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| Status |
Public on Jan 11, 2021 |
| Title |
Single-molecule long-read sequencing reveals a conserved intact long RNA profile in sperm |
| Organisms |
Homo sapiens; Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
Sperm contributes diverse RNAs to the zygote. While sperm small RNAs have been shown to impact offspring phenotypes, our knowledge of the sperm transcriptome, especially the composition of long RNAs has been limited by the lack of sensitive, high-throughput experimental techniques that can distinguish intact RNAs from fragmented RNAs, known to abound in sperm. Here, we integrate single-molecule long-read sequencing with short-read sequencing to detect sperm intact RNAs (spiRNAs). We identify 3,440 spiRNA species in mice and 4,100 in humans. The spiRNA profile consists of both mRNAs and long non-coding RNAs, is evolutionarily conserved between mice and humans, and displays an enrichment in mRNAs encoding for ribosome. In sum, we characterize the landscape of intact long RNAs in sperm, paving the way for future studies on their biogenesis and functions. Our experimental and bioinformatics approaches can be applied to other tissues and organisms to detect intact transcripts.
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| Overall design |
We used PacBio IsoSeq and Oxford Nanopore Technologies to sequence mouse sperm and testis RNAs, as well as human sperm RNAs. We also used Illumina short reads to sequence human sperm RNAs and mouse sperm RNAs.
The Summary.MousePacBio.ONT.xlsx table contains both PacBio and ONT data for mouse:
Mouse Sperm and Testis PacBio: Summary.MousePacBio.ONT.xlsx
Mouse Sperm ONT: Summary.MousePacBio.ONT.xlsx
The following three data files are linked to the corresponding sample records:
HumanSpermPacBio: Summary.HumanPacBio.xlsx
RNAseq.HumanSperm.cauda: RNAseq.HumanSperm.cauda.salmon.sf
RNAseq.MouseSperm.cauda.adult: RNAseq.MouseSperm.cauda.adult.salmon.sf
The following three GTF files are results of our PacBio assembly. They were based on both PacBio and Illumina sequencing data:
TranscriptomeAssembly.MouseTestis.mm10.gtf
TranscriptomeAssembly.spiRNA.HumanSperm.hg38.gtf
TranscriptomeAssembly.spiRNA.MouseSperm.mm10.gtf
These three fasta files are the full-length non-chimeric (FLNC) CCS reads for downstream analysis:
SpermPacBio_FLNC.fasta
TestisPacBio_FLNC.fasta
HumanSpermPacBio_FLNC.fasta
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| |
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| Contributor(s) |
Li XZ, Au KF, Sun YH, Wang A |
| Citation(s) |
33649327 |
| NIH grant(s) |
| Grant ID |
Grant title |
Affiliation |
Name |
| K99 HD078482 |
Dissect the piRNA regulatory mechanism during spermatogenesis |
UNIV OF MASSACHUSETTS MED SCHOOL |
Xin Li |
| R01 HG008759 |
Bioinformatics platform for Hybrid-Seq transcriptome data analysis |
OHIO STATE UNIVERSITY |
Kin Fai Au |
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| |
| Submission date |
Sep 16, 2019 |
| Last update date |
Mar 09, 2021 |
| Contact name |
Xin Li |
| E-mail(s) |
xin_li@urmc.rochester.edu
|
| Organization name |
University of Rochester Med Center
|
| Department |
Biochemistry and biophysics
|
| Lab |
Xin Li
|
| Street address |
601 Elmwood Ave.
|
| City |
Rochester |
| State/province |
NY |
| ZIP/Postal code |
14642 |
| Country |
USA |
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| Platforms (5)
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| Samples (15)
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| Relations |
| BioProject |
PRJNA565724 |
| SRA |
SRP221733 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE137490_HumanSpermPacBio_FLNC.fasta.gz |
149.8 Mb |
(ftp)(http) |
FASTA |
| GSE137490_RAW.tar |
1.6 Mb |
(http)(custom) |
TAR (of SF, XLSX) |
| GSE137490_SpermPacBio_FLNC.fasta.gz |
26.6 Mb |
(ftp)(http) |
FASTA |
| GSE137490_Summary.MousePacBio.ONT.xlsx |
662.7 Kb |
(ftp)(http) |
XLSX |
| GSE137490_TestisPacBio_FLNC.fasta.gz |
59.9 Mb |
(ftp)(http) |
FASTA |
| GSE137490_TranscriptomeAssembly.MouseTestis.mm10.gtf.gz |
2.0 Mb |
(ftp)(http) |
GTF |
| GSE137490_TranscriptomeAssembly.spiRNA.HumanSperm.hg38.gtf.gz |
804.4 Kb |
(ftp)(http) |
GTF |
| GSE137490_TranscriptomeAssembly.spiRNA.MouseSperm.mm10.gtf.gz |
426.3 Kb |
(ftp)(http) |
GTF |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
| Processed data provided as supplementary file |
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