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Sample GSM7060484 Query DataSets for GSM7060484
Status Public on Jun 30, 2023
Title maize_leaf, SG200, 6dpi, rep3
Sample type SRA
 
Source name Ustilago maydis-infected leaf
Organism Zea mays
Characteristics tissue: Ustilago maydis-infected leaf
cultivar: Golden Bantam
fungal strain: SG200
treatment: SG200
time point: 6dpi
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.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Description 6dpi, SG200, rep3
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.
 
Submission date Feb 23, 2023
Last update date Jun 30, 2023
Contact name Gunther Doehlemann
E-mail(s) g.doehlemann@uni-koeln.de
Organization name University of Cologne
Street address Zuelpicher Str. 47a
City Cologne
ZIP/Postal code 50674
Country Germany
 
Platform ID GPL25410
Series (1)
GSE225929 A transcriptional activator effector of Ustilago maydis regulates hyperplasia in maize during pathogen-induced tumor formation
Relations
BioSample SAMN33424258
SRA SRX19483384

Supplementary file Size Download File type/resource
GSM7060484_S63_counts.txt.gz 160.3 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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