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| Status |
Public on Jan 22, 2022 |
| Title |
Identification of regulatory factors promoting embryogenic callus formation in barley through transcriptome analysis |
| Organism |
Hordeum vulgare |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
The aim of this study was to uncover the differential transcription regulation pathways between immature embryo (IME)- and mature embryo (ME)-derived callus formation through transcriptome sequencing. We showed that incubation of embryos on auxin-rich medium caused dramatic changes in gene expression profiles within 48 h. A total of 9330 and 11318 differentially expressed genes (DEGs) were found in the IME and ME systems, respectively. 3880 DEGs were found specific to IME_0h/IME_48h, and protein phosphorylation, regulation of transcription, and oxidative-reduction process were the most common gene ontology categories of this group. Twenty-three IAA, 14 ARF, 8 SAUR, 3 YUC, and 4 PIN genes were found to be differentially expressed during callus formation. The effect of callus-inducing medium (CIM) on IAA genes was broader in the IME system than in the ME system, indicating that auxin response in regulating cell reprogramming during callus formation. BBM, LEC1 and PLT2 exhibited a significant increase in expression level during IME system but were not activated in the ME system, WUS showed a more substantial growth trend in the IME system than in the ME system, suggesting that these embryonic, shoot, and root meristems genes play crucial roles in determining the acquisition of competency. In addition, epigenetic regulators—including SUVH3A, SUVH2A, HDA19B/703—exhibited differential expression patterns between the two induction systems, indicating that epigenetic reprogramming might contribute to gene expression activation/suppression in this process.
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| Overall design |
The immature embryo samples were harvested at 0 h, 24 h, and 48 h after culture in CIM. The mature embryos were harvested at 0 h and 24 h after culture in CIM.
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| Contributor(s) |
qi Sj, lu Zc, hui Zz, pu lx, ning H |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
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| Submission date |
Jan 25, 2021 |
| Last update date |
Jan 22, 2022 |
| Contact name |
Suo jing qi |
| E-mail(s) |
11907039@zju.edu.cn
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| Organization name |
Zhejiang university
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| Department |
college of life sciences
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| Lab |
318
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| Street address |
866 Yuhangtang Rd
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| City |
Hangzhou |
| State/province |
Zhejiang |
| ZIP/Postal code |
310058 |
| Country |
China |
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| Platforms (1) |
| GPL29652 |
Illumina NovaSeq 6000 (Hordeum vulgare) |
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| Samples (15)
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| Relations |
| BioProject |
PRJNA694675 |
| SRA |
SRP303192 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE165487_1_genes_fpkm_expression.txt.gz |
5.7 Mb |
(ftp)(http) |
TXT |
| GSE165487_novel_transcripts.fa.gz |
3.6 Mb |
(ftp)(http) |
FA |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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