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Items: 1 to 20 of 248273

1.

High-throughput single-molecule long-read RNA sequencing analysis of tissue-specific genes and isoforms in lettuce

(Submitter supplied) This study utilized the HIT-ISOseq method for high-throughput sequencing of RNA isoforms across multiple lettuce samples, generating millions of long reads per PacBio Sequel II SMRT Cell. Analysis of six tissue types revealed tissue-specific gene expression and RNA isoforms, facilitating updates to the lettuce reference genome annotation with expanded functional annotations.
Organism:
Lactuca sativa
Type:
Expression profiling by high throughput sequencing
Platforms:
GPL34402 GPL34403
12 Samples
Download data: CSV, FASTA, GTF, XLS
Series
Accession:
GSE264560
ID:
200264560
2.

The genes expression in WT and XBAT31 mutant under normal and high temperature at reproductive stage of Arabidopsis.

(Submitter supplied) To investigate the genes which relay on XBAT31 under high temperature and are induced by high temperature.
Organism:
Arabidopsis thaliana
Type:
Expression profiling by high throughput sequencing
Platform:
GPL26208
12 Samples
Download data: TXT
Series
Accession:
GSE228349
ID:
200228349
3.

Multi-omics profiling of 5 Arabidopsis accessions in response to combined water and nitrogen deficiencies

(Submitter supplied) In this study, we build an in-depth multi-omics profile of 5 Arabidopsis accessions, in order to find the inner relations of N deficit, mild drought, and combined stress response at the physiological, metabolic and transcriptional level.
Organism:
Arabidopsis thaliana
Type:
Expression profiling by high throughput sequencing
Platform:
GPL19580
119 Samples
Download data: TSV
Series
Accession:
GSE206890
ID:
200206890
4.

The ATHB2 microProtein affects plant development and the shade avoidance response [Iso-seq]

(Submitter supplied) Plants display remarkable adaptability to varying light conditions, crucial for their optimal growth and development. Here, we investigate the functional significance of ATHB2-miP, a microProtein arising from an alternative transcript of the ATHB2 gene, in both white light and shade environments, supported by comprehensive phenotyping experiments. ATHB2, a homeodomain-leucine zipper transcription factor, is known for its involvement in growth regulation. more...
Organism:
Arabidopsis thaliana
Type:
Other
Platform:
GPL20197
3 Samples
Download data: FASTA
Series
Accession:
GSE267983
ID:
200267983
5.

Terminal nucleotidyl transferases govern secondary siRNA production at distinct steps in plants

(Submitter supplied) In this study, we aim at understanding the contributions from TUTases, HESO1 and URT1, in miRNA-targeted secondary siRNA production in Arabidopsis thaliana. We have sequenced small RNAs from various T-DNA insertation single/double/triple mutants and compared their capability of producing ectopic secondary siRNAs from endogenous miRNA targets. The DESeq analysis is also included.
Organism:
Arabidopsis thaliana
Type:
Non-coding RNA profiling by high throughput sequencing
Platform:
GPL19580
24 Samples
Download data: FASTQ, XLSX
Series
Accession:
GSE267947
ID:
200267947
6.

RNAseq and WGBS of Vaccinium corymbosum

(Submitter supplied) We did whole-genome methylation sequencing for 21 Vaccinium samples. This project attempts to analyze the improvement breeding process of cultivated blueberry from two aspects of heredity and epigenetic inheritance.
Organism:
Vaccinium darrowii; Vaccinium corymbosum
Type:
Methylation profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platforms:
GPL33769 GPL33280
36 Samples
Download data: BW, CGMAP
Series
Accession:
GSE228041
ID:
200228041
7.

ISRH-seq: a sensitive and robust methodology for R-loop profiling

(Submitter supplied) R-loops serve as key modulators in various biological processes in humans and plants.Current high-throughput methodologies for R-loop profiling have their own intrinsic pros and cons. Therefore, any robust, sensitive, and amenable methods, complementary and/or advantageous to existing methodologies, are much needed for advancing R-loop biology. We here present an RNase H based cleavage combined with DNA polymerase-mediated in situ biotin-dATP/dCTP labeling of newly synthesized DNA for sequencing, termed ISRH-seq, an antibody-independent approach for strand-specific mapping of R-loops. more...
Organism:
Oryza sativa
Type:
Other
Platform:
GPL27660
18 Samples
Download data: BW, TXT
Series
Accession:
GSE232347
ID:
200232347
8.

