title: Breast-tumour_53

city: Lund

first: Johan

last: Staaf

address: Medicon Village

country: Sweden

institute: SCIBLU - Swegene Centre for Integrative Biology at Lund University

description: Array CGH analysis was employed to identify and confirm changes in the gene expression of a number of different genes mapping to the 11q chromosomal region, associated with CCND1 amplification. The subsequent protein expression of these candidate genes was then examined in a clinical material of 500 primary breast cancers from premenopausal patients randomized to either tamoxifen or no adjuvant treatment. The protein expression was also compared to the CGH data in a subset of 56 breast cancer samples.

hyb_protocol: Samples were hybridised and washed as described in Jonsson et al. (Genes Chromosomes Cancer 2007).

scan_protocol: Arrays were scanned in Agilent Microarray scanner.

data_processing: Image analysis was performed using Genepix v4.0. Result files were uploaded into BASE (Saal et al., Genome Biology 2002) where they were filtered and pin-based lowess normalised.

source_name: Breast tumour

label_protocol: Samples were labelled using the Invitrogen BioPrime arrayCGH labelling module.

extract_protocol: Pre-treatment with Proteinase K (20 mg/ml) followed by the Promega Wizard Genomic Purification kit. Extracted DNA was purified by phenol/chloroform treatment.

value: Female, Tissue:Breast tumour

source_name: Promega reference male DNA

tag: Pooled genomic DNA from ten male individuals


title: Breast-tumour_55

status: Public on Oct 08 2008

type: genomic

molecule: genomic DNA

organism: Homo sapiens

tag: Gender


title: Breast-tumour_52


title: Breast-tumour_56


title: Breast-tumour_51


title: Breast-tumour_50


title: Breast-tumour_48


title: Breast-tumour_46


title: Breast-tumour_54


title: Breast-tumour_45


title: Breast-tumour_44


title: Breast-tumour_43


title: Breast-tumour_39


title: PBMC-Stenotic-Rep10 (17-0921)

type: RNA

city: CA

first: James

middle: A.

last: Wingrove

state: CA

address: 2500 Faber Place

country: USA

institute: CardioDx, Inc.

hyb_protocol: Labeled RNAs were hybridized using the Agilent protocol (Agilent, version 4.0.1) with the following exception: labeled reference samples were pooled in 1.06X Hybridization Buffer and 2X Blocking Buffer, the pooled samples were heated to 65 C for 5 minutes and then centrifuged at 13,000 rpm for 10 minutes

scan_protocol: Data was scanned on an Agilent Scanner (G2505B) and extracted using Agilent Feature Extraction Software (version 8.5.1.1)

data_processing:
Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and LOWESS normalization.
Data was imported into GeneSpring (Agilent, v 7.3.1) and normalized using the AgilentFE normalization scenario.  Retained features had a present or marginal call in at least one sample.

molecule: total RNA

source_name: PBMC - Stenotic

label_protocol: 100 ng of each patient PBMC RNA was labeled with Cy5 using the Low RNA Input Fluorescent Linear Amplification Kit from Agilent (PN 5184-3523), following the recommended protocol.  In parallel, 100 ng (per hybridization) of commercially available reference PBMC RNA (Clontech, PN 636580) was Cy3 labeled using the same protocol.

growth_protocol: Whole blood (16ml) was collected prior to angiography (BD Vacutainer® CPT); mononuclear cells were processed immediately following collection.

extract_protocol: RNA was extracted using a modification of the RNeasy method (Qiagen)

treatment_protocol: PBMC preps were processed using RLT buffer (Qiagen) prior to freezing at -80C

tag: Stenotic

source_name: PBMC Pool

tag: PBMC Pool - Clontech (PN # 636580)


title: Breast-tumour_34


title: Breast-tumour_38


title: Breast-tumour_49


title: 13256498 - Control vs ABA 10-5M

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

country: France

institute: INRA

description: The specific plant phosphorylated form of phosphatidic acid (PA), diacyglycerol pyrophosphate (DGPP) was recently shown to be a second messenger in abscisic acid (ABA) signaling. The aim of the project is to identify among the set of ABA-regulated genes the ones also regulated by DGPP and/or PA.

hyb_protocol: ABA 10-5M Cy5 / Control Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: GenePix Pro 3.0, Cy3:pmt voltage 532nm,650V,laser power 100%, Cy5:635nm,pmt voltage 620V,laser power 100%

data_processing: The raw data comprised the logarithm of median feature pixel intensity at wavelength 635 nm (red) and 532 nm (green). No background was subtracted. An array-by-array normalization was performed to remove systematic biases. First, we excluded spots that were considered badly formed features by the experimenter (Flags=-100). Then we performed a global intensity-dependent normalization using the loess procedure (see Yang et al., 2002) to correct the dye bias. Finally, on each block, the log-ratio median is subtracted from each value of the log-ratio of the block to correct a print-tip effect on each metablock.

organism: Arabidopsis thaliana

source_name: ABA 10-5M

label_protocol: labelling Cy3 and Cy5 direct, amplification=yes, aRNA 5 ug. Labelling protocol: 5 µg of aRNA (8µl) mixed with 2 µl of random nonamers 1µg/µl and 0.5 µl of RNAse Out 40 U/µl, denatured 10 min at 70 °C and chilled on ice. The followig components were added to the sample 4 µl of first strand buffer 5 X, 1 µl of 10 mM dNTP/2mM dCTP, 2 µl of 0.1 M DTT, 1.5 µl of Cy3-dCTP or Cy5-dCTP (Amersham Pharmacia Biotech, 25nmol tube, PA5502), 1 µl of SuperScript II RT 200U/µl. Then it was incubated at 42°C for 2.5 hours and chilled on ice. The sample was denaturated by adding 2 µl of NaOH 2.5M and incubated at 37 °C for exactly 15 min, then was added 10 µl of 2M MOPS and put on ice. The dyes were purified with the QIAquick PCR Purification Kit (QIAGEN).

growth_protocol: cell culture - Cells in suspension Media : Jouanneau and Peaud-Lenokl (Jouanneau and Peaud-Lenokl, 1967) Temperature : 22°C Light : 40 umol photon s-1 m-2

extract_protocol: Pool of extract, ABA 10-5M set1:0.5ug, ABA 10-5M set2:0.5ug, ABA 10-5M set3:0.5ug.

treatment_protocol: Name:ABA 10-5M - compound based treatment - compound addition,aba:quantity 0.01mM time 3hour . Five ml of 3 days-old suspension cells was incubated with ABA for 3 h under the conditions of culture. Lipids were emulsified by sonication for 1 mi, four times, at 4degre Celsius, in one ml of culture medium then added to 4 ml suspension cells. Cells were filtrated under vacuum, frozen in liquid nitrogen and RNA extracted.

tag: Arabidopsis thaliana (columbia)  - age:3day

source_name: Control

growth_protocol: cell culture - Cells in suspension. Media : Jouanneau and Peaud-Lenokl (Jouanneau and Peaud-Lenokl, 1967) Temperature : 22°C Light : 40 umol photon s-1 m-2

extract_protocol: Pool of extract, Control set1:0.5ug, Control set2:0.5ug, Control set3:0.5ug.

treatment_protocol: no treatment


title: Breast-tumour_40


title: Breast-tumour_41


title: Breast-tumour_33


title: Breast-tumour_37


title: Breast-tumour_36


title: Breast-tumour_30


title: HBMVEC+U87#2 array#2

city: Charlestown

first: Thomas

last: Wurdinger

state: MA

address: 149 13th Street

institute: MGH

hyb_protocol: For hybridization, membranes were first prehybridized in MicroHyb Hybridization Buffer (Invitrogen) at 37ºC for 30 min followed by an overnight hybridization in the same solution containing RNA probe.

scan_protocol: Following hybridization, membranes were washed and exposed to a phosphor storage screen, scanned using a Phosphor Imager, and hybridization signals were quantified using ImageQuant software (Molecular Dynamics).

data_processing:
The experiments included three independent biological replicates (3x HBMVEC and 3x HBMVEC exposed to U87-CFP) that each was analyzed on two different array membranes. Hybridization signals for each spot of the array and background values at 23 empty spots were measured. Raw data was further automatically processed in Microsoft Excel:

Each array datapoint is normalized against the total sum of array signal, so: miR-xxx array#1/total signal of array#1 was compared to miR-xxx array#2/total signal of array#2

Probe signals that showed high variance in biological replicates (more than 2-fold with p values <0.05) were excluded from further analysis. Subsequently, the three miRNA data sets of the HBMVECs were each independently compared to the three data sets of the HBMVECs that were exposed to U87-CFP cells. The expression ratio for each endothelial miRNA sample in the presence or absence of U87-CFP glioma cells was calculated as the ratio between the corresponding expression levels (see table on GSE13091).

source_name: Human brain microvascular endothelial cells exposed to U87 glioma cells

label_protocol: Ten micrograms of total RNA from endothelial cells were filtered through Microcon YM-100 concentrators to obtain a low molecular weight (LMW) fraction of RNA enriched in molecules under 60 nt. The LMW RNA was end-labeled with 30 µCi у33P dATP (3000 Ci/mmole) by T4 polynucleotide kinase (New England Biolabs) and purified using the Qiagen Nucleotide Removal Kit.

growth_protocol: Human brain microvascular endothelial cells (HBMVECs; Cell Systems ACBRI-376) were cultured in EGM medium (Cambrex) for no more than 10 passages. U87-CFP cells (U-87 MG; ATCC, transduced with Lentivector-CFP) were cultured in DMEM containing 10% FBS and antibiotics.

extract_protocol: Total RNA was isolated from endothelial cells passaged less than 7 times in culture and primary endothelial cells (passage 0) isolated from normal brain and glioma tissue. RNA isolation was carried out by adding 600 µl lysis buffer from the miRVANA miRNA isolation kit (Ambion) to the CD31-bead bound cells. The quality and quantity of the RNA was analyzed by photospectrometry and analytical 15% TBE-UREA gels (Biorad) after ethidium bromide staining.

treatment_protocol: Endothelial cells were isolated from HBMVECs cultured alone or for 24 hr in endothelial basal medium in the presence of U87-CFP glioma cells using CD31 Endothelial Cell Dynabeads (Dynal Biotech). Cells were trypsinized, and then trypsin was inactivated using trypsin neutralization solution (Cambrex). Single cell suspensions containing 1x10e6 cells were washed once in PBS and resuspended in 1 ml PBS to which 25 µl CD31 Dynabeads was added. The tubes were subjected to slow rotation for 20 min at 4ºC. Subsequently, the tubes were placed in a magnet for 2 min and washed 3 x with 1 ml PBS containing 0.1% BSA. Isolated endothelial cells were plated in EGM medium and analyzed for the presence of U87-CFP contamination by using a combination of light and fluorescence microscopy. Only an occasional sporadic U87-CFP cell was observed, indicating a >99.9% purity of the endothelial cell population.

tag: Human brain microvascular endothelial cells (HBMVEC)


title: Breast-tumour_32


title: HBMVEC+U87#3 array#2


title: Breast-tumour_31


title: Breast-tumour_27


title: Breast-tumour_28


title: HBMVEC+U87#1 array#2


title: Breast-tumour_29


title: HBMVEC+U87#2 array#1


title: Breast-tumour_25


title: HBMVEC+U87#1 array#1


title: HBMVEC#2 array#2

source_name: Human brain microvascular endothelial cells


title: HBMVEC#3 array#1


title: HBMVEC#3 array#2


title: HBMVEC#2 array#1


title: HBMVEC+U87#3 array#1


title: HBMVEC#1 array#1


title: Breast-tumour_23


title: Breast-tumour_24


title: Breast-tumour_21


title: Breast-tumour_19


title: Silberg2 (S11) 25091BE

city: Philadelphia

first: Anil

middle: K

last: Rustgi

state: PA

address: 415 Curie Blvd, 600 CRB

department: Medicine-Gastroenterology

institute: University of Pennsylvania

hyb_protocol: hybridization of cRNAs to Affymetrix chips were performed according manufacturer's instructions

scan_protocol: scanning of Affymetrix chips were performed according manufacturer's instructions

data_processing: The 19 CEL files were processed using Stratagene’s Array Lite 3.4 software using GC-RMA algorithm to calculate probeset intensity values and to calculate Absent/Present/Marginal flags.  These intensity values were log2 transformed.

