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Sample GSM1053022

Query DataSets for GSM1053022

Status

Public on Sep 30, 2013

Title

Δabpf2_48hpi reps1-3

Sample type

SRA

Source name

tissues containing both Arabidopsis thaliana plant leaves and Alternaria brassicicola fungal mycelia

Organism

Alternaria brassicicola

Characteristics

fungal pathogen: Alternaria brassicicola
pathogen genotype/variation: abpf2 deletion mutant
infected host plant: Arabidopsis thaliana
tissue: mixed tissues of plant leaves and fungal mycelia
developmental stage: early germination stage
time: 48hpi

Treatment protocol

Arabidopsis thaliana was infected with either wild type or abpf2 deletion mutant

Growth protocol

Arabidopsis thaliana (Col-0) were grown under 8/14 light and dark cycle for 5 weeks.

Extracted molecule

polyA RNA

Extraction protocol

Total RNA was extracted from mixed tissues of plant leaves and fungal mycelia. PolyA RNA was enriched and libraries were constructed using TruSeq RNA sample prep kit (Illumina)

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 2000

Description

enriched polyA RNA

Data processing

Image analysis, base-calling, and quality checks were performed with the Illumina data analysis pipeline CASAVA v1.8.0.
The sequenced reads were mapped to the genome sequence of Al. brassicicola (version 1; http://jgi.doe.gov/Abrassicicola) and the latest genome release of Ar. thaliana (TAIR10 ) (ftp://ftp.arabidopsis.org/home/tair/Genes/) using the programs Tophat 1.3.1 (Trapnell et al., 2009) and Bowtie 0.12.7 (Langmead et al., 2009).
The program Cuffdiff version 1.0.3 (which is part of Cufflinks, (Trapnell et al., 2010)) was used to identify reads overlapping with previously predicted genes.
The expression levels of each predicted gene were determined and normalized by the mapped Fragments Per Kilobase of exon model per Million (FPKM). Differentially expressed genes between the wild type and the mutant were determined by comparing FPKM from three biological replicates for both the wild type and the mutant. We also applied a cutoff of at least a two-fold change in expression value for differential expression. The bias correction method was used while running Cuffdiff (Roberts et al., 2011).
Genome_build: genome sequence of Al. brassicicola (version 1; http://jgi.doe.gov/Abrassicicola)
Genome_build: genome release of Ar. thaliana (TAIR10 )
Supplementary_files_format_and_content: Altbr1_expression_12hpi_48hpi.txt: ProteinId, A12W (normalized expression level of gene in the wild type Alternaria), A12F2 (normalized expression level of gene in the abpf2 mutant Alternaria), A48W (normalized expression level of gene in the abpf2 mutant Alternaria), A48F2 (normalized expression level of gene in the abpf2 mutant Alternaria), PFAM annotation, GO annotation, A12W -> A12F2: Up/Down, A12W -> A12F2: q value, A12W -> A12F2: >2-fold and significant difference?, A12W -> A48W: Up/Down, A12W -> A48W: q value, A12W -> A48W: >2-fold and significant difference?, , , A12F2 -> A48F2: Up/Down, A12F2 -> A48F2: q value, A12F2 -> A48F2: >2-fold and significant difference?, A48W -> A48F2: Up/Down, A48W -> A48F2: q value, A48W -> A48F2: >2-fold and significant difference?
Supplementary_files_format_and_content: Arabidopsis_expression_12hpi_48hpi.txt: ProteinId, A12W (normalized expression level of plant gene inoculated with wild type Alternaria), A12F2 (normalized expression level of plant gene inoculated with abpf2 mutant Alternaria), A48W, A48F2, PFAM annotation, GO annotation, A12W -> A12F2: Up/Down, A12W -> A12F2: q value, A12W -> A12F2: >2-fold and significant difference?, A12W -> A48W: Up/Down, A12W -> A48W: q value, A12W -> A48W: >2-fold and significant difference?, , , A12F2 -> A48F2: Up/Down, A12F2 -> A48F2: q value, A12F2 -> A48F2: >2-fold and significant difference?, A48W -> A48F2: Up/Down, A48W -> A48F2: q value, A48W -> A48F2: >2-fold and significant difference?

Submission date

Dec 13, 2012

Last update date

May 15, 2019

Contact name

Yangrae Cho

E-mail(s)

yangrae@hawaii.edu

Phone

808-956-5305

Organization name

University of Hawaii at Manoa