 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Jan 02, 2018 |
| Title |
ko2B_RNA-seq |
| Sample type |
SRA |
| |
|
| Source name |
yeast
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
genotype: CEN.PK ARP5::KAN
growth phase: RC mid
|
| Growth protocol |
Yeast grown in continuous culture to induce metabolic cycling; samples taken at different times across these metabolic cycles. The growth stages are described in Kuang, Z., Cai, L., Zhang, X., Ji, H., Tu, B.P., and Boeke, J.D. (2014). High-temporal-resolution view of transcription and chromatin states across distinct metabolic states in budding yeast. Nat Struct Mol Biol 21, 854 863. Samples A and B are technical replicates-- RNA was prepared separately from the same culture.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
yeast were harvested and flash frozen. RNA was extracted using MasterPure RNA extraction kit (MPY03100).
0.8 µg of RNA was used with the Illumina TruSeq mRNA kit (15031047) using standard protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
processed data file:
fpkmMatrix.csv
|
| Data processing |
Reads were aligned using Bowtie2 and analysed using DESeq2. Replicates were combined for analysis and genes with low reads (< 5 FPKM across all samples) were removed.
genome build: sacCer3 (April 2011)
processed data files format and content: FPKM
|
| |
|
| Submission date |
Jul 12, 2017 |
| Last update date |
Jan 03, 2018 |
| Contact name |
Graeme Gowans |
| E-mail(s) |
ggowans@stanford.edu
|
| Organization name |
Stanford University
|
| Department |
Biology
|
| Lab |
Ashby Morrison
|
| Street address |
Gilbert Building, 371 Serra Mall
|
| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305 |
| Country |
USA |
| |
|
| Platform ID |
GPL19756 |
| Series (1) |
| GSE101290 |
INO80 Chromatin Remodelling Coordinates Metabolic Homeostasis with Cell Division |
|
| Relations |
| BioSample |
SAMN07345705 |
| SRA |
SRX2997362 |
| Supplementary data files not provided |
SRA Run Selector |
| Processed data are available on Series record |
| Raw data are available in SRA |
|
|
|
|
 |