label: biotin

source_name: biopsy of Barrett's esophagus from the same patient as a matched normal esophagus biposy

label_protocol: cRNA with biotin labeling was performed according to Affymetrix protocols

extract_protocol: RNA was isolated by first homogenizing the tissue with a Brinkmann homogenizer, passing it through a QIAshredder (Qiagen,) column and isolating the RNA by RNeasy miniprep kit (Qiagen).


title: Silberg2 (S3) 23100BE


title: Breast-tumour_20


title: Breast-tumour_18


title: Breast-tumour_17


title: Silberg3 ( S5) 191102-1BE


title: Silberg2 (8) 021301BE


title: Silberg3 ( S2) 120902BE


title: control retina T48-sample3

city: Ann Arbor

first: Peter

middle: F.

last: Hitchcock

state: MI

address: 1000 Wall Street

department: Ophthy and Vis Sci

institute: University of Michigan

description: Gene Expression from lesioned retina 48hrs after light onset.

hyb_protocol: Following fragmentation, 5ug of cRNA were hybridized on GeneChip Zebrafish Array. GeneChips were washed and stained in the Affymetrix Fluidics Station.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.

data_processing: The data were analyzed with BRB Array Tools 3.6 using default analysis settings and global scaling for RMA normalization.

organism: Danio rerio

source_name: lesioned retina 48hrs after light onset

label_protocol: mRNA was amplified from total RNA using the RiboAmp HS RNA amplification kit (Arcturus, Molecular Devices Corporation.

extract_protocol: Pico Pure isolation kit (Arcturus, Molecular Devices Corporation)

tag: wild type, adult Danio retina


title: HBMVEC#1 array#2


title: control retina T24-sample4

description: Gene Expression from lesioned retina 24hrs after light onset.

source_name: lesioned retina 24hrs after light onset


title: control retina T48-sample4


title: Breast-tumour_16


title: control retina T48-sample2


title: Silberg2 (S1) 021101BE


title: Silberg2 (10) 130701BE


title: Breast-tumour_47


title: Breast-tumour_22


title: control retina T24-sample3


title: Breast-tumour_15


title: Breast-tumour_14


title: control retina T12-sample3

description: Gene Expression from lesioned retina 12hrs after light onset.

source_name: lesioned retina 12hrs after light onset


title: control retina T24-sample2


title: control retina T12-sample4


title: Silberg2 (S10) 25091NE

source_name: biopsy of normal esophagus from the same patient as a matched Barrett's esophagus biposy


title: Breast-tumour_13


title: Breast-tumour_12


title: control retina T12-sample2


title: Silberg2 (S4) 23100NE


title: Breast-tumour_10


title: Breast-tumour_26


title: Silberg3 ( S4) 191102-1NE


title: Breast-tumour_35


title: Silberg2 (9) 021301NE


title: Breast-tumour_11


title: Silberg3 ( S1) 120902NE


title: control retina T0-sample7

description: Gene Expression from unlesioned control retina.

source_name: unlesioned control retina


title: control retina T6-sample4

description: Gene Expression from lesioned retina 6hrs after light onset.

source_name: lesioned retina 6hrs after light onset


title: control retina T6-sample3


title: Breast-tumour_6


title: Breast-tumour_9


title: Breast-tumour_8


title: Silberg2 (S2) 021101NE


title: control retina T6-sample2


title: Breast-tumour_5


title: Rustgi PO1 SI4

source_name: biopsy of normal small intestine


title: Breast-tumour_7


title: control retina T0-sample6


title: Rustgi PO1 SI3


title: Rustgi PO1 SI6


title: Silberg2 (11) 130701NE


title: Breast-tumour_42


title: Breast-tumour_2


title: Breast-tumour_3


title: Breast-tumour_1


title: Rustgi PO1 SI2


title: control retina T0-sample5


title: Mutu (EBV positive) vs Mutu E1dn Cl. 1 (EBV negative)

status: Public on Oct 07 2008

city: New Orleans

first: Erik

last: Flemington

state: LA

address: 1430 Tulane Ave., SL79

department: Pathology

institute: Tulane Health Sciences Center

hyb_protocol: Hybridization is performed using a micro-circulation pump (Atactic Technologies).  The hybridization conditions are 100 µL 6xSSPE buffer (0.90 M NaCl, 60 mM Na2HPO4, 6 mM EDTA, pH 6.8) containing 25% formamide, 34 °C, and overnight.

scan_protocol: Hybridization images are collected using a laser scanner (GenePix 4000B, Molecular Device).  Scan resolution is set at 10 µ and PTM is set between 350 to 700 V.

data_processing: Data are analyzed by first subtracting the background and then normalization.  The background is determined using a regression-based background mapping method.  The regression is performed on 5% to 25% of the lowest intensity data points excluding blank spots.  Raw data matrix is then subtracted by the background matrix.  Normalization is carried out using a LOWESS (Locally-weighted Regression) method on the background-subtracted data.

source_name: Mutu E1dn Cl.1

label_protocol: Small RNAs (< 300 nt) are 3’-extended with a poly(A) tail using poly(A) polymerase.  An oligonucleotide tag is then ligated to the poly(A) tail for later fluorescent dye staining; two different tags are used for the two RNA samples in dual-sample experiments.

extract_protocol: Trizol preps followed by small RNA fractionation

tag: EBV negative derivative of the Burkitt's lymphoma line, Mutu, generated by double retroviral infection with dominant negative form of the EBV episomal replication factor, EBNA1.

source_name: Mutu (EBV positive - Bulk culture)

tag: EBV positive Burkitt's lymphoma cell line, Mutu I


title: Mutu (EBV positive) vs Mutu E1dn Cl. 3 (EBV negative)

source_name: Mutu E1dn Cl.3


title: EBV type III latency cell line, IB4 vs EBV type I latency cell line, Mutu I

hyb_protocol: Hybridization is performed using a micro-circulation pump (Atactic Technologies). The hybridization conditions are 100 µL 6xSSPE buffer (0.90 M NaCl, 60 mM Na2HPO4, 6 mM EDTA, pH 6.8) containing 25% formamide, 34 °C, and overnight.

scan_protocol: Hybridization images are collected using a laser scanner (GenePix 4000B, Molecular Device). Scan resolution is set at 10 µ and PTM is set between 350 to 700 V.

data_processing: Data are analyzed by first subtracting the background and then normalization. The background is determined using a regression-based background mapping method. The regression is performed on 5% to 25% of the lowest intensity data points excluding blank spots. Raw data matrix is then subtracted by the background matrix. Normalization is carried out using a LOWESS (Locally-weighted Regression) method on the background-subtracted data.

source_name: Mutu I cells

label_protocol: Small RNAs (< 300 nt) are 3’-extended with a poly(A) tail using poly(A) polymerase. An oligonucleotide tag is then ligated to the poly(A) tail for later fluorescent dye staining; two different tags are used for the two RNA samples in dual-sample experiments.

tag: EBV positive type I latency Burkitt's lymphoma cell line, Mutu I.

source_name: IB4 cells

tag: EBV infected B cell line, IB4.  Type III latency.


title: EBV positive type I latency Burkitt's lymphoma cell line, Rael vs EBV positive Type III latency cell line, JY

source_name: JY cells

tag: EBV immortalized B cell line, JY.  EBV latency type III

source_name: Rael cells

tag: EBV positive Burkitt's lymphoma cell line, Rael.  Type I latency.


title: EBV negative Burkitt's lymphoma cell line, DG75 vs EBV positive type III latency line, X50-7

source_name: X50-7 cells

tag: EBV infected B cell line, X50-7.  EBV type III latency.


title: Rustgi PO1 SI1


title: Breast-tumour_4

source_name: Breast tumour

source_name: Promega reference male DNA


title: breast tumor sample 175

city: San Diego

first: Jack

last: Yu

address: 3210 Merryfield Row

institute: Veridex, LLC

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: Affymetrix Microarray Suite version 5.0

source_name: breast tumor tissue

label_protocol: Approximately 5 µg of total RNA was processed to produce biotinylated cRNA targets.

extract_protocol: Total RNA was extracted from cell samples using the Trizol Kit.

tag: breast cancer


title: Mutu E1dn Cl. 9 (EBV negative) vs Mutu (EBV positive)

source_name: Mutu E1dn Cl. 9


title: breast tumor sample 3253


title: breast tumor sample 3263


title: EBV + Type III latency Burkitt's lymphoma vs EBV + Type I latency Burkitt's lymphoma

source_name: Akata I

tag: EBV positive Burkitt's lymphoma cell line, Akata. Type I latency cell line.

source_name: JIJOYE

tag: EBV Positive Burkitt's Lymphoma cell line, JIJOYE.  Type III latency cell line.


title: breast tumor sample 128


title: Mutu E1dn Cl. 6 (EBV negative) vs Mutu (EBV positive)

source_name: Mutu E1dn Cl.6


title: breast tumor sample 3276


title: K56Ac cell cycle, 120 min, array replicate 3 | array na_22_08

status: Public on Oct 04 2008

city: Worcester

first: Oliver

last: Rando

address: 364 Plantation St.

institute: UMass Medical School

description: BY4741 cells bearing a temperature sensitive mutation in cdc28 were arrested by shifting them from 22C to 37C for 3 hours.  To release from arrest, cold YPD media was added to shift back to 22C.  Cells were harvested after 120 minutes, crosslinked with formaldehyde (1%), washed with water and zymolyase treated.  Extracts of these cells were then digested with MNase to produce mononucleosomes, and subjected to immunoprecipitation with with 7 ul Upstate rabbit anti-H3K56Ac polyclonal antibody.  As a reference, DNA was obtained from a ChIP of unsynchronized cells with the same antibody.  The ChIP and reference samples were amplified via TLAD and labeled with cy5 and cy3 respectively, and co-hybridized to our custom nucleosomal arrays which contain oligos spanning chromosome III as well as select promoter regions from other chromosomes.

hyb_protocol: Amplified ChIP and ChIP input were mixed, purified by microcon, and hybridized to the microarrays in 3.4X SSC and 0.3% SDS for 16 hours at 55 degrees.

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with a GenePix 4000B fluorescent scanner at 5 micron resolution and image intensity data were extracted and analyzed with GenePix Pro 5.1 analysis software.

data_processing: After background correction and removal of flagged values, data was block normalized by dilation and log base 2 (Cy5/Cy3) ratios were calculated to produce the values given in the data table. The Cy5/Cy3 ratio represents the fold enrichment of the IP relative to the input, except in dye-flip samples, where it is the Cy3/Cy5 ratio.

organism: Saccharomyces cerevisiae

source_name: Mid-log H3K56Ac (unsynchronized)

label_protocol: The DNA were covalently coupled separately with either Cy5 or Cy3 monoreactive fluors in 50 mM sodium bicarbonate, pH 9.0. The Cy5 and Cy3 labelled DNAs were combined and purified with a Qiagen MinElute ERC cleanup kit and suspended in 50 µl of 3.4X SSC, 2 mg/ml of yeast tRNA, and 0.3% SDS for hybridization to the microarray.

extract_protocol: DNA was isolated from mononucleosomal cell extract via proteinase K digestion and phenol:chloroform extraction, and amplified by TLAD.

tag: Strain

source_name: 120 min

extract_protocol: Chromatin associated with the target epitope was immunoprecipitated from mononucleosomal cell extract and amplified by TLAD.


title: K56Ac cell cycle, 0 min, array replicate 3 | array na_22_10

description: BY4741 cells bearing a temperature sensitive mutation in cdc28 were arrested by shifting them from 22C to 37C for 3 hours.  To release from arrest, cold YPD media was added to shift back to 22C.  Cells were harvested after 0 minutes, crosslinked with formaldehyde (1%), washed with water and zymolyase treated.  Extracts of these cells were then digested with MNase to produce mononucleosomes, and subjected to immunoprecipitation with with 7 ul Upstate rabbit anti-H3K56Ac polyclonal antibody.  As a reference, DNA was obtained from a ChIP of unsynchronized cells with the same antibody.  The ChIP and reference samples were amplified via TLAD and labeled with cy5 and cy3 respectively, and co-hybridized to our custom nucleosomal arrays which contain oligos spanning chromosome III as well as select promoter regions from other chromosomes.

