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| Status |
Public on Oct 18, 2019 |
| Title |
gun1-1+NF1 |
| Sample type |
SRA |
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| Source name |
whole seedling
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| Organism |
Arabidopsis thaliana |
| Characteristics |
genotype: gun1-1
tissue: whole seedling
ecotype background: Col-0
age: 5d after germination
treatment: 5µM Norflurazon
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| Treatment protocol |
5µM Norflurazon (+NF) in growth media (MS). Additionally the gun5-1 mutant was germinated in the presence of 100µM piperonylic acid (+PIP) and +5µM NF
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| Growth protocol |
5d, 100µl photons m-2 s-1
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA-extraction protocol using citric acid described by Onate-Sanchez and Vicente-Carbajosa (2008). Total RNA of 5d old seedlings was extracted.
After the QC procedures, mRNA from eukaryotic organisms is enriched using oligo(dT) beads. For prokaryotic samples, rRNA is removed using the Ribo-Zero kit that leaves the mRNA. First, the mRNA is fragmented randomly by adding fragmentation buffer, then the cDNA is synthesized by using mRNA template and random hexamers primer, after which a custom second-strand synthesis buffer (Illumina) , dNTPs, RNase H and DNA polymerase I are added to initiate the second-strand synthesis. Second, after a series of terminal repair, A ligation and sequencing adaptor ligation, the double-stranded cDNA library is completed through size selection and PCR enrichment.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Description |
treatment with 5µM Noflurazon
Cuffdiff_Col-0+NF_gun1-1+NF
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| Data processing |
Analysis was performed using GALAXY-Webserver
Trimmomatic
TopHat alignment of reads to Arabidopsis thaliana Col-0 genome build (NCBI GenBank BioProject PRJNA10719), Araport11 Official Release
Cufflinks on TopHats "accepted hits"
Cuffmerge of all assembled transcripts togehter with Col-0 Araport11 (s.a.) annotation
Cuffdiff
Down stream analysis using GALAXY-tools (Filter, Cut, Paste), Microsoft Excel (offline handling of datasets), Perseus-Software (generation of heatmaps on FC, MPI biochemistry)
Genome_build: Arabidopsis thaliana Col-0 genome build (NCBI GenBank BioProject PRJNA10719)
Supplementary_files_format_and_content: Processed data files contain log2(FC) and p-value of control (Col-0+NF or gun5-1+NF for gun5-1+NF+PIP) vs mutant (gun1-1+NF, gun4-1+NF, gun5-1+NF, gun5-1+NF+PIP)
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| Submission date |
Oct 12, 2017 |
| Last update date |
Oct 18, 2019 |
| Contact name |
Andreas Sven Richter |
| Organization name |
University of Rostock
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| Department |
Institute for Biosciences
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| Lab |
Physiology of Plant Metabolism
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| Street address |
Albert-Einstein-Strasse 3
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| City |
Rostock |
| ZIP/Postal code |
18059 |
| Country |
Germany |
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| Platform ID |
GPL21785 |
| Series (1) |
| GSE104868 |
The genomes uncoupled dependent signaling pathway coordinates plastid biogenesis with the synthesis of anthocyanins |
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| Relations |
| BioSample |
SAMN07776221 |
| SRA |
SRX3275176 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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