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text: adult

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text: Protocols: Rats were kept in the animal facility of the Institute of Physiology, Czech Academy of Science (Prague, Czech Republic) in a climate-controlled environment with 12h light/dark cycles. Rats were housed in polystyrene cages containing wood shavings and fed standard rodent chow and water ad libitum. Six weeks old male rats were sacrificed by cervical dislocation and tissue (left ventricle of the heart and liver) was collected between 8 and 10 am, snap frozen in liquid nitrogen and stored at -80 C. All animal procedures were in accordance with the Animal Protection Law of the Czech Republic. ChIP samples were prepared as previously described (Barski, A. et al. High-resolution profiling of histone methylations in the human genome. Cell 129, 823-37, 2007) with following changes: Frozen LV and liver tissue was crunched using pestle and mortar. 125mg tissue was homogenized in a Potter- Elvehjem tissue grinder, nuclei were isolated and digested with MNase (Sigma- Aldrich) to generate native chromatin templates consisting mainly of mononucleosomes. Chromatin was precipitated with anti-H3K4me3 (NEB, 9751 S), anti-H3K27me3 (Millipore, 07-449), anti-H3K4me1 (Abcam, ab8895), or anti- H4K20me1 (Abcam, ab9051) and antibody-bound DNA fragments were purified by MinElute PCR Purification Kit (QIAGEN). Specificity of immunoprecipitation was confirmed with known genes by qPCR. 50ng of DNA was used for construction of ChIP-seq libraries according to the manufacturer's protocol (Illumina/Solexa).

characteristic: description

text: adult

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text: Rattus norvegicus


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text: Max-Delbrueck-Center, MDC, Berlin

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text: Max-Delbrueck-Center, MDC, Berlin

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text: Norway rat

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text: 6 week

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text: Max-Delbrueck-Center, MDC, Berlin

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characteristic: External Id

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text: adult

text: Rattus norvegicus

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text: Max-Delbrueck-Center, MDC, Berlin

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characteristic: description

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text: adult

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text: Max-Delbrueck-Center, MDC, Berlin

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text: ArrayExpress

text: Norway rat

text: Protocols: Rats were kept in the animal facility of the Institute of Physiology, Czech Academy of Science (Prague, Czech Republic) in a climate-controlled environment with 12h light/dark cycles. Rats were housed in polystyrene cages containing wood shavings and fed standard rodent chow and water ad libitum. Six weeks old male rats were sacrificed by cervical dislocation and tissue (left ventricle of the heart and liver) was collected between 8 and 10 am, snap frozen in liquid nitrogen and stored at -80 C. All animal procedures were in accordance with the Animal Protection Law of the Czech Republic. ChIP samples were prepared as previously described (Barski, A. et al. High-resolution profiling of histone methylations in the human genome. Cell 129, 823-37, 2007) with following changes: Frozen LV and liver tissue was crunched using pestle and mortar. 125mg tissue was homogenized in a Potter- Elvehjem tissue grinder, nuclei were isolated and digested with MNase (Sigma- Aldrich) to generate native chromatin templates consisting mainly of mononucleosomes. Chromatin was precipitated with anti-H3K4me3 (NEB, 9751 S), anti-H3K27me3 (Millipore, 07-449), anti-H3K4me1 (Abcam, ab8895), or anti- H4K20me1 (Abcam, ab9051) and antibody-bound DNA fragments were purified by MinElute PCR Purification Kit (QIAGEN). Specificity of immunoprecipitation was confirmed with known genes by qPCR. 50ng of DNA was used for construction of ChIP-seq libraries according to the manufacturer's protocol (Illumina/Solexa).

