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| Status |
Public on Aug 20, 2018 |
| Title |
CS3 |
| Sample type |
SRA |
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| Source name |
leaves
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| Organism |
Cucumis sativus |
| Characteristics |
strain: Cu-01
tissue: leaves
developmental stage: trifoliate
treatment: exposed to an air temperature of 6°C for 12 h
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s instructions.
In total, of 3 μg RNA per sample from four time points each with three independent biological replicates were used to construct 12 cDNA libraries designated as CS0, CS0-1, CS0-2, CS1, CS1-1, CS1-2, CS2, CS2-1, CS2-2, CS3, CS3-1, and CS3-2.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
CS0-VS-CS3.GeneDiffExpFilter.xls
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| Data processing |
Libraries were sequenced on an Illumina Hiseq platform (San Diego, CA, USA)
The reference genome and gene model annotation files were downloaded from the genome website （http://cucurbitgenomics.org/）. An index of the reference genome was built using Bowtie v.2.2.3 and paired-end clean reads were aligned to the reference genome using TopHat v.2.0.12.
Gene expression levels were calculated based on reads per kb per million reads. Differential expression analysis of eight samples (three biological replicates per condition) was performed using DESeq R package v.1.10.1. The false discovery rate (FDR) method was used to determine the threshold P value in multiple tests to identify DEGs; an adjusted log2 ratio ≥ 5 and FDR ≤ 0.001 were set as the threshold for differential expression.
Genome_build: the genome website （http://cucurbitgenomics.org/）
Supplementary_files_format_and_content: DESeq output
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| Submission date |
Mar 19, 2018 |
| Last update date |
Aug 20, 2018 |
| Contact name |
Zhiyong Liu |
| E-mail(s) |
lzyky99@163.com
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| Organization name |
Shenyang Agriculture University
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| Street address |
120
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| City |
Shenyang |
| ZIP/Postal code |
110866 |
| Country |
China |
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| Platform ID |
GPL20825 |
| Series (1) |
| GSE111998 |
Transcriptome Analysis of Cucumber (Cucumis sativus L.) Leaves Under Chilling Stress |
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| Relations |
| BioSample |
SAMN08731969 |
| SRA |
SRX3809900 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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