NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM4568403 Query DataSets for GSM4568403
Status Public on Sep 01, 2020
Title YPGal rep B
Sample type SRA
 
Source name YPGal_yeast cells
Organism Saccharomyces cerevisiae
Characteristics strain: JGY2000
genotype: Wild-type RPO21-FRB
growth medium: YP + 2% Galactose
culture stage: log phase
Treatment protocol none
Growth protocol Growth in the specified culture medium to mid-log phase except for diauxic cells, which were cultured for approximately 72 hours
Extracted molecule total RNA
Extraction protocol Hot acid phenol RNA extraction followed by Qiagen RNeasy purification
3' READS starting with 25µg total RNA (Jin, Y. et al., 2015 Curr Protoc Mol Biol 110, 4.23.21-24.23.17)
 
Library strategy OTHER
Library source transcriptomic
Library selection other
Instrument model Illumina NextSeq 500
 
Description 3' READS library
Data processing library strategy: 3' READS
Prep for mapping (removal of adapters, counting and removal of initial Ts, discarding reads with ambiguous base calls): python3
Mapping to yeast genome build Sac cer3 (first 17 non-A bases; accepting perfect matches and unique reads only): Bowtie (Langmead et al., 2009)
Discard mapped reads with fewer initial Ts than there are As in the adjacent genome: python3
Tally reads by UTR position if they map to the first 400nt after an ORF end: python3
Genome_build: Sac cer 3
Supplementary_files_format_and_content: tab-delimited text files with isoform expression percentages for every position in the first 400 nt after yeast genes
 
Submission date May 26, 2020
Last update date Jan 11, 2022
Contact name Zarmik Moqtaderi
Organization name Harvard Medical School
Department BCMP
Lab Struhl lab
Street address 240 Longwood Avenue C2-355
City Boston
State/province MA
ZIP/Postal code 02115
Country USA
 
Platform ID GPL19756
Series (1)
GSE151196 The transcriptional elongation rate regulates alternative polyadenylation in yeast
Relations
Reanalyzed by GSM5808423
BioSample SAMN15016303
SRA SRX8399841

Supplementary file Size Download File type/resource
GSM4568403_JGY2000_YPGal_RepB_RelCountsByPosition_1_to_400.txt.gz 2.3 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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