source_name: 0 min


title: K56Ac cell cycle, 140 min, array replicate 3 | array na_22_11

description: BY4741 cells bearing a temperature sensitive mutation in cdc28 were arrested by shifting them from 22C to 37C for 3 hours.  To release from arrest, cold YPD media was added to shift back to 22C.  Cells were harvested after 140 minutes, crosslinked with formaldehyde (1%), washed with water and zymolyase treated.  Extracts of these cells were then digested with MNase to produce mononucleosomes, and subjected to immunoprecipitation with with 7 ul Upstate rabbit anti-H3K56Ac polyclonal antibody.  As a reference, DNA was obtained from a ChIP of unsynchronized cells with the same antibody.  The ChIP and reference samples were amplified via TLAD and labeled with cy5 and cy3 respectively, and co-hybridized to our custom nucleosomal arrays which contain oligos spanning chromosome III as well as select promoter regions from other chromosomes.

source_name: 140 min


title: M phase turnover, 30 min, dye flip replicate | array na_28_092

description: BY4741 cells with the relevant genotype BY4741 MDY520 (MATa  ura3D  leu2D  his3D  met15D  bar1D::SpHIS5  [pGal1/10-FLAG-H3])  were arrested in M phase with Nocodazole and Benomyl at final concentrations of 10ug/ml and 30ug/ml respectively for 3 hrs at 30°C.  The cells were then induced to produce the FLAG-tagged histone H3, by the addition of galactose to a final concentration of 0.2%.  Cells were harvested after 30 minutes, crosslinked with formaldehyde (1%), washed with water and zymolyase treated.  Extracts of these cells were then digested with MNase to produce mononucleosomes, and subjected to immunoprecipitation with 20 ul Sigma anti-FLAG monoclonal antibody.  The ChIP and input samples were amplified via TLAD and labeled with cy5 and cy3 respectively, and co-hybridized to our custom nucleosomal arrays which contain oligos spanning chromosome III as well as select promoter regions from other chromosomes.

source_name: ChIP input

source_name: 30 min


title: M phase turnover, 90 min, dye flip replicate | array na_28_095

description: BY4741 cells with the relevant genotype BY4741 MDY520 (MATa  ura3D  leu2D  his3D  met15D  bar1D::SpHIS5  [pGal1/10-FLAG-H3])  were arrested in M phase with Nocodazole and Benomyl at final concentrations of 10ug/ml and 30ug/ml respectively for 3 hrs at 30°C.  The cells were then induced to produce the FLAG-tagged histone H3, by the addition of galactose to a final concentration of 0.2%.  Cells were harvested after 90 minutes, crosslinked with formaldehyde (1%), washed with water and zymolyase treated.  Extracts of these cells were then digested with MNase to produce mononucleosomes, and subjected to immunoprecipitation with 20 ul Sigma anti-FLAG monoclonal antibody.  The ChIP and input samples were amplified via TLAD and labeled with cy5 and cy3 respectively, and co-hybridized to our custom nucleosomal arrays which contain oligos spanning chromosome III as well as select promoter regions from other chromosomes.

source_name: 90 min


title: M phase turnover, 90 min, replicate 1 | array na_21_51

value: BY4741 MDY520 (MATa  ura3D  leu2D  his3D  met15D  bar1D::SpHIS5  [pGal1/10-FLAG-H3])


title: rtt109D, 90 min turnover, dye flip replicate 2 | array na_28_86

description: BY4741 cells with the relevant genotype BY4741 MDY520 (MATa  ura3D  leu2D  his3D  met15D  bar1D::SpHIS5  rtt109D::KanR  [pGal1/10-FLAG-H3]) were arrested in late G1 with alpha factor at a final concentration of 5ug/ml for 3 hrs at 30°C.  The cells were then induced to produce the FLAG-tagged histone H3, by the addition of galactose to a final concentration of 0.2%.  Cells were harvested after 90 minutes, crosslinked with formaldehyde (1%), washed with water and zymolyase treated.  Extracts of these cells were then digested with MNase to produce mononucleosomes, and subjected to immunoprecipitation with 20 ul Sigma anti-FLAG monoclonal antibody.  The ChIP and input samples were amplified via TLAD and labeled with cy5 and cy3 respectively, and co-hybridized to our custom nucleosomal arrays which contain oligos spanning chromosome III as well as select promoter regions from other chromosomes.


title: K56Ac cell cycle, 70 min, array replicate 3 | array na_22_07

description: BY4741 cells bearing a temperature sensitive mutation in cdc28 were arrested by shifting them from 22C to 37C for 3 hours.  To release from arrest, cold YPD media was added to shift back to 22C.  Cells were harvested after 70 minutes, crosslinked with formaldehyde (1%), washed with water and zymolyase treated.  Extracts of these cells were then digested with MNase to produce mononucleosomes, and subjected to immunoprecipitation with with 7 ul Upstate rabbit anti-H3K56Ac polyclonal antibody.  As a reference, DNA was obtained from a ChIP of unsynchronized cells with the same antibody.  The ChIP and reference samples were amplified via TLAD and labeled with cy5 and cy3 respectively, and co-hybridized to our custom nucleosomal arrays which contain oligos spanning chromosome III as well as select promoter regions from other chromosomes.

source_name: 70 min


title: M phase turnover, 45 min, replicate 1 | array na_21_49

description: BY4741 cells with the relevant genotype BY4741 MDY520 (MATa  ura3D  leu2D  his3D  met15D  bar1D::SpHIS5  [pGal1/10-FLAG-H3])  were arrested in M phase with Nocodazole and Benomyl at final concentrations of 10ug/ml and 30ug/ml respectively for 3 hrs at 30°C.  The cells were then induced to produce the FLAG-tagged histone H3, by the addition of galactose to a final concentration of 0.2%.  Cells were harvested after 45 minutes, crosslinked with formaldehyde (1%), washed with water and zymolyase treated.  Extracts of these cells were then digested with MNase to produce mononucleosomes, and subjected to immunoprecipitation with 20 ul Sigma anti-FLAG monoclonal antibody.  The ChIP and input samples were amplified via TLAD and labeled with cy5 and cy3 respectively, and co-hybridized to our custom nucleosomal arrays which contain oligos spanning chromosome III as well as select promoter regions from other chromosomes.

source_name: 45 min


title: K56Ac cell cycle, 160 min, array replicate 3 | array na_22_06

description: BY4741 cells bearing a temperature sensitive mutation in cdc28 were arrested by shifting them from 22C to 37C for 3 hours.  To release from arrest, cold YPD media was added to shift back to 22C.  Cells were harvested after 160 minutes, crosslinked with formaldehyde (1%), washed with water and zymolyase treated.  Extracts of these cells were then digested with MNase to produce mononucleosomes, and subjected to immunoprecipitation with with 7 ul Upstate rabbit anti-H3K56Ac polyclonal antibody.  As a reference, DNA was obtained from a ChIP of unsynchronized cells with the same antibody.  The ChIP and reference samples were amplified via TLAD and labeled with cy5 and cy3 respectively, and co-hybridized to our custom nucleosomal arrays which contain oligos spanning chromosome III as well as select promoter regions from other chromosomes.

source_name: 160 min


title: M phase turnover, 60 min, dye flip replicate | array na_28_094

description: BY4741 cells with the relevant genotype BY4741 MDY520 (MATa  ura3D  leu2D  his3D  met15D  bar1D::SpHIS5  [pGal1/10-FLAG-H3])  were arrested in M phase with Nocodazole and Benomyl at final concentrations of 10ug/ml and 30ug/ml respectively for 3 hrs at 30°C.  The cells were then induced to produce the FLAG-tagged histone H3, by the addition of galactose to a final concentration of 0.2%.  Cells were harvested after 60 minutes, crosslinked with formaldehyde (1%), washed with water and zymolyase treated.  Extracts of these cells were then digested with MNase to produce mononucleosomes, and subjected to immunoprecipitation with 20 ul Sigma anti-FLAG monoclonal antibody.  The ChIP and input samples were amplified via TLAD and labeled with cy5 and cy3 respectively, and co-hybridized to our custom nucleosomal arrays which contain oligos spanning chromosome III as well as select promoter regions from other chromosomes.

source_name: 60 min


title: M phase turnover, 120 min, dye flip replicate | array na_28_096

description: BY4741 cells with the relevant genotype BY4741 MDY520 (MATa  ura3D  leu2D  his3D  met15D  bar1D::SpHIS5  [pGal1/10-FLAG-H3])  were arrested in M phase with Nocodazole and Benomyl at final concentrations of 10ug/ml and 30ug/ml respectively for 3 hrs at 30°C.  The cells were then induced to produce the FLAG-tagged histone H3, by the addition of galactose to a final concentration of 0.2%.  Cells were harvested after 120 minutes, crosslinked with formaldehyde (1%), washed with water and zymolyase treated.  Extracts of these cells were then digested with MNase to produce mononucleosomes, and subjected to immunoprecipitation with 20 ul Sigma anti-FLAG monoclonal antibody.  The ChIP and input samples were amplified via TLAD and labeled with cy5 and cy3 respectively, and co-hybridized to our custom nucleosomal arrays which contain oligos spanning chromosome III as well as select promoter regions from other chromosomes.


title: rtt109D, 90 min turnover, dye flip replicate 1 | array na_27_23

description: BY4741 cells with the relevant genotype BY4741 MDY520 (MATa  ura3D  leu2D  his3D  met15D  bar1D::SpHIS5  rtt109D::KanR  [pGal1/10-FLAG-H3]) were arrested in late G1 with alpha factor at a final concentration of 5ug/ml of for 3 hrs at 30°C.  The cells were then induced to produce the FLAG-tagged histone H3, by the addition of galactose to a final concentration of 0.2%.  Cells were harvested after 90 minutes, crosslinked with formaldehyde (1%), washed with water and zymolyase treated.  Extracts of these cells were then digested with MNase to produce mononucleosomes, and subjected to immunoprecipitation with 20 ul Sigma anti-FLAG monoclonal antibody.  The ChIP and input samples were amplified via TLAD and labeled with cy5 and cy3 respectively, and co-hybridized to our custom nucleosomal arrays which contain oligos spanning chromosome III as well as select promoter regions from other chromosomes.


title: G1 phase turnover, 30 min | array na_26_72

description: BY4741 cells with the relevant genotype BY4741 MDY520 (MATa  ura3D  leu2D  his3D  met15D  bar1D::SpHIS5  [pGal1/10-FLAG-H3])  were arrested in late G1 with alpha factor at a final concentration of 5ug/ml of for 3 hrs at 30°C.  The cells were then induced to produce the FLAG-tagged histone H3, by the addition of galactose to a final concentration of 0.2%.  Cells were harvested after 30 minutes, crosslinked with formaldehyde (1%), washed with water and zymolyase treated.  Extracts of these cells were then digested with MNase to produce mononucleosomes, and subjected to immunoprecipitation with 20 ul Sigma anti-FLAG monoclonal antibody.  The ChIP and input samples were amplified via TLAD and labeled with cy5 and cy3 respectively, and co-hybridized to our custom nucleosomal arrays which contain oligos spanning chromosome III as well as select promoter regions from other chromosomes.


title: M phase turnover, 60 min, replicate 1 | array na_21_50


title: M phase turnover, 30 min, replicate 1 | array na_21_48


title: K56Ac cell cycle, 10 min, array replicate 2 | array na_20_91

description: BY4741 cells bearing a temperature sensitive mutation in cdc28 were arrested by shifting them from 22C to 37C for 3 hours.  To release from arrest, cold YPD media was added to shift back to 22C.  Cells were harvested after 10 minutes, crosslinked with formaldehyde (1%), washed with water and zymolyase treated.  Extracts of these cells were then digested with MNase to produce mononucleosomes, and subjected to immunoprecipitation with with 7 ul Upstate rabbit anti-H3K56Ac polyclonal antibody.  As a reference, DNA was obtained from a ChIP of unsynchronized cells with the same antibody.  The ChIP and reference samples were amplified via TLAD and labeled with cy5 and cy3 respectively, and co-hybridized to our custom nucleosomal arrays which contain oligos spanning chromosome III as well as select promoter regions from other chromosomes.

