text: University of Oxford

characteristic: GAL

text: NOT PROVIDED

text: EarlhamInstitute

characteristic: INSDC center name

text: public

text: NOT PROVIDED

characteristic: barcoding center

text: COPO

characteristic: broker name

text: Keiron Brown

characteristic: collected by

text: University of Oxford

characteristic: collecting institution

characteristic: collection date

text: common brandling worm

characteristic: elevation

text: United Kingdom

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Berkshire | Wytham woods

text: Woodland

characteristic: habitat

text: Keiron Brown

characteristic: identified by

text: University of Oxford

text: adult

characteristic: lifestage

text: Eisenia andrei

text: WHOLE ORGANISM

characteristic: organism part

text: DTOL

characteristic: project name

text: Eisenia andrei

text: NOT COLLECTED

characteristic: specimen id

characteristic: specimen voucher

text: 5ea7d3d7-7a42-4b89-936c-efeeaee518cd-DTOL-specimen

characteristic: tolid


status: PUBLIC

tag: attribute

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: University of Oxford

characteristic: GAL

text: NOT PROVIDED

text: EarlhamInstitute

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: NOT PROVIDED

text: COPO

text: Keiron Brown

text: University of Oxford

text: common brandling worm

characteristic: common name

unit: m

text: United Kingdom

characteristic: geographic location (country and/or sea)

unit: DD

text: Berkshire | Wytham woods

characteristic: geographic location (region and locality)

text: Woodland

text: Keiron Brown

text: University of Oxford

text: adult

text: Eisenia andrei

characteristic: organism

text: WHOLE ORGANISM

text: DTOL

text: Eisenia andrei

text: NOT COLLECTED

characteristic: sex

text: 194ba870-ad6b-47c8-8654-d8ef1b4b07fd-DTOL-specimen

characteristic: title

type: derived from


characteristic: ENA-CHECKLIST

text: Royal Botanic Garden Edinburgh

text: NOT PROVIDED

text: EarlhamInstitute

text: public

text: ROYAL BOTANIC GARDEN EDINBURGH

characteristic: barcoding center

text: COPO

characteristic: broker name

text: MARKUS RUHSAM

characteristic: collected by

text: ROYAL BOTANIC GARDEN EDINBURGH

characteristic: collecting institution

characteristic: collection date

text: United Kingdom

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Gorebridge

text: in garden

characteristic: habitat

text: MARKUS RUHSAM

characteristic: identified by

text: ROYAL BOTANIC GARDEN EDINBURGH

text: sporophyte

characteristic: lifestage

text: Trifolium dubium

text: WHOLE ORGANISM

characteristic: organism part

text: ERGA

characteristic: project name

text: DTOL

text: Trifolium dubium

text: HERMAPHRODITE MONOECIOUS

characteristic: specimen id

text: NOT PROVIDED

characteristic: specimen voucher

text: f5178aef-aa6c-44b1-bc12-a5f7299c1e0e-DTOL-specimen

characteristic: tolid


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Royal Botanic Garden Edinburgh

characteristic: GAL

text: NOT PROVIDED

text: EarlhamInstitute

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: ROYAL BOTANIC GARDEN EDINBURGH

text: COPO

text: MARKUS RUHSAM

text: ROYAL BOTANIC GARDEN EDINBURGH

text: United Kingdom

characteristic: geographic location (country and/or sea)

text: Gorebridge

characteristic: geographic location (region and locality)