Arabidopsis Lon1 disruption decreases autophagy flux affects seed development through brassinosteroid regulation

(Submitter supplied) Arabidopsis Lon1 serves dual roles as a mitochondrial protease and chaperone. Loss of Lon1 function reduced autophagy flux at transcriptional, protein and cellular levels. Meanwhile, changes occurred in the levels of cellular subunit proteins, especially a significant upregulation of mitochondrial proteins overall in lon1 mutants. Lon1 is a key enzyme in maintaining mitochondrial protein homeostasis. more...
Organism:
Arabidopsis thaliana
Type:
Expression profiling by high throughput sequencing
Platform:
GPL31102
6 Samples
Download data: TXT
Series
Accession:
GSE262650
ID:
200262650
9.

Premeiotic 24-nt phasiRNAs are present in the Zea genus and unique in biogenesis mechanism and molecular function [TraPR small RNA-seq]

(Submitter supplied) Reproductive phasiRNAs are broadly present in angiosperms and play crucial roles in sustaining male fertility. While the premeiotic 21-nt phasiRNAs and meiotic 24-nt phasiRNA pathways have been extensively studied in maize (Zea mays) and rice (Oryza sativa), a third putative category of reproductive phasiRNAs–named premeiotic 24-nt phasiRNAs–have recently been reported in barley (Hordeum vulgare) and wheat (Triticum aestivum). more...
Organism:
Zea mays subsp. mays
Type:
Other; Non-coding RNA profiling by high throughput sequencing
Platform:
GPL34147
11 Samples
Download data: TXT
Series
Accession:
GSE254583
ID:
200254583
10.

Premeiotic 24-nt phasiRNAs are present in the Zea genus and unique in biogenesis mechanism and molecular function [Smart-seq2+nanoPARE]

(Submitter supplied) Reproductive phasiRNAs are broadly present in angiosperms and play crucial roles in sustaining male fertility. While the premeiotic 21-nt phasiRNAs and meiotic 24-nt phasiRNA pathways have been extensively studied in maize (Zea mays) and rice (Oryza sativa), a third putative category of reproductive phasiRNAs–named premeiotic 24-nt phasiRNAs–have recently been reported in barley (Hordeum vulgare) and wheat (Triticum aestivum). more...
Organism:
Zea mays subsp. mays; Zea mays subsp. parviglumis; Zea mays subsp. mexicana; Zea luxurians
Type:
Expression profiling by high throughput sequencing
4 related Platforms
136 Samples
Download data: TSV
Series
Accession:
GSE254582
ID:
200254582
11.

Premeiotic 24-nt phasiRNAs are present in the Zea genus and unique in biogenesis mechanism and molecular function [small_RNA]

(Submitter supplied) Reproductive phasiRNAs are broadly present in angiosperms and play crucial roles in sustaining male fertility. While the premeiotic 21-nt phasiRNAs and meiotic 24-nt phasiRNA pathways have been extensively studied in maize (Zea mays) and rice (Oryza sativa), a third putative category of reproductive phasiRNAs–named premeiotic 24-nt phasiRNAs–have recently been reported in barley (Hordeum vulgare) and wheat (Triticum aestivum). more...
Organism:
Zea mays subsp. mexicana; Zea luxurians; Zea mays subsp. parviglumis; Zea mays subsp. mays
Type:
Non-coding RNA profiling by high throughput sequencing
4 related Platforms
69 Samples
Download data: TXT
Series
Accession:
GSE254581
ID:
200254581
12.

Premeiotic 24-nt phasiRNAs are present in the Zea genus and unique in biogenesis mechanism and molecular function.

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Zea luxurians; Zea mays subsp. parviglumis; Zea mays subsp. mays; Zea mays subsp. mexicana
Type:
Non-coding RNA profiling by high throughput sequencing; Expression profiling by high throughput sequencing; Other
4 related Platforms
216 Samples
Download data: TSV
Series
Accession:
GSE254584
ID:
200254584
13.

The ATHB2 microProtein affects plant development and the shade avoidance response

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Arabidopsis thaliana
Type:
Expression profiling by high throughput sequencing; Other
Platforms:
GPL17639 GPL21785 GPL20197
33 Samples
Download data: FASTA
Series
Accession:
GSE241976
ID:
200241976
14.

The ATHB2 microProtein affects plant development and the shade avoidance response (PEAT)

(Submitter supplied) Plants display remarkable adaptability to varying light conditions, crucial for their optimal growth and development. Here, we investigate the functional significance of ATHB2-miP, a microProtein arising from an alternative transcript of the ATHB2 gene, in both white light and shade environments, supported by comprehensive phenotyping experiments. ATHB2, a homeodomain-leucine zipper transcription factor, is known for its involvement in growth regulation. more...
Organism:
Arabidopsis thaliana
Type:
Other
Platform:
GPL17639
3 Samples
Download data: TXT
Series
Accession:
GSE241975
ID:
200241975
15.

