Solanum lycopersicum
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ABSTRACT:
PROVIDER: PRJNA344968 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:To understand the AtJUB1 mediated regulation of tomato fruit development. To test how the NAC transcription factor JUNGBRUNNEN1 from Arabidopsis thaliana (AtJUB1, identical to ANAC042; At2g43000) affects the development of tomato fruits, AtJUB1-GFP was expressed in transgenic tomato plants under the control of the CaMV 35S promoter. AtJUB1-GFP fusion protein was previously shown to encode a functionally active transcription factor in Arabidopsis (Wu et al., 2012). We then performed gene expression profiling of fruits from AtJUB1-GFP lines (AtJUB1-OX plants) and non-modified wild-type (WT) plants. Fruits at two developmental stages, namely mature green (MG) and Breaker+7 days (B+7), were analysed. To this end, the pericarp was separated from the rest of the fruits and quickly frozen in liquid nitrogen for subsequent RNA extraction. Gene expression analysis was performed using GeneChip Tomato Genome Arrays (Affymetrix). Probe preparation and microarray hybridizations were performed by ATLAS Biolabs (Berlin, Germany).
2017-03-31 | GSE87507 | GEO
Project description:By using parallel analysis of RNA ends (PARE) for global identification of miRNA targets and comparing four different stages of tomato fruit development we identified a large number of target genes of miRNAs. PARE libraries were produced, one each, for tomato fruits at 5 days after pollination, mature green fruit, Breaker fruit, and 7 days after Breaker stge fruits
2013-04-05 | E-GEOD-42661 | biostudies-arrayexpress
Project description:Gene expression in wild-type fruit. Strand-specific RNA-Seq data was used to calculate the gene expression value (RPKM) in four wild-type fruit developmental stages including immature fruit at 17DPA, mature green fruit (seeds development completes) at 39DPA, breaker fruit (onset of ripening) at 42DPA and fully ripe fruit at 52DPA. For each sample, two to four biological replicates were sequenced. Note: Samples in SRA were assigned the same sample accession. This is incorrect as there are different samples, hence âSource Nameâ was replaced with new values. Comment[ENA_SAMPLE] contains the original SRA sample accessions.
2011-10-07 | E-MTAB-4818 | biostudies-arrayexpress
Project description:Pepper fruits at four different developmental stages were collected: early fruit [EF; 1 cm long; 7 days after pollination (dap)], mature green fruit (MG; 6-7 cm length; 20 dap), breaking or turning red fruit (BR; fruit are partially red; 35 dap), and red ripe fruit (RR; fully red; 40 dap). Tomato fruits at corresponding developmental stages were also collected: EF (less than 1cm; 7 dap), MG (40 dap), BR (50 dap), and RR (55 dap). For the monitoring of fruit-specific and fruit ripening-related genes, we did array hybridization by using the leaves as a common reference and each corresponding fruit developmental stage sample.
2005-03-01 | E-MEXP-260 | biostudies-arrayexpress
Project description:We sequenced mRNA from immature green (15 days after anthesis) and red (Breaker+10 days) tomato (Solanum lycopersicum) fruit tissues from plants over-expressing SlGLK1 and SlGLK2 and from control plants 'M82' to compare gene expression levels between transgenic fruit and the control. Note: Samples in SRA were assigned the same sample accession. This is incorrect as there are different samples, hence “Source Name” was replaced with new values. Comment[ENA_SAMPLE] contains the original SRA sample accessions.
2013-06-01 | E-MTAB-4819 | biostudies-arrayexpress
Project description:High-throughput sequencing of small RNAs from different developmental stages of tomato fruits
| PRJNA119405 | ENA
Project description:To facilitate the functional annotation of the pepper genome, we generated 90.84 Gb of RNA-Seq data from 33 libraries representing all major tissue types and developmental stages of Zunla 1, as well as fruits from other accessions with significant phenotypic differences. Pepper ‘Zunla 1’ and other inbred lines were grown in a greenhouse as described in Table S1, with their different developmental stages Plants at full-bloom stage were harvested for roots, stems, and leaves as the same as the samples for phased small RNAs (see text S3.4.2 for details). Mature plants were harvested for unopened flower buds (buds) and fully open flowers (flowers). Additional flowers were allowed to self-pollinate and fruit was harvested at four pre-breaker stages (1-3cm, 3-4cm, 4-5cm fruit length, and mature green), the breaker stage (when the fruit was turning red) and three post-breaker stages (3, 5, and 7 days after breaker). These samples will respectively be referred to as Root, Stem, Leaf, Bud, Flower, F-Dev-1, F-Dev-2, F-Dev-3, F-Dev-4, F-Dev-5, F-Dev-6, F-Dev-7, F-Dev-8, and F-Dev-9. Similar roots, stems, leaves, immature fruit and red fruit were harvested from other inbred lines from domesticated Capsicum species. Meanwhile, chiltepin plants were grown under long days at controlled temperature and RNA was extracted from a mix of leaves from four stages (seedling, early blooming, full bloom, and fruit breaker phases), a mix of flowers from unopened flower buds (buds) and fully open flowers (flowers), and fruit at breaker and breaker plus five days respectively. All tissues were frozen in liquid nitrogen and then stored at -80℃. Total RNA was isolated from different samples by using the Trizol Reagent (Invitrogen) according to manufacturer’s instructions. Strand-specific RNA-Seq library preparations were performed as previously described (39) with 12 independently bar-coded samples sequenced on one lane of an Illumina HiSeq2000 system. The 200 bp paired-end libraries were sequenced using Illumina HiSeq 2000 (90 bp PE).
2014-03-14 | E-GEOD-45037 | biostudies-arrayexpress
Project description:In the present study, we demonstrated that application of CaCl2 to ‘Micro Tom’ tomato fruit (mature green stage) delayed fruit senescence and mature.
2017-09-28 | GSE73520 | GEO
Project description:To provide insights into how SUN regulates shape and whether this is accompanied with shifts in transcript profiles, we identified differentially expressed genes in eight pairwise comparisons of SUN and wild-type fruit tissues and time points. Lines nearly isogenic for SUN in the cultivated background Solanum lycopersicum c.v. SUN1642 were grown in the greenhouse in a completely randomized design. SA4 is like SUN1642 and SA3 is like WT LA1589 at SUN locus. Flowers at anthesis were tagged and self-pollinated on successive days. Anthesis is defined as when the flower opens. Pollination of flowers was staggered so fruit of all developmental stages would be harvested on the same day. Fruits at stage four, seven, and ten days post anthesis (dpa) were harvested and brought back to the laboratory. Septum, seed, and pericarp tissue were isolated and frozen in liquid nitrogen. Four dpa septum tissues is a mixture of septum and seed tissue. Four dpa pericarp is a mixture of pericarp and exocarp tissue due to small size of four dpa fruits. Seven and 10 dpa pericarp dont contain the exocarp (epidermal) tissues. Four replicates were collected. RNA was extracted using Trizol and Stand-specific libraries were prepared from total RNA and sequences of 51 bp were generated on an Illumina HiSeq2000.
2013-12-10 | E-MTAB-4837 | biostudies-arrayexpress
Project description:Gene expression in three stages of ripening tomato fruit (variety Ailsa Craig) was determined with the EUTOM3 Affymetrix array in order to compare with degradrome sequencing data from study GSE42661, treated as RNAseq. three replicates of each stage (MG, mature green; T, turning/breaker; RR, red ripe) were hybridized; Expression values were normalized for each sample and reported by iTAG2.3 cDNA identifier in the accompanying matrix table.
2013-04-05 | E-GEOD-42783 | biostudies-arrayexpress