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Sample GSM954713 Query DataSets for GSM954713
Status Public on Nov 14, 2013
Title Spike_infected_stage 2 (2011S2)
Sample type SRA
 
Source name the booting rice panicle
Organism Oryza sativa Indica Group
Characteristics cultivar: 9311
tissue: spike
disease stage: stage 2
infection: Ustilaginoidea virens
Treatment protocol At booting stage, each panicle was injected 2 ml 10^6/ml spore suspension ( 10^6/ml ) at 4:00-6:00, PM. Control was injiected with water. Each infected and control stages spikes were collected at 6 dpi.
Growth protocol Rice cultivar 9311 was grown in a glasshouse with an air temperature range of 28-31℃ and above 80% humidity under natural daylight at booting stage.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from frozen samples using standard protocols (Trizol) and then treated with DNase to remove potential genomic DNA contamination according to the manufactures’s protocols. Sample quality and concentration were evaluated using Qubit fluorometer (Invitrogen, CA) and Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, USA). mRNA was isolated from total RNA by binding the mRNA to a magnetic oligo(dT)bead, and break down it about 200nt by adding fragmentation buffer. Then the first strand cDNA is synthesized by random hexamer-primer using the mRNA fragments as templates. Buffer, dNTPs, RNase H and DNA polymerase I are added to sythsize the second strand. The double strand cDNA is purified with QiaQuick PCR extraction kit and washed with EB buffer for end repair and single nucleotide A (adenine) addition. Finally, sequencing adaptors are ligated to the fragments. The required fragments is purified by agrose gel electrophoresis and enriched by PCR amplification. The library products are ready for sequencing analysis via Illumina HiSeq™ 2000.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Data processing Illumina BCL Converter(BclConverter-1.9.0-11-03-08)software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to reference database (merged by integrating indica rice genome into japonica rice full-length cDNAs from the KOME with 95% threshold value) using SOAPaligner/soap2 V2.21t with parameters -m 0 -x 1000 -s 28 -l 32 -v 2 -r 2.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Poisson distribution model was used to identify differentially expressed genes between two samples(Referring to "The significance of digital gene expression profiles" from Audic S. et al.).In short, denote the number of unambiguous clean tags from gene A as x, given every gene's expression occupies only a small part of the library, p(x) will closely follow the Poisson distribution.
Expression pattern analysis of differentially expressed genes using Cluster with parameters -g 7 -e 7 -m a
Reference sequence then mapped to NR( from NCBI) using Blast v2.2.23 with parameters -p blastx -e 1e-5 -m 7, then mapped to GeneOntology using BLAST2GO v2.3.5 - 16.03.2009. And then, mapped to KEGG PATHWAY database using Blast v2.2.23 with parameters -o blastx -e 1e-5 -m 8.
Using hypergeometric test to find significantly enriched GO terms in differentially expressed genes comparing to the genome background.
Pathway enrichment analysis identifies significantly enriched metabolic pathways or signal transduction pathways in differentially expressed genes comparing with the whole genome background using hypergeometric test.
Genome_build: Reference database was merged by integrating indica rice genome into japonica rice full-length cDNAs from the KOME with 95% threshold value
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample
 
Submission date Jul 02, 2012
Last update date May 15, 2019
Contact name Chao Jin Quan
E-mail(s) tianwang208@163.com
Organization name Wuhan University
Department College of Life Sciences
Lab State Key lab of Hybrid Rice
Street address Bayi Road,Wuchang
City Wuhan
State/province Hubei
ZIP/Postal code 430072
Country China
 
Platform ID GPL14553
Series (2)
GSE39048 Genome-wide analysis rice transcriptional change during the early stages of false smut formation caused by Ustilaginoidea virens [2011].
GSE39049 Genome-wide analysis rice transcriptional change during the early stages of false smut formation caused by Ustilaginoidea virens
Relations
SRA SRX157304
BioSample SAMN01085211

Supplementary file Size Download File type/resource
GSM954713_S2.Gene.SESoap.txt.gz 441.8 Mb (ftp)(http) TXT
GSM954713_S2.Gene.rpkm.txt.gz 2.1 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Processed data provided as supplementary file
Processed data are available on Series record
Raw data are available in SRA

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