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Sample GSM724118 Query DataSets for GSM724118
Status Public on Sep 26, 2012
Title H3shutoff-RNA-3hr-rep3
Sample type SRA
 
Source name H3shutoff-RNA-3hr
Organism Saccharomyces cerevisiae
Characteristics strain: DCB200.1
carbon source: dextrose
time point: 3 hours
od: 0.8-1
Treatment protocol Cells were collected by filtration using a 0.2ul filter, washed with media containing 1% yeast extract, 2% peptone, 2% dextrose, and resuspended at the intial concentration in fresh media containing 1% yeast extract, 2% peptone, 2% dextrose.
Growth protocol Cells were grown with shaking at 30C in media containing 1% yeast extract, 2% peptone, 2% galactose and grown to an OD600 of between 0.8 and 1.
Extracted molecule total RNA
Extraction protocol RNA was isolated using the hot acidic phenol method (Xiao et al., 2003) from wildtype and H3-shutoff cells grown as previously described and transitioned to dextrose-containing media for 3 hours. RNA was cleaned up using the RNEasy Mini Kit (Qiagen 74104). Ribosomal RNA was removed using the RiboMinus system (Invitrogen K155003). Quality of RNA and absence of ribosomal RNA was confirmed by gel electrophoresis. 4.5ug of ribo-minus RNA was then fragmented at 70C for 5 minutes (Ambion AM8740) and used as input for double-strand cDNA synthesis using Invitrogen Double-Stranded cDNA synthesis kit (Invitrogen 11917-010) with random priming (Invitrogen 48190-011). The resulting cDNA was then prepared for Solexa sequencing using UNC HTSF protocol v. 2.5 for single-end, multiplex sequencing.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina Genome Analyzer IIx
 
Description RNA isolation from wildtype cells after 3 hours in dextrose
Data processing RNA-seq reads from three biological replicates each of H3 shutoff and wildtype cells were mapped to the S. cerevisiae sacCer1 genome using TopHat (v. 1.1.0) and Bowtie (v. 0.12.6.0) with a maximum intron size of 1 kb. Samtools (v. 0.1.8.0) was used to determine pileups at each base in the genome.
 
Submission date May 14, 2011
Last update date May 15, 2019
Contact name Jason D Lieb
E-mail(s) jlieb@bio.unc.edu
Phone 919-843-3228
URL http://www.bio.unc.edu/faculty/lieb/labpages/default.shtml
Organization name University of North Carolina at Chapel Hill
Department Biology
Lab Jason Lieb
Street address 203 Fordham Hall
City Chapel Hill
State/province NC
ZIP/Postal code 27599
Country USA
 
Platform ID GPL13272
Series (2)
GSE29293 Effects of Histone H3 depletion on nucleosome occupancy and positioning through the S. cerevisiae genome [RNA_seq]
GSE29294 Effects of Histone H3 depletion on nucleosome occupancy and positioning through the S. cerevisiae genome
Relations
SRA SRX066584
BioSample SAMN00622017

Supplementary file Size Download File type/resource
GSM724118_AG306_unique_hits_pileup.wig.gz 17.2 Mb (ftp)(http) WIG
SRA Run SelectorHelp
Raw data not provided for this record
Processed data provided as supplementary file
Raw data are available in SRA

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