{"database":"EGA","file_versions":[],"scores":null,"additional":{"omics_type":["Genomics"],"dataset_type":["Illumina HiSeq 2500;ILLUMINA"],"full_dataset_link":["https://ega-archive.org/datasets/EGAD00001004062"],"sample_count":["198"],"description":["EGA dataset EGAD00001004062"],"repository":["EGA"],"title":["Whole genome sequencing of 198 epileptic individuals."],"name_synonyms":["Vasp, VASP, DmelCG15112, ENHANCER OF ATNSI ACTIVITY, Data Set, MENA, NDPP1, l(2)02029, Enb, enb, ENA, Ena, CG15112, 2018., ENA/VASP"],"description_synonyms":["biotin--protein ligase activity, chemical properties, BamF, biml, determination, methionine aminopeptidase activity, BamC, [X]Other epilepsy (disorder), Epilectic attack, Sepharose C1 4B, Seizure disorder (disorder), Biotin apo-protein ligase, bam, instrument configuration, Epilepsy (disorder), Xkl-1, biotin-acetyl-CoA carboxylase synthetase, ran, prevention, Long Term, KL receptor activity, unspecified, ranGap, ranGAP, Gsfsco1, B37, Hominids, SCO5, rbm9a, rbm9b, 2, SCO1, Software Engineering, Epileptic attack, Polymerase Chain, AAF30287, DmelCG10422, Gsfsow3, Gsfsco5, prevention and control, Effect, Computer Program, peptidase M activity, SOW3, RTA, GPR168, DmelCG9999, adenomas, average, Other forms of epilepsy and recurrent seizures, Sepharose, hnrbp2, rabGAPLP, thymus nucleic acid, rangap, biotin-acetyl-CoA-carboxylase ligase activity, L-methionine aminopeptidase activity, Biotin--[propionyl-CoA-carboxylase [ATP-hydrolyzing]] ligase, reference sample, Genomes, HCAP, Epileptic seizure, entire life cycle, rbfox2-a, Open, SD, Inverse Polymerase Chain Reaction, Computer Programs and Programming, nucleic acid library preparation, HardwareType, RabGAP-5, biotin:apocarboxylase ligase activity, W, CDLS3, free, Fast, rta, Biotin--[acetyl-CoA-carboxylase] ligase, preventive measures, C1 4B, Generalized seizure, scientific observation, Hominin, RUSC3, Reaction, rbm9-b, BMH., rbm9-a, Bs, Sd, Other forms of epilepsy NOS (disorder), Double-Stranded DNA, deoxyribonucleic acids, homozygous 2P16 deletion syndrome, DNAn, ran-1, Natriumhydroxid, hydroxyde de sodium, Sl, Long-Term Effects, FAST, Hominid, Anchored Polymerase Chain Reaction, preventive therapy, Generalized seizure (finding), chemical characterization, acetyl CoA holocarboxylase synthetase activity, HRS, Data Set, Epileptic seizures, CT28175, Other forms of epilepsy (disorder), CYC, 4B, homozygous 2P21 deletion syndrome, MYH-associated polyposis, Genome Sequencing, Longterm Effect, autosomal recessive familial adenomatous polyposis, Maps, Tr-kit, ham, FASTK, Epileptic fits, Double-Stranded, HSC, Fox-2, CG14670, Source Softwares, xran, Software Tools, Programs, (Deoxyribonucleotide)n+m, NOD, PBT, Program, Computer Applications, Epileptic disorder, Complete Genome, [4)-3, Computer Applications Software, Sepharose C1, Computer Applications Softwares, kl1-A, NOS, EPILEPSY NOS W INTR EPIL, Softwares, KIT, seizure disorder, desoxyribose nucleic acid, HCS, END, PCR, Rasl2-8, autosomal recessive, tyrosine-protein kinase Kit, pbt, RUTBC3, xrbm9, biotin holoenzyme synthetase activity, Software Applications, NaOH, Nested Polymerase Chain Reaction, instrument, Source Software, life, whole genome, kit, alpha, chemical content, sodium hydrate, hcs, HiSeq 2500, dRanGAP, polymerase chain reaction, RABGAP5, Biotin--[methylcrotonoyl-CoA-carboxylase] ligase, without mention of intractable epilepsy, Applications, Epilepsy NOS, dJ106I20.3, Epileptic, BIM, ds DNA, multiple colorectal, Sepharose 4B, acetyl coenzyme A holocarboxylase synthetase activity, GPR140, SMC3L1, CG9999, 6.3.4.