NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM4407049 Query DataSets for GSM4407049
Status Public on Jun 16, 2020
Title A23 exp1 rep1 [AS_an.exp1.A23.d6053]
Sample type SRA
 
Source name A23 exp1
Organism Saccharomyces cerevisiae
Characteristics strain background: S288C
strain: A23
growth phase/cell type: Exponentially Growing Cells
extract_protocol: Illumina Truseq
Growth protocol Selected complex aneuploid strains were grown on YEPD + 2% glucose plate for 2 days at 25ºC. Colonies were inoculated overnight in 25 mL YEPD + 2% glucose and grown at 25ºC. After 12-14 hours of growth at 25ºC, cells were diluted to approximately OD(600nm) = 0.1 and grown for an additional 4 hours at 25ºC.
Extracted molecule total RNA
Extraction protocol 3-5 mL samples of culture were taken, spun down at 3000rpm for 5 minutes, washed with 1 mL DEPC water, and transferred to a 2 mL RNase-free screw-cap tube. Samples were spun again at 8000rpm for 3 minutes, and supernatant was aspirated. Cells were snap frozen with liquid nitrogen and stored at -80C. RNA samples were prepared with RNeasy mini kit from Qiagen and treated with DNase on-column treatment (RNase-free) from Qiagen.
Illumina Truseq or KAPA
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Description processed data file: terhorst_l2tpm.txt.gz
AS_an.exp1.A23.d6053
Data processing HiSeq2000 using v3 chemistry. Software: Control v2.2.58, RTA 1.18.64. BCL files were converted to fastq using bcl2qseq. Indexes were split using custom scripts allowing 1 mismatch.
Reads were aligned to a S. cerevisiae transcriptome with STAR version 2.5.3a and gene expression was quantified with RSEM version 1.3.0. Transcript per million (TPM) values were offset by +1 and transformed to log 2 space.
Genome_build: SacCer3 plus spike-ins with an ensembl annotation
Supplementary_files_format_and_content: text format file of log2 TPM with a +1 offset of protein coding genes
 
Submission date Mar 11, 2020
Last update date Jun 16, 2020
Contact name Charles Arthur Whittaker
E-mail(s) charliew@mit.edu
Organization name Koch Institute
Street address 77 Mass Ave 76-189
City Cambridge
State/province MA
ZIP/Postal code 02152
Country USA
 
Platform ID GPL13821
Series (1)
GSE146791 The environmental stress response causes ribosome loss in aneuploid yeast cells. 
Relations
BioSample SAMN14354911
SRA SRX7894824

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap