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Sample GSM3037964 Query DataSets for GSM3037964
Status Public on Feb 12, 2019
Title tmk1-2
Sample type SRA
 
Source name apical hook
Organism Arabidopsis thaliana
Characteristics age: 45hours old plant
tissue: apical hook
genotype: tmk1-1
Growth protocol Arabidopsis is grown in growth chamber at 22C under dark condition
Extracted molecule total RNA
Extraction protocol The hook shaped structure without cotyledons (~2mm) were cut from the seedlings by blades. Total RNA was isolated from ~50 hooks per sample by using TRIzol™ Reagent (Invitrogen)
Total RNA (1μg) was used for performing the library preparation with NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England BioLabs, E7420L) according to the manufacturer’s instructions with 9 different barcodes (triplicate biological samples)
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Data processing Illumina Casava1.7 software used for basecalling.
Raw reads were first subject to 3’ adapter removal and quality filtering (Q > 17 and length >= 25 bp). Clean reads were mapped to the Arabidopsis thaliana genome sequence (http://mtweb.cs.ucl.ac.uk/mus/www/19genomes/fasta/MASKED/ler_0.v7.PR_in_lowercase.fas) using HISAT. Read counts of each gene were summarized by the HTSeq-count. Lowly expressed genes were removed and only genes with an expression level of at least 1 CPM (counts per million) in at least two samples were kept for further analysis.
Genome_build: v2i
Supplementary_files_format_and_content: Tab-delimited text file include RPM(Reads per Million) values for 9 Samples .
 
Submission date Mar 12, 2018
Last update date Feb 12, 2019
Contact name Renyi Liu
E-mail(s) rliu.bicomp@gmail.com
Phone 02157078228
Organization name Shanghai Center for Plant Stress Biology
Department Bioinformatics
Street address 3888 Chenhua Road
City Shanghai
State/province Shanghai
ZIP/Postal code 201602
Country China
 
Platform ID GPL13222
Series (1)
GSE111716 TMK1-mediated transcriptional auxin signaling guides differential growth in plant
Relations
BioSample SAMN08687538
SRA SRX3782548

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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