The ATHB2 microProtein affects plant development and the shade avoidance response (RNA-Seq)

(Submitter supplied) Plants display remarkable adaptability to varying light conditions, crucial for their optimal growth and development. Here, we investigate the functional significance of ATHB2-miP, a microProtein arising from an alternative transcript of the ATHB2 gene, in both white light and shade environments, supported by comprehensive phenotyping experiments. ATHB2, a homeodomain-leucine zipper transcription factor, is known for its involvement in growth regulation. more...
Organism:
Arabidopsis thaliana
Type:
Expression profiling by high throughput sequencing
Platform:
GPL21785
27 Samples
Download data: TXT
Series
Accession:
GSE241974
ID:
200241974
16.

Replacement of Arabidopsis H2A.Z with human H2A.Z orthologs reveals extensive functional conservation and limited importance of the N-terminal tail sequence for Arabidopsis development

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Arabidopsis thaliana
Type:
Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL26208
24 Samples
Download data: BW, TXT
Series
Accession:
GSE263313
ID:
200263313
17.

Replacement of Arabidopsis H2A.Z with human H2A.Z orthologs reveals extensive functional conservation and limited importance of the N-terminal tail sequence for Arabidopsis development (ChIP-Seq)

(Submitter supplied) To investigate the functional conservation of H2A.Z histones during eukaryotic evolution we transformed h2a.z deficient plants with three human H2A.Z proteins to assess their ability to rescue the mutant defects. We discovered that human H2A.Z.1 and H2A.Z.2.1 fully complement the phenotypic abnormalities of h2a.z plants even though Arabidopsis and human H2A.Z N-terminal tail sequences are divergent, while the brain-specific splice variant H2A.Z.2.2 has a dominant-negative effect in wild-type plants. more...
Organism:
Arabidopsis thaliana
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL26208
9 Samples
Download data: BW, TXT
Series
Accession:
GSE263312
ID:
200263312
18.

Replacement of Arabidopsis H2A.Z with human H2A.Z orthologs reveals extensive functional conservation and limited importance of the N-terminal tail sequence for Arabidopsis development (WT, h2a.z + HsH2A.Z. RNA-Seq)

(Submitter supplied) To investigate the functional conservation of H2A.Z histones during eukaryotic evolution we transformed h2a.z deficient plants with three human H2A.Z proteins to assess their ability to rescue the mutant defects. We discovered that human H2A.Z.1 and H2A.Z.2.1 fully complement the phenotypic abnormalities of h2a.z plants even though Arabidopsis and human H2A.Z N-terminal tail sequences are divergent, while the brain-specific splice variant H2A.Z.2.2 has a dominant-negative effect in wild-type plants. more...
Organism:
Arabidopsis thaliana
Type:
Expression profiling by high throughput sequencing
Platform:
GPL26208
6 Samples
Download data: TXT
Series
Accession:
GSE263311
ID:
200263311
19.

Replacement of Arabidopsis H2A.Z with human H2A.Z orthologs reveals extensive functional conservation and limited importance of the N-terminal tail sequence for Arabidopsis development (WT, h2a.z, h2a.z + AtHTA11 RNA-Seq)

(Submitter supplied) To investigate the functional conservation of H2A.Z histones during eukaryotic evolution we transformed h2a.z deficient plants with three human H2A.Z proteins to assess their ability to rescue the mutant defects. We discovered that human H2A.Z.1 and H2A.Z.2.1 fully complement the phenotypic abnormalities of h2a.z plants even though Arabidopsis and human H2A.Z N-terminal tail sequences are divergent, while the brain-specific splice variant H2A.Z.2.2 has a dominant-negative effect in wild-type plants. more...
Organism:
Arabidopsis thaliana
Type:
Expression profiling by high throughput sequencing
Platform:
GPL26208
9 Samples
Download data: TXT
Series
Accession:
GSE263310
ID:
200263310
20.

Dynamic evolution of the heterochromatin sensing histone demethylase IBM1

(Submitter supplied) Heterochromatin constitutes a fundamental aspect of genomes that is crucial for maintaining genome stability. In flowering plants, maintenance of heterochromatin relies on a positive feedback loop involving the histone 3 lysine nine methyltransferase (H3K9), KRYPTONITE (KYP), and the DNA methyltransferase, CHROMOMETHYLASE3 (CMT3). An H3K9 demethylase, INCREASED IN BONSAI METHYLATION 1 (IBM1), has evolved to modulate the activity of KYP-CMT3 within transcribed genes. more...
Organism:
Raphanus raphanistrum; Isatis lusitanica; Arabidopsis thaliana
Type:
Methylation profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platforms:
GPL34074 GPL26208 GPL34073
12 Samples
Download data: TSV
Series
Accession:
GSE252913
ID:
200252913
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