Solanum vitiense - GEO DataSets

Select item 2002454721.

Transcriptomic exploration of Solanum spp. resistance upon early-stage broomrape parasitism

(Submitter supplied) Tomato (Solanum lycopersicum) is a major crop of high economic value. Phelipanche and Orobanche genera (broomrapes) are parasitic weeds, constituting biotic stressors that impact tomato production. Developing varieties with tolerance to broomrapes has become imperative for sustainable agriculture. Solanum pennellii, a wild tomato species, has been used as breeding material for S. lycopersicum. In the present study a commercial tomato hybrid and two Introgression Lines (ILs), (S. more...

Organism:: Solanum lycopersicum; Solanum lycopersicum x Solanum pennellii

Type:: Expression profiling by high throughput sequencing

Platforms:: GPL27957 GPL33844
18 Samples

Download data: RESULTS

Series

Accession:: GSE245472

ID:: 200245472

Select item 2002699972.

Histone demethylase JMJ4 interacts with transcription factor BLH3 to modulate jasmonate biosynthesis in tomato response to cold stress [RNA-seq]

(Submitter supplied) To investigate the difference of gene expression regulated by JMJ4, we performed RNA-seq assay of jmj4 mutant and wild type plants under control and cold treatment conditions.

Organism:: Solanum lycopersicum

Type:: Expression profiling by high throughput sequencing

Platform:: GPL27957
12 Samples

Download data: TXT

Series

Accession:: GSE269997

ID:: 200269997

Select item 2002699963.

Histone demethylase JMJ4 interacts with transcription factor BLH3 to modulate jasmonate biosynthesis in tomato response to cold stress [ChIP-seq]

(Submitter supplied) To clarify the specific regulating mechanism of JMJ4 under cold treatment, we performed ChIP-seq assay of jmj4 mutant and wild type plants under control and cold treatment conditions.

Organism:: Solanum lycopersicum

Type:: Genome binding/occupancy profiling by high throughput sequencing

Platform:: GPL27957
15 Samples

Download data: BW

Series

Accession:: GSE269996

ID:: 200269996

Select item 2002606684.

Transcriptome-wide mapping of RNA:protein interactions of GFP-RS2Z35 and GFP-RS2Z36 in tomato (Solanum lycopersicum) leaves.

(Submitter supplied) We performed iCLIP2 in tomato leaves stably expressing GFP-tagged RS2Z35 or RS2Z36.

Organism:: Solanum lycopersicum

Type:: Other

Platform:: GPL21762
8 Samples

Download data: BED, BW

Series

Accession:: GSE260668

ID:: 200260668

Select item 2002439115.

THE EPIGENOME PLAYS A MAJOR ROLE IN TOMATO 3D CHROMATIN ORGANIZATION

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:: Solanum lycopersicum

Type:: Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Other

Platform:: GPL21762
17 Samples

Download data: BIGWIG, BROADPEAK, NARROWPEAK

Series

Accession:: GSE243911

ID:: 200243911

Select item 2002439106.

THE EPIGENOME PLAYS A MAJOR ROLE IN TOMATO 3D CHROMATIN ORGANIZATION [RNA-seq]

(Submitter supplied) Understanding the 3D genome organization in the nucleus is becoming increasingly crucial given its involvement in many processes from transcription to the integrity of the nucleus itself, which play a role in every stage of an organism's life. Beyond the linear genome defined by its nucleotide sequence, this organization is also governed by its epigenome, but how the latter controls the 3D architecture of the nucleus is poorly understood. more...

Organism:: Solanum lycopersicum

Type:: Expression profiling by high throughput sequencing

Platform:: GPL21762
4 Samples

Download data: TXT

Series

Accession:: GSE243910

ID:: 200243910

Select item 2002439097.

THE EPIGENOME PLAYS A MAJOR ROLE IN TOMATO 3D CHROMATIN ORGANIZATION [Hi-C]

(Submitter supplied) Understanding the 3D genome organization in the nucleus is becoming increasingly crucial given its involvement in many processes from transcription to the integrity of the nucleus itself, which play a role in every stage of an organism's life. Beyond the linear genome defined by its nucleotide sequence, this organization is also governed by its epigenome, but how the latter controls the 3D architecture of the nucleus is poorly understood. more...

Organism:: Solanum lycopersicum

Type:: Other

Platform:: GPL21762
4 Samples

Download data

Series

Accession:: GSE243909

ID:: 200243909

Select item 2002439088.