source_name: 10 min


title: M phase turnover, 120 min, replicate 1 | array na_21_52


title: K56Ac cell cycle, 100 min, array replicate 3 | array na_22_09

description: BY4741 cells bearing a temperature sensitive mutation in cdc28 were arrested by shifting them from 22C to 37C for 3 hours.  To release from arrest, cold YPD media was added to shift back to 22C.  Cells were harvested after 100 minutes, crosslinked with formaldehyde (1%), washed with water and zymolyase treated.  Extracts of these cells were then digested with MNase to produce mononucleosomes, and subjected to immunoprecipitation with with 7 ul Upstate rabbit anti-H3K56Ac polyclonal antibody.  As a reference, DNA was obtained from a ChIP of unsynchronized cells with the same antibody.  The ChIP and reference samples were amplified via TLAD and labeled with cy5 and cy3 respectively, and co-hybridized to our custom nucleosomal arrays which contain oligos spanning chromosome III as well as select promoter regions from other chromosomes.

source_name: 100 min


title: G1 phase turnover, 45 min | array na_26_73

description: BY4741 cells with the relevant genotype BY4741 MDY520 (MATa  ura3D  leu2D  his3D  met15D  bar1D::SpHIS5  [pGal1/10-FLAG-H3])  were arrested in late G1 with alpha factor at a final concentration of 5ug/ml of for 3 hrs at 30°C.  The cells were then induced to produce the FLAG-tagged histone H3, by the addition of galactose to a final concentration of 0.2%.  Cells were harvested after 45 minutes, crosslinked with formaldehyde (1%), washed with water and zymolyase treated.  Extracts of these cells were then digested with MNase to produce mononucleosomes, and subjected to immunoprecipitation with 20 ul Sigma anti-FLAG monoclonal antibody.  The ChIP and input samples were amplified via TLAD and labeled with cy5 and cy3 respectively, and co-hybridized to our custom nucleosomal arrays which contain oligos spanning chromosome III as well as select promoter regions from other chromosomes.


title: M phase turnover, 150 min, dye flip replicate | array na_28_097

description: BY4741 cells with the relevant genotype BY4741 MDY520 (MATa  ura3D  leu2D  his3D  met15D  bar1D::SpHIS5  [pGal1/10-FLAG-H3])  were arrested in M phase with Nocodazole and Benomyl at final concentrations of 10ug/ml and 30ug/ml respectively for 3 hrs at 30°C.  The cells were then induced to produce the FLAG-tagged histone H3, by the addition of galactose to a final concentration of 0.2%.  Cells were harvested after 150 minutes, crosslinked with formaldehyde (1%), washed with water and zymolyase treated.  Extracts of these cells were then digested with MNase to produce mononucleosomes, and subjected to immunoprecipitation with 20 ul Sigma anti-FLAG monoclonal antibody.  The ChIP and input samples were amplified via TLAD and labeled with cy5 and cy3 respectively, and co-hybridized to our custom nucleosomal arrays which contain oligos spanning chromosome III as well as select promoter regions from other chromosomes.

source_name: 150 min


title: G1 phase turnover, 90 min | array na_26_75

description: BY4741 cells with the relevant genotype BY4741 MDY520 (MATa  ura3D  leu2D  his3D  met15D  bar1D::SpHIS5  [pGal1/10-FLAG-H3])  were arrested in late G1 with alpha factor at a final concentration of 5ug/ml of for 3 hrs at 30°C.  The cells were then induced to produce the FLAG-tagged histone H3, by the addition of galactose to a final concentration of 0.2%.  Cells were harvested after 90 minutes, crosslinked with formaldehyde (1%), washed with water and zymolyase treated.  Extracts of these cells were then digested with MNase to produce mononucleosomes, and subjected to immunoprecipitation with 20 ul Sigma anti-FLAG monoclonal antibody.  The ChIP and input samples were amplified via TLAD and labeled with cy5 and cy3 respectively, and co-hybridized to our custom nucleosomal arrays which contain oligos spanning chromosome III as well as select promoter regions from other chromosomes.


title: K56Ac cell cycle, 90 min, array replicate 2 | array na_20_92

description: BY4741 cells bearing a temperature sensitive mutation in cdc28 were arrested by shifting them from 22C to 37C for 3 hours.  To release from arrest, cold YPD media was added to shift back to 22C.  Cells were harvested after 90 minutes, crosslinked with formaldehyde (1%), washed with water and zymolyase treated.  Extracts of these cells were then digested with MNase to produce mononucleosomes, and subjected to immunoprecipitation with with 7 ul Upstate rabbit anti-H3K56Ac polyclonal antibody.  As a reference, DNA was obtained from a ChIP of unsynchronized cells with the same antibody.  The ChIP and reference samples were amplified via TLAD and labeled with cy5 and cy3 respectively, and co-hybridized to our custom nucleosomal arrays which contain oligos spanning chromosome III as well as select promoter regions from other chromosomes.


title: K56Ac cell cycle, 80 min, array replicate 2 | array na_21_100

description: BY4741 cells bearing a temperature sensitive mutation in cdc28 were arrested by shifting them from 22C to 37C for 3 hours.  To release from arrest, cold YPD media was added to shift back to 22C.  Cells were harvested after 80 minutes, crosslinked with formaldehyde (1%), washed with water and zymolyase treated.  Extracts of these cells were then digested with MNase to produce mononucleosomes, and subjected to immunoprecipitation with with 7 ul Upstate rabbit anti-H3K56Ac polyclonal antibody.  As a reference, DNA was obtained from a ChIP of unsynchronized cells with the same antibody.  The ChIP and reference samples were amplified via TLAD and labeled with cy5 and cy3 respectively, and co-hybridized to our custom nucleosomal arrays which contain oligos spanning chromosome III as well as select promoter regions from other chromosomes.

source_name: 80 min


title: K56Ac cell cycle, 170 min, array replicate 2 | array na_20_82

description: BY4741 cells bearing a temperature sensitive mutation in cdc28 were arrested by shifting them from 22C to 37C for 3 hours.  To release from arrest, cold YPD media was added to shift back to 22C.  Cells were harvested after 170 minutes, crosslinked with formaldehyde (1%), washed with water and zymolyase treated.  Extracts of these cells were then digested with MNase to produce mononucleosomes, and subjected to immunoprecipitation with with 7 ul Upstate rabbit anti-H3K56Ac polyclonal antibody.  As a reference, DNA was obtained from a ChIP of unsynchronized cells with the same antibody.  The ChIP and reference samples were amplified via TLAD and labeled with cy5 and cy3 respectively, and co-hybridized to our custom nucleosomal arrays which contain oligos spanning chromosome III as well as select promoter regions from other chromosomes.

source_name: 170 min


title: K56Ac cell cycle, 0 min, array replicate 2 | array na_20_90

description: BY4741 cells bearing a temperature sensitive mutation in cdc28 were arrested by shifting them from 22C to 37C for 3 hours.  To release from arrest, cold YPD media was added to shift back to 22C.  Cells were harvested after 0 minutes, crosslinked with formaldehyde (1%), washed with water and zymolyase treated.  Extracts of these cells were then digested with MNase to produce mononucleosomes, and subjected to immunoprecipitation with with 7 ul Upstate rabbit anti-H3K56Ac polyclonal antibody.  As a reference, DNA was obtained from a ChIP of unsynchronized cells with the same antibody.  The ChIP and reference samples were amplified via TLAD and labeled with cy5 and cy3 respectively, and co-hybridized to our custom nucleosomal arrays which contain oligos spanning chromosome III as well as select promoter regions from other chromosomes.


title: K56Ac cell cycle, 150 min, array replicate 2 | array na_20_88

description: BY4741 cells bearing a temperature sensitive mutation in cdc28 were arrested by shifting them from 22C to 37C for 3 hours.  To release from arrest, cold YPD media was added to shift back to 22C.  Cells were harvested after 150 minutes, crosslinked with formaldehyde (1%), washed with water and zymolyase treated.  Extracts of these cells were then digested with MNase to produce mononucleosomes, and subjected to immunoprecipitation with with 7 ul Upstate rabbit anti-H3K56Ac polyclonal antibody.  As a reference, DNA was obtained from a ChIP of unsynchronized cells with the same antibody.  The ChIP and reference samples were amplified via TLAD and labeled with cy5 and cy3 respectively, and co-hybridized to our custom nucleosomal arrays which contain oligos spanning chromosome III as well as select promoter regions from other chromosomes.


title: K56Ac cell cycle, 40 min, array replicate 2 | array na_20_81

description: BY4741 cells bearing a temperature sensitive mutation in cdc28 were arrested by shifting them from 22C to 37C for 3 hours.  To release from arrest, cold YPD media was added to shift back to 22C.  Cells were harvested after 40 minutes, crosslinked with formaldehyde (1%), washed with water and zymolyase treated.  Extracts of these cells were then digested with MNase to produce mononucleosomes, and subjected to immunoprecipitation with with 7 ul Upstate rabbit anti-H3K56Ac polyclonal antibody.  As a reference, DNA was obtained from a ChIP of unsynchronized cells with the same antibody.  The ChIP and reference samples were amplified via TLAD and labeled with cy5 and cy3 respectively, and co-hybridized to our custom nucleosomal arrays which contain oligos spanning chromosome III as well as select promoter regions from other chromosomes.

source_name: 40 min


title: K56Ac cell cycle, 60 min, array replicate 3 | array na_22_05

description: BY4741 cells bearing a temperature sensitive mutation in cdc28 were arrested by shifting them from 22C to 37C for 3 hours.  To release from arrest, cold YPD media was added to shift back to 22C.  Cells were harvested after 60 minutes, crosslinked with formaldehyde (1%), washed with water and zymolyase treated.  Extracts of these cells were then digested with MNase to produce mononucleosomes, and subjected to immunoprecipitation with with 7 ul Upstate rabbit anti-H3K56Ac polyclonal antibody.  As a reference, DNA was obtained from a ChIP of unsynchronized cells with the same antibody.  The ChIP and reference samples were amplified via TLAD and labeled with cy5 and cy3 respectively, and co-hybridized to our custom nucleosomal arrays which contain oligos spanning chromosome III as well as select promoter regions from other chromosomes.

source_name: Mid-log H3K56Ac (unsynchronized)


title: K56Ac cell cycle, 70 min, array replicate 2 | array na_20_89

description: BY4741 cells bearing a temperature sensitive mutation in cdc28 were arrested by shifting them from 22C to 37C for 3 hours.  To release from arrest, cold YPD media was added to shift back to 22C.  Cells were harvested after 70 minutes, crosslinked with formaldehyde (1%), washed with water and zymolyase treated.  Extracts of these cells were then digested with MNase to produce mononucleosomes, and subjected to immunoprecipitation with with 7 ul Upstate rabbit anti-H3K56Ac polyclonal antibody.  As a reference, DNA was obtained from a ChIP of unsynchronized cells with the same antibody.  The ChIP and reference samples were amplified via TLAD and labeled with cy5 and cy3 respectively, and co-hybridized to our custom nucleosomal arrays which contain oligos spanning chromosome III as well as select promoter regions from other chromosomes.


title: M phase turnover, 150 min, replicate 1 | array na_21_53


title: K56Ac cell cycle, 60 min, array replicate 2 | array na_20_77


title: K56Ac cell cycle, 130 min, array replicate 2 | array na_20_73

description: BY4741 cells bearing a temperature sensitive mutation in cdc28 were arrested by shifting them from 22C to 37C for 3 hours.  To release from arrest, cold YPD media was added to shift back to 22C.  Cells were harvested after 130 minutes, crosslinked with formaldehyde (1%), washed with water and zymolyase treated.  Extracts of these cells were then digested with MNase to produce mononucleosomes, and subjected to immunoprecipitation with with 7 ul Upstate rabbit anti-H3K56Ac polyclonal antibody.  As a reference, DNA was obtained from a ChIP of unsynchronized cells with the same antibody.  The ChIP and reference samples were amplified via TLAD and labeled with cy5 and cy3 respectively, and co-hybridized to our custom nucleosomal arrays which contain oligos spanning chromosome III as well as select promoter regions from other chromosomes.

