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| Status |
Public on Jun 21, 2023 |
| Title |
Salt stress treatment of grafted seedlings (24h) [PS7] |
| Sample type |
SRA |
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| Source name |
Leaves
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| Organism |
Solanum lycopersicum |
| Characteristics |
agent: Salt stress
tissue: Grafted seedling
time point: 24h
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| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol RNA
RNA libraries were prepared for sequencing using standard Illumina protocolsA total amount of 3 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
PS7
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| Data processing |
After cluster generation, the library preparations were sequenced on an Illumina Hiseq platform and 125 bp/150 bp paired-end reads were generated.
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing read containing adapter, reads containing ploy-N and low quality reads from raw data.At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.16.1). DESeq2 provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate . Genes with an adjusted P-value <0.05 found by DESeq2 were assigned as differentially expressed.
Gene Ontology (GO) enrichment analysis of differentially expressed genes wasimplemented by the clusterProfiler R package, in which gene length bias wascorrected. GO terms with corrected Pvalue less than 0.05 were considered significantly enriched by differential expressed genes.KEGG is a database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from molecular-level information, especially large-scale molecular datasets generated by genome sequencing and other high-through put experimental technologie (http://www.genome.jp/kegg/). We used clusterProfiler R package to test the statistical enrichment of differential expression genes in KEGG pathways
Fusion gene is refers to the two genes of all or part of the sequences performfusion ,results of the chimeric gene, usually caused by reasons such as chromosome translocation and problem.We used star-fusion(1.2.0) software analysis and detection of fusion genes. Fusion gene list were filtered with star-fusion by standard filter method and other parameters(--annotate; -examine_coding_effect; --FusionInspector inspect; --denovo_reconstruct; --min_junction_reads 1 ; --min_sum_frags 2)
Assembly: Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5
Supplementary files format and content: featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
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| Submission date |
May 23, 2023 |
| Last update date |
Jun 21, 2023 |
| Contact name |
ding yuan |
| E-mail(s) |
yuanding534@gmail.com
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| Organization name |
Hebei Agricultural University
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| Street address |
lekainan
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| City |
Baoding |
| ZIP/Postal code |
071000 |
| Country |
China |
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| Platform ID |
GPL16345 |
| Series (1) |
| GSE233233 |
Transcriptome analysis showed that tomato-rootstock enhanced salt tolerance of grafted seedlings was accompanied by multiple metabolic processes and gene differences |
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| Relations |
| BioSample |
SAMN35330015 |
| SRA |
SRX20487488 |
| 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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