|
Status |
Public on Jul 26, 2023 |
Title |
Mp, BoGa, rep3 |
Sample type |
SRA |
|
|
Source name |
3 weeks old thallus; entire plants (1 replicate = 3 plants)
|
Organism |
Marchantia polymorpha |
Characteristics |
age: 3 weeks old tissue: thallus genotype: BoGa (WT) treatment: none
|
Treatment protocol |
No treatment was performed.
|
Growth protocol |
BoGa, Mpb-gata1-1 and Mpb-gata1-2 were grown on 1/2 Gamborg's B5 medium in long day conditions (16L/8D) at 40 µmol m-2 s-1 and 22°C for three weeks.
|
Extracted molecule |
total RNA |
Extraction protocol |
Total RNA was extracted using a NucleoSpin RNA kit (Macherey-Nagel). TruSeq stranded mRNA Kit (Illumina, San Diego, USA) with TruSeq RNA Adapter Box Set B (Illumina, San Diego, USA) and protocol 1000000040498v00 (Elution-2-Frag-Prime step: 4 minutes at 94°C; 15 cycles enrichment).
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2500 |
|
|
Data processing |
CLC Genomics Workbench v20.0.2 Sequence reads were trimmed using CLC Genomics Workbench - Quality limit: 0.05. Trimmed sequence reads were mapped to the MpTak1v5.1 release of Marchantia polymorpha Tak1 genome using CLC Genomics Workbench - Mismath cost: 2, Insertion cost: 3, Deletion cost: 3, Length fraction: 0.5, Similarity fraction: 0.8. Read count extraction and normalization were performed using CLC Genomics Workbench. Assembly: MpTak1v5.1 release of Marchantia polymorpha Tak1. Supplementary files format and content: Tab-delimited text files, including TPM.
|
|
|
Submission date |
Jul 19, 2022 |
Last update date |
Jul 26, 2023 |
Contact name |
Peter Michael Schröder |
E-mail(s) |
p.schroeder@tum.de
|
Organization name |
Technical University of Munich
|
Department |
School of Life Sciences
|
Lab |
Plant Systems Biology
|
Street address |
Emil-Ramann-Straße 8, Gebäude 4223
|
City |
Freising |
State/province |
Bavaria |
ZIP/Postal code |
85354 |
Country |
Germany |
|
|
Platform ID |
GPL28942 |
Series (2) |
GSE208557 |
Comparative transcriptomic analysis of Marchantia polymorpha BoGa and the MpB-GATA1 mutants Mpb-gata1-1 and Mpb-gata1-2 |
GSE208563 |
Conserved roles of B-GATAs in the regulation of photosynthesis and high-light stress response |
|
Relations |
BioSample |
SAMN29828390 |
SRA |
SRX16342317 |