characteristic: INSDC center name

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text: public

characteristic: INSDC status

text: E-MTAB-11825:ATAC18_HOL1_m_PBMCcorce_fresh_tn15_lib1

text: ArrayExpress

text: mononuclear cell

text: cattle

text: Protocols: Blood samples were collected from the tail or jugular vein using K2-EDTA blood collection tubes. White blood cells (WBC) were enriched by lysing erythrocytes using eBioscience 10X RBC Lysis Buffer (Thermo Fisher Scientific, Waltham, MA). Peripheral blood mononuclear cells (PBMC) were prepared by a density gradient centrifugation using either Ficoll-Paque PLUS (Cytiva, Marlborough, MA) or Lymphoprep (STEMCELL technologies, Vancouver, Canada) and SepMate-50 tubes (STEMCELL technologies). Animals were humanely euthanized and tissues were collected in ice-cold BELZER UW cold storage solution (Bridge to Life, London, United Kingdom) and processed in three ways. (1) Fresh sample (its file name contains a word fresh): Tissue kept in the UW cold storage solution was directly used for constructing ATAC-seq libraries in the day of sampling. (2) Cryopreserved sample (its file name contains slow): Tissue was cut into ~3 mm cubes and transferred to cryotubes filled with 1 ml of STEM-CELLBANKER DMSO-free cell freezing media (Amsbio, Abingdon, United Kingdom). The tubes were kept on ice for ~10 minutes and transferred in dry-ice during other samples being processed. The samples were stored in a -80 Celsius freezer until a library construction. (3) Snap-frozen sample (file name contains a word snap): Tissue was cut into ~3 mm cubes and transferred to cryotubes. The sample was snap-frozen in liquid nitrogen and stored at -80 Celsius until use. ATAC-seq libraries were constructed following the Omni ATAC-seq protocol (Corces et al., 2017) with some modifications. Tissue homogenization: A cryopreserved tissue in a vial was quickly thaw in a 37 Celsius water bath and transferred to an excess amount of ice-cold DPBS. The cryopreserved or fresh tissue was dissociated into a single-cell suspension using gentleMACS dissociator (with one or two cycles of the program B1. Miltenyi Biotec, Gladbach, Germany) with 3 ml of ice-cold Omni 1 x Homogenization Buffer in a gentleMACS C-tube. A snap-frozen sample was pulverized using a mortar and pestle chilled in liquid nitrogen. The cell suspension or pulverized tissue was transferred to a Dounce Tissue Grinder (D9063. Merck, Darmstadt, Germany) on ice with 3 ml of ice-cold Omni 1 x Homogenization buffer. The sample was homogenized with an A-pestle until resistance went away and further with a B-pestle (3 ~ 10 strokes each) so as to disrupt cellular plasma membranes. Cell debris was removed by passing the sample through stackable cell strainers (100, 70 and 30 um MACS SmartStrainers, Miltenyi Biotec). The flowthrough was further clarified by a brief centrifugation at 100 x g for 1 minute at 4 Celsius. Supernatant was mixed with an equal volume of ice-cold Omni 50% Iodixanol solution (final 25% Iodixanol). Purification of nuclei: Two layers of Iodixanol cushions were prepared in a 2 ml LoBind tube (Eppendorf, Hamburg, Germany) by placing 600 ul of ice-cold 40% Iodixanol solution on the bottom and overlaying 600 ul of ice-cold 29% Iodixanol solution using wide-bore tips. On the top, 800 ul of the cell suspension (25% Iodixanol) was placed. Density gradient centrifugation was done using a swing rotor at 6,000 x g for 30 minutes at 4 Celsius with a soft brake setting. Top layers were carefully removed down to ~2 mm above of the bottom layer. A nuclear fraction between the bottom and middle layers was collected (~ 400 ul) to a new LoBind tube on ice. The number of nuclei was counted by mixing 20 ul of the sample with 20 ul of 100 x diluted Hoechst 33342 (Fisher) using a hemocytometer under a fluorescence microscope. Tagmentation: Approximately 50,000 nuclei each were transferred to two of 1.5 ml LoBind tubes filled with1 ml of ice-cold ATAC-RSB + 0.1% Tween-20 buffer and centrifuged at 500 x g for 10 minutes at 4 Celsius. After carefully removing supernatant, nuclei were resuspended in 50 ul of Omni-ATAC reaction mix containing Tn5 Transposase TDE1 enzyme (Illumina, San Diego, CA). As effectiveness of Tn5 enzyme varied slightly among tissue types, we used two different amounts of the enzyme per sample. After mixing the sample by pipetting six times using a P200 fine tip, tagmentation reaction was carried out using Eppendorf Thermomixer at 37 Celsius at 500 rpm for 30 minutes. The reaction was stopped by adding 300 ul of PB buffer in MinElute PCR purification kit (Qiagen, Venlo, Netherlands) and 10 ul of 3M sodium acetate, pH 5.2. The sample was mixed, kept at room temperature for 10 min and stored at -20 Celsius until DNA purification. Library preparation: The tagmented DNA was purified and eluted in 21 ul elution buffer using the MinElute PCR purification kit. The DNA was amplified using NEBNext High-Fidelity 2X PCR Master Mix with Ad1 and Ad2 primers (Buenrostro et al., 2013) for 13 PCR-cycles. The amplified libraries were purified and eluted in 51 ul elution buffer using the MinElute PCR purification kit. Library size distribution was monitored using 10 ul of the library by QIAxcel capillary electrophoresis (Qiagen). Large DNA fragments were eliminated using AMPure XP magnetic beads (Beckman Coulter, Brea, CA) by a right-side size selection using 0.55 x followed by 1.5 x ratio of beads to sample. Library concentration was estimated using KAPA Library Quantification kit (Kapa Biosystems, Wilmington, MA).

text: infant

characteristic: developmental stage

text: normal

characteristic: disease

text: wild type genotype

characteristic: genotype

characteristic: individual

text: not applicable

characteristic: isolate

text: Bos taurus

characteristic: organism

text: Bos taurus

text: blood

text: Bos taurus

text: male

text: Holstein

text: fresh tissue, TDE1=1.5 ul


status: PUBLIC

tag: attribute

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text: E-MTAB-11825:ATAC18_HOL1_m_PBMCcorce_fresh_tn20_lib1

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text: mononuclear cell

text: cattle

characteristic: common name

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text: infant

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text: not applicable

text: Bos taurus

text: Bos taurus

text: blood

characteristic: organism part

characteristic: sampling site

text: Bos taurus

text: male

characteristic: sex

text: Holstein

characteristic: strain

text: fresh tissue, TDE1=2.0 ul

characteristic: tissue with known storage state

characteristic: title


text: Unit of Animal Genomics, GIGA Institute, University of Liege

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text: E-MTAB-11825:ATAC27_HOL1_m_PeyersPatch_slow_tn10_lib1

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text: cattle

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characteristic: developmental stage

text: normal

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text: wild type genotype

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text: not applicable

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text: Bos taurus

characteristic: organism

text: Bos taurus

text: Peyer's patch

text: Bos taurus

text: male

text: Holstein

text: slowly-frozen tissue, TDE1=1.0 ul


characteristic: ENA-CHECKLIST

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text: E-MTAB-11825:ATAC25_HOL1_m_PinealGland_slow_tn10_lib1

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text: ArrayExpress

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text: cattle

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text: infant

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text: Bos taurus

text: Bos taurus

text: pineal complex

text: Bos taurus

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text: slowly-frozen tissue, TDE1=1.0 ul


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text: E-MTAB-11825:ATAC19_HOL1_m_PituitaryAnterior_fresh_tn05_lib1

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text: Bos taurus

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text: Bos taurus

characteristic: organism

text: Bos taurus

text: pituitary gland

text: Bos taurus

text: male

text: Holstein

text: fresh tissue, TDE1=1.0 ul


characteristic: INSDC center name

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text: E-MTAB-11825:ATAC27_HOL1_m_Pons_slow_tn10_lib1

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text: public

text: E-MTAB-11825:ATAC36_HOL2_m_Prostate_snap_tn15_lib1

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text: Bos taurus

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text: Bos taurus

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text: E-MTAB-11825:ATAC36_HOL2_m_Prostate_snap_tn20_lib1

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text: Bos taurus

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text: Bos taurus

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text: cattle

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text: Bos taurus

text: Bos taurus

text: prostate gland

text: Bos taurus

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text: Holstein

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text: Bos taurus

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characteristic: organism part

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text: Bos taurus

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text: Holstein

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text: snap-frozen tissue, TDE1=2.0 ul

characteristic: tissue with known storage state

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text: E-MTAB-11825:ATAC34_HOL2_m_PulmonaryVein_snap_tn15_lib1

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characteristic: genotype

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text: not applicable

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text: Bos taurus

characteristic: organism

text: Bos taurus

text: pulmonary vein

text: Bos taurus

text: male

text: Holstein

text: snap-frozen tissue, TDE1=1.5 ul


characteristic: INSDC center name

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text: E-MTAB-11825:ATAC34_HOL2_m_PulmonaryVein_snap_tn20_lib1

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text: cattle

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text: infant

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text: not applicable

text: Bos taurus

text: Bos taurus

text: pulmonary vein

text: Bos taurus

text: male

text: Holstein

text: snap-frozen tissue, TDE1=2.0 ul


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text: E-MTAB-11825:ATAC37_HOL1_m_PulmonaryVein_snap_tn15_lib1

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text: infant

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text: not applicable

text: Bos taurus

text: Bos taurus

text: pulmonary vein

characteristic: organism part

characteristic: sampling site

text: Bos taurus

text: male

characteristic: sex

text: Holstein

characteristic: strain

text: snap-frozen tissue, TDE1=1.5 ul

characteristic: tissue with known storage state

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text: E-MTAB-11825:ATAC37_HOL1_m_PulmonaryVein_snap_tn20_lib1

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text: infant

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text: wild type genotype

characteristic: genotype

characteristic: individual

text: not applicable

characteristic: isolate

text: Bos taurus

characteristic: organism

text: Bos taurus

text: pulmonary vein

text: Bos taurus

text: male

text: Holstein

text: snap-frozen tissue, TDE1=2.0 ul


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text: E-MTAB-11825:ATAC28_HOL1_m_Pylorus_slow_tn08_lib1

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text: ArrayExpress

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text: cattle

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text: infant

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text: Bos taurus

text: Bos taurus

text: pylorus

text: Bos taurus

text: male

text: Holstein

text: slowly-frozen tissue, TDE1=0.8 ul


characteristic: INSDC center name

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text: public

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text: E-MTAB-11825:ATAC26_HOL1_m_Rectum_slow_tn10_lib1

text: ArrayExpress

text: cattle

text: Protocols: Blood samples were collected from the tail or jugular vein using K2-EDTA blood collection tubes. White blood cells (WBC) were enriched by lysing erythrocytes using eBioscience 10X RBC Lysis Buffer (Thermo Fisher Scientific, Waltham, MA). Peripheral blood mononuclear cells (PBMC) were prepared by a density gradient centrifugation using either Ficoll-Paque PLUS (Cytiva, Marlborough, MA) or Lymphoprep (STEMCELL technologies, Vancouver, Canada) and SepMate-50 tubes (STEMCELL technologies). Animals were humanely euthanized and tissues were collected in ice-cold BELZER UW cold storage solution (Bridge to Life, London, United Kingdom) and processed in three ways. (1) Fresh sample (its file name contains a word fresh): Tissue kept in the UW cold storage solution was directly used for constructing ATAC-seq libraries in the day of sampling. (2) Cryopreserved sample (its file name contains slow): Tissue was cut into ~3 mm cubes and transferred to cryotubes filled with 1 ml of STEM-CELLBANKER DMSO-free cell freezing media (Amsbio, Abingdon, United Kingdom). The tubes were kept on ice for ~10 minutes and transferred in dry-ice during other samples being processed. The samples were stored in a -80 Celsius freezer until a library construction. (3) Snap-frozen sample (file name contains a word snap): Tissue was cut into ~3 mm cubes and transferred to cryotubes. The sample was snap-frozen in liquid nitrogen and stored at -80 Celsius until use. ATAC-seq libraries were constructed following the Omni ATAC-seq protocol (Corces et al., 2017) with some modifications. Tissue homogenization: A cryopreserved tissue in a vial was quickly thaw in a 37 Celsius water bath and transferred to an excess amount of ice-cold DPBS. The cryopreserved or fresh tissue was dissociated into a single-cell suspension using gentleMACS dissociator (with one or two cycles of the program B1. Miltenyi Biotec, Gladbach, Germany) with 3 ml of ice-cold Omni 1 x Homogenization Buffer in a gentleMACS C-tube. A snap-frozen sample was pulverized using a mortar and pestle chilled in liquid nitrogen. The cell suspension or pulverized tissue was transferred to a Dounce Tissue Grinder (D9063. Merck, Darmstadt, Germany) on ice with 3 ml of ice-cold Omni 1 x Homogenization buffer. The sample was homogenized with an A-pestle until resistance went away and further with a B-pestle (3 ~ 10 strokes each) so as to disrupt cellular plasma membranes. Cell debris was removed by passing the sample through stackable cell strainers (100, 70 and 30 um MACS SmartStrainers, Miltenyi Biotec). The flowthrough was further clarified by a brief centrifugation at 100 x g for 1 minute at 4 Celsius. Supernatant was mixed with an equal volume of ice-cold Omni 50% Iodixanol solution (final 25% Iodixanol). Purification of nuclei: Two layers of Iodixanol cushions were prepared in a 2 ml LoBind tube (Eppendorf, Hamburg, Germany) by placing 600 ul of ice-cold 40% Iodixanol solution on the bottom and overlaying 600 ul of ice-cold 29% Iodixanol solution using wide-bore tips. On the top, 800 ul of the cell suspension (25% Iodixanol) was placed. Density gradient centrifugation was done using a swing rotor at 6,000 x g for 30 minutes at 4 Celsius with a soft brake setting. Top layers were carefully removed down to ~2 mm above of the bottom layer. A nuclear fraction between the bottom and middle layers was collected (~ 400 ul) to a new LoBind tube on ice. The number of nuclei was counted by mixing 20 ul of the sample with 20 ul of 100 x diluted Hoechst 33342 (Fisher) using a hemocytometer under a fluorescence microscope. Tagmentation: Approximately 50,000 nuclei each were transferred to two of 1.5 ml LoBind tubes filled with1 ml of ice-cold ATAC-RSB + 0.1% Tween-20 buffer and centrifuged at 500 x g for 10 minutes at 4 Celsius. After carefully removing supernatant, nuclei were resuspended in 50 ul of Omni-ATAC reaction mix containing Tn5 Transposase TDE1 enzyme (Illumina, San Diego, CA). As effectiveness of Tn5 enzyme varied slightly among tissue types, we used two different amounts of the enzyme per sample. After mixing the sample by pipetting six times using a P200 fine tip, tagmentation reaction was carried out using Eppendorf Thermomixer at 37 Celsius at 500 rpm for 30 minutes. The reaction was stopped by adding 300 ul of PB buffer in MinElute PCR purification kit (Qiagen, Venlo, Netherlands) and 10 ul of 3M sodium acetate, pH 5.2. The sample was mixed, kept at room temperature for 10 min and stored at -20 Celsius until DNA purification. Library preparation: The tagmented DNA was purified and eluted in 21 ul elution buffer using the MinElute PCR purification kit. The DNA was amplified using NEBNext High-Fidelity 2X PCR Master Mix with Ad1 and Ad2 primers (Buenrostro et al., 2013) for 13 PCR-cycles. The amplified libraries were purified and eluted in 51 ul elution buffer using the MinElute PCR purification kit. Library size distribution was monitored using 10 ul of the library by QIAxcel capillary electrophoresis (Qiagen). Large DNA fragments were eliminated using AMPure XP magnetic beads (Beckman Coulter, Brea, CA) by a right-side size selection using 0.55 x followed by 1.5 x ratio of beads to sample. Library concentration was estimated using KAPA Library Quantification kit (Kapa Biosystems, Wilmington, MA).

text: infant

text: normal

text: wild type genotype

text: not applicable

text: Bos taurus

text: Bos taurus

text: rectum

characteristic: organism part

characteristic: sampling site

text: Bos taurus

text: male

characteristic: sex

text: Holstein

characteristic: strain

text: slowly-frozen tissue, TDE1=1.0 ul

characteristic: tissue with known storage state

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Unit of Animal Genomics, GIGA Institute, University of Liege

text: public

text: E-MTAB-11825:ATAC34_HOL2_m_Reticulum_snap_tn15_lib1

text: ArrayExpress

text: cattle

text: infant

characteristic: developmental stage

text: normal

characteristic: disease

text: wild type genotype

characteristic: genotype

characteristic: individual

text: not applicable

characteristic: isolate

text: Bos taurus

characteristic: organism

text: Bos taurus

text: ruminant reticulum

text: Bos taurus

text: male

text: Holstein

text: snap-frozen tissue, TDE1=1.5 ul


characteristic: INSDC center name

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text: E-MTAB-11825:ATAC34_HOL2_m_Reticulum_snap_tn20_lib1

characteristic: Submitter Id

characteristic: age

text: ArrayExpress

characteristic: broker name

text: cattle

characteristic: common name

characteristic: description

text: infant

text: normal

text: wild type genotype

text: not applicable

text: Bos taurus

text: Bos taurus

text: ruminant reticulum

text: Bos taurus

text: male

text: Holstein

text: snap-frozen tissue, TDE1=2.0 ul


characteristic: ENA-CHECKLIST

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text: E-MTAB-11825:ATAC36_HOL1_m_Reticulum_snap_tn15_lib1

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text: cattle

text: infant

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text: wild type genotype

text: not applicable

text: Bos taurus

text: Bos taurus

text: ruminant reticulum

characteristic: organism part

characteristic: sampling site

text: Bos taurus

text: male

characteristic: sex

text: Holstein

characteristic: strain

text: snap-frozen tissue, TDE1=1.5 ul

characteristic: tissue with known storage state

characteristic: title


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text: E-MTAB-11825:ATAC36_HOL1_m_Reticulum_snap_tn20_lib1

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text: normal

characteristic: disease

text: wild type genotype

characteristic: genotype

characteristic: individual

text: not applicable

characteristic: isolate

text: Bos taurus

characteristic: organism

text: Bos taurus

text: ruminant reticulum

text: Bos taurus

text: male

text: Holstein

text: snap-frozen tissue, TDE1=2.0 ul


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text: E-MTAB-11825:ATAC36_HOL2_m_RibBone_snap_tn15_lib1

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text: ArrayExpress

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text: cattle

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text: infant

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text: Bos taurus

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text: Bos taurus

text: male

text: Holstein

text: snap-frozen tissue, TDE1=1.5 ul


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text: rib

characteristic: organism part

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text: Bos taurus

text: male

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text: public

text: E-MTAB-11825:ATAC29_HOL1_m_RumenDorsal_snap_tn08_lib1

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text: dorsal

text: cattle

text: infant

characteristic: developmental stage

text: normal

characteristic: disease

text: wild type genotype

characteristic: genotype

characteristic: individual

text: not applicable

characteristic: isolate

text: Bos taurus

characteristic: organism

text: Bos taurus

text: rumen

text: Bos taurus

text: male

text: Holstein

text: snap-frozen tissue, TDE1=0.8 ul


characteristic: INSDC center name

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text: E-MTAB-11825:ATAC29_HOL1_m_RumenDorsal_snap_tn12_lib1

characteristic: Submitter Id

characteristic: age

text: ArrayExpress

characteristic: broker name

text: dorsal

text: cattle

characteristic: common name

characteristic: description

text: infant

text: normal

text: wild type genotype

text: not applicable

text: Bos taurus

text: Bos taurus

text: rumen

text: Bos taurus

text: male

text: Holstein

text: snap-frozen tissue, TDE1=1.2 ul


characteristic: ENA-CHECKLIST

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text: public

text: E-MTAB-11825:ATAC34_HOL2_m_RumenDorsal_snap_tn15_lib1

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text: dorsal

text: cattle

text: infant

text: normal

text: wild type genotype

text: not applicable

text: Bos taurus

text: Bos taurus

text: rumen

characteristic: organism part

characteristic: sampling site

text: Bos taurus

text: male

characteristic: sex

text: Holstein

characteristic: strain

text: snap-frozen tissue, TDE1=1.5 ul

characteristic: tissue with known storage state

characteristic: title


characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-11825:ATAC34_HOL2_m_RumenDorsal_snap_tn20_lib1

text: ArrayExpress

text: dorsal

text: cattle

text: infant

characteristic: developmental stage

text: normal

characteristic: disease

text: wild type genotype

characteristic: genotype

characteristic: individual

text: not applicable

characteristic: isolate

text: Bos taurus

characteristic: organism

text: Bos taurus

text: rumen

text: Bos taurus

text: male

text: Holstein

text: snap-frozen tissue, TDE1=2.0 ul


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

characteristic: SRA accession

text: E-MTAB-11825:ATAC25_HOL1_m_SalivaryGland_slow_tn10_lib1

characteristic: Submitter Id

characteristic: age

text: ArrayExpress

characteristic: broker name

text: cattle

characteristic: common name

characteristic: description

text: infant

text: normal

text: wild type genotype

text: not applicable

text: Bos taurus

text: Bos taurus

text: salivary gland

text: Bos taurus

text: male

text: Holstein

text: slowly-frozen tissue, TDE1=1.0 ul


characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-11825:ATAC27_HOL1_m_SeminalVesicle_slow_tn10_lib1

text: ArrayExpress

text: cattle

text: infant

text: normal

text: wild type genotype

text: not applicable

text: Bos taurus

text: Bos taurus

text: seminal vesicle

characteristic: organism part

characteristic: sampling site

text: Bos taurus

text: male

characteristic: sex

text: Holstein

characteristic: strain

text: slowly-frozen tissue, TDE1=1.0 ul

characteristic: tissue with known storage state

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: E-MTAB-11825:ATAC35_BOV1_f_Skin_snap_tn15_lib1

text: ArrayExpress

text: cattle

text: infant

characteristic: developmental stage

text: normal

characteristic: disease

text: wild type genotype

characteristic: genotype

characteristic: individual

text: not applicable

characteristic: isolate

text: Bos taurus

characteristic: organism

text: Bos taurus

text: skin

text: Bos taurus

text: female

text: snap-frozen tissue, TDE1=1.5 ul


characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-11825:ATAC35_BOV1_f_Skin_snap_tn20_lib1

characteristic: Submitter Id

characteristic: age

text: ArrayExpress

characteristic: broker name

text: cattle

characteristic: common name

characteristic: description

text: infant

text: normal

text: wild type genotype

text: not applicable

text: Bos taurus

text: Bos taurus

text: skin

text: Bos taurus

text: female

text: snap-frozen tissue, TDE1=2.0 ul


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: E-MTAB-11825:ATAC35_BOV2_m_Skin_snap_tn15_lib1

text: ArrayExpress

text: cattle

text: juvenile stage

text: normal

text: wild type genotype

text: not applicable

text: Bos taurus

text: Bos taurus

text: skin

characteristic: organism part

characteristic: sampling site

text: Bos taurus

text: male

characteristic: sex

characteristic: strain

text: snap-frozen tissue, TDE1=1.5 ul

characteristic: tissue with known storage state

characteristic: title


characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-11825:ATAC35_BOV2_m_Skin_snap_tn20_lib1

text: ArrayExpress

text: cattle

text: Protocols: Blood samples were collected from the tail or jugular vein using K2-EDTA blood collection tubes. White blood cells (WBC) were enriched by lysing erythrocytes using eBioscience 10X RBC Lysis Buffer (Thermo Fisher Scientific, Waltham, MA). Peripheral blood mononuclear cells (PBMC) were prepared by a density gradient centrifugation using either Ficoll-Paque PLUS (Cytiva, Marlborough, MA) or Lymphoprep (STEMCELL technologies, Vancouver, Canada) and SepMate-50 tubes (STEMCELL technologies). Animals were humanely euthanized and tissues were collected in ice-cold BELZER UW cold storage solution (Bridge to Life, London, United Kingdom) and processed in three ways. (1) Fresh sample (its file name contains a word fresh): Tissue kept in the UW cold storage solution was directly used for constructing ATAC-seq libraries in the day of sampling. (2) Cryopreserved sample (its file name contains slow): Tissue was cut into ~3 mm cubes and transferred to cryotubes filled with 1 ml of STEM-CELLBANKER DMSO-free cell freezing media (Amsbio, Abingdon, United Kingdom). The tubes were kept on ice for ~10 minutes and transferred in dry-ice during other samples being processed. The samples were stored in a -80 Celsius freezer until a library construction. (3) Snap-frozen sample (file name contains a word snap): Tissue was cut into ~3 mm cubes and transferred to cryotubes. The sample was snap-frozen in liquid nitrogen and stored at -80 Celsius until use. ATAC-seq libraries were constructed following the Omni ATAC-seq protocol (Corces et al., 2017) with some modifications. Tissue homogenization: A cryopreserved tissue in a vial was quickly thaw in a 37 Celsius water bath and transferred to an excess amount of ice-cold DPBS. The cryopreserved or fresh tissue was dissociated into a single-cell suspension using gentleMACS dissociator (with one or two cycles of the program B1. Miltenyi Biotec, Gladbach, Germany) with 3 ml of ice-cold Omni 1 x Homogenization Buffer in a gentleMACS C-tube. A snap-frozen sample was pulverized using a mortar and pestle chilled in liquid nitrogen. The cell suspension or pulverized tissue was transferred to a Dounce Tissue Grinder (D9063. Merck, Darmstadt, Germany) on ice with 3 ml of ice-cold Omni 1 x Homogenization buffer. The sample was homogenized with an A-pestle until resistance went away and further with a B-pestle (3 ~ 10 strokes each) so as to disrupt cellular plasma membranes. Cell debris was removed by passing the sample through stackable cell strainers (100, 70 and 30 um MACS SmartStrainers, Miltenyi Biotec). The flowthrough was further clarified by a brief centrifugation at 100 x g for 1 minute at 4 Celsius. Supernatant was mixed with an equal volume of ice-cold Omni 50% Iodixanol solution (final 25% Iodixanol). Purification of nuclei: Two layers of Iodixanol cushions were prepared in a 2 ml LoBind tube (Eppendorf, Hamburg, Germany) by placing 600 ul of ice-cold 40% Iodixanol solution on the bottom and overlaying 600 ul of ice-cold 29% Iodixanol solution using wide-bore tips. On the top, 800 ul of the cell suspension (25% Iodixanol) was placed. Density gradient centrifugation was done using a swing rotor at 6,000 x g for 30 minutes at 4 Celsius with a soft brake setting. Top layers were carefully removed down to ~2 mm above of the bottom layer. A nuclear fraction between the bottom and middle layers was collected (~ 400 ul) to a new LoBind tube on ice. The number of nuclei was counted by mixing 20 ul of the sample with 20 ul of 100 x diluted Hoechst 33342 (Fisher) using a hemocytometer under a fluorescence microscope. Tagmentation: Approximately 50,000 nuclei each were transferred to two of 1.5 ml LoBind tubes filled with1 ml of ice-cold ATAC-RSB + 0.1% Tween-20 buffer and centrifuged at 500 x g for 10 minutes at 4 Celsius. After carefully removing supernatant, nuclei were resuspended in 50 ul of Omni-ATAC reaction mix containing Tn5 Transposase TDE1 enzyme (Illumina, San Diego, CA). As effectiveness of Tn5 enzyme varied slightly among tissue types, we used two different amounts of the enzyme per sample. After mixing the sample by pipetting six times using a P200 fine tip, tagmentation reaction was carried out using Eppendorf Thermomixer at 37 Celsius at 500 rpm for 30 minutes. The reaction was stopped by adding 300 ul of PB buffer in MinElute PCR purification kit (Qiagen, Venlo, Netherlands) and 10 ul of 3M sodium acetate, pH 5.2. The sample was mixed, kept at room temperature for 10 min and stored at -20 Celsius until DNA purification. Library preparation: The tagmented DNA was purified and eluted in 21 ul elution buffer using the MinElute PCR purification kit. The DNA was amplified using NEBNext High-Fidelity 2X PCR Master Mix with Ad1 and Ad2 primers (Buenrostro et al., 2013) for 13 PCR-cycles. The amplified libraries were purified and eluted in 51 ul elution buffer using the MinElute PCR purification kit. Library size distribution was monitored using 10 ul of the library by QIAxcel capillary electrophoresis (Qiagen). Large DNA fragments were eliminated using AMPure XP magnetic beads (Beckman Coulter, Brea, CA) by a right-side size selection using 0.55 x followed by 1.5 x ratio of beads to sample. Library concentration was estimated using KAPA Library Quantification kit (Kapa Biosystems, Wilmington, MA).

text: juvenile stage

characteristic: developmental stage

text: normal

characteristic: disease

text: wild type genotype

characteristic: genotype

characteristic: individual

text: not applicable

characteristic: isolate

text: Bos taurus

characteristic: organism

text: Bos taurus

text: skin

text: Bos taurus

text: male

text: snap-frozen tissue, TDE1=2.0 ul


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Unit of Animal Genomics, GIGA Institute, University of Liege

text: public

characteristic: SRA accession

text: E-MTAB-11825:ATAC19_HOL1_m_SpinalCordCervical_fresh_tn05_lib1

characteristic: Submitter Id

characteristic: age

text: ArrayExpress

characteristic: broker name

text: cattle

characteristic: common name

characteristic: description

text: infant

text: normal

text: wild type genotype

text: not applicable

text: Bos taurus

text: Bos taurus

text: cervical spinal cord

text: Bos taurus

text: male

text: Holstein

text: fresh tissue, TDE1=0.5 ul


characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-11825:ATAC19_HOL1_m_SpinalCordCervical_fresh_tn10_lib1

text: ArrayExpress

text: cattle

text: infant

text: normal

text: wild type genotype

text: not applicable

text: Bos taurus

text: Bos taurus

text: cervical spinal cord

characteristic: organism part

characteristic: sampling site

text: Bos taurus

text: male

characteristic: sex

text: Holstein

characteristic: strain

text: fresh tissue, TDE1=1.0 ul

characteristic: tissue with known storage state

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: E-MTAB-11825:ATAC28_HOL1_m_SpinalCordDosal_slow_tn08_lib1

text: ArrayExpress

text: cattle

text: infant

characteristic: developmental stage

text: normal

characteristic: disease

text: wild type genotype

characteristic: genotype

characteristic: individual

text: not applicable

characteristic: isolate

text: Bos taurus

characteristic: organism

text: Bos taurus

text: spinal cord dorsal column

text: Bos taurus

text: male

text: Holstein

text: slowly-frozen tissue, TDE1=0.8 ul


characteristic: INSDC center name

characteristic: INSDC first public

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text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-11825:ATAC19_HOL1_m_Spleen_fresh_tn05_lib1

characteristic: Submitter Id

characteristic: age

text: ArrayExpress

characteristic: broker name

text: cattle

characteristic: common name

characteristic: description

text: infant

text: normal

text: wild type genotype

text: not applicable

text: Bos taurus

text: Bos taurus

text: spleen

text: Bos taurus

text: male

text: Holstein

text: fresh tissue, TDE1=0.5 ul


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

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characteristic: External Id

text: public

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text: cattle

text: infant

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text: wild type genotype

text: not applicable

text: Bos taurus

text: Bos taurus

text: spleen

characteristic: organism part

characteristic: sampling site

text: Bos taurus

text: male

characteristic: sex

text: Holstein

characteristic: strain

text: fresh tissue, TDE1=1.0 ul

characteristic: tissue with known storage state

characteristic: title


characteristic: INSDC center name

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text: public

characteristic: INSDC status

text: E-MTAB-11825:ATAC22_HOL1_m_Spleen_slow_tn05_lib1

text: ArrayExpress

text: cattle

text: infant

characteristic: developmental stage

text: normal

characteristic: disease

text: wild type genotype

characteristic: genotype

characteristic: individual

text: not applicable

characteristic: isolate

text: Bos taurus

characteristic: organism

text: Bos taurus

text: spleen

text: Bos taurus

text: male

text: Holstein

text: slowly-frozen tissue, TDE1=0.5 ul


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

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characteristic: External Id

text: public

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text: E-MTAB-11825:ATAC22_HOL1_m_Spleen_slow_tn10_lib1

characteristic: Submitter Id

characteristic: age

text: ArrayExpress

characteristic: broker name

text: cattle

characteristic: common name

characteristic: description

text: infant

text: normal

text: wild type genotype

text: not applicable

text: Bos taurus

text: Bos taurus

text: spleen

text: Bos taurus

text: male

text: Holstein

text: slowly-frozen tissue, TDE1=1.0 ul


characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-11825:ATAC19_HOL1_m_Testicle_fresh_tn05_lib1

text: ArrayExpress

text: cattle

text: infant

text: normal

text: wild type genotype

text: not applicable

text: Bos taurus

text: Bos taurus

text: testicle

characteristic: organism part

characteristic: sampling site

text: Bos taurus

text: male

characteristic: sex

text: Holstein

characteristic: strain

text: fresh tissue, TDE1=0.5 ul

characteristic: tissue with known storage state

characteristic: title


characteristic: ENA-CHECKLIST

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characteristic: External Id

text: public

text: E-MTAB-11825:ATAC19_HOL1_m_Testicle_fresh_tn10_lib1

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text: cattle

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characteristic: disease

text: wild type genotype

characteristic: genotype

characteristic: individual

text: not applicable

characteristic: isolate

text: Bos taurus

characteristic: organism

text: Bos taurus

text: testicle

text: Bos taurus

text: male

text: Holstein

text: fresh tissue, TDE1=1.0 ul


characteristic: INSDC center name

characteristic: INSDC first public

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text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-11825:ATAC29_HOL1_m_Testicle_slow_tn08_lib1

characteristic: Submitter Id

characteristic: age

text: ArrayExpress

characteristic: broker name

text: cattle

characteristic: common name

characteristic: description

text: infant

text: normal

text: wild type genotype

text: not applicable

text: Bos taurus

text: Bos taurus

text: testicle

text: Bos taurus

text: male

text: Holstein

text: slowly-frozen tissue, TDE1=0.8 ul


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: E-MTAB-11825:ATAC29_HOL1_m_Testicle_slow_tn12_lib1

text: ArrayExpress

text: cattle

text: infant

text: normal

text: wild type genotype

text: not applicable

text: Bos taurus

text: Bos taurus

text: testicle

characteristic: organism part

characteristic: sampling site

text: Bos taurus

text: male

characteristic: sex

text: Holstein

characteristic: strain

text: slowly-frozen tissue, TDE1=1.2 ul

characteristic: tissue with known storage state

characteristic: title


characteristic: INSDC center name

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characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-11825:ATAC29_HOL1_m_Testicle_snap_tn08_lib1

text: ArrayExpress

text: cattle

text: infant

characteristic: developmental stage

text: normal

characteristic: disease

text: wild type genotype

characteristic: genotype

characteristic: individual

text: not applicable

characteristic: isolate

text: Bos taurus

characteristic: organism

text: Bos taurus

text: testicle

text: Bos taurus

text: male

text: Holstein

text: snap-frozen tissue, TDE1=0.8 ul


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

characteristic: SRA accession

text: E-MTAB-11825:ATAC29_HOL1_m_Testicle_snap_tn12_lib1

characteristic: Submitter Id

characteristic: age

text: ArrayExpress

characteristic: broker name

text: cattle

characteristic: common name

characteristic: description

text: infant

text: normal

text: wild type genotype

text: not applicable

text: Bos taurus

text: Bos taurus

text: testicle

text: Bos taurus

text: male

text: Holstein

text: snap-frozen tissue, TDE1=1.2 ul


characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-11825:ATAC35_BOV2_m_Testicle_snap_tn15_lib1

text: ArrayExpress

text: cattle

text: juvenile stage

text: normal

text: wild type genotype

text: not applicable

text: Bos taurus

text: Bos taurus

text: testicle

characteristic: organism part

characteristic: sampling site

text: Bos taurus

text: male

characteristic: sex

characteristic: strain

text: snap-frozen tissue, TDE1=1.5 ul

characteristic: tissue with known storage state

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: E-MTAB-11825:ATAC35_BOV2_m_Testicle_snap_tn20_lib1

text: ArrayExpress

text: cattle

text: juvenile stage

characteristic: developmental stage

text: normal

characteristic: disease

text: wild type genotype

characteristic: genotype

characteristic: individual

text: not applicable

characteristic: isolate

text: Bos taurus

characteristic: organism

text: Bos taurus

text: testicle

text: Bos taurus

text: male

text: snap-frozen tissue, TDE1=2.0 ul


characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-11825:ATAC23_HOL1_m_Thalamus_slow_tn10_lib1

characteristic: Submitter Id

characteristic: age

text: ArrayExpress

characteristic: broker name

text: cattle

characteristic: common name

text: Protocols: Blood samples were collected from the tail or jugular vein using K2-EDTA blood collection tubes. White blood cells (WBC) were enriched by lysing erythrocytes using eBioscience 10X RBC Lysis Buffer (Thermo Fisher Scientific, Waltham, MA). Peripheral blood mononuclear cells (PBMC) were prepared by a density gradient centrifugation using either Ficoll-Paque PLUS (Cytiva, Marlborough, MA) or Lymphoprep (STEMCELL technologies, Vancouver, Canada) and SepMate-50 tubes (STEMCELL technologies). Animals were humanely euthanized and tissues were collected in ice-cold BELZER UW cold storage solution (Bridge to Life, London, United Kingdom) and processed in three ways. (1) Fresh sample (its file name contains a word fresh): Tissue kept in the UW cold storage solution was directly used for constructing ATAC-seq libraries in the day of sampling. (2) Cryopreserved sample (its file name contains slow): Tissue was cut into ~3 mm cubes and transferred to cryotubes filled with 1 ml of STEM-CELLBANKER DMSO-free cell freezing media (Amsbio, Abingdon, United Kingdom). The tubes were kept on ice for ~10 minutes and transferred in dry-ice during other samples being processed. The samples were stored in a -80 Celsius freezer until a library construction. (3) Snap-frozen sample (file name contains a word snap): Tissue was cut into ~3 mm cubes and transferred to cryotubes. The sample was snap-frozen in liquid nitrogen and stored at -80 Celsius until use. ATAC-seq libraries were constructed following the Omni ATAC-seq protocol (Corces et al., 2017) with some modifications. Tissue homogenization: A cryopreserved tissue in a vial was quickly thaw in a 37 Celsius water bath and transferred to an excess amount of ice-cold DPBS. The cryopreserved or fresh tissue was dissociated into a single-cell suspension using gentleMACS dissociator (with one or two cycles of the program B1. Miltenyi Biotec, Gladbach, Germany) with 3 ml of ice-cold Omni 1 x Homogenization Buffer in a gentleMACS C-tube. A snap-frozen sample was pulverized using a mortar and pestle chilled in liquid nitrogen. The cell suspension or pulverized tissue was transferred to a Dounce Tissue Grinder (D9063. Merck, Darmstadt, Germany) on ice with 3 ml of ice-cold Omni 1 x Homogenization buffer. The sample was homogenized with an A-pestle until resistance went away and further with a B-pestle (3 ~ 10 strokes each) so as to disrupt cellular plasma membranes. Cell debris was removed by passing the sample through stackable cell strainers (100, 70 and 30 um MACS SmartStrainers, Miltenyi Biotec). The flowthrough was further clarified by a brief centrifugation at 100 x g for 1 minute at 4 Celsius. Supernatant was mixed with an equal volume of ice-cold Omni 50% Iodixanol solution (final 25% Iodixanol). Purification of nuclei: Two layers of Iodixanol cushions were prepared in a 2 ml LoBind tube (Eppendorf, Hamburg, Germany) by placing 600 ul of ice-cold 40% Iodixanol solution on the bottom and overlaying 600 ul of ice-cold 29% Iodixanol solution using wide-bore tips. On the top, 800 ul of the cell suspension (25% Iodixanol) was placed. Density gradient centrifugation was done using a swing rotor at 6,000 x g for 30 minutes at 4 Celsius with a soft brake setting. Top layers were carefully removed down to ~2 mm above of the bottom layer. A nuclear fraction between the bottom and middle layers was collected (~ 400 ul) to a new LoBind tube on ice. The number of nuclei was counted by mixing 20 ul of the sample with 20 ul of 100 x diluted Hoechst 33342 (Fisher) using a hemocytometer under a fluorescence microscope. Tagmentation: Approximately 50,000 nuclei each were transferred to two of 1.5 ml LoBind tubes filled with1 ml of ice-cold ATAC-RSB + 0.1% Tween-20 buffer and centrifuged at 500 x g for 10 minutes at 4 Celsius. After carefully removing supernatant, nuclei were resuspended in 50 ul of Omni-ATAC reaction mix containing Tn5 Transposase TDE1 enzyme (Illumina, San Diego, CA). As effectiveness of Tn5 enzyme varied slightly among tissue types, we used two different amounts of the enzyme per sample. After mixing the sample by pipetting six times using a P200 fine tip, tagmentation reaction was carried out using Eppendorf Thermomixer at 37 Celsius at 500 rpm for 30 minutes. The reaction was stopped by adding 300 ul of PB buffer in MinElute PCR purification kit (Qiagen, Venlo, Netherlands) and 10 ul of 3M sodium acetate, pH 5.2. The sample was mixed, kept at room temperature for 10 min and stored at -20 Celsius until DNA purification. Library preparation: The tagmented DNA was purified and eluted in 21 ul elution buffer using the MinElute PCR purification kit. The DNA was amplified using NEBNext High-Fidelity 2X PCR Master Mix with Ad1 and Ad2 primers (Buenrostro et al., 2013) for 13 PCR-cycles. The amplified libraries were purified and eluted in 51 ul elution buffer using the MinElute PCR purification kit. Library size distribution was monitored using 10 ul of the library by QIAxcel capillary electrophoresis (Qiagen). Large DNA fragments were eliminated using AMPure XP magnetic beads (Beckman Coulter, Brea, CA) by a right-side size selection using 0.55 x followed by 1.5 x ratio of beads to sample. Library concentration was estimated using KAPA Library Quantification kit (Kapa Biosystems, Wilmington, MA).

characteristic: description

text: infant

text: normal

text: wild type genotype

text: not applicable

text: Bos taurus

text: Bos taurus

text: thalamic complex

text: Bos taurus

text: male

text: Holstein

text: slowly-frozen tissue, TDE1=1.0 ul


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Unit of Animal Genomics, GIGA Institute, University of Liege

text: public

text: E-MTAB-11825:ATAC34_HOL2_m_Thymus_snap_tn15_lib1

text: ArrayExpress

text: cattle

text: infant

text: normal

text: wild type genotype

text: not applicable

text: Bos taurus

text: Bos taurus

text: thymus gland

characteristic: organism part

characteristic: sampling site

text: Bos taurus

text: male

characteristic: sex

text: Holstein

characteristic: strain

text: snap-frozen tissue, TDE1=1.5 ul

characteristic: tissue with known storage state

characteristic: title


characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-11825:ATAC34_HOL2_m_Thymus_snap_tn20_lib1

text: ArrayExpress

text: cattle

text: infant

characteristic: developmental stage

text: normal

characteristic: disease

text: wild type genotype

characteristic: genotype

characteristic: individual

text: not applicable

characteristic: isolate

text: Bos taurus

characteristic: organism

text: Bos taurus

text: thymus gland

text: Bos taurus

text: male

text: Holstein

text: snap-frozen tissue, TDE1=2.0 ul


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

characteristic: SRA accession

text: E-MTAB-11825:ATAC24_HOL1_m_ThyroidGland_slow_tn10_lib1

characteristic: Submitter Id

characteristic: age

text: ArrayExpress

characteristic: broker name

text: cattle

characteristic: common name

characteristic: description

text: infant

text: normal

text: wild type genotype

text: not applicable

text: Bos taurus

text: Bos taurus

text: thyroid gland

text: Bos taurus

text: male

text: Holstein

text: slowly-frozen tissue, TDE1=1.0 ul


characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-11825:ATAC32_HOL1_m_Tongue_snap_tn10_lib1

text: ArrayExpress

text: cattle

text: infant

text: normal

text: wild type genotype

text: not applicable

text: Bos taurus

text: Bos taurus

text: tongue

characteristic: organism part

characteristic: sampling site

text: Bos taurus

text: male

characteristic: sex

text: Holstein

characteristic: strain

text: snap-frozen tissue, TDE1=1.0 ul

characteristic: tissue with known storage state

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: E-MTAB-11825:ATAC34_HOL2_m_Tongue_snap_tn15_lib1

text: ArrayExpress

text: cattle

text: infant

characteristic: developmental stage

text: normal

characteristic: disease

text: wild type genotype

characteristic: genotype

characteristic: individual

text: not applicable

characteristic: isolate

text: Bos taurus

characteristic: organism

text: Bos taurus

text: tongue

text: Bos taurus

text: male

text: Holstein

text: snap-frozen tissue, TDE1=1.5 ul


characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-11825:ATAC34_HOL2_m_Tongue_snap_tn20_lib1

characteristic: Submitter Id

characteristic: age

text: ArrayExpress

characteristic: broker name

text: cattle

characteristic: common name

characteristic: description

text: infant

text: normal

text: wild type genotype

text: not applicable

text: Bos taurus

text: Bos taurus

text: tongue

text: Bos taurus

text: male

text: Holstein

text: snap-frozen tissue, TDE1=2.0 ul


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: E-MTAB-11825:ATAC26_HOL1_m_Tonsil_slow_tn10_lib1

text: ArrayExpress

text: cattle

text: infant

text: normal

text: wild type genotype

text: not applicable

text: Bos taurus

text: Bos taurus

text: tonsil

characteristic: organism part

characteristic: sampling site

text: Bos taurus

text: male

characteristic: sex

text: Holstein

characteristic: strain

text: slowly-frozen tissue, TDE1=1.0 ul

characteristic: tissue with known storage state

characteristic: title


characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-11825:ATAC35_BOV1_f_Uterus_snap_tn15_lib1

text: ArrayExpress

text: cattle

text: infant

characteristic: developmental stage

text: normal

characteristic: disease

text: wild type genotype

characteristic: genotype

characteristic: individual

text: not applicable

characteristic: isolate

text: Bos taurus

characteristic: organism

text: Bos taurus

text: uterus

text: Bos taurus

text: female

text: snap-frozen tissue, TDE1=1.5 ul


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

characteristic: SRA accession

text: E-MTAB-11825:ATAC35_BOV1_f_Uterus_snap_tn20_lib1

characteristic: Submitter Id

characteristic: age

text: ArrayExpress

characteristic: broker name

text: cattle

characteristic: common name

characteristic: description

text: infant

text: normal

text: wild type genotype

text: not applicable

text: Bos taurus

text: Bos taurus

text: uterus

text: Bos taurus

text: female

text: snap-frozen tissue, TDE1=2.0 ul


characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-11825:ATAC17_BBB1_f_WBCbuen_fresh_tn15_lib1

unit: year

text: ArrayExpress

text: leukocyte

text: cattle

text: adult

text: normal

text: wild type genotype

text: not applicable

text: Bos taurus

text: Bos taurus

text: blood

characteristic: organism part

characteristic: sampling site

text: Bos taurus

text: female

characteristic: sex

text: Belgian Blue

characteristic: strain

text: fresh tissue, TDE1=1.5 ul

characteristic: tissue with known storage state

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: E-MTAB-11825:ATAC17_BBB1_f_WBCbuen_fresh_tn20_lib1

text: ArrayExpress

text: leukocyte

text: cattle

text: adult

characteristic: developmental stage

text: normal

characteristic: disease

text: wild type genotype

characteristic: genotype

characteristic: individual

text: not applicable

characteristic: isolate

text: Bos taurus

characteristic: organism

text: Bos taurus

text: blood

text: Bos taurus

text: female

text: Belgian Blue

text: fresh tissue, TDE1=2.0 ul


characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-11825:ATAC17_BBB1_f_WBCcorc_fresh_tn15_lib1

characteristic: Submitter Id

characteristic: age

text: ArrayExpress

characteristic: broker name

text: leukocyte

text: cattle

characteristic: common name

characteristic: description

text: adult

text: normal

text: wild type genotype

text: not applicable

text: Bos taurus

text: Bos taurus

text: blood

text: Bos taurus

text: female

text: Belgian Blue

text: fresh tissue, TDE1=1.5 ul


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: E-MTAB-11825:ATAC17_BBB1_f_WBCcorc_fresh_tn20_lib1

text: ArrayExpress

text: leukocyte

text: cattle

text: adult

text: normal

text: wild type genotype

text: not applicable

text: Bos taurus

text: Bos taurus

text: blood

characteristic: organism part

characteristic: sampling site

text: Bos taurus

text: female

characteristic: sex

text: Belgian Blue

characteristic: strain

text: fresh tissue, TDE1=2.0 ul

characteristic: tissue with known storage state

characteristic: title


characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-11825:ATAC18_BBB1_f_WBCcorc_slow_tn15_lib1

text: ArrayExpress

text: leukocyte

text: cattle

text: adult

characteristic: developmental stage

text: normal

characteristic: disease

text: wild type genotype

characteristic: genotype

characteristic: individual

text: not applicable

characteristic: isolate

text: Bos taurus

characteristic: organism

text: Bos taurus

text: blood

text: Bos taurus

text: female

text: Belgian Blue

text: slowly-frozen tissue, TDE1=1.5 ul


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

characteristic: SRA accession

text: E-MTAB-11825:ATAC18_BBB1_f_WBCcorc_slow_tn20_lib1

characteristic: Submitter Id

characteristic: age

text: ArrayExpress

characteristic: broker name

text: leukocyte

text: cattle

characteristic: common name

characteristic: description

text: adult

text: normal

text: wild type genotype

text: not applicable

text: Bos taurus

text: Bos taurus

text: blood

text: Bos taurus

text: female

text: Belgian Blue

text: slowly-frozen tissue, TDE1=2.0 ul


characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-11825:ATAC18_HOL1_m_WBCcorc_fresh_tn15_lib1

text: ArrayExpress

text: leukocyte

text: cattle

text: Protocols: Blood samples were collected from the tail or jugular vein using K2-EDTA blood collection tubes. White blood cells (WBC) were enriched by lysing erythrocytes using eBioscience 10X RBC Lysis Buffer (Thermo Fisher Scientific, Waltham, MA). Peripheral blood mononuclear cells (PBMC) were prepared by a density gradient centrifugation using either Ficoll-Paque PLUS (Cytiva, Marlborough, MA) or Lymphoprep (STEMCELL technologies, Vancouver, Canada) and SepMate-50 tubes (STEMCELL technologies). Animals were humanely euthanized and tissues were collected in ice-cold BELZER UW cold storage solution (Bridge to Life, London, United Kingdom) and processed in three ways. (1) Fresh sample (its file name contains a word fresh): Tissue kept in the UW cold storage solution was directly used for constructing ATAC-seq libraries in the day of sampling. (2) Cryopreserved sample (its file name contains slow): Tissue was cut into ~3 mm cubes and transferred to cryotubes filled with 1 ml of STEM-CELLBANKER DMSO-free cell freezing media (Amsbio, Abingdon, United Kingdom). The tubes were kept on ice for ~10 minutes and transferred in dry-ice during other samples being processed. The samples were stored in a -80 Celsius freezer until a library construction. (3) Snap-frozen sample (file name contains a word snap): Tissue was cut into ~3 mm cubes and transferred to cryotubes. The sample was snap-frozen in liquid nitrogen and stored at -80 Celsius until use. ATAC-seq libraries were constructed following the Omni ATAC-seq protocol (Corces et al., 2017) with some modifications. Tissue homogenization: A cryopreserved tissue in a vial was quickly thaw in a 37 Celsius water bath and transferred to an excess amount of ice-cold DPBS. The cryopreserved or fresh tissue was dissociated into a single-cell suspension using gentleMACS dissociator (with one or two cycles of the program B1. Miltenyi Biotec, Gladbach, Germany) with 3 ml of ice-cold Omni 1 x Homogenization Buffer in a gentleMACS C-tube. A snap-frozen sample was pulverized using a mortar and pestle chilled in liquid nitrogen. The cell suspension or pulverized tissue was transferred to a Dounce Tissue Grinder (D9063. Merck, Darmstadt, Germany) on ice with 3 ml of ice-cold Omni 1 x Homogenization buffer. The sample was homogenized with an A-pestle until resistance went away and further with a B-pestle (3 ~ 10 strokes each) so as to disrupt cellular plasma membranes. Cell debris was removed by passing the sample through stackable cell strainers (100, 70 and 30 um MACS SmartStrainers, Miltenyi Biotec). The flowthrough was further clarified by a brief centrifugation at 100 x g for 1 minute at 4 Celsius. Supernatant was mixed with an equal volume of ice-cold Omni 50% Iodixanol solution (final 25% Iodixanol). Purification of nuclei: Two layers of Iodixanol cushions were prepared in a 2 ml LoBind tube (Eppendorf, Hamburg, Germany) by placing 600 ul of ice-cold 40% Iodixanol solution on the bottom and overlaying 600 ul of ice-cold 29% Iodixanol solution using wide-bore tips. On the top, 800 ul of the cell suspension (25% Iodixanol) was placed. Density gradient centrifugation was done using a swing rotor at 6,000 x g for 30 minutes at 4 Celsius with a soft brake setting. Top layers were carefully removed down to ~2 mm above of the bottom layer. A nuclear fraction between the bottom and middle layers was collected (~ 400 ul) to a new LoBind tube on ice. The number of nuclei was counted by mixing 20 ul of the sample with 20 ul of 100 x diluted Hoechst 33342 (Fisher) using a hemocytometer under a fluorescence microscope. Tagmentation: Approximately 50,000 nuclei each were transferred to two of 1.5 ml LoBind tubes filled with1 ml of ice-cold ATAC-RSB + 0.1% Tween-20 buffer and centrifuged at 500 x g for 10 minutes at 4 Celsius. After carefully removing supernatant, nuclei were resuspended in 50 ul of Omni-ATAC reaction mix containing Tn5 Transposase TDE1 enzyme (Illumina, San Diego, CA). As effectiveness of Tn5 enzyme varied slightly among tissue types, we used two different amounts of the enzyme per sample. After mixing the sample by pipetting six times using a P200 fine tip, tagmentation reaction was carried out using Eppendorf Thermomixer at 37 Celsius at 500 rpm for 30 minutes. The reaction was stopped by adding 300 ul of PB buffer in MinElute PCR purification kit (Qiagen, Venlo, Netherlands) and 10 ul of 3M sodium acetate, pH 5.2. The sample was mixed, kept at room temperature for 10 min and stored at -20 Celsius until DNA purification. Library preparation: The tagmented DNA was purified and eluted in 21 ul elution buffer using the MinElute PCR purification kit. The DNA was amplified using NEBNext High-Fidelity 2X PCR Master Mix with Ad1 and Ad2 primers (Buenrostro et al., 2013) for 13 PCR-cycles. The amplified libraries were purified and eluted in 51 ul elution buffer using the MinElute PCR purification kit. Library size distribution was monitored using 10 ul of the library by QIAxcel capillary electrophoresis (Qiagen). Large DNA fragments were eliminated using AMPure XP magnetic beads (Beckman Coulter, Brea, CA) by a right-side size selection using 0.55 x followed by 1.5 x ratio of beads to sample. Library concentration was estimated using KAPA Library Quantification kit (Kapa Biosystems, Wilmington, MA).

text: infant

text: normal

text: wild type genotype

text: not applicable

text: Bos taurus

text: Bos taurus

text: blood

characteristic: organism part

characteristic: sampling site

text: Bos taurus

text: male

characteristic: sex

text: Holstein

characteristic: strain

text: fresh tissue, TDE1=1.5 ul

characteristic: tissue with known storage state

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Unit of Animal Genomics, GIGA Institute, University of Liege

text: public

text: E-MTAB-11825:ATAC18_HOL1_m_WBCcorc_fresh_tn20_lib1

text: ArrayExpress

text: leukocyte

text: cattle

text: infant

characteristic: developmental stage

text: normal

characteristic: disease

text: wild type genotype

characteristic: genotype

characteristic: individual

text: not applicable

characteristic: isolate

text: Bos taurus

characteristic: organism

text: Bos taurus

text: blood

text: Bos taurus

text: male

text: Holstein

text: fresh tissue, TDE1=2.0 ul


characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-11825:ATAC31_HOL2_m_WBCcorc_fresh_tn20_lib1

characteristic: Submitter Id

characteristic: age

text: ArrayExpress

characteristic: broker name

text: leukocyte

text: cattle

characteristic: common name

characteristic: description

text: infant

text: normal

text: wild type genotype

text: not applicable

text: Bos taurus

text: Bos taurus

text: blood

text: Bos taurus

text: male

text: Holstein

text: fresh tissue, TDE1=2.0 ul


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: E-MTAB-11825:ATAC31_HOL2_m_WBCcorc_fresh_tnD15_lib1

text: ArrayExpress

text: leukocyte

text: cattle

text: infant

text: normal

text: wild type genotype

text: not applicable

text: Bos taurus

text: Bos taurus

text: blood

characteristic: organism part

characteristic: sampling site

text: Bos taurus

text: male

characteristic: sex

text: Holstein

characteristic: strain

text: fresh tissue, TDE1=1.5 ul

characteristic: tissue with known storage state

characteristic: title


characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

tag: Namespace:University of Zurich, Institute of Parasitology

text: dog

text: Canis lupus familiaris

characteristic: organism

text: Canis lupus familiaris


text: University of Zurich, Institute of Parasitology

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: dog

characteristic: common name

text: Canis lupus familiaris

text: Canis lupus familiaris


text: 3-spined stickleback

characteristic: ArrayExpress-Species

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

text: three-spined stickleback

text: Gasterosteus aculeatus

text: Gasterosteus aculeatus


text: 3-spined stickleback

characteristic: ArrayExpress-SPECIES

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

text: public

text: three-spined stickleback

text: Gasterosteus aculeatus

text: Gasterosteus aculeatus


text: University of Basel

text: public

tag: Namespace:University of Basel

text: Posieux field data 1

characteristic: description

text: metagenome

text: metagenome


text: University of Basel

text: public

text: Posieux field data 2

text: metagenome

text: metagenome


text: Nector americanus

text: SC

text: public

text: Nector americanus

text: Necator americanus

text: Necator americanus


text: Streptococcus agalactiae

text: SC

text: public

text: Streptococcus agalactiae

text: Streptococcus agalactiae

text: Streptococcus agalactiae

text: Streptococcus agalactiae


text: Streptococcus agalactiae

text: SC

text: public

text: Streptococcus agalactiae

text: Streptococcus pneumoniae

text: Streptococcus pneumoniae

text: Streptococcus agalactiae


text: Streptococcus agalactiae

text: SC

text: public

text: Streptococcus agalactiae

text: Streptococcus pyogenes

text: Streptococcus pyogenes

text: Streptococcus agalactiae


text: Streptococcus agalactiae

text: SC

text: public

text: Streptococcus agalactiae

text: Streptococcus downei

text: Streptococcus downei

text: Streptococcus agalactiae


text: Streptococcus agalactiae

text: SC

text: public

text: Streptococcus agalactiae

text: Streptococcus parasanguinis

text: Streptococcus parasanguinis

text: Streptococcus agalactiae


text: Streptococcus agalactiae

text: SC

text: public

text: Streptococcus agalactiae

text: Streptococcus sp. 'group B'

text: Streptococcus sp. 'group B'

text: Streptococcus agalactiae


text: Streptococcus agalactiae

text: SC

text: public

text: Streptococcus agalactiae

text: Streptococcus sp. 'group G'

text: Streptococcus sp. 'group G'

text: Streptococcus agalactiae


text: Streptococcus agalactiae

text: SC

text: public

text: Streptococcus agalactiae

text: Blautia hansenii

text: Blautia hansenii

text: Streptococcus agalactiae


text: Streptococcus agalactiae

text: SC

text: public

text: Streptococcus agalactiae

text: Faecalicoccus pleomorphus

text: Faecalicoccus pleomorphus

text: Streptococcus agalactiae


text: Streptococcus agalactiae

text: SC

text: public

text: Streptococcus agalactiae

text: Streptococcus sp. G148

text: Streptococcus sp. G148

text: Streptococcus agalactiae


text: Streptococcus agalactiae

text: SC

text: public

text: Streptococcus agalactiae

text: Streptococcus sp. GX7805

text: Streptococcus sp. GX7805

text: Streptococcus agalactiae


text: Streptococcus agalactiae

text: SC

text: public

text: Streptococcus agalactiae

text: Streptococcus acidominimus

text: Streptococcus acidominimus

text: Streptococcus agalactiae


text: Streptococcus agalactiae

text: SC

text: public

text: Streptococcus agalactiae

text: Streptococcus alactolytiens

text: Streptococcus alactolytiens

text: Streptococcus agalactiae


text: Streptococcus agalactiae

text: SC

text: public

text: Streptococcus agalactiae

text: Streptococcus anginosus

text: Streptococcus anginosus

text: Streptococcus agalactiae


text: Streptococcus agalactiae

text: SC

text: public

text: Streptococcus agalactiae

text: Streptococcus canis

text: Streptococcus canis

text: Streptococcus agalactiae


text: Streptococcus agalactiae

text: SC

text: public

text: Streptococcus agalactiae

text: Streptococcus criae

text: Streptococcus criae

text: Streptococcus agalactiae


E-MTAB-11860:HCC1806 siControl.1

text: public

text: E-MTAB-11860:HCC1806 siControl.1

tag: Namespace:University Medical Center Gottingen Department of Gynecology and Obstetrics Molecular Gynecology

text: ArrayExpress

characteristic: broker name

text: human

text: Protocols: HCC1806 cells were grown in RPMI GlutaMax medium supplemented with 10% fetal bovine serum, 100 units/ml penicillin and 100 μg/ml streptomycin at 37°C and 5% CO2. siRNA transfections were performed using Lipofectamine® RNAiMAX (Invitrogen) according to the manufacturer’s instructions. RNA was extracted usiung QIAzol® Lysis Reagent (Qiagen) according to the manufacturer's protocol. Libraries were prepared using NEXTflex™ Rapid Illumina Directional RNA-Seq Library Prep Kit (Illumina®) after verifying the RNA integrity on an agarose gel. Library quality was assessed using an Agilent Bioanalyzer 2100.

text: triple-negative breast cancer

characteristic: disease

text: wild type genotype

characteristic: genotype

text: not applicable

characteristic: isolate

text: Homo sapiens

text: Homo sapiens

text: mammary gland

characteristic: organism part

text: Homo sapiens

text: HCC1806 siControl.1


E-MTAB-11860:HCC1806 siControl.2

text: University Medical Center Gottingen Department of Gynecology and Obstetrics Molecular Gynecology

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-11860:HCC1806 siControl.2

text: ArrayExpress

text: human

text: triple-negative breast cancer

text: wild type genotype

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: mammary gland

text: Homo sapiens

text: HCC1806 siControl.2

characteristic: title


E-MTAB-11860:HCC1806 siControl.3

text: public

characteristic: SRA accession

text: E-MTAB-11860:HCC1806 siControl.3

characteristic: Submitter Id

text: ArrayExpress

text: human

characteristic: common name

text: triple-negative breast cancer

text: wild type genotype

text: not applicable

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: mammary gland

text: Homo sapiens

text: HCC1806 siControl.3


E-MTAB-11860:HCC1806 siRNF40.1

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: public

text: E-MTAB-11860:HCC1806 siRNF40.1

text: ArrayExpress

text: human

text: triple-negative breast cancer

text: wild type genotype

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: mammary gland

text: Homo sapiens

text: HCC1806 siRNF40.1


E-MTAB-11860:HCC1806 siRNF40.2

characteristic: External Id

text: public

text: E-MTAB-11860:HCC1806 siRNF40.2

text: ArrayExpress

characteristic: broker name

text: human

characteristic: description

text: triple-negative breast cancer

text: wild type genotype

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: mammary gland

text: Homo sapiens

text: HCC1806 siRNF40.2


E-MTAB-11860:HCC1806 siRNF40.3

text: public

text: E-MTAB-11860:HCC1806 siRNF40.3

text: ArrayExpress

text: human

text: triple-negative breast cancer

characteristic: disease

text: wild type genotype

characteristic: genotype

text: not applicable

characteristic: isolate

text: Homo sapiens

text: Homo sapiens

text: mammary gland

text: Homo sapiens

text: HCC1806 siRNF40.3


text: Anopheles gambiae

characteristic: ArrayExpress-SPECIES

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: African malaria mosquito

text: Anopheles gambiae

text: Anopheles gambiae


text: CGR

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: Norway rat

text: Rattus norvegicus

text: Rattus norvegicus

characteristic: title


text: public

characteristic: SRA accession

tag: Namespace:MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY

characteristic: Submitter Id

text: Euplotes crassus DP1 MAC DNA

text: Moneuplotes crassus

text: Moneuplotes crassus

characteristic: strain


text: Not Applicable

characteristic: ArrayExpress-PHENOTYPE

text: unknown

characteristic: ArrayExpress-SEX

text: Mus musculus

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Unknown

characteristic: GENDER

text: SC

text: public

text: Not Applicable

characteristic: PHENOTYPE

text: house mouse

characteristic: common name

text: Mus musculus

characteristic: organism

text: Mus musculus


text: Escherichia coli

characteristic: ArrayExpress-Species

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

text: public

text: Escherichia coli

text: Escherichia coli

text: Escherichia coli


text: Escherichia coli

characteristic: ArrayExpress-SPECIES

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: Escherichia coli

text: Escherichia coli

text: Escherichia coli


text: CGR

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: European woodmouse

characteristic: description

text: Apodemus sylvaticus

text: Apodemus sylvaticus

characteristic: title


text: Streptococcus agalactiae

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

text: Streptococcus agalactiae

text: Streptococcus agalactiae

text: Bacterial DNA

text: Streptococcus agalactiae

characteristic: strain

text: Streptococcus agalactiae


text: Streptococcus agalactiae

text: SC

text: public

text: Streptococcus agalactiae

characteristic: common name

text: Streptococcus agalactiae

text: Streptococcus agalactiae


text: Streptococcus agalactiae

text: SC

text: public

text: Streptococcus agalactiae

text: Streptococcus agalactiae

characteristic: organism

text: Streptococcus agalactiae

text: Streptococcus agalactiae


text: Streptococcus agalactiae

text: SC

text: public

text: Streptococcus agalactiae

text: Streptococcus agalactiae

text: Streptococcus agalactiae

text: Streptococcus agalactiae


text: public

tag: Namespace:Key Laboratory of Environmental and Applied Microbiology, CAS

characteristic: collection date

text: soil

text: soil

characteristic: environment (biome)

text: soil

characteristic: environment (feature)

text: soil

characteristic: environment (material)

text: China

characteristic: geographic location (country and/or sea)

unit: m

characteristic: geographic location (depth)

characteristic: geographic location (elevation)

unit: DD

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome

characteristic: investigation type

text: gut metagenome

text: Corpse

characteristic: project name

text: gut metagenome

characteristic: sequencing method

text: soil

characteristic: soil environmental package

text: soil


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Key Laboratory of Environmental and Applied Microbiology, CAS

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: soil

characteristic: description

text: soil

text: soil

text: soil

text: China

text: metagenome

text: gut metagenome

text: Corpse

text: gut metagenome

text: soil

text: soil

characteristic: title


text: public

characteristic: collection date

text: fecal

characteristic: environment (biome)

text: fecal

characteristic: environment (feature)

text: fecal

characteristic: environment (material)

text: China

characteristic: geographic location (country and/or sea)

characteristic: geographic location (depth)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome

text: gut metagenome

characteristic: organism

text: fecal

text: gut metagenome

text: fecal

text: water

characteristic: water environmental package


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

tag: Namespace:GFZ German Research Centre for Geosciences

text: BMA3 drill core from the Opalinus Clay geological formation at the Mt. Terri Rock Laboratory (St-Ursanne, Switzerland) depth 3,85-4,15m

text: rock

text: rock

text: rock

text: Switzerland

characteristic: geographic location (elevation)

text: mimarks-survey

characteristic: investigation type

text: miscellaneous natural or artificial environment

characteristic: miscellaneous environmental package

text: metagenome

text: 515F (GTGYCAGCMGCCGCGGTAA) 806R (GGACTACNVGGGTWTCTAAT)

characteristic: pcr primers

text: Opalinus Clay-associated microbial communities

characteristic: project name

text: metagenome

text: Illumina MiSeq v3 2x300bp

characteristic: sequencing method

text: 16S rRNA

characteristic: target gene

text: 16S V4

characteristic: target subfragment


text: GFZ German Research Centre for Geosciences

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

characteristic: description

text: rock

characteristic: environment (biome)

text: rock

characteristic: environment (feature)

text: rock

characteristic: environment (material)

text: Switzerland

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: mimarks-survey

text: metagenome

text: metagenome

text: Illumina MiSeq v3 2x300bp

text: 16S rRNA

text: 16S V4

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: BMA3 drill core from the Opalinus Clay geological formation at the Mt. Terri Rock Laboratory (St-Ursanne, Switzerland) depth 5,7-5,95m

text: rock

text: rock

text: rock

text: Switzerland

characteristic: geographic location (elevation)

text: mimarks-survey

characteristic: investigation type

characteristic: miscellaneous environmental package

text: metagenome

characteristic: organism

characteristic: pcr primers

characteristic: project name

text: metagenome

text: Illumina MiSeq v3 2x300bp

text: 16S rRNA

text: 16S V4


characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

text: BMA4 drill core from the Opalinus Clay geological formation at the Mt. Terri Rock Laboratory (St-Ursanne, Switzerland) depth 4,26-4,4m

characteristic: description

text: rock

characteristic: environment (biome)

text: rock

characteristic: environment (feature)

text: rock

characteristic: environment (material)

text: Switzerland

text: mimarks-survey

text: metagenome

text: metagenome

text: Illumina MiSeq v3 2x300bp

characteristic: sequencing method

text: 16S rRNA

characteristic: target gene

text: 16S V4

characteristic: target subfragment


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: BMA3 drill core from the Opalinus Clay geological formation at the Mt. Terri Rock Laboratory (St-Ursanne, Switzerland) depth 10,75 - 11

text: rock

text: rock

text: rock

text: Switzerland

characteristic: geographic location (country and/or sea)

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: mimarks-survey

characteristic: investigation type

text: metagenome

text: metagenome

text: Illumina MiSeq v3 2x300bp

text: 16S rRNA

text: 16S V4

characteristic: title


characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

text: BMA4 drill core from the Opalinus Clay geological formation at the Mt. Terri Rock Laboratory (St-Ursanne, Switzerland) depth 6,56-6,71m

characteristic: description

text: rock

characteristic: environment (biome)

text: rock

characteristic: environment (feature)

text: rock

text: Switzerland

text: mimarks-survey

characteristic: miscellaneous environmental package

text: metagenome

characteristic: organism

characteristic: pcr primers

characteristic: project name

text: metagenome

text: Illumina MiSeq v3 2x300bp

text: 16S rRNA

text: 16S V4


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: BMA3 drill core from the Opalinus Clay geological formation at the Mt. Terri Rock Laboratory (St-Ursanne, Switzerland) depth 7,25-7,5

text: rock

text: rock

text: rock

characteristic: environment (material)

text: Switzerland

characteristic: geographic location (country and/or sea)

characteristic: geographic location (elevation)

text: mimarks-survey

text: metagenome

text: metagenome

text: Illumina MiSeq v3 2x300bp

characteristic: sequencing method

text: 16S rRNA

characteristic: target gene

text: 16S V4

characteristic: target subfragment


characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

text: BMA4 drill core from the Opalinus Clay geological formation at the Mt. Terri Rock Laboratory (St-Ursanne, Switzerland) depth 8,9-9,13m

characteristic: description

text: rock

characteristic: environment (biome)

text: rock

characteristic: environment (feature)

text: rock

text: Switzerland

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: mimarks-survey

characteristic: investigation type

text: metagenome

text: metagenome

text: Illumina MiSeq v3 2x300bp

text: 16S rRNA

text: 16S V4

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: Negative PCR

text: rock

text: rock

text: rock

characteristic: environment (material)

text: Switzerland

characteristic: geographic location (country and/or sea)

text: mimarks-survey

characteristic: miscellaneous environmental package

text: metagenome

characteristic: organism

characteristic: pcr primers

characteristic: project name

text: metagenome

text: Illumina MiSeq v3 2x300bp

text: 16S rRNA

text: 16S V4


characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

text: Nitrogengas

characteristic: description

text: rock

characteristic: environment (biome)

text: rock

characteristic: environment (feature)

text: rock

text: Switzerland

characteristic: geographic location (elevation)

text: mimarks-survey

text: metagenome

text: metagenome

text: Illumina MiSeq v3 2x300bp

characteristic: sequencing method

text: 16S rRNA

characteristic: target gene

text: 16S V4

characteristic: target subfragment


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: Gas Glovebox

text: rock

text: rock

text: rock

characteristic: environment (material)

text: Switzerland

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: mimarks-survey

characteristic: investigation type

text: metagenome

text: metagenome

text: Illumina MiSeq v3 2x300bp

text: 16S rRNA

text: 16S V4

characteristic: title


characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

text: Negative Extraction Kit

characteristic: description

text: rock

characteristic: environment (biome)

text: rock

characteristic: environment (feature)

text: rock

text: Switzerland

text: mimarks-survey

characteristic: miscellaneous environmental package

text: metagenome

characteristic: organism

characteristic: pcr primers

characteristic: project name

text: metagenome

text: Illumina MiSeq v3 2x300bp

text: 16S rRNA

text: 16S V4


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: Negative control PCR

text: rock

text: rock

text: rock

characteristic: environment (material)

text: Switzerland

characteristic: geographic location (country and/or sea)

characteristic: geographic location (elevation)

text: mimarks-survey

text: metagenome

text: metagenome

text: Illumina MiSeq v3 2x300bp

characteristic: sequencing method

text: 16S rRNA

characteristic: target gene

text: 16S V4

characteristic: target subfragment


characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

text: Positive control 10

characteristic: description

text: rock

characteristic: environment (biome)

text: rock

characteristic: environment (feature)

text: rock

text: Switzerland

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: mimarks-survey

characteristic: investigation type

text: metagenome

text: metagenome

text: Illumina MiSeq v3 2x300bp

text: 16S rRNA

text: 16S V4

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: Positive control even

text: rock

text: rock

text: rock

characteristic: environment (material)

text: Switzerland

characteristic: geographic location (country and/or sea)

text: mimarks-survey

characteristic: miscellaneous environmental package

text: metagenome

characteristic: organism

characteristic: pcr primers

characteristic: project name

text: metagenome

text: Illumina MiSeq v3 2x300bp

text: 16S rRNA

text: 16S V4


characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

text: Positive control uneven

characteristic: description

text: rock

characteristic: environment (biome)

text: rock

characteristic: environment (feature)

text: rock

text: Switzerland

characteristic: geographic location (elevation)

text: mimarks-survey

text: metagenome

text: metagenome

text: Illumina MiSeq v3 2x300bp

characteristic: sequencing method

text: 16S rRNA

characteristic: target gene

text: 16S V4

characteristic: target subfragment


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: DKFZ

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: ena-upload-cli

text: naked mole-rat

characteristic: common name

text: DMBA or vehicle treated naked mole rat fibroblasts

text: Heterocephalus glaber

text: Heterocephalus glaber

characteristic: title


text: Pseudomonas aeruginosa

characteristic: ArrayExpress-SPECIES

text: SC

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: Pseudomonas aeruginosa

text: Pseudomonas aeruginosa

characteristic: organism

text: Pseudomonas aeruginosa


text: Quadram Institute Bioscience

text: public

tag: Namespace:Quadram Institute Bioscience

characteristic: age

text: ArrayExpress

characteristic: broker name

text: human

text: Protocols: Hepatic artery samples were collected from patients at the time of liver transplantation at Addenbrookes NHS Trust, Cambridge University Hospitals, Cambridge, UK. Hepatic arterial samples were collected from patients with confirmed cirrhosis and clinically significant portal hypertension with a diagnosis of primary sclerosing cholangitis involving both intra- and extra-hepatic bile ducts, or alcohol-related liver disease or non-alcohol related fatty liver disease. The hepatic artery samples were identified and resected during surgery by the attending transplant surgeon. The samples were approximately 1 cm in length and were taken from the main artery at the hilum of the liver, just proximal to the bifurcation into the left and right hepatic artery. The proximity to the bifurcation was chosen for consistency and to ensure the same area was sampled across all specimens. Once collected, samples were frozen in liquid nitrogen and stored at -80°C prior to further analysis to allow for batched processing. RNA was extracted with the Qiagen RNeasy Mini Kit following the manufacturer’s protocol. Nucleic acid library construction was performed by the Sanger Institute

characteristic: description

text: adult

characteristic: developmental stage

text: normal

characteristic: disease

characteristic: individual

text: not applicable

characteristic: isolate

text: Homo sapiens

text: Homo sapiens

text: hepatic artery

characteristic: organism part

text: Homo sapiens

text: male

characteristic: sex


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Quadram Institute Bioscience

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: ArrayExpress

text: human

characteristic: common name

text: adult

text: normal

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: hepatic artery

text: Homo sapiens

text: female


text: Quadram Institute Bioscience

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: human

text: adult

text: primary sclerosing cholangitis

text: not applicable

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: hepatic artery

text: Homo sapiens

text: female

characteristic: title


text: Quadram Institute Bioscience

text: public

characteristic: age

text: ArrayExpress

characteristic: broker name

text: human

characteristic: description

text: adult

characteristic: developmental stage

text: primary sclerosing cholangitis

characteristic: disease

characteristic: individual

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: hepatic artery

text: Homo sapiens

text: male


E-MTAB-11914:DAOY KO empty vector

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: public

text: E-MTAB-11914:DAOY KO empty vector

tag: Namespace:European Research Institute for the Biology of Ageing University Medical Center Groningen

text: ArrayExpress

text: Daoy

text: human

text: Protocols: Half a million cells were plated on six well plates. After 48 hours, cells were harvested using Tryple. Pelleted cells were washed with 1xPBS before being stored as dry pellets at -80 degree Celsius. For whole transcriptome analysis, RNA was isolated using the RNeasy mini kit (Qiagen) in accordance to manufacturer's protocol and RNA quality was examined using the Agilent 2100 Bioanalyzer (Agilent Technologies). 250-500 ng of total RNA was used as input for mRNA enrichment using NEXTflex Poly(A) Beads (Bio Scientific) followed by library preparation using a NEXTflex Rapid Directional qRNA-Seq Kit (Bio Scientific).

text: juvenile stage

text: desmoplastic/nodular medulloblastoma

text: VAPB -/-

characteristic: genotype

text: not applicable

characteristic: isolate

text: Homo sapiens

text: Homo sapiens

text: posterior cranial fossa

characteristic: organism part

text: Homo sapiens

text: DAOY KO empty vector


E-MTAB-11914:USP13 KO empty vector

characteristic: External Id

text: European Research Institute for the Biology of Ageing University Medical Center Groningen

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-11914:USP13 KO empty vector

text: ArrayExpress

text: human

characteristic: common name

text: juvenile stage

text: medulloblastoma

text: VAPB -/-

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: mixed brain and cerebellum

text: Homo sapiens

text: USP13 KO empty vector