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| Status |
Public on Feb 23, 2015 |
| Title |
Sample_4-E1 |
| Sample type |
SRA |
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| Source name |
apical meristem
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| Organism |
Solanum lycopersicum |
| Characteristics |
tissue: apical meristem
cultivar: Rutgers
genotype: wild type
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| Treatment protocol |
regular growth condition
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| Growth protocol |
Plants in the greenhouse were germinated on MetroMix 200 medium (SunGro,USA) and maintained at 26-28°C with 15-h daylengthand at 20-22.8 °C with 9-h dark periods.
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| Extracted molecule |
total RNA |
| Extraction protocol |
At 4-weeks after sow , apical meristem tissues were quickly removed, frozen in liquid N2, and stored at –80°C. Total RNA was isolated from materials by using TRIzol Reagent (Invitrogen cat#: P/N 15596-018), followed by further purification by Qiagen RNeasy Mini Kit (P/N 74104). RNA qualities were assessed using an Agilent BioAnalyzer 2100 system (Agilent Technologies).
RNA libraries were constructed as described by TruSeq® RNA Sample Preparation v2 Guide. These libraries were sequenced at a final concentration of 5pM in a Hi-Seq 2500 rapid 100 bp single read runat theSequencing and Microarray Core Facilities of the University of Nebraska Medical Center.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
4-weeks apical meristem, Rutgers wild type, biological replicate 1
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| Data processing |
adapter sequences and the barcodes were removed. FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) was used to confirmsequencing quality.
Bowtie-2.1.0 (Langmead et al, 2009) and Tophat-2.0.10 (Kim D et al, 2013) (with the default parameter) were used to map the reads of tomato samples to gene models in the tomato reference genome ITAG 2.4
DESeq2 (Anders et al, 2010)was used to identify differentially expressed genes (DEGs)between each mutant and the wild-type control. Raw P-values were adjusted using theBenjamini-Hochberg procedure (Benjamini et al, 1995), and a cut-off value of adjusted p< 0.05 was used to identify significant DEGs. For cross comparison, BLAST was used to identify orthologs of tomato genes in Arabidopsis, with the match having the lowest E-value used in each case. After corresponding orthologs were identified, lists of differentially expressed genes in tomato msh1-RNAi and Arabidopsis msh1 (compared to their wild-type counterparts) were compared for overlap.
Genome_build: tomato reference genome ITAG 2.4 (ftp://ftp.solgenomics.net/tomato_genome/annotation/ITAG2.4_release/).
Supplementary_files_format_and_content: Tab delimited files containing FPKM gene-level values for each sample, as well as a cuffdiff generated and further annotated tab-delimited files containing fold-changes and q-values of AL versus AP and LL versus LP.
Supplementary_files_format_and_content: Annotation files are tab-delimited annotated cuffdiff file (log2 fold changes, q-value, gene annotation)
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| Submission date |
Jan 23, 2015 |
| Last update date |
Oct 29, 2019 |
| Contact name |
Hardik Kundariya |
| E-mail(s) |
hsk13@psu.edu
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| Organization name |
The Pennsylvania State University
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| Street address |
361 N. Frear
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| City |
University Park |
| State/province |
PA |
| ZIP/Postal code |
16801 |
| Country |
USA |
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| Platform ID |
GPL19694 |
| Series (1) |
| GSE65242 |
Global transcriptomic changes induced by manipulate MSH1 gene in tomato using next generation sequencing |
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| Relations |
| BioSample |
SAMN03292463 |
| SRA |
SRX851871 |
| 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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