-, DNA, humans, krk1, Computer Software Applications, 6.3.4.9, lifespan, bim, DNS, (Deoxyribonucleotide)n, Effects, Generalized fit, with intractable epilepsy, STK10, SCF receptor activity, dran, Polymerase Chain Reactions, Computer, Inverse, Hominini, aligned, Seizure disorder, Other forms of epilepsy, Deoxyribonucleic acids, ara24, gDNA, hardware, Buffer, RanGAP, fs(3)neo61, Apes, CG10422, HRNBP2, Inverse PCR, Sd-RanGAP, Sd-RanGap, 6.3.4.11, Deoxyribonucleic Acid, scfr, 6.3.4.10, DmelCG1404, Homo, bim-beta7, 6.3.4.15, Epileptic Seizure, Epileptic seizure (finding), SCFR, familial adenomatous polyposis, EP - Epilepsy, Application, MAP, Other forms of epilepsy NOS, Open Source Softwares, FOX2, D12S755E, Fdc, Complete, Whole Genome, Longterm, entire lifespan, bim-beta6, Software Application, familial adenomatous polyposis 2, Complete Genome Sequencing, nucleic acid library construction, Open Source Software, Double Stranded, Pongidae, Deoxyribonucleic acid, HNRBP2, soude caustique, Long-Term, Sequencing, Epileptic fit, Computer Software Application, MRGF, Hominins, autosomal recessive multiple colorectal adenomas, fox-2, Tools, ATP:Fas-activated serine/threonine protein phosphotransferase activity, Whole, Agarose, rbfox2, Generalised convulsion, hrnbp2, NEST:bs27h05, fox2, Long-Term Effect, (Deoxyribonucleotide)m, Anchored PCR, EF - Epileptic fit, CSPG6, Generalised fit, 6-An-alpha-L-Galp-(1->3)-beta-D-Galp-(1->]n, chemical structure, biotin-acetyl coenzyme A carboxylase synthetase activity, C21orf120, HHT1, Epileptic convulsions, chemical composition, Controlled, epilepsy, Applications Software, measuring, proto-oncogene c-Kit, Open Source, Controlling, biotin:apo-acetyl-CoA:carbon-dioxide ligase (ADP-forming) ligase (AMP-forming), Computer Software, MUTYH-Associated Polyposis, Edg, biotin--[acetyl-CoA carboxylase] synthetase activity, Biotin--[methylmalonyl-CoA-carboxytransferase] ligase, DNAn+1, ran10A, DRPLA, aligned to, BOD, RBM9, buffer, Homininus, gsp1, OK/SW-cl.81, CG1404, Tool, TC4, tc4, Software Tool, rbm9, KIT ligand receptor activity, EPILEP NEC W/O INTR EPIL, chemical analysis, Long Term Effects, caustic soda, DmelCG14670, high content screening, bod, ds-DNA, soda lye, Fxh, Software, Library, bimel, [X]Other epilepsy, XKrk1, EPILEPSY NEC W INTR EPIL, Anchored, c-KIT, l(1)G0075, Epilepsy, Reactions, Nested, ARA24, library construction, prophylaxis, RanGap1, Engineering, fxh, CD117, MYH-Associated Polyposis, Epilepsy NOS (disorder), Epilepsy and recurrent seizures, EPILEP NOS W/O INTR EPIL, acetyl-CoA carboxylase biotin holoenzyme synthetase activity, Longterm Effects, Computer Programs, THC4, c-kit, Holocarboxylase synthetase, Generalized convulsion, Applications Softwares, C-Kit, control, Bam-C, Ssm, BAM, Generalised seizure, Gsp1, Bam, Desoxyribonukleinsaeure, xkl-1, Nested PCR, Aetznatron, MAP syndrome, assay, Ape, ORW1, Scl, formerly, PRED81, FAP2, Ran, colorectal adenomatous polyposis"],"additional_accession":[]},"is_claimable":false,"name":"ena-DATASET-CRCHUM-28-03-2018-14:35:08:309-2886 - samples","description":"This dataset includes whole genome sequencing of 198 epileptic individuals.\n\nLibraries preparation and whole-genome sequencing: gDNA was cleaned up using ZR-96 DNA Clean & ConcentratorTM-5 Kit (Zymo) prior to being quantified using the Quant-iTTM PicoGreen dsDNA Assay Kit (Life Technologies) and its integrity assessed on agarose gels. Libraries were generated using the TruSeq DNA PCR-Free Library Preparation Kit (Illumina) according to the manufacturer’s recommendations. Libraries were quantified using the Quant-iTTM PicoGreen dsDNA Assay Kit (Life Technologies) and the Kapa Illumina GA with Revised Primers-SYBR Fast Universal kit (Kapa Biosystems). Average size fragment was determined using a LabChip GX (PerkinElmer) instrument. The libraries were denatured in 0.05N NaOH and diluted to 8pM using HT1 buffer. The clustering was done on a Illumina cBot and the flowcell was ran on a HiSeq 2500 for 2x125 cycles (paired-end mode) using v4 chemistry and following the manufacturer's instructions. A phiX library was used as a control and mixed with libraries at 0.01 level.\n\nBioinformatics: The Illumina control software was HCS 2.2.58, the real-time analysis program was RTA v. 1.18.64. Program bcl2fastq v1.8.4 was used to demultiplex samples and generate fastq reads. The filtered reads were aligned to reference Homo_sapiens assembly b37. Each readset was aligned to creates a Binary Alignment Map file (.bam).","dates":{"updated":"2020-07-16 15:33:08"},"accession":"EGAD00001004062","cross_references":{"TAXONOMY":["9606"],"EGA":["EGAC00001000827","EGAS00001002825"]}}