|
| Status |
Public on Nov 12, 2020 |
| Title |
Target rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Target, yeast cells
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: BY4742
treatment: 2 mg/L NP
|
| Treatment protocol |
Cultures at the beginning of incubation were treated with 2 mg/L NP prepared in ethanol while controls were treated with the same volume of ethanol for 22 h. At the end of 22 hour of exposure, 1 mL sample was taken from each of the cultures, centrifuged, and supernatants were discarded. The precipitated cells were suspended in 1 mL of liquid YPD medium. This process was repeated three times to remove possible NP residuals. After the washing procedure, suspended cells were transferred to the new 100 mL YPD in 500 mL flasks and NP was added to the cultures to reach the above mentioned final concentrations of NP, and the second round of the exposure was initiated. The long-term exposure was performed for 40 rounds by repeating the above steps.
|
| Growth protocol |
YPD broth was inoculated with 1% of yeast pre-culture and incubated at 30⁰C, 180 RPM in incubator shaker
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Extraction of total RNA was performed with RNeasy Mini Kit (Qiagen) according to the manufacturer's instructions. 1μg of total RNA was used for RNA-seq analysis.Libraries for RNA-Seq were prepared using the following procedure. At first, poly-A containing mRNA molecules were purified using poly-T oligo-attached magnetic beads. After purification, the mRNA was fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers. This was followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. These cDNA fragments then had the addition of a single 'A' base and subsequent ligation of the adapter. The products were then purified and enriched with PCR amplification. Then the PCR yield was quantified by Qubit and pooled samples together to make a single strand DNA circle (ssDNA circle), which gave the final library. DNA nanoballs (DNBs) were generated with the ssDNA circle by rolling circle replication (RCR) to enlarge the fluorescent signals at the sequencing process. The DNBs were loaded into the patterned nanoarrays and pair-end reads of 100 bp were read through on the BGISEQ-500 platform for further data analysis. For this step, the BGISEQ-500 platform was combined the DNA nanoball-based nanoarrays and stepwise sequencing using Combinational Probe-Anchor Synthesis Sequencing Method.
RNA libraries were prepared for sequencing using standard BGI protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
BGISEQ-500 |
| |
|
| Description |
Gene expression data from yeast RNA
|
| Data processing |
RNA-Seq data was analyzed using Partek Genomic Flow software (Partek).
The raw data files were first analyzed for sequence quality using pre-alignment QA/QC.
The reads were then aligned to the S. cerevisiae genome (R64-1-1) using STAR 2.5.3a aligner index.
Genome assembly and annotation files were obtained from Ensembl genome browser.
The generated counts were normalized using counts per million (CPM) method and the differentially regulated genes were identified using differential gene expression (GSA) algorithm.
Gene ontology (GO) enrichment anaylsis was performed to determine GO terms. For pathway analysis KEGG pathway database was used. False discovery rate (FDR) was set to 0.05, p value to 0.05 and fold change +/- 1.5 fold.
Genome_build: R64-1-1
Supplementary_files_format_and_content: xlsx file includes differentially expressed genes, GO terms and pathways
|
| |
|
| Submission date |
Sep 17, 2020 |
| Last update date |
Nov 12, 2020 |
| Contact name |
Ceyhun Bereketoglu |
| E-mail(s) |
ceyhunbereketoglu@gmail.com
|
| Organization name |
Iskenderun Technical University
|
| Department |
Biomedical Engineering
|
| Street address |
Iskenderun Technical University Main Campus, Iskenderun
|
| City |
Hatay |
| ZIP/Postal code |
31200 |
| Country |
Turkey |
| |
|
| Platform ID |
GPL25927 |
| Series (1) |
| GSE158124 |
Transcriptomic Analysis of Nonylphenol Effect on Saccharomyces cerevisiae |
|
| Relations |
| BioSample |
SAMN16193115 |
| SRA |
SRX9140851 |
