RNA-seq Expression data from several developmental stages of P. patens Gransden WT and Reute WT.
Gd: Gransden WT
Re: Reute WT
Note: Gametophores with sexual organs were considered Adult gametophores.
Dry spores and imbibed spores from Grandsen and protonema Klq, gametophore ksl and adult gametophore ksl from Reute were published in Fernandez-Pozo et al., 2020. The rest of the experiments were published in Perroud et al., 2018. All samples were normalized to RPKM.
| Media | Abbreviations |
|---|---|
| BCDA (ammonium) liquid | BlqA |
| BCD solid | Bsl |
| BCDA (ammonium) solid | BslA |
| Knop liquid | Klq |
| Knop solid | Ksl |
RNA-seq expression data of P. patens experiments conducted in sexual organs and first stages of the sporophyte development.
All samples were normalized to RPKM.
The experiments of this dataset were published in Genau et al., 2021 (Gametophore apices),
Meyberg et al., 2020 (antheridia 21 DAI),
Julca et al., 2021 (Gransden antheridia development, sperm cell packages, mature archegonia and Granden sporophyte development),
Haas et al., 2020 (Laser Capture Microdissection of egg cell and E0 embryo together with venter cells of their corresponding unfertilized and fertilized archegonia. Also Bulk RNAseq of ES1),
Szövényi et al., 2017 (E0/E1/E2, ES/ES1, green sporophyte premeiotic).
Due to the small tissue size all samples but the gametophore apices required PCR amplification. For more information about RNA-seq extraction, amplification and mapped reads see the file sample_information.xlsx.
Re: Reute WT
Gd: Gransden WT
Vx: Villersexel WT
DAI: days after induction
DAF: days after fecundation
2 DAW: 2 days after watering
Note: Gametophores apices were collected to study gene expression in sexual organs.
Figure 1. Sporophyte developmental stages
| Abb. | Developmental stage | Description |
|---|---|---|
| E0 | Embryo 0 |
Embryos of archegonia 2 days after watering/fertilization (8 cells aprox/stage E0 following Meyberg et al 2020 stage specification) |
| E1 | Embryo 1 |
Developing embryo; the upper, chloroplast rich half will develop into the spherical, spore-containing spore capsule, whereas the lower part will connect to the gametophore for nourishment of the developing sporophyte. |
| E2 | Embryo 2 |
Elongated embryo without developed stomata. Connection between gametophore and sporophyte still loose but cells started to differentiate. |
| ES | Early sporophyte | Stomata are developed, clear separation of capsule (inflation) and developing seta (2n). |
| PM | Premeiotic sporophyte | Spherical green translucend sporophyte containing spore mother cells (2n), seta starts to turn brownish. |
| M | Meiotic sporophyte | Opaque green sporophyte containing tetrades which will later form each four spores (1n, meiosis occured). |
| Y | Yellow sporophyte | Contains early spores of the final size covered by a plasma membrane, seta darkend during the maturation process. |
| LB | Light brown sporophyte | Spores started to mature, the spore wall thickens by exine deposition. |
| B | Brown sporophyte | Spores are mature, spore wall consists of a thick perine layer with spikes, exine, seperating layer and intine, sporophyte detaches easily. |
Expression data from multiple hormone treatments for Gransden WT protonema on several media.
These data were published in Perroud et al., 2018.
| Abbreviations | |
|---|---|
| BCD solid | BSL |
| BCDA (ammonium) solid | BSLA |
| Gibberellin A9 methyl-ester | GA9 |
| 12-oxophytodienoic acid | OPDA |
Note: OPDA is a precursor of jasmonic acid.
Expression data from several experimental conditions for Gransden WT protonema on several media.
These data were published in Perroud et al., 2018.
| Abbreviations | |
|---|---|
| BCD solid | BSL |
| BCDA (ammonium) solid | BSLA |
| Knop liquid | KLQ |
| Knop liquid ammonium | KLQA |
| Knop solid | KSL |
Time series of RNA-seq expression data of P. patens Gransden WT protonema with and without Pi deficency.
This dataset was published in Fernandez-Pozo et al., 2020.
Expression data from several experimental conditions for Gransden WT gametophore on several media.
These data were published in Perroud et al., 2018.
| Abbreviations | |
|---|---|
| BCD solid | BSL |
| hydroponic | hydr |
Combimatrix microarray expression data from several developmental stages of P. patens Gransden WT and Reute WT.
Gd: Gransden WT
Re: Reute WT
Note: Gametophores with sexual organs are considered Adult gametophores.
These data were published in Hiss et al., 2014. The data are from the CombiMatrix microarray platform and all the samples were normalized by a median value of 12.
Gene models: v1.2 Phypa.
| Abbreviations | |
|---|---|
| Knop solid | Ksl |
| Knop liquid | Klq |
| Knop liquid ammonium | KlqA |
Combimatrix microarray expression data from multiple experimental conditions for P. patens Gransden WT protonema in liquid Knop medium.
The data are derived from the CombiMatrix microarray platform and all samples were normalized by a median value of 12. Transition experiments from pH 5.8 to pH4.5 were published in Hiss et al., 2014. The ABA time series experiment is under preparation.
Gene models: v1.2 Phypa.
| Abbreviations | |
|---|---|
| Knop solid | Ksl |
| Knop liquid | Klq |
| Knop liquid ammonium | KlqA |
Expression data of several experimental conditions for Gransden WT juvenile gametophores on solid Knop medium.
The data are derived from the CombiMatrix microarray platform and all the samples were normalized by a median value of 12. All experiments but the red light and cold time series were published in Hiss et al., 2014. The cold time series was published in Beike et al., 2015. The red light experiment was published in Possart et al., 2017.
Gene models: v1.2 Phypa.
Detached Leaflet (phyllid) development time series from 0 to 96 hours (Experiment time points have one single measurement, no replicates).
All samples were normalized by a median value of 12. Combimatrix microarray expression data was published in Busch et al., 2013 and Hiss et al., 2014.
Gene models: v1.2 Phypa.
Generation of a transcriptome atlas covering most phases in the life cycle of the model bryophyte P. patens, including detailed sporophyte developmental progression.
The processed data from Ortiz-Ramirez et al., 2016 (RMA normalized) were scaled to a median value of 12.
Gene models: v1.6.
Expression data of heat treatment and mycorrhiza interaction experiments for Gransden WT juvenile gametophores on solid Knop medium and developmental stages for Reute ecotype.
Gd: Gransden WT
Re: Reute WT
AdGam: Adult Gametophores
JuvGam: Juvenile Gametophores
Note: Gametophores with sexual organs were considered Adult gametophores.
The processed data from Ortiz-Ramirez et al., 2016 (RMA normalized) were scaled to a median value of 12.
Gene models: v1.6.
Developmental gene expression data from Spirogyra pratensis.
RNA-seq expression data from Spirogyra pratensis under Cytokinin Treatment.
RNA-seq expression data from Spirogyra pratensis under osmotic stress.
Comprehensive dataset of Spirogyra pratensis gene expression across a gradient of 42 samples with different exposure to light intensity and temperature, plus control samples, covering 43 samples in total.
Figure 1. Schematic representation of the enviromental conditions.
| Abbreviations | |
|---|---|
| um | μmol photons s−1 m−2 |
| C | °C |
Vegetative Chara braunii S276 cultures were kept at 22°C in a 16 h light: 8 h dark cycle with white light lateral illumination (30–70 μmol photons m−2 s−1).
Nodal cells were cut out and pooled from several algae and total RNA extracted from both pooled nodal cells and a whole thallus.
Poly(a)+ selected cDNA libraries were generated via service and sequenced on an Illumina NextSeq 500 system using 75 bp read length.
Data analysis was performed on the European instance galaxy server: reads were trimmed via cutadapt, mapped and counting of reads was performed using RNA STAR.
Samples are based into one replicate normalized to TPM.
Published by Heß et al., 2023
Figure on right: Specimen of Chara baunii. Detailed view of Chara braunii S276. Shown is the area with the interior node cells confined by two internodal cells. Nodal cells pinched off peripheric cells from which branchlets developed with a structure analogous to the main stem consisting of branchlet nodal and internodal cells. Branchlet nodal cells are the origin for the development of antheridia (shown) and the typical charophytic oogonia after proliferation.
Vegetative Chara braunii S276 cultures were pre-cultivated at 21°C with a light intensity of 50–60 μmol photons m−2 s−1 under a 16 h light: 8 h dark cycle. To evaluate osmoregulatory ability, the alga was then incubated for 6, 24, and 48 h at an elevated salinity of 5 PSU sea salt and whole thalli without the rhizome were harvested. Poly(a)+ selected cDNA libraries were generated via service using the Illumina TruSeq stranded protocol and paired-end sequenced using 2x100 bp read length.
Data analysis was performed on the European instance galaxy server: reads were trimmed via cutadapt, mapped and counting of reads was performed using RNA STAR and time series gene expression analysis was performed using DESeq2.
Samples are based into two replicates normalized to TPM.
Published by Heß et al., 2023
Vegetative Chara braunii S276 cultures were cultivated at 21°C with a light intensity of 50-60 μmol photons m−2 s−1 under a 16 h light: 8 h dark cycle.
Cultivation under ambient air conditions (0.04% CO2) was defined as a low-inorganic carbon (LC) condition.
To evaluate response to fluctuating inorganic carbon conditions, medium of the algae (LC) was exchanged with high-inorganic carbon medium (HC, 10 mM NaHCO3). Both HC and LC algae were acclimated for 7 d, after which the liquid medium was exchanged with the respective other (HC to LC and LC to HC) and thalli samples sans rhizome collected 24 and 48h after the shift. Poly(a)+ selected cDNA libraries were generated via service using the Illumina TruSeq stranded protocol and paired-end sequenced using 2x100 bp read length.
Data analysis was performed on the European instance galaxy server: reads were trimmed via cutadapt, mapped and counting of reads was performed using RNA STAR and time series gene expression analysis (HC to LC and LC to HC) was performed using DESeq2.
Samples are based into two replicates normalized to ???.
Published by Heise et al., 2025
