 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Jun 29, 2024 |
| Title |
ssk1𝛥kss1𝛥, 0, 15min, rep3 |
| Sample type |
SRA |
| |
|
| Source name |
single cell
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
cell type: single cell
genotype: ssk1deltakss1delta
treatment: no treatment
|
| Treatment protocol |
350 mM KCl for 15 min
|
| Growth protocol |
Cells were grown from a single colony to saturation overnight. Next day, cells were diluted and grown to OD600nm of 0.7 (~107 cells/mL). Then, cells were treated with 350 mM KCl, 30 μM mating pheromone or the combination of both for 15 min. At the 13-min mark, cells were harvested by centrifugation at 16,000 x g for two min and flash frozen in liquid nitrogen and stored on dry ice
|
| Extracted molecule |
total RNA |
| Extraction protocol |
We submit sample to Azenta Life Science for RNA extraction, sequencing and data analysis. Used Rnaeasy kit for extraction (Qiagen)
The RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina using manufacturer’s instructions (New England Biolabs, Ipswich, MA, USA). Briefly, mRNAs were initially enriched with Oligo d(T) beads.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1500 |
| |
|
| Description |
GroupE-vs-GroupK
|
| Data processing |
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36
The trimmed reads were mapped to the Saccharomyces cerevisiae S288c reference genome available on ENSEMBL using the STAR aligner v.2.5.2b
The STAR aligner is a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences.
BAM files were generated as a result of this step.
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2
Assembly: S288c
Supplementary files format and content: txt format of raw counts and differential expression analysis tables, including volcano, PCA, MA, PTM plots.
|
| |
|
| Submission date |
Jun 25, 2024 |
| Last update date |
Jun 29, 2024 |
| Contact name |
Henrik Gunnar Dohlman |
| E-mail(s) |
hdohlman@med.unc.edu
|
| Organization name |
UNC Chapel Hill
|
| Street address |
120 Mason Farm Rd
|
| City |
Chapel Hill |
| ZIP/Postal code |
27599 |
| Country |
USA |
| |
|
| Platform ID |
GPL18085 |
| Series (1) |
| GSE270781 |
Shared and redundant proteins coordinate signal cross-talk between MAPK pathways in yeast |
|
| Relations |
| BioSample |
SAMN42042484 |
| SRA |
SRX25061576 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
|
|
|
|
 |
