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| Status |
Public on Feb 13, 2017 |
| Title |
NM+K rep1 |
| Sample type |
SRA |
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| Source name |
NM+K
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| Organism |
Medicago truncatula |
| Characteristics |
host genotype: Jemalong A17
inoculation: control
growth protocol: +K
tissue: roots
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| Extracted molecule |
total RNA |
| Extraction protocol |
Frozen root tissues were ground in liquid nitrogen, and total RNA was extracted from the resulting powder using PureLink® RNA Mini Kit (Thermofisher), and treated with TURBOTM DNase (Thermofisher). RNA quality was assessed using the Agilent 2100 BioAnalyzer technology (Agilent Technologies, Santa Clara, CA, USA).
Six micrograms of total RNA were used to construct polyA selection libraries using the Illumina TrueSeq RNA Sample Preparation kit; 100-nt single-end reads were obtained on an Illumina Hiseq2000 platform using TruSeq v3 (University of Wisconsin Biotechnology Center DNA Sequencing Facility, USA).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
nmk1
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| Data processing |
RNA-sequencing (RNA-Seq) data were processed to obtain differentially expressed genes (DEGs) using TopHat2-SE, Cufflinks2, Cuffmerge2 and Cuffdiff2 applications from the iPlant Collaborative platform (http://www.iplantcollaborative.org).
The DESeq Bioconductor package version 3.3 for R (Anders and Huber, 2010) was used for the analysis of DEGs. Cuffdiff2 sequencing data were analyzed using the cummeRbund package to generate principal component and multidimensional scaling analyses on biological and technical replicates.
Genome_build: Mt4.0v1
Supplementary_files_format_and_content: tab-delimited text file displaying FPKM values for each condition
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| Submission date |
Jan 30, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Jean-Michel Ané |
| E-mail(s) |
[email protected]
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| Organization name |
University of Wisconsin-Madison
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| Department |
Bacteriology
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| Lab |
Ané lab
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| Street address |
1550 Linden Drive
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| City |
Madison |
| State/province |
WI |
| ZIP/Postal code |
53706-1521 |
| Country |
USA |
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| Platform ID |
GPL17491 |
| Series (1) |
| GSE94266 |
RNA-seq of mycorrhizal Medicago truncatula roots under K+ deprivation |
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| Relations |
| BioSample |
SAMN06279704 |
| SRA |
SRX2527539 |
| 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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