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Sample GSM969707 Query DataSets for GSM969707
Status Public on Nov 22, 2012
Title The triple mutant (pen2 pad4 sag101) challenged with Bgh K1 isolate at 24hpi, replicate 3
Sample type SRA
 
Source name Bgh K1-infected pps leaves, 24hpi
Organism Arabidopsis thaliana
Characteristics plant strain: Columbia-0 pen2-1 pad4-1 sag101-2 mutant
tissue: leaves
fungal isolate: Blumeria graminis f. sp. hordei isolate K1
virulence: virulent
time: 24hpi
virulence_time (as used for model): virulent_24hpi
Treatment protocol Inoculation of the pathogens was perfomed as described in V. Lipka, et al., Science 310, 1180 (2005) (PMID 16293760).
Growth protocol Growth of plants and pathogens was performed as described in V. Lipka, et al., Science 310, 1180 (2005) (PMID 16293760).
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using the RNeasy Plant Mini Kit (Qiagen). RNA-seq libraries were prepared from an input of 4 ug total RNA according to recommendations of the supplier (TruSeq RNA sample preparation v2 guide, Illumina). Libraries were quantified by fluorometry, immobilized and processed onto a flow cell with a cBot (Illumina) followed by sequencing-by-synthesis with TruSeq v3 chemistry on a HiSeq 2000. Library construction and sequencing were performed by the Max Planck Genome Center Cologne (http://mpgc.mpipz.mpg.de).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Description pps_K1_24hpi_3
PolyA-enriched RNA
Data processing Illumina Casava 1.8 software was used for basecalling.
Sequenced reads were mapped to the TAIR10 whole genome using tophat v1.3.2 with parameters -p 12 -a 10 -g 5 --library-type fr-unstranded -G TAIR10_GFF3_genes.gff
Read counts per gene per sample were obtained using the bedTools suite v2.13.2 (function coverageBed).
Genome_build: TAIR10
Supplementary_files_format_and_content: CompleteCountTable_At.txt: Tab-delimited text file including raw read counts per gene for each sample. This file is linked to the Series record as a supplementary file.
 
Submission date Jul 18, 2012
Last update date May 15, 2019
Contact name Emiel Ver Loren van Themaat
E-mail(s) themaat@mpiz-koeln.mpg.de
Organization name Max Planck Institute
Street address Carl von linneweg
City Cologne
ZIP/Postal code 50823
Country Germany
 
Platform ID GPL13222
Series (1)
GSE39463 Time-course RNA-seq analysis of the barley MLA1 immune receptor-mediated response to barley powdery mildew fungus Bgh in Arabidopsis thaliana
Relations
Reanalyzed by GSM1057683
SRA SRX160963
BioSample SAMN01091819

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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