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Dataset results
9 results for “cultivated tomato”
FASTA file containing to the MYB encoding gene Ant1 genomic sequences corresponding to wild and cultivated tomato accessions
<p>Fasta sequence correspond to the MYB encoding gene <em>An2-like</em>. The genomic sequences correspond to <em>Solanum galagpagnese</em> accession LA1141 (this study), <em>S. lycopersicum</em> variety OH8245 (this study), <em>S. lycopersicum</em> variety Heinz 1706 reference genome, and 84 tomato accessions published as part of The 100 Tomato Genome Sequencing Consortium (The 100 Tomato Genome Sequencing Consortium et al., 2014). Local sequences databases were made and retrieved using BLAST version/2018-08 for 84 accessions from The 100 Tomato Genome Sequencing Consortium (The 100 Tomato Genome Sequencing Consortium et al., 2014). Sequences corresponding to Heinz 1706 (Hosmani et al., 2018), were accessed using the Basic Local Alignment Search Tool (BLAST) tool available from the Sol Genomics Network (SGN) (available at <a href="https://solgenomics.net/tools/blast/">https://solgenomics.net/tools/blast/</a>).</p>
FASTA file containing the MYB encoding gene An2-like genomic sequences corresponding to wild and cultivated tomato accessions
<p>FASTA sequence corresponds to the MYB encoding gene <em>An2-like</em>. The genomic sequences correspond to <em>Solanum galagpagnese</em> accession LA1141 (this study), <em>S. lycopersicum</em> variety OH8245 (this study), <em>S. lycopersicum</em> variety Heinz 1706 reference genome (Hosmani et al., 2019), <em>S. lycopersicum </em>variety Indigo Rose (Yan et al., 2020), <em>S. lycopersicum</em> accession LA1996 [MN242011.1 (Colanero et al., 2020)], <em>S. chilense </em>accession LA1930 [MN242012.1 (Colanero et al., 2020)], and 84 tomato accessions published as part of The 100 Tomato Genome Sequencing Consortium (The 100 Tomato Genome Sequencing Consortium et al., 2014). Local sequences databases were made and retrieved using BLAST version/2018-08 for 84 accessions from The 100 Tomato Genome Sequencing Consortium (The 100 Tomato Genome Sequencing Consortium et al., 2014). Sequences corresponding to Heinz 1706 (Hosmani et al., 2018), Indigo Rose [MN433087 (Yan et al., 2020)], <em>S. lycopersicum </em>accession LA1996 [MN242011.1, EF433417.1 (Sapir et al., 2008; Colanero et al., 2020)], <em>S. chilense</em> accession LA1930 [MN242012.1 (Colanero et al., 2020)] were accessed using the Basic Local Alignment Search Tool (BLAST) tool available from the Sol Genomics Network (SGN) (available at <a href="https://solgenomics.net/tools/blast/">https://solgenomics.net/tools/blast/</a>) and the National Center for Biotechnology Information (NCBI)(available at NCBI: <a href="https://www.ncbi.nlm.nih.gov">https://www.ncbi.nlm.nih.gov</a>).</p>
FASTA file containing the MYB encoding genes at the Aft locus with genomic sequences corresponding to wild and cultivated tomato accessions
<p>FASTA sequences correspond to the MYB encoding genes <em>An2-like </em>and <em>Ant1</em>. The genomic sequences were combined correspond to <em>Solanum galagpagnese</em> accession LA1141 (this study), <em>S. lycopersicum</em> variety OH8245 (this study), <em>S. lycopersicum</em> variety Heinz 1706 reference genome (Hosmani et al., 2019), LA1996 [MN242011.1, EF433417.1(Sapir et al., 2008; Colanero et al., 2020)], and 84 tomato accessions published as part of The 100 Tomato Genome Sequencing Consortium (The 100 Tomato Genome Sequencing Consortium et al., 2014). Local sequences databases were made and retrieved using BLAST version/2018-08 for 84 accessions from The 100 Tomato Genome Sequencing Consortium (The 100 Tomato Genome Sequencing Consortium et al., 