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| Status |
Public on Jul 01, 2021 |
| Title |
Integrated analysis of RNA-seq and microRNA-seq depicts miRNA-mRNA networks involved in stripe patterns of Botia superciliaris skin [RNA-seq] |
| Organism |
Sinibotia superciliaris |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Purpose:In order to elucidate the molecular mechanism of the stripe patterns in B. superciliaris skin.These results will enhance understanding of molecular mechanisms underlying skin pigmentation and facilitate molecular-assisted selection of highly valued skin colors.
Methods:In this study, Illumina sequencing was employed to identify the mRNAs and miRNAs involved in stripe pattern formation in B. superciliaris skin. target prediction revealed a variety of putative target genes; differentially expressed mRNAs and miRNAs patterns were observed in 5 mRNAs and mir-217 by qRT-PCR.
Results:Based on the zebrafish genome, a total of 44,206,176 and 46,941,318 high-quality transcriptome reads were generated, which resulted in 134,586 unigenes that were used as reference sequences. A total of 24,113 genes exhibited significantly different expression patterns (fold-change ≥ 2 or ≤ 0.5 and q ≤ 0.05), including 15,117 up-regulated genes and 8,996 down-regulated genes associated with black and yellow stripes.These genes were enriched in 65 GO terms and 7 KEGG pathways (q ≤ 0.05), which included melanogenesis, and contained 32 up-regulated genes and 12 down-regulated genes. High-throughput miRNA sequencing identified a total of 355 miRNAs, which included 38 novel miRNAs. Furthermore, 87 differentially expressed miRNAs that contained 50 up-regulated and 37 down-regulated miRNAs were identified in different color skin
Conclusions:This study provides novel insight into the mechanism that produces different color stripes in B. superciliaris by combining RNA-seq with small RNA-seq. 5 genes and 1 miRNAs were selected arbitrarily for verification . Compared with previous fish studies, revealed that these DE mRNAs and miRNAs are likely involved in melanin synthesis, and the quantitative mRNA/miRNA data and pathway information presented here provide a strong basis for elucidation of the detailed functions of mRNAs and miRNAs associated with black and yellow stripe formation in aquarium fish.
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| Overall design |
Black and yellow skin tissue samples were collected from 6 individuals . and mRNA and miRNA library construction and sequencing
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| Contributor(s) |
Zhou J, Zhao H |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
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| Submission date |
Jul 30, 2018 |
| Last update date |
Jul 02, 2021 |
| Contact name |
jideng Ma |
| E-mail(s) |
jideng_ma@sina.com
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| Organization name |
Sichuan Agricultural University(SICAU),
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| Street address |
Xinkang road
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| City |
Yaan |
| ZIP/Postal code |
625014 |
| Country |
China |
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| Platforms (1) |
| GPL25404 |
Illumina HiSeq 2000 (Sinibotia superciliaris) |
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| Samples (2) |
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| This SubSeries is part of SuperSeries: |
| GSE118321 |
Integrated analysis of RNA-seq and microRNA-seq depicts miRNA-mRNA networks involved in stripe patterns of Botia superciliaris skin |
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| Relations |
| BioProject |
PRJNA485176 |
| SRA |
SRP156789 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE117894_RAW.tar |
1.5 Mb |
(http)(custom) |
TAR (of TXT) |
| GSE117894_Trinotate_report_all.txt.gz |
2.1 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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