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| Status |
Public on Jun 12, 2017 |
| Title |
5mMVanillin-BY4741-2A |
| Sample type |
SRA |
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| Source name |
5mMVanillin-BY4741
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| Organism |
Saccharomyces cerevisiae BY4741 |
| Characteristics |
strain: BY4741
stress: vanillin
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| Treatment protocol |
SD added 5mM vanillin
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| Growth protocol |
The control medium was SD medium (1.7 g/L yeast nitrogen base(Sangon, China), 5 g/L ammonium sulfate(Sangon, China), CSM(MP Biomedicals,Solon,OH,USA) supplying 20 g/L glucose). The experimental medium was SD added 5mM vanillin. All the cultures were at 30℃,200rpm.
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| Extracted molecule |
total RNA |
| Extraction protocol |
The pre-cultured cells of BY4741 and BY4741(yrr1Δ) in SD medium were transferred into fresh SD or SD added 5mM vanillin with an initial OD600 of 0.2. The cells were harvested during the log phase (OD600≈1.6-2.0) and quick frozen using liquid nitrogen. UNIQ-10 Trizol RNA Purification Kit (Sangon Biotech, China) was used to extract total RNA.
After the total RNA extraction and DNase I treatment, magnetic beads with Oligo (dT) are used to isolate mRNA(for eukaryotes) or by removing rRNAs from the total RNA (for prokaryotes). Mixed with the fragmentation buffer, the mRNA is fragmented into short fragments. Then cDNA is synthesized using the mRNA fragments as templates. Short fragments are purified and resolved with EB buffer for end reparation and single nucleotide A (adenine) addition. After that, the short fragments are connected with adapters. After agarose gel electrophoresis, the suitable fragments are selected for the PCR amplification as templates.After that, the short fragments are connected with adapters. After agarose gel electrophoresis, the suitable fragments are selected for the PCR amplification as templates.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Description |
BY4741 as the control strain cultured in SD medium with 5mM vanillin(Another parallel)
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| Data processing |
Raw reads was produced by Illumina HiSeqTM 4000.
Raw reads was subjected to quality control (QC).
After QC, raw reads are filtered into clean reads which will be aligned to the reference sequences.
The alignment data is utilized to calculate distribution of reads on reference genes and mapping ratio.
If alignment result passes QC, we will proceed with downstream analysis including gene and isoform expression,deep analysis based on gene expression(PCA/correlation/screening differentially expressed genes and so on),exon expression, gene structure,refinement, alternative splicing, novel transcript prediction and annotation, SNP detection, Indel detection, gene fusion. Deep analysis based on DEGs,including Gene Ontology (GO) enrichment analysis,Pathway enrichment analysis, cluster analysis, protein-protein interaction network analysis and finding transcriptor were performed.
We define "dirty" raw reads as reads which contain the sequence of adapter, high content of unknown bases and low quality reads. They need to be removed before data analysis. Filtering steps are as follows to make clean data:
1) Remove reads with adapters;
2) Remove reads in which unknown bases are more than 10%;
3) Remove low quality reads (the percentage of low quality bases is over 50% in a read, we define the low quality base to be the base whose sequencing quality is no more than 10).
Genome_build: R64
Supplementary_files_format_and_content: .txt files report FPKMs and differential expression of genes
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| Submission date |
Nov 15, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Xiaoming Bao |
| E-mail(s) |
bxm@sdu.edu.cn
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| Phone |
(86) 053188365826
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| Organization name |
Shandong University
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| Department |
State Key Laboratory of Microbial Technology
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| Lab |
Bao lab
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| Street address |
Shanda Nan Road 27
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| City |
Jinan |
| State/province |
Shandong |
| ZIP/Postal code |
250100 |
| Country |
China |
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| Platform ID |
GPL22674 |
| Series (1) |
| GSE89854 |
BY4741 and BY4741（Δyrr1）transcriptional differences under vanillin stress |
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| Relations |
| BioSample |
SAMN06017502 |
| SRA |
SRX2348733 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2391639_5mMVanillin-BY4741-2A.gene.FPKM.txt.gz |
74.3 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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