2014). Sequences corresponding to Heinz 1706 (Hosmani et al., 2018), <em>S. lycopersicum </em>accession LA1996 [MN242011.1, EF433417.1 (Sapir et al., 2008; Colanero et al., 2020)], <em>S. chilense</em> accession LA1930 [MN242012.1 (Colanero et al., 2020)] were accessed using the Basic Local Alignment Search Tool (BLAST) tool available from the Sol Genomics Network (SGN) (available at <a href="https://solgenomics.net/tools/blast/">https://solgenomics.net/tools/blast/</a>) and the National Center for Biotechnology Information (NCBI) (available at NCBI: <a href="https://www.ncbi.nlm.nih.gov/">https://www.ncbi.nlm.nih.gov</a>).</p>
FASTA file containing the MYB encoding gene An2-like and Ant1 coding sequences corresponding to wild and cultivated tomato accessions
<p>The coding sequence (CDS) of the MYB encoding genes <em>Ant1</em> and <em>An2-like</em>. Sequences were retrieved from regions corresponding to the<em> Aft</em> locus from <em>Solanum galapagense </em>accession LA1141, <em>S. lycopersicum</em> variety OH8245, and 84 tomato accessions published as part of The 100 Tomato Genome Sequencing Consortium (The 100 Tomato Genome Sequencing Consortium et al., 2014). Sequences were compared to available CDS available from the Sol genomics network (SGN) and the National Center for Biotechnology Information. The CDS was retrieved from <em>S. lycopersicum</em> variety Indigo Rose [MN433087 (Yan et al., 2020)], <em>S. lycopersicum</em> accession LA1996 [MN242011.1, EF433417.1( Sapir et al., 2008; Colanero et al., 2020)], and <em>S. chilense </em>accession LA1930 [MN242012.1 (Colanero et al., 2020)], The orthologous CDS corresponding to the <em>Aft </em>MYB encoding genes from <em>Solanum tuberosum</em> L. Group Phureja clone DM1-3 genome (PGSC DM v4.03 Pseudomolecules) was retrieved from the Potato Genome Sequence Consortium (PGSC: Potato Genome Sequencing Consortium et al., 2011), and the Capsicum annum cv. CM334 genome was retrieved from <em>Capsicum annuum </em>cv CM334 genome chromosome release 1.55 (Hulse-Kemp et al. 2018). These CDS were obtained using the Basic Local Alignment Search Tool (BLAST) tool available from the Sol Genomics Network (SGN) (available at https://solgenomics.net/tools/blast/). Comparison of syntenic chromosomal regions using known positions of tomato, potato, and pepper markers with comparative map viewer from SGN: (available at https://solgenomics.net/cview) on chromosome 10, was used as a quality check for S.<em> tuberosom</em> and <em>C. annuum.</em> Orthologous CDS corresponding to <em>Salvia miltiorrhiza, Arabidopsis thaliana</em>, [NM_105308.2, NM_105310.4 (Teng et al., 2005, Cominelli et al., 2008; Beradini et al., 2015)] were chosen based on tomato <em>Aft</em> sequence homology and gene annotations of positive R2R3 MYB regulation of anthocyanin. The CDS corresponding to the <em>Aft</em> genes were retrieved from the CDS reference genomes available from the Sol Genomics Network SGN: Tomato Genome CDS (ITAG release 4.0), Potato PGSC DM v3.4 CDS sequences, <em>Capsicum annuum </em>cv CM334 Genome CDS (release 1.55), or from the National Center for Biotechnology Information (NCBI: https://www.ncbi.nlm.nih.gov) reference sequences (RefSeq) section of the Genbank records. When accessed from Genank records, the CDS sequence was extracted from the “features” section and exported as a FASTA file.</p>
Selection strategies to introgress water deficit tolerance derived from Solanum galapagense accession LA1141 into cultivated tomato (datasets)
<p>This dataset includes best linear unbiased predictors (BLUPs) used for composite interval mapping in the LA1141 × OH8245 BC<sub>2</sub>S<sub>3</sub> families (tab - BC2S3_BLUP_data_for_CIM), greenhouse data corresponding to the BC<sub>2</sub>S<sub>5</sub> advanced lines (tab - BC2S5_GH_trial), and field performance data corresponding to the BC<sub>2</sub>S<sub>5</sub> advanced lines (tab - BC2S5_Field_Trial).</p>
