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Single Cell Sequencing of Sperm (scSperm)

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.Project 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.Altogether, 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.

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Studies are experimental investigations of a particular phenomenon, e.g., case-control studies on a particular trait or cancer research projects reporting matching cancer normal genomes from patients.

Study ID Study Title Study Type
EGAS00001000935 Population Genomics

This table displays only public information pertaining to the files in the dataset. If you wish to access this dataset, please submit a request. If you already have access to these data files, please consult the download documentation.

ID File Type Size Located in
EGAF00000722607 cram 20.9 GB
EGAF00000722608 cram 17.9 GB
EGAF00000722609 cram 18.6 GB
EGAF00000722610 cram 19.9 GB
EGAF00000722962 cram 20.3 GB
EGAF00000722963 cram 18.1 GB
EGAF00000722964 cram 21.1 GB
EGAF00000722965 cram 15.3 GB
EGAF00000722966 cram 21.9 GB
EGAF00000722967 cram 21.1 GB
EGAF00000722968 cram 20.6 GB
EGAF00000722969 cram 22.0 GB
EGAF00000722970 cram 20.4 GB
EGAF00000722971 cram 20.5 GB
EGAF00000722972 cram 20.3 GB
EGAF00000722973 cram 19.1 GB
EGAF00000722974 cram 22.2 GB
EGAF00000722975 cram 21.2 GB
EGAF00000722976 cram 21.7 GB
EGAF00000722977 cram 19.9 GB
EGAF00000722978 cram 19.9 GB
EGAF00000722979 cram 20.0 GB
EGAF00000722980 cram 16.0 GB
EGAF00000722981 cram 23.3 GB
EGAF00000830458 cram 7.4 GB
EGAF00000830459 cram 7.2 GB
EGAF00000830460 cram 7.3 GB
EGAF00000830461 cram 7.1 GB
EGAF00000830462 cram 7.5 GB
EGAF00000830463 cram 7.2 GB
EGAF00000830464 cram 7.4 GB
EGAF00000830465 cram 7.2 GB
EGAF00000830466 cram 7.4 GB
EGAF00000830467 cram 7.2 GB
EGAF00000830468 cram 7.3 GB
EGAF00000830469 cram 7.1 GB
EGAF00000830470 cram 7.3 GB
EGAF00000830471 cram 7.1 GB
EGAF00000830472 cram 7.0 GB
EGAF00000830473 cram 6.8 GB
40 Files (597.4 GB)