|
| Status |
Public on Jan 01, 2013 |
| Title |
mtr3-1 |
| Sample type |
SRA |
| |
|
| Source name |
2 hour temperature-shifted culture, mtr3-1
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: T208
genotype: mtr3 mutation
treatment: temperature shift (OD600 of 0.4 @ 30 degrees, then 2 hours @ 37 degrees)
|
| Treatment protocol |
Yeast strains were grown in 50 mL of YPD in a 250 mL flask at 30°C and 250 rpm to a final OD600 of 0.4, and were temperature shifted for 2 hours at 37°C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA libraries were generated using an Illumina poly-A select mRNA kit, and a unique 3-base barcode was included into each library. All libraries were simultaneously sequenced in a single lane of an Illumina GAIIx at the Microarray and Genomic Analysis Core Facility of the Huntsman Cancer Institute, University of Utah. 36 cycles of sequencing were performed, and each read resulted in 1.1 billion filter-passed bases. The resulting data were split by barcodes using SplitBarcode (Christopher Maxwell, U. of Utah).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
RNA-seq of total RNA, selected for poly-A+.
|
| Data processing |
All individual samples were groomed using the FASTQ groomer in the NGS: QC and Manipulation tab, and aligned to the sacCer2 reference genome using the Map with Bowtie for Illumina function of the NGS: Mapping tab of the Galaxy website http://main.g2.bx.psu.edu/.
The aligned files were then uploaded into Avadis NGS software (STRAND Scientific Intelligence Inc.), reads were normalized, then numerical values were exported and analyzed using Microsoft Excel and Access suites. Genes included in mitosis-related GO terms were examined in detail, and their levels compared to WT were calculated. These values are included in the Excel file 'Table_S3_family_YEAST.xls', which is linked to the Series record as a supplementary file.
|
| |
|
| Submission date |
May 02, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Daniel Louis Kiss |
| E-mail(s) |
dlk13@case.edu
|
| Phone |
216-368-0385
|
| Fax |
216-368-3055
|
| Organization name |
Case Western Reserve University
|
| Department |
Molceular Biology and Microbiology
|
| Lab |
Andrulis
|
| Street address |
2109 Adelbert Road
|
| City |
Cleveland |
| State/province |
OH |
| ZIP/Postal code |
44106 |
| Country |
USA |
| |
|
| Platform ID |
GPL13272 |
| Series (1) |
| GSE29018 |
Pronounced and Extensive Microtubule Defects in a Saccharomyces cerevisiae DIS3 Mutant |
|
| Relations |
| SRA |
SRX060140 |
| BioSample |
SAMN00262776 |
