title: T8-R1-G
organism: Saccharomyces cerevisiae
description: Protocols: After incubation at 37°C, cells were returned to an air incubator set to 24°C, 180 rpm, and incubated under these conditions for the duration of sample collection. Samples were collected once an hour, over an 8 h time span with the first sample collected immediately after cells were returned to 24°C. For transcriptomic sample collection, cells were added to ice- chilled 50 mL falcon tubes containing approx. 25 mL ice then immediately pelleted in 4°C pre-chilled centrifuge for 3 min at 5500 g. Supernatant was discarded and pellets were snap frozen with liquid nitrogen and stored at -80°C until further notice. The yeast Saccharomyces cerevisiae CEN.PK 113-11A HIS3 TRP1 SPC42tmCherry cdc15-2 was used. Three individual colonies were inoculated into 10 mL Delft minimal medium respectively, with 2% glucose used as the carbon source, and cells were grown 3 x overnight (180 rpm, 24°C). Cultures were then used to inoculate 500 mL Delft medium to an optical density measured at 600 nm (OD600) of approx. 0.025. Once cells had reached an OD600 of approx. 0.08, cultures were switched to another air incubator set to 37°C, 180 rpm, and incubated for 4 h. RNA was extracted and purified using Qiagen RNeasy Mini Kit extraction and DNA degradation according to the user's manual (Qiagen, Hilden, Germany). Integrity of the product was verified using 2100 Bioanalyzer instrument according to its user's manual (Agilent Technologies, Santa Clara, California, United States). RNA concentration was determined by a NanoDrop 2000 (Thermo Fisher Scientific) and Qubit (Life Technologies). The cDNA libraries were generated by using Illumina TruSeq Stranded mRNA Library Prep (96 Samples) kit (Illumina Inc., USA) with following modifications. Briefly, 2.5 ug of total undegraded RNA was diluted in 50 µL nuclease free water and mRNA was purified by oligo-dT selection by following the company's protocol. Purified mRNA was enzymatically fragmented for 8 minutes to approx. 250 bp average fragment size. Finally, the adapter-modified cDNA fragments were enriched by 10 cycles enrichment PCR. All the purification and size-selection steps along the protocol were conducted by using Kapa Pure Beads (Roche Molecular Systems, Inc., Switzerland).
attributes.tag: ENA-FIRST-PUBLIC
attributes.value: 2020-12-17T04:05:18Z
attributes.tag: ENA-LAST-UPDATE
attributes.value: 2019-12-20T12:16:46Z
attributes.tag: External Id
attributes.value: SAMEA6434560
attributes.tag: INSDC center name
attributes.value: Dept of Biochemistry and Biophysics, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Stockholm University
attributes.tag: INSDC first public
attributes.value: 2020-12-17T04:05:18Z
attributes.tag: INSDC last update
attributes.value: 2019-12-20T12:16:46Z
attributes.tag: INSDC status
attributes.value: public
attributes.tag: Submitter Id
attributes.value: E-MTAB-8626:T8-R1-G
attributes.tag: broker name
attributes.value: ArrayExpress
attributes.tag: common name
attributes.value: baker's yeast
attributes.tag: genotype
attributes.value: HIS3 TRP1 SPC42tmCherry cdc15-2
attributes.tag: growth condition
attributes.value: Delft minimal medium with 2% glucose
attributes.tag: organism part
attributes.value: whole organism
attributes.tag: sample name
attributes.value: E-MTAB-8626:T8-R1-G
attributes.tag: scientific_name
attributes.value: Saccharomyces cerevisiae
attributes.tag: strain
attributes.value: CEN.PK 113-11A