{"database":"EGA","file_versions":[],"scores":null,"additional":{"omics_type":["Genomics"],"technology_type":["Illumina HiSeq 2000"],"study_type":["Population Genomics"],"full_dataset_link":["https://ega-archive.org/studies/EGAS00001000935"],"host":["EGA"],"description":["EGA study EGAS00001000935"],"dataset_title":["Single Cell Sequencing of Sperm (scSperm)"],"repository":["EGA"],"category":["restricted"],"name_synonyms":["X-Chromosome-Bearing Sperm, sperm cell, Y-Chromosome-Bearing, X-Chromosome-Bearing, X-Bearing Sperm, Sperm, X-Bearing, ejaculate., X-Bearing Sperms, Y-Chromosome-Bearing Sperm, spermatozoid, X Bearing Sperm, X-Chromosome-Bearing Sperms, spermatozoon, seminal fluid, Y Chromosome Bearing Sperm, Y-Bearing Sperms, Y-Bearing Sperm, sperm, X Chromosome Bearing Sperm, Sperms, Y-Chromosome-Bearing Sperms, Spermatozoon, SPERM, Y-Bearing, Y Bearing Sperm"],"description_synonyms":["HSN1E, multiple endocrine neoplasia syndrome, prostate fluid, Aging, Mutation Frequency, CG11121, Mutations, dmTAF[[II]]230, old, Biological, GRP1, Grp1, Mutation Frequencies, X-Chromosome-Bearing Sperm, Senescence, sperm cell, X-Bearing, thymus nucleic acid, TFIID TAF250, Genomes, cel, PTPSTEP, Boys, SO, Core Genome., Y Chromosome Bearing Sperm, Biological Aging, Y-Bearing Sperm, X Chromosome Bearing Sperm, ELL1, l(2)k08110, Y-Chromosome-Bearing Sperms, Ell1, sample, Double-Stranded DNA, deoxyribonucleic acids, DNAn, Frequency, CXXC finger protein 9, So, GPH, ejaculate, Y-Chromosome-Bearing, dTAF[[II]]230, Multiple endocrine neoplasms, DmelCG10120, TAF200, Double-Stranded, TAFII-250, TAF250/230, familial endocrine, (Deoxyribonucleotide)n+m, TAFII250, Seminal Plasma, Frequencies, 3.1.3.48, multiple endocrine adenomatosis, desoxyribose nucleic acid, ADCADN, X-Chromosome-Bearing, UNQ203/PRO229, Step, CG11628, DNA (cytosine-5-)-methyltransferase 1, Adenomatosis, Striatum-enriched protein-tyrosine phosphatase, CG17603, spermatozoid, TAF[[II]], X Bearing Sperm, seminal fluid, Endocrine neoplasia, multiple, Taf250, STEP, C19orf17, SR3-5, Sperms, ds DNA, anon-WO0118547.278, DNA, multiple endocrine neoplasia syndrome(s), Mdh-NADP, TAF230, Sperm, d230, DNS, GRP1/cytohesin 1, (Deoxyribonucleotide)n, men syndromes, Multiple endocrine neoplasia, dTAFII250, Y-Chromosome-Bearing Sperm, EfW1, Deoxyribonucleic acids, CG11633, cytohesin/GRP1, Aim, AIM, Rate, Deoxyribonucleic Acid, DmelCG11121, dmTAF1, Taf230, Core Genome, Spermatozoon, Y Bearing Sperm, TAF250, DNMT1, Taf200, somda, dTAF[[II]]250, DNMT1_HUMAN, cell, Accessory Genome, l(2)SH2 0323, multiple endocrine neoplasia, Double Stranded, Taf1p, Deoxyribonucleic acid, X-Bearing Sperms, Outlines, Genotypes, X-Chromosome-Bearing Sperms, API6, dTAF250, prostatic fluid, men syndrome, Neural-specific protein-tyrosine phosphatase, sperm, SPERM, (Deoxyribonucleotide)m, TAF, DNA MTase HsaI, Drl, DNA (cytosine-5)-methyltransferase 1, X-Bearing Sperm, TAF[[II]]250, DNAn+1, Multiple Endocrine Neoplasia, MDH, DNMT, l(3)84Ab, stepk, BG:DS00004.13, ME, MCMT, Pangenome, Cell, spermatozoon, Mdu, dTAF230, Genogroup, mda, p230, DNA methyltransferase HsaI, Familial endocrine adenomatosis, Mutation Rates, sequence, TAF[[II]]250/230, TFIID, MEN, Men, ds-DNA, Me, Y-Bearing, l(2)SH0323, Mutation, ami, CXXC9, CYH1, Plasma, Taf[[II]]250, Rates, TAF[[II]]230, CT-2, med, mem, TAF[II]250, men, CXXC-type zinc finger protein 9, primary structure of sequence macromolecule, sample population, DmelCG11628, Genogroups, Y-Bearing Sperms, PPP1R68, Pan-genome, DmelCG17603, Desoxyribonukleinsaeure, Multiple endocrine adenomatosis, Seminal, CLEC2C, m.HsaI, CG10120, TAF1"],"additional_accession":[]},"is_claimable":false,"name":"Single Cell Sequencing of Sperm  scSperm ","description":"The aim of this project is to genotype and sequence single spermatozoa from two men, one in his twenties and the other in his seventies. The resulting data is used to quantify the mutations that have arisen in the gametes of both individuals in order to better understand the effect of aging on mutation rates and modes.\n\nProject Outline. In order to quantify mutations, semen from two individuals are sequenced. 48 single sperm cells are isolated from each individual, and their DNA is extracted. The resulting genomes are amplified using PicoPlex, GenomiPhi MDA, Repli-G MDA, and MALBAC. QC step is applied to check the quality of WGA DNA using standard Sequenom plex (26 SNPs). A subset of 32 amplification products which pass the intiall QC, are genotyped using Affymetrix SNP6 chips. 12 of the genotyped amplification products are also sequenced. In addition, one multi-cell sample per individual is sequenced as a reference and for validation purposes.\n\nAltogether, 12 single cell sperm genomes and two multi-cell genomes are sequenced, coming to a total of 14 genomes. Of the single cell sperm genomes, 2 are sequenced to 50x coverage, and the other 10 to 25x coverage. Both multi-cell genomes are sequenced to 25x coverage.","dates":{"updated":"2017-07-26 15:39:25"},"accession":"EGAS00001000935","cross_references":{"TAXONOMY":["9606"],"EGA":["EGAD00001001216","EGAC00001000205"]}}