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| Status |
Public on Jun 30, 2023 |
| Title |
maize_leaf, SG200, 6dpi, rep1 |
| Sample type |
SRA |
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| Source name |
Ustilago maydis-infected leaf
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| Organism |
Zea mays |
| Characteristics |
tissue: Ustilago maydis-infected leaf
cultivar: Golden Bantam
fungal strain: SG200
treatment: SG200
time point: 6dpi
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested from frozen and homogenized samples using TRIzol reagent (Invitrogen, Darmstadt, Germany). The Turbo DNA-Free Kit from Ambion (Ambion Life TechnologiesTM, Carlsbad, USA) was used to exclude DNA contamination.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
6dpi, SG200, rep1
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| Data processing |
The Trinity software (v2.9.1) option trimmomatic was used for quality filtering of the paired-end reads.
bowtie2 (2.3.5.1) was used for the mapping of the quality-filtered reads to the reference genome of maize.
The R package Rsubread (v1.34.7) was used to count the mapped reads.
edgeR (3.26.8) was used for the differential gene expression analysis.
Assembly: Combined assembly of Ustilago maydis and Zea mays B73 version 5
Supplementary files format and content: Gzipped text files containing transcript counts for each sample.
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| Submission date |
Feb 23, 2023 |
| Last update date |
Jun 30, 2023 |
| Contact name |
Gunther Doehlemann |
| E-mail(s) |
g.doehlemann@uni-koeln.de
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| Organization name |
University of Cologne
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| Street address |
Zuelpicher Str. 47a
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| City |
Cologne |
| ZIP/Postal code |
50674 |
| Country |
Germany |
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| Platform ID |
GPL25410 |
| Series (1) |
| GSE225929 |
A transcriptional activator effector of Ustilago maydis regulates hyperplasia in maize during pathogen-induced tumor formation |
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| Relations |
| BioSample |
SAMN33424260 |
| SRA |
SRX19483382 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7060482_S61_counts.txt.gz |
160.1 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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