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Series GSE62874 Query DataSets for GSE62874
Status Public on Jul 08, 2015
Title The Partitioning of RNAs in sperm
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary A diverse pool of RNAs remain encapsulated within the transcriptionally and translationally silent spermatozoon. These transcripts persist within the male gamete despite the dramatic reduction in cellular volume achieved through expulsion of the cytoplasm and quite possibly the nucleoplasm. The precise location of RNAs retained within the sperm cell remains largely unknown. However, early evidence suggested that many are embedded within the nucleus (1). To discern the global pattern of transcript compartmentalization in sperm, total RNA was extracted from whole mouse spermatozoa and detergent demembranated nuclei fractionated through a sucrose gradient. Isolated RNAs were subjected to RNA-sequencing (RNA-seq) and their abundance used to infer localization. Transcripts enriched in the unfractionated cells were related to the production and function of mitochondria and surprisingly, exosomes. The absence of these extracellular vesicles associated RNAs within the inner-nuclear compartment was suggestive of an origin other than sperm. This contributes to the growing evidence for sperm-bound exosomes rich in RNA. In comparison, the majority of the remaining sperm RNAs were associated with the nucleus. This included the abundant fragmented ribosomal transcripts which likely persist between the nuclear envelope and the perinuclear theca. The spermatozoal inner-nuclear compartment was also enriched in repetitive transcribed sequences. This included LINE elements and simple repeat sequences both of which have been shown to contribute to chromatin structure in other cell types suggesting that they may serve parallel roles in the spermatozoon.
Overall design RNA-seq analysis of whole mouse sperm and fractionated nuclei
Contributor(s) Johnson GD, Krawet SA
Citation(s) 26071953, 26224537
Submission date Oct 30, 2014
Last update date May 15, 2019
Contact name Graham Johnson
Organization name WSUSOM
Department CMMG
Lab Krawetz
Street address 275 E. Hancock
City Detroit
State/province Michigan
ZIP/Postal code 48201
Country USA
Platforms (1)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
Samples (6)
GSM1535340 nuc1_run1
GSM1535341 nuc2_run1
GSM1535342 whole_run1
BioProject PRJNA265872
SRA SRP049420

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Supplementary file Size Download File type/resource
GSE62874_Genomic_Coordinates_of_Novel_Transcripts.txt.gz 28.0 Kb (ftp)(http) TXT
GSE62874_adj_w_subcount.txt.gz 90.1 Kb (ftp)(http) TXT
GSE62874_nuc1_subcount.txt.gz 97.7 Kb (ftp)(http) TXT
GSE62874_nuc2_subcount.txt.gz 95.5 Kb (ftp)(http) TXT
GSE62874_unadjusted_RPKMs.txt.gz 454.2 Kb (ftp)(http) TXT
GSE62874_w_subcount.txt.gz 99.4 Kb (ftp)(http) TXT
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