|
| Status |
Public on Aug 04, 2023 |
| Title |
WT3h-R1 |
| Sample type |
SRA |
| |
|
| Source name |
cell
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: CEN.PK
genotype: WT
treatment: switch to minimal medium for 3h
|
| Treatment protocol |
Cells were washed with SL medium once and then transferred to SL medium for culturing.
|
| Growth protocol |
Yeast cells grown to log phase in YPL medium from 0.1 OD.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using Lucigen MasterPure Yeast RNA Purification Kit
1 μg total RNA was used for following library preparation. Next generation sequencing library preparations were constructed according to the Illumina protocol
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Pass filter data of fastq format were processed by Cutadapt (V1.9.1).
Reference genome sequences and gene model annotation files of relative species were downloaded from genome website UCSC. Then Hisat2 (v2.0.1) was used to index reference genome sequence. Finally, clean data were aligned to reference genome via software Hisat2 (v2.0.1).
In the beginning transcripts in fasta format are converted from known gff annotation file and indexed properly. Then, with the file as a reference gene file, HTSeq (v0.6.1) estimated gene and isoform expression levels from the pair-end clean data.
Genome_build: sacCer3
Supplementary_files_format_and_content: all.fpkm_anno.txt (Matrix table with raw gene counts and FPKMs for every gene and every sample
|
| |
|
| Submission date |
Aug 07, 2021 |
| Last update date |
Aug 04, 2023 |
| Contact name |
Zhu Yibing |
| E-mail(s) |
davidyb@zju.edu.cn
|
| Phone |
19817865403
|
| Organization name |
Zhejiang University
|
| Department |
Life Of Science
|
| Street address |
Xihu
|
| City |
Hangzhou |
| ZIP/Postal code |
310000 |
| Country |
China |
| |
|
| Platform ID |
GPL27812 |
| Series (1) |
| GSE181620 |
Reciprocal regulation of phosphatidylcholine synthesis and H3K36 methylation programs metabolic adaptation |
|
| Relations |
| BioSample |
SAMN20606255 |
| SRA |
SRX11667720 |
