characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC last update

text: public

characteristic: SRA accession

text: ArrayExpress

text: fibroblast of dermis

text: human

text: normal

text: wild type genotype

text: xugn

text: Homo sapiens

text: Homo sapiens

text: dermis

characteristic: organism part

text: Homo sapiens

text: male

characteristic: sex


status: PUBLIC

tag: attribute

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: INSDC status

tag: Namespace:EMBL - EBI & Wellcome Trust Sanger Institute

characteristic: Submitter Id

unit: year

characteristic: age

text: ArrayExpress

characteristic: broker name

text: fibroblast of dermis

characteristic: cell type

text: human

characteristic: common name

text: Protocols: Cells were washed with PBS and then lysed in RLT plus buffer (Qiagen) Cells were stimulated with 0.5ug/mL of High-Molecular Weight poly I:C (Invivogen, Cat. Code: tlrl-pic), transfected with 1uL/mL Lipofectamin 2,000, for 0,2 or 6 hours before collection. Total RNA was extracted using the RNeasy Plus Mini kit(Qiagen, Cat Number 74136), using QIAcube (Qiagen). Libraries were produced using the Kapa Stranded mRNA-seq Kit (Kapa Biosystems, Kit code: KK8421). The Kapa library construction protocol was modified for automated library preparation by Bravo (Agilent Technologies). cDNA was amplified in 13 PCR cycles, and purified by Ampure XP beads (Beckman Coulter, Cat Number A63882) (1.8x volume) using Zephyr (Perkin Elmer). Prior to sequencing, libraries were quantified using MiSeq (25bp PE). This data was used for pooling libraries in equimolar amounts by Coulter NX (Span-8, Beckman).

characteristic: description

text: normal

characteristic: disease

text: wild type genotype

characteristic: genotype

text: xugn

characteristic: individual

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: dermis

text: Homo sapiens

text: male

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMBL - EBI & Wellcome Trust Sanger Institute

characteristic: INSDC last update

text: public

characteristic: SRA accession

text: ArrayExpress

text: fibroblast of dermis

text: human

text: normal

text: wild type genotype

text: xuja

text: Homo sapiens

text: Homo sapiens

text: dermis

characteristic: organism part

text: Homo sapiens

text: female

characteristic: sex


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: INSDC status

characteristic: Submitter Id

text: ArrayExpress

text: fibroblast of dermis

text: human

text: normal

text: wild type genotype

text: zihe

text: Homo sapiens

text: Homo sapiens

text: dermis

text: Homo sapiens

text: female


text: public

characteristic: age

text: ArrayExpress

characteristic: broker name

text: fibroblast of dermis

characteristic: cell type

text: human

characteristic: common name

characteristic: description

text: normal

characteristic: disease

text: wild type genotype

text: zoxy

text: Homo sapiens

text: Homo sapiens

text: dermis

text: Homo sapiens

text: female


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: 30 to 55

text: ArrayExpress

text: fibroblast of dermis

text: human

text: Protocols: Cells were washed with PBS and then trypsinized. Cells were grown in DMEM, high glucose, GlutaMAX Supplement, pyruvate (Life Technologies / 10569-010) + Fetal Bovine Serum (Lab Tech / FB-1001) + Penicillin - Streptomycin (Life Technologies / 15140122). Cells were stimulated with 0.5ug/mL of High-Molecular Weight poly I:C (Invivogen, Cat. Code: tlrl-pic), transfected with 1uL/mL Lipofectamin 2,000, for 2 or 6 hours before collection. Sorted plates were processed according to the Smart-seq2 protocol(Picelli et al., 2014): Oligo-dT primer (IDT), dNTPs (ThermoFisher, Cat Number 10319879) and ERCC RNA Spike-In Mix (1:25,000,000 final dilution, Ambion, Cat Number 4456740) were added to each well, and Reverse Transcription (using 50U SmartScribe, Clontech Cat Number 639538) and PCR were performed following the original protocol with 25 PCR cycles. cDNA libraries were prepared using Nextera XT DNA Sample Preparation Kit (Illumina, Cat Number FC-131-1096), according to the protocol supplied by Fluidigm (PN 100-5950 B1). Quality Checks on cDNA were done using a Bioanalyser 2100 (Agilent Technologies). Libraries from 96 single cells were quantified using the LightCycler 480 (Roche), pooled and purified using AMPure XP beads (Beckman Coulter) with Hamilton 384 head robot (Hamilton Robotics). Pooled samples were sequenced on an Illumina HiSeq 2500 instrument, using paired-end 125-bp reads.

text: normal

text: wild type genotype

characteristic: genotype

text: mix of wuye, wetu, vass

characteristic: individual

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: dermis

text: Homo sapiens

text: female

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC last update

text: public

characteristic: SRA accession

text: 40 to 44

text: ArrayExpress

text: fibroblast of dermis

text: human

text: Protocols: Cells were sorted with Becton Dickinson INFLUX into wells containing 2uL of Lysis Buffer (1:20 solution of RNase Inhibitor (Clontech, Cat Number 2313A) in 0.2% v/v Triton X-100 (Sigma-Aldrich, Cat Number T9284), spun down and immediately frozen at -80°. Cell were grown in ATCC fibroblast growth medium (Fibroblast Basal Medium (ATCC, ATCC-PCS-201-030) with Fibroblast Growth Kit-Low serum (ATCC, PCS-201-041) Cells were grown in three parallel time courses - each treated with 1ug/mL dsRNA (poly I:C) and LF-2,000. In one time course the poly I:C was replaced by fresh medium after 30mins, in a second time course the poly I:C was replaced after 1 hour; and in the third it was kept in the medium throughout the time course. Cells were then collected after 2,4 and 6 hours. Sorted plates were processed according to the Smart-seq2 protocol(Picelli et al., 2014): Oligo-dT primer (IDT), dNTPs (ThermoFisher, Cat Number 10319879) and ERCC RNA Spike-In Mix (1:25,000,000 final dilution, Ambion, Cat Number 4456740) were added to each well, and Reverse Transcription (using 50U SmartScribe, Clontech Cat Number 639538) and PCR were performed following the original protocol with 25 PCR cycles. cDNA libraries were prepared using Nextera XT DNA Sample Preparation Kit (Illumina, Cat Number FC-131-1096), according to the protocol supplied by Fluidigm (PN 100-5950 B1). Quality Checks on cDNA were done using a Bioanalyser 2100 (Agilent Technologies). Libraries from 96 single cells were quantified using the LightCycler 480 (Roche), pooled and purified using AMPure XP beads (Beckman Coulter) with Hamilton 384 head robot (Hamilton Robotics).

text: normal

text: wild type genotype

text: oapg

text: Homo sapiens

text: Homo sapiens

text: dermis

characteristic: organism part

text: Homo sapiens

text: female

characteristic: sex


characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: INSDC status

tag: Namespace:Philipps-University Marburg, Genomics Core Facility

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

characteristic: cell line

text: embryonic stem cell

text: house mouse

text: Protocols: Approximately 5x10e7 PGK12.1XX cells per 15 cm plate were cross-linked with 2 mM DSG (disuccinimidyl glutarate, Thermo Scientific) in PBS for 45 min at room temperature, washed three times with PBS, and formaldehyde (Polysciences) was added to a final concentration of 1 % for 10 min at room temperature. Formaldehyde was quenched using glycine (0.125 M). Mouse PGK12.1 XX ES cells were cultivated feeder-cell free on gelatin-coated dishes in Dulbecco's Modified Eagle Medium (DMEM, Life Technologies) supplemented with 15% fetal calf serum, 2 mM L-glutamine, 1x non-essential amino acids, 50 μM 2-mercaptoethanol, and 1000U/ml ESGRO leukemia inhibitory factor. Generation of FLAG-SMARCAD1 expressing PGK12.1 XX ES cells: The coding sequence of SMARCAD1 was amplified from mouse ES cell cDNA and inserted into a chicken beta actin promoter (CAG)-driven expression vector, with an N-terminal triple FLAG tag. Tagged wild-type Smarcad1 construct along with the empty FLAG vector control were transfected into PGK12.1 ES cells using Lipofectamine 2000 (Life Technologies), followed by 1.7 µg/ml puromycin selection and clonal expansion. Chromatin was eluted in 1% SDS, 100mM NaHCO3 and DNA purified by Qiaquick PCR cleanup columns (Qiagen). Library preparation was performed using the MicroPlex Library Preparation Kit v2 (Diagenode) according to manufacturer’s instructions. Briefly: 7ng DNA was used for each sample. Adapter-ligated DNA was subject to 9 cycles of PCR amplification before size selection and DNA purification by AMPure XP beads (Agencourt).

text: normal

text: wild type genotype

text: Mus musculus

text: Mus musculus

text: inner cell mass

text: Mus musculus

text: PGK x 129P2/Ola/Hsd

characteristic: strain


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Philipps-University Marburg, Genomics Core Facility

text: public

text: ArrayExpress

text: embryonic stem cell

characteristic: cell type

text: house mouse

characteristic: common name

characteristic: description

text: normal

characteristic: disease

characteristic: genotype

text: Mus musculus

text: Mus musculus

text: inner cell mass

text: Mus musculus

text: PGK x 129P2/Ola/Hsd


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: EMBL-EBI and Wellcome Sanger Institute

characteristic: INSDC last update

text: public

characteristic: SRA accession

tag: Namespace:EMBL-EBI and Wellcome Sanger Institute

characteristic: age

text: ArrayExpress

text: fibroblast of dermis

text: human

text: Protocols: Cells were grown in DMEM, high glucose, GlutaMAX Supplement, pyruvate (Life Technologies / 10569-010) + Fetal Bovine Serum (Lab Tech / FB-1001) + Penicillin - Streptomycin (Life Technologies / 15140122). Cells were stimulated with 1000 IU IFNB (human IFNB - R&D Systems / 11410-2) for 2 or 6 hours Reverse transcription and cDNA amplification was performed according to the SmartSeq2 protocol (Picelli et al., 2014) Library preparation was performed using an Illumina Nextera kit.

text: normal

text: wild type genotype

text: joxm

characteristic: individual

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: dermis

text: Homo sapiens

text: female

text: interferon beta

characteristic: stimulus

characteristic: title


text: EMBL-EBI and Wellcome Sanger Institute

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: INSDC status

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: fibroblast of dermis

text: human

text: normal

text: wild type genotype

text: pelm

text: Homo sapiens

text: Homo sapiens

text: dermis

characteristic: organism part

text: Homo sapiens

text: female

characteristic: sex

text: interferon beta


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMBL-EBI and Wellcome Sanger Institute

text: public

text: ArrayExpress

text: fibroblast of dermis

characteristic: cell type

text: human

characteristic: common name

characteristic: description

text: normal

characteristic: disease

text: wild type genotype

characteristic: genotype

text: vass

text: Homo sapiens

text: Homo sapiens

text: dermis

text: Homo sapiens

text: female

text: interferon beta


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: EMBL-EBI and Wellcome Sanger Institute

characteristic: INSDC last update

text: public

characteristic: SRA accession

characteristic: age

text: ArrayExpress

text: fibroblast of dermis

text: human

text: normal

text: wild type genotype

text: wetu

characteristic: individual

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: dermis

text: Homo sapiens

text: female

text: interferon beta


text: EMBL-EBI and Wellcome Sanger Institute

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: INSDC status

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: fibroblast of dermis

text: human

text: normal

text: wild type genotype

text: wuye

text: Homo sapiens

text: Homo sapiens

text: dermis

text: Homo sapiens

text: female

text: interferon beta

characteristic: stimulus

characteristic: title


SPEDE

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UNIVERSITY OF COPENHAGEN

text: public

text: SPEDE

tag: Namespace:UNIVERSITY OF COPENHAGEN

characteristic: collection date

text: Denmark

characteristic: geographic location (country and/or sea)

text: Gallus domesticus

characteristic: host scientific name

text: E. coli

characteristic: isolate

text: laboratory

characteristic: isolation source

text: Escherichia coli

text: Escherichia coli

text: SPEDE


sPEBC

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: UNIVERSITY OF COPENHAGEN

characteristic: INSDC last update

text: public

characteristic: SRA accession

text: sPEBC

text: Denmark

text: Gallus domesticus

text: E. coli

text: laboratory

text: Escherichia coli

text: Escherichia coli

text: sPEBC


potE

text: UNIVERSITY OF COPENHAGEN

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: potE

text: Denmark

text: Gallus domesticus

text: E. coli

text: laboratory

text: Escherichia coli

characteristic: organism

text: Escherichia coli

text: potE


text: MMRI

text: public

characteristic: INSDC status

characteristic: Submitter Id

text: human

characteristic: common name

text: Whole-genome bisulfite sequencing (WGBS) applied to NeuN+ neuronal nuclei isolated from patient CTRL-36 hippocampus

characteristic: description

text: Homo sapiens

text: Homo sapiens


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: NATIONAL VETERINARY INSTITUTE (SVA)

text: public

tag: Namespace:NATIONAL VETERINARY INSTITUTE (SVA)

text: The isolates were collected between 1988 and 2016 and originated from rainbow trout (Oncorhynchus mykiss, n=36), arctic charr (Salvelinus alpinus, n=2), brown trout (Salmo trutta, n=1) and fish farm water samples (n=2). Of the fish isolates, 33 were from kidneys, one each was from skin, fin, gill and abscess samples while the remaining were from unspecified tissues.