THE EPIGENOME PLAYS A MAJOR ROLE IN TOMATO 3D CHROMATIN ORGANIZATION [ChIP-seq]

(Submitter supplied) Understanding the 3D genome organization in the nucleus is becoming increasingly crucial given its involvement in many processes from transcription to the integrity of the nucleus itself, which play a role in every stage of an organism's life. Beyond the linear genome defined by its nucleotide sequence, this organization is also governed by its epigenome, but how the latter controls the 3D architecture of the nucleus is poorly understood. more...

Organism:: Solanum lycopersicum

Type:: Genome binding/occupancy profiling by high throughput sequencing

Platform:: GPL21762
9 Samples

Download data: BIGWIG, BROADPEAK, NARROWPEAK, TXT

Series

Accession:: GSE243908

ID:: 200243908

Select item 2002638619.

Nuclear factors NF-YC3 and NF-YBs positively regulate arbuscular mycorrhizal symbiosis in tomato

(Submitter supplied) The involvement of nuclear factor Y (NF-Y) in transcriptional reprogramming during arbuscular mycorrhizal symbiosis has been demonstrated in several plant species. However, a comprehensive picture is lacking. We showed that the spatial expression of NF-YC3 was observed in cortical cells containing arbuscules via the cis-regulatory element GCC boxes. Moreover, NF-YC3 promoter was transactivated by the combination of CYCLOPS and autoactive CCaMK via GCC boxes. more...

Organism:: Solanum lycopersicum

Type:: Expression profiling by high throughput sequencing

Platform:: GPL27957
12 Samples

Download data: XLSX

Series

Accession:: GSE263861

ID:: 200263861

Select item 20023282810.

Local and systemic transcriptome and spliceome changes induced by Meloidigyne incognita in tomato roots.

(Submitter supplied) The aim of study is to investigate DEGs, long non-coding RNAs and alternative splicing events in the development of galls and neighboring region compared to the non-infected whole root induced by root-knot nematode (RKN, Meloidogyne incognita). Total RNA was extracted, ribosomal depleted libraries were prepared, and then high throughput RNA sequencing was performed using the Illumina NovaSeq 6000. High quality, paired-end reads were then aligned to the tomato reference genome (Heinz1706 assembly SL4.0) and uniquely mapped reads were counted using Htseq. more...

Organism:: Solanum lycopersicum

Type:: Expression profiling by high throughput sequencing

Platform:: GPL27957
18 Samples

Download data: XLSX

Series

Accession:: GSE232828

ID:: 200232828

Select item 20026255211.

Tomato RS2Z35 and RS2Z36

(Submitter supplied) Assessment of RS2Z protein function under heat stress in Solanum Lycopersicum via RNASeq and iCLIP2. This SuperSeries is composed of the SubSeries listed below.

Organism:: Solanum lycopersicum

Type:: Expression profiling by high throughput sequencing; Other

Platforms:: GPL21762 GPL27957
32 Samples

Download data: BW, TAB

Series

Accession:: GSE262552

ID:: 200262552

PubMed Similar studies

Select item 20026181612.

Effect of RS2Z35 and RS2Z36 single and double knockout on gene expression and splicing during control and heat stress conditions in tomato (Solanum Lycopersicum) leaf tissue

(Submitter supplied) To investigate the role of Serine/Arginine-rich proteins RS2Z35 and RS2Z36 in tomato heat stress response and thermotolerance, we established single and double knockouts of the respective splicing factor(s) in tomato We then performed gene expression and splicing analysis using data obtained from RNA-seq of wildtype, single knockout and double knockout plants under control and heat stress conditions (1 h 40°C)

Organism:: Solanum lycopersicum

Type:: Expression profiling by high throughput sequencing

Platform:: GPL27957
24 Samples

Download data: TAB

Series

Accession:: GSE261816

ID:: 200261816

PubMed Similar studies

Select item 20025623813.

iSB09 elicits ABA-responsive gene expression in Solanum lycopersicum seedlings

(Submitter supplied) To compare the genome-wide transcriptional effect of ABA and iSB09 in tomato plants, we performed RNA-seq analysis of mock-, 10 uM ABA- or 20 uM iSB09-treated plants. Differential gene expression analysis between mock- and ABA-treated or iSB09-treated seedlings was done with DESeq2 and genes with an absolute value of log2 fold change (log2FC) > 1 or (log2FC) < -1 and p-adjusted value (padj) < 0.05 were selected. more...

Organism:: Solanum lycopersicum

Type:: Expression profiling by high throughput sequencing

Platform:: GPL28981
9 Samples

Download data: TSV

Series

Accession:: GSE256238

ID:: 200256238

Select item 20020855914.

Next generation sequencing analysis of tea plant transcriptomes in response to Colletotrichum camelliae infection.

(Submitter supplied) Next generation sequencing (NGS) was performed to identify genes changed in tea plant upon Colletotrichum camelliae infection. The goal of the work is to find interesting genes involved in tea plant in response to fungi infection. The object is to reveal the molecular mechanism of tea plant defense.

Organism:: Camellia sinensis

Type:: Expression profiling by high throughput sequencing

Platform:: GPL23285
9 Samples

Download data: XLSX

Series

Accession:: GSE208559

ID:: 200208559

Select item 20026443015.

KRYPTONITE shapes TAD-like boundaries through the control of H3K9ac [ChIP-Seq]

(Submitter supplied) Employing high-throughput sequencing and advanced microscopy techniques, we explored twenty-six histone modifications and Pol II distribution landscape in tomato (Solanum lycopersicum). Our findings revealed a comprehensive epigenetic landscape, uncovering distinct chromatin states associated with heterochromatin formation and gene silencing, allowing for the classification of genomic regions.

Organism:: Solanum lycopersicum

Type:: Genome binding/occupancy profiling by high throughput sequencing

Platform:: GPL21762
4 Samples

Download data: BIGWIG, NARROWPEAK

Series

Accession:: GSE264430

ID:: 200264430

PubMed Full text in PMC Similar studies

Select item 20026442916.

KRYPTONITE shapes TAD-like boundaries through the control of H3K9ac [ATAC-Seq]

(Submitter supplied) Employing high-throughput sequencing and advanced microscopy techniques, we explored twenty-six histone modifications and Pol II distribution landscape in tomato (Solanum lycopersicum). Our findings revealed a comprehensive epigenetic landscape, uncovering distinct chromatin states associated with heterochromatin formation and gene silencing, allowing for the classification of genomic regions.

Organism:: Solanum lycopersicum

Type:: Genome binding/occupancy profiling by high throughput sequencing

Platform:: GPL21762
4 Samples

Download data: BIGWIG

Series

Accession:: GSE264429

ID:: 200264429

PubMed Full text in PMC Similar studies

Select item 20024552917.

KRYPTONITE shapes TAD-like boundaries through the control of H3K9ac

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:: Solanum lycopersicum

Type:: Genome binding/occupancy profiling by high throughput sequencing; Other; Expression profiling by high throughput sequencing

Platforms:: GPL27957 GPL21762
47 Samples

Download data: BIGWIG, BROADPEAK, NARROWPEAK

Series

Accession:: GSE245529

ID:: 200245529

PubMed Full text in PMC Similar studies

Select item 20024552818.

KRYPTONITE shapes TAD-like boundaries through the control of H3K9ac [RNA-seq]

(Submitter supplied) Employing high-throughput sequencing and advanced microscopy techniques, we explored twenty-six histone modifications and Pol II distribution landscape in tomato (Solanum lycopersicum). Our findings revealed a comprehensive epigenetic landscape, uncovering distinct chromatin states associated with heterochromatin formation and gene silencing, allowing for the classification of genomic regions.

Organism:: Solanum lycopersicum

Type:: Expression profiling by high throughput sequencing

Platform:: GPL27957
6 Samples

Download data: TXT

Series

Accession:: GSE245528

ID:: 200245528

PubMed Full text in PMC Similar studies

Select item 20024552719.

KRYPTONITE shapes TAD-like boundaries through the control of H3K9ac [Hi-C]

(Submitter supplied) Employing high-throughput sequencing and advanced microscopy techniques, we explored twenty-six histone modifications and Pol II distribution landscape in tomato (Solanum lycopersicum). Our findings revealed a comprehensive epigenetic landscape, uncovering distinct chromatin states associated with heterochromatin formation and gene silencing, allowing for the classification of genomic regions.

Organism:: Solanum lycopersicum

Type:: Other

Platform:: GPL21762
5 Samples

Download data: TXT

Series

Accession:: GSE245527

ID:: 200245527

PubMed Full text in PMC Similar studies

Select item 20024552520.

KRYPTONITE shapes TAD-like boundaries through the control of H3K9ac [ChIP-seq]

(Submitter supplied) Employing high-throughput sequencing and advanced microscopy techniques, we explored twenty-six histone modifications and Pol II distribution landscape in tomato (Solanum lycopersicum). Our findings revealed a comprehensive epigenetic landscape, uncovering distinct chromatin states associated with heterochromatin formation and gene silencing, allowing for the classification of genomic regions.

Organism:: Solanum lycopersicum

Type:: Genome binding/occupancy profiling by high throughput sequencing

Platform:: GPL21762
28 Samples

Download data: BIGWIG, BROADPEAK, NARROWPEAK

Series

Accession:: GSE245525

ID:: 200245525

PubMed Full text in PMC Similar studies

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