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Sample GSM4985008 Query DataSets for GSM4985008
Status Public on May 04, 2021
Title Col-0_r1
Sample type SRA
Source name seedlings
Organism Arabidopsis thaliana
Characteristics genotype: wild type
age: 7 days old
tissue: whole seedling
Growth protocol For seed germination, seeds were sterilized and then stratified for 3 days at 4 ℃ under dark condition; seeds were germinated on 1/2 Murashige and Skoog (MS) plates containing 0.8% Phytagel. Seedlings were grown in growth chamber with 16-h light/8-h dark cycles at 22℃.
Extracted molecule total RNA
Extraction protocol Total RNA was isolaed from 7-day-old seedlings using Purelink Plant RNA Regent (Invitrogen) according to manufacturer's instructions.
RNA-Seq libraries were prepared by NEBNext Ultra™ Directional RNA Library Prep Kit for Illumina (E7420) according to the manufacturer’s instructions.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
Data processing Raw reads wer mapped to the TAIR10 Arabidopsis genome using HISAT2 with default parameters
Featurecount was used to count read numbers of each gene
edgeR was used to identify differentially expressed genes
Genome_build: TAIR 10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values of each gene for each sample
Submission date Dec 23, 2020
Last update date May 04, 2021
Contact name Wei Zong
Organization name University of Texas at Austin
Department Molecular Biosciences
Street address NMS 5.268, Stop A5000
City Austin
State/province Texas
ZIP/Postal code 78712
Country USA
Platform ID GPL19580
Series (1)
GSE163742 RNA-Seq of Col-0, dek3-2, dek4-2, and dek3-2 dek4-2 (dd-2) 7-day-old seedlings in Arabidopsis
BioSample SAMN17142423
SRA SRX9721556

Supplementary file Size Download File type/resource
GSM4985008_Col-0_r1.txt.gz 905.5 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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