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145 results for “trichomes”
Insights into the transcriptional cascade involved in the initial and early phases of glandular trichome development in Nicotiana tabacum [RNAseq_MIXTA]
GEO Series GSE263485. Nicotiana tabacum. 12 samples. Type: Expression profiling by high throughput sequencing.
Comparison of gene expression in Arabidopsis trichome between gtl1-1 mutant and wild type
GEO Series GSE40518. Arabidopsis thaliana. 6 samples. Type: Expression profiling by array.
Insights into the transcriptional cascade involved in the initial and early phases of glandular trichome development in Nicotiana tabacum [DAPseq_MIXTA_ZFP8]
GEO Series GSE263486. Nicotiana tabacum. 9 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
FIGURE. Alsophila erinacea (H. Karst.) D.S. Conant., Sean Feeney 1(C) & DA/RP3 (TCD). A. Laminae; B. Indusia present and without trichomes. Veins with star-like trichomes abaxially. in Ferns and Lycophytes of Honduras: A new annotated checklist
FIGURE. Alsophila erinacea (H. Karst.) D.S. Conant., Sean Feeney 1(C) & DA/RP3 (TCD). A. Laminae; B. Indusia present and without trichomes. Veins with star-like trichomes abaxially.
Stochastic Turing patterns of trichomes in Arabidopsis leaves. Data and Software.
<p>Data and Software.</p>
Different gene expression in the tomato trichome and leaf
GEO Series GSE117766. Solanum lycopersicum. 8 samples. Type: Expression profiling by high throughput sequencing.
⁶⁰Co-γ radiation-induced GDH64 NtCYC mutation enhances the glandular trichome density and aroma quality of tobacco via physiological, biochemical, and molecular mechanisms
GEO Series GSE296296. Nicotiana tabacum. 6 samples. Type: Expression profiling by high throughput sequencing.
Stem trichome mRNA-Seq dataset from the 20 accessions (files part 2)
<p><strong>RNA isolation and sequencing</strong> </p> <p>Total RNA were isolated using the RNeasy Plant Mini Kit (QIAGEN) from 50 to 150mg of stem trichome material. RNA concentration and quality was assessed using the Agilent 2100 Bioanalyzer instrument (Agilent). mRNA sequencing was done using the Proton Ion system using PI chips and yielded between 25 and 33 million reads per sample.</p> <p><strong>Table of genotypes used</strong></p> <p> </p> <pre><code class="language-markdown">| accession | species | accession nr | synonym | origin | |------------|--------------------------------|--------------|---------|-------------| | LA2172 | S. arcanum | TR0009 | - | Peru | | LA1401* | S. cheesmaniae f. minor | EA00652 | - | Ecuador | | LA1840 | S. chmielewskii | - | - | unknown | | LA2695 | S. chmielewskii | EA00759 | - | Peru | | LA0407 | S. habrochaites f. glabratum | EA00558 | - | Ecuador | | LA1777 | S. habrochaites f. hirsutum | EA00703 | - | Peru | | PI134418 | S. habrochaites f. glabratum | TR00015 | LYC38 | unknown | | LYC4 | S. habrochaites f. hirsutum | TR00017 | - | unknown | | LA1718 | S. habrochaites f. glabratum | EA00699 | LYC4934 | Peru | | PI127826 | S. habrochaites f. hirsutum | - | - | Peru | | LA1364 | S. huaylasense | TR00030 | - | Peru | | Moneymaker | S. lycopersicum | - | C32 | Netherlands | | LA4024 | S. lycopersicum | TA209 | - | unknown | | LA2133 | S. neorickii/L. parviflorum | EA00729 | - | Peru | | LA0735 | S. neorickii | TR00025 | LYC140 | unknown | | LA0716 | S. pennellii | EA00585 | - | Peru | | LA1278 | S. peruvianum/pimpinellifolium | TR00005 | - | unknown | | LA1954 | S. peruvianum | EA00713 | - | Peru | | LA1578 | S. pimpinellifolium | EA00674 | - | Peru |</code></pre> <p> </p>
Stem trichome mRNA-Seq dataset from the 20 accessions (part 1)
<p><strong>RNA isolation and sequencing</strong> </p> <p>Total RNA were isolated using the RNeasy Plant Mini Kit (QIAGEN) from 50 to 150mg of stem trichome material. RNA concentration and quality was assessed using the Agilent 2100 Bioanalyzer instrument (Agilent). mRNA sequencing was done using the Proton Ion system using PI chips and yielded between 25 and 33 million reads per sample.</p> <p><strong>Table of genotypes used</strong></p> <p> </p> <pre><code class="language-markdown">| accession | species | accession nr | synonym | origin | |------------|--------------------------------|--------------|---------|-------------| | LA2172 | S. arcanum | TR0009 | - | Peru | | LA1401* | S. cheesmaniae f. minor | EA00652 | - | Ecuador | | LA1840 | S. chmielewskii | - | - | unknown | | LA2695 | S. chmielewskii | EA00759 | - | Peru | | LA0407 | S. habrochaites f. glabratum | EA00558 | - | Ecuador | | LA1777 | S. habrochaites f. hirsutum | EA00703 | - | Peru | | PI134418 | S. habrochaites f. glabratum | TR00015 | LYC38 | unknown | | LYC4 | S. habrochaites f. hirsutum | TR00017 | - | unknown | | LA1718 | S. habrochaites f. glabratum | EA00699 | LYC4934 | Peru | | PI127826 | S. habrochaites f. hirsutum | - | - | Peru | | LA1364 | S. huaylasense | TR00030 | - | Peru | | Moneymaker | S. lycopersicum | - | C32 | Netherlands | | LA4024 | S. lycopersicum | TA209 | - | unknown | | LA2133 | S. neorickii/L. parviflorum | EA00729 | - | Peru | | LA0735 | S. neorickii | TR00025 | LYC140 | unknown | | LA0716 | S. pennellii | EA00585 | - | Peru | | LA1278 | S. peruvianum/pimpinellifolium | TR00005 | - | unknown | | LA1954 | S. peruvianum | EA00713 | - | Peru | | LA1578 | S. pimpinellifolium | EA00674 | - | Peru |</code></pre> <p> </p>
Stem trichome mRNA-Seq dataset from the 20 accessions (part 5)
<p><strong>RNA isolation and sequencing</strong> </p> <p>Total RNA were isolated using the RNeasy Plant Mini Kit (QIAGEN) from 50 to 150mg of stem trichome material. RNA concentration and quality was assessed using the Agilent 2100 Bioanalyzer instrument (Agilent). mRNA sequencing was done using the Proton Ion system using PI chips and yielded between 25 and 33 million reads per sample.</p> <p><strong>Table of genotypes used</strong></p> <p> </p> <pre><code class="language-markdown">| accession | species | accession nr | synonym | origin | |------------|--------------------------------|--------------|---------|-------------| | LA2172 | S. arcanum | TR0009 | - | Peru | | LA1401* | S. cheesmaniae f. minor | EA00652 | - | Ecuador | | LA1840 | S. chmielewskii | - | - | unknown | | LA2695 | S. chmielewskii | EA00759 | - | Peru | | LA0407 | S. habrochaites f. glabratum | EA00558 | - | Ecuador | | LA1777 | S. habrochaites f. hirsutum | EA00703 | - | Peru | | PI134418 | S. habrochaites f. glabratum | TR00015 | LYC38 | unknown | | LYC4 | S. habrochaites f. hirsutum | TR00017 | - | unknown | | LA1718 | S. habrochaites f. glabratum | EA00699 | LYC4934 | Peru | | PI127826 | S. habrochaites f. hirsutum | - | - | Peru | | LA1364 | S. huaylasense | TR00030 | - | Peru | | Moneymaker | S. lycopersicum | - | C32 | Netherlands | | LA4024 | S. lycopersicum | TA209 | - | unknown | | LA2133 | S. neorickii/L. parviflorum | EA00729 | - | Peru | | LA0735 | S. neorickii | TR00025 | LYC140 | unknown | | LA0716 | S. pennellii | EA00585 | - | Peru | | LA1278 | S. peruvianum/pimpinellifolium | TR00005 | - | unknown | | LA1954 | S. peruvianum | EA00713 | - | Peru | | LA1578 | S. pimpinellifolium | EA00674 | - | Peru |</code></pre> <p> </p>
