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| Status |
Public on Jul 20, 2016 |
| Title |
sl-myc |
| Sample type |
SRA |
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| Source name |
root
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| Organism |
Solanum lycopersicum |
| Characteristics |
inoculated with: Rhizophagus irregularis
tissue: root
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| Treatment protocol |
For mycorrhizal treatment, plants were inoculated with Rhizophagus irregularis (BGC HEB07D, a mixture of soil, spores, hyphae and root material from Institute of Plant Nutrition and Resources, Beijing Academy of Agriculture and Forestry Sciences).
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| Growth protocol |
Seeds of tomato (Solanum lycopersicum) were surfaced sterilized with 8% sodium hypochlorite for 6 min by gently shaking, and rinsed six times in sterile distilled water. Surface sterilized tomato seed were germinated at 24 °C for two days on 0.8% water Agar. After germinating, the seeds were transferred to a plastic pot filled with 650g sands. Plants were cultivated under 16h light (300 μmol photons m–2 s–1) at 24 °C and 8h dark at 22 °C. All plants were watered two times per week with half-strength Hoagland solution containing 20 μM phosphate (Arnon and Hoagland 1940).
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from tomato roots were isolated using TRIzol reagent (Invitrogen, Carlsbad, CA, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols.
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| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
Sequences were mapped to Solanum lycopersicum whole genome using bowtie
The counts of reads were normalized by the formula: actual miRNA count/ total count of clean reads*1000000
Genome_build: Solanum lycopersicum (Assembly number: GCA_000188115.2)
Supplementary_files_format_and_content: abundance measurements
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| Submission date |
Dec 21, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Ping Wu |
| E-mail(s) |
winslow9223@gmail.com
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| Phone |
15996319570
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| Organization name |
Nanjing University
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| Street address |
163 Xianlin Avenue
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| City |
Nanjing |
| ZIP/Postal code |
210046 |
| Country |
China |
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| Platform ID |
GPL16345 |
| Series (1) |
| GSE76204 |
Small RNA sequencing in tomato roots with and without Rhizophagus irregularis |
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| Relations |
| BioSample |
SAMN04358129 |
| SRA |
SRX1493987 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1976413_T_AM.txt.gz |
34.5 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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