txid3983[Organism] - GEO DataSets

(Submitter supplied) The gene expression profiling analysis from WT and cold treated samples of cassava that were used with other multi-omics data to build gene model annotation of Cassava.

Organism:: Manihot esculenta

Type:: Expression profiling by high throughput sequencing

Platform:: GPL28909
8 Samples

Download data: BEDGRAPH, TXT

Series

Accession:: GSE225365

ID:: 200225365

PubMed Similar studies

Select item 2002253643.

STRIPE-Seq of transcripts from cassava, Maihot esculenta variety TM12

(Submitter supplied) The start site analysis of transcripts from WT and cold treated samples of cassava that were used with other multi-omics data to build gene model annotation of Cassava.

Organism:: Manihot esculenta

Type:: Expression profiling by high throughput sequencing

Platform:: GPL33130
8 Samples

Download data: BEDGRAPH

Series

Accession:: GSE225364

ID:: 200225364

PubMed Similar studies

Select item 2002253634.

3'-end sequencing of transcripts from cassava, Manihot esculenta variety TM12

(Submitter supplied) Quant-Seq (3'-end sequencing technique) of mRNAs to identify the 3'-ends of transcripts to analyse the 3'-UTR that were used with other multi-omics data to build gene model annotation of Cassava.

Organism:: Manihot esculenta

Type:: Expression profiling by high throughput sequencing

Platform:: GPL21635
8 Samples

Download data: BEDGRAPH

Series

Accession:: GSE225363

ID:: 200225363

PubMed Similar studies

Select item 2002253615.

Oxford nanopore transcriptome of cassava, Manihot esculenta variety TM12

(Submitter supplied) Full length long read transcript sequences were used as guides along with other multi-omics data to build gene model annotation of Cassava.

Organism:: Manihot esculenta

Type:: Expression profiling by high throughput sequencing

Platform:: GPL33129
2 Samples

Download data: BED

Series

Accession:: GSE225361

ID:: 200225361

PubMed Similar studies

Select item 2001690606.

Small RNA profiles of Sri Lankan Cassava Mosaic Virus (SLCMV) infected Cassava plants

(Submitter supplied) We reported the small RNA profiles of disease free and SLCMV infected leaves of susceptible and tolerant genotypes of cassava. The sRNA data generated through high throughput small RNA sequencing revealed critical regulatory role of host and pathogen derived small RNAs during SLCMV infection.

Organism:: Manihot esculenta

Type:: Non-coding RNA profiling by high throughput sequencing

Platform:: GPL21982
3 Samples

Download data: FA

Series

Accession:: GSE169060

ID:: 200169060

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 2002347127.

Induction of leaf curling in cassava plants by the cassava mealybug Phenacoccus manihoti (Hemiptera: Pseudococcidae)

(Submitter supplied) Certain phytophagous insects can induce leaf curling in their host plants that may provide protected and nutrient-rich habitats. However, the mechanisms of this induction remain poorly understood. The cassava mealybug, Phenacoccus manihoti Matile-Ferrero (Hemiptera: Pseudococcidae), is a serious pest of the cassava and causes leaf curling. To reveal the mechanisms of leaf-curl induction, we first inoculated varying numbers of mealybugs in different locations, namely, the apical meristem and the stem, on cassava seedlings. more...

Organism:: Manihot esculenta

Type:: Expression profiling by high throughput sequencing

Platform:: GPL27820
14 Samples

Download data: TXT

Series

Accession:: GSE234712

ID:: 200234712

Select item 2001870228.

Improving disease resistance in plants by editing the epigenome

(Submitter supplied) Pathogens rely on expression of host susceptibility (S) genes to promote infection and disease. DNA methylation is an epigenetic modification that affects gene expression. Theoretically, blocking access to S genes through targeted methylation could increase disease resistance. Xanthomonas axonopodis pv. manihotis, the causal agent of cassava bacterial blight (CBB), uses transcription activator-like20 (TAL20) to induce expression of the S gene MeSWEET10a. more...

Organism:: Manihot esculenta

Type:: Methylation profiling by high throughput sequencing

Platform:: GPL28909
3 Samples

Download data: BW

Series

Accession:: GSE187022

ID:: 200187022

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 2001411259.

Field transcriptome analysis reveals a molecular mechanism of the cassava-flowering phenomena in a mountainous environment in Southeast Asia

(Submitter supplied) We report the sequencing data for time series profiling of cassava.This study provides transcriptome profile during floweing and non-flowering in cassava.

Organism:: Manihot esculenta

Type:: Expression profiling by high throughput sequencing

Platform:: GPL27820
44 Samples

Download data: XLSX

Series

Accession:: GSE141125

ID:: 200141125

PubMed Similar studies SRA Run Selector

Select item 20019274810.

Whole genome bisulfite sequencing data of cassava

(Submitter supplied) Cassava mosaic disease (CMD) suppresses cassava yields across the tropics. It has been reported that landraces lose CMD resistance after regeneration through de novo morphogenesis. We sequenced WGBS data of 14 samples.

Organism:: Manihot esculenta

Type:: Methylation profiling by high throughput sequencing

Platform:: GPL28909
14 Samples

Download data: BW

Series

Accession:: GSE192748

ID:: 200192748

PubMed Full text in PMC Similar studies

Select item 20016968511.

Agrobacterium-mediated cassava transformation for the Asian-elite variety KU50

(Submitter supplied) Agrobacterium-mediated cassava transformation via friable embryogenic callus (FEC) has allowed the robust production of transgenic cassava. So far, the transformation has been performed mostly for 60444 (the model cassava variety for transformation) and African varieties due to the high ability of callus induction and good regeneration capacity from embryogenic tissues. It is important to develop the transformation methods for elite cassava varieties in Asian area which is one of main cassava production area in the world, however, the suitable transformation method for Asian elite variety via FEC has not been reported. more...

Organism:: Manihot esculenta

Type:: Expression profiling by array

Platform:: GPL22197
8 Samples

Download data: TXT

Series

Accession:: GSE169685

ID:: 200169685

Select item 20014327812.

Integrative omics approaches revealed a crosstalk among phytohormones during tuberous root development in cassava

(Submitter supplied) Tuberous root formation is a complex process consisting of phase changes as well as cell division and elongation for radial growth. We performed an integrated analysis to clarify the relationships among metabolites, phytohormones, and gene transcription during tuberous root formation in cassava (Manihot esculenta Crantz). We also confirmed the effects of the auxin (AUX), cytokinin (CK), abscisic acid (ABA), jasmonic acid (JA), gibberellin (GA), brassinosteroid (BR), salicylic acid (SA), and indole-3-acetic acid conjugated with aspartic acid (IAAsp) on tuberous root development. more...

Organism:: Manihot esculenta

Type:: Expression profiling by array

Platform:: GPL22197
42 Samples

Download data: TXT

Series

Accession:: GSE143278

ID:: 200143278

Select item 20015663813.

Transcriptome of cassava seedling under different treatments

(Submitter supplied) Transcriptome of cassava seedling were analysised in 7% PEG and 50 μmol of ABA by RNA-seq.The goal of this study was to compare the phenotypic and transcriptome differences between treatment and WT plants, and to analyze how treatment changed the expression patterns.

Organism:: Manihot esculenta

Type:: Expression profiling by high throughput sequencing

Platforms:: GPL27820 GPL28909
9 Samples

Download data: XLS

Series

Accession:: GSE156638

ID:: 200156638

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20015494814.

Transcriptome Analysis of Wild Type and Histone H1.2(MeH1.2) Transgenic Plants by RNA-seq in Cassava.

(Submitter supplied) Transcriptome Analysis of Wild Type and Histone H1.2(MeH1.2) Transgenic Plants by RNA-seq in Cassava.The goal of this study was to compare the phenotypic and transcriptome differences between transgenic and WT plants, and to analyze how overexpression of MeH1.2 gene changed the expression patterns. MeH1.2 overexpressed transgenic cassava plant (HOE) were was made. The 2-month-old seedlings of HOE were significantly smaller and weaker than of the wild type (WT) under Murashige and Skoog (MS) medium, while, the leave leaf became yellow senescence and the number of branch root increased significantly in HOE than in WT. more...

Organism:: Manihot esculenta

Type:: Expression profiling by high throughput sequencing

Platforms:: GPL28909 GPL27820
9 Samples

Download data: TXT

Series

Accession:: GSE154948

ID:: 200154948

SRA Run Selector

Select item 20008997115.

Formation of Friable Embryogenic Callus is Enhanced under Nitrate, Potassium and Phosphate Limited Condition in Cassava.

(Submitter supplied) Agrobacterium-mediated transformation is an important research tool and a practical tool for an improvement of cassava cultivar. The induction of friable embryogenic callus (FEC) is considered as a one of key step in cassava transformation. In this article, we optimized a media composition for improving the frequency of FEC induction and investigated about the physiological mechanism of FEC induction under optimized media condition using the transcriptome analysis. more...