Stem trichome mRNA-Seq dataset from the 20 accessions (part 4)
<p><strong>RNA isolation and sequencing</strong> </p> <p>Total RNA were isolated using the RNeasy Plant Mini Kit (QIAGEN) from 50 to 150mg of stem trichome material. RNA concentration and quality was assessed using the Agilent 2100 Bioanalyzer instrument (Agilent). mRNA sequencing was done using the Proton Ion system using PI chips and yielded between 25 and 33 million reads per sample.</p> <p><strong>Table of genotypes used</strong></p> <p> </p> <pre><code class="language-markdown">| accession | species | accession nr | synonym | origin | |------------|--------------------------------|--------------|---------|-------------| | LA2172 | S. arcanum | TR0009 | - | Peru | | LA1401* | S. cheesmaniae f. minor | EA00652 | - | Ecuador | | LA1840 | S. chmielewskii | - | - | unknown | | LA2695 | S. chmielewskii | EA00759 | - | Peru | | LA0407 | S. habrochaites f. glabratum | EA00558 | - | Ecuador | | LA1777 | S. habrochaites f. hirsutum | EA00703 | - | Peru | | PI134418 | S. habrochaites f. glabratum | TR00015 | LYC38 | unknown | | LYC4 | S. habrochaites f. hirsutum | TR00017 | - | unknown | | LA1718 | S. habrochaites f. glabratum | EA00699 | LYC4934 | Peru | | PI127826 | S. habrochaites f. hirsutum | - | - | Peru | | LA1364 | S. huaylasense | TR00030 | - | Peru | | Moneymaker | S. lycopersicum | - | C32 | Netherlands | | LA4024 | S. lycopersicum | TA209 | - | unknown | | LA2133 | S. neorickii/L. parviflorum | EA00729 | - | Peru | | LA0735 | S. neorickii | TR00025 | LYC140 | unknown | | LA0716 | S. pennellii | EA00585 | - | Peru | | LA1278 | S. peruvianum/pimpinellifolium | TR00005 | - | unknown | | LA1954 | S. peruvianum | EA00713 | - | Peru | | LA1578 | S. pimpinellifolium | EA00674 | - | Peru |</code></pre> <p> </p>
Stem trichome mRNA-Seq dataset from the 20 accessions (part 3)
<p><strong>RNA isolation and sequencing</strong> </p> <p>Total RNA were isolated using the RNeasy Plant Mini Kit (QIAGEN) from 50 to 150mg of stem trichome material. RNA concentration and quality was assessed using the Agilent 2100 Bioanalyzer instrument (Agilent). mRNA sequencing was done using the Proton Ion system using PI chips and yielded between 25 and 33 million reads per sample.</p> <p><strong>Table of genotypes used</strong></p> <p> </p> <pre><code class="language-markdown">| accession | species | accession nr | synonym | origin | |------------|--------------------------------|--------------|---------|-------------| | LA2172 | S. arcanum | TR0009 | - | Peru | | LA1401* | S. cheesmaniae f. minor | EA00652 | - | Ecuador | | LA1840 | S. chmielewskii | - | - | unknown | | LA2695 | S. chmielewskii | EA00759 | - | Peru | | LA0407 | S. habrochaites f. glabratum | EA00558 | - | Ecuador | | LA1777 | S. habrochaites f. hirsutum | EA00703 | - | Peru | | PI134418 | S. habrochaites f. glabratum | TR00015 | LYC38 | unknown | | LYC4 | S. habrochaites