title: Synchronized cells, 130 min, cell cycle CCA | array yofG_86T

description: BY4741 bar1- cells were arrested with the addition of alpha factor (final conc. 1 ug/ml) for 3 hours.  To release from arrest, cells were filtered on a 0.45 um Millipore filter, rinsed with 500 ml sterile water, and dropped into fresh YPD medium supplemented with 5 ug/ml.  Cells were harvested 130 minutes later, 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)

source_name: 130 min


title: nla4 cells 4h replicate 3

status: Public on Jan 28 2009

type: RNA

city: Syracuse

first: Anthony

last: Garza

state: NY

address: 212 BRL,  130 College Place

department: Biology

country: USA

institute: Syracuse University

description: Biological replicate 3

hyb_protocol: cDNA was resuspended in 9 µl of 0.1 M sodium bicarbonate (pH 9.0). The cDNA was labeled with Cy3 (Reference: mixed wild type cDNA) or Cy5 (mutant developmental cDNA) (Amersham Pharmacia) by the addition of 4.5 µl of dye dissolved in 73 µl of dimethyl sulfoxide, and incubated for 1 hour in the dark.

scan_protocol: Post-hybridized DNA microarrays were scanned using a GenePix 4100A microarray scanner and read using GenePix Pro 6.0 (Axon Inc. Union City, CA) Images were quantified using GenePix Pro 6.0 (Axon Inc). Data extracted from the images were transferred to the software package Acuity 4.0 (Axon Instruments) for normalization and statistical analysis

data_processing: LOWESS normalized, background subtracted VALUE data obtained from log2 of processed Green signal/processed Red signal.

molecule: total RNA

organism: Myxococcus xanthus

source_name: cells undergoing development for 4 hours

label_protocol: Fifty µg of total RNA were used to synthesize cDNA using 10 µg of pdN6 primers (Amersham Pharmacia) in the presence of 40 µg/µl RNase inhibitor (Promega)

growth_protocol: Strains were grown at 28° or 32 °C in flasks containing 350 ml of CTTYE broth [1.0% Casitone, 10 mM Tris-HCl (pH 8.0), 1 mM KH2PO4, 8 mM MgSO4, and 0.5% yeast extract] with vigorous swiriling.  CTTYE broth was supplemented with 40 mg/ml of kanamycin sulfate as needed.

extract_protocol: Total RNA was extracted using the Hot-Phenol-Chloroform method (Sambrook et al., 1989) and subsequently purified using Agilent Technologies Total RNA Purification Kit

treatment_protocol: After culutres reached a density of 5 X 108 cells/ml, 40 ml aliquts of the cells were pelleted by centrifugation, the supernatants were removed, the cells were quick-frozen in dry ice/ethanol mixure, and the cells were stored at -80 °C as the vegetative (0 hour) test samples.  The cells in the remaining 350 ml culture wre pelleded by centrifugatin, the supernatants were removed and cells were resuspended in MC7 starvation buffer (10 mM morpholinepropanesulfonic acid [pH 7.0], 1 mM Ca cl2) to a density of 5 X 109 cells/ml.  Four ml of the concentrated cells were added to 28 ml of MC7 buffer and the cells were allowed to develop in a petri dish at 32°C.  At certain time points (1, 2, 4, 6, 12, 24 hours post-starvation) in development, the cells were detatched from the bottoms of the petri dishes using a cell scraper, pelleted by centrifugation, and the supernatants were removed.  The cells were quick-frozen in dry ice/ethanol mixure, and the stored at -80° C as developmental samples.

tag: Stain

source_name: Total RNA from pooled M. xanthus cells at developmental time points

tag: Strain


title: nla4 cells 6h replicate 1

description: Biological replicate 1

source_name: cells undergoing development for 6 hours


title: nla4 cells 6h replicate 2

description: Biological replicate 2


title: nla4 cells 4h replicate 2

description: Biological replicate 2


title: nla4 cells 4h replicate 1

description: Biological replicate 1


title: nla4 cells 2h replicate 3

description: Biological replicate 3

source_name: cells undergoing development for 2 hours


title: Synchronized cells, 150 min, cell cycle CCA | array yofG_87T

city: Worcester

first: Oliver

last: Rando

state: MA

address: 364 Plantation St.

institute: UMass Medical School

description: BY4741 bar1- cells were arrested with the addition of alpha factor (final conc. 1 ug/ml) for 3 hours.  To release from arrest, cells were filtered on a 0.45 um Millipore filter, rinsed with 500 ml sterile water, and dropped into fresh YPD medium supplemented with 5 ug/ml.  Cells were harvested 150 minutes later, 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.

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 expression ratios (Cy5/Cy3) were calculated to produce the values given in the data table.

organism: Saccharomyces cerevisiae

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.

source_name: 150 min

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: BW25113 sdiA-empty vector 12h biofilm cells at 30oC

city: College Station

first: Jintae

last: Lee

state: TX

department: Chemical Engineering

institute: Texas A&M University

description: For the microarray experiments, 10 g glass wool (Corning Glass Works, Corning, N.Y.) were used to form biofilms in 250 mL LB ( 1 mM IPTG + Cm30) in 1 L Erlenmeyer shake flasks which were inoculated with overnight cultures diluted that were 1:100.  The cells were shaken at 250 rpm and 30C for 12 hours to form biofilms on the glass wool, and RNA was isolated from the biofilm cells

hyb_protocol: The biotin-labeled target was hybridized to the Affymetrix GeneChip E. coli array at 45C for 16 hour at 60 rpm using the Hybridization Oven 640 (Affymetrix), then a three-step fluorescent staining was conducted using the Fluidics Station 450 (Affymetrix) during the washing and staining procedure.

scan_protocol: The microarray was scanned at 570 nm to get an image file by the GeneChip Scanner 3000 (Affymetrix).  Using GeneChip® Operating Software, total cell intensity was scaled automatically in the software to an average value of 500.

data_processing: MAS 5.0 Expression Analysis Default Setting

label: biotin

organism: Escherichia coli

source_name: Channel 1

label_protocol: The total RNA samples were first converted into cDNA through a reverse transcription reaction with poly-A RNA controls spiked into the same reaction mixture to monitor the entire target labeling process.  The cDNA was then digested with DNase I (Amersham Biosciences) to produce 50-200 bp fragments, which was checked by running the fragmented cDNA on a 2% agarose gel.  The fragmented cDNA was labeled at the 3’ termini by the Enzo BioArray Terminal Labeling Kit with Biotin-ddUTP (Affymetrix, P/N 900181).

extract_protocol: To lyse the cells, 1.0 mL RLT buffer (Qiagen, Inc., Valencia, CA) and 0.2 mL 0.1 mm zirconia/silica beads (Biospec) were added to the frozen bead beater tubes containing the cell pellets. The tubes were closed tightly and beat for 50 seconds at the maximum speed in a mini bead beater (cat. no. 3110BX, Biospec). The total RNA was isolated by following the protocol of the RNeasy Mini Kit (Qiagen) including an on-column DNase digestion with RNase-free DNase I (Qiagen).

tag: RNA extracted from biofilm cells of K-12 sdiA-no SdiA 1 after 12h of growth in LB + 1 mMIPTG and 30 microM Cm with glass wool at 30oC


title: nla4 cells 2h replicate 2

description: Biological replicate 2


title: BW25113_yjgK_deleted_mutant_8_h_biofilm_LB

city: State College

first: Thomas

middle: K.

last: Wood

state: PA

address: Room 161 Fenske Laboratory, University Park

department: Chemical Engineering & Biochemistry and Molecular Biology

institute: Pennsylvania State University

description: RNA extracted from biofilm cells of E. coli K-12 BW25113 yjgK deleted mutant after 8 h of growth in LB with glass wool at 37ºC

hyb_protocol: The biotin-labeled target was hybridized to the Affymetrix GeneChip E. coli array at 45ºC for 16 hour at 60 rpm using the Hybridization Oven 640 (Affymetrix), then a three-step fluorescent staining was conducted using the Fluidics Station 450 (Affymetrix) during the washing and staining procedure.

