NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM7060478 Query DataSets for GSM7060478
Status Public on Jun 30, 2023
Title maize_leaf, Sts2-ko, 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 Sts2-ko
treatment: Sts2-ko
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, Sts2-ko, 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 SAMN33424264
SRA SRX19483378

Supplementary file Size Download File type/resource
GSM7060478_K63_counts.txt.gz 159.8 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap