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| Status |
Public on Dec 15, 2021 |
| Title |
control wheat roots rep2 |
| Sample type |
SRA |
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| Source name |
Triticum aestivum L.
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| Organism |
Triticum aestivum |
| Characteristics |
variety: Jimai 22
tissue: root
treatment: Control
time point: four days after treatment
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| Treatment protocol |
The seedlings selected for uniform growth were separately transplanted into plastic pots (50 cm in diameter and 40 cm in height; 10 plants per pot) containing the 1/4 Hoagland nutrient solution (pH 5.2) with 0 μM NaCl to form the control group and various types of stress (150 mM NaCl, 5 mM 3-MA, or 5 mM 3-MA+ 150 mM NaCl) to form the NaCl treatment groups. 3-MA (Sigma Aldrich, Saint Louis, MO, USA) was added to the medium 5 h prior to NaCl treatment. The nutrient solution was changed every 2 d. For each treatment, seedlings from three pots were separately sampled or measured as replicates. Four days after NaCl and 3-MA treatment, the roots and the third leaves were collected respectively with every 10 of them being mixed as one biological replicate for each treatment. Every treatment had four biological replicates. Each sample was ground respectively into powder in a mortar using liquid nitrogen. Total RNA was extracted from samples using a Trizol reagent (Invitrogen). There were six sample groups, including CG: the control wheat roots, TG: 150 mM NaCl treated wheat roots, TMG: 5 mM 3-MA + 150 mM NaCl treated wheat roots, CY: the control wheat leaves, TY: 150 mM NaCl treated wheat leaves, and TMY: 5 mM 3-MA + 150 mM NaCl treated wheat leaves.
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| Growth protocol |
The test species were NaCl-tolerant Jimai 22 wheat varieties. Jimai 22 is a medium gluten wheat variety with super high yield, multi resistance and high quality. The Jimai 22 seeds were first washed with tap water and then rinsed with distilled water thrice before being soaked in distilled water for 12 h. The seeds were then germinated on moist gauze. A small amount of distilled water was sprayed onto the seeds for culture at ambient temperature. The distilled water was changed every 24 h until the seedlings grew to the one-leaf-and-one-bud stage. The uniform seedlings were transplanted into plastic pots containing 1/4 Hoagland solution for further culture. The nutrient solution was changed every 2 d until the seedlings grew to the two-leaf-and-one-bud stage.
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| Extracted molecule |
total RNA |
| Extraction protocol |
The roots and leaves samples were flash frozen on dry ice respectively, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
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 2000 |
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| Description |
CG2
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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 mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata.
Reads Per Kilobase of exon per Megabase of library size (RPKM) 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.
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumina) according to the manufacturer’s instructions.
The Triticum aestivum L. reference genome and gene model annotation files were downloaded from ftp://ftp.ensemblgenomes.org/pub/release-45/plants/fasta/triticum_aestivum/dna/Triticum_aestivum.IWGSC.dna.toplevel.fa.gz. The paired-end clean RNA-seq reads were aligned to the reference genome using Hisat2 (version 2.0.5,) was used to count the number of reads mapped to each gene.
Genome_build: ftp://ftp.ensemblgenomes.org/pub/release-45/plants/fasta/triticum_aestivum/dna/Triticum_aestivum.IWGSC.dna.toplevel.fa.gz
Supplementary_files_format_and_content: ExpressionProfile.txt: Matrix table with raw gene counts and FPKM values for every gene and every sample.
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| Submission date |
Feb 05, 2021 |
| Last update date |
Dec 15, 2021 |
| Contact name |
Jieyu Yue |
| E-mail(s) |
skyyjy@tjnu.edu.cn
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| Phone |
86-022-23766533
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| Organization name |
Tianjin Normal University
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| Street address |
Road Binshuixidao NO.393
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| City |
Tianjin |
| State/province |
Tianjin |
| ZIP/Postal code |
300387 |
| Country |
China |
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| Platform ID |
GPL17701 |
| Series (1) |
| GSE166260 |
Next-Generation Sequencing Facilitates Quantitative Analysis of Transcriptomes Mechanism for Autophagy Inhibition Enhanced Salt Stress Sensitivity of Wheat Seedling |
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| Relations |
| BioSample |
SAMN17812778 |
| SRA |
SRX10038120 |
| 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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