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| Status |
Public on Jun 01, 2012 |
| Title |
F6DPI |
| Sample type |
SRA |
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| Source name |
Fusarium oxysporum infected whole plants
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| Organism |
Arabidopsis thaliana |
| Characteristics |
developmental stage: 3 week old seedling
ecotype: Col-0
tissue: whole plants
treatment: Fusarium oxysporum infected
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| Treatment protocol |
Fusarium oxysporum inoculation was perfomed using root dipping with 2 week old seedlings
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| Growth protocol |
Plants were grown under 16h light.
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| Extracted molecule |
total RNA |
| Extraction protocol |
The libraries were constructed according to the procedures detailed in the SOLiDTM Whole Transcriptome Analysis Kit using 1 μg of RQ1 DNase-treated and rRNA-depleted (two rounds of depletion using the RiboMinusTM Plant Kit, Invitrogen) total RNA
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
AB SOLiD System |
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| Description |
rRNA depleted total RNA
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| Data processing |
F6DPI_TAIR10.bed; genome build: TAIR10
F6DPI_TAIR10_ROI.csv; genome build: TAIR10
RNA-seq reads were aligned to the TAIR10 Arabidopsis/Fusarium pseudo genome using the aligner Kanga. Alignment parameters were set to allow up to 5 aligner induced substitutions, microIndels up to 5 bp, splice junctions up to 10000 bp, and only accepting uniquely aligned reads which are at least one Hamming from any other putative alignment. Aligned reads were filtered and only those reads exclusively aligning to the TAIR10 Arabidopsis assembly were retained for subsequent processing. Retained Arabidopsis aligned reads were then mapped on to TAIR10 annotation loci for each individual class of annotation (protein-coding, psuedogene, transposon, miRNA, snoRNA, tRNA, ncRNA and geneid). The digital expression levels (RPKM, reads per kilobase of exon model per million mapped reads) of each annotated protein-coding gene were then calculated and used to identify differentially expressed genes in Fusarium oxysporum infected samples.)
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| Submission date |
Dec 07, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Stuart Stephen |
| E-mail(s) |
stuart.stephen@csiro.au
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| Organization name |
CSIRO
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| Department |
Plant Industry
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| Lab |
Computational Biology
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| Street address |
Black Mountain
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| City |
Canberra |
| State/province |
ACT |
| ZIP/Postal code |
2601 |
| Country |
Australia |
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| Platform ID |
GPL13396 |
| Series (1) |
| GSE34241 |
RNA-seq-based analysis of the pathogen-induced defense transcriptome in Arabidopsis |
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| Relations |
| SRA |
SRX110622 |
| BioSample |
SAMN00763682 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM845433_F6DPI_TAIR10.bed.gz |
19.6 Mb |
(ftp)(http) |
BED |
| GSM845433_F6DPI_TAIR10_ROI.csv.gz |
25.2 Kb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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