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| Status |
Public on May 17, 2021 |
| Title |
1 dpt inf R3 |
| Sample type |
SRA |
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| Source name |
Roots
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| Organism |
Arabidopsis thaliana |
| Characteristics |
ecotype: Col-0
tissue: whole root
treatment: Fusarium oxysporum 5176
days post treatment: 1
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| Treatment protocol |
For hydroponic infections, the roots of 10-day-old seedlings were infected with 20µl of a solution containing 107 microconidia/ml Fo5176. All pots were incubated for 30 minutes at 100 rpm on a rotary shaker. The media of the infected plants was then replaced with fresh ½ MS media. The plants were further grown under the same conditions until the roots were harvested for RNA extraction or for imaging at 0, 1, 2, 3, 4, and 6 days post treatment. For Fo5176 transcriptomics in the absence of a plant host, 107 microconidia/ml were germinated in ½ MS + 1% (w/v) sucrose overnight at 180rpm at 28°C in the dark. The germinated microconidia were harvested via two centrifugation steps at 4000 xg for 15 minutes at 10° C, washed twice with water, discarding supernatant in between washes.
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| Growth protocol |
Arabidopsis seeds were germinated at 24° C, long day conditions, on 2 mm foam plugs suspended on 200 ml ½ MS + 1% sucrose media in 330ml pots at pH 5.7 adjusted by KOH. The media was exchanged 6 days after germination to ½ MS and seedlings were further grown.
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
For Fo5176 transcriptomics in the absence of a plant host, 107 microconidia/ml were germinated in ½ MS + 1% (w/v) sucrose overnight at 180rpm at 28°C in the dark. The germinated microconidia were harvested via two centrifugation steps at 4000 xg for 15 minutes at 10° C, washed twice with water, discarding supernatant in between washes.
3’mRNA-libraries were prepared using the 3’mRNA-Seq library Prep Kit (QuantSeq, Lexogen). The manual from the supplier was followed with the following modifications. At least 1 µg RNA was used as input. For first strand synthesis of cDNA the incubation time at step 4 was increased to 60 min. For library indexing and amplification 13-17 amplification cycles of the given PCR were used depending on the amount of input RNA. 17 µl of the purified library was transferred to a fresh tube. The finished libraries were stored at -20° C until quality control and pooling.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
sequenced reads were trimmed for low-quality bases with Trimmomatic, version 0.36
sequencing adapters were removed with Flexbar, version 3.0.3
Reads were mapped against the Arabidopsis thaliana genome (TAIR10) with STAR version 2.6.1c
Reads were mapped against the Fusarium oxysporum 5176 genome (Fokkens et al., 2020, G3) with STAR version 2.6.1c
Uniquely mapped reads were counted by featureCounts, based on the R package Rsubread (version 1.32.1)
Genome_build: ASM1311235v1
Genome_build: TAIR10
Supplementary_files_format_and_content: Processed data files include the raw counts of reads mapped uniquely against the reference genomes in .txt format.
Supplementary_files_format_and_content: Processed data files include the normalized counts per million for the samples and time points used afterwards to draw conclusions (counts were normalized using trimmed means of M-values (TMM) normalization in EdgeR version 3.24.3; Robinson and Oshlack, 2010)
Supplementary_files_format_and_content: Samples and time points taken into account to calculate differential gene expression in Fusarium oxysporum 5176 using the protocols described for EdgeR. Reads are normalized to counts per million using the TMM-method described by Robinson and Oshlack, 2010.
Supplementary_files_format_and_content: Samples and time points taken into account to calculate differential gene expression in Arabidopsis thaliana Col-0 using the protocols described for EdgeR. Reads are normalized to counts per million using the TMM-method described by Robinson and Oshlack, 2010.
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| Submission date |
Mar 02, 2021 |
| Last update date |
May 18, 2021 |
| Contact name |
Susanne Dora |
| E-mail(s) |
[email protected]
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| Organization name |
ETH Zürich
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| Department |
D-Biology, Institute for molecular plant biology
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| Lab |
Plant Cell Biology
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| Street address |
Universitätsstrasse 2
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| City |
Zürich |
| ZIP/Postal code |
8092 |
| Country |
Switzerland |
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| Platform ID |
GPL17639 |
| Series (2) |
| GSE168015 |
mRNA-profiles of Arabidopsis thaliana (Col-0) roots infected with Fusarium oxysporum 5176 over a time course of six days |
| GSE168919 |
A primary cell wall cellulose-dependent defense mechanism against vascular pathogens revealed by time-resolved dual-transcriptomics |
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| Relations |
| BioSample |
SAMN18105264 |
| SRA |
SRX10204654 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5123790_1_dpt_inf_R3_At.txt.gz |
111.7 Kb |
(ftp)(http) |
TXT |
| GSM5123790_1_dpt_inf_R3_Fo.txt.gz |
43.0 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
| Processed data provided as supplementary file |
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