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| Status |
Public on Sep 04, 2019 |
| Title |
Seedling, Cold_2h |
| Sample type |
SRA |
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| Source name |
seedling
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| Organism |
Medicago truncatula |
| Characteristics |
strain: Jemalong A17
tissue: seedling
age: 4 weeks
genotype: Wild type
stress: Cold
time: 2h
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| Growth protocol |
Plants were grown under long day (14 h light/ 10 h darkness) conditions at 22-24°C
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| Extracted molecule |
total RNA |
| Extraction protocol |
Medicago truncatula seedlings were collected, frozen in liquid nitrogen, and RNA was harvested using Trizol reagent.
Total RNA was isolated at each time point for each treatment using the TRIzol purification system (Invitrogen). The 3’-tag digital gene expression libraries were prepared using the Illumina Gene Expression Sample Prep Kit. The library was sequenced on an Illumina HiSeq3000.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
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| Data processing |
The raw data comprised 100-bp paired-end sequences, and the cleaned reads were then mapped to M. truncatula genome (Mt4.0) using default settings of TOPHATv2.0.8.
The duplicated reads were removed and alignments with MAPQ score > 20 were used for further analysis.
RNA-seq alignments were processed using HTSeq-count, and differentially expressed genes were identified using DESeq with |log2 fold change| > 3.5
Genome_build: M. truncatula genome (Mt4.0)
Supplementary_files_format_and_content: FPKM
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| Submission date |
Sep 03, 2019 |
| Last update date |
Sep 04, 2019 |
| Contact name |
Jianbo Song |
| E-mail(s) |
thinkskier@163.com
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| Phone |
18579059335
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| Organization name |
Jiang Xi Agricultural University
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| Street address |
Department of Biochemistry and Molecular Biology, College of Science, Jiang Xi Agricultural University, Nanchang 330045, China
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| City |
Nanchang |
| State/province |
Jiang Xi |
| ZIP/Postal code |
330045 |
| Country |
China |
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| Platform ID |
GPL23002 |
| Series (1) |
| GSE136739 |
The U-box family genes in Medicago truncatula: key elements in response to salt, cold, and drought stresses |
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| Relations |
| BioSample |
SAMN12676129 |
| SRA |
SRX6792713 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4056947_Cold_2_FPKM.txt.gz |
398.7 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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