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Items: 10

1.

Whole-genome transcriptome analysis of tomato and Arabidopsis roots in the shade

(Submitter supplied) RNA-seq analysis of arabidopsis and tomato roots in shaded and unshaded seedlings.
Organism:
Arabidopsis thaliana; Solanum lycopersicum
Type:
Expression profiling by high throughput sequencing
Platforms:
GPL19580 GPL29032
40 Samples
Download data: CSV
Series
Accession:
GSE175963
ID:
200175963

PubMed Full text in PMC Similar studies SRA Run Selector

2.

Comprehensive characterization of cistrome and epicistrome involved in fruit ripening

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Solanum lycopersicum
Type:
Genome binding/occupancy profiling by high throughput sequencing; Methylation profiling by high throughput sequencing
Platform:
GPL29032
824 Samples
Download data: BED, BW
Series
Accession:
GSE173213
ID:
200173213

3.

Comprehensive characterization of cistrome and epicistrome involved in fruit ripening [Bisulfite-seq]

(Submitter supplied) The biggest advantage of DAP-seq is that it’s capable of measuring the influence of DNA methylation on TF binding, without disturbing of other epigenetic markers. Here, by utilizing DNA affinity purification sequencing, we generated two binding sets which were incubated with DNA libraries that representing methylomes in different developmental stage. And we made the most of our data to predict DNA methylation impact on TF binding in two dimensions: prediction by comparing genome-wide binding signal in motif-matched regions with or without methylation in single stage, and prediction by comparing binding signal variation in motif-matched regions with or without methylation variation.
Organism:
Solanum lycopersicum
Type:
Methylation profiling by high throughput sequencing
Platform:
GPL29032
2 Samples
Download data: BW
Series
Accession:
GSE173212
ID:
200173212

SRA Run Selector

4.

Comprehensive characterization of cistrome and epicistrome involved in fruit ripening [ChIP-seq]

(Submitter supplied) Here we generated ChIP-seq data of a tomato ERF family TF Sl-ERF_F_4 in red fruit stage and green fruit stage to validate the accuracy of DAP-seq data.
Organism:
Solanum lycopersicum
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL29032
12 Samples
Download data: BW, TXT
Series
Accession:
GSE173208
ID:
200173208

SRA Run Selector

5.

Comprehensive characterization of cistrome and epicistrome involved in fruit ripening [red fruit]

(Submitter supplied) The biggest advantage of DAP-seq is that it’s capable of measuring the influence of DNA methylation on TF binding, without disturbing of other epigenetic markers. Here, by utilizing DNA affinity purification sequencing, we generated two binding sets which were incubated with DNA libraries that representing methylomes in different developmental stage. And we made the most of our data to predict DNA methylation impact on TF binding in two dimensions: prediction by comparing genome-wide binding signal in motif-matched regions with or without methylation in single stage, and prediction by comparing binding signal variation in motif-matched regions with or without methylation variation.
Organism:
Solanum lycopersicum
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL29032
393 Samples
Download data: BED, BW, TXT
Series
Accession:
GSE172260
ID:
200172260

SRA Run Selector

6.

Comprehensive characterization of cistrome and epicistrome involved in fruit ripening [green fruit]

(Submitter supplied) The biggest advantage of DAP-seq is that it’s capable of measuring the influence of DNA methylation on TF binding, without disturbing of other epigenetic markers. Here, by utilizing DNA affinity purification sequencing, we generated two binding sets which were incubated with DNA libraries that representing methylomes in different developmental stage. And we made the most of our data to predict DNA methylation impact on TF binding in two dimensions: prediction by comparing genome-wide binding signal in motif-matched regions with or without methylation in single stage, and prediction by comparing binding signal variation in motif-matched regions with or without methylation variation.
Organism:
Solanum lycopersicum
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL29032
393 Samples
Download data: BED, BW, TXT
Series
Accession:
GSE172249
ID:
200172249

SRA Run Selector

7.

Comprehensive characterization of cistrome and epicistrome involved in fruit ripening [pre-experiment]

(Submitter supplied) The biggest advantage of DAP-seq is that it’s capable of measuring the influence of DNA methylation on TF binding, without disturbing of other epigenetic markers. Here, by utilizing DNA affinity purification sequencing, we generated two binding sets which were incubated with DNA libraries that representing methylomes in different developmental stage. And we made the most of our data to predict DNA methylation impact on TF binding in two dimensions: prediction by comparing genome-wide binding signal in motif-matched regions with or without methylation in single stage, and prediction by comparing binding signal variation in motif-matched regions with or without methylation variation.
Organism:
Solanum lycopersicum
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL29032
24 Samples
Download data: BED, BW
Series
Accession:
GSE171493
ID:
200171493

SRA Run Selector

8.

Time course of trans-species miRNAs from Cuscuta campestris grown on Solanum lycopersicum

(Submitter supplied) Cuscuta campestris is an obligate stem parasite which uses an organ called the haustoria to divert water and photosynthates from the host.  Previously, we have identified that at the haustorial interface between Cuscuta campestris and Arabidopsis thaliana, miRNAs generated by the parasite are able to move into the host and regulate host gene expression.  This study identifies how long after attachment does trans-species miRNA transcription begin in Arabidopsis thaliana and Solanum lycopersicum, as well as identifying which stage of haustoria development they become detectable.  A time course was performed by harvesting interfaces every 24 hours post attachment, and samples were subjected to RNA extraction and sRNA sequencing. more...
Organism:
Solanum lycopersicum
Type:
Non-coding RNA profiling by high throughput sequencing
Platform:
GPL29032
42 Samples
Download data: CSV
Series
Accession:
GSE184642
ID:
200184642

PubMed Full text in PMC Similar studies SRA Run Selector

9.

Single cell mRNA-Seq of developing stem-borne roots in tomato

(Submitter supplied) Plants adjust their growth in response to environmental cues by forming new organs in different development contexts. Underground lateral roots initiate from prepatterned cells in the main root, but cells can also bypass the root/shoot trajectory separation and generate shoot-borne-roots through an unknown mechanism. Here, we mapped tomato (Solanum lycoperiscum) shoot-borne-roots development at single-cell resolution and show that they initiate from differentiated phloem-associated cells via a unique transitional stem-cell-like state. more...
Organism:
Solanum lycopersicum
Type:
Expression profiling by high throughput sequencing
Platform:
GPL29032
1 Sample
Download data: CSV, TXT
Series
Accession:
GSE159055
ID:
200159055

PubMed Similar studies SRA Run Selector

10.

Vein and Intervein Drought RNAseq

(Submitter supplied) We report here the RNAseq data generated from a drought experiment using tomato leaves (Solanum lycopersicum), in which three timepoints and two treatments were collected. More specifically, RNAseq was generated from tomato plants prior to drought (T0), during a period of drought (T1) and after a period of recovery from drought (T2). At timepoints 1 and 2 (T1 & T2), a control set of plants that were continuously watered are also included. more...
Organism:
Solanum lycopersicum
Type:
Expression profiling by high throughput sequencing
Platform:
GPL29032
30 Samples
Download data: XLSX
Series
Accession:
GSE156402
ID:
200156402

SRA Run Selector

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