Similar Datasets
Project description:Bisulfite treatment libraries were made to characterize the DNA methylome of tea tree
2018-09-15 | GSE119992 | GEO
Project description:Bisulfite treatment libraries were made to characterize DNA methylaiton of potato
2017-12-06 | GSE102651 | GEO
Project description:Bisulfite treatment libraries were made to characterize DNA methylation of Norway spruce
2016-11-22 | GSE86983 | GEO
Project description:Bisulfite treatment, and mRNA libraries were made to characterize DNA methylation and expression of cassava.
2015-10-12 | GSE73644 | GEO
Project description:Bisulfite treatment, and mRNA libraries were made to characterize DNA methylation and expression of cassava.
2015-10-12 | GSE73643 | GEO
Project description:Here we have undertaken a pilot study analysing the proteome of MD2 pineapple using Liquid Chromatography coupled with Mass Spectrometry (LC-MS/MS) and identified 3,818 peptides from 1,781 candidate proteins in the annotated V3 genome sequenced. In addition, a further 603 peptide identifications were found that mapped exclusively to an independent MD2 transcriptome-derived database and were not found in the standard V3 annotated proteome. Peptide identifications derived from the MD2 transcripts were also cross-referenced to a more recent and complete MD2 genome annotation, resulting in 402 non overlapping peptides with either of the genomes. Subsequently, cross-referencing these peptide identifications via their parent transcripts, 30 high-quality gene candidates novel to the V3 pineapple genomes were identified. These analyses add to the knowledge of experimentally validated pineapple genes and demonstrate the utility of transcript-derived proteomics to discover both novel genes and genetic structure in plant genome, and can help improve its annotation.
2024-05-24 | PXD045998 | Pride
Project description:Pineapple (Ananas comosus var. comosus) and ornamental bromeliads are commercially induced to flower by treatment with ethylene or its analogs. The apex is transformed from a vegetative to a floral meristem and shows morphological changes in 8 to 10 days, with flowers developing 8 to 10 weeks later. During eight sampling stages ranging from 6 hours to 8 days after treatment, 7,961 genes were found to exhibit differential expression (DEG) after the application of ethylene. In the first 3 days after treatment, there was little change in ethylene synthesis or in the early stages of the ethylene response. Subsequently, three ethylene response transcription factors (ERTF) were up-regulated and the potential gene targets were predicted to be the positive flowering regulator CONSTANS (CO), a WUSCHEL gene, two APETALA1/FRUTFULL (AP1/FUL) genes, an epidermal patterning gene and a jasmonic acid synthesis gene. We confirm that pineapple has lost the flowering repressor FLOWERING LOCUS C. At the initial stages, the SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 (SOC1) was not significantly involved in this transition. Another WUSCHEL gene and a PHD homeobox transcription factor, though not apparent direct targets of ERTF, were up-regulated within a day of treatment, their predicted targets being the up-regulated CO, auxin response factors, SQUAMOSA, and histone H3 genes with suppression of abscisic acid response genes. The FLOWERING LOCUS T (FT), TERMINAL FLOWER (TFL), AGAMOUS-like APETELAR (AP2) and SEPETALA (SEP) increased rapidly within 2 to 3 days after ethylene treatment. Two FT genes were up-regulated in the apex and not the leaf bases after treatment, suggesting that transport did not occur. These results indicated that the ethylene response in pineapple and possibly most bromeliads acts directly to promote the vegetative to flower transition via APETALA1/FRUITFULL (AP1/FUL) and its interaction with SPL, FT, TFL, SEP and AP2.
2023-11-22 | GSE239489 | GEO
Project description:Pineapple (Ananas comosus var. comosus) and ornamental bromeliads are commercially induced to flower by treatment with ethylene or its analogs. The apex is transformed from a vegetative to a floral meristem and shows morphological changes in 8 to 10 days, with flowers developing 8 to 10 weeks later. During eight sampling stages ranging from 6 hours to 8 days after treatment, 7,961 genes were found to exhibit differential expression (DEG) after the application of ethylene. In the first 3 days after treatment, there was little change in ethylene synthesis or in the early stages of the ethylene response. Subsequently, three ethylene response transcription factors (ERTF) were up-regulated and the potential gene targets were predicted to be the positive flowering regulator CONSTANS (CO), a WUSCHEL gene, two APETALA1/FRUTFULL (AP1/FUL) genes, an epidermal patterning gene and a jasmonic acid synthesis gene. We confirm that pineapple has lost the flowering repressor FLOWERING LOCUS C. At the initial stages, the SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 (SOC1) was not significantly involved in this transition. Another WUSCHEL gene and a PHD homeobox transcription factor, though not apparent direct targets of ERTF, were up-regulated within a day of treatment, their predicted targets being the up-regulated CO, auxin response factors, SQUAMOSA, and histone H3 genes with suppression of abscisic acid response genes. The FLOWERING LOCUS T (FT), TERMINAL FLOWER (TFL), AGAMOUS-like APETELAR (AP2) and SEPETALA (SEP) increased rapidly within 2 to 3 days after ethylene treatment. Two FT genes were up-regulated in the apex and not the leaf bases after treatment, suggesting that transport did not occur. These results indicated that the ethylene response in pineapple and possibly most bromeliads acts directly to promote the vegetative to flower transition via APETALA1/FRUITFULL (AP1/FUL) and its interaction with SPL, FT, TFL, SEP and AP2.
2023-11-22 | GSE241286 | GEO
Project description:Bisulfite sequencing is a valuable tool for mapping the position of 5-methylcytosine in the genome at single base resolution. However, the associated chemistry renders the majority of DNA fragments unsequenceable, thus necessitating PCR amplification. Furthermore, bisulfite conversion generates an A,T-rich DNA library that leads to major PCR biases that may confound methylation analysis. Here we report a method that enables accurate methylation analysis, by rebuilding the damaged DNA library after bisulfite treatment. This recovery after bisulfite treatment (ReBuilT) approach enables PCR-free bisulfite sequencing from low nanogram quantities of genomic DNA. We applied the ReBuilT method for whole methylome analysis of the A,T rich genome of Plasmodium berghei. We demonstrate substantial improvements in coverage and the reduction of sequence-context biases as compared to classical methylome analysis. Our method will be widely applicable for accurate, quantitative methylation analysis, even for technically challenging genomes, and where limited sample DNA is available. From the same DNA sample we prepared 3 PCR-free Bisulfite-Seq replicates (ReBuilT) and 2 standard Bisulfite-Seq replicates (PCR-BS).
2016-03-16 | E-GEOD-65116 | biostudies-arrayexpress