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| Status |
Public on Jun 30, 2016 |
| Title |
Williams82_SMV-G7_RNA-seq |
| Sample type |
SRA |
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| Source name |
leaves tissues
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| Organism |
Glycine max |
| Characteristics |
cultivar: Williams82
cultivar: Susceptible
agent: SMV-G7
age: 14 days post-inoculation
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| Treatment protocol |
Leaves were mechanically inoculated by SMV-L, SMV-LRB,SMV-G7 and Mock (buffer) after germination at 10 days.
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| Growth protocol |
Soybeans were grown in a growth chamber under a 16 h light at 22°C and 8 h dark at 18°C.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA and small RNA fractions (≤ 200 nt) were extracted from the leaves inoculated by SMV-L,SMV-LRB,SMV-G7 and Mock using a mirVana miRNA isolation kit (Ambion) and the Poly (A)+ RNA was isolated using the NucleoTrap@ mRNA purification kits (Machery-Nagel) according to the instructions of the supplier.
RNA-seq and sRNA-seq libraries were prepared following the manufacturer's instructions using Illumina TruSeq Stranded Total RNA Sample Prep Kit (Cat#RS-122-2501) and TruSeq Small RNA Sample Prep Kit (Cat#RS-200-0012),respectively. Degradome-seq libraries were constructed as previously described using Illumina TruSeq Small RNA Sample Prep Kit (Cat#RS-200-0024)(German, M. A. et al., Nature Biotechology, 2008; German et al., Nature Protocols, 2009; Zhai et al., 2014).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina MiSeq |
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| Description |
Williams82_RNA-seq_Alignment_Report.txt
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| Data processing |
For RNA-seq analysis, the raw sequences were aligned to the soybean reference transcriptome (Glyma1, Ensembl genes and transcripts) using the Strand NGS software (Strand Life Sciences, version 2.1) following RNA alignment and RNA-seq analysis pipeline with standard parameters.
For sRNA-seq analysis, after the low quality reads and the adapter sequences were trimmed, the sequences were mapped to the Glycine max reference genome (Glyma1, Ensembl) and aligned to the known miRNA gene of Glycine max (miRBase 21) using the Strand NGS software (Strand Life Sciences, version 2.1) following small RNA alignment and small RNA analysis pipeline with standard parameters.
For degradome-seq analysis, the adaptor sequences, tRNA/rRNA sequences and low complexity sequences were removed from raw reads, then the length of degradome sequences and small RNA sequences were trimmed to 20-21 nt and 19-24 nt, respectively. Any sequences without a match to the soybean genome (Glyma1, Ensembl) were also removed from further analysis. The potential targets of small RNAs were identified and validated using the UEA small RNA workbench following the PAREsnip pipeline under a high stringency setting with the Glycine max reference genome (Glyma1, Ensembl) and the known miRNAs of Glycine max (miRBase 21).
Genome_build: Soybean reference transcriptome (Glyma1, Ensembl) and soybean known miRNA (miRBase 21)
Supplementary_files_format_and_content: The txt files of alignment reports were geneated using the Strand NGS software (Strand Life Sciences, version 2.1) following various alignment and analysis pipeline with standard parameters.
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| Submission date |
Jan 07, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Hui Chen |
| E-mail(s) |
Hui.Chen@agr.gc.ca
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| Phone |
001-519-953-6710
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| Organization name |
Agriculture and Agri-Food Canada
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| Street address |
1391 Sandford St.
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| City |
London |
| State/province |
Ontario |
| ZIP/Postal code |
N5V 4T3 |
| Country |
Canada |
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| Platform ID |
GPL21309 |
| Series (1) |
| GSE76636 |
Genome-wide investigation using sRNA-seq, degradome-seq and transcriptome-seq reveals regulatory networks of microRNAs and their target genes in soybean during Soybean mosaic virus infection |
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| Relations |
| BioSample |
SAMN04388357 |
| SRA |
SRX1521265 |
| Supplementary data files not provided |
SRA Run Selector |
| Processed data are available on Series record |
| Raw data are available in SRA |
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