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Sample GSM3893768 Query DataSets for GSM3893768
Status Public on Aug 20, 2020
Title Col-0 flower bud RNA-Seq_S_91
Sample type SRA
 
Source name Flower bud
Organism Arabidopsis thaliana
Characteristics strain: Col-0
Growth protocol The plants were grown under long-day photoperiod with 16-h light (150 μmol/m2/s)/ 8-h darkness at 21°C and 19°C, respectively.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from 10-50 mg of floral buds or open flowers from both WT and ask1 primary inflorescences five hours after dawn using the NucleoSpin® RNA kit (Macherey-Nagel).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Description Pair end 150-mer RNA-Seq
Data processing Adapter and low-quality sequences in the raw FASTQ sequencing data were removed to produce valid sequences using Trimmomatic (phred=33, minimum length=36; (Bolger et al., 2014)), which were further aligned to the A. thaliana Col-0 reference genome (TAIR10; www.arabidopsis.org) via TOPHAT2 (Kim et al., 2013a) to identify accepted hits of each locus. HTSeq was then used to calculate an absolute expression level (counts) of each locus based on the accepted hits (Anders et al., 2015).
 
Submission date Jun 17, 2019
Last update date Aug 21, 2020
Contact name Zhihua Hua
E-mail(s) hua@ohio.edu
Phone 7405931123
Organization name Ohio University
Department Department of Environmental and Plant Biology
Lab Hua Lab
Street address 22 Richland Ave
City Athens
State/province Ohio
ZIP/Postal code 45701
Country USA
 
Platform ID GPL26208
Series (1)
GSE132841 Generation of a fertile ask1 mutant uncovers a comprehensive set of SCF‐mediated intracellular functions
Relations
BioSample SAMN12078909
SRA SRX6078343

Supplementary file Size Download File type/resource
GSM3893768_s_9Col0Bud_htseq_counts.txt.gz 127.1 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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