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353 results for “mRNA-seq”
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 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>
mRNA-seq of immortailized bone marrow derived macrophages (iBMDM) infected with type II Toxoplasma gondii
GEO Series GSE128752. Mus musculus. 6 samples. Type: Expression profiling by high throughput sequencing.
The post-translational modifications and translation-regulatory role of METTL14 in 5-fluorouracil-resistant colorectal cancer [mRNA-seq]
GEO Series GSE219171. Homo sapiens. 4 samples. Type: Expression profiling by high throughput sequencing.
mRNA-seq study performed on MCF-7 breast cancer cells treated with a combination of vitamins A and D
GEO Series GSE221019. Homo sapiens. 6 samples. Type: Expression profiling by high throughput sequencing.
mRNA-seq of Pea3 triple mutants in 10ss Danio rerio larvae
GEO Series GSE155013. Danio rerio. 6 samples. Type: Expression profiling by high throughput sequencing.
Comparative anterior pituitary miRNA and mRNA expression profiles of Bama minipigs and Landrace pigs reveal potential molecular network involved in animal postnatal growth [mRNA-Seq]
GEO Series GSE68490. Sus scrofa. 2 samples. Type: Expression profiling by high throughput sequencing.
mRNA-seq analysis of rex-1 deletion in C. elegans
GEO Series GSE265989. Caenorhabditis elegans. 6 samples. Type: Expression profiling by high throughput sequencing.
Dysregulated ac4C modification of mRNA in a mouse model of early stage Alzheimer's disease [mRNA-seq]
GEO Series GSE281343. Mus musculus. 6 samples. Type: Expression profiling by high throughput sequencing.
Heat stress effects on gene expression in the grape berry. Comparison of pre- and post-véraison berries and microarray versus mRNA-seq datasets.
GEO Series GSE33222. Vitis vinifera. 8 samples. Type: Expression profiling by high throughput sequencing.
mRNA-seq analysis of early adult C. elegans fatty acid synthesis mutant following extended L1 arrest
GEO Series GSE178171. Caenorhabditis elegans. 4 samples. Type: Expression profiling by high throughput sequencing.
mRNA-Seq of brain tissue from honeybee (Apis mellifera) drones (male), workers (female) and queens (female).
GEO Series GSE45408. Apis mellifera carnica. 9 samples. Type: Expression profiling by high throughput sequencing.
mRNA-Seq identifies the differentially expressed mRNA in negative control and METTL3 knockdown HULEC-5a
GEO Series GSE200649. Homo sapiens. 4 samples. Type: Expression profiling by high throughput sequencing.
mRNA-seq of wild-type or ZUFSP knockout THP1 cells after vesicular stomatitis virus infection
GEO Series GSE239783. Homo sapiens. 4 samples. Type: Expression profiling by high throughput sequencing.
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