|
| Status |
Public on Oct 02, 2023 |
| Title |
Early_control, rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Saccharomyces cerevisiae strain BY4742
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: BY4742
treatment: Control
time of treatment: Less than 72 hr after inoculation
|
| Treatment protocol |
Early (before 72 hours inoculation) or Late (after 72 hours inoculation) NaHS treatments.
|
| Growth protocol |
Yeast cells were grown in synthetic dextrose complete (SDC) according to Longo et al., 2007.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The total RNA was extracted using TRIzol Reagent according to the manufacturer’s instructions (Invitrogen) and genomic DNA was removed using DNase I (TaKara, China).
RNA-seq transcriptome library was prepared using TruSeq RNA sample preparation Kit from Illumina (San Diego, CA). Libraries were size selected for cDNA target fragments of 200–300 bp on 2% Low Range Ultra Agarose followed by PCR amplified using Phusion DNA polymerase (NEB) for 15 PCR cycles. After quantified by TBS380, paired-end RNA-seq sequencing library was sequenced with the Illumina NovaSeq 6000 sequencer. The raw paired end reads were trimmed and quality controlled by SeqPrep and Sickle software with default parameters. Then clean reads were separately aligned to reference genome with orientation mode using TopHat software.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Yeast
Early without Treatment
Early_control_vs_Early_NaHS_treatment.txt
|
| Data processing |
Illumina NovaSeq 6000 sequencer software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to R64-1-1 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.
Genome_build: R64-1-1
Supplementary_files_format_and_content: *.txt: Tab-delimited text files include FPKM values for each Sample.
|
| |
|
| Submission date |
Oct 26, 2020 |
| Last update date |
Oct 02, 2023 |
| Contact name |
Arman Ali Shah |
| E-mail(s) |
armanbio11@gmail.com
|
| Phone |
008613032865903
|
| Organization name |
Sichuan University
|
| Street address |
Wangjiang road 29, Key Laboratory of Bio-resources and Eco-environment of the Ministry of Education, College of Life Sciences, Sichuan University, Chengdu
|
| City |
Chengdu |
| State/province |
Sichuan |
| ZIP/Postal code |
610064 |
| Country |
China |
| |
|
| Platform ID |
GPL27812 |
| Series (1) |
| GSE160162 |
Hydrogen sulfide treatment at the late growth stage of Saccharomyces cerevisiae extends chronological lifespan |
|
| Relations |
| BioSample |
SAMN16556753 |
| SRA |
SRX9366155 |
