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| Status |
Public on Feb 13, 2018 |
| Title |
JSCK_3 |
| Sample type |
SRA |
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| Source name |
sweet potato_JSCK
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| Organism |
Ipomoea batatas |
| Characteristics |
cultivar: JinShan 57(JS57)
resistance phenotype: highly resistance to Fusarium wilt
inoculated with: nonpathogenic F. oxyspurum f.sp.batatas Fo-04
timepoint: 24 hours after inoculation
tissue: stem
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| Treatment protocol |
Seedling stems were cut freshly with 20 cm long, grew in a glass bottle containing conidial solutions of 1 × 10^7 conidia/mL of Fob-07 (strong pathogenic),or of Fob-04 (nonpathogenic), respectively. Control was set in which the seedling grew in the water.
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| Growth protocol |
The sweet potato seedlings were field grown for at least 28 d until they were cut and used as experimental material. After treatment the seedlings were grown in growth chambers at 28°C for 24 hours,
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from each sample respectively using RNAprep pure plant kit (polysaccharides and polyphenolics-rich, Tianen biotech,Beijing,China), according to the manufacturer’s instructions.
Sequencing libraries were generated using NEBNext Ultra™ RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. mRNA was purified and cDNA synthesis was subsequently performed. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structurewere ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system. Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Hiseq 2500 platform and paired-end reads were generated
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
Basecalls performed using CASAVA version 1.7
The clean reads with high quality were obtained by removing reads containing adapter, reads that containing N (indefinite base) higher than 10% and reads with low quality from raw reads
Transcriptome assembly was accomplished using Trinity (version:r20140413p1).
The level of gene expression was determined by normalizing the number of unambiguous tags in each library to expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced (FPKM). For the samples with biological replicates, differential expression analysis of two groups was performed using the DESeq R package (1.10.1)(qvalue< 0.005 &|log2(foldchange)| > 1)
Genome_build: Trinity.fasta
Supplementary_files_format_and_content: Fastq files of clean data were generated including error rate and Q20, Q30
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| Submission date |
Oct 28, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Xuanyang Chen |
| E-mail(s) |
cxy@fafu.edu.cn
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| Organization name |
Fujian Agriculture and Forestry University
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| Street address |
15,Shangxiadian road,cangshan district
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| City |
Fuzhou |
| ZIP/Postal code |
350002 |
| Country |
China |
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| Platform ID |
GPL22614 |
| Series (1) |
| GSE89290 |
Transcriptome profiling and digital gene expression analysis of sweet potato challenged with Fusarium oxysporum f. sp.batatas. |
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| Relations |
| BioSample |
SAMN05951919 |
| SRA |
SRX2281894 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2364833_JSCK_3.Readcount_FPKM.txt.gz |
521.8 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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