text: Finland

text: fish farm water

text: Flavobacterium psychrophilum

text: Flavobacterium psychrophilum

text: Salmonid fish tissue

characteristic: title


text: NATIONAL VETERINARY INSTITUTE (SVA)

text: public

characteristic: collection date

text: Finland

characteristic: geographic location (country and/or sea)

text: diseased

characteristic: host health state

text: Oncorhynchus mykiss

characteristic: host scientific name

text: kidney

text: Flavobacterium psychrophilum

text: Flavobacterium psychrophilum

text: Salmonid fish tissue


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: NATIONAL VETERINARY INSTITUTE (SVA)

text: public

text: Sweden

text: diseased

text: Oncorhynchus mykiss

text: kidney

characteristic: isolation source

text: Flavobacterium psychrophilum

text: Flavobacterium psychrophilum

text: Salmonid fish tissue


text: NATIONAL VETERINARY INSTITUTE (SVA)

characteristic: INSDC center name

characteristic: INSDC last update

text: public

characteristic: SRA accession

text: Sweden

text: diseased

text: Oncorhynchus mykiss

text: Flavobacterium psychrophilum

text: Flavobacterium psychrophilum

text: Salmonid fish tissue


text: NATIONAL VETERINARY INSTITUTE (SVA)

characteristic: INSDC first public

text: public

characteristic: INSDC status

text: Sweden

text: diseased

text: Oncorhynchus mykiss

text: skin

text: Flavobacterium psychrophilum

characteristic: organism

text: Flavobacterium psychrophilum

text: Salmonid fish tissue


text: NATIONAL VETERINARY INSTITUTE (SVA)

text: public

characteristic: Submitter Id

characteristic: description

text: Sweden

text: diseased

text: Salmo trutta

text: fin

text: Flavobacterium psychrophilum

text: Flavobacterium psychrophilum

text: Salmonid fish tissue


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: NATIONAL VETERINARY INSTITUTE (SVA)

text: public

text: Sweden

text: diseased

text: Oncorhynchus mykiss

text: abscess

text: Flavobacterium psychrophilum

text: Flavobacterium psychrophilum

text: Salmonid fish tissue


text: NATIONAL VETERINARY INSTITUTE (SVA)

text: public

characteristic: collection date

text: Sweden

text: diseased

text: Salvelinus alpinus

text: kidney

text: Flavobacterium psychrophilum

text: Flavobacterium psychrophilum

text: Salmonid fish tissue

characteristic: title


text: NATIONAL VETERINARY INSTITUTE (SVA)

text: public

text: Sweden

characteristic: geographic location (country and/or sea)

text: diseased

characteristic: host health state

text: Salvelinus alpinus

text: gill

text: Flavobacterium psychrophilum

text: Flavobacterium psychrophilum

text: Salmonid fish tissue


characteristic: ENA-CHECKLIST

text: University Hospital Munster

text: public

tag: Namespace:University Hospital Munster

text: Germany

text: restricted access

text: human

characteristic: host scientific name

characteristic: isolate

text: human

text: Staphylococcus aureus

text: Staphylococcus aureus

text: Early LA-MRSA CC398 isolate


characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC center name

text: public

tag: Namespace:University of Chinese Academy of Sciences

text: change of breN2002

text: wheat

characteristic: environment (biome)

text: agriculture

characteristic: environment (feature)

text: soil

characteristic: environment (material)

text: China

unit: m

characteristic: geographic location (depth)

characteristic: geographic location (elevation)

unit: DD

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome

characteristic: investigation type

text: soil metagenome

text: rhizosphere

characteristic: project name

text: soil metagenome

text: Illumina

characteristic: sequencing method

text: soil

characteristic: soil environmental package


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: University of Chinese Academy of Sciences

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

text: change of breN2003

characteristic: description

text: wheat

text: agriculture

text: soil

text: China

characteristic: geographic location (country and/or sea)

text: metagenome

text: soil metagenome

characteristic: organism

text: rhizosphere

text: soil metagenome

text: Illumina

text: soil

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC center name

text: public

text: change of breN4001

text: wheat

characteristic: environment (biome)

text: agriculture

characteristic: environment (feature)

text: soil

characteristic: environment (material)

text: China

characteristic: geographic location (depth)

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome

text: soil metagenome

text: rhizosphere

text: soil metagenome

text: Illumina

text: soil


characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: change of breN4002

text: wheat

text: agriculture

text: soil

text: China

text: metagenome

characteristic: investigation type

text: soil metagenome

text: rhizosphere

characteristic: project name

text: soil metagenome

text: Illumina

characteristic: sequencing method

text: soil

characteristic: soil environmental package


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC center name

text: public

characteristic: Submitter Id

characteristic: collection date

text: change of breN4003

characteristic: description

text: wheat

characteristic: environment (biome)

text: agriculture

text: soil

text: China

characteristic: geographic location (country and/or sea)

text: metagenome

text: soil metagenome

characteristic: organism

text: rhizosphere

text: soil metagenome

text: Illumina

text: soil

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: change of breN6001

text: wheat

text: agriculture

characteristic: environment (feature)

text: soil

characteristic: environment (material)

text: China

characteristic: geographic location (depth)

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome

text: soil metagenome

text: rhizosphere

text: soil metagenome

text: Illumina

text: soil


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC center name

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: change of breN6002

text: wheat

text: agriculture

text: soil

text: China

text: metagenome

characteristic: investigation type

text: soil metagenome

text: rhizosphere

characteristic: project name

text: soil metagenome

text: Illumina

characteristic: sequencing method

text: soil

characteristic: soil environmental package


characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: collection date

text: change of breN6003

characteristic: description

text: wheat

characteristic: environment (biome)

text: agriculture

text: soil

text: China

characteristic: geographic location (country and/or sea)

text: metagenome

text: soil metagenome

characteristic: organism

text: rhizosphere

text: soil metagenome

text: Illumina

text: soil

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC center name

text: public

characteristic: INSDC status

text: change of fseN03

text: wheat

text: agriculture

characteristic: environment (feature)

text: soil

characteristic: environment (material)

text: China

characteristic: geographic location (depth)

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome

text: soil metagenome

text: rhizosphere

text: soil metagenome

text: Illumina

text: soil


characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: change of fseN6002

text: wheat

text: agriculture

text: soil

text: China

text: metagenome

characteristic: investigation type

text: soil metagenome

text: rhizosphere

characteristic: project name

text: soil metagenome

text: Illumina

characteristic: sequencing method

text: soil

characteristic: soil environmental package


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC center name

text: public

characteristic: INSDC status

characteristic: collection date

text: change of tfsN02

characteristic: description

text: wheat

characteristic: environment (biome)

text: agriculture

text: soil

text: China

characteristic: geographic location (country and/or sea)

text: metagenome

text: soil metagenome

characteristic: organism

text: rhizosphere

text: soil metagenome

text: Illumina

text: soil

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: change of fstN03

text: wheat

text: agriculture

characteristic: environment (feature)

text: soil

characteristic: environment (material)

text: China

characteristic: geographic location (depth)

