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| Status |
Public on May 14, 2014 |
| Title |
wt #2 |
| Sample type |
SRA |
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| Source name |
wild type_BrdU IP
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| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain background: W303
genotype/variation: wild type
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| Treatment protocol |
Samples were released from alpha-factor arrest in the presence of 200 mM HU (hydroxyurea).
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| Growth protocol |
Cells were grown on YPD at 25°C
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
For immunoprecipitation of BrdU-labelled DNA, 1.5x10^9 cells were lysed for 5 x 2 minutes in NIB buffer (17 % glycerol, 50 mM MOPS buffer, 150mM potassium acetate, 2 mM magnesium chloride, 500 µM spermidine and 150 µM spermine, pH7.2) with Zirconium beads on a Vibrax (VXR basic, Ika) at 4C. DNA was isolated using Qiagen Genomic DNA extraction kit and sonicated to reach an average DNA size of 300-600 bp. For each immunoprecipitation, 10 µl of mouse anti-BrdU IgG1 (BDBioscience 555627) was prebound to Dynabeads M-280 Sheep anti-mouse IgG (Invitrogen 112.02) and added to the denatured purified DNA. For immunoprecipitation of BrdU-labelled DNA, 1.5x109 cells were lysed for 5 x 2 minutes in NIB buffer (17 % glycerol, 50 mM MOPS buffer, 150mM potassium acetate, 2 mM magnesium chloride, 500 µM spermidine and 150 µM spermine, pH7.2) with Zirconium beads on a Vibrax (VXR basic, Ika) at 4C. DNA was isolated using Qiagen Genomic DNA extraction kit and sonicated to reach an average DNA size of 300-600 bp.
Libraries were constructed using standard Illumina kits (TruSeq SBS Kit v3) and protocols
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
BrdU IP
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| Data processing |
Basecalls performed using HiSeq Control Software 1.5.15.1, RTA 1.13.48.0 and CASAVA version 1.8.2
BrdU-IP-seq reads were aligned to the sacCer3 genome assembly using using Bowtie 2, version 2.1.0, , allowing only perfect matches
Alignement against rDNA repeats were performed using a sequence retrieved on SGD (http://www.yeastgenome.org) by entering the coordinates ChrXII:459797..468931 into GBrowse or Gene/Sequence Resources.
Nucleosomes were positioned using NSeq ( Nellore et al. (2012). Front Genet 3, 320.)
Genome_build: sacCer3
Supplementary_files_format_and_content: SGR files correspond to signal log ratio smoothed with a 1000 bp window and a 100 bp step
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| Submission date |
May 13, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Philippe Pasero |
| E-mail(s) |
ppasero@igh.cnrs.fr
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| Organization name |
Institute of Human Genetics - CNRS
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| Lab |
Pasero
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| Street address |
141 rue de la Cardonille
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| City |
Montpellier |
| ZIP/Postal code |
34396 |
| Country |
France |
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| Platform ID |
GPL13821 |
| Series (2) |
| GSE57617 |
HDACs act on ribosomal DNA to control the yeast replication program and the competition between origins for limiting initiation factors [ChIP-seq] |
| GSE57619 |
HDACs act on ribosomal DNA to control the yeast replication program and the competition between origins for limiting initiation factors |
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| Relations |
| BioSample |
SAMN02776980 |
| SRA |
SRX541158 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1385578_log2Ratio_0to1_wt_IP_GYC-30_VS_0to1_wt_input_GYC-26_Smooth1000_Step100.sgr.gz |
924.3 Kb |
(ftp)(http) |
SGR |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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