text: in garden

text: MARKUS RUHSAM

text: ROYAL BOTANIC GARDEN EDINBURGH

text: sporophyte

text: Trifolium dubium

characteristic: organism

text: WHOLE ORGANISM

text: ERGA

text: DTOL

text: Trifolium dubium

text: HERMAPHRODITE MONOECIOUS

characteristic: sex

text: NOT PROVIDED

text: 63d72ed0-5bb9-4fbd-bea8-fdd3ebad77dd-DTOL-specimen

characteristic: title


characteristic: ENA-CHECKLIST

text: Royal Botanic Garden Edinburgh

text: NOT PROVIDED

text: EarlhamInstitute

text: public

text: ROYAL BOTANIC GARDEN EDINBURGH

characteristic: barcoding center

text: COPO

characteristic: broker name

text: MARKUS RUHSAM

characteristic: collected by

text: ROYAL BOTANIC GARDEN EDINBURGH

characteristic: collecting institution

characteristic: collection date

text: United Kingdom

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Gorebridge

text: in garden

characteristic: habitat

text: MARKUS RUHSAM

characteristic: identified by

text: ROYAL BOTANIC GARDEN EDINBURGH

text: sporophyte

characteristic: lifestage

text: Trifolium dubium

text: WHOLE ORGANISM

characteristic: organism part

text: ERGA

characteristic: project name

text: DTOL

text: Trifolium dubium

text: HERMAPHRODITE MONOECIOUS

characteristic: specimen id

text: NOT PROVIDED

characteristic: specimen voucher

text: 4c7dc569-3d3c-429d-9d13-f5de204ba74f-DTOL-specimen


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Royal Botanic Garden Edinburgh

characteristic: GAL

text: NOT PROVIDED

text: EarlhamInstitute

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: ROYAL BOTANIC GARDEN EDINBURGH

text: COPO

text: MARKUS RUHSAM

text: ROYAL BOTANIC GARDEN EDINBURGH

text: United Kingdom

characteristic: geographic location (country and/or sea)

text: Gorebridge

characteristic: geographic location (region and locality)

text: in garden

text: MARKUS RUHSAM

text: ROYAL BOTANIC GARDEN EDINBURGH

text: sporophyte

text: Trifolium dubium

characteristic: organism

text: WHOLE ORGANISM

text: ERGA

text: DTOL

text: Trifolium dubium

text: HERMAPHRODITE MONOECIOUS

characteristic: sex

text: NOT PROVIDED

text: e38e7e52-ea97-483f-ac23-f97cb6984a84-DTOL-specimen

characteristic: tolid


characteristic: ENA-CHECKLIST

text: Royal Botanic Garden Edinburgh

text: NOT PROVIDED

text: EarlhamInstitute

text: public

text: ROYAL BOTANIC GARDEN EDINBURGH

characteristic: barcoding center

text: COPO

characteristic: broker name

text: MARKUS RUHSAM

characteristic: collected by

text: ROYAL BOTANIC GARDEN EDINBURGH

characteristic: collecting institution

characteristic: collection date

text: United Kingdom

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Gorebridge

text: in garden

characteristic: habitat

text: MARKUS RUHSAM

characteristic: identified by

text: ROYAL BOTANIC GARDEN EDINBURGH

text: sporophyte

characteristic: lifestage

text: Trifolium dubium

text: WHOLE ORGANISM

characteristic: organism part

text: ERGA

characteristic: project name

text: DTOL

text: Trifolium dubium

text: HERMAPHRODITE MONOECIOUS

characteristic: specimen id

text: NOT PROVIDED

text: 360aa897-cb0f-4317-8a7b-df8ede050f45-DTOL-specimen

characteristic: title


text: Plasmodium falciparum

characteristic: ArrayExpress-SPECIES

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: malaria parasite P. falciparum

