GEO DataSets

(Submitter supplied) Comparative analysis of nascent transcription among plant species

Organism:

Arabidopsis thaliana; Chlamydomonas reinhardtii; Zea mays; Carica papaya; Physcomitrium patens; Hordeum vulgare; Drosophila melanogaster; Selaginella moellendorffii

Type:

Expression profiling by high throughput sequencing; Other; Non-coding RNA profiling by high throughput sequencing

17 related Platforms

68 Samples

Download data: BED, TXT, XLSX

(Submitter supplied) In this study, we identified the main genes of the m6A methyltransferase complex (MTC) in P. patens and we demonstrate that their inactivation by genome editing leads to loss of m6A presence in mRNA and results in defects in the moss life cycle. We detected a delay in the formation of gametophore buds, affecting the transition from 2D to 3D growth and subsequent gametophore formation in all MTC mutant plants. more...

Organism:

Physcomitrium patens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30955

4 Samples

Download data: TXT

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

Organism:

Physcomitrium patens

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL30955

6 Samples

Download data

(Submitter supplied) In this study, we identified the main genes of the m6A methyltransferase complex (MTC) in P. patens and we demonstrate that their inactivation by genome editing leads to loss of m6A presence in mRNA and results in defects in the moss life cycle. We detected a delay in the formation of gametophore buds, affecting the transition from 2D to 3D growth and subsequent gametophore formation in all MTC mutant plants. more...

Organism:

Physcomitrium patens

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL30955

2 Samples

Download data: BED

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

Organism:

Physcomitrium patens

Type:

Methylation profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platforms:

GPL30513 GPL29161 GPL30955

8 Samples

Download data: GFF

(Submitter supplied) We mutated PpDDM1 and the early land plant. Using BS-seq and RNA-seq, we here show that though DNA methylation is disrupted in all contexts development isn't and TE and gene differential expression are minute

Organism:

Physcomitrium patens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL30955 GPL30513

6 Samples

Download data: TXT

(Submitter supplied) We mutated PpDDM1 and the early land plant. Using BS-seq and RNA-seq, we here show that though DNA methylation is disrupted in all contexts development isn't and TE and gene differential expression are minute

Organism:

Physcomitrium patens

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL29161

2 Samples

Download data: GFF

(Submitter supplied) To investigate transcriptomic profiles when auxin-dependent transcription factor ARFC2 from Physcomitrium patens is expressed, we established an inducible overexpressor line for PpARFC2. We then perform bulk RNA-seq on protonemata tissues that have been mock-treated or induced by beta-estradiol for 16 h.

Organism:

Physcomitrium patens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL32682

5 Samples

Download data: TXT

(Submitter supplied) The goal of this study is to identify genes whose expression is affected by decapitation and auxin in moss gametophores Project ngs2017_09_moss1-auxin in CATdb What genes are misregulated in response to decapitation or auxin response?

Organism:

Physcomitrium patens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30955

21 Samples

Download data: TXT

(Submitter supplied) Functional targeting of PpPINC gene in Physcomitrella, researching it's role during gametangia and sporophyte development.

Organism:

Physcomitrium patens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL32248

12 Samples

Download data: TXT

(Submitter supplied) Eukaryotic RNA molecules undergo multiple regulatory steps prior to being translated as proteins. Two features of post-transcriptional regulation are RNA secondary structure and RNA-binding protein (RBP) interactions with mRNAs. Here we reveal the global landscape of RBP-RNA interactions the bryophyte Physcomitrella patens undergoes as part of its response to the phytohormone abscisic acid (ABA). We show that P. more...

Organism:

Physcomitrium patens

Type:

Other

Platform:

GPL17793

24 Samples

Download data: BED, BED12

(Submitter supplied) Eukaryotic RNA molecules undergo multiple regulatory steps prior to being translated as proteins. Two features of post-transcriptional regulation are RNA secondary structure and RNA-binding protein (RBP) interactions with mRNAs. Here we reveal the global landscape of RBP-RNA interactions the bryophyte Physcomitrella patens undergoes as part of its response to the phytohormone abscisic acid (ABA). We show that P. more...

Organism:

Physcomitrium patens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17793

6 Samples

Download data: TXT

(Submitter supplied) We used single cell laser-assisted microdissection (LAM) to perform egg cell transcriptome analysis for comparison with available expression profiles of vegetative tissues and male reproductive organs. We observed an overlap in gene activity between bryophyte and angiosperm egg cells, but also clear differences. Strikingly, several processes that are male germline-specific in Arabidopsis are active in the P. more...

Organism:

Physcomitrium patens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30513

4 Samples

Download data: TXT

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

Organism:

Physcomitrium patens; Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing

5 related Platforms

29 Samples

Download data: GFF

(Submitter supplied) Cytosine methylation is commonly targeted to symmetrical CG sites, as well as to non-CGs, such as the symmetrical-CHG and asymmetric-CHH sites in plants (H= A, C or T). Thus far, depletion of CG methylation in plants was associated with ample transcriptional activation of transposons. Here, we profiled transcription in various context specific methylation mutants in the early-diverged plant, Physcomitrella patens. more...

Organism:

Physcomitrium patens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL17793 GPL27916

20 Samples

Download data: TXT

(Submitter supplied) Cytosine methylation is commonly targeted to symmetrical CG sites, as well as to non-CGs, such as the symmetrical-CHG and asymmetric-CHH sites in plants (H= A, C or T). Thus far, depletion of CG methylation in plants was associated with ample transcriptional activation of transposons. Here, we profiled transcription in various context specific methylation mutants in the early-diverged plant, Physcomitrella patens. more...

Organism:

Physcomitrium patens

Type:

Methylation profiling by high throughput sequencing

Platforms:

GPL29161 GPL14798

3 Samples

Download data: GFF

(Submitter supplied) Pentatricopeptide repeat (PPR) proteins are RNA binding proteins that function in posttranscriptional regulation as gene-specific regulators of RNA metabolism in plant organelles. Plant PPR proteins are divided into four classes: P, PLS, E and DYW. The E- and DYW-class proteins are mainly implicated in RNA editing, whereas most of the P-class proteins predominantly participate in RNA cleavage, splicing and stabilization. more...

Organism:

Physcomitrium patens

Type:

Expression profiling by array

Platform:

GPL25703

4 Samples

Download data: TXT

(Submitter supplied) transcriptomic analysis by a high-throughput sequencing platform.

Organism:

Physcomitrium patens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28239

10 Samples

Download data: TXT, XLSX

(Submitter supplied) The moss Physcomitrella patens was employed to study abiotic stress responses in order to understand the effects of mild (30°C) and strong (37°C) continuous heat stresses from 1h to 24h at a transcriptomic level.

Organism:

Physcomitrium patens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17793

24 Samples

Download data: TXT

(Submitter supplied) Chloroplast gene expression is controlled by numerous nuclear-encoded RNA-binding proteins. Among them, pentatricopeptide repeat (PPR) proteins are known to be a key player in posttranscriptional regulation in chloroplasts. However, the functions of many PPR proteins remain unknown. In this study, we characterized the function of a chloroplast-localized P-class PPR protein PpPPR_21 in Physcomitrella patens. more...

Organism:

Physcomitrium patens

Type:

Expression profiling by array

Platform:

GPL25703

4 Samples

Download data: TXT