scan_protocol: The microarray was scanned at 570 nm to get an image file by the GeneChip Scanner 3000 (Affymetrix). Using GeneChip® Operating Software, total cell intensity was scaled automatically in the software to an average value of 500.

source_name: BW25113 yjgK deleted mutant

label_protocol: The total RNA samples were first converted into cDNA through a reverse transcription reaction with poly-A RNA controls spiked into the same reaction mixture to monitor the entire target labeling process. The cDNA was then digested with DNase I (Amersham Biosciences) to produce 50-200 bp fragments, which was checked by running the fragmented cDNA on a 2% agarose gel. The fragmented cDNA was labeled at the 3’ termini by the Enzo BioArray Terminal Labeling Kit with Biotin-ddUTP (Affymetrix, P/N 900181).

extract_protocol: The overnight culture (2.5 ml) was used to inoculate 250 ml of fresh LB medium with 10 g of glass wool (Corning Glass Works, Corning, NY) for forming biofilm. After incubation for 8 h at 37°C with shaking (250 rpm), the glass wool was carefully and quickly removed and rinsed with 100 ml of sterile 0.85% NaCl solution at 0°C. Biofilm cells were removed by sonicating the glass wool in 200 ml of sterile 0.85% NaCl solution at 0°C. After breaking the cells with a bead beater (cat. no. 3110BX, Biospec), and the total RNA was isolated with Qiagen RNeasy mini Kit (Cat# 74104) including an on-column DNase digestion with RNase-free DNase I (Qiagen).

tag: RNA extracted from biofilm cells of E. coli K-12 BW25113 yjgK deleted mutant after 8 h of growth with glass wool at 37oC


title: Synchronized cells, 110 min, cell cycle CCA | array yofG_84T

description: BY4741 bar1- cells were arrested with the addition of alpha factor (final conc. 1 ug/ml) for 3 hours.  To release from arrest, cells were filtered on a 0.45 um Millipore filter, rinsed with 500 ml sterile water, and dropped into fresh YPD medium supplemented with 5 ug/ml.  Cells were harvested 110 minutes later, 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: nla4 cells 2h replicate 1

description: Biological replicate 1


title: Biofilm cells of E. coli K-12 LVM100 delta 5 TA mutant

description: RNA extracted from biofilm cells of E. coli K-12 LVM100 delta 5 TA mutant after 15 h of growth in LB with glass wool at 37ºC

source_name: biofilm cells of E. coli K-12 LVM100 delta 5 TA mutant grown at 37oC for 15 h

extract_protocol: The overnight culture (2.5 ml) was used to inoculate 250 ml of fresh LB medium with 10 g of glass wool (Corning Glass Works, Corning, NY) for forming biofilm. After incubation for 15 h at 37°C with shaking (250 rpm), the glass wool was carefully and quickly removed and rinsed with 100 ml of sterile 0.85% NaCl solution at 0°C. Biofilm cells were removed by sonicating the glass wool in 200 ml of sterile 0.85% NaCl solution at 0°C. After breaking the cells with a bead beater (cat. no. 3110BX, Biospec), and the total RNA was isolated with Qiagen RNeasy mini Kit (Cat# 74104) including an on-column DNase digestion with RNase-free DNase I (Qiagen).

tag: RNA extracted from biofilm cells of E. coli K-12 LVM100 delta 5 TA mutant after 15 h of growth with glass wool at 37oC


title: BW25113_wild_type_8_h_biofilm_LB

description: RNA extracted from biofilm cells of E. coli K-12 BW25113 after 8 h of growth in LB with glass wool at 37ºC

source_name: BW25113 wild-type

tag: RNA extracted from biofilm cells of E. coli K-12 BW25113 after 8 h of growth with glass wool at 37oC


title: nla4 cells 1h replicate 3

description: Biological replicate 3

source_name: cells undergoing development for 1 hour


title: Biofilm cells of E. coli K-12 MG1655

description: RNA extracted from biofilm cells of E. coli K-12 MG1655 after 15 h of growth in LB with glass wool at 37ºC

source_name: biofilm cells of E. coli K-12 MG1655 grown at 37oC for 15 h

tag: RNA extracted from biofilm cells of E. coli K-12 MG1655 after 15 h of growth with glass wool at 37oC


title: nla4 cells 1h replicate 2

description: Biological replicate 2


title: Synchronized cells, 120 min, cell cycle CCA | array yofG_86B

description: BY4741 bar1- cells were arrested with the addition of alpha factor (final conc. 1 ug/ml) for 3 hours.  To release from arrest, cells were filtered on a 0.45 um Millipore filter, rinsed with 500 ml sterile water, and dropped into fresh YPD medium supplemented with 5 ug/ml.  Cells were harvested 120 minutes later, 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: BW25113 sdiA-WTSdiA 12h biofilm cells at 30oC

description: For the microarray experiments, 10 g glass wool (Corning Glass Works, Corning, N.Y.) were used to form biofilms in 250 mL LB ( 1 mM IPTG + Cm30) in 1 L Erlenmeyer shake flasks which were inoculated with overnight cultures diluted that were 1:100.  The cells were shaken at 250 rpm and 30C for 12 hours to form biofilms on the glass wool, and RNA was isolated from the suspension cells and the biofilm.

hyb_protocol: The biotin-labeled target was hybridized to the Affymetrix GeneChip E. coli array at 45C for 16 hour at 60 rpm using the Hybridization Oven 640 (Affymetrix), then a three-step fluorescent staining was conducted using the Fluidics Station 450 (Affymetrix) during the washing and staining procedure.

source_name: wild type SdiA

tag: RNA extracted from biofilm cells of K-12 sdiA-WTSdiA after 12h of growth in LB + 1 mMIPTG and 30 microM Cm with glass wool at 30oC


title: Synchronized cells, 140 min, cell cycle CCA | array yofG_87B

description: BY4741 bar1- cells were arrested with the addition of alpha factor (final conc. 1 ug/ml) for 3 hours.  To release from arrest, cells were filtered on a 0.45 um Millipore filter, rinsed with 500 ml sterile water, and dropped into fresh YPD medium supplemented with 5 ug/ml.  Cells were harvested 140 minutes later, 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: nla4 cells 0h replicate 3

description: Biological replicate 3

source_name: actively growing cells - 0h


title: BW25113 sdiA-SdiA1E11 12h biofilm cells at 30oC

source_name: mutant SdiA1E11

tag: RNA extracted from biofilm cells of K-12 sdiA-SdiA1E11 after 12h of growth in LB + 1 mMIPTG and 30 microM Cm with glass wool at 30oC


title: nla4 cells 1h replicate 1

description: Biological replicate 1


title: nla4 cells 0h replicate 2

description: Biological replicate 2


title: nla4 cells 0h replicate 1

description: Biological replicate 1


title: Control wild-type 24h replicate 2

description: Biological replicate 2

source_name: cells undergoing development for 24 hours


title: ChIP Input cell cycle CCA, 130 min | array na_13_023

type: genomic

description: BY4741 cells bearing a deletion in bar1 were grown to an OD of 0.25 and arrested by adding alpha factor to a final concentration of 1 ug/ml and incubated for 3 hours.  To release from arrest, cells were filtered with 0.22 uM Whatman filter, washed with sterile MilliQ water, and the filter paper placed in a flask prewarmed to 30C, containing 450 ml YPD and 22.5 mg pronase.  Upon release, 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 (ChIP Input).  As a reference, DNA was obtained from sonication of unsynchronized cells.  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, labeled ChIP DNA were mixed, purified by microcon, and hybridized to the microarrays in 3.4X SSC and 0.3% SDS for 16 hours at 55 degrees.

data_processing: After background correction and removal of flagged values, data was block normalized by dilation and log base 2 ratios (Cy5/Cy3) were calculated to produce the values given in the data table.

molecule: genomic DNA

source_name: Amplified sonicated DNA

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 cDNAs 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.

value: BY4741 bar1(del)

source_name: 130 min


title: ChIP Input cell cycle CCA, 140 min | array na_13_070

description: BY4741 cells bearing a deletion in bar1 were grown to an OD of 0.25 and arrested by adding alpha factor to a final concentration of 1 ug/ml and incubated for 3 hours.  To release from arrest, cells were filtered with 0.22 uM Whatman filter, washed with sterile MilliQ water, and the filter paper placed in a flask prewarmed to 30C, containing 450 ml YPD and 22.5 mg pronase.  Upon release, 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 (ChIP Input).  As a reference, DNA was obtained from sonication of unsynchronized cells.  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: Control wild-type 24h replicate 1

description: Biological replicate 1

source_name: Total RNA from pooled M. xanthus cells at developmental time points


title: Control wild-type 24h replicate 4

description: Biological replicate 4


title: Control wild-type 18h replicate 2

description: Biological replicate 2

source_name: cells undergoing development for 18 hours


title: Control wild-type 18h replicate 4

description: Biological replicate 4


title: Control wild-type 18h replicate 5

description: Biological replicate 5


title: Control wild-type 24h replicate 5

description: Biological replicate 5


title: ChIP Input cell cycle CCA, 100 min | array na_13_021

description: BY4741 cells bearing a deletion in bar1 were grown to an OD of 0.25 and arrested by adding alpha factor to a final concentration of 1 ug/ml and incubated for 3 hours.  To release from arrest, cells were filtered with 0.22 uM Whatman filter, washed with sterile MilliQ water, and the filter paper placed in a flask prewarmed to 30C, containing 450 ml YPD and 22.5 mg pronase.  Upon release, 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 (ChIP Input).  As a reference, DNA was obtained from sonication of unsynchronized cells.  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: ChIP Input cell cycle CCA, 110 min | array na_13_073

description: BY4741 cells bearing a deletion in bar1 were grown to an OD of 0.25 and arrested by adding alpha factor to a final concentration of 1 ug/ml and incubated for 3 hours.  To release from arrest, cells were filtered with 0.22 uM Whatman filter, washed with sterile MilliQ water, and the filter paper placed in a flask prewarmed to 30C, containing 450 ml YPD and 22.5 mg pronase.  Upon release, 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 (ChIP Input).  As a reference, DNA was obtained from sonication of unsynchronized cells.  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: ChIP Input cell cycle CCA, 120 min | array na_13_072

description: BY4741 cells bearing a deletion in bar1 were grown to an OD of 0.25 and arrested by adding alpha factor to a final concentration of 1 ug/ml and incubated for 3 hours.  To release from arrest, cells were filtered with 0.22 uM Whatman filter, washed with sterile MilliQ water, and the filter paper placed in a flask prewarmed to 30C, containing 450 ml YPD and 22.5 mg pronase.  Upon release, 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 (ChIP Input).  As a reference, DNA was obtained from sonication of unsynchronized cells.  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: ChIP Input cell cycle CCA, 90 min | array na_13_020

description: BY4741 cells bearing a deletion in bar1 were grown to an OD of 0.4 and arrested by adding alpha factor to a final concentration of 1 ug/ml and incubated for 3 hours.  To release from arrest, cells were filtered with 0.22 uM Whatman filter, washed with sterile MilliQ water, and the filter paper placed in a flask prewarmed to 30C, containing 450 ml YPD and 22.5 mg pronase.  Upon release, 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 (ChIP Input).  As a reference, DNA was obtained from sonication of unsynchronized cells.  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: Control wild-type 24h replicate 3

description: Biological replicate 3


title: Control wild-type 18h replicate 1

description: Biological replicate 1


title: ChIP Input cell cycle CCA, 80 min | array na_13_077

description: BY4741 cells bearing a deletion in bar1 were grown to an OD of 0.4 and arrested by adding alpha factor to a final concentration of 1 ug/ml and incubated for 3 hours.  To release from arrest, cells were filtered with 0.22 uM Whatman filter, washed with sterile MilliQ water, and the filter paper placed in a flask prewarmed to 30C, containing 450 ml YPD and 22.5 mg pronase.  Upon release, 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 (ChIP Input).  As a reference, DNA was obtained from sonication of unsynchronized cells.  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: ChIP Input cell cycle CCA, 50 min | array na_13_024

description: BY4741 cells bearing a deletion in bar1 were grown to an OD of 0.4 and arrested by adding alpha factor to a final concentration of 1 ug/ml and incubated for 3 hours.  To release from arrest, cells were filtered with 0.22 uM Whatman filter, washed with sterile MilliQ water, and the filter paper placed in a flask prewarmed to 30C, containing 450 ml YPD and 22.5 mg pronase.  Upon release, 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 (ChIP Input).  As a reference, DNA was obtained from sonication of unsynchronized cells.  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: Control wild-type 18h replicate 3

description: Biological replicate 3


title: Control wild-type 12h replicate 4

description: Biological replicate 4

source_name: cells undergoing development for 12 hours


title: MCF7_CRY2KO_Rep2

status: Public on Jan 29 2009

city: New Haven

first: Aaron

middle: Ezra

last: Hoffman

state: CT

address: 60 College St.

department: LEPH

institute: Yale School of Medicine

description: All protocols performed by an Agilent-certified service provider

hyb_protocol: Agilent's Gene Expression Hybridization Kit followed by Agilent's Gene Expression Wash Buffer Kit

scan_protocol: Agilent’s Microarray Scanner with SureScan technology

data_processing: Agilent Feature Extraction Software, data were analyzed using the Rosetta Luminator gene expression data analysis system.  Value = log10 (intensity2/intensity1)

organism: Homo sapiens

source_name: MCF7 Negative Control siRNA

label_protocol: mRNA converted to Cyanine 3-labeled cRNA using Agilent's Quick Amp Labeling Kit, two-color

extract_protocol: Qiagen RNeasy mini kit with on-column DNase digestion

tag: MCF7 cells transfected with a negative control siRNA

source_name: MCF7 CRY2 siRNA

label_protocol: mRNA converted to Cyanine 5-labeled cRNA using Agilent's Quick Amp Labeling Kit, two-color

tag: MCF7 cells transfected with a CRY2-targeting siRNA


title: ChIP Input cell cycle CCA, 70 min | array na_13_075

description: BY4741 cells bearing a deletion in bar1 were grown to an OD of 0.4 and arrested by adding alpha factor to a final concentration of 1 ug/ml and incubated for 3 hours.  To release from arrest, cells were filtered with 0.22 uM Whatman filter, washed with sterile MilliQ water, and the filter paper placed in a flask prewarmed to 30C, containing 450 ml YPD and 22.5 mg pronase.  Upon release, 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 (ChIP Input).  As a reference, DNA was obtained from sonication of unsynchronized cells.  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: ChIP Input cell cycle CCA, 10 min | array na_13_069

description: BY4741 cells bearing a deletion in bar1 were grown to an OD of 0.7 and arrested by adding alpha factor to a final concentration of 1 ug/ml and incubated for 3 hours.  To release from arrest, cells were filtered with 0.22 uM Whatman filter, washed with sterile MilliQ water, and the filter paper placed in a flask prewarmed to 30C, containing 450 ml YPD and 22.5 mg pronase.  Upon release, 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 (ChIP Input).  As a reference, DNA was obtained from sonication of unsynchronized cells.  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: Control wild-type 12h replicate 2

description: Biological replicate 2


title: Control wild-type 6h replicate 5

description: Biological replicate 5

source_name: cells undergoing development for 6 hours


title: Control wild-type 12h replicate 3

description: Biological replicate 3


title: Control wild-type 6h replicate 4

description: Biological replicate 4


title: ChIP Input cell cycle CCA, 150 min | array na_13_022

description: BY4741 cells bearing a deletion in bar1 were grown to an OD of 0.25 and arrested by adding alpha factor to a final concentration of 1 ug/ml and incubated for 3 hours.  To release from arrest, cells were filtered with 0.22 uM Whatman filter, washed with sterile MilliQ water, and the filter paper placed in a flask prewarmed to 30C, containing 450 ml YPD and 22.5 mg pronase.  Upon release, 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 (ChIP Input).  As a reference, DNA was obtained from sonication of unsynchronized cells.  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: 150 min


title: Control wild-type 12h replicate 1

description: Biological replicate 1


title: ChIP Input cell cycle CCA, 20 min | array na_13_074

description: BY4741 cells bearing a deletion in bar1 were grown to an OD of 0.7 and arrested by adding alpha factor to a final concentration of 1 ug/ml and incubated for 3 hours.  To release from arrest, cells were filtered with 0.22 uM Whatman filter, washed with sterile MilliQ water, and the filter paper placed in a flask prewarmed to 30C, containing 450 ml YPD and 22.5 mg pronase.  Upon release, cells were harvested after 20 minutes, crosslinked with formaldehyde (1%), washed with water and zymolyase treated.  Extracts of these cells were then digested with MNase (ChIP Input).  As a reference, DNA was obtained from sonication of unsynchronized cells.  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: 20 min


title: ChIP Input cell cycle CCA, 0 min | array na_13_071

description: BY4741 cells bearing a deletion in bar1 were grown to an OD of 0.7 and arrested by adding alpha factor to a final concentration of 1 ug/ml and incubated for 3 hours.  To release from arrest, cells were filtered with 0.22 uM Whatman filter, washed with sterile MilliQ water, and the filter paper placed in a flask prewarmed to 30C, containing 450 ml YPD and 22.5 mg pronase.  Upon release, cells were immediately harvested, crosslinked with formaldehyde (1%), washed with water and zymolyase treated.  Extracts of these cells were then digested with MNase (ChIP Input).  As a reference, DNA was obtained from sonication of unsynchronized cells.  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: ChIP Input cell cycle CCA, 60 min | array na_13_068

description: BY4741 cells bearing a deletion in bar1 were grown to an OD of 0.4 and arrested by adding alpha factor to a final concentration of 1 ug/ml and incubated for 3 hours.  To release from arrest, cells were filtered with 0.22 uM Whatman filter, washed with sterile MilliQ water, and the filter paper placed in a flask prewarmed to 30C, containing 450 ml YPD and 22.5 mg pronase.  Upon release, 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 (ChIP Input).  As a reference, DNA was obtained from sonication of unsynchronized cells.  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: Amplified sonicated DNA

source_name: 60 min


title: Control wild-type 6h replicate 2

description: Biological replicate 2

source_name: Total RNA from pooled M. xanthus cells at developmental time points


title: H3K4Me3 ChIP cell cycle CCA, 130 min | array na_13_043

description: BY4741 cells bearing a deletion in bar1 were grown to an OD of 0.25 and arrested by adding alpha factor to a final concentration of 1 ug/ml and incubated for 3 hours.  To release from arrest, cells were filtered with 0.22 uM Whatman filter, washed with sterile MilliQ water, and the filter paper placed in a flask prewarmed to 30C, containing 450 ml YPD and 22.5 mg pronase.  Upon release, 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, and subjected to immunoprecipitation with with 4 ul Abcam rabbit anti-H3K4Me3 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 H3K4Me3 (unsynchronized)

source_name: 130 min


title: H3K4Me3 ChIP cell cycle CCA, 120 min | array na_13_031

description: BY4741 cells bearing a deletion in bar1 were grown to an OD of 0.25 and arrested by adding alpha factor to a final concentration of 1 ug/ml and incubated for 3 hours.  To release from arrest, cells were filtered with 0.22 uM Whatman filter, washed with sterile MilliQ water, and the filter paper placed in a flask prewarmed to 30C, containing 450 ml YPD and 22.5 mg pronase.  Upon release, 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, and subjected to immunoprecipitation with with 4 ul Abcam rabbit anti-H3K4Me3 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: Control wild-type 6h replicate 3

description: Biological replicate 3


title: Control wild-type 6h replicate 1

description: Biological replicate 1


title: H3K4Me3 ChIP cell cycle CCA, 140 min | array na_13_028

description: BY4741 cells bearing a deletion in bar1 were grown to an OD of 0.25 and arrested by adding alpha factor to a final concentration of 1 ug/ml and incubated for 3 hours.  To release from arrest, cells were filtered with 0.22 uM Whatman filter, washed with sterile MilliQ water, and the filter paper placed in a flask prewarmed to 30C, containing 450 ml YPD and 22.5 mg pronase.  Upon release, 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, and subjected to immunoprecipitation with with 4 ul Abcam rabbit anti-H3K4Me3 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: ChIP Input cell cycle CCA, 30 min | array na_13_078

description: BY4741 cells bearing a deletion in bar1 were grown to an OD of 0.7 and arrested by adding alpha factor to a final concentration of 1 ug/ml and incubated for 3 hours.  To release from arrest, cells were filtered with 0.22 uM Whatman filter, washed with sterile MilliQ water, and the filter paper placed in a flask prewarmed to 30C, containing 450 ml YPD and 22.5 mg pronase.  Upon release, 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 (ChIP Input).  As a reference, DNA was obtained from sonication of unsynchronized cells.  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: Control wild-type 4h replicate 5

description: Biological replicate 5

source_name: cells undergoing development for 4 hours


title: Control wild-type 4h replicate 3

description: Biological replicate 3


title: Control wild-type 4h replicate 1

description: Biological replicate 1


title: ChIP Input cell cycle CCA, 5 min | array na_13_076

description: BY4741 cells bearing a deletion in bar1 were grown to an OD of 0.7 and arrested by adding alpha factor to a final concentration of 1 ug/ml and incubated for 3 hours.  To release from arrest, cells were filtered with 0.22 uM Whatman filter, washed with sterile MilliQ water, and the filter paper placed in a flask prewarmed to 30C, containing 450 ml YPD and 22.5 mg pronase.  Upon release, cells were harvested after 5 minutes, crosslinked with formaldehyde (1%), washed with water and zymolyase treated.  Extracts of these cells were then digested with MNase (ChIP Input).  As a reference, DNA was obtained from sonication of unsynchronized cells.  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: 5 min


title: H3K4Me3 ChIP cell cycle CCA, 100 min | array na_13_034

description: BY4741 cells bearing a deletion in bar1 were grown to an OD of 0.25 and arrested by adding alpha factor to a final concentration of 1 ug/ml and incubated for 3 hours.  To release from arrest, cells were filtered with 0.22 uM Whatman filter, washed with sterile MilliQ water, and the filter paper placed in a flask prewarmed to 30C, containing 450 ml YPD and 22.5 mg pronase.  Upon release, 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, and subjected to immunoprecipitation with with 4 ul Abcam rabbit anti-H3K4Me3 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: H3K4Me3 ChIP cell cycle CCA, 90 min | array na_13_042

description: BY4741 cells bearing a deletion in bar1 were grown to an OD of 0.4 and arrested by adding alpha factor to a final concentration of 1 ug/ml and incubated for 3 hours.  To release from arrest, cells were filtered with 0.22 uM Whatman filter, washed with sterile MilliQ water, and the filter paper placed in a flask prewarmed to 30C, containing 450 ml YPD and 22.5 mg pronase.  Upon release, 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, and subjected to immunoprecipitation with with 4 ul Abcam rabbit anti-H3K4Me3 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: Control wild-type 4h replicate 4

description: Biological replicate 4


title: Control wild-type 4h replicate 2

description: Biological replicate 2


title: H3K4Me3 ChIP cell cycle CCA, 110 min | array na_13_029

description: BY4741 cells bearing a deletion in bar1 were grown to an OD of 0.25 and arrested by adding alpha factor to a final concentration of 1 ug/ml and incubated for 3 hours.  To release from arrest, cells were filtered with 0.22 uM Whatman filter, washed with sterile MilliQ water, and the filter paper placed in a flask prewarmed to 30C, containing 450 ml YPD and 22.5 mg pronase.  Upon release, 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, and subjected to immunoprecipitation with with 4 ul Abcam rabbit anti-H3K4Me3 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: Control wild-type 2h replicate 5

description: Biological replicate 5

source_name: cells undergoing development for 2 hours


title: ChIP Input cell cycle CCA, 15 min | array na_13_025

description: BY4741 cells bearing a deletion in bar1 were grown to an OD of 0.7 and arrested by adding alpha factor to a final concentration of 1 ug/ml and incubated for 3 hours.  To release from arrest, cells were filtered with 0.22 uM Whatman filter, washed with sterile MilliQ water, and the filter paper placed in a flask prewarmed to 30C, containing 450 ml YPD and 22.5 mg pronase.  Upon release, cells were harvested after 15 minutes, crosslinked with formaldehyde (1%), washed with water and zymolyase treated.  Extracts of these cells were then digested with MNase (ChIP Input).  As a reference, DNA was obtained from sonication of unsynchronized cells.  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: 15 min


title: Control wild-type 2h replicate 4

description: Biological replicate 4


title: Control wild-type 2h replicate 6

description: Biological replicate 6


title: Control wild-type 2h replicate 2

description: Biological replicate 2


title: Control wild-type 2h replicate 1

description: Biological replicate 1


title: H3K4Me3 ChIP cell cycle CCA, 20 min | array na_13_035

description: BY4741 cells bearing a deletion in bar1 were grown to an OD of 0.7 and arrested by adding alpha factor to a final concentration of 1 ug/ml and incubated for 3 hours.  To release from arrest, cells were filtered with 0.22 uM Whatman filter, washed with sterile MilliQ water, and the filter paper placed in a flask prewarmed to 30C, containing 450 ml YPD and 22.5 mg pronase.  Upon release, cells were harvested after 20 minutes, crosslinked with formaldehyde (1%), washed with water and zymolyase treated.  Extracts of these cells were then digested with MNase, and subjected to immunoprecipitation with with 4 ul Abcam rabbit anti-H3K4Me3 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: 20 min


title: H3K4Me3 ChIP cell cycle CCA, 15 min | array na_13_036

description: BY4741 cells bearing a deletion in bar1 were grown to an OD of 0.7 and arrested by adding alpha factor to a final concentration of 1 ug/ml and incubated for 3 hours.  To release from arrest, cells were filtered with 0.22 uM Whatman filter, washed with sterile MilliQ water, and the filter paper placed in a flask prewarmed to 30C, containing 450 ml YPD and 22.5 mg pronase.  Upon release, cells were harvested after 15 minutes, crosslinked with formaldehyde (1%), washed with water and zymolyase treated.  Extracts of these cells were then digested with MNase, and subjected to immunoprecipitation with with 4 ul Abcam rabbit anti-H3K4Me3 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: H3K4Me3 ChIP cell cycle CCA, 70 min | array na_13_038

description: BY4741 cells bearing a deletion in bar1 were grown to an OD of 0.4 and arrested by adding alpha factor to a final concentration of 1 ug/ml and incubated for 3 hours.  To release from arrest, cells were filtered with 0.22 uM Whatman filter, washed with sterile MilliQ water, and the filter paper placed in a flask prewarmed to 30C, containing 450 ml YPD and 22.5 mg pronase.  Upon release, 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, and subjected to immunoprecipitation with with 4 ul Abcam rabbit anti-H3K4Me3 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: H3K4Me3 ChIP cell cycle CCA, 30 min | array na_13_030

description: BY4741 cells bearing a deletion in bar1 were grown to an OD of 0.7 and arrested by adding alpha factor to a final concentration of 1 ug/ml and incubated for 3 hours.  To release from arrest, cells were filtered with 0.22 uM Whatman filter, washed with sterile MilliQ water, and the filter paper placed in a flask prewarmed to 30C, containing 450 ml YPD and 22.5 mg pronase.  Upon release, 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, and subjected to immunoprecipitation with with 4 ul Abcam rabbit anti-H3K4Me3 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: H3K4Me3 ChIP cell cycle CCA, 60 min | array na_13_039

description: BY4741 cells bearing a deletion in bar1 were grown to an OD of 0.4 and arrested by adding alpha factor to a final concentration of 1 ug/ml and incubated for 3 hours.  To release from arrest, cells were filtered with 0.22 uM Whatman filter, washed with sterile MilliQ water, and the filter paper placed in a flask prewarmed to 30C, containing 450 ml YPD and 22.5 mg pronase.  Upon release, 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, and subjected to immunoprecipitation with with 4 ul Abcam rabbit anti-H3K4Me3 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: Control wild-type 1h replicate 6

description: Biological replicate 6

source_name: cells undergoing development for 1 hour


title: H3K4Me3 ChIP cell cycle CCA, 80 min | array na_13_026

description: BY4741 cells bearing a deletion in bar1 were grown to an OD of 0.4 and arrested by adding alpha factor to a final concentration of 1 ug/ml and incubated for 3 hours.  To release from arrest, cells were filtered with 0.22 uM Whatman filter, washed with sterile MilliQ water, and the filter paper placed in a flask prewarmed to 30C, containing 450 ml YPD and 22.5 mg pronase.  Upon release, 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, and subjected to immunoprecipitation with with 4 ul Abcam rabbit anti-H3K4Me3 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: Control wild-type 1h replicate 5

description: Biological replicate 5

source_name: Total RNA from pooled M. xanthus cells at developmental time points


title: ChIP Input cell cycle CCA, 40 min | array na_13_079

description: BY4741 cells bearing a deletion in bar1 were grown to an OD of 0.4 and arrested by adding alpha factor to a final concentration of 1 ug/ml and incubated for 3 hours.  To release from arrest, cells were filtered with 0.22 uM Whatman filter, washed with sterile MilliQ water, and the filter paper placed in a flask prewarmed to 30C, containing 450 ml YPD and 22.5 mg pronase.  Upon release, 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 (ChIP Input).  As a reference, DNA was obtained from sonication of unsynchronized cells.  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: Amplified sonicated DNA

source_name: 40 min


title: Control wild-type 1h replicate 4

description: Biological replicate 4


title: H3K4Me3 ChIP cell cycle CCA, 40 min | array na_13_040

description: BY4741 cells bearing a deletion in bar1 were grown to an OD of 0.4 and arrested by adding alpha factor to a final concentration of 1 ug/ml and incubated for 3 hours.  To release from arrest, cells were filtered with 0.22 uM Whatman filter, washed with sterile MilliQ water, and the filter paper placed in a flask prewarmed to 30C, containing 450 ml YPD and 22.5 mg pronase.  Upon release, 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, and subjected to immunoprecipitation with with 4 ul Abcam rabbit anti-H3K4Me3 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 H3K4Me3 (unsynchronized)


title: H3K4Me3 ChIP cell cycle CCA, 10 min | array na_13_037

description: BY4741 cells bearing a deletion in bar1 were grown to an OD of 0.7 and arrested by adding alpha factor to a final concentration of 1 ug/ml and incubated for 3 hours.  To release from arrest, cells were filtered with 0.22 uM Whatman filter, washed with sterile MilliQ water, and the filter paper placed in a flask prewarmed to 30C, containing 450 ml YPD and 22.5 mg pronase.  Upon release, 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, and subjected to immunoprecipitation with with 4 ul Abcam rabbit anti-H3K4Me3 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: Control wild-type 1h replicate 1

description: Biological replicate 1


title: Control wild-type 0h replicate 5

description: Biological replicate 5

source_name: actively growing cells - 0h


title: Control wild-type 0h replicate 3

description: Biological replicate 3


title: H3K4Me3 ChIP cell cycle CCA, 5 min | array na_13_027

description: BY4741 cells bearing a deletion in bar1 were grown to an OD of 0.7 and arrested by adding alpha factor to a final concentration of 1 ug/ml and incubated for 3 hours.  To release from arrest, cells were filtered with 0.22 uM Whatman filter, washed with sterile MilliQ water, and the filter paper placed in a flask prewarmed to 30C, containing 450 ml YPD and 22.5 mg pronase.  Upon release, cells were harvested after 5 minutes, crosslinked with formaldehyde (1%), washed with water and zymolyase treated.  Extracts of these cells were then digested with MNase, and subjected to immunoprecipitation with with 4 ul Abcam rabbit anti-H3K4Me3 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: Control wild-type 0h replicate 4

description: Biological replicate 4


title: Control wild-type 0h replicate 2

description: Biological replicate 2


title: Control wild-type 0h replicate 1

description: Biological replicate 1


title: ChIP Input cell cycle CCTS, 150 min, array replicate 2 | array na_22_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 150 minutes, crosslinked with formaldehyde (1%), washed with water and zymolyase treated.  Extracts of these cells were then digested with MNase to produce mononucleosomes (ChIP input).  As a reference, ChIP input time points from the entire time course were combined together in equal mass proportion to form a pool.  The ChIP input 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: ChIP Input pool

source_name: 150 min


title: ChIP Input cell cycle CCTS, 170 min, array replicate 2 | array na_22_77

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 (ChIP input).  As a reference, ChIP input time points from the entire time course were combined together in equal mass proportion to form a pool.  The ChIP input 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: ChIP Input cell cycle CCTS, 160 min, array replicate 2 | array na_23_36

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 (ChIP input).  As a reference, ChIP input time points from the entire time course were combined together in equal mass proportion to form a pool.  The ChIP input 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: Control wild-type 1h replicate 3

description: Biological replicate 3


title: ChIP Input cell cycle CCTS, 130 min, array replicate 2 | array na_23_35

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 (ChIP input).  As a reference, ChIP input time points from the entire time course were combined together in equal mass proportion to form a pool.  The ChIP input 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: ChIP Input cell cycle CCTS, 100 min, array replicate 2 | array na_22_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 100 minutes, crosslinked with formaldehyde (1%), washed with water and zymolyase treated.  Extracts of these cells were then digested with MNase to produce mononucleosomes (ChIP input).  As a reference, ChIP input time points from the entire time course were combined together in equal mass proportion to form a pool.  The ChIP input 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: ChIP Input cell cycle CCTS, 120 min, array replicate 2 | array na_22_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 (ChIP input).  As a reference, ChIP input time points from the entire time course were combined together in equal mass proportion to form a pool.  The ChIP input 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: ChIP Input cell cycle CCTS, 90 min, array replicate 2 | array na_22_85

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 (ChIP input).  As a reference, ChIP input time points from the entire time course were combined together in equal mass proportion to form a pool.  The ChIP input 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: ChIP Input cell cycle CCTS, 110 min, array replicate 2 | array na_22_75

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 (ChIP input).  As a reference, ChIP input time points from the entire time course were combined together in equal mass proportion to form a pool.  The ChIP input 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: H3K4Me3 ChIP cell cycle CCA, 50 min | array na_13_033

description: BY4741 cells bearing a deletion in bar1 were grown to an OD of 0.4 and arrested by adding alpha factor to a final concentration of 1 ug/ml and incubated for 3 hours.  To release from arrest, cells were filtered with 0.22 uM Whatman filter, washed with sterile MilliQ water, and the filter paper placed in a flask prewarmed to 30C, containing 450 ml YPD and 22.5 mg pronase.  Upon release, 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, and subjected to immunoprecipitation with with 4 ul Abcam rabbit anti-H3K4Me3 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: Control wild-type 2h replicate 3

description: Biological replicate 3

source_name: cells undergoing development for 2 hours


title: ChIP Input cell cycle CCTS, 140 min, array replicate 2 | array na_22_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 140 minutes, crosslinked with formaldehyde (1%), washed with water and zymolyase treated.  Extracts of these cells were then digested with MNase to produce mononucleosomes (ChIP input).  As a reference, ChIP input time points from the entire time course were combined together in equal mass proportion to form a pool.  The ChIP input 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: ChIP Input cell cycle CCTS, 70 min, array replicate 2 | array na_22_83

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 (ChIP input).  As a reference, ChIP input time points from the entire time course were combined together in equal mass proportion to form a pool.  The ChIP input 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: ChIP Input cell cycle CCTS, 80 min, array replicate 2 | array na_22_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 80 minutes, crosslinked with formaldehyde (1%), washed with water and zymolyase treated.  Extracts of these cells were then digested with MNase to produce mononucleosomes (ChIP input).  As a reference, ChIP input time points from the entire time course were combined together in equal mass proportion to form a pool.  The ChIP input 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: Colon mucosa from rats 7 and 8  vs control pool

city: Florence

first: Maria del Mar

last: Larrosa Pérez

address: Viale G. Pieracinni 6

country: Italy

institute: Department of Pharmacology

hyb_protocol: Gene Expression hybridization kit Agilent hybridization was carried out at 64º C 18h

scan_protocol: GenePix 4000B microarray scanner (Axon Instruments, Foster City, CA, USA)

data_processing: Images were quantified using Agilent Feature Extraction Software (version A.7.5). The log-ratio of the background adjusted intensity on the red channel vs. green channel was normalized by loess to rescale the log-ratios to zero, using R software (http://www.Rproject.org) and the Limma library of Bioconductor (http://www.bioconductor.org). The normalized log-ratios of multiple probes corresponding to a single gene were collapsed using the median to obtain one normalized log-ratios for single gene. Genes with log-ratios not present at least on three arrays were removed during the quality control step.

organism: Rattus norvegicus

source_name: RNA colon mucosa from rats fed with resveratrol + 5% DSS

label_protocol: indirect labelling with CyDye Mono-Reactive Dye Pack, Amersham

growth_protocol: Treated rats were fed with resveratrol 1mg/kg/day for 20d and control rats with standard chow

extract_protocol: Qiagen RNA total extraction kit following manufacturer´s instructions

treatment_protocol: After 20d colitis was induced adding 5% dextran sodium sulphate in drinking water for 5d

tag: Fisher 344 rats

source_name: RNA colon mucosa from rats 5% DSS 5d


title: ChIP Input cell cycle CCTS, 60 min, array replicate 2 | array na_22_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 60 minutes, crosslinked with formaldehyde (1%), washed with water and zymolyase treated.  Extracts of these cells were then digested with MNase to produce mononucleosomes (ChIP input).  As a reference, ChIP input time points from the entire time course were combined together in equal mass proportion to form a pool.  The ChIP input 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: 60 min


title: ChIP Input cell cycle CCTS, 50 min, array replicate 2 | array na_22_87

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 (ChIP input).  As a reference, ChIP input time points from the entire time course were combined together in equal mass proportion to form a pool.  The ChIP input 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: ChIP Input pool


title: Control vs. Global Ischemia

city: Boston

first: James

middle: D

last: McCully

address: 77 Avenue Louis Pasteur

department: Cardiothoracic Surgery

institute: BIDMC/Harvard Medical School

description: New Zealand White rabbits (male, 15-20 weeks; 3 to 4 kg) were used fro Langendorff perfusion.  All rabbits were sedated with acepromazine (0.5 mg/kg, im) and anesthetized with  pentobarbital (50 mg/kg, iv) and received heparin (200 U/kg, iv) via marginal ear vein. Hearts were removed by thoracotomy under deep anesthesia. Control hearts (n=6) were perfused with of Krebs-Ringer solution 100mM NaCl, 4.7 mM KCl, 1.1 mM KH2PO4, 1.2 mM MgSO4, 25 mM NaHCO3, 1.7 mM CaCl2, 11.5 mM glucose, 4.9 mM pyruvic acid, and 5.4 mM fumaric acid)equilibrated with 95% O2 and 5% CO2 (pH 7.4 at 37ºC) at 37°C for 210 minutes.At the completion of Langendorff perfusion the hearts wer snap frozen and stored in liquid nitrogen prior to the isolation of RNA.

hyb_protocol: Hybridization: Contro heart samples were labeled with Cy3-dUTP and  experimental hearts samples (Global ischemia and cardioplegia) were  labeled with Cy5-dUTP and then  combined with 30 uL hybridization solution (stock solution containing 100 uL DIG EasyHyb hybridization solution (Roche), 5 uL yeast tRNA (10 mg/mL), 5 uL human COT1 DNA, 5 uL Poly-dA, and 5 uL salmon sperm DNA (10 mg/mL).  In the case of Global Ischemia vs. Cardioplegia, Global ischemia samples were labeled with Cy3-dUTP and  Cardioplegia  heart samples  were  labeled with Cy5-dUTP and then  combined with 30 uL hybridization solution. The probe solution was hybridized to the arrayed slide at 37 C overnight.  The following day, slides were  washed first with 1x SSC to remove the cover slip (Hybri-Slips, Sigma) , then 3 successive washes of 1x SSC / 0.1% SDS for 15 minutes each at 50 oC, followed by a rinse with 1x SSC.  The slides were dried in individual 50 mL conical tubes and centrifuged at 500 rpm to remove excess fluid.

scan_protocol: Scanning of the slides was performed using the GMS 418 scanner (Affymetrix) at 532 nm (Cy3) and 635 nm (Cy5).

data_processing: Dye-swap, lowess normalization

label: Cy3, Cy5

organism: Oryctolagus cuniculus

source_name: control

label_protocol: Labeling reaction  Total RNA was isolated separately from Control, Global ischemia and Cardioplegia treated  New Zealnad White Rabbit heart tissue using Trizol reagent (Gibco BRL- Life Technologies), according to the manufacturer’s protocol.  Integrity of the RNA was determined by 1% agarose gel containing 3% formaldehyde, 0.02 M MOPS pH 7.4 (3-[N-morpholino] propanesulfonic acid) and 0.001 M disodium EDTA (ethylenediamine tetraacetic acid).RNA (35 ug) from control and experimental groups was used separately for first strand cDNA synthesis using an oligo-dT primer (0.5ug /uL). Following incubation at 65 oC for 5 min. the reaction was  put on ice and the following added:  4uL first strand buffer; 2uL 0.1M DTT;  2L 10X low dTTP–dNTP (5 mM dATP, dCTP, dGTP, and 2 mM dTTP); 2L CyanineX-dUTP (1 mM ; Cyanine3; Cy3 for control; green and Cyanine5; Cy5 for experimental; Amersham, Pharmacia Biotech); 1uL RNasin and 1uL of Superscript II (GIBCO) and incubated at 42 oC  for 30 min. then and another 1uL Superscript II added and the reaction allowed to continue a further 40 min. at 42 oC. The reaction was stopped with the addition of  2.5 uL 500 mM EDTA and heating to 65 oC for 1 min. The RNA template was hydrolyzed with the addition of 5 uL 1M NaOH and incubation at 65 oC for 10 min. and then neutralized by adding 12.5 uL 1M Tris pH 7.5 immediately to neutralize the pH. The labeled cDNA probes were purified by gel exclusion chromatography (ProbeQuant G-50, Amersham) and the volume reduced to 5-10 uL using a Speedvac.

extract_protocol: Total heart (atria and ventricles) RNA extracted using Trizol

treatment_protocol: Langendorff perfusion. New Zealand White rabbits (male,15-20 weeks; 3 to 4 kg) were used fro Langendorff perfusion.  All rabbits were sedated with acepromazine (0.5 mg/kg, im) and anesthetized with  pentobarbital (50 mg/kg, iv) and received heparin (200 U/kg, iv) via marginal ear vein. Hearts were removed by thoracotomy under deep anesthesia. Control hearts (n=6) were perfused with of Krebs-Ringer solution 100mM NaCl, 4.7 mM KCl, 1.1 mM KH2PO4, 1.2 mM MgSO4, 25 mM NaHCO3, 1.7 mM CaCl2, 11.5 mM glucose, 4.9 mM pyruvic acid, and 5.4 mM fumaric acid)equilibrated with 95% O2 and 5% CO2 (pH 7.4 at 37ºC) at 37°C for 210 minutes(11). Global ischemia hearts (GI; N=6) were perfused for 60 minutes and then subjected to 30 minutes global ischemia and 120 minutes of reperfusion. Global ischemia was achieved by cross-clamping the perfusion line. Reperfusion was achieved by release of the crossclamp. Cardioplegia hearts (n=6) received normothermic (37°C) cardioplegia (K/Mg cardioplegia; K+, 20 mmol/L, Mg2+, 20 mmol/L containing  50 µM diazoxide in Krebs-Ringer solution), perfused for 5 minutes prior to global ischemia (4).  Diazoxide was dissolved in dimethyl sulfoxide (DMSO, Fisher Scientific Co., Fair Lawn, NJ) before being added into Krebs-Ringer solution.  The final concentration of DMSO was less than 0.1%. DMSO was added to Control and GI hearts at the same concentration. At the completion of Langendorff perfusion the hearts wer snap frozen and stored in liquid nitrogen prior to the isolation of RNA.

source_name: global ischemia


title: Colon mucosa from rats 5 and 6  vs control pool


title: Global Ischemia vs. Cardioplegia

description: New Zealand White rabbits (male,15-20 weeks; 3 to 4 kg) were used fro Langendorff perfusion.  All rabbits were sedated with acepromazine (0.5 mg/kg, im) and anesthetized with  pentobarbital (50 mg/kg, iv) and received heparin (200 U/kg, iv) via marginal ear vein. Hearts were removed by thoracotomy under deep anesthesia.ardioplegia hearts (n=6) received normothermic (37°C) cardioplegia (K/Mg cardioplegia; K+, 20 mmol/L, Mg2+, 20 mmol/L containing  50 µM diazoxide in Krebs-Ringer solution), perfused for 5 minutes prior to global ischemia (4).  Diazoxide was dissolved in dimethyl sulfoxide (DMSO, Fisher Scientific Co., Fair Lawn, NJ) before being added into Krebs-Ringer solution.  The final concentration of DMSO was less than 0.1%. DMSO was added to Control and GI hearts at the same concentration. At the completion of Langendorff perfusion the hearts wer snap frozen and stored in liquid nitrogen prior to the isolation of RNA.

tag: New Zealand White rabbits (male, 15-20 weeks; 3 to 4 kg)

source_name: cardioplegia


title: Control vs. Cardioplegia

description: New Zealand White rabbits (male,15-20 weeks; 3 to 4 kg) were used fro Langendorff perfusion.  All rabbits were sedated with acepromazine (0.5 mg/kg, im) and anesthetized with  pentobarbital (50 mg/kg, iv) and received heparin (200 U/kg, iv) via marginal ear vein. Hearts were removed by thoracotomy under deep anesthesia.Global ischemia hearts (GI; N=6) were perfused for 60 minutes and then subjected to 30 minutes global ischemia and 120 minutes of reperfusion. Global ischemia was achieved by cross-clamping the perfusion line. Reperfusion was achieved by release of the crossclamp.At the completion of Langendorff perfusion the hearts wer snap frozen and stored in liquid nitrogen prior to the isolation of RNA.


title: Colon mucosa from rats 1 and 2  vs control pool


title: ChIP Input cell cycle CCTS, 40 min, array replicate 2 | array na_22_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 40 minutes, crosslinked with formaldehyde (1%), washed with water and zymolyase treated.  Extracts of these cells were then digested with MNase to produce mononucleosomes (ChIP input).  As a reference, ChIP input time points from the entire time course were combined together in equal mass proportion to form a pool.  The ChIP input 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: Colon mucosa from rats 3 and 4  vs control pool


title: tetC (tetC-Myc) induced MEFs

city: Los Angeles

first: Kathrin

last: Plath

state: CA

address: 615 Charles E. Young Drive South

department: Biological Chemistry

institute: UCLA

hyb_protocol: standard Affymetrix protocol (UCLA Clinical Microarray Core)

data_processing: all data were quantile normalized

organism: Mus musculus

source_name: Cell culture

extract_protocol: Trizol and RNEasy purification

tag: tetC-Myc induced MEFs


title: tetS (tet-Sox2) induced MEFs

scan_protocol: standard Affymetrix protocol (UCLA Clinical Microarray Core)

tag: tet-Sox2 induced MEFs


title: ChIP Input cell cycle CCTS, 20 min, array replicate 2 | array na_22_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 20 minutes, crosslinked with formaldehyde (1%), washed with water and zymolyase treated.  Extracts of these cells were then digested with MNase to produce mononucleosomes (ChIP input).  As a reference, ChIP input time points from the entire time course were combined together in equal mass proportion to form a pool.  The ChIP input 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: 20 min


title: ChIP Input cell cycle CCTS, 10 min, array replicate 2 | array na_22_84

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 (ChIP input).  As a reference, ChIP input time points from the entire time course were combined together in equal mass proportion to form a pool.  The ChIP input 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: ChIP Input cell cycle CCTS, 30 min, array replicate 2 | array na_23_34

