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| Status |
Public on Dec 18, 2008 |
| Title |
YPD 6 biological replicates (4 non-crosslinked, 2 crosslinked) |
| Sample type |
SRA |
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| Source name |
S. cerevisiae BY4741
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| Organism |
Saccharomyces cerevisiae |
| Characteristics |
yeast strain: BY4741
genomic dna: chromatin
growth condition: Dextrose
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| Treatment protocol |
As indicated in sample protocols
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| Growth protocol |
Mononucleosomes were isolated from S. cerevisiae were grown to an OD600 of 0.8 in YPD medium as described in Segal et. al, Nature 442, 772-8 (2006). For crosslinked sample, yeast were grown to an OD600 of 0.8 in YPD and fixed with 1% formaldehyde for 15 min at 30C before spheroplasting as in Segal et. al, Nature 2006. Spheroplasts were treated with Mnase as in Shivaswamy et al, PLoS Biol 6, e65 (2008), and nucleosomal DNA isolated as in Sekinger, Moqtaderi, and Struhl, Mol Cell 18, 735-48 (2005).
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| 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.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer II |
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| Description |
library source : genomic
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| 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.
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| Submission date |
Dec 16, 2008 |
| Last update date |
May 15, 2019 |
| Contact name |
Desiree Tillo |
| E-mail(s) |
[email protected]
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| Phone |
+1-240-760-7289
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| Organization name |
NIH/NCI
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| Street address |
41 Center Dr, Room D310
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| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
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| Platform ID |
GPL9377 |
| Series (1) |
| GSE13622 |
The DNA-Encoded Nucleosome Organization of a Eukaryotic Genome |
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| Relations |
| SRA |
SRX008315 |
| BioSample |
SAMN00003107 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM351492_SRA_README.txt.gz |
105 b |
(ftp)(http) |
TXT |
| GSM351492_YPD_CL_R2.tab.gz |
11.3 Mb |
(ftp)(http) |
TAB |
| GSM351492_YPD_CL_R3.tab.gz |
8.9 Mb |
(ftp)(http) |
TAB |
| GSM351492_YPD_NOCL_R1.tab.gz |
8.3 Mb |
(ftp)(http) |
TAB |
| GSM351492_YPD_NOCL_R2.tab.gz |
12.1 Mb |
(ftp)(http) |
TAB |
| GSM351492_YPD_NOCL_R3.tab.gz |
11.8 Mb |
(ftp)(http) |
TAB |
| GSM351492_YPD_NOCL_R4.tab.gz |
13.0 Mb |
(ftp)(http) |
TAB |
| GSM351492_YPD_normalized.tab.gz |
42.0 Mb |
(ftp)(http) |
TAB |
SRA Run Selector |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
| Processed data included within Sample table |
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