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Status |
Public on Jan 19, 2016 |
Title |
Cold1 |
Sample type |
SRA |
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Source name |
Cold
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Organism |
Zea mays subsp. mexicana |
Characteristics |
subspecies: mexicana developmental stage: Seedling cultivar: 8493 age: Thirteen days after germination stress: cold tissue: Root, Stem and Leave
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Treatment protocol |
Thirteen days after germination, samples were divided into 3 groups for different treatments: control (no stress); cold treated and drought treated. For cold treatments, seedlings were treated with 4℃ low temperature under the same light condition for 12 h. For drought treatment, seedlings were treated with Hoagland solution mixed with PEG2000 (20%) for 3 h with same light condition. Each sample were selected three seedlings randomly and two replications.
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Growth protocol |
Selected plump seeds were washed 3 times with distilled water, then soaked in 75% ethanol and 2% sodium hypochlorite for 10 min and 3 min, respectively, and washed 3 times with distilled water. Sterilized seeds were planted in plastic boxes (54 cm length, 28 cm width and 7 cm height) with soil substrates (Jiffy, Netherlands, http://www.jiffygroup.com/en/substrates/). The boxes were placed in a climate control box (RXZ 500-C, JIANGNAN Instrument) (25℃ under a 10-h light/14-h dark photoperiod, humidity of 60%).
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Extracted molecule |
total RNA |
Extraction protocol |
Total RNA of 6 samples were extracted by TRIzol® reagent (Invitrogen, Carlsbad, USA) according to the manufacturer's instructions. RNA was purified with the RNase-free DNase I (Takara, Japan) to degrade any possible DNA. The integrity and concentration of the total RNA was identified by agilent 2100 bioanalyzer (Agilent Technologies, Palo Alto, CA) and NanoDrop 8000 spectrophotometer (NanoDrop, Wilmington, DE) and checked by running a gel electrophoresis in 1.5% (w/v) agarose gels. RNA libraries were prepared for sequencing using standard Illumina protocols
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2500 |
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Data processing |
Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then merged and de novo to generate all transcripts set by Trinity with default parameter, which will be treated as reference genome. The number of paired-reads of each sample were mapped to reference genome by Bowtie software v1.1.1 and the number of mapped reads were calculated by RSEM. Fragments per kilobase of transcript per million fragments mapped (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library. Supplementary_files_format_and_content: tab-delimited text file includes FPKM values for each Sample
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Submission date |
Jan 18, 2016 |
Last update date |
May 15, 2019 |
Contact name |
Xiang LU |
E-mail(s) |
xiang.lu@utas.edu.au
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Organization name |
University of Tasmania
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Department |
Tasmania of Institute Agriculture
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Street address |
Private Bag 98
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City |
Hobart |
State/province |
TAS |
ZIP/Postal code |
7001 |
Country |
Australia |
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Platform ID |
GPL21342 |
Series (1) |
GSE76939 |
RNA-Seq analysis, transcriptome assembly and gene expression profile analysis for Zea may ssp. mexicana L. under cold and drought stress |
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Relations |
BioSample |
SAMN04420624 |
SRA |
SRX1533948 |
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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