characteristic: common name

text: Plasmodium falciparum

characteristic: organism

text: Plasmodium falciparum


text: unidentified

characteristic: ENA-CHECKLIST

text: SC

text: public

text: unidentified

text: unidentified

text: unidentified


text: Streptococcus agalactiae

text: SC

text: public

text: Streptococcus agalactiae

text: Streptococcus agalactiae

text: Streptococcus agalactiae


text: mixed

characteristic: ArrayExpress-SEX

text: Vibrio cholerae

text: Vibrio cholerae

text: Mixed

characteristic: GENDER

text: SC

text: public

text: Vibrio cholerae

text: Vibrio cholerae

text: Vibrio cholerae

text: Bacteria


text: Boletus edulis

text: SC

text: public

text: Boletus edulis

text: Boletus edulis

text: Boletus edulis


text: Natural History Museum

characteristic: GAL

text: NOT PROVIDED

text: EarlhamInstitute

text: public

text: NOT PROVIDED

characteristic: barcoding center

text: COPO

characteristic: broker name

text: EMMA SHERLOCK | CHRIS FLETCHER

characteristic: collected by

text: NATURAL HISTORY MUSEUM | NATURAL HISTORY MUSEUM

characteristic: collecting institution

characteristic: collection date

text: common brandling worm

text: United Kingdom

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: England|Natural History Museum Wildlife Garden

characteristic: geographic location (region and locality)

text: NOT COLLECTED

characteristic: habitat

text: EMMA SHERLOCK

characteristic: identified by

text: NATURAL HISTORY MUSEUM

text: adult

characteristic: lifestage

text: Eisenia andrei

text: WHOLE ORGANISM

characteristic: organism part

text: DTOL

characteristic: project name

text: Eisenia andrei

text: NOT COLLECTED

characteristic: sex

characteristic: specimen id

text: 7ac9e01d-d6dc-41a8-9e65-29fea1cbb070-DTOL-specimen

characteristic: tolid


text: Pseudomonas aeruginosa

characteristic: ArrayExpress-SPECIES

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: Pseudomonas aeruginosa

characteristic: common name

text: Pseudomonas aeruginosa

characteristic: organism

text: Pseudomonas aeruginosa

characteristic: title


text: Pseudomonas aeruginosa

text: SC

text: public

text: Pseudomonas aeruginosa

text: Pseudoalteromonas atlantica

text: Pseudoalteromonas atlantica


text: Royal Botanic Gardens Kew

characteristic: GAL

text: NOT PROVIDED

text: EarlhamInstitute

text: public

text: ROYAL BOTANIC GARDEN EDINBURGH

characteristic: barcoding center

text: COPO

characteristic: broker name

text: Maarten Christenhusz

characteristic: collected by

text: Independent

characteristic: collecting institution

characteristic: collection date

characteristic: elevation

text: United Kingdom

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: SURREY | KEW

characteristic: geographic location (region and locality)

text: weed in flower bed

characteristic: habitat

text: Maarten Christenhusz

characteristic: identified by

text: Independent

text: vegetative structure

characteristic: lifestage

text: Symphytum orientale

text: WHOLE ORGANISM

characteristic: organism part

characteristic: original collection date

text: UNITED KINGDOM | SURREY | KEW

characteristic: original collection location

text: DTOL

characteristic: project name

text: Symphytum orientale

text: HERMAPHRODITE MONOECIOUS

characteristic: sex

characteristic: specimen voucher

text: bb3f2a92-6019-4ac1-b591-a50977e2d0f3-DTOL-specimen


text: Boletus aereus

characteristic: ArrayExpress-SPECIES

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: Boletus aereus

characteristic: common name

text: Boletus aereus

characteristic: organism

text: Boletus aereus

characteristic: title


text: Sanger Institute

characteristic: GAL

text: NOT PROVIDED

text: Tree of Life Programme

text: public

tag: Namespace:Tree of Life Programme

text: STEWART ROSELL

characteristic: collected by

text: University of Cambridge

characteristic: collecting institution

characteristic: collection date

text: apple ermine moth

text: United Kingdom

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Cambridge | King's College

characteristic: geographic location (region and locality)

text: NOT COLLECTED

characteristic: habitat

text: Richard Durbin

characteristic: identified by

text: University of Cambridge

text: adult

characteristic: lifestage

text: Yponomeuta malinellus

text: WHOLE ORGANISM

characteristic: organism part

text: DTOL

characteristic: project name

text: Yponomeuta malinellus

text: NOT COLLECTED

characteristic: specimen id

text: NOT COLLECTED

text: N

characteristic: symbiont

characteristic: tolid


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Sanger Institute

text: NOT PROVIDED

text: Tree of Life Programme

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: STEWART ROSELL

text: University of Cambridge

text: United Kingdom

text: Cambridge | Cambridge University Botanic Gardens

text: NOT COLLECTED

text: Richard Durbin

text: University of Cambridge

text: adult

text: Yponomeuta cagnagella

characteristic: organism

text: WHOLE ORGANISM

text: DTOL

text: Yponomeuta cagnagella

text: NOT COLLECTED

characteristic: sex

text: NOT COLLECTED

characteristic: specimen voucher

text: N

characteristic: title


text: Sanger Institute

characteristic: GAL

text: NOT PROVIDED

text: Tree of Life Programme

text: public

text: STEWART ROSELL

characteristic: collected by

text: University of Cambridge

characteristic: collecting institution

characteristic: collection date

text: apple ermine moth

characteristic: common name

text: United Kingdom

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Cambridge | King's College

characteristic: geographic location (region and locality)

text: NOT COLLECTED

characteristic: habitat

text: Richard Durbin

characteristic: identified by

text: University of Cambridge

text: adult

characteristic: lifestage

text: Yponomeuta malinellus

text: WHOLE ORGANISM

characteristic: organism part

text: ToL

characteristic: project name

characteristic: sample same as

text: Yponomeuta malinellus

text: NOT COLLECTED

characteristic: specimen id

text: NOT COLLECTED

text: N


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Sanger Institute

text: NOT PROVIDED

text: Tree of Life Programme

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: STEWART ROSELL

text: University of Cambridge

text: United Kingdom

text: NOT COLLECTED

text: Richard Durbin

text: University of Cambridge

text: adult

text: Yponomeuta cagnagella

characteristic: organism

text: WHOLE ORGANISM

text: ToL

text: Yponomeuta cagnagella

text: NOT COLLECTED

characteristic: sex

text: NOT COLLECTED

characteristic: specimen voucher

text: N

characteristic: symbiont

characteristic: title

characteristic: tolid


text: Lorraine University

text: public

tag: Namespace:Lorraine University

text: human

characteristic: common name

text: AlkAnilineSeq analysis of tRNA fraction, WT cell line

characteristic: description

text: Homo sapiens

text: Homo sapiens

text: � C4 small 1


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Lorraine University

text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: � C4 small 2


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Lorraine University

text: public

text: human

text: AlkAnilineSeq analysis of tRNA fraction, METTL1 KO cell line

text: Homo sapiens

text: Homo sapiens

text: 117 C1 small 1


text: Lorraine University

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: 117 C1 small 2


characteristic: INSDC last update

text: public

characteristic: INSDC status

text: Male mice with IVIg

text: metagenome

text: metagenome


text: Gut Metagenome

characteristic: ArrayExpress-SPECIES

text: SC

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: Gut Metagenome

text: gut metagenome

text: gut metagenome


text: public

text: E-MTAB-11825:ATAC32_HOL1_m_Abomasum_snap_tn15_lib1

tag: Namespace:Unit of Animal Genomics, GIGA Institute, University of Liege

unit: month

characteristic: age

text: ArrayExpress

characteristic: broker name

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: abomasum

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: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

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

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-11825:ATAC36_HOL2_m_AdiposeCardiac_snap_tn15_lib1

text: ArrayExpress

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: adipose tissue

text: heart

text: Bos taurus

text: male

text: Holstein

text: snap-frozen tissue, TDE1=1.5 ul

characteristic: title


text: public

characteristic: SRA accession

text: E-MTAB-11825:ATAC36_HOL2_m_AdiposeCardiac_snap_tn20_lib1

characteristic: Submitter Id

characteristic: age

text: ArrayExpress

characteristic: broker name

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: adipose tissue

text: heart

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

characteristic: INSDC center name

text: public

text: E-MTAB-11825:ATAC37_HOL1_m_AdiposeCardiac_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: adipose tissue

characteristic: organism part

text: heart

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: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-11825:ATAC37_HOL1_m_AdiposeCardiac_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: adipose tissue

text: heart

text: Bos taurus

text: male

text: Holstein

text: snap-frozen tissue, TDE1=2.0 ul

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: E-MTAB-11825:ATAC19_HOL1_m_AdrenalGland_fresh_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: adrenal gland

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

characteristic: SRA accession

text: E-MTAB-11825:ATAC19_HOL1_m_AdrenalGland_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: adrenal gland

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: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: E-MTAB-11825:ATAC34_HOL2_m_Atrioventricular_snap_tn15_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: atrioventricular valve

text: Bos taurus

text: male

text: Holstein

text: snap-frozen tissue, TDE1=1.5 ul

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_Atrioventricular_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: atrioventricular valve

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:ATAC37_HOL1_m_Atrioventricular_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: atrioventricular 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


characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-11825:ATAC37_HOL1_m_Atrioventricular_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: atrioventricular vein

text: Bos taurus

text: male

text: Holstein

text: snap-frozen tissue, TDE1=2.0 ul

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: E-MTAB-11825:ATAC26_HOL1_m_Bladder_slow_tn10_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: urinary bladder

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

characteristic: SRA accession

text: E-MTAB-11825:ATAC24_HOL1_m_BoneMarrow_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: bone marrow

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: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: E-MTAB-11825:ATAC28_HOL1_m_CartilageEpiglottis_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: epiglottic cartilage

text: Bos taurus

text: male

text: Holstein

text: slowly-frozen tissue, TDE1=0.8 ul

characteristic: title


characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-11825:ATAC28_HOL1_m_Cecum_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: caecum

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

characteristic: SRA accession

text: E-MTAB-11825:ATAC24_HOL1_m_Cerebellum_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: cerebellum

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: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-11825:ATAC19_HOL1_m_CerebralFrontal_fresh_tn05_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: frontal lobe

text: Bos taurus

text: male

text: Holstein

text: fresh tissue, TDE1=0.5 ul

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:ATAC19_HOL1_m_CerebralFrontal_fresh_tn10_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: frontal lobe

text: Bos taurus

text: male

text: Holstein

text: fresh tissue, TDE1=1.0 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:ATAC24_HOL1_m_ColonDescend_slow_tn05_lib1

text: ArrayExpress

text: cattle

text: infant

text: normal

text: wild type genotype

text: not applicable

text: Bos taurus

text: Bos taurus

text: descending colon

characteristic: organism part

characteristic: sampling site

text: Bos taurus

text: male

characteristic: sex

text: Holstein

characteristic: strain

text: slowly-frozen tissue, TDE1=0.5 ul

characteristic: tissue with known storage state


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: E-MTAB-11825:ATAC25_HOL1_m_ColonSpiral_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: spiral colon

text: Bos taurus

text: male

text: Holstein

text: slowly-frozen tissue, TDE1=1.0 ul

characteristic: title


characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-11825:ATAC25_HOL1_m_CorpusCallosum_slow_tn10_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: corpus callosum

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: public

characteristic: SRA accession

text: E-MTAB-11825:ATAC19_HOL1_m_Duodenum_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: duodenum

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: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-11825:ATAC19_HOL1_m_Duodenum_fresh_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: duodenum

text: Bos taurus

text: male

text: Holstein

text: fresh tissue, TDE1=1.0 ul

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: E-MTAB-11825:ATAC26_HOL1_m_Epididymis_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: epididymis

text: Bos taurus

text: male

text: Holstein

text: slowly-frozen tissue, TDE1=0.5 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:ATAC36_HOL2_m_Epididymis_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: epididymis

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: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: E-MTAB-11825:ATAC36_HOL2_m_Epididymis_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: epididymis

text: Bos taurus

text: male

text: Holstein

text: snap-frozen tissue, TDE1=2.0 ul

characteristic: title


characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-11825:ATAC37_HOL1_m_Epididymis_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: epididymis

text: Bos taurus

text: male

text: Holstein

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:ATAC37_HOL1_m_Epididymis_snap_tn20_lib1

text: ArrayExpress

text: cattle

text: infant

text: normal

text: wild type genotype

text: not applicable

text: Bos taurus

text: Bos taurus

text: epididymis

characteristic: organism part

characteristic: sampling site

text: Bos taurus

text: male

characteristic: sex

text: Holstein

characteristic: strain

text: snap-frozen tissue, TDE1=2.0 ul

characteristic: tissue with known storage state


characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-11825:ATAC25_HOL1_m_Esophagus_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: esophagus

text: Bos taurus

text: male

text: Holstein

text: slowly-frozen tissue, TDE1=1.0 ul

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: E-MTAB-11825:ATAC32_HOL1_m_Esophagus_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: esophagus

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_Esophagus_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: esophagus

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: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: E-MTAB-11825:ATAC34_HOL2_m_Esophagus_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: esophagus

text: Bos taurus

text: male

text: Holstein

text: snap-frozen tissue, TDE1=2.0 ul

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_Heart_snap_tn15_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: heart

text: Bos taurus

text: male

text: snap-frozen tissue, TDE1=1.5 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:ATAC35_BOV2_m_Heart_snap_tn20_lib1

text: ArrayExpress

text: cattle

text: juvenile stage

text: normal

text: wild type genotype

text: not applicable

text: Bos taurus

text: Bos taurus

text: heart

characteristic: organism part

characteristic: sampling site

text: Bos taurus

text: male

characteristic: sex

characteristic: strain

text: snap-frozen tissue, TDE1=2.0 ul

characteristic: tissue with known storage state


characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-11825:ATAC24_HOL1_m_Hippocampus_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: hippocampal formation

text: Bos taurus

text: male

text: Holstein

text: slowly-frozen tissue, TDE1=1.0 ul

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: E-MTAB-11825:ATAC23_HOL1_m_Hypothalamus_slow_tn10_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: hypothalamus

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

characteristic: SRA accession

text: E-MTAB-11825:ATAC26_HOL1_m_Ileum_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: ileum

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: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: E-MTAB-11825:ATAC27_HOL1_m_Jejunum_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: jejunum

text: Bos taurus

text: male

text: Holstein

text: slowly-frozen tissue, TDE1=1.0 ul

characteristic: title


characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-11825:ATAC19_HOL1_m_KidneyCortex_fresh_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: cortex of kidney

text: Bos taurus

text: male

text: Holstein

text: fresh tissue, TDE1=0.5 ul


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

characteristic: SRA accession

text: E-MTAB-11825:ATAC19_HOL1_m_KidneyCortex_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: cortex of kidney

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: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-11825:ATAC26_HOL1_m_KidneyMedulla_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: renal medulla

text: Bos taurus

text: male

text: Holstein

text: slowly-frozen tissue, TDE1=1.0 ul

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: E-MTAB-11825:ATAC24_HOL1_m_Lung_slow_tn10_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: lung

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

characteristic: SRA accession

text: E-MTAB-11825:ATAC23_HOL1_m_LymphMandibula_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: mandibular lymph node

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: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: E-MTAB-11825:ATAC25_HOL1_m_LymphMediastinal_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: mediastinal lymph node

text: Bos taurus

text: male

text: Holstein

text: slowly-frozen tissue, TDE1=1.0 ul

characteristic: title


characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-11825:ATAC28_HOL1_m_LymphMesenteric_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: mesenteric lymph node

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

characteristic: SRA accession

text: E-MTAB-11825:ATAC28_HOL1_m_LymphPrescapular_slow_tn08_lib1

text: ArrayExpress

text: cattle

text: infant

text: normal

text: wild type genotype

text: not applicable

text: Bos taurus

text: Bos taurus

text: prescapular lymph node

characteristic: organism part

characteristic: sampling site

text: Bos taurus

text: male

characteristic: sex

text: Holstein

characteristic: strain

text: slowly-frozen tissue, TDE1=0.8 ul

characteristic: tissue with known storage state


characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-11825:ATAC29_HOL4_f_MammaryGland_snap_tn08_lib1

characteristic: Submitter Id

characteristic: age

text: ArrayExpress

characteristic: broker name

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: mammary gland

text: Bos taurus

text: female

text: Holstein

text: snap-frozen tissue, TDE1=0.8 ul

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: E-MTAB-11825:ATAC29_HOL4_f_MammaryGland_snap_tn12_lib1

text: ArrayExpress

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: mammary gland

text: Bos taurus

text: female

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

characteristic: SRA accession

text: E-MTAB-11825:ATAC32_HOL5_f_MammaryGland_snap_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: adult

text: normal

text: wild type genotype

text: not applicable

text: Bos taurus

text: Bos taurus

text: mammary gland

characteristic: organism part

characteristic: sampling site

text: Bos taurus

text: female

characteristic: sex

text: Holstein

characteristic: strain

text: snap-frozen tissue, TDE1=1.0 ul

characteristic: tissue with known storage state


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:ATAC32_HOL5_f_MammaryGland_snap_tn15_lib1

characteristic: Submitter Id

characteristic: age

text: ArrayExpress

characteristic: broker name

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: mammary gland

text: Bos taurus

text: female

text: Holstein

text: snap-frozen tissue, TDE1=1.5 ul

characteristic: title


characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-11825:ATAC32_HOL6_f_MammaryGland_snap_tn10_lib1

text: ArrayExpress

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: mammary gland

text: Bos taurus

text: female

text: Holstein

text: snap-frozen tissue, TDE1=1.0 ul


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

characteristic: SRA accession

text: E-MTAB-11825:ATAC32_HOL6_f_MammaryGland_snap_tn15_lib1

text: ArrayExpress

text: cattle

text: adult

text: normal

text: wild type genotype

text: not applicable

text: Bos taurus

text: Bos taurus

text: mammary gland

characteristic: organism part

characteristic: sampling site

text: Bos taurus

text: female

characteristic: sex

text: Holstein

characteristic: strain

text: snap-frozen tissue, TDE1=1.5 ul

characteristic: tissue with known storage state


characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-11825:ATAC32_HOL7_f_MammaryGland_snap_tn05_lib1

characteristic: Submitter Id

characteristic: age

text: ArrayExpress

characteristic: broker name

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: mammary gland

text: Bos taurus

text: female

text: Holstein

text: snap-frozen tissue, TDE1=0.5 ul

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: E-MTAB-11825:ATAC32_HOL7_f_MammaryGland_snap_tn10_lib1

text: ArrayExpress

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: mammary gland

text: Bos taurus

text: female

text: Holstein

text: snap-frozen tissue, TDE1=1.0 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:ATAC32_HOL8_f_MammaryGland_snap_tn05_lib1

text: ArrayExpress

text: cattle

text: adult

text: normal

text: wild type genotype

text: not applicable

text: Bos taurus

text: Bos taurus

text: mammary gland

characteristic: organism part

characteristic: sampling site

text: Bos taurus

text: female

characteristic: sex

text: Holstein

characteristic: strain

text: snap-frozen tissue, TDE1=0.5 ul

characteristic: tissue with known storage state


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: E-MTAB-11825:ATAC32_HOL8_f_MammaryGland_snap_tn10_lib1

characteristic: Submitter Id

characteristic: age

text: ArrayExpress

characteristic: broker name

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: mammary gland

text: Bos taurus

text: female

text: Holstein

text: snap-frozen tissue, TDE1=1.0 ul

characteristic: title


characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-11825:ATAC27_HOL1_m_MedullaOblongata_slow_tn10_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: medulla oblongata

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: public

characteristic: SRA accession

text: E-MTAB-11825:ATAC24_HOL1_m_Mesencephalon_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: mesencephalon

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: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-11825:ATAC28_HOL1_m_MuscleBiceps_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: biceps femoris

text: Bos taurus

text: male

text: Holstein

text: slowly-frozen tissue, TDE1=0.8 ul

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: E-MTAB-11825:ATAC26_HOL1_m_MuscleDP_slow_tn10_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: muscle of pelvic diaphragm

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

characteristic: SRA accession

text: E-MTAB-11825:ATAC19_HOL1_m_MuscleLD_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: longissimus muscle

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: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: E-MTAB-11825:ATAC19_HOL1_m_MuscleLD_fresh_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: longissimus muscle

text: Bos taurus

text: male

text: Holstein

text: fresh tissue, TDE1=1.0 ul

characteristic: title


characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-11825:ATAC25_HOL1_m_MusclePsoas_slow_tn10_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: psoas major muscle

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: public

characteristic: SRA accession

text: E-MTAB-11825:ATAC27_HOL1_m_MuscleSM_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: semimembranosus muscle

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: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-11825:ATAC27_HOL1_m_MuscleSS_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: supraspinatus muscle

text: Bos taurus

text: male

text: Holstein

text: slowly-frozen tissue, TDE1=1.0 ul

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:ATAC36_HOL2_m_NerveSciatic_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: sciatic nerve

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:ATAC36_HOL2_m_NerveSciatic_snap_tn20_lib1

text: ArrayExpress

text: cattle

text: infant

text: normal

text: wild type genotype

text: not applicable

text: Bos taurus

text: Bos taurus

text: sciatic nerve

characteristic: organism part

characteristic: sampling site

text: Bos taurus

text: male

characteristic: sex

text: Holstein

characteristic: strain

text: snap-frozen tissue, TDE1=2.0 ul

characteristic: tissue with known storage state


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: E-MTAB-11825:ATAC37_HOL1_m_NerveSciatic_snap_tn15_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: sciatic nerve

text: Bos taurus

text: male

text: Holstein

text: snap-frozen tissue, TDE1=1.5 ul

characteristic: title


characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-11825:ATAC37_HOL1_m_NerveSciatic_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: sciatic nerve

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_OlfactoryBulb_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: olfactory bulb

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: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-11825:ATAC36_HOL1_m_Omasum_snap_tn15_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: omasum

text: Bos taurus

text: male

text: Holstein

text: snap-frozen tissue, TDE1=1.5 ul

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: E-MTAB-11825:ATAC36_HOL1_m_Omasum_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: omasum

text: Bos taurus

text: male

text: Holstein

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:ATAC35_BOV1_f_Ovary_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: ovary

characteristic: organism part

characteristic: sampling site

text: Bos taurus

text: female

characteristic: sex

characteristic: strain

text: snap-frozen tissue, TDE1=1.5 ul

characteristic: tissue with known storage state


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: E-MTAB-11825:ATAC35_BOV1_f_Ovary_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: ovary

text: Bos taurus

text: female

text: snap-frozen tissue, TDE1=2.0 ul

characteristic: title


characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-11825:ATAC19_HOL1_m_Pancreas_fresh_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: pancreas

text: Bos taurus

text: male

text: Holstein

text: fresh tissue, TDE1=0.5 ul


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

characteristic: SRA accession

text: E-MTAB-11825:ATAC19_HOL1_m_Pancreas_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: pancreas

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: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-11825:ATAC17_BBB1_f_PBMCcorce_fresh_tn15_lib1

characteristic: Submitter Id

unit: year

characteristic: age

text: ArrayExpress

characteristic: broker name

text: mononuclear cell

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: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: E-MTAB-11825:ATAC17_BBB1_f_PBMCcorce_fresh_tn20_lib1

text: ArrayExpress

text: mononuclear cell

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:ATAC18_BBB1_f_PBMCcorce_slow_tn15_lib1

text: ArrayExpress

text: mononuclear cell

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: slowly-frozen tissue, TDE1=1.5 ul

characteristic: tissue with known storage state


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: E-MTAB-11825:ATAC18_BBB1_f_PBMCcorce_slow_tn20_lib1

characteristic: Submitter Id

characteristic: age

text: ArrayExpress

characteristic: broker name

text: mononuclear cell

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: title