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| Status |
Public on Jul 01, 2024 |
| Title |
Transcriptomic Analysis of the Spatiotemporal Axis of Oogenesis and Fertilization in C. elegans |
| Organism |
Caenorhabditis elegans |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
The oocyte germline of the C. elegans hermaphrodite presents a unique model to study the formation of oocytes. However, the size of the model animal and difficulties in retrieval of specific stages of the germline have obviated closer systematic studies of this process throughout the years. Here, we present a transcriptomic level analysis into the oogenesis of C. elegans hermaphrodites. We dissected a hermaphrodite gonad into seven sections corresponding to the mitotic distal region, the pachytene, the diplotene, the early diakinesis region and the 3 most proximal oocytes, and deeply sequenced the transcriptome of each of them along with that of the fertilized egg using a single-cell RNA-seq protocol. We identified specific gene expression events as well as gene splicing events in finer detail along the oocyte germline and provided novel insights into underlying mechanisms of the oogenesis process. These results expand our knowledge of the transcriptomic space of the C. elegans germline and lay a foundation on which future studies of the germline can be based upon.
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| Overall design |
we combined microdissection with scRNA-seq technique, and profiled the transcriptomes in the proliferative zone, pachytene zone, diplotene zone, early diakinesis zone (before -3 oocyte stage), later diakinesis zone (-3, -2, -1 oocytes), and the zygote. We identified not only many genes that were known to play roles in oogenesis and fertilization, but also many novel candidate genes that may be significant in each of the stages.
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| Contributor(s) |
Su Y, Shea J, DeStephanis D, Su Z |
| Citation(s) |
38895354, 39224437 |
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| Submission date |
Mar 17, 2024 |
| Last update date |
Oct 01, 2024 |
| Contact name |
Yangqi Su |
| E-mail(s) |
ysu13@uncc.edu
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| Organization name |
UNC Charlotte
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| Department |
Bioinformatics
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| Street address |
9201 University City Blvd
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| City |
Charlotte |
| State/province |
NC |
| ZIP/Postal code |
28262 |
| Country |
USA |
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| Platforms (1) |
| GPL18245 |
Illumina HiSeq 2500 (Caenorhabditis elegans) |
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| Samples (146)
|
| GSM8151760 |
C. elegans gonad, Unknown Worm 1, Zygote |
| GSM8151761 |
C. elegans gonad, Unknown Worm 2, Early Embryo |
| GSM8151762 |
C. elegans gonad, Unknown Worm 3, Early Embryo |
| GSM8151763 |
C. elegans gonad, Unknown Worm 4, Early Embryo |
| GSM8151764 |
C. elegans gonad, WormA, Mitotic Region and Transition Zone |
| GSM8151765 |
C. elegans gonad, WormB, Mitotic Region and Transition Zone |
| GSM8151766 |
C. elegans gonad, WormB, Diplotene Loop |
| GSM8151767 |
C. elegans gonad, WormC, Mitotic Region and Transition Zone |
| GSM8151768 |
C. elegans gonad, WormC, Pachytene Zone |
| GSM8151769 |
C. elegans gonad, WormC, -1 Oocyte |
| GSM8151770 |
C. elegans gonad, WormC, -2 Oocyte |
| GSM8151771 |
C. elegans gonad, WormD, Pachytene Zone |
| GSM8151772 |
C. elegans gonad, WormD, -1 Oocyte |
| GSM8151773 |
C. elegans gonad, WormE, -1 Oocyte |
| GSM8151774 |
C. elegans gonad, WormE, Mitotic Region and Transition Zone |
| GSM8151775 |
C. elegans gonad, WormE, Diplotene Loop |
| GSM8151776 |
C. elegans gonad, WormF, -1 Oocyte |
| GSM8151777 |
C. elegans gonad, WormF, -2 Oocyte |
| GSM8151778 |
C. elegans gonad, WormF, Diakinesis |
