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| Status |
Public on Jul 27, 2018 |
| Title |
Transcriptomic analysis of tomato sperm cell lineage development |
| Organism |
Solanum lycopersicum |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Sperm cell (SC) lineage development from the haploid microspore to SCs represents a unique biological process. We isolated tomato (Solanum lycopersicum) microspores, generative cells and sperm cells, and performed the genome-wide transcriptomic analysis of lncRNAs and mRNAs. SC lineage development involves global repression of genes for pluripotency, somatic development and metabolism following microspore asymmetric division and coordinated upregulation of GC/SC preferential genes. This process is accompanied by progressive loss of the active marks H3K4me3 and H3K9ac, and accumulation of the repressive marks H3K9 methylation. The SC lineage has a higher ratio of lncRNAs to mRNAs and preferentially expresses a larger percentage of lncRNAs than does the non-SC lineage. A co-expression network showed that the largest set of lncRNAs in these nodes, with more than 100 links, are GC-preferential, and a small portion of lncRNAs co-express with their neighboring genes. Single molecular FISH showed that several candidate genes may be markers distinguishing the three cell types of the SC lineage. Our findings reveal the molecular programming and potential roles of lncRNAs for SC lineage development.
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| Overall design |
Seven cell types were examined, including microspores, generative cells, sperm cells, callus, fully expanded leaves, pistil and mature pollen grain (MPG). Each cell type has three biological replicates.
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| Contributor(s) |
Wang T, Lu Y |
| Citation(s) |
30047180 |
| Submission date |
Jul 16, 2018 |
| Last update date |
Jul 27, 2018 |
| Contact name |
Tai Wang |
| E-mail(s) |
twang@ibcas.ac.cn
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| Organization name |
Institute of Botany, CAS
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| Street address |
Nanxincun 20, Xiangshan
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| City |
Beijing |
| ZIP/Postal code |
100093 |
| Country |
China |
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| Platforms (1) |
| GPL16345 |
Illumina HiSeq 2000 (Solanum lycopersicum) |
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| Samples (21)
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| Relations |
| BioProject |
PRJNA481375 |
| SRA |
SRP154001 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE117185_List_of_expressed_mRNAs_and_lncRNAs.txt.gz |
3.6 Mb |
(ftp)(http) |
TXT |
| GSE117185_tomato_wlq_IGDBV1.gene.fasta.gz |
52.1 Mb |
(ftp)(http) |
FASTA |
| GSE117185_tomato_wlq_IGDBV1.gff.gz |
20.3 Mb |
(ftp)(http) |
GFF |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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