source_name: 130 min


title: K56Ac cell cycle, 140 min, array replicate 2 | array na_20_80

description: BY4741 cells bearing a temperature sensitive mutation in cdc28 were arrested by shifting them from 22C to 37C for 3 hours.  To release from arrest, cold YPD media was added to shift back to 22C.  Cells were harvested after 140 minutes, crosslinked with formaldehyde (1%), washed with water and zymolyase treated.  Extracts of these cells were then digested with MNase to produce mononucleosomes, and subjected to immunoprecipitation with with 7 ul Upstate rabbit anti-H3K56Ac polyclonal antibody.  As a reference, DNA was obtained from a ChIP of unsynchronized cells with the same antibody.  The ChIP and reference samples were amplified via TLAD and labeled with cy5 and cy3 respectively, and co-hybridized to our custom nucleosomal arrays which contain oligos spanning chromosome III as well as select promoter regions from other chromosomes.


title: K56Ac cell cycle, 160 min, array replicate 2 | array na_20_74

description: BY4741 cells bearing a temperature sensitive mutation in cdc28 were arrested by shifting them from 22C to 37C for 3 hours.  To release from arrest, cold YPD media was added to shift back to 22C.  Cells were harvested after 160 minutes, crosslinked with formaldehyde (1%), washed with water and zymolyase treated.  Extracts of these cells were then digested with MNase to produce mononucleosomes, and subjected to immunoprecipitation with with 7 ul Upstate rabbit anti-H3K56Ac polyclonal antibody.  As a reference, DNA was obtained from a ChIP of unsynchronized cells with the same antibody.  The ChIP and reference samples were amplified via TLAD and labeled with cy5 and cy3 respectively, and co-hybridized to our custom nucleosomal arrays which contain oligos spanning chromosome III as well as select promoter regions from other chromosomes.


title: K56Ac cell cycle, 100 min, array replicate 2 | array na_20_78


title: K56Ac cell cycle, 110 min, array replicate 2 | array na_20_76

description: BY4741 cells bearing a temperature sensitive mutation in cdc28 were arrested by shifting them from 22C to 37C for 3 hours.  To release from arrest, cold YPD media was added to shift back to 22C.  Cells were harvested after 110 minutes, crosslinked with formaldehyde (1%), washed with water and zymolyase treated.  Extracts of these cells were then digested with MNase to produce mononucleosomes, and subjected to immunoprecipitation with with 7 ul Upstate rabbit anti-H3K56Ac polyclonal antibody.  As a reference, DNA was obtained from a ChIP of unsynchronized cells with the same antibody.  The ChIP and reference samples were amplified via TLAD and labeled with cy5 and cy3 respectively, and co-hybridized to our custom nucleosomal arrays which contain oligos spanning chromosome III as well as select promoter regions from other chromosomes.

source_name: 110 min


title: K56Ac cell cycle, 80 min, array replicate 1 | array na_19_76


title: K56Ac cell cycle, 60 min, array replicate 1 | array na_19_66


title: K56Ac cell cycle, 120 min, array replicate 2 | array na_20_79

description: BY4741 cells bearing a temperature sensitive mutation in cdc28 were arrested by shifting them from 22C to 37C for 3 hours.  To release from arrest, cold YPD media was added to shift back to 22C.  Cells were harvested after 120 minutes, crosslinked with formaldehyde (1%), washed with water and zymolyase treated.  Extracts of these cells were then digested with MNase to produce mononucleosomes, and subjected to immunoprecipitation with with 7 ul Upstate rabbit anti-H3K56Ac polyclonal antibody.  As a reference, DNA was obtained from a ChIP of unsynchronized cells with the same antibody.  The ChIP and reference samples were amplified via TLAD and labeled with cy5 and cy3 respectively, and co-hybridized to our custom nucleosomal arrays which contain oligos spanning chromosome III as well as select promoter regions from other chromosomes.

source_name: 120 min


title: K56Ac cell cycle, 150 min, array replicate 1 | array na_19_65


title: K56Ac cell cycle, 100 min, array replicate 1 | array na_19_70

description: BY4741 cells bearing a temperature sensitive mutation in cdc28 were arrested by shifting them from 22C to 37C for 3 hours.  To release from arrest, cold YPD media was added to shift back to 22C.  Cells were harvested after 100 minutes, crosslinked with formaldehyde (1%), washed with water and zymolyase treated.  Extracts of these cells were then digested with MNase to produce mononucleosomes, and subjected to immunoprecipitation with with 7 ul Upstate rabbit anti-H3K56Ac polyclonal antibody.  As a reference, DNA was obtained from a ChIP of unsynchronized cells with the same antibody.  The ChIP and reference samples were amplified via TLAD and labeled with cy5 and cy3 respectively, and co-hybridized to our custom nucleosomal arrays which contain oligos spanning chromosome III as well as select promoter regions from other chromosomes.


title: K56Ac cell cycle, 0 min, array replicate 1 | array na_19_74

source_name: 0 min


title: K56Ac cell cycle, 40 min, array replicate 1 | array na_19_78


title: K56Ac cell cycle, 120 min, array replicate 1 | array na_19_73


title: K56Ac cell cycle, 70 min, array replicate 1 | array na_19_68


title: K56Ac cell cycle, 50 min, array replicate 1 | array na_19_72

description: BY4741 cells bearing a temperature sensitive mutation in cdc28 were arrested by shifting them from 22C to 37C for 3 hours.  To release from arrest, cold YPD media was added to shift back to 22C.  Cells were harvested after 50 minutes, crosslinked with formaldehyde (1%), washed with water and zymolyase treated.  Extracts of these cells were then digested with MNase to produce mononucleosomes, and subjected to immunoprecipitation with with 7 ul Upstate rabbit anti-H3K56Ac polyclonal antibody.  As a reference, DNA was obtained from a ChIP of unsynchronized cells with the same antibody.  The ChIP and reference samples were amplified via TLAD and labeled with cy5 and cy3 respectively, and co-hybridized to our custom nucleosomal arrays which contain oligos spanning chromosome III as well as select promoter regions from other chromosomes.

source_name: 50 min


title: K56Ac cell cycle, 30 min, array replicate 1 | array na_19_64

description: BY4741 cells bearing a temperature sensitive mutation in cdc28 were arrested by shifting them from 22C to 37C for 3 hours.  To release from arrest, cold YPD media was added to shift back to 22C.  Cells were harvested after 30 minutes, crosslinked with formaldehyde (1%), washed with water and zymolyase treated.  Extracts of these cells were then digested with MNase to produce mononucleosomes, and subjected to immunoprecipitation with with 7 ul Upstate rabbit anti-H3K56Ac polyclonal antibody.  As a reference, DNA was obtained from a ChIP of unsynchronized cells with the same antibody.  The ChIP and reference samples were amplified via TLAD and labeled with cy5 and cy3 respectively, and co-hybridized to our custom nucleosomal arrays which contain oligos spanning chromosome III as well as select promoter regions from other chromosomes.

source_name: 30 min


title: Mid-log H3K56Ac (unsynchronized), biological replicate 2, Grunstein Ab | array na_18_68

description: BY4741 cells bearing a temperature sensitive mutation in cdc28 were growin in mid-log, crosslinked with formaldehyde (1%), washed with water and zymolyase treated.  Extracts of these cells were then digested with MNase to produce mononucleosomes, and subjected to immunoprecipitation with with 25 ul rabbit anti-H3K56Ac polyclonal antibody from the Grunstein Lab.  The ChIP and input samples were amplified via TLAD and labeled with cy5 and cy3 respectively, and co-hybridized to our custom nucleosomal arrays which contain oligos spanning chromosome III as well as select promoter regions from other chromosomes.  Second biological replicate.

source_name: ChIP input


title: K56Ac cell cycle, 30 min, array replicate 2 | array na_20_72


title: K56Ac cell cycle, 140 min, array replicate 1 | array na_19_77

source_name: 140 min


title: K56Ac cell cycle, 90 min, array replicate 1 | array na_19_69

description: BY4741 cells bearing a temperature sensitive mutation in cdc28 were arrested by shifting them from 22C to 37C for 3 hours.  To release from arrest, cold YPD media was added to shift back to 22C.  Cells were harvested after 90 minutes, crosslinked with formaldehyde (1%), washed with water and zymolyase treated.  Extracts of these cells were then digested with MNase to produce mononucleosomes, and subjected to immunoprecipitation with with 7 ul Upstate rabbit anti-H3K56Ac polyclonal antibody.  As a reference, DNA was obtained from a ChIP of unsynchronized cells with the same antibody.  The ChIP and reference samples were amplified via TLAD and labeled with cy5 and cy3 respectively, and co-hybridized to our custom nucleosomal arrays which contain oligos spanning chromosome III as well as select promoter regions from other chromosomes.

source_name: 90 min


title: Mid-log H3K56Ac (unsynchronized), biological replicate 1, array replicate 2, Upstate Ab | array na_19_25

description: BY4741 cells bearing a temperature sensitive mutation in cdc28 were growin in mid-log, crosslinked with formaldehyde (1%), washed with water and zymolyase treated.  Extracts of these cells were then digested with MNase to produce mononucleosomes, and subjected to immunoprecipitation with with 10 ul Upstate rabbit anti-H3K56Ac polyclonal antibody.  The ChIP and input samples were amplified via TLAD and labeled with cy5 and cy3 respectively, and co-hybridized to our custom nucleosomal arrays which contain oligos spanning chromosome III as well as select promoter regions from other chromosomes.  First biological replicate, second array replicate.


title: K56Ac cell cycle, 160 min, array replicate 1 | array na_19_75

source_name: 160 min


title: Mid-log H3K56Ac (unsynchronized), biological replicate 1, Grunstein Ab | array na_19_26

description: BY4741 cells bearing a temperature sensitive mutation in cdc28 were growin in mid-log, crosslinked with formaldehyde (1%), washed with water and zymolyase treated.  Extracts of these cells were then digested with MNase to produce mononucleosomes, and subjected to immunoprecipitation with with 20 ul rabbit anti-H3K56Ac polyclonal antibody from the Grunstein Lab.  The ChIP and input samples were amplified via TLAD and labeled with cy5 and cy3 respectively, and co-hybridized to our custom nucleosomal arrays which contain oligos spanning chromosome III as well as select promoter regions from other chromosomes.  First biological replicate.


title: K56Ac cell cycle, 50 min, array replicate 2 | array na_20_75


title: Mid-log H3K56Ac (unsynchronized), biological replicate 2, array replicate 2 Upstate Ab | array na_18_67

description: BY4741 cells bearing a temperature sensitive mutation in cdc28 were growin in mid-log, crosslinked with formaldehyde (1%), washed with water and zymolyase treated.  Extracts of these cells were then digested with MNase to produce mononucleosomes, and subjected to immunoprecipitation with with 4 ul Upstate rabbit anti-H3K56Ac polyclonal antibody.  The ChIP and input samples were amplified via TLAD and labeled with cy5 and cy3 respectively, and co-hybridized to our custom nucleosomal arrays which contain oligos spanning chromosome III as well as select promoter regions from other chromosomes.  Second biological replicate, second array replicate.


title: K56Ac cell cycle, 130 min, array replicate 1 | array na_19_61


title: Expt VIII, vps75D, 90 min turnover | array na_33_36

description: Strain PKY4231 was cultured in YPA raffinose medium supplemented with 300 ug/ml hygromycin and treated for 3 hrs with alpha factor (5 ?g/ml) to induce G1 arrest. Expression of the plasmid-borne FLAG-tagged H3 was induced for 90 min by the addition of 0.2% galactose.  Cells were then crosslinked with formaldehyde (1%), washed with water and zymolyase treated.  Extracts of these cells were then digested with MNase to produce mononucleosomes, and subjected to immunoprecipitation with 20 ul Sigma anti-FLAG monoclonal antibody.  The ChIP and input samples were amplified via TLAD and labeled with cy5 and cy3, respectively, and co-hybridized to our custom nucleosomal arrays which contain oligos spanning chromosome III as well as select promoter regions from other chromosomes.