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome

text: soil metagenome

text: rhizosphere

text: soil metagenome

text: Illumina

text: soil


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC center name

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: change of fstN4001

text: wheat

text: agriculture

text: soil

text: China

text: metagenome

characteristic: investigation type

text: soil metagenome

text: rhizosphere

characteristic: project name

text: soil metagenome

text: Illumina

characteristic: sequencing method

text: soil

characteristic: soil environmental package


characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: collection date

text: change fstN6001

characteristic: description

text: wheat

characteristic: environment (biome)

text: agriculture

text: soil

text: China

characteristic: geographic location (country and/or sea)

text: metagenome

text: soil metagenome

characteristic: organism

text: rhizosphere

text: soil metagenome

text: Illumina

text: soil

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC center name

text: public

characteristic: INSDC status

tag: Namespace:HELMHOLTZ CENTRE FOR ENVIRONMENTAL RESEARCH - UFZ

text: biogas reactor

text: full-scale agricultural biogas plant; mesophillic

characteristic: environment (feature)

text: digestate from biogas reactor

characteristic: environment (material)

text: Germany

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: mimarks-survey

text: miscellaneous natural or artificial environment

characteristic: miscellaneous environmental package

text: uncultured bacterium

text: Biogas production from glycolate

text: uncultured bacterium

text: amplicon sequencing (Illumina)

text: Glycolate-biogas-production


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: HELMHOLTZ CENTRE FOR ENVIRONMENTAL RESEARCH - UFZ

characteristic: INSDC first public

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: biogas reactor

text: digestate from biogas reactor

text: Germany

text: mimarks-survey

characteristic: investigation type

text: uncultured bacterium

text: Biogas production from glycolate

characteristic: project name

text: uncultured bacterium

text: amplicon sequencing (Illumina)

characteristic: sequencing method

text: Glycolate-biogas-production


characteristic: ENA-CHECKLIST

characteristic: INSDC last update

text: public

characteristic: collection date

text: biogas reactor

characteristic: environment (biome)

text: digestate from biogas reactor

text: Germany

characteristic: geographic location (country and/or sea)

text: mimarks-survey

text: uncultured archaeon

characteristic: organism

text: Biogas production from glycolate

text: uncultured archaeon

text: amplicon sequencing (Illumina)

text: Glycolate-biogas-production

characteristic: title


text: Enterococcus faecium

characteristic: ArrayExpress-SPECIES

characteristic: ENA-FIRST-PUBLIC

text: SC

characteristic: INSDC center name

text: public

characteristic: INSDC status

text: Enterococcus faecium

characteristic: common name

text: Enterococcus faecium

text: Enterococcus faecium

characteristic: subject id


text: Staphylococcus aureus

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

characteristic: INSDC first public

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: Staphylococcus aureus

text: Staphylococcus aureus

text: Staphylococcus aureus


CLIP 2015/00305

characteristic: ENA-CHECKLIST

text: INSTITUT PASTEUR

characteristic: INSDC last update

text: public

text: CLIP 2015/00305

tag: Namespace:INSTITUT PASTEUR

text: Listeria sp. CLIP 2015/00305

text: Listeria sp. CLIP 2015/00305

text: Listeria thailandensis CLIP 2015/00305


text: HEINRICH HEINE UNIVERSITY DUESSELDORF

text: public

tag: Namespace:HEINRICH HEINE UNIVERSITY DUESSELDORF

characteristic: collection date

text: protists associated with Q. suber and Q. ilex

characteristic: description

text: terrestrial biome

characteristic: environment (biome)

text: organic feature

characteristic: environment (feature)

text: root matter

characteristic: environment (material)

text: Spain

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

characteristic: host taxid

text: metagenome

characteristic: investigation type

text: uncultured Oomycetes

text: plant-associated

characteristic: plant-associated environmental package

text: Cork and holm oak associated oomycete communities

characteristic: project name

text: uncultured Oomycetes

text: Illumina

characteristic: sequencing method

characteristic: target gene

text: Protist microbiome Quercus


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: INSDC status

characteristic: SRA accession

tag: Namespace:LEIBNIZ INSTITUTE FOR AGE RESEARCH - FRITZ LIPMANN

text: yellowtail clownfish

characteristic: common name

text: These samples were used to create a transcript catalog of Amphiprion clarkii.

text: Amphiprion clarkii

characteristic: organism

text: Amphiprion clarkii

text: brain

characteristic: tissue type

text: Amphiprion clarkii individual 1 transcriptome assembly samples

characteristic: title


characteristic: ENA-CHECKLIST

text: LEIBNIZ INSTITUTE FOR AGE RESEARCH - FRITZ LIPMANN

characteristic: INSDC last update

text: public

characteristic: Submitter Id

text: yellowtail clownfish

characteristic: description

text: Amphiprion clarkii

text: Amphiprion clarkii

text: brain

text: Amphiprion clarkii individual 2 transcriptome assembly samples


text: public

text: yellowtail clownfish

text: Amphiprion clarkii

text: Amphiprion clarkii

text: brain

text: Amphiprion clarkii individual 3 transcriptome assembly samples


text: public

text: orange clownfish

text: These samples were used to create a transcript catalog of Amphiprion percula.

text: Amphiprion percula

text: Amphiprion percula

text: brain

text: Amphiprion percula individual 1 transcriptome assembly samples


text: public

text: orange clownfish

text: Amphiprion percula

text: Amphiprion percula

text: brain

text: Amphiprion percula individual 2 transcriptome assembly samples


text: public

text: orange clownfish

text: Amphiprion percula

text: Amphiprion percula

text: brain

text: Amphiprion percula individual 3 transcriptome assembly samples


text: public

text: blue green damselfish

text: These samples were used to create a transcript catalog of Chromis viridis.

text: Chromis viridis

text: Chromis viridis

text: brain

text: Chromis viridis individual 1 transcriptome assembly samples


text: public

text: blue green damselfish

text: Chromis viridis

text: Chromis viridis

text: brain

text: Chromis viridis individual 2 transcriptome assembly samples


text: public

text: blue green damselfish

text: Chromis viridis

text: Chromis viridis

text: brain

text: Chromis viridis individual 3 transcriptome assembly samples


text: Hospital Universitari de Bellvitge

text: public

tag: Namespace:Hospital Universitari de Bellvitge

characteristic: collection date

text: Spain

characteristic: geographic location (country and/or sea)

text: diseased

characteristic: host health state

text: Homo sapiens

characteristic: host scientific name

characteristic: isolate

text: Blood

characteristic: isolation source

characteristic: lat lon

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Hospital Universitari de Bellvitge

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: INSDC status

text: Spain

text: diseased

text: Homo sapiens

text: bronchoalveolar lavage

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae


text: European Otter

characteristic: ArrayExpress-SPECIES

characteristic: ENA-CHECKLIST

text: SC

text: public

characteristic: SRA accession

text: Eurasian river otter

characteristic: common name

text: Lutra lutra

characteristic: organism

text: Lutra lutra

characteristic: subject id

characteristic: title


E-MTAB-6985:Sample 37 ChIP

text: UNIVERSITYOFABERDEEN

characteristic: INSDC last update

text: public

text: E-MTAB-6985:Sample 37 ChIP

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: baker's yeast

text: Protocols: All strains were grown on YPD plates at 30 degrees Celsius prior to inoculation for ChIP-Seq experiment. OD600 0.25 cells were arrested in S-phase by addition of alpha factor. After 2 hours, cells were released into S-phase by adding Pronase at 23 degrees Celsius into YPD medium containing 0.2M Hydroxyurea and incubated for 60 minutes. Formaldehyde was then added to a final concentration of 1%. Cells were then incubated at room temperature for 20 minutes and then in cold room overnight. Cells were then washed with ice cold 1X PBS thrice. Cell pellet was frozen at -80 degrees Celsius until further processing. Cells were disrupted using Multi-beads shocker (MB400U, Yasui Kikai) Anti-HA monoclonal antibody HA.11 (16B12) was used for Immunoprecipitation. DNA from Input and ChIP fractions were sheared to an average size of 150 bp using a Covaris Ultra. DNA was then subjected to end repair and ligation of primers before eight rounds of amplification and the samples were sequenced using ABI Solid version 4.0 system according to manufacturer instructions.

characteristic: description

text: elg1 - Mata arg4::natMX4 his31 leu20 lys20 ura30 RTT106-6HA::hphNT1 elg1::KanMX4

characteristic: genotype

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: hydroxyurea block

characteristic: stimulus

characteristic: strain

text: Sample 37 ChIP


E-MTAB-6985:Sample 38 ChIP

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UNIVERSITYOFABERDEEN

characteristic: INSDC center name

text: public

text: E-MTAB-6985:Sample 38 ChIP

text: ArrayExpress

text: baker's yeast

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: hydroxyurea block

text: Sample 38 ChIP


E-MTAB-6985:Sample 35 ChIP

characteristic: ENA-CHECKLIST

text: UNIVERSITYOFABERDEEN

characteristic: INSDC first public

text: public

characteristic: INSDC status

text: E-MTAB-6985:Sample 35 ChIP

text: ArrayExpress

text: baker's yeast

text: wild type genotype - Mata arg4::natMX4 his31 leu20 lys20 ura30 RTT106-6HA::hphNT1

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: hydroxyurea block

text: Sample 35 ChIP


E-MTAB-6985:Sample 36 ChIP

text: UNIVERSITYOFABERDEEN

text: public

characteristic: SRA accession

text: E-MTAB-6985:Sample 36 ChIP

text: ArrayExpress

text: baker's yeast

characteristic: common name

text: Saccharomyces cerevisiae

characteristic: organism

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: hydroxyurea block

text: Sample 36 ChIP


E-MTAB-6985:Sample 25 MNase

text: UNIVERSITYOFABERDEEN

characteristic: INSDC last update

text: public

text: E-MTAB-6985:Sample 25 MNase

text: ArrayExpress

text: baker's yeast

text: Protocols: All strains were plated on YPAD overnight, day cultures were incubated at 30 Celsius in YPAD plus ampicillin, 3.2x10^5 cells were incubated in YPAD plus ampicillin overnight at 30 Celsius, 300ml cells OD 0.2 in YPAD plus ampicillin were grown to OD 0.6 (generally ~3 hours). OD660 0.66 cells were arrested with 50ng/ml final α-factor for 2.5 hours at 30 Celsius and then checked for adequate schmooing under brightfield. G1 control samples were fixed with 1% formaldehyde followed by glycine quench as per below. Cells were filter washed with 800 ml YPAD+ampicillin (30 Celsius) in vacuum trap and Whatman 1.2um 100mm diameter membrane filters cat.10400821, and brought up in 350ml YPAD+ampicillin+50uM EdU (final). 50ml aliquots were harvested at defined time course and formaldehyde-fixed 10’ room temperature shaking followed by addition of 2.25ml 2.5M Glycine for 5’ shaking, and then placed on ice. Cells were washed 3X with cold TBS (20mM Tris pH8.0, 150mM NaCl) and frozen at -80 Celsius. Frozen cell pellets were brought up in ice cold Spheroplast Digestion Buffer (1M Sorbitol, 50mM NaCl, 10mM Tris-HCl pH 7.5, 5mM MgCl2, 1mM CaCl2, and 0.075% v/v Nonidet p40 alternative supplemented with 1mM 2-mercaptoethanol, and 0.5mM of each of the following: Spermidine, Pepstatin, Aprotinin, benzamidine, E64, and ABSF) and lysed in a Mini-Bead Beater 8 ® at 4 degrees Celsius. MNase was titrated to give 80% mononucleosomal DNA bands, typically 30 units for 15m at 37 degrees Celsius. Samples were incubated overnight at 65 degrees Celsius with proteinase K and the supernatant was treated with RNase A for 1h at 37 degrees Celsius, followed by phenol-chloroform extraction and isopropanol precipitation. Excized mononucleosome bands from agarose size-selection gel were purified using Freeze-n-Squeeze columns followed by phenol-chloroform extraction and cold ethanol precipitation. A Click-iT ® NascentRNACapture Kit (Invitrogen, C10365) was used to biotinylate EdU-labelled nascent DNA, which was pulled down with Streptavidin MyOneTM Dynabeads ® (Invitrogen, 65601) as per Invitrogen protocols. DNA was blunt-ended, an A-overhang was added, and Illumina adapters were ligated on, with Agencourt Ampure XP bead washes after each step. PCR amplification was performed with 18 or fewer cycles using Illumina barcoded primers and primer PE 1.0, followed by a final Ampure bead purification.

text: cac1 - Mat-a ura3::GPD-TK(Thymidine Kinase)::URA3 (5 copies) aur1::Padh1-hENT1::AUR1C ade2-1 trp1-1 leu2-3,112 his3-11,15 bar1::TRP1 cac1::LEU2

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: -factor block

text: Sample 25 MNase

characteristic: title


E-MTAB-6985:Sample 13 MNase

text: UNIVERSITYOFABERDEEN

text: public

text: E-MTAB-6985:Sample 13 MNase

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: baker's yeast

text: elg1 - Mat-a ura3::GPD-TK(Thymidine Kinase)::URA3(5 copies) aur1::Padh1-hENT1::AUR1C ade2-1 trp1-1 leu2-3,112 his3-11,15 bar1::TRP1 elg1::KanMX4

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: -factor block

text: Sample 13 MNase


E-MTAB-6985:Sample 19 MNase

text: UNIVERSITYOFABERDEEN

text: public

text: E-MTAB-6985:Sample 19 MNase

text: ArrayExpress

text: baker's yeast

characteristic: description

characteristic: genotype

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: -factor block

text: Sample 19 MNase


E-MTAB-6985:Sample 33 ChIP

text: UNIVERSITYOFABERDEEN

text: public

text: E-MTAB-6985:Sample 33 ChIP

text: ArrayExpress

text: baker's yeast

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: -factor block

characteristic: stimulus

characteristic: strain

text: Sample 33 ChIP


E-MTAB-6985:Sample 34 ChIP

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: UNIVERSITYOFABERDEEN

text: public

text: E-MTAB-6985:Sample 34 ChIP

text: ArrayExpress

text: baker's yeast

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: -factor block

text: Sample 34 ChIP


E-MTAB-6985:Sample 1 MNase

characteristic: External Id

text: UNIVERSITYOFABERDEEN

characteristic: INSDC center name

text: public

text: E-MTAB-6985:Sample 1 MNase

text: ArrayExpress

text: baker's yeast

text: wild type genotype - Mat-a ura3::GPD-TK(Thymidine Kinase)::URA3 (5 copies) aur1::Padh1-hENT1::AUR1C ade2-1 trp1-1 leu2-3,112 his3-11,15 bar1::TRP1

