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Sample GSM1553427 Query DataSets for GSM1553427
Status Public on Aug 26, 2015
Title WT_flg22_R1
Sample type SRA
 
Source name seedlings_wildtype_flg22
Organism Arabidopsis thaliana
Characteristics cultivar: Col-0
genotype: wildtype
age: 10-day old
tissue: whole plant
Treatment protocol Ten days old seedlings were transferred to a 6-well tissue culture plate with 2 ml water for overnight, and then treated with 100 mM flg22 for 30 min.
Growth protocol Seedlings were germinated on ½ Murashige and Skoog (MS) plate containing 1% sucrose, 0.8% Agar.Plants were grown in a growth room at 23°C, 45% humidity and 75μE m-2s-1 light with a 12 hr light/12 hr dark photoperiod.
Extracted molecule total RNA
Extraction protocol Total RNA from 10-day-old seedlings was extracted by TRIzol reagent (Invitrogen) and quantified with NanoDrop (Thermo Scientific).
cDNA libraries were made using Illumina TruSeq RNA prep kit as per the manufacturer's protocol and 1 μg total RNA was used for one sample.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Data processing Sequence cluster identification, quality prefiltering, base calling and uncertainty assessment were done in real time using Illumina's HCS 2.2.38 and RTA 1.18.61 software with default parameter settings
Sequencer .bcl basecall files were formatted into .fastq files using bcl2fastq 1.8.4 script configureBclToFastq.pl
Samples are demultiplexed during the execution of the configureBclToFastq.pl script. Three metrics are examined upon sample demultiplexing: (1) demultiplexing balance, (2) rate of prefiltering, and (3) the presence of technical adapter sequence at the ends of reads using cutadapt 1.0.
Reads were aligned to the Arabidopsis genome using Tophat v2.0.12 with default parameter settings
Normalized abundance measurements of FPKM value were generated using the Cuffdiff v2.2.1
Genome_build: Arabidopsis TAIR10 genome annotation
Supplementary_files_format_and_content: txt format, gene relative expression level of fragments per kilobase of exon per million fragments mapped (FPKM)
 
Submission date Nov 24, 2014
Last update date May 15, 2019
Contact name Libo Shan
Organization name Texas A&M University
Department Department of Plant Pathology and Microbiology
Lab Institute for Plant Genomics and Biotechnology
Street address Norman Borlaug Center 136, TAMU2123
City College Station
State/province Texas
ZIP/Postal code 77845
Country USA
 
Platform ID GPL17639
Series (1)
GSE63603 RNA-seq analysis of flg22-induced gene expression changes in wild type, asr3-1 mutant and OX9 overexpression line
Relations
BioSample SAMN03219221
SRA SRX767321

Supplementary file Size Download File type/resource
GSM1553427_WT_flg22_R1.txt.gz 172.8 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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