|
| Status |
Public on Nov 01, 2023 |
| Title |
221205L17_exp221129_MS95_SCGEuri-20nM-BE_1hr-5uM-EU-32min-chase_polyA-input-RNA-seq |
| Sample type |
SRA |
| |
|
| Source name |
221205L17_exp221129_MS95_SCGEuri-20nM-BE_1hr-5uM-EU-32min-chase_polyA-input-RNA-seq
|
| Organisms |
Schizosaccharomyces pombe; Saccharomyces cerevisiae |
| Characteristics |
sample: cDNA of polyA-enriched RNA from a mixture S. cerevisiae (MS95) and S. pombe (PN10597). MS95 was cultured in the prescence of 20nM beta-estradiol and was collected 32min after EU washout from media.
cell type: yeast
chip-antibody: n/a
|
| Growth protocol |
S. pombe: Standard yeast cell culture practices were followed. Cells were cultured at 30C in Edinburgh Minimal Media (EMM).
C. Glabrata: Standard yeast cell culture practices were followed. Cells were cultured at 30C in synthetic complete media with either 2% glucose (SCD) or 2% glycerol + 1% ethanol (SCGE) as a carbon source.
S. cerevisiae: Standard yeast cell culture practices were followed. Cells were cultured at 30C in synthetic complete media with either 2% glucose (SCD) or 2% glycerol + 1% ethanol (SCGE) as a carbon source.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
S. cerevisiae and S. pombe cells were separately pelleted and snap-frozen in liquid nitrogen. Pellets were thawed in ice-cold PBS and mixed. 30 µl of cells in PBS were added to 300 µl TRI Reagent (Zymo Research) and lysed by bead beating using a Fastprep 24. Cell debris was pelleted (14k rpm, 1 minute) and the supernatant recovered. RNA was then extracted using the direct-zol RNA microprep kit (Zymo Research). mRNA was enriched using the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB, E7490).
Indexed sequencing libraries were generated using the NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB, #E7775), pooled, and then sequenced by paired-end (2x150bp) Illumina sequencing.
spike-in normalised polyA RNA-seq
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
cDNA of polyA-enriched RNA from a mixture S. cerevisiae (MS95) and S. pombe (PN10597). MS95 was cultured in the prescence of 20nM beta-estradiol and was collected 32min after EU washout from media.
|
| Data processing |
read alignment, ChIP-seq and gDNA data Bowtie (version 1.0.1)
read alignment, RNA-seq data STAR (version 2.5.3a
bigWig file generation custom code
Assembly: sacCer3
Supplementary files format and content: bigWig
|
| |
|
| Submission date |
Sep 11, 2023 |
| Last update date |
Nov 01, 2023 |
| Contact name |
Georgi Kolev Marinov |
| Organization name |
STANFORD UNIVERSITY
|
| Department |
Genetics
|
| Street address |
279 Campus Drive West, Beckman Center, B-257A/259
|
| City |
Stanford |
| State/province |
California |
| ZIP/Postal code |
94305-5101 |
| Country |
USA |
| |
|
| Platform ID |
GPL29170 |
| Series (1) |
| GSE242874 |
RNA polymerase II dynamics and mRNA stability feedback scale mRNA amounts with cell size |
|
| Relations |
| BioSample |
SAMN37351233 |
| SRA |
SRX21748784 |
