|
| Status |
Public on Sep 26, 2017 |
| Title |
msn2Δmsn4Δ-RNA-t10 |
| Sample type |
SRA |
| |
|
| Source name |
yeast cells in metabolic cycles
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: ZKY763: CEN.PK MATa msn2<delta>::hygMX msn4<delta>::KanMX6
time: t10
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
2 OD cycling cells were collected and flash frozen. RNA was extracted with the Qiagen RNeasy Mini kit (QIAGEN, 74104, Valencia, CA).
RNA-seq libraries were prepared using Illumina Trueseq RNAseq v2 library kit (Illumina, San Diego, CA). PolyA beads were used for mRNA selection. 500 ng of RNA per sample was used as input and 12 cycles of PCR were run for amplification.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Additionally time points representing the relative time of WT samples in the RC phase
|
| Data processing |
Sequence reads were mapped to the Saccharomyces.cerevisiae (sacCer2) using TopHat (--bowtie1 -i 40 --genome-read-mismatches 4 --no-coverage-search -G genes.gtf). FPKM counts were calculated by Cuffidff.
Supplementary_files_format_and_content: FPKM file contains FPKM values for each gene in 7 WT and 11 mutant cells.
Genome_build: sacCer2
|
| |
|
| Submission date |
Aug 21, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Zheng Kuang |
| Organization name |
UT Southwestern medical center
|
| Department |
Immunology
|
| Lab |
Lora Hooper
|
| Street address |
6000 Harry Hines Blvd. NA7.500
|
| City |
Dallas |
| State/province |
TX |
| ZIP/Postal code |
75390 |
| Country |
USA |
| |
|
| Platform ID |
GPL17342 |
| Series (1) |
| GSE72263 |
DynaMO, a package identifying transcription factor binding sites in dynamical ChIPSeq/RNASeq datasets, identifies transcription factors driving yeast ultradian and mammalian circadian cycles |
|
| Relations |
| BioSample |
SAMN04005550 |
| SRA |
SRX1163858 |