Datasets for article: "Growth, yield and fruit quality of tomato Solanum lycopersicum L grown in sewage-based compost in a semi-hydroponic cultivation system"
<p>These are datasets for the article "<a href="https://url6649.tandfonline.com/ls/click?upn=odl8Fji2pFaByYDqV3bjGMQo8st9of2228V6AcSFNq3t86qU90pAx-2BEad4OTI0D6N9KC9sSb13y7BPhSaI63naXaZgVk1tHid9RTOJaM-2BnU-3D7KXJ_7lAorwd83bcaLkCsHwQvGOB9-2B-2BBAnxWbMvsKY6LNfdeMZIZaDBN1qcEGaoB68Zm3oQJMrVyC4lonL7Ijzn3jC4mP-2Bn0By4CgI-2Fsl-2BpH9f-2FkHHDAmcaic3SupThlJumHH0OlnLYxK7sBZVFoAIGTbzWYuCGoTD1OiI-2B9hCV2q3oeUlwNt7LmUWEphiiU2jLHJPhc-2BtmWrqknunT7zsH-2BOotCufae3hHE9Cd6sCbxN0xWhC1N6Eabvq83S0YBORSx-2FVsTVIIbd0BQgD74rizmahhXmrvA5f9Q8Ac7C8oSBVeY-3D">Growth, yield and fruit quality of tomato Solanum lycopersicum L grown in sewage-based compost in a semi-hydroponic cultivation system</a> "</p>
A naturally unique variation in Al-activated malate transporter 9 determines fruit malate in cultivated tomato
GEO Series GSE89772. Solanum lycopersicum. 2 samples. Type: Expression profiling by high throughput sequencing.
SlWRKY33 confers cold tolerance through activation of various downstream signaling pathways in cultivated tomato
GEO Series GSE202902. Solanum lycopersicum. 4 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Solanum section Lycopersicon (cultivated and wild tomato genotypes) trichome pictures
<p><strong>Stem trichome pictures of various genotypes from the <em>Solanum</em> section Lycopersicon:</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 | | 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><strong>Pictures were taken in March 2018 following this two-step protocol:</strong></p> <pre><code class="language-markdown"># Making high-quality pictures of tomato trichomes This protocol is to take high-quality pictures of trichomes and stack them into one unique final picture. The stem from the 4th leaf from the top will be used to make a picture. This protocol is composed of two parts: - Firstly: take a series of pictures (15 to 30 pictures) using a stereomicroscope - Secondly: photo stacking using Photoshop # First part: taking pictures using the Leica MZFLII 1. Turn on the microscope zoom mechanism 2. Turn on the ebq 100 lamp and the Olympus Highlight 2000 lamp 3. Make sure no filter (e.g. dsRed) is applied 4. Open the Nikon NIS-Elements program. 5. Take a piece of stem and place it horizontally (---) under the microscope. . 6. Zoom out completely. 7. Zoom in at 10,000x on the side of the branch ("labeled 10.0 on the microscope). 8. Focus on a few trichomes. Get them as much as possible in focus. This is going to be your first picture (foreground). 9. Zoom in about a few trichome layers away. There should not be too much overlap between the different trichomes (otherwise they get merged together during the stacking phase). This will be your background. 10. Zoom out to go back to the foreground (= your first picture). 11. Depending on the number of trichomes in-between your foreground and background, you need to take a variable number of pictures. - If trichome density is high, then trichomes will overlap during the stacking meaning that you need to take more pictures (~30) and reduce the distance between your foreground and background. - If trichome density is low, then trichomes won't overlap and you need less pictures (~10) # Second part: alignment of pictures using Photoshop See the trichome layer photography protocol (PDF file)made by Maurice Heilijgers (August 2018).</code></pre> <p> </p>
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.