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| Status |
Public on Sep 14, 2020 |
| Title |
WT elongation rep2 |
| Sample type |
SRA |
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| Source name |
Root
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| Organism |
Solanum lycopersicum |
| Characteristics |
cultivar: Ailsa Craig
tissue: Elongation zone
genotype: WT
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| Growth protocol |
Three biological replicates for each tissue and genotype were performed. Seven-day old tomato (Solanum lycopersicum) wild-type and dgt1-1 plants in the ‘AilsaCraig’ background7were used. Seeds were sterilized in 20% commercial bleach for 30 min and rinsed four times for 10 min with sterile water. Sterilized seeds were incubated at 4C for 2d to ensure even germination and then planted on media containing 0.2× Murashige and Skoog basal medium with vitamins (PhytoTechnology; http://www.phytotechlab.com), 1 % sucrose, 10 mM MES buffer pH5.7,and 0.8% agar. Seeds were germinated in Magenta dishes (16 seeds per dish) in a growth chamber at 21C under long day (16h light, 8h dark) conditions and light intensity as in Ivanchenko et al. (2013). Root samples were dissected under DIC optics at 4× objective as in Ivanchenko et al. (2006). On average, 50–100 root portions were collected per biological replicate. The meristem was dissected between the root tip and the root portion where tissue becomes more transparent. The elongation zone was collected from the proximal meristem border and the first hair bulge, and approximately 1 cm portions were collected above the first hair bulge for the differentiation zone.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Tissue was ground in liquid N2 and RNA extracted with Plant RNA Reagent (Life Technologies; http://www.lifetechnologies.com). Total RNA was treated with 1X RNA Secure Reagent (Ambion; http://www.lifetechnologies.com) at 65C for 10 min, treated with DNase I (Ambion; http://www.lifetechnologies.com) at 37C for 10 min, and purified with RNeasy kit (Qiagen; http://www.qiagen.com) following the manufacturer's instructions.
RNA-Seq library preparation and sequencing was performed at the Oregon State University Center for Genome Research and Biocomputing. Libraries were prepared using the TruSeq RNA Sample Prep Kit v2 (Illumina, San Diego, CA) and sequenced as single-end 51 bpreads on two lanes of the Illumina HiSeq 2000.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
Illumina Casava v1.8.2 software used for basecalling.
Reference transcripts were extracted and preprocessed from the NCBI Heinz 1706 genome sequence and gene annotation (GCF_000188115.4) using RSEM’s (RNA-Seq by Expectation Maximization, version 1.3.1) rsem-prepare-reference function
Using RSEM, raw sequence reads wer aligned to the reference transcript sequences and relative abundances were calculated using default parameters. Resulting gene-level estimates from biological replicates were merged into a single input matrix and EBSeq (version 1.26.0) was then used to test for differential expression between dgt and WT for each root-tip zone.
Genome_build: GCF_000188115.4
Supplementary_files_format_and_content: genes.results.txt files contain tab-delimited expression estimates including TPM and FPKM from RSEM at a gene-level, and isoforms.results.txt files contain the same estimate types at an isoform-level. Txt files present differential expression analysis from EBSeq of dgt as compared to WT.
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| Submission date |
Aug 18, 2020 |
| Last update date |
Sep 15, 2020 |
| Contact name |
Molly Megraw |
| E-mail(s) |
megrawm@science.oregonstate.edu
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| Organization name |
Oregon State University
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| Street address |
2082 Cordley Hall
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| City |
Corvallis |
| State/province |
Oregon |
| ZIP/Postal code |
97331 |
| Country |
USA |
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| Platform ID |
GPL16345 |
| Series (1) |
| GSE156398 |
RNA-Seq analysis of genes affected by Cyclophilin A/DIAGEOTROPICA (DGT) in tomato root development |
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| Relations |
| BioSample |
SAMN15847799 |
| SRA |
SRX8961646 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4730154_AC-E2.genes.results.txt.gz |
613.4 Kb |
(ftp)(http) |
TXT |
| GSM4730154_AC-E2.isoforms.results.txt.gz |
854.9 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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