|
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.
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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.
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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)
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|
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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 |