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| Status |
Public on Aug 01, 2024 |
| Title |
root, Spermidine 0.1mM + NaCl 100mM, T2 |
| Sample type |
SRA |
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| Source name |
root
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| Organism |
Oryza sativa |
| Characteristics |
treatment: Spermidine 0.1mM + NaCl 100mM
genetic background: WT
tissue: root
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| Treatment protocol |
Spermidine, NaCl or Spermidine+NaCl for 72hrs
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extraction, poly-A pulling, reverse transcription, 3'end adenylation, linker ligation, and PCR amplification
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Basecalling with Illumina Casava 1.8 software
3' adapter trimming with FastX-toolkit
Library sorting based on sample barcode sequence with custom script
random barcode triming with custom script
Alignment with bowtie2
Read quantitation using RSEM
Genome_build: Assembled transcriptome using Trinity
Supplementary_files_format_and_content: csv file contains nine types of information: 1. ID;2-13. FPKM for each sample;3. KEGG; 4. NR; 5. SwissProt; 6. TrEMBL; 7.KOG; 8. GO; 9. Pfam
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| Submission date |
Nov 27, 2021 |
| Last update date |
Aug 01, 2024 |
| Contact name |
Mingming Chen |
| Organization name |
Guangdong Ocean University
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| Street address |
Haida Street No.1
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| City |
Zhanjiang |
| ZIP/Postal code |
524088 |
| Country |
China |
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| Platform ID |
GPL27660 |
| Series (1) |
| GSE189665 |
Spermidine augments salt stress resilience in rice roots potentially by enhancing OsbZIP73’s RNA binding capacity |
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| Relations |
| BioSample |
SAMN23470174 |
| SRA |
SRX13242146 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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