source_name: vps75D, Gal90', anti-FLAG IP

source_name: vps75D, Gal90', input


title: Mid-log H3K56Ac (unsynchronized), biological replicate 2, array replicate 1, Upstate Ab | array na_18_37

description: BY4741 cells bearing a temperature sensitive mutation in cdc28 were growin in mid-log, crosslinked with formaldehyde (1%), washed with water and zymolyase treated.  Extracts of these cells were then digested with MNase to produce mononucleosomes, and subjected to immunoprecipitation with with 4 ul Upstate rabbit anti-H3K56Ac polyclonal antibody.  The ChIP and input samples were amplified via TLAD and labeled with cy5 and cy3 respectively, and co-hybridized to our custom nucleosomal arrays which contain oligos spanning chromosome III as well as select promoter regions from other chromosomes.  Second biological replicate, first array replicate.


title: Expt VIII, vps75D, 90 min turnover | array na_33_38


title: Expt IV, vps75D, 90 min turnover | array na_30_155


title: K56Ac cell cycle, 170 min, array replicate 1 | array na_19_67

description: BY4741 cells bearing a temperature sensitive mutation in cdc28 were arrested by shifting them from 22C to 37C for 3 hours.  To release from arrest, cold YPD media was added to shift back to 22C.  Cells were harvested after 170 minutes, crosslinked with formaldehyde (1%), washed with water and zymolyase treated.  Extracts of these cells were then digested with MNase to produce mononucleosomes, and subjected to immunoprecipitation with with 7 ul Upstate rabbit anti-H3K56Ac polyclonal antibody.  As a reference, DNA was obtained from a ChIP of unsynchronized cells with the same antibody.  The ChIP and reference samples were amplified via TLAD and labeled with cy5 and cy3 respectively, and co-hybridized to our custom nucleosomal arrays which contain oligos spanning chromosome III as well as select promoter regions from other chromosomes.


title: K56Ac cell cycle, 110 min, array replicate 1 | array na_19_62


title: rtt109D, 90 min turnover, replicate 2 | array na_28_85

description: BY4741 cells with the relevant genotype BY4741 MDY520 (MATa  ura3D  leu2D  his3D  met15D  bar1D::SpHIS5  rtt109D::KanR  [pGal1/10-FLAG-H3]) were arrested in late G1 with alpha factor at a final concentration of 5ug/ml for 3 hrs at 30°C.  The cells were then induced to produce the FLAG-tagged histone H3, by the addition of galactose to a final concentration of 0.2%.  Cells were harvested after 90 minutes, crosslinked with formaldehyde (1%), washed with water and zymolyase treated.  Extracts of these cells were then digested with MNase to produce mononucleosomes, and subjected to immunoprecipitation with 20 ul Sigma anti-FLAG monoclonal antibody.  The ChIP and input samples were amplified via TLAD and labeled with cy3 and cy5 respectively, and co-hybridized to our custom nucleosomal arrays which contain oligos spanning chromosome III as well as select promoter regions from other chromosomes.


title: Mid-log H3K56Ac (unsynchronized), biological replicate 1, array replicate 1, Upstate Ab | array na_18_26

description: BY4741 cells bearing a temperature sensitive mutation in cdc28 were growin in mid-log, crosslinked with formaldehyde (1%), washed with water and zymolyase treated.  Extracts of these cells were then digested with MNase to produce mononucleosomes, and subjected to immunoprecipitation with with 10 ul Upstate rabbit anti-H3K56Ac polyclonal antibody.  The ChIP and input samples were amplified via TLAD and labeled with cy5 and cy3 respectively, and co-hybridized to our custom nucleosomal arrays which contain oligos spanning chromosome III as well as select promoter regions from other chromosomes.  First biological replicate, first array replicate.


title: K56Ac cell cycle, 10 min, array replicate 1 | array na_19_63

description: BY4741 cells bearing a temperature sensitive mutation in cdc28 were arrested by shifting them from 22C to 37C for 3 hours.  To release from arrest, cold YPD media was added to shift back to 22C.  Cells were harvested after 10 minutes, crosslinked with formaldehyde (1%), washed with water and zymolyase treated.  Extracts of these cells were then digested with MNase to produce mononucleosomes, and subjected to immunoprecipitation with with 7 ul Upstate rabbit anti-H3K56Ac polyclonal antibody.  As a reference, DNA was obtained from a ChIP of unsynchronized cells with the same antibody.  The ChIP and reference samples were amplified via TLAD and labeled with cy5 and cy3 respectively, and co-hybridized to our custom nucleosomal arrays which contain oligos spanning chromosome III as well as select promoter regions from other chromosomes.

source_name: 10 min


title: M phase turnover, 30 min, replicate 2 | array na_28_098

description: BY4741 cells with the relevant genotype BY4741 MDY520 (MATa  ura3D  leu2D  his3D  met15D  bar1D::SpHIS5  [pGal1/10-FLAG-H3])  were arrested in M phase with Nocodazole and Benomyl at final concentrations of 10ug/ml and 30ug/ml respectively for 3 hrs at 30°C.  The cells were then induced to produce the FLAG-tagged histone H3, by the addition of galactose to a final concentration of 0.2%.  Cells were harvested after 30 minutes, crosslinked with formaldehyde (1%), washed with water and zymolyase treated.  Extracts of these cells were then digested with MNase to produce mononucleosomes, and subjected to immunoprecipitation with 20 ul Sigma anti-FLAG monoclonal antibody.  The ChIP and input samples were amplified via TLAD and labeled with cy3 and cy5 respectively, and co-hybridized to our custom nucleosomal arrays which contain oligos spanning chromosome III as well as select promoter regions from other chromosomes.


title: Expt V, vps75D, 90 min turnover | array na_30_247


title: Mid-log H3K56Ac (unsynchronized), biological replicate 3, Grunstein Ab | array na_18_61

description: BY4741 cells bearing a temperature sensitive mutation in cdc28 were growin in mid-log, crosslinked with formaldehyde (1%), washed with water and zymolyase treated.  Extracts of these cells were then digested with MNase to produce mononucleosomes, and subjected to immunoprecipitation with with 25 ul rabbit anti-H3K56Ac polyclonal antibody from the Grunstein Lab.  The ChIP and input samples were amplified via TLAD and labeled with cy5 and cy3 respectively, and co-hybridized to our custom nucleosomal arrays which contain oligos spanning chromosome III as well as select promoter regions from other chromosomes.  Third biological replicate.


title: M phase turnover, 120 min, replicate 2 | array na_30_128

description: BY4741 cells with the relevant genotype BY4741 MDY520 (MATa  ura3D  leu2D  his3D  met15D  bar1D::SpHIS5  [pGal1/10-FLAG-H3])  were arrested in M phase with Nocodazole and Benomyl at final concentrations of 10ug/ml and 30ug/ml respectively for 3 hrs at 30°C.  The cells were then induced to produce the FLAG-tagged histone H3, by the addition of galactose to a final concentration of 0.2%.  Cells were harvested after 120 minutes, crosslinked with formaldehyde (1%), washed with water and zymolyase treated.  Extracts of these cells were then digested with MNase to produce mononucleosomes, and subjected to immunoprecipitation with 20 ul Sigma anti-FLAG monoclonal antibody.  The ChIP and input samples were amplified via TLAD and labeled with cy3 and cy5 respectively, and co-hybridized to our custom nucleosomal arrays which contain oligos spanning chromosome III as well as select promoter regions from other chromosomes.


title: M phase turnover, 45 min, replicate 2 | array na_28_099

description: BY4741 cells with the relevant genotype BY4741 MDY520 (MATa  ura3D  leu2D  his3D  met15D  bar1D::SpHIS5  [pGal1/10-FLAG-H3])  were arrested in M phase with Nocodazole and Benomyl at final concentrations of 10ug/ml and 30ug/ml respectively for 3 hrs at 30°C.  The cells were then induced to produce the FLAG-tagged histone H3, by the addition of galactose to a final concentration of 0.2%.  Cells were harvested after 45 minutes, crosslinked with formaldehyde (1%), washed with water and zymolyase treated.  Extracts of these cells were then digested with MNase to produce mononucleosomes, and subjected to immunoprecipitation with 20 ul Sigma anti-FLAG monoclonal antibody.  The ChIP and input samples were amplified via TLAD and labeled with cy3 and cy5 respectively, and co-hybridized to our custom nucleosomal arrays which contain oligos spanning chromosome III as well as select promoter regions from other chromosomes.

source_name: 45 min


title: M phase turnover, 150 min, replicate 2 | array na_30_129

description: BY4741 cells with the relevant genotype BY4741 MDY520 (MATa  ura3D  leu2D  his3D  met15D  bar1D::SpHIS5  [pGal1/10-FLAG-H3])  were arrested in M phase with Nocodazole and Benomyl at final concentrations of 10ug/ml and 30ug/ml respectively for 3 hrs at 30°C.  The cells were then induced to produce the FLAG-tagged histone H3, by the addition of galactose to a final concentration of 0.2%.  Cells were harvested after 150 minutes, crosslinked with formaldehyde (1%), washed with water and zymolyase treated.  Extracts of these cells were then digested with MNase to produce mononucleosomes, and subjected to immunoprecipitation with 20 ul Sigma anti-FLAG monoclonal antibody.  The ChIP and input samples were amplified via TLAD and labeled with cy3 and cy5 respectively, and co-hybridized to our custom nucleosomal arrays which contain oligos spanning chromosome III as well as select promoter regions from other chromosomes.

source_name: 150 min


title: G1 phase turnover, 60 min, dye flip replicate | array na_26_79

description: BY4741 cells with the relevant genotype BY4741 MDY520 (MATa  ura3D  leu2D  his3D  met15D  bar1D::SpHIS5  [pGal1/10-FLAG-H3])  were arrested in late G1 with alpha factor at a final concentration of 5ug/ml of for 3 hrs at 30°C.  The cells were then induced to produce the FLAG-tagged histone H3, by the addition of galactose to a final concentration of 0.2%.  Cells were harvested after 60 minutes, crosslinked with formaldehyde (1%), washed with water and zymolyase treated.  Extracts of these cells were then digested with MNase to produce mononucleosomes, and subjected to immunoprecipitation with 20 ul Sigma anti-FLAG monoclonal antibody.  The ChIP and input samples were amplified via TLAD and labeled with cy3 and cy5 respectively, and co-hybridized to our custom nucleosomal arrays which contain oligos spanning chromosome III as well as select promoter regions from other chromosomes.

source_name: 60 min


title: G1 phase turnover, 90 min, dye flip replicate | array na_26_80

description: BY4741 cells with the relevant genotype BY4741 MDY520 (MATa  ura3D  leu2D  his3D  met15D  bar1D::SpHIS5  [pGal1/10-FLAG-H3])  were arrested in late G1 with alpha factor at a final concentration of 5ug/ml of for 3 hrs at 30°C.  The cells were then induced to produce the FLAG-tagged histone H3, by the addition of galactose to a final concentration of 0.2%.  Cells were harvested after 90 minutes, crosslinked with formaldehyde (1%), washed with water and zymolyase treated.  Extracts of these cells were then digested with MNase to produce mononucleosomes, and subjected to immunoprecipitation with 20 ul Sigma anti-FLAG monoclonal antibody.  The ChIP and input samples were amplified via TLAD and labeled with cy3 and cy5 respectively, and co-hybridized to our custom nucleosomal arrays which contain oligos spanning chromosome III as well as select promoter regions from other chromosomes.


title: rtt109D, 90 min turnover, replicate 1 | array na_27_24

description: BY4741 cells with the relevant genotype BY4741 MDY520 (MATa  ura3D  leu2D  his3D  met15D  bar1D::SpHIS5  rtt109D::KanR  [pGal1/10-FLAG-H3]) were arrested in late G1 with alpha factor at a final concentration of 5ug/ml of for 3 hrs at 30°C.  The cells were then induced to produce the FLAG-tagged histone H3, by the addition of galactose to a final concentration of 0.2%.  Cells were harvested after 90 minutes, crosslinked with formaldehyde (1%), washed with water and zymolyase treated.  Extracts of these cells were then digested with MNase to produce mononucleosomes, and subjected to immunoprecipitation with 20 ul Sigma anti-FLAG monoclonal antibody.  The ChIP and input samples were amplified via TLAD and labeled with cy3 and cy5 respectively, and co-hybridized to our custom nucleosomal arrays which contain oligos spanning chromosome III as well as select promoter regions from other chromosomes.


title: M phase turnover, 90 min, replicate 2 | array na_30_127

description: BY4741 cells with the relevant genotype BY4741 MDY520 (MATa  ura3D  leu2D  his3D  met15D  bar1D::SpHIS5  [pGal1/10-FLAG-H3])  were arrested in M phase with Nocodazole and Benomyl at final concentrations of 10ug/ml and 30ug/ml respectively for 3 hrs at 30°C.  The cells were then induced to produce the FLAG-tagged histone H3, by the addition of galactose to a final concentration of 0.2%.  Cells were harvested after 90 minutes, crosslinked with formaldehyde (1%), washed with water and zymolyase treated.  Extracts of these cells were then digested with MNase to produce mononucleosomes, and subjected to immunoprecipitation with 20 ul Sigma anti-FLAG monoclonal antibody.  The ChIP and input samples were amplified via TLAD and labeled with cy3 and cy5 respectively, and co-hybridized to our custom nucleosomal arrays which contain oligos spanning chromosome III as well as select promoter regions from other chromosomes.


title: M phase turnover, 60 min, replicate 2 | array na_30_126

description: BY4741 cells with the relevant genotype BY4741 MDY520 (MATa  ura3D  leu2D  his3D  met15D  bar1D::SpHIS5  [pGal1/10-FLAG-H3])  were arrested in M phase with Nocodazole and Benomyl at final concentrations of 10ug/ml and 30ug/ml respectively for 3 hrs at 30°C.  The cells were then induced to produce the FLAG-tagged histone H3, by the addition of galactose to a final concentration of 0.2%.  Cells were harvested after 60 minutes, crosslinked with formaldehyde (1%), washed with water and zymolyase treated.  Extracts of these cells were then digested with MNase to produce mononucleosomes, and subjected to immunoprecipitation with 20 ul Sigma anti-FLAG monoclonal antibody.  The ChIP and input samples were amplified via TLAD and labeled with cy3 and cy5 respectively, and co-hybridized to our custom nucleosomal arrays which contain oligos spanning chromosome III as well as select promoter regions from other chromosomes.


title: Synchronized cells, 160 min, biological replicate F | array yoG_19B

description: BY4741 cells bearing a temperature sensitive mutation in cdc28 were arrested by shifting them from 22C to 37C for 3 hours.  To release from arrest, cold YPD media was added to shift back to 22C.  Cells were harvested after 160 minutes, centrifuged at 3000 x rpm for 2 minutes, and flash-frozen on nitrogen.  mRNA was isolated and labeled with Cy5 fluorescent dye (red).  mRNA from unarrested cells growing in mid-log was isolated and labeled with Cy3 fluorescent dye (green).  These two probes were mixed together and hybridized to microarrays printed with oligonucleotides probes corresponding to each ORF in the yeast genome.

hyb_protocol: Labeled samples were combined, concentrated in Microcon YM-30 columns, and hybridized to the microarrays in 3.4X SSC and 0.3% SDS for 16 hours at 65 degrees.

data_processing: After background correction and removal of flagged values, data was block normalized by dilation and log base 2 expression (Cy5/Cy3) ratios were calculated to produce the values given in the data table.  The Cy5/Cy3 ratio represents the fold change in expression level for the indicated time point relative to unsynchronized cells growing in mid-log phase.

source_name: Mid-log mRNA (unsynchronized)

label_protocol: The mRNA was reverse-transcribed, incorporating amino-allyl dUTP and then coupled with Cy3 NHS ester, and cleaned up with the Qiagen MinElute kit.

extract_protocol: Cells were lysed in a buffered SDS solution and extracted twice with hot phenol and once with chloroform, and then precipiated with 0.1 volume sodium acetate and 2.5 volumes of 100% ethanol.  Total RNA pellets were washed and resuspended, and mRNA was purified using the Qiagen Oligotex kit following manuf. instructions.

label_protocol: The mRNA was reverse-transcribed, incorporating amino-allyl dUTP and then coupled with Cy5 NHS ester, and cleaned up with the Qiagen MinElute kit.


title: K56Ac cell cycle, 80 min, array replicate 3 | array na_22_13

description: BY4741 cells bearing a temperature sensitive mutation in cdc28 were arrested by shifting them from 22C to 37C for 3 hours.  To release from arrest, cold YPD media was added to shift back to 22C.  Cells were harvested after 80 minutes, crosslinked with formaldehyde (1%), washed with water and zymolyase treated.  Extracts of these cells were then digested with MNase to produce mononucleosomes, and subjected to immunoprecipitation with with 7 ul Upstate rabbit anti-H3K56Ac polyclonal antibody.  As a reference, DNA was obtained from a ChIP of unsynchronized cells with the same antibody.  The ChIP and reference samples were amplified via TLAD and labeled with cy5 and cy3 respectively, and co-hybridized to our custom nucleosomal arrays which contain oligos spanning chromosome III as well as select promoter regions from other chromosomes.

source_name: Mid-log H3K56Ac (unsynchronized)

source_name: 80 min


title: G1 phase turnover, 30 min, dye flip replicate | array na_26_78

description: BY4741 cells with the relevant genotype BY4741 MDY520 (MATa  ura3D  leu2D  his3D  met15D  bar1D::SpHIS5  [pGal1/10-FLAG-H3])  were arrested in late G1 with alpha factor at a final concentration of 5ug/ml of for 3 hrs at 30°C.  The cells were then induced to produce the FLAG-tagged histone H3, by the addition of galactose to a final concentration of 0.2%.  Cells were harvested after 30 minutes, crosslinked with formaldehyde (1%), washed with water and zymolyase treated.  Extracts of these cells were then digested with MNase to produce mononucleosomes, and subjected to immunoprecipitation with 20 ul Sigma anti-FLAG monoclonal antibody.  The ChIP and input samples were amplified via TLAD and labeled with cy3 and cy5 respectively, and co-hybridized to our custom nucleosomal arrays which contain oligos spanning chromosome III as well as select promoter regions from other chromosomes.


title: Synchronized cells, 40 min, biological replicate F | array yoG_15B

description: BY4741 cells bearing a temperature sensitive mutation in cdc28 were arrested by shifting them from 22C to 37C for 3 hours.  To release from arrest, cold YPD media was added to shift back to 22C.  Cells were harvested after 40 minutes, centrifuged at 3000 x rpm for 2 minutes, and flash-frozen on nitrogen.  mRNA was isolated and labeled with Cy5 fluorescent dye (red).  mRNA from unarrested cells growing in mid-log was isolated and labeled with Cy3 fluorescent dye (green).  These two probes were mixed together and hybridized to microarrays printed with oligonucleotides probes corresponding to each ORF in the yeast genome.

source_name: 40 min


title: Synchronized cells, 20 min, biological replicate F | array yoG_63T

description: BY4741 cells bearing a temperature sensitive mutation in cdc28 were arrested by shifting them from 22C to 37C for 3 hours.  To release from arrest, cold YPD media was added to shift back to 22C.  Cells were harvested after 20 minutes, centrifuged at 3000 x rpm for 2 minutes, and flash-frozen on nitrogen.  mRNA was isolated and labeled with Cy5 fluorescent dye (red).  mRNA from unarrested cells growing in mid-log was isolated and labeled with Cy3 fluorescent dye (green).  These two probes were mixed together and hybridized to microarrays printed with oligonucleotides probes corresponding to each ORF in the yeast genome.

source_name: 20 min


title: Synchronized cells, 70 min, biological replicate F | array yoG_16T

description: BY4741 cells bearing a temperature sensitive mutation in cdc28 were arrested by shifting them from 22C to 37C for 3 hours.  To release from arrest, cold YPD media was added to shift back to 22C.  Cells were harvested after 70 minutes, centrifuged at 3000 x rpm for 2 minutes, and flash-frozen on nitrogen.  mRNA was isolated and labeled with Cy5 fluorescent dye (red).  mRNA from unarrested cells growing in mid-log was isolated and labeled with Cy3 fluorescent dye (green).  These two probes were mixed together and hybridized to microarrays printed with oligonucleotides probes corresponding to each ORF in the yeast genome.

source_name: 70 min


title: Synchronized cells, 120 min, biological replicate F | array yoG_18T

description: BY4741 cells bearing a temperature sensitive mutation in cdc28 were arrested by shifting them from 22C to 37C for 3 hours.  To release from arrest, cold YPD media was added to shift back to 22C.  Cells were harvested after 120 minutes, centrifuged at 3000 x rpm for 2 minutes, and flash-frozen on nitrogen.  mRNA was isolated and labeled with Cy5 fluorescent dye (red).  mRNA from unarrested cells growing in mid-log was isolated and labeled with Cy3 fluorescent dye (green).  These two probes were mixed together and hybridized to microarrays printed with oligonucleotides probes corresponding to each ORF in the yeast genome.

source_name: 120 min


title: K56Ac cell cycle, 130 min, array replicate 3 | array na_22_21

description: BY4741 cells bearing a temperature sensitive mutation in cdc28 were arrested by shifting them from 22C to 37C for 3 hours.  To release from arrest, cold YPD media was added to shift back to 22C.  Cells were harvested after 130 minutes, crosslinked with formaldehyde (1%), washed with water and zymolyase treated.  Extracts of these cells were then digested with MNase to produce mononucleosomes, and subjected to immunoprecipitation with with 7 ul Upstate rabbit anti-H3K56Ac polyclonal antibody.  As a reference, DNA was obtained from a ChIP of unsynchronized cells with the same antibody.  The ChIP and reference samples were amplified via TLAD and labeled with cy5 and cy3 respectively, and co-hybridized to our custom nucleosomal arrays which contain oligos spanning chromosome III as well as select promoter regions from other chromosomes.

source_name: 130 min


title: Synchronized cells, 140 min, biological replicate F | array yoG_66T

description: BY4741 cells bearing a temperature sensitive mutation in cdc28 were arrested by shifting them from 22C to 37C for 3 hours.  To release from arrest, cold YPD media was added to shift back to 22C.  Cells were harvested after 140 minutes, centrifuged at 3000 x rpm for 2 minutes, and flash-frozen on nitrogen.  mRNA was isolated and labeled with Cy5 fluorescent dye (red).  mRNA from unarrested cells growing in mid-log was isolated and labeled with Cy3 fluorescent dye (green).  These two probes were mixed together and hybridized to microarrays printed with oligonucleotides probes corresponding to each ORF in the yeast genome.

source_name: 140 min


title: Synchronized cells, 10 min, biological replicate F | array yoG_13B

description: BY4741 cells bearing a temperature sensitive mutation in cdc28 were arrested by shifting them from 22C to 37C for 3 hours.  To release from arrest, cold YPD media was added to shift back to 22C.  Cells were harvested after 10 minutes, centrifuged at 3000 x rpm for 2 minutes, and flash-frozen on nitrogen.  mRNA was isolated and labeled with Cy5 fluorescent dye (red).  mRNA from unarrested cells growing in mid-log was isolated and labeled with Cy3 fluorescent dye (green).  These two probes were mixed together and hybridized to microarrays printed with oligonucleotides probes corresponding to each ORF in the yeast genome.


title: Synchronized cells, 100 min, biological replicate F | array yoG_16B

description: BY4741 cells bearing a temperature sensitive mutation in cdc28 were arrested by shifting them from 22C to 37C for 3 hours.  To release from arrest, cold YPD media was added to shift back to 22C.  Cells were harvested after 100 minutes, centrifuged at 3000 x rpm for 2 minutes, and flash-frozen on nitrogen.  mRNA was isolated and labeled with Cy5 fluorescent dye (red).  mRNA from unarrested cells growing in mid-log was isolated and labeled with Cy3 fluorescent dye (green).  These two probes were mixed together and hybridized to microarrays printed with oligonucleotides probes corresponding to each ORF in the yeast genome.

