|
| Status |
Public on Nov 22, 2012 |
| Title |
The triple mutant (pen2 pad4 sag101) challenged with Bgh K1 isolate at 12hpi, replicate 1 |
| Sample type |
SRA |
| |
|
| Source name |
Bgh K1-infected pps leaves, 12hpi
|
| 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: 12hpi
virulence_time (as used for model): virulent_12hpi
|
| 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_12hpi_1
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 |
GSM1057669 |
| SRA |
SRX160949 |
| BioSample |
SAMN01091805 |
