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Sample GSM6351348 Query DataSets for GSM6351348
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

Supplementary file Size Download File type/resource
GSM6351348_WT4_S9_R1_001_GE.txt.gz 646.7 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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