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Sample GSM2041247

Query DataSets for GSM2041247

Status

Public on Jan 19, 2016

Title

CK2

Sample type

SRA

Source name

Control

Organism

Zea mays subsp. mexicana

Characteristics

subspecies: mexicana
developmental stage: Seedling
cultivar: 8493
age: Thirteen days after germination
stress: control
tissue: Root, Stem and Leave

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.

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%).

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

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 2500

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

Submission date

Jan 18, 2016

Last update date

May 15, 2019

Contact name

Xiang LU

E-mail(s)

xiang.lu@utas.edu.au

Organization name

University of Tasmania

Department

Tasmania of Institute Agriculture