source_name: 100 min


title: Synchronized cells, 30 min, biological replicate F | array yoG_15T

description: BY4741 cells bearing a temperature sensitive mutation in cdc28 were arrested by shifting them from 22C to 37C for 3 hours.  To release from arrest, cold YPD media was added to shift back to 22C.  Cells were harvested after 30 minutes, centrifuged at 3000 x rpm for 2 minutes, and flash-frozen on nitrogen.  mRNA was isolated and labeled with Cy5 fluorescent dye (red).  mRNA from unarrested cells growing in mid-log was isolated and labeled with Cy3 fluorescent dye (green).  These two probes were mixed together and hybridized to microarrays printed with oligonucleotides probes corresponding to each ORF in the yeast genome.

source_name: 30 min


title: K56Ac cell cycle, 170 min, array replicate 3 | array na_22_20

description: BY4741 cells bearing a temperature sensitive mutation in cdc28 were arrested by shifting them from 22C to 37C for 3 hours.  To release from arrest, cold YPD media was added to shift back to 22C.  Cells were harvested after 170 minutes, crosslinked with formaldehyde (1%), washed with water and zymolyase treated.  Extracts of these cells were then digested with MNase to produce mononucleosomes, and subjected to immunoprecipitation with with 7 ul Upstate rabbit anti-H3K56Ac polyclonal antibody.  As a reference, DNA was obtained from a ChIP of unsynchronized cells with the same antibody.  The ChIP and reference samples were amplified via TLAD and labeled with cy5 and cy3 respectively, and co-hybridized to our custom nucleosomal arrays which contain oligos spanning chromosome III as well as select promoter regions from other chromosomes.

source_name: 170 min


title: Expt V, asf1D, 90 min turnover | array na_30_245B

description: Strain PKY4214 was cultured in YPA raffinose medium supplemented with 300 ug/ml hygromycin and treated for 3 hrs with alpha factor (5 ?g/ml) to induce G1 arrest. Expression of the plasmid-borne FLAG-tagged H3 was induced for 90 min by the addition of 0.2% galactose.  Cells were then crosslinked with formaldehyde (1%), washed with water and zymolyase treated.  Extracts of these cells were then digested with MNase to produce mononucleosomes, and subjected to immunoprecipitation with 20 ul Sigma anti-FLAG monoclonal antibody.  The ChIP and input samples were amplified via TLAD and labeled with cy5 and cy3, respectively, and co-hybridized to our custom nucleosomal arrays which contain oligos spanning chromosome III as well as select promoter regions from other chromosomes.

source_name: asf1D, Gal 90', input

source_name: asf1D, Gal 90', anti-FLAG IP


title: Expt IV, wild-type, 90 min turnover | array na_30_151

description: Strain PKY4212 was cultured in YPA raffinose medium supplemented with 300 ug/ml hygromycin and treated for 3 hrs with alpha factor (5 ?g/ml) to induce G1 arrest. Expression of the plasmid-borne FLAG-tagged H3 was induced for 90 min by the addition of 0.2% galactose.  Cells were then crosslinked with formaldehyde (1%), washed with water and zymolyase treated.  Extracts of these cells were then digested with MNase to produce mononucleosomes, and subjected to immunoprecipitation with 20 ul Sigma anti-FLAG monoclonal antibody.  The ChIP and input samples were amplified via TLAD and labeled with cy5 and cy3, respectively, and co-hybridized to our custom nucleosomal arrays which contain oligos spanning chromosome III as well as select promoter regions from other chromosomes.

source_name: wild-type, Gal 90', input

source_name: wild-type, Gal 90', anti-FLAG IP


title: Synchronized cells, 150 min, biological replicate F | array yoG_19T

description: BY4741 cells bearing a temperature sensitive mutation in cdc28 were arrested by shifting them from 22C to 37C for 3 hours.  To release from arrest, cold YPD media was added to shift back to 22C.  Cells were harvested after 150 minutes, centrifuged at 3000 x rpm for 2 minutes, and flash-frozen on nitrogen.  mRNA was isolated and labeled with Cy5 fluorescent dye (red).  mRNA from unarrested cells growing in mid-log was isolated and labeled with Cy3 fluorescent dye (green).  These two probes were mixed together and hybridized to microarrays printed with oligonucleotides probes corresponding to each ORF in the yeast genome.

source_name: 150 min


title: K56Ac cell cycle, 90 min, array replicate 3 | array na_22_19

description: BY4741 cells bearing a temperature sensitive mutation in cdc28 were arrested by shifting them from 22C to 37C for 3 hours.  To release from arrest, cold YPD media was added to shift back to 22C.  Cells were harvested after 90 minutes, crosslinked with formaldehyde (1%), washed with water and zymolyase treated.  Extracts of these cells were then digested with MNase to produce mononucleosomes, and subjected to immunoprecipitation with with 7 ul Upstate rabbit anti-H3K56Ac polyclonal antibody.  As a reference, DNA was obtained from a ChIP of unsynchronized cells with the same antibody.  The ChIP and reference samples were amplified via TLAD and labeled with cy5 and cy3 respectively, and co-hybridized to our custom nucleosomal arrays which contain oligos spanning chromosome III as well as select promoter regions from other chromosomes.

source_name: 90 min


title: Synchronized cells, 170 min, biological replicate F | array yoG_66B

description: BY4741 cells bearing a temperature sensitive mutation in cdc28 were arrested by shifting them from 22C to 37C for 3 hours.  To release from arrest, cold YPD media was added to shift back to 22C.  Cells were harvested after 170 minutes, centrifuged at 3000 x rpm for 2 minutes, and flash-frozen on nitrogen.  mRNA was isolated and labeled with Cy5 fluorescent dye (red).  mRNA from unarrested cells growing in mid-log was isolated and labeled with Cy3 fluorescent dye (green).  These two probes were mixed together and hybridized to microarrays printed with oligonucleotides probes corresponding to each ORF in the yeast genome.

source_name: Mid-log mRNA (unsynchronized)


title: Expt V, wild-type, 90 min turnover | array na_30_243


title: Synchronized cells, 90 min, biological replicate F | array yoG_65T

description: BY4741 cells bearing a temperature sensitive mutation in cdc28 were arrested by shifting them from 22C to 37C for 3 hours.  To release from arrest, cold YPD media was added to shift back to 22C.  Cells were harvested after 90 minutes, centrifuged at 3000 x rpm for 2 minutes, and flash-frozen on nitrogen.  mRNA was isolated and labeled with Cy5 fluorescent dye (red).  mRNA from unarrested cells growing in mid-log was isolated and labeled with Cy3 fluorescent dye (green).  These two probes were mixed together and hybridized to microarrays printed with oligonucleotides probes corresponding to each ORF in the yeast genome.


title: 48hpi_rep1

city: Brisbane

first: Elizabeth

middle: A

last: Williams

state: QLD

address: St Lucia campus

department: School of Integrative Biology

country: Australia

institute: University of Queensland

description: loop design

hyb_protocol: 4X SSC, 40% deionized formamide (Astral Scientific) and 0.1% SDS were added to the probe mix to create the hybridisation buffer. Following incubation at 95ºC for 5 min and 45ºC for 90 min, the labelled probe mix was loaded onto the microarray chip, and placed in a hybridisation chamber (Corning) with 10 μl H2O at each end in a 45 ºC oven for 16 h (as per Woods et al. 2004).

scan_protocol: Following hybridisation, chips were washed once in a 0.2X SSC, 0.05% SDS solution and twice in 0.2X SSC solution, then dried by low speed centrifugation. Washed slides were scanned using a GenePix 4000B Microarray Scanner (Molecular Devices). Spot intensities from raw scan data were quantified using GenePix Pro 6.0 software (Molecular Devices). Spots were flagged as present or absent based on circularity and diameter (circularity </= 70 and diameter < 100 = absent) or sum of means (Cy5 intensity/Cy3 intensity < 200 = absent).

data_processing: Quantified data was transferred as a one-colour analysis into Genespring version 7.0 (Silicon Genetics). Raw data was normalised per chip to the 50th percentile and per gene to the median, and measurements < 0.01 were set to 0.01. Median polishing was performed per chip and per gene.

organism: Haliotis asinina

source_name: pooled whole postlarvae

label_protocol: 2.5 μg total RNA was used to prepare labelled cDNA for each developmental stage. cDNA was transcribed with an oligo(dT)15 primer using a dNTP mix with a ratio of 4:1 aminoallyl-dUTP to dTTP (Sigma) and Superscript III Reverse Transcriptase (Invitrogen) according to manufacturers’ instructions. Aminoallyl-labelled cDNA (aa-cDNA) was purified, dried and redissolved in 100 mM sodium carbonate pH 9. Cy3 and Cy5 reactive dyes (Amersham) were added to their respective aa-cDNA samples and the coupling reaction allowed to proceed. After 1 h, 4.5 μl 4 M hydroxylamine was added to remove unincorporated dyes. Cy3- and Cy5-labeled cDNA were combined and purified with a PCR cleanup kit (Qiagen). To prevent non-specific binding, 10 μg human Cot1 DNA (Invitrogen) and 0.125 A260 units poly dA (Roche) were added to the purified probe mix. This solution was dehydrated in a speed-vac to a volume of 8 μl.

growth_protocol: Spawning of adult Haliotis asinina and larval culture were carried out at Heron Island Research Station on the Great Barrier Reef, Australia (23°27’S; 151°55’E) as previously described (Counihan et al. 2001; Jackson et al. 2005). Larval cultures were derived from gametic contributions from at least 3 females and 3 males, and were treated for 2 hours daily with 20 μg/L rifampicin to protect against bacterial invasion. Larvae were allowed to develop to 96 hours post fertilisation (hpf), at which time a subset were introduced into 0.5 L plastic chambers containing ~11.5 cm2 surface area of the encrusting coralline algae, Mastophora pacifica, previously shown to be an effective inducer of Haliotis asinina metamorphosis (Jackson et al. 2005). After 2 h, chambers were supplied with a gentle flow of seawater, such that any larvae not in constant contact with the coralline algae were washed out of the chamber. At 8 h after their introduction, the algal shards were removed from chambers and all attached larvae were washed into fresh 0.5 L plastic chambers using a jet of 0.22 μM filtered seawater (FSW). Once again, chambers were supplied with a gentle flow of seawater so that only larvae exhibiting constant crawling behaviour were maintained. Washed larvae were allowed to develop for a further 48 h, at which point the experiment ended. Throughout the induction experiment, postlarvae were treated with rifampicin as described above. A subset of larvae were maintained in the original culture chambers to act as an non-induced control.

extract_protocol: Abalone larvae were collected for RNA extraction at 66, 78, 90, 108, 120 and 144 hpf. Competent larvae were induced by exposure to coralline algae at 96 hpf (see above) and postlarval samples were collected at 12, 24 and 48 hpi. This meant that postlarvae 12, 24 and 48 hpi were actually the same age as larvae 108, 120 and 144 hpf. Total RNA was extracted using TRIreagent (Sigma) as described by the manufacturer. Quantity and quality of RNA was assessed using UV spectrophotometry (Nanodrop ND-1000) and agarose gel electrophoresis.

tag: SOURCE POP

value: Heron Island

tag: CHIP #

tag: HYB DATE


title: Synchronized cells, 110 min, biological replicate F | array yoG_65B

description: BY4741 cells bearing a temperature sensitive mutation in cdc28 were arrested by shifting them from 22C to 37C for 3 hours.  To release from arrest, cold YPD media was added to shift back to 22C.  Cells were harvested after 110 minutes, centrifuged at 3000 x rpm for 2 minutes, and flash-frozen on nitrogen.  mRNA was isolated and labeled with Cy5 fluorescent dye (red).  mRNA from unarrested cells growing in mid-log was isolated and labeled with Cy3 fluorescent dye (green).  These two probes were mixed together and hybridized to microarrays printed with oligonucleotides probes corresponding to each ORF in the yeast genome.

source_name: 110 min


title: 144hpf_rep4

description: loop design

source_name: pooled whole larvae