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Sample GSM8173073 Query DataSets for GSM8173073
Status Public on May 15, 2024
Title Arabidopsis, lon1_2atg5_3, rep3
Sample type SRA
 
Source name seedling
Organism Arabidopsis thaliana
Characteristics tissue: seedling
genotype: double mutant
treatment: normal conditions
Treatment protocol treat under normal conditions
Growth protocol Arabidopsis grown best under 16/8 hours light / dark cycle at room temperature (18-22 ° C), with light intensity of 120-150 µ mol / m2 (normal conditions).
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using the mirVana miRNA Isolation Kit (Ambion) following the manufacturer’s protocol. RNA integrity was evaluated using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). The samples with RNA Integrity Number (RIN) ≥ 7 were subjected to the subsequent analysis
The libraries were constructed using TruSeq Stranded mRNA LT Sample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions. Then these libraries were sequenced on the Illumina sequencing platform (DNBSEQ-T7) and 125bp/150bp paired-end reads were generated.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model DNBSEQ-T7
 
Data processing The transcriptome sequencing and analysis were conducted by OE biotech Co., Ltd. (Shanghai, China).
Raw data (raw reads) were processed using Trimmomatic.
The reads containing ploy-N and the low quality reads were removed to obtain the clean reads.
Then the clean reads were mapped to reference genome using hisat2
Assembly: TAIR10.1
Supplementary files format and content: FPKM value of each gene was calculated using cufflinks, and the read counts of each gene were obtained by htseq-count.
Supplementary files format and content: DEGs were identified using the DESeq(2012) R package functions estimateSizeFactors and nbinomTest. Pvalue < 0.05 and foldChange >2 or foldChange < 0.5 was set as the threshold for significantly differential expression.
 
Submission date Mar 27, 2024
Last update date May 15, 2024
Contact name Ce Song
E-mail(s) Ce.song@outlook.com
Organization name Nankai University
Street address Weijin road NO.94
City Tianjin
ZIP/Postal code 300000
Country China
 
Platform ID GPL31102
Series (1)
GSE262650 Lon1 Inactivation Downregulates Autophagic Flux and Brassinosteroid Biogenesis, Modulating Mitochondrial Proportion and Seed Development in Arabidopsis
Relations
BioSample SAMN40632919
SRA SRX24082066

Supplementary file Size Download File type/resource
GSM8173073_lon1_2atg5_3_FPKM.txt.gz 206.6 Kb (ftp)(http) TXT
GSM8173073_lon1_2atg5_3_counts.txt.gz 109.4 Kb (ftp)(http) TXT
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Raw data are available in SRA

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