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Series GSE136603 Query DataSets for GSE136603
Status Public on Aug 30, 2019
Title Severe sperm acrosome overgrowth and infertility in mice lacking chromosome 18 pachytene piRNA
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary Purpose: piRNAs are a class of germline-specific, small non-coding RNAs required to maintain genome integrity and preserve RNA homeostasis essential for male gametogenesis. During mouse spermatogenesis, male germ cells transcribe piRNAs at pre-pachytene anad pachytene stages of development from genetically distince loci. The most well-studied and conserved function of pre-pachytene piRNAs is repression of transposons to ensure the integrity of the germline genome. In contrast to pre-pachytene piRNAs, the mode of action and function of pachytene piRNA is much less understood. To investigate and characterize the functional importance of pachytene piRNAs in spermatogenesis and male fertility, we have used CRISPR/Cas9 and established mutant mice which have deleted a bi-directional promoter of the pachytene piRNA cluster on Chr18. Mutant mice have a male sterile phenotype with acrosome overgrowth and defective motility.
 
Overall design Methods: Testes mRNA and ncRNA profiles of P28 wild-type (+/+), heterozygous (+/-), and homozygous (-/-) mice were generated by deep sequencing , in triplicate, using Illumina's TruSeq Stranded Total RNA kit with Ribo-Zero following the manufacturer instruction. The fragment size of RNAseq libraries was verified using the Agilent 2100 Bioanalyzer and the concentrations were determined using Qubit instrument. The libraries were loaded onto the Illumina Hiseq 3000 for 2X50 bp paired end read sequencing. The fastq files were generated using the bcl2fastq software for further analysis.
 
Contributor(s) Choi H, Palmer CD, Dean J
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Submission date Aug 29, 2019
Last update date Sep 01, 2019
Contact name Heejin Choi
E-mail(s) choih5@nih.gov
Phone 3015941405
Organization name NIH
Street address 50 South drive, Building 50, Room 3131
City Bethesda
State/province Maryland
ZIP/Postal code 20892
Country USA
 
Platforms (2)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
GPL21493 Illumina HiSeq 3000 (Mus musculus)
Samples (15)
GSM4052565 Chr18+/+ ssRNA-seq (HC3802-1)
GSM4052566 Chr18+/+ ssRNA-seq (HC3802-2)
GSM4052567 Chr18+/+ ssRNA-seq (HC3802-3)
Relations
BioProject PRJNA562845
SRA SRP219704

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE136603_RAW.tar 35.2 Mb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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