| GSM8151779 |
C. elegans gonad, WormG, -1 Oocyte |
| GSM8151780 |
C. elegans gonad, WormG, -2 Oocyte |
| GSM8151781 |
C. elegans gonad, WormH, -2 Oocyte |
| GSM8151782 |
C. elegans gonad, WormH, -3 Oocyte |
| GSM8151783 |
C. elegans gonad, WormH, Diakinesis |
| GSM8151784 |
C. elegans gonad, WormI, Diakinesis |
| GSM8151785 |
C. elegans gonad, WormJ, Diakinesis |
| GSM8151786 |
C. elegans gonad, WormJ, -3 Oocyte |
| GSM8151787 |
C. elegans gonad, Unkown Worm A, Zygote |
| GSM8151788 |
C. elegans gonad, Unkown Worm B, Zygote |
| GSM8151789 |
C. elegans gonad, Worm1, Mitotic Region and Transition Zone |
| GSM8151790 |
C. elegans gonad, Worm1, Pachytene Zone |
| GSM8151791 |
C. elegans gonad, Worm1, Diplotene Loop |
| GSM8151792 |
C. elegans gonad, Worm1, -1 Oocyte |
| GSM8151793 |
C. elegans gonad, Worm1, Diakinesis |
| GSM8151794 |
C. elegans gonad, Worm2, Zygote |
| GSM8151795 |
C. elegans gonad, Worm2, Mitotic Region and Transition Zone |
| GSM8151796 |
C. elegans gonad, Worm2, Pachytene Zone |
| GSM8151797 |
C. elegans gonad, Worm2, Diplotene Loop |
| GSM8151798 |
C. elegans gonad, Worm2, -1 Oocyte |
| GSM8151799 |
C. elegans gonad, Worm2, -2 Oocyte |
| GSM8151800 |
C. elegans gonad, Worm2, Diakinesis |
| GSM8151801 |
C. elegans gonad, Worm3, Mitotic Region and Transition Zone |
| GSM8151802 |
C. elegans gonad, Worm3, Pachytene Zone |
| GSM8151803 |
C. elegans gonad, Worm3, Diplotene Loop |
| GSM8151804 |
C. elegans gonad, Worm3, Diakinesis |
| GSM8151805 |
C. elegans gonad, Worm4, Zygote |
| GSM8151806 |
C. elegans gonad, Worm5, Mitotic Region and Transition Zone |
| GSM8151807 |
C. elegans gonad, Worm5, Pachytene Zone |
| GSM8151808 |
C. elegans gonad, Worm5, Diplotene Loop |
| GSM8151809 |
C. elegans gonad, Worm6, Pachytene Zone |
| GSM8151810 |
C. elegans gonad, Worm7, -1 Oocyte |
| GSM8151811 |
C. elegans gonad, Worm7, Diplotene Loop |
| GSM8151812 |
C. elegans gonad, Worm8, Zygote |
| GSM8151813 |
C. elegans gonad, Worm9, Zygote |
| GSM8151814 |
C. elegans gonad, Worm10, Zygote |
| GSM8151815 |
C. elegans gonad, Worm11, Mitotic Region and Transition Zone |
| GSM8151816 |
C. elegans gonad, Worm12, Mitotic Region and Transition Zone |
| GSM8151817 |
C. elegans gonad, Worm12, Diplotene Loop |
| GSM8151818 |
C. elegans gonad, Worm12, Diakinesis |
| GSM8151819 |
C. elegans gonad, Worm11, Pachytene Zone |
| GSM8151820 |
C. elegans gonad, Worm11, Diplotene Loop |
| GSM8151821 |
C. elegans gonad, Worm13, Mitotic Region and Transition Zone |
| GSM8151822 |
C. elegans gonad, Worm13, Pachytene Zone |
| GSM8151823 |
C. elegans gonad, Worm14, Mitotic Region and Transition Zone |
| GSM8151824 |
C. elegans gonad, Worm14, Pachytene Zone |
| GSM8151825 |
C. elegans gonad, Worm14, Diplotene Loop |
| GSM8151826 |
C. elegans gonad, Worm15, Mitotic Region and Transition Zone |
| GSM8151827 |
C. elegans gonad, Worm15, Pachytene Zone |
| GSM8151828 |
C. elegans gonad, Worm15, -1 Oocyte |
| GSM8151829 |
C. elegans gonad, Worm16, Mitotic Region and Transition Zone |
| GSM8151830 |
C. elegans gonad, Worm17, Mitotic Region and Transition Zone |
| GSM8151831 |
C. elegans gonad, Worm17, Pachytene Zone |
| GSM8151832 |
C. elegans gonad, Worm17, Diplotene Loop |
| GSM8151833 |
C. elegans gonad, Worm17, -2 Oocyte |
| GSM8151834 |
C. elegans gonad, Worm18, Pachytene Zone |
| GSM8151835 |
C. elegans gonad, Worm18, Diplotene Loop |
| GSM8151836 |
C. elegans gonad, Worm18, -1 Oocyte |
| GSM8151837 |
C. elegans gonad, Worm19, Pachytene Zone |
| GSM8151838 |
C. elegans gonad, Worm19, Diplotene Loop |
| GSM8151839 |
C. elegans gonad, Worm20, -1 Oocyte |
| GSM8151840 |
C. elegans gonad, Worm20, -2 Oocyte |
| GSM8151841 |
C. elegans gonad, Worm20, Diakinesis |
| GSM8151842 |
C. elegans gonad, Worm20, -3 Oocyte |
| GSM8151843 |
C. elegans gonad, Worm21, Pachytene Zone |
| GSM8151844 |
C. elegans gonad, Worm21 NA |
| GSM8151845 |
C. elegans gonad, Worm21, -1 Oocyte |
| GSM8151846 |
