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Sample GSM2794350

Query DataSets for GSM2794350

Status

Public on Dec 25, 2018

Title

Pi sufficient leaf-rep2

Sample type

SRA

Source name

Leaf

Organism

Glycine max

Characteristics

cultivar: Williams 82
tissue: first trifoliate true leaf
developmental stage: 18 days after germination

Treatment protocol

After 18 days of cultivation, soybean seedlings with the first trifoliate true leaves fully expanded were transferred into Pi-sufficient (500 μM KH2PO4) or Pi-deficient (0 μM KH2PO4, K2SO4 was substituted for KH2PO4) nutrient solutions.

Growth protocol

Soybean (Glycine max var. Williams 82) seeds were soaked in sterilized water for 4 hours, and then incubated at room temperature in the dark between two layers of moistened filter paper. Four days later, seedlings were grown hydroponically in a 10 L tank filled with half-strength modified Hoagland nutrient solution containing 2.5 mM Ca(NO3)2, 2.5 mM KNO3, 0.5 mM KH2PO4, 1.25 mM MgSO4, 10.0 μM Fe-EDTA, 3.4 μM MnSO4, 0.16 μM CuSO4, 0.38 μM ZnSO4, 23.0 μM H3BO3, 0.25 μM Na2MoO4, with pH adjusted to 5.6. Nutrient solution was changed every two days. Plants were grown in a growth chamber with a photoperiod set at 16-h-light/8-h-dark at 26/22 ◦C and light intensity set at 150 μmol m-2 s-1.

Extracted molecule

total RNA

Extraction protocol

Roots and leaves of soybean seedlings were separately sampled after treatment of Pi-deficiency for 24 hours, frozen in liquid nitrogen and stored at -80°C until RNA preparation.
RNA libraries were prepared for sequencing using standard Illumina protocols

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 2000

Data processing

The initial base calling and quality filtering of the reads generated with the Illumina analysis pipeline (Fastq format) were performed using a custom Perl script and the default parameters of the Illumina pipeline (http://www.illumina.com). Additional filtering for poor-quality bases was performed using the FASTX-toolkit available in the FastQC software package (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/)..
To facilitate the read mapping, the Glycine max reference genome (Gmax2.0 version) was indexed by Bowtie2 (http://www.phytozome.net). The read mapping was performed using the Tophat software package.
Tophat allows multiple alignments per read (up to 40) and a maximum of two mismatches when mapping the reads to the reference genome.
The reads were first mapped directly to the genome using indexing and then the unmapped reads were used to identify novel splicing events. The aligned read files were processed by Cufflinks to measure the relative abundances of the transcripts by using the normalized RNA-seq fragement counts.
The estimated gene abundance was measured in terms of the fragments per kilobase of transcript per million mapped reads (FPKM). The differentially expressed genes (DEGs) between the two sets of samples were identified using Cuffdiff. Only the genes with a log2 fold change ≥1 or ≤−1, and a p-value ≤0.05 were considered as significantly DEGs.
Genome_build: the Glycine max reference genome (Gmax2.0 version)
Supplementary_files_format_and_content: one excel file includes FPKM values for each sample

Submission date

Sep 26, 2017

Last update date

May 15, 2019

Contact name

Houqing Zeng

E-mail(s)

zenghq@hznu.edu.cn

Phone

+8657328865199

Organization name

Hangzhou Normal University