|
| Status |
Public on Feb 10, 2017 |
| Title |
small_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
BY4741
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
sample type: small particles
genotype/variation: Mat a; his3^1leu2^0 ura3^0 met15^0
|
| Growth protocol |
S. cerevisiae strains were grown in YPD (1% yeast extract, 2% peptone, 2% glucose) at 30ºC. Microencapsulation of individual yeast cells in alginate microspheres (no more than one cell per microparticle) was performed using a Cellena microencapsulator (Ingeniatrics), as described (Gómez-Herreros et al, NAR 2011). Encapsulated cells were incubated together in YPD medium under standard culturing conditions. After ethanol fixation, microcolonies were analysed and sorted using a BioSorter large-particle flow cytometer (Union Biometrica). A detailed protocol of the sorting procedures is described in (Delgado-Ramos et al, G3 2014).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated by a standard hot phenol method and treated with RNase-free DNaseI using Turbo DNA-free kit (Ambion)
Genome-wide quantification of gene expression and poly(A) site usage was performed using 3’T-fill approach (Wilkening et al 2013; PMID: 23295673). We used 500-3000 ng of total RNA as starting material.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
RACE |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Microcolonies encapsulated in alginate, EtOH fixed, small colonies.Barcode in the beginning of the second read - TACAAG. Excluded due to low quality.
|
| Data processing |
Base-calling was done during processing of sequencing data with the illumina pipeline casava v1.8.2
Reads were mapped to S. cerevisiae genome (SGD R64-1-1) using the GSNAP version 2012-01-11
Genome_build: R64-1-1 (sacCer3)
Supplementary_files_format_and_content: Count table containing the 3' polyadenylation sites identified.
|
| |
|
| Submission date |
Aug 14, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Vicent Pelechano |
| E-mail(s) |
[email protected]
|
| Organization name |
ScilifeLab - Karolinska Institutet
|
| Department |
MTC
|
| Street address |
Nobels väg 16
|
| City |
Solna |
| ZIP/Postal code |
SE-17177 |
| Country |
Sweden |
| |
|
| Platform ID |
GPL13821 |
| Series (1) |
| GSE72092 |
Transcriptional analysis of wild-type budding yeast microcolonies encapsulated in alginate particles |
|
| Relations |
| BioSample |
SAMN03995095 |
| SRA |
SRX1150826 |
