|
Status |
Public on Aug 31, 2017 |
Title |
WT_gal_glu_5m |
Sample type |
SRA |
|
|
Source name |
Saccharomyces cerevisiae
|
Organism |
Saccharomyces cerevisiae |
Characteristics |
genotype/variation: WT protocol: gal_glu time point: 5m 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
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|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 4000 |
|
|
Description |
WT_gal_glu_5m_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
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|
|
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 |
SAMN07572966 |
SRA |
SRX3146041 |