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: -factor block

text: Sample 1 MNase


E-MTAB-6985:Sample 7 MNase

characteristic: ENA-CHECKLIST

text: UNIVERSITYOFABERDEEN

characteristic: INSDC first public

text: public

text: E-MTAB-6985:Sample 7 MNase

text: ArrayExpress

text: baker's yeast

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: -factor block

text: Sample 7 MNase


E-MTAB-6985:Sample 31 ChIP

text: UNIVERSITYOFABERDEEN

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-6985:Sample 31 ChIP

text: ArrayExpress

text: baker's yeast

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: -factor block

text: Sample 31 ChIP


E-MTAB-6985:Sample 32 ChIP

text: UNIVERSITYOFABERDEEN

text: public

text: E-MTAB-6985:Sample 32 ChIP

text: ArrayExpress

text: baker's yeast

characteristic: common name

text: Saccharomyces cerevisiae

characteristic: organism

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: -factor block

text: Sample 32 ChIP


E-MTAB-6985:Sample 26 MNase

text: UNIVERSITYOFABERDEEN

characteristic: INSDC last update

text: public

text: E-MTAB-6985:Sample 26 MNase

text: ArrayExpress

text: baker's yeast

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: -factor block

text: Sample 26 MNase

characteristic: title


E-MTAB-6985:Sample 27 MNase

text: UNIVERSITYOFABERDEEN

text: public

text: E-MTAB-6985:Sample 27 MNase

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: baker's yeast

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: -factor block

text: Sample 27 MNase


E-MTAB-6985:Sample 28 MNase

text: UNIVERSITYOFABERDEEN

text: public

text: E-MTAB-6985:Sample 28 MNase

text: ArrayExpress

text: baker's yeast

characteristic: description

characteristic: genotype

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: -factor block

text: Sample 28 MNase


E-MTAB-6985:Sample 29 MNase

text: UNIVERSITYOFABERDEEN

text: public

text: E-MTAB-6985:Sample 29 MNase

text: ArrayExpress

text: baker's yeast

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: -factor block

characteristic: stimulus

characteristic: strain

text: Sample 29 MNase


E-MTAB-6985:Sample 30 MNase

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: UNIVERSITYOFABERDEEN

text: public

text: E-MTAB-6985:Sample 30 MNase

text: ArrayExpress

text: baker's yeast

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: -factor block

text: Sample 30 MNase


E-MTAB-6985:Sample 14 MNase

characteristic: External Id

text: UNIVERSITYOFABERDEEN

characteristic: INSDC center name

text: public

text: E-MTAB-6985:Sample 14 MNase

text: ArrayExpress

text: baker's yeast

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: -factor block

text: Sample 14 MNase


E-MTAB-6985:Sample 20 MNase

characteristic: ENA-CHECKLIST

text: UNIVERSITYOFABERDEEN

characteristic: INSDC first public

text: public

text: E-MTAB-6985:Sample 20 MNase

text: ArrayExpress

text: baker's yeast

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: -factor block

text: Sample 20 MNase


E-MTAB-6985:Sample 15 MNase

text: UNIVERSITYOFABERDEEN

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-6985:Sample 15 MNase

text: ArrayExpress

text: baker's yeast

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: -factor block

text: Sample 15 MNase


E-MTAB-6985:Sample 21 MNase

text: UNIVERSITYOFABERDEEN

text: public

text: E-MTAB-6985:Sample 21 MNase

text: ArrayExpress

text: baker's yeast

characteristic: common name

text: Saccharomyces cerevisiae

characteristic: organism

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: -factor block

text: Sample 21 MNase


E-MTAB-6985:Sample 16 MNase

text: UNIVERSITYOFABERDEEN

characteristic: INSDC last update

text: public

text: E-MTAB-6985:Sample 16 MNase

text: ArrayExpress

text: baker's yeast

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: -factor block

text: Sample 16 MNase

characteristic: title


E-MTAB-6985:Sample 22 MNase

text: UNIVERSITYOFABERDEEN

text: public

text: E-MTAB-6985:Sample 22 MNase

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: baker's yeast

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: -factor block

text: Sample 22 MNase


E-MTAB-6985:Sample 17 MNase

text: UNIVERSITYOFABERDEEN

text: public

text: E-MTAB-6985:Sample 17 MNase

text: ArrayExpress

text: baker's yeast

characteristic: description

characteristic: genotype

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: -factor block

text: Sample 17 MNase


E-MTAB-6985:Sample 23 MNase

text: UNIVERSITYOFABERDEEN

text: public

text: E-MTAB-6985:Sample 23 MNase

text: ArrayExpress

text: baker's yeast

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: -factor block

characteristic: stimulus

characteristic: strain

text: Sample 23 MNase


E-MTAB-6985:Sample 18 MNase

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: UNIVERSITYOFABERDEEN

text: public

text: E-MTAB-6985:Sample 18 MNase

text: ArrayExpress

text: baker's yeast

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: -factor block

text: Sample 18 MNase


E-MTAB-6985:Sample 24 MNase

characteristic: External Id

text: UNIVERSITYOFABERDEEN

characteristic: INSDC center name

text: public

text: E-MTAB-6985:Sample 24 MNase

text: ArrayExpress

text: baker's yeast

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: -factor block

text: Sample 24 MNase


E-MTAB-6985:Sample 2 MNase

characteristic: ENA-CHECKLIST

text: UNIVERSITYOFABERDEEN

characteristic: INSDC first public

text: public

text: E-MTAB-6985:Sample 2 MNase

text: ArrayExpress

text: baker's yeast

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: -factor block

text: Sample 2 MNase


E-MTAB-6985:Sample 8 MNase

text: UNIVERSITYOFABERDEEN

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-6985:Sample 8 MNase

text: ArrayExpress

text: baker's yeast

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: -factor block

text: Sample 8 MNase


E-MTAB-6985:Sample 3 MNase

text: UNIVERSITYOFABERDEEN

text: public

text: E-MTAB-6985:Sample 3 MNase

text: ArrayExpress

text: baker's yeast

characteristic: common name

text: Saccharomyces cerevisiae

characteristic: organism

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: -factor block

text: Sample 3 MNase


E-MTAB-6985:Sample 9 MNase

text: UNIVERSITYOFABERDEEN

characteristic: INSDC last update

text: public

text: E-MTAB-6985:Sample 9 MNase

text: ArrayExpress

text: baker's yeast

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: -factor block

text: Sample 9 MNase

characteristic: title


E-MTAB-6985:Sample 10 MNase

text: UNIVERSITYOFABERDEEN

text: public

text: E-MTAB-6985:Sample 10 MNase

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: baker's yeast

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: -factor block

text: Sample 10 MNase


E-MTAB-6985:Sample 4 MNase

text: UNIVERSITYOFABERDEEN

text: public

text: E-MTAB-6985:Sample 4 MNase

text: ArrayExpress

text: baker's yeast

characteristic: description

characteristic: genotype

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: -factor block

text: Sample 4 MNase


E-MTAB-6985:Sample 11 MNase

text: UNIVERSITYOFABERDEEN

text: public

text: E-MTAB-6985:Sample 11 MNase

text: ArrayExpress

text: baker's yeast

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: -factor block

characteristic: stimulus

characteristic: strain

text: Sample 11 MNase


E-MTAB-6985:Sample 5 MNase

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: UNIVERSITYOFABERDEEN

text: public

text: E-MTAB-6985:Sample 5 MNase

text: ArrayExpress

text: baker's yeast

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: -factor block

text: Sample 5 MNase


E-MTAB-6985:Sample 12 MNase

characteristic: External Id

text: UNIVERSITYOFABERDEEN

characteristic: INSDC center name

text: public

text: E-MTAB-6985:Sample 12 MNase

text: ArrayExpress

text: baker's yeast

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: -factor block

text: Sample 12 MNase


E-MTAB-6985:Sample 6 MNase

characteristic: ENA-CHECKLIST

text: UNIVERSITYOFABERDEEN

characteristic: INSDC first public

text: public

text: E-MTAB-6985:Sample 6 MNase

text: ArrayExpress

text: baker's yeast

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: -factor block

text: Sample 6 MNase


E-MTAB-6945:Sample 1

text: UNIVERSITY OF CAMBRIDGE

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-6945:Sample 1

tag: Namespace:UNIVERSITY OF CAMBRIDGE

unit: day

characteristic: age

text: ArrayExpress

text: CD8-Positive T-Lymphocytes

characteristic: cell type

text: house mouse

text: Protocols: Thymuses were dissected from postnatal day (PND)6 neonates and homogenised in PBS before passing through a 40 µm filter. Cells were counted and diluted to 200,000 cells / mL in PBS/0.1% BSA for processing according to Drop-Seq protocol (Macosko et al, 2015) Exon U2 was deleted from the Igf2 locus to prevent expression of the placenta-specific Igf2 transcript, P0. This gene is paternally expressed, so by crossing wild type females with heterozygous males, both wild type and affected neonates grow within the same environment. Single cells were encapsulated in droplets with primer barcoded beads. After RNA binding to the oligo-dT portion of the primer, the droplets were broken to pool beads for reverse transcription. Exonuclease treatment removed unused primers from the beads prior to PCR amplification at up to 8,000 beads / tube (~400 cells/tube). Samples were pooled up to 4,000 cells / sample and purified before determining concentration. DNA was fragmented and tagged with Illumina adapter and index sequencers using Nextera Sequencing kit and 600 pg DNA/sample. Samples were diluted 1:1 in ddH20 water before double-sided purification with Agencourt Ampure beads using 0.6x beads to remove large fragments and 1x beads twice to remove contaminating primers.

text: neonate

characteristic: developmental stage

text: normal

characteristic: disease

text: wild type genotype

characteristic: individual

text: Mus musculus

text: Mus musculus

text: thymus

characteristic: organism part

text: Mus musculus

text: male

characteristic: sex

text: Sample 1


E-MTAB-6945:Sample 2

text: UNIVERSITY OF CAMBRIDGE

characteristic: INSDC last update

text: public

text: E-MTAB-6945:Sample 2

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: CD8-Positive T-Lymphocytes

text: house mouse

characteristic: common name

characteristic: description

text: neonate

text: normal

text: wild type genotype

characteristic: genotype

text: Mus musculus

characteristic: organism

text: Mus musculus

text: thymus

text: Mus musculus

text: male

text: Sample 2

characteristic: title


E-MTAB-6945:Sample 3

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UNIVERSITY OF CAMBRIDGE

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: INSDC status

text: E-MTAB-6945:Sample 3

text: ArrayExpress

text: CD8-Positive T-Lymphocytes

text: house mouse

text: neonate

text: normal

text: wild type genotype

text: Mus musculus

text: Mus musculus

text: thymus

text: Mus musculus

text: male

characteristic: strain

text: Sample 3


E-MTAB-6945:Sample 4

text: UNIVERSITY OF CAMBRIDGE

text: public

characteristic: SRA accession

text: E-MTAB-6945:Sample 4

characteristic: age

text: ArrayExpress

text: CD8-Positive T-Lymphocytes

characteristic: cell type

text: house mouse

text: neonate

characteristic: developmental stage

text: normal

characteristic: disease

text: wild type genotype

characteristic: individual

text: Mus musculus

text: Mus musculus

text: thymus

characteristic: organism part

text: Mus musculus

text: male

characteristic: sex

text: Sample 4


E-MTAB-6945:Sample 5

text: UNIVERSITY OF CAMBRIDGE

characteristic: INSDC last update

text: public

text: E-MTAB-6945:Sample 5

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: CD8-Positive T-Lymphocytes