f. hirsutum | TR00017 | - | unknown | | LA1718 | S. habrochaites f. glabratum | EA00699 | LYC4934 | Peru | | PI127826 | S. habrochaites f. hirsutum | - | - | Peru | | LA1364 | S. huaylasense | TR00030 | - | Peru | | Moneymaker | S. lycopersicum | - | C32 | Netherlands | | LA4024 | S. lycopersicum | TA209 | - | unknown | | LA2133 | S. neorickii/L. parviflorum | EA00729 | - | Peru | | LA0735 | S. neorickii | TR00025 | LYC140 | unknown | | LA0716 | S. pennellii | EA00585 | - | Peru | | LA1278 | S. peruvianum/pimpinellifolium | TR00005 | - | unknown | | LA1954 | S. peruvianum | EA00713 | - | Peru | | LA1578 | S. pimpinellifolium | EA00674 | - | Peru |</code></pre> <p> </p>
Scaled counts of trichome mRNA-seq from the 20 accessions
<p><strong>mRNA-seq scaled counts from stem trichomes of the 20 accessions. </strong></p> <p>Pipeline: rnaseq-analysis-kallisto-sleuth: release v0.2.2</p> <p><a href="https://github.com/BleekerLab/rnaseq-analysis-kallisto-sleuth/releases">https://github.com/BleekerLab/rnaseq-analysis-kallisto-sleuth/releases</a></p> <p> </p> <p>Transcriptome used: S. lycopersicum ITAG4.0 cDNA</p> <p><strong>Table of genotypes</strong></p> <p> </p> <pre><code class="language-markdown">| accession | species | accession nr | synonym | origin | |------------|--------------------------------|--------------|---------|-------------| | LA2172 | S. arcanum | TR0009 | - | Peru | | LA1401* | S. cheesmaniae f. minor | EA00652 | - | Ecuador | | LA1840 | S. chmielewskii | - | - | unknown | | LA2695 | S. chmielewskii | EA00759 | - | Peru | | LA0407 | S. habrochaites f. glabratum | EA00558 | - | Ecuador | | LA1777 | S. habrochaites f. hirsutum | EA00703 | - | Peru | | PI134418 | S. habrochaites f. glabratum | TR00015 | LYC38 | unknown | | LYC4 | S. habrochaites f. hirsutum | TR00017 | - | unknown | | LA1718 | S. habrochaites f. glabratum | EA00699 | LYC4934 | Peru | | PI127826 | S. habrochaites f. hirsutum | - | - | Peru | | LA1364 | S. huaylasense | TR00030 | - | Peru | | Moneymaker | S. lycopersicum | - | C32 | Netherlands | | LA4024 | S. lycopersicum | TA209 | - | unknown | | LA2133 | S. neorickii/L. parviflorum | EA00729 | - | Peru | | LA0735 | S. neorickii | TR00025 | LYC140 | unknown | | LA0716 | S. pennellii | EA00585 | - | Peru | | LA1278 | S. peruvianum/pimpinellifolium | TR00005 | - | unknown | | LA1954 | S. peruvianum | EA00713 | - | Peru | | LA1578 | S. pimpinellifolium | EA00674 | - | Peru |</code></pre> <p> </p> <p> </p>
Stem trichome small RNA-Seq from the 20 accessions
<p><strong>Total and Small RNA Isolation</strong></p> <p>Total RNA from stem trichomes (n = 1) were isolated using concentrated TRIzol reagent (Life Technologies). Total RNA was isolated using the E.Z.N.A.<sup>®</sup> MicroElute RNA Clean Up Kit (Omega Bio-Tek). Briefly, TRIzol Reagent (Life Technologies) and chloroform was added according to the manufacturer's instructions. After centrifugation, the RNA-containing aqueous phase was collected, mixed with 1.5 volume of 100% ethanol and applied to a MicroElute spin column (Omega Bio-Tek). The column was washed according to the manufacturers's instructions: once with RWT buffer (Qiagen), once with RPE washing buffer (Qiagen) and finally with 80% ethanol. The RNA concentration was measured on a NanoDrop ND-2000 (Thermo Scientific) and RNA integrity was examined using the 2200 TapeStation System with Agilent RNA ScreenTapes (Agilent Technologies).