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| Status |
Public on Oct 31, 2021 |
| Title |
LCY001_GE_rep3 |
| Sample type |
SRA |
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| Source name |
BY4741
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| Organism |
Saccharomyces cerevisiae |
| Characteristics |
stain: LCY001
genotype: his3{delta}1 leu2{delta}0 met15{delta}0 ura3{delta}0 CEN-HIS3
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| Growth protocol |
The yeast strains (BY4741, LCY001 and LCY002) were cultured in SC-His media, overnight. Then dilute into three different cultures – containing either glucose, galactose or ethanol/glycerol as the carbon source – at OD600 of 0.1/ml. Grow until OD600 reached about 1.0. Every sample had three repeats from individual colonies. Cells (30 OD) were collected by centrifugation at 4°C at 3000 rpm for 10 min, washed with iced PBS buffer and frozen in liquid nitrogen, then stored at -80°C.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Yeast RNA was extracted using the TRIzol® method following the manufacturer’s protocol. Bulk cells or filamentous fungus are grounded to a powder using liquid nitrogen, and the powder was transferred into the 2 mL tube contains 1.5 mL Trizol reagent. The mix was shaked for 3 min, and kept for 5 min at room temperature, then was Centrifuged at 10,000×g for 5 min at 4 °C. The supernatant was added 200 μL of chloroform/isoamyl alcohol (24:1) with 1 mL lysis reagents. After centrifuged at 10,000×g for 10 min at 4 °C, the supernatant was transferred into another new tube with equal volume of isopropanol and put in the refrigerator at -20 °C for 1 h. After centrifuged at 13,600×g for 20 min at 4 °C, the supernatant was precipitated by 1 mL of 75% ethanol and let dry for 3-5 min. The RNA pellet was dissolved with 30-100 μL of DEPC water or RNase-free water. The concentration of the extracted RNA samples was determined using a Nanodrop system (NanoDrop, Madison, USA), and the integrity of the RNA was examined by the RNA integrity number (RIN) using an Agilent 2100 bioanalyzer (Agilent, Santa Clara, USA).
Oligo(dT)-attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then first-strand cDNA was generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. Afterwards, a Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR, and products were purified by Ampure XP Beads, then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA (ssCir DNA) was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300 copies of one molecular, DNBs were loaded into the patterned nanoarray and single end 50 bases reads were generated on BGIseq500 platform (BGI-Shenzhen, China).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
BGISEQ-500 |
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| Data processing |
The sequencing data was filtered with SOAPnuke (v1.4.0) by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format.
The clean reads were mapped to the reference genome using HISAT2 (v2.1.0)
Bowtie2 (v2.2.5) was applied to align the clean reads to the reference coding gene set
expression level of gene was calculated by RSEM (v1.2.8)
Genome_build: Saccharomyces_cerevisiae_S288C R64
Supplementary_files_format_and_content: results files include FPKM values for each Sample
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| Submission date |
Feb 08, 2021 |
| Last update date |
Oct 31, 2021 |
| Contact name |
Li Cheng |
| E-mail(s) |
li.cheng@siat.ac.cn
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| Organization name |
Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences
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| Department |
Institute of Synthetic Biology
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| Street address |
Xueyuan Boulevard
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| City |
Shenzhen |
| ZIP/Postal code |
518055 |
| Country |
China |
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| Platform ID |
GPL25927 |
| Series (1) |
| GSE166328 |
transcript analysis of strains with or without plasmid containing 40 genes in three different culture conditions |
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| Relations |
| BioSample |
SAMN17833202 |
| SRA |
SRX10046649 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5068609_LCY001_GE_3.genes.results.txt.gz |
111.2 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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