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Sample GSM3612823 Query DataSets for GSM3612823
Status Public on May 15, 2019
Title Col00Rt2
Sample type SRA
Source name Root
Organism Arabidopsis thaliana
Characteristics genotype: wild type
tissue: root
treatment: iron deficient
Treatment protocol Grown for 3 days on iron sufficient (+Fe) or iron deficient (-Fe) media
Growth protocol Germinated and grown for 12 days on B5, followed by 3 days on iron sufficient (+Fe) or iron deficient (-Fe) media; 16/8 light/dark cycle at 22°C
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from fresh Arabidopsis root tissue using Plant RNA Isolation Kit (Agilent) per manufacturer's instructions.
RNA libraries were prepared for sequencing using TruSeq Stranded mRNA Library Prep Kit
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
Data processing Illumina Casava1.8 software used for basecalling.
Raw reads were filgered to remove reads containing adapters or reads of low quality, then mapped to Arabidopsis TAIR10 reference genome using TopHat2 (TMR>70%; MMR<10%)
RPKM (Reads Per Kilo bases per Million reads) method (Mortazavi et al 2008)
Genome_build: TAIR10
Supplementary_files_format_and_content: RPKM
Submission date Feb 19, 2019
Last update date May 15, 2019
Contact name Jeeyon Jeong
Organization name Amherst College
Department Biology
Lab Jeong
Street address 25 East Drive
City Amherst
State/province MA
ZIP/Postal code 01002
Country USA
Platform ID GPL26208
Series (1)
GSE126782 PRC2-mediated H3K27me3 contributes to transcriptional regulation of FIT-mediated iron deficiency response
BioSample SAMN10968253
SRA SRX5392812

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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