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| Status |
Public on May 15, 2024 |
| Title |
Arabidopsis, atg5_1_3, rep3 |
| Sample type |
SRA |
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| Source name |
seedling
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| Organism |
Arabidopsis thaliana |
| Characteristics |
tissue: seedling
genotype: ATG5 knockout
treatment: normal conditions
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| Treatment protocol |
treat under normal conditions
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| 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).
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| 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.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
DNBSEQ-T7 |
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| 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.
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| Submission date |
Mar 27, 2024 |
| Last update date |
May 15, 2024 |
| Contact name |
Ce Song |
| E-mail(s) |
Ce.song@outlook.com
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| Organization name |
Nankai University
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| Street address |
Weijin road NO.94
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| City |
Tianjin |
| ZIP/Postal code |
300000 |
| Country |
China |
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| Platform ID |
GPL31102 |
| Series (1) |
| GSE262650 |
Lon1 Inactivation Downregulates Autophagic Flux and Brassinosteroid Biogenesis, Modulating Mitochondrial Proportion and Seed Development in Arabidopsis |
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| Relations |
| BioSample |
SAMN40632922 |
| SRA |
SRX24082063 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8173070_atg5_1_3_FPKM.txt.gz |
206.4 Kb |
(ftp)(http) |
TXT |
| GSM8173070_atg5_1_3_counts.txt.gz |
109.2 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
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