title: 1h mock, 0-60 min 200µM 4sU nt-RNA Rep.1

description: 60 min newly transcribed RNA (nt-RNA)

source_name: NIH-3T3 cells

growth_protocol: 37°C, 5% CO2, DMEM + 5%NCS + P/S

tag: NIH-3T3 cells 1h mock, 0-60min 200µM 4sU

tag: NIH-3T3 cells split 24 h before start of experiment


title: 1h mock, 0-60 min 200µM 4sU nt-RNA Rep.2

status: Public on Sep 30 2009

type: RNA

city: Cambridge

first: Lars

last: Dölken

state: Cambridgeshire

address: Addenbrookes Hospital, Hills Road

department: Medicine

country: United Kingdom

institute: University of Cambridge

description: 60 min newly transcribed RNA (nt-RNA)

hyb_protocol: Affymetrix standard

scan_protocol: GeneChips were scanned using the Affymetrix 7G Scanner

data_processing: GCRMA

label: biotin

molecule: total RNA

organism: Mus musculus

label_protocol: Affymetrix one cycle target labeling protocol

extract_protocol: Trizol extraction of total RNA was performed following the modified protocol described by Chomczynski et al.

treatment_protocol: NIH-3T3 cells (5th to 15th passage after thawing) were plated at 40% density 24 h before the begin of the experiment (=> 80% density at start of experiment)


title: 1h mock, 0-60 min 200µM 4sU tc-RNA Rep. 2

description: total cellular RNA (tc-RNA)

growth_protocol: DMEM + 5%NCS + P/S, 37°C, 5% CO2


title: 1h mock, 0-60 min 200µM 4sU nt-RNA Rep.3

description: 60 min newly transcribed RNA (nt-RNA)


title: BL41 60 min nt-RNA Rep.2

description: newly transcribed RNA (nt-RNA)

organism: Homo sapiens

source_name: B41 human B-cells

growth_protocol: RPMI, 10% FCS, P/S, 37°C, 5% CO2

treatment_protocol: 60 min 100 µM 4sU

tag: Burkitt lymphoma cell line


title: 1h mock, 0-60 min 200µM 4sU tc-RNA Rep. 1

description: total cellular RNA (tc-RNA)


title: 1h mock, 0-60 min 200µM 4sU tc-RNA Rep. 3

description: total cellular RNA (tc-RNA)


title: Chromosomal distribution of Mis6 in cd39 (#2)

status: Public on Aug 22 2008

type: genomic

city: Kami

first: Kojiro

last: Ishii

state: Kochi

address: 185 Miyanokuchi, Tosayamada

country: Japan

institute: Kochi University of Technology

description: Comparing between genome DNA (Cy3) and DNA co-immunopurified with Mis6 (Cy5) from the Schizosaccharomyces pombe cen1 deletion survivor cd39

hyb_protocol: Hybridisation was carried out at 65 °C for 40 h against the 4 x 44K slide of S. pombe whole genome ChIP-on-chip microarray (G4810A, Agilent Technologies) according to the manufacturer’s instructions. The slide was then washed with Wash Buffer 1 for 5 min at room temperature and with Wash Buffer 2 for 5 min at 31 ºC, according to the manufacturer’s instructions (Agilent Technologies), in ozone-depleted surroundings.

scan_protocol: Microarray slide was scanned using the Agilent Microarray Scanner G2505B and Scan Control Software G2565BA, followed by extraction of information from the probe features using Agilent Feature Extraction Software 9.5.1.1.

data_processing: For each data set, intra-array Lowess (intensity-dependent) normalization was performed using the Agilent ChIP Analytics Software 1.3.1, and the enrichment ratios were calculated by dividing the normalised ChIP (Cy5) signals over corresponding WCE (Cy3) signals.

molecule: genomic DNA

organism: Schizosaccharomyces pombe

source_name: Chromatin-immunoprecipitated (ChIP) DNA for Mis6

label_protocol: ChIP-purified DNA was treated with RNase A, flush-ended using T7 DNA polymerase, and ligated with the double-stranded DNA linker using T4 DNA ligase. Linker-ligated DNA was PCR-amplified using AmpliTaq DNA polymerase, and then labelled with Cy5-dUTP by using the Invitrogen BioPrime Array CGH Genomic Labeling System.

growth_protocol: Cells were fixed with 3% formaldehyde at 18 °C for 35 min, and the fixation reaction was terminated by adding 330 mM final concentration of glycine and incubating for 10 min; the cells were collected by centrifugation and washed 3 times with 1x PBS.

extract_protocol: Cell lysates were prepared by glass bead vortexing in FA-lysis buffer (50 mM HEPES-KOH (pH 7.5), 150 mM NaCl, 1 mM EDTA, 0.1% sodium deoxycholate, 1x Complete) containing 0.5% SDS. The cross-linked chromatin was then pelleted by centrifuging the lysate, and after a wash with ice-cold FA-lysis buffer containing 0.1% SDS, the chromatin pellet was sonicated to yield soluble fragments with an average size of 500 bp and a range between 300 and 1000 bp. The reaction was clarified by centrifugation, and the chromatin solution was supplemented with 1% Triton X-100 and applied for the immunoprecipitation using anti-GFP (Roche) and Dynabeads M-280 (Dynal). The beads were subsequently washed 3 times in ice-cold FA-lysis buffer containing 0.1% SDS and 1% Triton X-100; once in the same buffer containing 0.5 M NaCl; once in 10 mM Tris-HCl (pH 8.0), 250 mM LiCl, 1 mM EDTA, 0.5% NP-40, and 0.5% sodium deoxycholate; and once in TE (10 mM Tris-HCl (pH 8.0), 1 mM EDTA). To elute DNA and revert cross-links, the beads were incubated with SDS-TE (1% SDS, 10 mM Tris-HCl (pH 8.0), 1 mM EDTA) for 15 h at 65 °C, followed by digestion with proteinase K at 42 °C. After extraction with phenol, DNA was precipitated with isopropanol and resuspended in TE.

treatment_protocol: Exponentially growing fission yeast cells were asynchromously cultured at 33 °C in YES, and transferred to 18 °C for 2 h prior to fixation.

tag: neocentric cell; h- leu1 ura4 cen1D::kanR cd39 mis6-GFP strain

source_name: Chromatin-input DNA (WCE) for Mis6

label_protocol: WCE DNA was treated with RNase A, flush-ended using T7 DNA polymerase, and ligated with the double-stranded DNA linker using T4 DNA ligase. Linker-ligated DNA was PCR-amplified using AmpliTaq DNA polymerase, and then labelled with Cy3-dUTP by using the Invitrogen BioPrime Array CGH Genomic Labeling System.

extract_protocol: Cell lysates were prepared by glass bead vortexing in FA-lysis buffer (50 mM HEPES-KOH (pH 7.5), 150 mM NaCl, 1 mM EDTA, 0.1% sodium deoxycholate, 1x Complete) containing 0.5% SDS. The cross-linked chromatin was then pelleted by centrifuging the lysate, and after a wash with ice-cold FA-lysis buffer containing 0.1% SDS, the chromatin pellet was sonicated to yield soluble fragments with an average size of 500 bp and a range between 300 and 1000 bp. The reaction was clarified by centrifugation, and the chromatin solution was supplemented with 1% Triton X-100. To elute DNA and revert cross-links, the beads were incubated with SDS-TE (1% SDS, 10 mM Tris-HCl (pH 8.0), 1 mM EDTA) for 15 h at 65 °C, followed by digestion with proteinase K at 42 °C. After extraction with phenol, DNA was precipitated with isopropanol and resuspended in TE.


title: Chromosomal distribution of H3me2K9 in WT (#2, dye-swapped)

description: Comparing between genome DNA (Cy5) and DNA co-immunopurified with H3me2K9 (Cy3) from the Schizosaccharomyces pombe wild-type

data_processing: For each data set, intra-array Lowess (intensity-dependent) normalization was performed using the Agilent ChIP Analytics Software 1.3.1, and the enrichment ratios were calculated by dividing the normalised ChIP (Cy3) signals over corresponding WCE (Cy5) signals.

source_name: Chromatin-input DNA (WCE) for H3me2K9

label_protocol: WCE DNA was treated with RNase A, flush-ended using T7 DNA polymerase, and ligated with the double-stranded DNA linker using T4 DNA ligase. Linker-ligated DNA was PCR-amplified using AmpliTaq DNA polymerase, and then labelled with Cy5-dUTP by using the Agilent Genomic DNA Labeling Kit PLUS.

tag: wild-type; h- leu1 ura4 mis6-GFP strain

source_name: Chromatin-immunoprecipitated (ChIP) DNA for H3me2K9

label_protocol: ChIP-purified DNA was treated with RNase A, flush-ended using T7 DNA polymerase, and ligated with the double-stranded DNA linker using T4 DNA ligase. Linker-ligated DNA was PCR-amplified using AmpliTaq DNA polymerase, and then labelled with Cy3-dUTP by using the Agilent Genomic DNA Labeling Kit PLUS.

extract_protocol: Cell lysates were prepared by glass bead vortexing in FA-lysis buffer (50 mM HEPES-KOH (pH 7.5), 150 mM NaCl, 1 mM EDTA, 0.1% sodium deoxycholate, 1x Complete) containing 0.5% SDS. The cross-linked chromatin was then pelleted by centrifuging the lysate, and after a wash with ice-cold FA-lysis buffer containing 0.1% SDS, the chromatin pellet was sonicated to yield soluble fragments with an average size of 500 bp and a range between 300 and 1000 bp. The reaction was clarified by centrifugation, and the chromatin solution was supplemented with 1% Triton X-100 and applied for the immunoprecipitation using anti-H3me2K9 (Abcam) and Dynabeads M-280 (Dynal). The beads were subsequently washed 3 times in ice-cold FA-lysis buffer containing 0.1% SDS and 1% Triton X-100; once in the same buffer containing 0.5 M NaCl; once in 10 mM Tris-HCl (pH 8.0), 250 mM LiCl, 1 mM EDTA, 0.5% NP-40, and 0.5% sodium deoxycholate; and once in TE (10 mM Tris-HCl (pH 8.0), 1 mM EDTA). To elute DNA and revert cross-links, the beads were incubated with SDS-TE (1% SDS, 10 mM Tris-HCl (pH 8.0), 1 mM EDTA) for 15 h at 65 °C, followed by digestion with proteinase K at 42 °C. After extraction with phenol, DNA was precipitated with isopropanol and resuspended in TE.


title: Chromosomal distribution of H3me2K9 in WT (#2)

description: Comparing between genome DNA (Cy3) and DNA co-immunopurified with H3me2K9 (Cy5) from the Schizosaccharomyces pombe wild-type

label_protocol: ChIP-purified DNA was treated with RNase A, flush-ended using T7 DNA polymerase, and ligated with the double-stranded DNA linker using T4 DNA ligase. Linker-ligated DNA was PCR-amplified using AmpliTaq DNA polymerase, and then labelled with Cy5-dUTP by using the Agilent Genomic DNA Labeling Kit PLUS.

label_protocol: WCE DNA was treated with RNase A, flush-ended using T7 DNA polymerase, and ligated with the double-stranded DNA linker using T4 DNA ligase. Linker-ligated DNA was PCR-amplified using AmpliTaq DNA polymerase, and then labelled with Cy3-dUTP by using the Agilent Genomic DNA Labeling Kit PLUS.


title: Chromosomal distribution of H3me2K9 in cd39 (#3, dye-swapped)

description: Comparing between genome DNA (Cy5) and DNA co-immunopurified with H3me2K9 (Cy3) from the Schizosaccharomyces pombe cen1 deletion survivor cd39


title: Chromosomal distribution of H3me2K9 in cd39 (#2)

description: Comparing between genome DNA (Cy3) and DNA co-immunopurified with H3me2K9 (Cy5) from the Schizosaccharomyces pombe cen1 deletion survivor cd39


title: Chromosomal distribution of H3me2K9 in cd39 (#3)


title: Chromosomal distribution of Mis6 in cd60 (#2)

description: Comparing between genome DNA (Cy3) and DNA co-immunopurified with Mis6 (Cy5) from the Schizosaccharomyces pombe cen1 deletion survivor cd60

tag: neocentric cell; h- leu1 ura4 cen1D::kanR cd60 mis6-GFP strain


title: Chromosomal distribution of H3me2K9 in cd39 (#2, dye-swapped)


title: Chromosomal distribution of Swi6 in cd60

description: Comparing between genome DNA (Cy3) and DNA co-immunopurified with Swi6 (Cy5) from the Schizosaccharomyces pombe cen1 deletion survivor cd60

source_name: Chromatin-immunoprecipitated (ChIP) DNA for Swi6

extract_protocol: Cell lysates were prepared by glass bead vortexing in FA-lysis buffer (50 mM HEPES-KOH (pH 7.5), 150 mM NaCl, 1 mM EDTA, 0.1% sodium deoxycholate, 1x Complete) containing 0.5% SDS. The cross-linked chromatin was then pelleted by centrifuging the lysate, and after a wash with ice-cold FA-lysis buffer containing 0.1% SDS, the chromatin pellet was sonicated to yield soluble fragments with an average size of 500 bp and a range between 300 and 1000 bp. The reaction was clarified by centrifugation, and the chromatin solution was supplemented with 1% Triton X-100 and applied for the immunoprecipitation using anti-Swi6 (Abcam) and Dynabeads M-280 (Dynal). The beads were subsequently washed 3 times in ice-cold FA-lysis buffer containing 0.1% SDS and 1% Triton X-100; once in the same buffer containing 0.5 M NaCl; once in 10 mM Tris-HCl (pH 8.0), 250 mM LiCl, 1 mM EDTA, 0.5% NP-40, and 0.5% sodium deoxycholate; and once in TE (10 mM Tris-HCl (pH 8.0), 1 mM EDTA). To elute DNA and revert cross-links, the beads were incubated with SDS-TE (1% SDS, 10 mM Tris-HCl (pH 8.0), 1 mM EDTA) for 15 h at 65 °C, followed by digestion with proteinase K at 42 °C. After extraction with phenol, DNA was precipitated with isopropanol and resuspended in TE.

source_name: Chromatin-input DNA (WCE) for Swi6


title: Chromosomal distribution of H3me2K9 in cd60

description: Comparing between genome DNA (Cy3) and DNA co-immunopurified with H3me2K9 (Cy5) from the Schizosaccharomyces pombe cen1 deletion survivor cd60


title: Chromosomal distribution of Mis12 in cd60

description: Comparing between genome DNA (Cy3) and DNA co-immunopurified with Mis12 (Cy5) from the Schizosaccharomyces pombe cen1 deletion survivor cd60

source_name: Chromatin-immunoprecipitated (ChIP) DNA for Mis12

tag: neocentric cell; h- leu1 ura4 cen1D::kanR cd60 mis12-GFP strain

source_name: Chromatin-input DNA (WCE) for Mis12


title: Chromosomal distribution of Mis6 in WT (#2)

description: Comparing between genome DNA (Cy3) and DNA co-immunopurified with Mis6 (Cy5) from the Schizosaccharomyces pombe wild-type


title: Chromosomal distribution of Cnp3 in cd60

description: Comparing between genome DNA (Cy3) and DNA co-immunopurified with Cnp3 (Cy5) from the Schizosaccharomyces pombe cen1 deletion survivor cd60

source_name: Chromatin-immunoprecipitated (ChIP) DNA for Cnp3

tag: neocentric cell; h- leu1 ura4 cen1D::kanR cd60 Cnp3-GFP strain

source_name: Chromatin-input DNA (WCE) for Cnp3


title: Chromosomal distribution of H3me2K9 in cd39


title: Chromosomal distribution of Mis6 in cd60


title: Chromosomal distribution of Swi6 in WT

description: Comparing between genome DNA (Cy3) and DNA co-immunopurified with Swi6 (Cy5) from the Schizosaccharomyces pombe wild-type


title: Chromosomal distribution of Cnp1 in cd60

description: Comparing between genome DNA (Cy3) and DNA co-immunopurified with Cnp1 (Cy5) from the Schizosaccharomyces pombe cen1 deletion survivor cd60

source_name: Chromatin-immunoprecipitated (ChIP) DNA for Cnp1

extract_protocol: Cell lysates were prepared by glass bead vortexing in FA-lysis buffer (50 mM HEPES-KOH (pH 7.5), 150 mM NaCl, 1 mM EDTA, 0.1% sodium deoxycholate, 1x Complete) containing 0.5% SDS. The cross-linked chromatin was then pelleted by centrifuging the lysate, and after a wash with ice-cold FA-lysis buffer containing 0.1% SDS, the chromatin pellet was sonicated to yield soluble fragments with an average size of 500 bp and a range between 300 and 1000 bp. The reaction was clarified by centrifugation, and the chromatin solution was supplemented with 1% Triton X-100 and applied for the immunoprecipitation using anti-Cnp1 (Takayama et al. (2008) Mol. Biol. Cell 19 682-690) and Dynabeads M-280 (Dynal). The beads were subsequently washed 3 times in ice-cold FA-lysis buffer containing 0.1% SDS and 1% Triton X-100; once in the same buffer containing 0.5 M NaCl; once in 10 mM Tris-HCl (pH 8.0), 250 mM LiCl, 1 mM EDTA, 0.5% NP-40, and 0.5% sodium deoxycholate; and once in TE (10 mM Tris-HCl (pH 8.0), 1 mM EDTA). To elute DNA and revert cross-links, the beads were incubated with SDS-TE (1% SDS, 10 mM Tris-HCl (pH 8.0), 1 mM EDTA) for 15 h at 65 °C, followed by digestion with proteinase K at 42 °C. After extraction with phenol, DNA was precipitated with isopropanol and resuspended in TE.

source_name: Chromatin-input DNA (WCE) for Cnp1


title: Chromosomal distribution of Mis6 in cd39


title: Chromosomal distribution of Swi6 in cd39

description: Comparing between genome DNA (Cy3) and DNA co-immunopurified with Swi6 (Cy5) from the Schizosaccharomyces pombe cen1 deletion survivor cd39


title: Chromosomal distribution of Cnp1 in cd39

description: Comparing between genome DNA (Cy3) and DNA co-immunopurified with Cnp1 (Cy5) from the Schizosaccharomyces pombe cen1 deletion survivor cd39


title: Chromosomal distribution of H3me2K9 in WT


title: Chromosomal distribution of Mis6 in WT


title: Chromosomal distribution of Cnp1 in WT

description: Comparing between genome DNA (Cy3) and DNA co-immunopurified with Cnp1 (Cy5) from the Schizosaccharomyces pombe wild-type