|
| Status |
Public on Jan 31, 2023 |
| Title |
wildtype, biol rep 3 |
| Sample type |
SRA |
| |
|
| Source name |
budding yeast cells
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
cell type: budding yeast cells
strain: BY4742
genotype: MAT{alpha} his3{delta}1 leu2{delta}0 lys2{delta}0 ura3{delta}0
treatment: none
|
| Treatment protocol |
no treatment
|
| Growth protocol |
Strains were grown in standard synthetic complete (SC) media at 28°C for 24 hours
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Cells were washed with 10 mM NaF/NaN3 and lysed using beating with glass beads. RNA was isolated using RNeasy® Plus Mini Kit (includes gDNA removal columns) followed by DNA digestion with DNase Max® Kit. mRNA was enriched by polyA selection.
polyA
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
1C_S13_L001_R1_001
|
| Data processing |
rRNA and tRNA removed using SortMeRNA
Filtered reads aligned to S288C genome reference using GSNAP
Differential gene expression analyzed using DESeq2 (including LFC shrinkage and count normalization using the median of ratios method(DESeq() command)
For PCA and hierarchical clustering, rlog2 transformed counts were used
Assembly: S288C_reference_genome_R64-3-1_20210421 (obtained from the SGD)
Supplementary files format and content: DESeqDataSet.tsv - gene expression counts normalized by median of ratios method (command: DESeq(dds, parallel = TRUE)); tab-delimited matrix
Supplementary files format and content: DESeqTransform.tsv - regularized log2 transformation of DESeqDataSet (command: rlog(dds, blind = FALSE)); tab-delimited matrix
|
| |
|
| Submission date |
Aug 19, 2022 |
| Last update date |
Jan 31, 2023 |
| Contact name |
Jakub Zahumensky |
| E-mail(s) |
jakub.zahumensky@iem.cas.cz
|
| Organization name |
Institute of Experimental Medicine, CAS
|
| Department |
Functional Organization of Biomembranes
|
| Street address |
Videnska 1083
|
| City |
Prague |
| ZIP/Postal code |
14220 |
| Country |
Czech Republic |
| |
|
| Platform ID |
GPL19756 |
| Series (1) |
| GSE211649 |
Absence of the eisosome causes general transcriptome remodeling of the yeast cell |
|
| Relations |
| BioSample |
SAMN30413248 |
| SRA |
SRX17153008 |