</p> <p>Total RNA was spiked with ERCCs spike-in mix 1 (Life Technologies) as well as a synthetic spike-in set for Size Range Quality Control (SRQC) together with an External Reference for Data Normalization (ERDN; <a href="https://www.frontiersin.org/articles/10.3389/fpls.2016.01759/full#B38">Locati et al., 2015</a>). The total RNA was divided in a large and a small fraction. The large RNA fraction was bound to a mirVana™ spin column (mirVana™ miRNA Isolation Kit, Life Technologies) according to the manufacturer's instructions. Small RNAs (<200 nts) were purified from the flow-through by adding ethanol to a final concentration of 65% (v/v) and bound to an E.Z.N.A.<sup>®</sup> MicroElute spin column. The column was washed once with RWT buffer, once with RPE buffer and once with 80% ethanol (Qiagen). The concentration and integrity of small RNA was examined as described above.</p> <p><strong>Next-Generation Sequencing</strong></p> <p>Bar-coded small RNA libraries were generated according to the manufacturer's protocols using the Ion Total RNA-Seq Kit v2 and the Ion Xpress™ RNA-Seq bar-coding kit (Life Technologies). The size distribution and yield of the bar-coded libraries were assessed using the 2200 TapeStation System with Agilent D1K ScreenTapes (Agilent Technologies). Sequencing templates were prepared on the Ion Chef™ System using the Ion PI Hi-Q Chef Kit (Life Technologies). Sequencing was performed on an Ion Proton™ System using Ion PI v3 chips (Life Technologies) according to the manufacturer's instructions.</p> <p><strong>References</strong></p> <p>Locati et al. 2015. Improving small RNA-seq by using a synthetic spike-in set for size-range quality control together with a set for data normalization. <a href="https://www.ncbi.nlm.nih.gov/pubmed/25870415#">Nucleic Acids Res.</a> (2015). 43(14):e89. doi: 10.1093/nar/gkv303. </p> <p><strong>Table of genotypes used</strong></p> <pre><code class="language-markdown">| accession | species | accession nr | synonym | origin | |------------|--------------------------------|--------------|---------|-------------| | LA2172 | S. arcanum | TR0009 | - | Peru | | LA1401* | S. cheesmaniae f. minor | EA00652 | - | Ecuador | | LA1840 | S. chmielewskii | - | - | unknown | | LA2695 | S. chmielewskii | EA00759 | - | Peru | | LA0407 | S. habrochaites f. glabratum | EA00558 | - | Ecuador | | LA1777 | S. habrochaites f. hirsutum | EA00703 | - | Peru | | PI134418 | S. habrochaites f. glabratum | TR00015 | LYC38 | unknown | | LYC4 | S. habrochaites f. hirsutum | TR00017 | - | unknown | | LA1718 | S. habrochaites f. glabratum | EA00699 | LYC4934 | Peru | | PI127826 | S. habrochaites f. hirsutum | - | - | Peru | | LA1364 | S. huaylasense | TR00030 | - | Peru | | Moneymaker | S. lycopersicum | - | C32 | Netherlands | | LA4024 | S. lycopersicum | TA209 | - | unknown | | LA2386 | S. lycopersicoides | - | - | Peru | LA2133 | S. neorickii/L. parviflorum | EA00729 | - | Peru | | LA0735 | S. neorickii | TR00025 | LYC140 | unknown | | LA0716 | S. pennellii | EA00585 | - | Peru | | LA1278 | S. peruvianum/pimpinellifolium | TR00005 | - | unknown | | LA1954 | S. peruvianum | EA00713 | - | Peru | | LA1578 | S. pimpinellifolium | EA00674 | - | Peru |</code></pre>
Stem trichome mRNA-Seq from lycopersicum x habrochaites crosses (Parents and F1)
