NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM2410200 Query DataSets for GSM2410200
Status Public on Nov 01, 2021
Title RNA-seq_H4_shutoff_t2_R2
Sample type SRA
 
Source name cultured cells
Organism Saccharomyces cerevisiae
Characteristics strain: UKY403
time point (hrs): 2
Treatment protocol For time-course experiments, cells were initially inoculated in 5ml YPG liquid media and cultured at 30C. Logarithmically growing cells were then transferred and diluted into larger 1-1.5L YPG cultures for growth overnight at 30C while shaking in containers with 4x equivalent free-air volume. The following morning, mid-log phase cells (OD600 ~0.6-1.2) were collected by centrifugation, washed 2x within 5 minutes with ~250-500ml YP dextrose (YPD), and re-suspended in equivalent volume of YPD media for 0, 2, and 4 hours of continued growth at 30C.
Growth protocol H4 shutoff (UKY403) and isogenic control (UKY412) strains of S. cerevisiae were obtained from the Grunstein lab. Cells were maintained on agar plates containing YPG media (1% yeast extract, 2% peptone, 2% galactose).
Extracted molecule polyA RNA
Extraction protocol Total RNA was isolated using TRIzol Reagent following standard protocols. RNA was further purified using the RNEasy Mini Kit with on-column DNase digestion (Qiagen). Quality of extracted RNA was confirmed using an Agilent Bioanalyzer and samples with RIN > 8 were selected for sequencing. RNA from biological replicates for each control time-point and three biological replicates for each experimental (H4 Shutoff) time-point were collected.
RNA-seq was performed on all samples using the standard illumina protocol, which includes cDNA synthesis via random priming and ribosomal RNA depletion.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina Genome Analyzer II
 
Description RNA-seq during histone H4 shutoff
Data processing TopHat       VN:1.4.1 sgd_r64/SacCer3 (genes.gtf from iGenomes build)
Genome_build: SacCer3
Supplementary_files_format_and_content: Bam Files where generated with Tophat (vn 1.4.1)
Supplementary_files_format_and_content: Abundance measurments contain FPKM measurements generated with cuffdiff VN:2.1.1 with saccer3 gene annotations
 
Submission date Nov 29, 2016
Last update date Nov 01, 2021
Contact name Michael Buck
E-mail(s) mjbuck@buffalo.edu
Phone 7168817569
Organization name SUNY at Buffalo
Department Biochemistry
Street address 701 Ellicott St
City Buffalo
State/province NY
ZIP/Postal code 14203
Country USA
 
Platform ID GPL9377
Series (2)
GSE90669 Nucleosomes inhibit intragenic binding of Rap1p and subsequent cryptic transcription [RNA-seq]
GSE92468 Nucleosomes inhibit intragenic binding of Rap1p and subsequent cryptic transcription
Relations
BioSample SAMN06145906
SRA SRX2426614

Supplementary file Size Download File type/resource
GSM2410200_403-Rep2-t2.fpkm_tracking.gz 207.5 Kb (ftp)(http) FPKM_TRACKING
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