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| Status |
Public on Mar 10, 2024 |
| Title |
Root_CK_3 |
| Sample type |
SRA |
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| Source name |
Root
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| Organism |
Oryza sativa Japonica Group |
| Characteristics |
cultivar: Nipponbare
tissue: Root
treatment: CK
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| Extracted molecule |
total RNA |
| Extraction protocol |
Roots sample were flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
Root_NvsRoot_CK_deg
Root_PvsRoot_CK_deg
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| Data processing |
Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using hisat2 v2.0.5 with parameters hisat2 [options]* -x <hisat2-idx> {-1 <m1> -2 <m2> | -U <r> | --sra-acc <SRA accession number>} [-S <hit>]
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell,Cole et al., Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol, 2010. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: rap-db (http://rapdb.dna.affrc.go.jp/download/irgsp1.html)
Supplementary files format and content: tab-delimited text files include FPKM values, log2FoldChange, padj and gene information for each Sample ...
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| Submission date |
Mar 10, 2023 |
| Last update date |
Mar 10, 2024 |
| Contact name |
Fei Wang |
| E-mail(s) |
lowfei@126.com
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| Phone |
123456789
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| Organization name |
浙江大学
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| Street address |
紫金港校区
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| City |
杭州 |
| State/province |
浙江 |
| ZIP/Postal code |
310058 |
| Country |
China |
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| Platform ID |
GPL18525 |
| Series (1) |
| GSE227072 |
Integrated transcriptomic analysis identifies coordinated responses to nitrogen and phosphate deficiency in rice |
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| Relations |
| BioSample |
SAMN33711597 |
| SRA |
SRX19782185 |
| 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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