C. elegans gonad, Worm22, Pachytene Zone |
| GSM8151847 |
C. elegans gonad, Worm22, Diplotene Loop |
| GSM8151848 |
C. elegans gonad, Worm23, Mitotic Region and Transition Zone |
| GSM8151849 |
C. elegans gonad, Worm23, Pachytene Zone |
| GSM8151850 |
C. elegans gonad, Worm23, -2 Oocyte |
| GSM8151851 |
C. elegans gonad, Worm23, Diplotene Loop |
| GSM8151852 |
C. elegans gonad, Worm23, -1 Oocyte |
| GSM8151853 |
C. elegans gonad, Worm24, Mitotic Region and Transition Zone |
| GSM8151854 |
C. elegans gonad, Worm25 NA |
| GSM8151855 |
C. elegans gonad, Worm25, Pachytene Zone |
| GSM8151856 |
C. elegans gonad, Worm25, -1 Oocyte |
| GSM8151857 |
C. elegans gonad, Worm25, Diakinesis |
| GSM8151858 |
C. elegans gonad, Worm25, -2 Oocyte |
| GSM8151859 |
C. elegans gonad, Worm26, -1 Oocyte |
| GSM8151860 |
C. elegans gonad, Worm26, Diakinesis |
| GSM8151861 |
C. elegans gonad, Worm26, -2 Oocyte |
| GSM8151862 |
C. elegans gonad, Worm30, Mitotic Region and Transition Zone |
| GSM8151863 |
C. elegans gonad, Worm30, Pachytene Zone |
| GSM8151864 |
C. elegans gonad, Worm30, -1 Oocyte |
| GSM8151865 |
C. elegans gonad, Worm30, -2 Oocyte |
| GSM8151866 |
C. elegans gonad, Worm30, Diplotene Loop |
| GSM8151867 |
C. elegans gonad, Worm31, Mitotic Region and Transition Zone |
| GSM8151868 |
C. elegans gonad, Worm31, Pachytene Zone |
| GSM8151869 |
C. elegans gonad, Worm31, -2 Oocyte |
| GSM8151870 |
C. elegans gonad, Worm31, Diakinesis |
| GSM8151871 |
C. elegans gonad, Worm32, -1 Oocyte |
| GSM8151872 |
C. elegans gonad, Worm32, Mitotic Region and Transition Zone |
| GSM8151873 |
C. elegans gonad, Worm32, Pachytene Zone |
| GSM8151874 |
C. elegans gonad, Worm32, Diplotene Loop |
| GSM8151875 |
C. elegans gonad, Worm32, -2 Oocyte |
| GSM8151876 |
C. elegans gonad, Worm32, Diakinesis |
| GSM8151877 |
C. elegans gonad, Worm33, Mitotic Region and Transition Zone |
| GSM8151878 |
C. elegans gonad, Worm33, Zygote |
| GSM8151879 |
C. elegans gonad, Worm33, Diplotene Loop |
| GSM8151880 |
C. elegans gonad, Worm33, -2 Oocyte |
| GSM8151881 |
C. elegans gonad, Worm33, -3 Oocyte |
| GSM8151882 |
C. elegans gonad, Worm34, Pachytene Zone |
| GSM8151883 |
C. elegans gonad, Worm34, Diakinesis |
| GSM8151884 |
C. elegans gonad, Worm34, Mitotic Region and Transition Zone |
| GSM8151885 |
C. elegans gonad, Worm29, Mitotic Region and Transition Zone |
| GSM8151886 |
C. elegans gonad, Worm29, Pachytene Zone |
| GSM8151887 |
C. elegans gonad, Worm29, Diplotene Loop |
| GSM8151888 |
C. elegans gonad, Worm29, Diakinesis |
| GSM8151889 |
C. elegans gonad, Worm29, -1 Oocyte |
| GSM8151890 |
C. elegans gonad, Worm27, -3 Oocyte |
| GSM8151891 |
C. elegans gonad, Worm28, Mitotic Region and Transition Zone |
| GSM8151892 |
C. elegans gonad, Worm28, Diplotene Loop |
| GSM8151893 |
C. elegans gonad, Worm28, Pachytene Zone |
| GSM8151894 |
C. elegans gonad, Worm28, -1 Oocyte |
| GSM8151895 |
C. elegans gonad, Worm28, -2 Oocyte |
| GSM8151896 |
C. elegans gonad, Worm28, -3 Oocyte |
| GSM8151897 |
C. elegans gonad, Worm28, Diakinesis |
| GSM8151898 |
C. elegans gonad, Unknown Worm 5, Zygote |
| GSM8151899 |
C. elegans gonad, Unknown Worm 6, Zygote |
| GSM8151900 |
C. elegans gonad, Unknown Worm 7, Early Embryo |
| GSM8151901 |
C. elegans gonad, Unknown Worm 8, Early Embryo |
| GSM8151902 |
C. elegans gonad, Unknown Worm 9, Early Embryo |
| GSM8151903 |
C. elegans gonad, Unknown Worm 10, Early Embryo |
| GSM8151904 |
C. elegans gonad, Unknown Worm 11, Early Embryo |
| GSM8151905 |
C. elegans gonad, Unknown Worm 12, Early Embryo |
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| Relations |
| BioProject |
PRJNA1088873 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE261784_HISAT_raw_counts.txt.gz |
2.1 Mb |
(ftp)(http) |
TXT |
| GSE261784_SALMON_tpm.txt.gz |
5.7 Mb |
(ftp)(http) |
TXT |
| GSE261784_sample_qc_meta.txt.gz |
14.8 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
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