|
| Status |
Public on Aug 31, 2017 |
| Title |
WT_gal_fru_10m |
| Sample type |
SRA |
| |
|
| Source name |
Saccharomyces cerevisiae
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
genotype/variation: WT
protocol: gal_fru
time point: 10m
strain: DBY12000
|
| Treatment protocol |
cultures were sampled at log phase (t=0), then glucose or fructose was added (to a final concentration of 2%) and subsequent time-points were taken
|
| Growth protocol |
100 mL cultures were grown in 500 mL baffled flasks overnight in YNB + 2% galactose media to log phase (OD600 between 0.230 and 0.273)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
total RNA was extracted using a standard yeast RNA extraction protocol (using hot, acidic phenol); briefly, cells are resuspended in a lysis buffer and acidic phenol, then incubated at 65C for 30 minutes to dissolve the proteins/membranes and release the RNA. Next RNA is purified using alcohol precipitation.
libraries were prepared using Illumina's Tru-seq stranded mRNA prep kit (poly-dT selection of polyA transcripts)(using Invitrogen's SuperScriptIV); fragments ranging from 200-600 bp were selected using a Pippin-HT
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
WT_gal_fru_10m_0
|
| Data processing |
Basecalls performed using CASAVA version 1.4
We aligned sequencing reads to SacCer3 assembly and the SGD transcriptome (Harrow et al. 2012) using TopHat2 (Trapnell, Pachter, and Salzberg 2009) with options -p 4 --library-type fr-firststrand and -M.
We estimated gene abundances per condition using the Cuffllinks CuffNorm option with default options
Genome_build: sacCer3
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample at gene level
|
| |
|
| Submission date |
Aug 30, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
David G Hendrickson |
| E-mail(s) |
david.gillis.hendrickson@gmail.com
|
| Organization name |
Harvard
|
| Street address |
725 Parsons
|
| City |
Boston |
| ZIP/Postal code |
02138 |
| Country |
USA |
| |
|
| Platform ID |
GPL21656 |
| Series (1) |
| GSE103285 |
Gene expression response to glucose/fructose in WT vs. tps1- |
|
| Relations |
| BioSample |
SAMN07572974 |
| SRA |
SRX3146028 |
