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| Status |
Public on Jul 29, 2020 |
| Title |
BN207 normal potassium rep3 |
| Sample type |
SRA |
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| Source name |
Wheat roots
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| Organism |
Triticum aestivum |
| Characteristics |
strain: bainong207
phenotype: K-deficiency sensitive
tissue: Wheat roots
treatment: normal potassium
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Aglient 2100 Bioanalyzer and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0.
Poly(A) RNA was purified from total RNA using poly-T oligo-attached magnetic beads by two rounds of purification. Following purification, the mRNA was fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the TruSeq Stranded mRNA Library Prep Kit (Illumina, San Diego, USA).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Description |
SCK14_3
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| Data processing |
Illumina Casava1.8 software used for basecalling.
Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20) were removed.
We aligned reads of samples to the reference genome using HISAT2 package.
The mapped reads of each sample were assembled using StringTie. Then, all transcriptomes from Samples were merged to reconstruct a comprehensive transcriptome. After the final transcriptome was generated, StringTie and edgeR was used to estimate the expression levels of all transcripts.
Genome_build: Triticum_aestivum (Chinese Spring) IWGSC RefSeq v1.0
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
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| Submission date |
Jul 28, 2020 |
| Last update date |
Jul 29, 2020 |
| Contact name |
KE XU |
| E-mail(s) |
xuke1214@sina.com
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| Organization name |
Hebei agricultural university
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| Street address |
KEKAI2596
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| City |
Baoding |
| State/province |
Hebei |
| ZIP/Postal code |
071000 |
| Country |
China |
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| Platform ID |
GPL23509 |
| Series (1) |
| GSE155319 |
Multi-omics Analyses Reveal Molecular Mechanisms of Potassium Deprivation Adaption in Wheat (Triticum aestivum L.) |
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| Relations |
| BioSample |
SAMN15662671 |
| SRA |
SRX8840963 |
| 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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