|
| Status |
Public on Jun 25, 2021 |
| Title |
ML3287 (OAY470), in raffinose and induced with galactose, replicate 1 |
| Sample type |
SRA |
| |
|
| Source name |
ML3287 (OAY470) in exponential phase, grown in raffinose and induced with galactose
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
growth stage: exponential phase
strain: ML3287
media: YEP + 2% raffinose
|
| Treatment protocol |
Cells were induced with 2 % galactose for 6 hr.
|
| Growth protocol |
Strains were grown in YEP with indicated carbon souce to specified OD and 2 % galactose was added for 6 hr for GapR induction.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was extracted by hot phenol method followed by gDNA removal and mRNA enrichment using poly(dT) pulldown with the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB).
Sequencing libraries were processed as previously reported (Culviner and Laub, 2018).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Strains were grown in YEP+2% raffinose to OD 0.05, and 2% galactose was added. Cells were grown for 6 hr (maintaining OD <1.0) and RNA was extracted and processed into sequencing libraries as described.
|
| Data processing |
Reads were aligned to SacCer3 using bowtie2 with default parameters with duplicated reads filtered out.
Bowtie alignments were converted to wiggle files with custom Python scripts. The position of each alignment is evenly distributed over the length of the read.
To calculate mRNA abundance, a pseudocount was added to all positions and the number of reads mapped to a gene was divided by the length of the gene and normalized to yield the mean number of reads per kilobase per million sequencing reads (RPKM).
Genome_build: SacCer3
Supplementary_files_format_and_content: Tab delimited files, columns containing index positions, chromosome, chromosome positions, number of reads, and normalized number of reads. For RNA-seq, two files are provided, one for forward and reverse strand.
|
| |
|
| Submission date |
Jan 04, 2021 |
| Last update date |
Jun 25, 2021 |
| Contact name |
Monica S Guo |
| E-mail(s) |
msguo@uw.edu
|
| Organization name |
University of Washington
|
| Department |
Microbiology
|
| Lab |
Guo
|
| Street address |
750 Republican St
|
| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98109 |
| Country |
USA |
| |
|
| Platform ID |
GPL19756 |
| Series (2) |
| GSE152882 |
High-resolution, genome-wide mapping of positive supercoiling in chromosomes |
| GSE164186 |
High-resolution, genome-wide mapping of positive supercoiling in chromosomes [RNA-Seq 2] |
|
| Relations |
| BioSample |
SAMN17208748 |
| SRA |
SRX9773819 |