Organism:: Manihot esculenta

Type:: Expression profiling by array

Platform:: GPL22197
8 Samples

Download data: TXT

Series

Accession:: GSE89971

ID:: 200089971

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 20012214016.

Acetic Acid Treatment Enhances the Drought Avoidance in Cassava (Manihot esculenta Crantz)

(Submitter supplied) External application of acetic acid has been recently reported to enhance the survival to drought in plants such as Arabidopsis, rapeseed, maize, rice and wheat, but the effects of acetic acid application on increased drought tolerance in woody plants such as a tropical crop “cassava” remain elusive. A molecular understanding of acetic acid-induced drought avoidance in cassava will contribute to the development of technology that can be used to enhance drought tolerance without resorting to transgenic technology or advancements in cassava cultivation. more...

Organism:: Manihot esculenta

Type:: Expression profiling by array

Platform:: GPL22197
6 Samples

Download data: TXT

Series

Accession:: GSE122140

ID:: 200122140

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 20009309817.

Genome-wide expression of HD-Zip genes in cassava

(Submitter supplied) To reveal the expression of HD-Zip genes in different tissues of cassava, samples from leaf (90 days after planting), stem (90 days after planting), early storage root (ESR, 90 days after planting), middle storage root (MSR, 150 days after planting) and last storage root (LSR, 210 days after planting) were collected for RNA-seq analysis. In addition, their expression was also examined in folded leaf (FL), full expanded leaf (FEL) and bottom leaf (BL), as well as root (RT) at 0, 3, 24 h after the treatment of PEG 6000.

Organism:: Manihot esculenta

Type:: Expression profiling by high throughput sequencing

Platform:: GPL17194
24 Samples

Download data: TXT

Series

Accession:: GSE93098

ID:: 200093098

SRA Run Selector

Select item 20009853718.

RNA-Seq gives insights into genetic regulation of the drought-stress response in the cassava leaves

(Submitter supplied) Cassava is a drought–resistant food crop in tropical and subtropical regions. Although cassava is a relatively drought-tolerant species, the development and yields are greatly affected by the adverse drought conditions. Information about molecular breeding will obtain by studying genetic regulatory mechanism. In this study, we demonstrate the drought-tolerant mechanisms in leaves of both cassava varieties(Xinxuan048 and KU50) by using RNA-Seq technique. more...

Organism:: Manihot esculenta

Type:: Expression profiling by high throughput sequencing

Platform:: GPL17194
4 Samples

Download data: TXT

Series

Accession:: GSE98537

ID:: 200098537

SRA Run Selector

Select item 20011475819.

RNA polymerase mapping in plants identifies enhancers enriched in causal variants

(Submitter supplied) Promoter-proximal pausing and divergent transcription at promoters and enhancers, which are prominent features in animals, have been reported to be absent in plants based on a study of Arabidopsis thaliana. Here, our PRO-Seq analysis in cassava (Manihot esculenta) identified peaks of transcriptionally-engaged RNA polymerase II (Pol2) at both 5’ and 3’ ends of genes, consistent with paused or slowly-moving Pol2, and divergent transcription at potential intragenic enhancers. more...

Organism:: Manihot esculenta; Zea mays

Type:: Expression profiling by high throughput sequencing

Platforms:: GPL21982 GPL17628
2 Samples

Download data: BW

Series

Accession:: GSE114758

ID:: 200114758

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20010031920.

Provitamin A-enriched Golden Cassava generated through metabolic engineering has reduced dry matter, elevated oil content and enhanced shelf-life

(Submitter supplied) In this study, β-carotene concentrations in cassava storage roots were enhanced by co-expression of transgenes for deoxyxylulose-5-phosphate synthase (DXS) and bacterial phytoene synthase (crtB), mediated by the patatin type-1 promoter. Storage roots harvested from field-grown plants accumulated carotenoids to ≤50 μg/g DW, a 15- to 20-fold increase relative to roots from non-transgenic plants. Approximately 85-90% of these carotenoids accumulated as all-trans-β-carotene, the most nutritionally efficacious carotenoid. more...

Organism:: Manihot esculenta

Type:: Expression profiling by high throughput sequencing

Platform:: GPL17194
9 Samples

Download data: TSV

Series

Accession:: GSE100319

ID:: 200100319

PubMed Full text in PMC Similar studies SRA Run Selector

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