuantSeq, Applications Software, DmelCG43443, proto-oncogene c-Kit, Hts-RC, Open Source, RNA, cou, Computer Software, Edg, synthesize, D10Wsu136e, DmelCG31211, Messenger RNA, split, RNS, cDNA, Libraries, Tool, read, count in organism, Software Tool, Lr, l(2)k02514, GLI3-190, DmCycE, KIT ligand receptor activity, yeast nucleic acid, Poly(A)+ mRNA, chemical analysis, Long Term Effects, hemorrhaged, INSDC_feature:mRNA, Dmel_CG34197, DNA Library, Polyadenylated RNA, CyeE, Software, Library, Bph, XKrk1, torn, ribonucleic acid, Anchored, c-KIT, Poly(A)+ RNA, Ligatures, l(2)k02602, Reactions, Nested, mRNA, Poly(A) Tail, library construction, adducin, Non Polyadenylated RNA, Ntup1, l(2)35Dd, Engineering, Non-Polyadenylated, 2310012C15Rik, Ribonucleic Acid, CD117, CG14732, cDNA Libraries, Longterm Effects, plan specification, Computer Programs, DmelCG7004, D-CycE, c-kit, Applications Softwares, C-Kit, Therapeutic, Ssm, cardinality, xkl-1, Bra, Nested PCR, Treatment, PE, Attention Deficit Hyperactivity Disorder, assay, AI450383, ORW1, Polyadenylated mRNA, EST D, CG3938"],"additional_accession":[]},"is_claimable":false,"name":"Transcriptome Sequencing PPGL","description":"RNA library preparation of samples with RNA Integrity Number (RIN) > 5.5 (median 7.1; range 5.6-8.9) was performed as described in the TruSeq Stranded mRNA Library Prep Kit (Illumina, RS-122-2101). Briefly, 0.7-1 µg total RNA PolyA+ fraction was purified and randomly fragmented, converted to double stranded cDNA and processed through subsequent enzymatic treatments of end-repair, dA-tailing, and ligation to adapters. Adapter-ligated library was completed by PCR with Illumina PE primers. The resulting purified cDNA library was applied to an Illumina flow cell for cluster generation and sequenced on an Illumina HiSeq2500 on a 51bp single-read format following manufacturer's protocols.\ncDNA libraries from FFPE tumors and low integrity RNA’s (RIN<5.5) from FF tumors (median 2.4; range 1-5.5) but % of fragments > 200 nucleotides higher than 20% (median 57.5; range 20-96) were prepared using QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen, 015) with a UMI Second Strand Synthesis Module for QuantSeq FWD (Lexogen, 081), vendor’s protocol for low input/ low quality/ FFPE RNA using 200-500 ng of total RNA, according to availability, was used as starting material. PCR Add-on Kit for Illumina (Lexogen, 020) was used to adjust the library amplification number of cycles. Libraries were applied to an Illumina flow cell for cluster generation and sequenced on NovaSeq6000. \nImage analysis, per-cycle basecalling and quality score assignment was performed with Illumina Real Time Analysis software. Demultiplexing of BCL files to FASTQ format was performed with the bcl2fastq Software (Illumina).","dates":{"updated":"2023-01-20 12:12:21"},"accession":"EGAS00001006044","cross_references":{"TAXONOMY":["9606"],"EGA":["EGAD00001008578","EGAC00001002543"]}}