Comment[ArrayExpressAccession]	E-MTAB-2388
MAGE-TAB Version	1.1
Investigation Title	DNA:RNA Immunoprecipitation and Tiling Microarray (DRIP-chip)
Comment[Submitted Name]	DNA:RNA Immunoprecipitation and Tiling Microarray (DRIP-chip)
Experiment Description	Experiment to obtain the genome-wide distribution of DNA:RNA hybrid prone loci in Saccharomyces cerevisiae by DNA:RNA immunoprecipitation and tiling microarray (DRIP-chip). Samples: wild type, Rnase H deletion mutant, hpr1 deletion mutant, sen1-1 temperature sensitive mutant.
Experimental Design	in_vivo_design	binding site identification design
Comment[AEExperimentType]	ChIP-chip by array
Comment[AEExperimentDisplayName]	DNA:RNA immunoprecipitation and tiling microarray (DRIP-chip) to obtain the genome-wide distribution of DNA:RNA hybrid prone loci in Saccharomyces cerevisiae
Experimental Factor Name	genotype	immunoprecipitate
Experimental Factor Type	genotype	immunoprecipitate
Quality Control Type	biological replicate
Quality Control Term Source REF	EFO
Public Release Date	2014-05-06
Person Last Name	Chan
Person First Name	Yujia Alina
Person Mid Initials
Person Email	alinayujiachan@gmail.com
Person Phone	604 822 5936
Person Address	2185 East Mall, University of British Columbia, Vancouver, BC, Canada V6T1Z4
Person Affiliation	University of British Columbia
Person Roles	submitter
PubMed ID	24743342
Publication Author List	Yujia A Chan, Maria J Aristizabal, Phoebe YT Lu, Zongli Luo, Akil Hamza, Michael S Kobor, Peter C Stirling, Philip Hieter
Publication Title	Genome-Wide Profiling of Yeast DNA:RNA Hybrid Prone Sites with DRIP-Chip
Publication Status	in preparation
Protocol Name	P-MTAB-37885	P-MTAB-37886	P-MTAB-37887	P-MTAB-37888	P-MTAB-37889	P-MTAB-37890
Protocol Type	growth protocol	nucleic acid extraction protocol	nucleic acid labeling protocol	nucleic acid hybridization to array protocol	array scanning and feature extraction protocol	normalization data transformation protocol
Protocol Description	ChIP-on-chip cultures were grown overnight in YPD, diluted to 0.15 OD600 and grown to 0.5-0.6 OD600 units. Cultures were cross-linked with 1% formaldehyde for 20 min and harvested by centrifugation.	Chromatin immunoprecipitation and genome-wide location analyses were performed as described previously, using the adapted linear amplification method that involves two rounds of T7 RNA polymerase amplification (van Bakel et al., 2008). In brief, 500 ml yeast cells were grown in a rich medium to an OD600 0.8-0.9 and were cross-linked with 1% formaldehyde for 20 min before chromatin was extracted. The chromatin was sonicated (Bioruptor, Diagenode: 10 cycles,30s on/off, high setting) to yield an average DNA fragment of 500 bp. 40ug of S9.6 antibody was coupled to 60 ul of protein A magnetic beads (Invitrogen). After reversal of the crosslinking and DNA purification, the immunoprecipitated and input DNA were amplified to about 6 ug aRNA using T7 RNA polymerase in two rounds. 	Samples were labeled with biotin. cRNA from second T7 round amplification was labeled with Biotin-X-X-NHS for 1hr at 25C. (Parameters: Amplification = none, Mass unit = Micro gram)	Hybridization was carried out according to manufacturer specifications. The immunoprecipitated and input sample were hybridized to two Affymetrix 1.0R S. cerevisiae microarrays.	Data were scanned using MicroArraySuite 5.0 according to manufacturer specifications.	We used an adapted version of the Model-based Analysis of Tiling-arrays (MAT) algorithm to reliably detect enriched regions (Schulze, Gottardo, Kobor, manuscript in preparation) (Johnson et al., 2006). MAT was applied to corresponding immunoprecipitated and input sample array, and the probe behavior model was estimated by examining the signal intensity, sequence, and copy number of all probes on an array. After probe behavior model fitting, the residuals between the model and observation were normally distributed and centered at 0. MAT uses a score function to identify regions of ChIP enrichment, which allows robust p-value and false discovery rate calculations. MATscores are calculated from all probes within a 300-bp sliding window and returns a MATscore for each probe.  All samples were normalized to input. Normalized files corresponding to biological replicates were quantile normalized and averaged.
Protocol Term Source REF	EFO	EFO	EFO	EFO	EFO	EFO
Term Source Name	ArrayExpress	EFO
Term Source File	http://www.ebi.ac.uk/ArrayExpress	http://www.ebi.ac.uk/efo
SDRF File	E-MTAB-2388.sdrf.txt
Publication DOI	10.1371/journal.pgen.1004288