<p><strong>Stem trichome mRNA-Seq datasets from different crossing materials.</strong></p> <p>Genetic material</p> <p>Obtained from ENZA Zaden. The pollen from <em>S. habrochaites</em> LA1777 or PI127826 was placed on the pistil of <em>S. lycopersicum to obtain </em>interspecific crosses. </p> <p>The pollen of <em>S. habrochaites</em> LA1777 was placed on the pistil of PI127826 to obtain <em>S. habrochaites</em> F1.</p> <p><strong>Sample collection</strong></p> <p>....</p> <p><strong>Total RNA isolation</strong></p> <p><strong>....</strong></p> <p><strong>Sequencing </strong></p> <p>...</p> <p>Sample table</p> <pre><code class="language-markdown">| sample | species | cross | |--------------------- |--------------------------------------- |---------- | | 14865_PI127826_F1 | S. lycopersicum x S. habrochaites | F1 | | LA1777_4 | S. habrochaites | Parent | | LA1777_F1_3 | S. lycopersicum x S. habrochaites | F1 | | LA1777_P1_Cv_4 | S. lycopersicum | Parent | | PI26_P1_cv_i | S. lycopersicum | Parent | | PI26_P2_w_4 | S. habrochaites f. hirsutum | Parent | | PI26xLA1777_F1_J | S. habrochaites | F1 |</code></pre> <p> </p>
Stem trichome mRNA-Seq from S. lycopersicum x S. habrochaites PI127826 crosses (F2 lines)
<p><strong>Stem trichome mRNA-Seq datasets from different crossing materials.</strong></p> <p>Genetic material</p> <p>Obtained from ENZA Zaden. The pollen from <em>S. habrochaites</em> PI127826 was placed on the pistil of <em>S. lycopersicum to obtain </em>interspecific crosses. </p> <p><strong>Sample collection</strong></p> <p>....</p> <p><strong>Total RNA isolation</strong></p> <p><strong>....</strong></p> <p><strong>Sequencing </strong></p> <p>...</p> <p><strong>Sample table</strong></p> <p>See the samples.csv file.</p> <p> </p>
Comparative Transcriptomics Identifies Differentially Expressed Genes Regulating endoreplication and trichome branching
GEO Series GSE185717. Arabidopsis thaliana. 6 samples. Type: Expression profiling by high throughput sequencing.
The B-type cyclin gene, SlCycB2, is essential to multicellular trichome-mediated defense against herbivores and reproductive organ development in tomato
GEO Series GSE90747. Solanum lycopersicum. 2 samples. Type: Expression profiling by high throughput sequencing.
Expression data from trichomes and pavement cells
GEO Series GSE14053. Arabidopsis thaliana. 2 samples. Type: Expression profiling by array.
BSc project data repository, In silico analysis of microRNA regulation of tomato trichome-based specialized metabolism
<p>Data repository of the bachelor project of Sjors Huizinga (April - June, 2020).</p> <p>The following files are present:</p> <p>README.txt</p> <p>NDA_SjorsHuizinga.pdf<br> Contains the non-disclosure agreement signed before the start of the project.</p> <p>Scripts_Github_Repository.txt<br> Contains the URL of the github repostory in which all custom scripts created<br> and used during the project are stored.</p> <p>The following subfolders are present:</p> <p>ProjectPlan<br> Contains the research proposal.</p> <p>RawData<br> Contains raw data that is considered read-only; degradome data, metabolite<br> data, miRNA data, and trichome count data.</p> <p>Results<br> Contains figures, tables, and data generated during the project; annotation<br> target prediction, degradome analysis, etc.</p>
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