NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM351494 Query DataSets for GSM351494
Status Public on Dec 18, 2008
Title Ethanol 4 replicates (2 non-crosslinked, 2 crosslinked)
Sample type SRA
 
Source name S. cerevisiae BY4741
Organism Saccharomyces cerevisiae
Characteristics yeast strain: BY4741
genomic dna: chromatin
growth condition: Ethanol
Treatment protocol As indicated in sample protocols
Growth protocol Cells were grown in YP media supplemented by 2% galactose or 2.8% ethanol.
Extracted molecule genomic DNA
Extraction protocol Samples were extracted as indicated in sample protocols. All samples were then blunted using END-IT DNA Repair Kit #ER0720 from Epicentre (< 5µg DNA, 5uL 10x buffer, 5uL dNTP mix, 5uL ATP solution, 1uL enzyme mix, water to 50uL. Incubated at room temp for 60 minutes, then cleaned up using Qiagen buffer QG on QiaQuick columns with 2 PE buffer washes, eluted with 30uL EB), then A-tailed using #KL06041K from Epicentre (Klenow Exo-minus) (30uL DNA solution, 5uL Klenow, 1uL 10mM dATP, 1uL Klenow, water to 50uL, 60 min at room temp, then cleaned up with Qiagen MinElute columns and eluted in 10uL EB). Solexa adapters were ligated using a Fast Link Kit (#LK11025 from Epicentre) (10uL DNA, 1.5uL 10x buffer, 0.75 uL 10mM ATP, 1uL of Solexa adapters, 1uL ligase, and water to 50uL incubated for 60 min at room temp, then 7.5uL water, 1uL 10x buffer, 0.5uL 10mM ATP, and 1uL ligase were added and the entire reaction incubated at 16C overnight before purification on QiaQuick columns as in blunting reaction). Samples were run out on a 2% agarose gel and the mononucleosome sized band (~147bp) was extracted using Qiagen Gel Extraction columns. Samples were amplified by PCR (Stratagen PfuUltra II Fusion #600670) (30uL ligated DNA, 2uL Solexa PCR primers, 10uL 10x buffer, 10uL 2.5mM dNTP, 1uL enzyme, water to 100uL for PCR [95C 1 min, (95C 50'', 65C 1', 72C 30'') x 15 cycles, 72C 5min, 4C hold] and then cleaned on QiaQuick columns) before being sequenced on Illumina Genome Analyzer II machines.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer II
 
Description library source : genomic
Data processing Mapped Reads: Unique reads mapped to the yeast genome, and extended to the average fragment length in the experiment (140-170 bp).
Normalized Tracks: For each Sample, we used the map reads to calculate at every basepair the log-ratio between the number of reads that cover that basepair and the average number of reads per basepair across the genome. We then set the genomic mean in each sample to zero by subtracting the genome-wide mean from every basepair. Finally, we averaged the replicates within each experimental condition, resulting in four tracks of log-normalized nucleosome coccupancy. One file for each biological condition, four files in total.
 
Submission date Dec 16, 2008
Last update date May 15, 2019
Contact name Desiree Tillo
E-mail(s) desiree.tillo@nih.gov
Phone +1-240-760-7289
Organization name NIH/NCI
Street address 41 Center Dr, Room D310
City Bethesda
State/province MD
ZIP/Postal code 20892
Country USA
 
Platform ID GPL9377
Series (1)
GSE13622 The DNA-Encoded Nucleosome Organization of a Eukaryotic Genome
Relations
SRA SRX008317
BioSample SAMN00003109

Supplementary file Size Download File type/resource
GSM351494_SRA_README.txt.gz 96 b (ftp)(http) TXT
GSM351494_YPEtOH_CL_R1.tab.gz 10.2 Mb (ftp)(http) TAB
GSM351494_YPEtOH_CL_R2.tab.gz 12.7 Mb (ftp)(http) TAB
GSM351494_YPEtOH_NOCL_R1.tab.gz 8.1 Mb (ftp)(http) TAB
GSM351494_YPEtOH_NOCL_R2.tab.gz 11.8 Mb (ftp)(http) TAB
GSM351494_YPEtOH_normalized.tab.gz 40.6 Mb (ftp)(http) TAB
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA
Processed data included within Sample table

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