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 (ChIP input).  As a reference, ChIP input time points from the entire time course were combined together in equal mass proportion to form a pool.  The ChIP input 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: ChIP Input cell cycle CCTS, 170 min, array replicate 1 | array na_23_47

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 (ChIP input).  As a reference, ChIP input time points from the entire time course were combined together in equal mass proportion to form a pool.  The ChIP input 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: ChIP Input cell cycle CCTS, 0 min, array replicate 2 | array na_22_78

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 immediately, crosslinked with formaldehyde (1%), washed with water and zymolyase treated.  Extracts of these cells were then digested with MNase to produce mononucleosomes (ChIP input).  As a reference, ChIP input time points from the entire time course were combined together in equal mass proportion to form a pool.  The ChIP input 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: OCK Clone 3 - generated from Oct4/c-Myc/Klf4 infected MEFs

label_protocol: standard Affymetrix protocol (UCLA Clinical Microarray Core)

tag: Clones generated from Oct4/c-Myc/Klf4 infected MEFs


title: tetO (tet-Oct4) induced MEFs

tag: tet-Oct4 induced MEFs


title: H3K4Me3 ChIP cell cycle CCA, 0 min | array na_13_032

description: BY4741 cells bearing a deletion in bar1 were grown to an OD of 0.7 and arrested by adding alpha factor to a final concentration of 1 ug/ml and incubated for 3 hours.  To release from arrest, cells were filtered with 0.22 uM Whatman filter, washed with sterile MilliQ water, and the filter paper placed in a flask prewarmed to 30C, containing 450 ml YPD and 22.5 mg pronase.  Upon release, cells were immediately harvested, crosslinked with formaldehyde (1%), washed with water and zymolyase treated.  Extracts of these cells were then digested with MNase, and subjected to immunoprecipitation with with 4 ul Abcam rabbit anti-H3K4Me3 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 H3K4Me3 (unsynchronized)


title: tetK (tet-Klf4) induced MEFs

tag: tet-Klf4 induced MEFs


title: ChIP Input cell cycle CCTS, 150 min, array replicate 1 | array na_22_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 150 minutes, crosslinked with formaldehyde (1%), washed with water and zymolyase treated.  Extracts of these cells were then digested with MNase to produce mononucleosomes (ChIP input).  As a reference, ChIP input time points from the entire time course were combined together in equal mass proportion to form a pool.  The ChIP input 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.

tag: Strain

source_name: 150 min


title: ChIP Input cell cycle CCTS, 140 min, array replicate 1 | array na_23_48

source_name: 140 min


title: ChIP Input cell cycle CCTS, 160 min, array replicate 1 | array na_22_71

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 (ChIP input).  As a reference, ChIP input time points from the entire time course were combined together in equal mass proportion to form a pool.  The ChIP input 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: ChIP Input cell cycle CCTS, 130 min, array replicate 1 | array na_22_61

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 (ChIP input).  As a reference, ChIP input time points from the entire time course were combined together in equal mass proportion to form a pool.  The ChIP input 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: ChIP Input cell cycle CCTS, 120 min, array replicate 1 | array na_22_65

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 (ChIP input).  As a reference, ChIP input time points from the entire time course were combined together in equal mass proportion to form a pool.  The ChIP input 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: OCK Clone 2 - generated from Oct4/c-Myc/Klf4 infected MEFs


title: ChIP Input cell cycle CCTS, 90 min, array replicate 1 | array na_22_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 90 minutes, crosslinked with formaldehyde (1%), washed with water and zymolyase treated.  Extracts of these cells were then digested with MNase to produce mononucleosomes (ChIP input).  As a reference, ChIP input time points from the entire time course were combined together in equal mass proportion to form a pool.  The ChIP input 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: ChIP Input pool

source_name: 90 min


title: ChIP Input cell cycle CCTS, 60 min, array replicate 1 | array na_22_68

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 (ChIP input).  As a reference, ChIP input time points from the entire time course were combined together in equal mass proportion to form a pool.  The ChIP input 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: 60 min


title: T Cells Replicate 3

city: Pamplona

first: Raquel

last: Malumbres

state: Navarra

address: Avenida Pio XII 55

department: Hemato-Oncology

country: Spain

institute: University of Navarra/ Clínica Universidad de Navarra

description: Biological replicate 3 of 3. T cell, untreated, purified from reactive tonsils

hyb_protocol: Hybridization was performed overnight on a µParaflo microfluidic chip using a microcirculation pump. Hybridization solution consisted of 100 µL of 6× SSPE buffer (0.90 M NaCl, 60 mM Na2HPO4, 6 mM EDTA, pH 6.8) containing 25% formamide at 34°C. After hybridization, the miRNAs were detected by fluorescence labeling using tag-specific Cy3 and Cy5 dyes

scan_protocol: Scanned on a GenePix 4000B (Molecular Device) laser scanner Images were quantified using Array-Pro image analysis software (Media Cybernetics)

data_processing: Median normalized, background subtracted data was used to calculate the ratio of processed Green signal/processed Red signal, and ratios were then log2 transformed. Probes hsa-miR-377 and hsa-miR-542-5p were excluded due to systematic dye bias, following manufacturer instructions.

source_name: Tonsilar T cells

label_protocol: The assay started with 5 µg of total RNA sample. The RNA was size-fractionated using a YM-100 Microcon centrifugal filter (GE Millipore), and the 3′ ends of the small RNAs (<300 nt) were extended with a poly(A) tail using poly(A) polymerase. An oligonucleotide tag was then ligated to the poly(A) tail for later fluorescent dye staining; two different tags were used for the two RNA samples in the dual-sample experiments

extract_protocol: Total RNA extracted using mirVana™ miRNA Isolation Kit (Ambion) following manufacturer's instructions

tag: Extracted from reactive tonsils

source_name: FirstChoice® Human Skeletal Muscle Total RNA (Ambion)

tag: Total RNA from healthy human skeletal muscle

tag: Tissue

value: skeletal muscle


title: 10 colonies from 1A2 partial iPS clone (1A2-col)

source_name: Cell culture

tag: 10 colonies of the 1A2 clone (1A2-col)


title: ChIP Input cell cycle CCTS, 20 min, array replicate 1 | array na_22_66

source_name: 20 min


title: ChIP Input cell cycle CCTS, 100 min, array replicate 1 | array na_22_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 (ChIP input).  As a reference, ChIP input time points from the entire time course were combined together in equal mass proportion to form a pool.  The ChIP input 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: ChIP Input cell cycle CCTS, 50 min, array replicate 1 | array na_23_46

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 (ChIP input).  As a reference, ChIP input time points from the entire time course were combined together in equal mass proportion to form a pool.  The ChIP input 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: ChIP Input cell cycle CCTS, 30 min, array replicate 1 | array na_22_62

source_name: 30 min


title: uninduced MEFs for tet experiments

tag: uninduced MEFs


title: Control wild-type 1h replicate 2

description: Biological replicate 2

source_name: cells undergoing development for 1 hour

source_name: Total RNA from pooled M. xanthus cells at developmental time points


title: ChIP Input cell cycle CCTS, 0 min, array replicate 1 | array na_22_72

source_name: 0 min


title: ChIP Input cell cycle CCTS, 40 min, array replicate 1 | array na_22_73

source_name: 40 min


title: H3K4Me3 cell cycle CCTS, 160 min, array replicate 2 | array na_20_12

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 5 ul Upstate mouse anti-H3K4Me3 monoclonal antibody clone MC315.  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 H3K4Me3 (unsynchronized)

source_name: 160 min


title: H3K4Me3 cell cycle CCTS, 170 min, array replicate 2 | array na_20_17

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 5 ul Upstate mouse anti-H3K4Me3 monoclonal antibody clone MC315.  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