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Status |
Public on Apr 18, 2022 |
Title |
Ri, 150mM, root, sample 1 |
Sample type |
SRA |
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Source name |
root
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Organism |
Oryza sativa |
Characteristics |
tissue: root genotype: wild type inoculation treatment: Rhizophagus irregularis salt treatment: 150mM NaCl time: 8 weeks post inoculation
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Extracted molecule |
total RNA |
Extraction protocol |
Total RNA was extracted from 100 mg shoot or root tissue by using TRIzol Reagent (Invitrogen™) following the manufacturer’s instructions. A total amount of RNA (≥ 4 μg) per sample were used for transcriptome sequencing. Strand-specific sequencing libraries were obtained following the handbook for the NEBNext® Ultra™ RNA Library Prep Kit for Illumina®
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 4000 |
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Description |
R-150-r-1
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Data processing |
The quality control of raw reads was evaluated using FastQC software v0.11.8 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). The low-quality reads (Q-value < 20) and adaptors were removed using the sequence preprocessing tool Trimmomatic v0.39 (Bolger et al., 2014). After low-quality reads and adaptors were removed, all cleaned reads were assembled into contigs using Trinity (Grabherr et al., 2011). To get a more specific gene list, we used CD-HIT-EST version CD-HIT4 to cluster the redundancy of transcripts and removed the shorter redundant transcripts (Li and Godzik, 2006;Fu et al., 2012). In this analysis, Bowtie2 version V2.3.2 and RSEM version v1.2.31 software were used to map short reads to the Trinity de novo assembly and quantify the read counts that matched to each contig (Li and Dewey, 2011;Langmead and Salzberg, 2012). Then, Transdecoder was used to identify candidate coding regions for gene prediction. Next, to distinguish the de novo assembled sequences between those of the rice and fungal species, the Basic Local Alignment Search Tool (BLAST) searches against the Orygenes database (https://orygenesdb.cirad.fr/) for rice (O. sativa) and the National Center for Biotechnology Information (NCBI) database for AM fungi (R. irregularis), was performed for annotation, respectively (Altschul et al., 1990;Droc et al., 2006;Coordinators, 2016). Assembly: Orygenes database (https://orygenesdb.cirad.fr/) for rice (O. sativa) and the National Center for Biotechnology Information (NCBI) database for AM fungi (R. irregularis) Supplementary files format and content: tab-delimited excel files include raw count values for each Sample
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Submission date |
Apr 15, 2022 |
Last update date |
Apr 18, 2022 |
Contact name |
Shu-Yi Yang |
E-mail(s) |
shuyiyang@ntu.edu.tw
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Phone |
+886-2-3366-2533
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Organization name |
Institute of Plant Biology
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Lab |
R1047
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Street address |
Life Science Building, NTU. No. 1, Sec. 4, Roosevelt Rd
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City |
Taipei |
ZIP/Postal code |
10617 |
Country |
Taiwan |
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Platform ID |
GPL23013 |
Series (1) |
GSE200863 |
Transcriptome analysis provides insights into the mechanism of salt tolerance in rice colonized by arbuscular mycorrhizal fungi |
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Relations |
BioSample |
SAMN27596913 |
SRA |
SRX14868626 |
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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