text: adult

text: Rattus norvegicus

text: Rattus norvegicus

text: liver

text: Rattus norvegicus


text: Max-Delbrueck-Center, MDC, Berlin

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-1102:lv-H3K4me3-HXB10-male-bio1-tech1.bam

text: 6 week

text: ArrayExpress

text: Norway rat

text: adult

text: Rattus norvegicus

text: Rattus norvegicus

text: heart

text: Rattus norvegicus


text: Max-Delbrueck-Center, MDC, Berlin

text: public

text: E-MTAB-1102:liver-H3K4me3-HXB25-male-bio1-tech1.bam

characteristic: Submitter Id

text: 6 week

text: ArrayExpress

characteristic: broker name

text: Norway rat

text: adult

text: Rattus norvegicus

text: Rattus norvegicus

text: liver

text: Rattus norvegicus


text: Max-Delbrueck-Center, MDC, Berlin

text: public

text: E-MTAB-1102:liver-H3K27me3-HXB01-male-bio1-tech1.bam

text: 6 week

text: ArrayExpress

text: Norway rat

characteristic: common name

characteristic: description

text: adult

text: Rattus norvegicus

text: Rattus norvegicus

text: liver

text: Rattus norvegicus


text: Max-Delbrueck-Center, MDC, Berlin

text: public

text: E-MTAB-1102:lv-H3K4me3-HXB24-male-bio1-tech1.bam

text: 6 week

text: ArrayExpress

text: Norway rat

text: adult

text: Rattus norvegicus

characteristic: organism

text: Rattus norvegicus

text: heart

text: Rattus norvegicus

characteristic: title


text: Max-Delbrueck-Center, MDC, Berlin

text: public

characteristic: StrainOrLine

text: E-MTAB-1102:liver-H3K27me3-HXB22-male-bio1-tech1.bam

text: 6 week

characteristic: age

text: ArrayExpress

text: Norway rat

text: adult

text: Rattus norvegicus

text: Rattus norvegicus

text: liver

text: Rattus norvegicus


text: Max-Delbrueck-Center, MDC, Berlin

text: public

text: SHR

text: E-MTAB-1102:liver-input-SHR-male-bio1-tech1.bam

text: 6 week

text: ArrayExpress

text: Norway rat

text: adult

characteristic: developmental stage

text: Rattus norvegicus

text: Rattus norvegicus

text: liver

characteristic: organism part

text: Rattus norvegicus


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: Max-Delbrueck-Center, MDC, Berlin

text: public

text: E-MTAB-1102:lv-H3K4me3-BXH13-male-bio1-tech1.bam

text: 6 week

text: ArrayExpress

text: Norway rat

text: adult

text: Rattus norvegicus

text: Rattus norvegicus

text: heart

text: Rattus norvegicus


characteristic: External Id

text: Max-Delbrueck-Center, MDC, Berlin

characteristic: INSDC center name

text: public

text: E-MTAB-1102:liver-H3K4me3-HXB24-male-bio1-tech1.bam

text: 6 week

text: ArrayExpress

text: Norway rat

text: adult

text: Rattus norvegicus

text: Rattus norvegicus

text: liver

text: Rattus norvegicus


text: Max-Delbrueck-Center, MDC, Berlin

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-1102:lv-H3K27me3-HXB05-male-bio1-tech1.bam

text: 6 week

text: ArrayExpress

text: Norway rat

text: adult

text: Rattus norvegicus

text: Rattus norvegicus

text: heart

text: Rattus norvegicus


text: Max-Delbrueck-Center, MDC, Berlin

text: public

characteristic: INSDC status

characteristic: SRA accession

text: SHR

text: E-MTAB-1102:liver-H3K4me3-SHR-male-bio4-tech1.bam

text: 6 week

text: ArrayExpress

text: Norway rat

text: adult

text: Rattus norvegicus

text: Rattus norvegicus

text: liver

text: Rattus norvegicus


text: Max-Delbrueck-Center, MDC, Berlin

text: public

text: E-MTAB-1102:lv-H3K27me3-BXH11-male-bio1-tech2.bam

characteristic: Submitter Id

text: 6 week

text: ArrayExpress

characteristic: broker name

text: Norway rat

text: adult

text: Rattus norvegicus

text: Rattus norvegicus

text: heart

text: Rattus norvegicus


text: Max-Delbrueck-Center, MDC, Berlin

text: public

text: E-MTAB-1102:lv-H3K27me3-BXH06-male-bio1-tech1.bam

text: 6 week

text: ArrayExpress

text: Norway rat

characteristic: common name

characteristic: description

text: adult

text: Rattus norvegicus

text: Rattus norvegicus

text: heart

text: Rattus norvegicus


text: IDOM FGC UPenn

text: public

tag: Namespace:IDOM FGC UPenn

text: ArrayExpress

text: human

text: Protocols: Pdx1 ChIP was performed as previously described (Deramaudt et al. JBC 2006).

text: Mus musculus

characteristic: organism

text: Homo sapiens

text: Pancreas

text: Homo sapiens

characteristic: title


text: IDOM FGC UPenn

text: public

text: ArrayExpress

text: human

text: Homo sapiens

text: Homo sapiens

text: Pancreas

text: Homo sapiens


text: Chlamydia trachomatis

characteristic: ArrayExpress-Species

characteristic: ArrayExpress-StrainOrLine

text: SC

text: public

text: Chlamydia trachomatis

text: Chlamydia trachomatis

characteristic: strain


text: Chlamydia trachomatis

characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

text: S3257MDA-sc-2011-11-28T12:56:50Z-1312427

text: Chlamydia trachomatis

text: Chlamydia trachomatis


text: Chlamydia trachomatis

characteristic: ENA-LAST-UPDATE

text: SC

text: public

text: S3489MDA-sc-2011-11-28T12:56:49Z-1312426

text: Chlamydia trachomatis

text: Chlamydia trachomatis


text: Chlamydia trachomatis

characteristic: ENA-CHECKLIST

characteristic: External Id

text: SC

text: public

characteristic: collection date

characteristic: collection day

characteristic: collection month

text: Russia: St Petersburg

characteristic: geographic location (country and/or sea)

text: disease

characteristic: host health state

text: cervical

characteristic: isolation source

text: Chlamydia trachomatis

characteristic: pmid

text: St Petersburg

characteristic: region

text: Chlamydia trachomatis

characteristic: scientific name

text: Chlamydia trachomatis

text: not known

characteristic: serovar

text: human

characteristic: specific host

characteristic: tax id

text: Chlamydia trachomatis; Chlamydia trachomatis


text: Chlamydia trachomatis

characteristic: ArrayExpress-Species

characteristic: ArrayExpress-StrainOrLine

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: S3344MDA-sc-2011-11-28T12:56:51Z-1312428

characteristic: Submitter Id

text: Chlamydia trachomatis

characteristic: organism

text: Chlamydia trachomatis

characteristic: strain


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

text: public

characteristic: collection date

text: Sweden

characteristic: geographic location (country and/or sea)

text: Cervix

characteristic: isolation source

text: Chlamydia trachomatis

characteristic: pubmed id

text: Chlamydia trachomatis

text: F

text: Homo sapiens


text: Chlamydia trachomatis

characteristic: ArrayExpress-Species

text: SC

text: public

text: S3270MDA-sc-2011-11-28T12:56:48Z-1312425

text: Chlamydia trachomatis

text: Chlamydia trachomatis


text: Chlamydia trachomatis

characteristic: ArrayExpress-StrainOrLine

text: SC

text: public

text: S2459MDA-sc-2011-11-28T12:56:51Z-1312429

text: Chlamydia trachomatis

text: Chlamydia trachomatis


text: Chlamydia trachomatis

text: SC

characteristic: INSDC center name

text: public

text: 688IMSMDA-sc-2011-12-22T13:11:27Z-1328377

text: Chlamydia trachomatis

text: Chlamydia trachomatis


text: Chlamydia trachomatis

text: SC

characteristic: INSDC first public

text: public

text: S4410MDA-sc-2011-11-28T12:56:52Z-1312430

text: Chlamydia trachomatis

text: Chlamydia trachomatis


text: SC

characteristic: INSDC last update

text: public

text: Chlamydia trachomatis

text: Chlamydia trachomatis


characteristic: ENA-CHECKLIST

text: SC

text: public

characteristic: INSDC status

characteristic: anonymized name

text: Russia

characteristic: country

text: diseased

characteristic: host status

text: Swab

text: Chlamydia trachomatis

text: Chlamydia trachomatis

text: H

characteristic: serovar

text: Homo sapiens

characteristic: specific host

characteristic: title


text: Chlamydia trachomatis

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

text: public

characteristic: SRA accession

text: Soton145-sc-2011-11-28T12:56:26Z-1312397

characteristic: Submitter Id

text: Chlamydia trachomatis

characteristic: organism

text: Chlamydia trachomatis

characteristic: strain


text: Chlamydia trachomatis

characteristic: ArrayExpress-Species

characteristic: ArrayExpress-StrainOrLine

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: Soton159-sc-2011-11-28T12:56:27Z-1312398

text: Chlamydia trachomatis

text: Chlamydia trachomatis


text: Chlamydia trachomatis

text: SC

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: Soton120-sc-2011-11-28T12:56:26Z-1312396

text: Chlamydia trachomatis

text: Chlamydia trachomatis


text: Chlamydia trachomatis

text: SC

text: public

text: Jali16MDA-sc-2011-11-28T12:56:19Z-1312390

text: Chlamydia trachomatis

text: Chlamydia trachomatis


text: Chlamydia trachomatis

text: SC

text: public

text: ND12899M-sc-2011-12-22T13:11:01Z-1328346

text: Chlamydia trachomatis

text: Chlamydia trachomatis


text: Chlamydia trachomatis

text: SC

text: public

text: Chlamydia trachomatis

text: Chlamydia trachomatis


text: Chlamydia trachomatis

characteristic: ENA-CHECKLIST

text: SC

text: public

characteristic: collection date

characteristic: collection day

characteristic: collection month

text: Russia: St Petersburg

characteristic: geographic location (country and/or sea)

text: disease

characteristic: host health state

text: urethra

characteristic: isolation source

text: Chlamydia trachomatis

characteristic: pmid

text: St Petersburg

characteristic: region

text: Chlamydia trachomatis

characteristic: scientific name

text: Chlamydia trachomatis

text: not known

text: human

characteristic: tax id


text: Chlamydia trachomatis

characteristic: ArrayExpress-Species

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

text: public

characteristic: SRA accession

text: Soton116-sc-2011-11-28T12:56:25Z-1312395

characteristic: Submitter Id

text: Chlamydia trachomatis

characteristic: organism

text: Chlamydia trachomatis

characteristic: strain


characteristic: ENA-CHECKLIST

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: anonymized name

characteristic: collection date

text: UK

characteristic: country

text: diseased

characteristic: host status

text: Not known

text: Chlamydia trachomatis

text: Chlamydia trachomatis

characteristic: serovar

text: Homo sapiens

characteristic: specific host

characteristic: title


text: Chlamydia trachomatis

characteristic: ArrayExpress-Species

characteristic: ArrayExpress-StrainOrLine

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

text: public

characteristic: collection day

characteristic: collection month

text: Russia: St Petersburg

characteristic: geographic location (country and/or sea)

text: disease

characteristic: host health state

text: cervical

characteristic: isolation source

text: Chlamydia trachomatis

characteristic: pmid

text: St Petersburg

characteristic: region

text: Chlamydia trachomatis

characteristic: scientific name

text: Chlamydia trachomatis

text: not known

text: human

characteristic: tax id


characteristic: ENA-CHECKLIST

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: anonymized name

characteristic: collection date

text: Sweden

characteristic: country

text: diseased

characteristic: host status

text: Swab

text: Chlamydia trachomatis

characteristic: organism

text: Chlamydia trachomatis

text: H

characteristic: serovar

text: Homo sapiens

characteristic: strain