text: house mouse

characteristic: common name

characteristic: description

text: neonate

text: normal

text: igf2-p0 heterozygous knockout

characteristic: genotype

text: Mus musculus

characteristic: organism

text: Mus musculus

text: thymus

text: Mus musculus

text: male

text: Sample 5

characteristic: title


E-MTAB-6945:Sample 6

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UNIVERSITY OF CAMBRIDGE

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: INSDC status

text: E-MTAB-6945:Sample 6

text: ArrayExpress

text: CD8-Positive T-Lymphocytes

text: house mouse

text: neonate

text: normal

text: igf2-p0 heterozygous knockout

text: Mus musculus

text: Mus musculus

text: thymus

text: Mus musculus

text: female

characteristic: strain

text: Sample 6


E-MTAB-6945:Sample 7

text: UNIVERSITY OF CAMBRIDGE

text: public

characteristic: SRA accession

text: E-MTAB-6945:Sample 7

characteristic: age

text: ArrayExpress

text: CD8-Positive T-Lymphocytes

characteristic: cell type

text: house mouse

text: neonate

characteristic: developmental stage

text: normal

characteristic: disease

text: igf2-p0 heterozygous knockout

characteristic: individual

text: Mus musculus

text: Mus musculus

text: thymus

characteristic: organism part

text: Mus musculus

text: male

characteristic: sex

text: Sample 7


E-MTAB-7031:12 weeks sample 4

text: University of Leeds

characteristic: INSDC last update

text: public

text: E-MTAB-7031:12 weeks sample 4

tag: Namespace:University of Leeds

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: human

characteristic: common name

text: Protocols: Human fetal hearts were collected after elective terminations of pregnancy, with informed written parental consent obtained from all subjects. All experimental protocols were approved by local ethical committees (Study Code LREC 08/S1101/1). 3 developmental stages were successfully collected: 9, 12 and 16 weeks of gestation. Individual pregnancies carried on independently to this study. They were terminated after parental decision. All fetuses used for this study were healthy, as assessed by the clinicians. Fetuses and their tissues were not treated prior to the experiments. Whole hearts were homogenised by pestle and mortar in liquid nitrogen. 100 mg of the resulting powder was used to extract RNA. The extraction method was followed as outlined in the BioRad Aurum Total RNA Fatty and Fibrous Tissue Kit (cat no. 732-6830). Briefly, the sample was disrupted in PureZol, after which chloroform was added and the lysate centrifuged. RNA was extracted in the aqueous phase and an equal amount of ethanol was added. The mixture was transferred to a RNA binding column and centrifuged. Low stringency wash solution, DNase I, high stringency wash buffer followed by low stringency wash solution was used to purify the RNA, which was then eluted and stored at -80C until use. All RNA extraction were performed at the same time to eliminate the variable of interest, i.e. gestational age. Illumina compatible barcoded mRNA sequencing libraries were made from 100 ng of total RNA after polyA selection for mature mRNAs using the TruSeq Stranded mRNA Sample Preparation Kit’s high sample protocol (Illumina). Before pooling the libraries were visualised using a Tapestation (Agilent) to determine insert size, while their concentration was calculated using the Picogreen dsDNA quantification assay (Thermofisher Scientific).

characteristic: description

text: gestational week 12

text: normal

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: heart

text: Homo sapiens

text: male

text: 12 weeks sample 4

characteristic: title


E-MTAB-7031:12 weeks sample 5

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: University of Leeds

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: INSDC status

text: E-MTAB-7031:12 weeks sample 5

text: ArrayExpress

text: human

text: gestational week 12

text: normal

text: Homo sapiens

text: Homo sapiens

text: heart

text: Homo sapiens

text: female

text: 12 weeks sample 5


E-MTAB-7031:12 weeks sample 6

text: University of Leeds

text: public

characteristic: SRA accession

text: E-MTAB-7031:12 weeks sample 6

text: ArrayExpress

text: human

text: gestational week 12

characteristic: developmental stage

text: normal

characteristic: disease

text: Homo sapiens

text: Homo sapiens

text: heart

text: Homo sapiens

text: male

text: 12 weeks sample 6


E-MTAB-7031:16 weeks sample 7

text: University of Leeds

characteristic: INSDC last update

text: public

text: E-MTAB-7031:16 weeks sample 7

text: ArrayExpress

text: human

text: gestational week 16

text: normal

text: Homo sapiens

text: Homo sapiens

text: heart

characteristic: organism part

text: Homo sapiens

text: male

characteristic: sex

text: 16 weeks sample 7


E-MTAB-7031:16 weeks sample 8

text: University of Leeds

text: public

text: E-MTAB-7031:16 weeks sample 8

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: human

characteristic: common name

text: gestational week 16

text: normal

text: Homo sapiens

text: Homo sapiens

text: heart

text: Homo sapiens

text: male

text: 16 weeks sample 8


E-MTAB-7031:16 weeks sample 9

text: University of Leeds

text: public

text: E-MTAB-7031:16 weeks sample 9

text: ArrayExpress

text: human

characteristic: description

text: gestational week 16

text: normal

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: heart

text: Homo sapiens

text: female

text: 16 weeks sample 9

characteristic: title


E-MTAB-7031:9 weeks sample 1

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: University of Leeds

text: public

text: E-MTAB-7031:9 weeks sample 1

text: ArrayExpress

text: human

text: gestational week 9

text: normal

text: Homo sapiens

text: Homo sapiens

text: heart

text: Homo sapiens

text: female

text: 9 weeks sample 1


E-MTAB-7031:9 weeks sample 2

characteristic: External Id

text: University of Leeds

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-7031:9 weeks sample 2

text: ArrayExpress

text: human

text: gestational week 9

text: normal

text: Homo sapiens

text: Homo sapiens

text: heart

text: Homo sapiens

text: male

text: 9 weeks sample 2


E-MTAB-7031:9 weeks sample 3

text: University of Leeds

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-7031:9 weeks sample 3

text: ArrayExpress

text: human

text: gestational week 9

characteristic: developmental stage

text: normal

text: Homo sapiens

text: Homo sapiens

text: heart

text: Homo sapiens

text: female

text: 9 weeks sample 3


characteristic: INSDC last update

text: public

tag: Namespace:University of Michigan Medical School: Department of Internal Medicine, Division of Gastroenterology

text: ArrayExpress

characteristic: cell line

text: intestinal epithelial cell

characteristic: cell type

text: human

text: Protocols: Human derived epithelial organoids (HdEs) or transplanted human derived epithelial organoids (tHdEs)were collected as pools from individual wells of a 24-well plate and seperated manually from the culture matrix prior to RNA extraction. Generation of HdEs and tHdEs from HIOs and tHIOs was performed using previously described methods to isolate the epithelium (Finkbeiner et al., 2015b; Hill et al., 2017; Tsai et al., 2018). In summary, HIOs and tHIOs were incubated in dispase (07923; STEMCELL Technologies) for 30 minutes on ice. Following incubation, dispase was removed and replaced with 100% fetal bovine serum for 15 minutes on ice. To mechanically separate the epithelium from mesenchyme, a volume of advanced Dulbecco's modified Eagle medium/F12 (12634010; Gibco) equal to the initial volume of fetal bovine serum was added to the tissue before vigorously pipetting the mixture several times. Epithelial fragments then settled to the bottom where they were collected manually on a stereoscope by pipet. The epithelium was washed with ice-cold advanced Dulbecco's modified Eagle medium/F12 and allowed to settle to the bottom of a 1.5-mL Eppendorf tube. The media was then withdrawn from the loose tissue pellet and replaced with Matrigel on ice. The Matrigel containing the isolated epithelium was gently mixed to evenly suspend the cells before being pipetted into individual 50-μL droplets in a 24-well plate. The plate containing the droplets was incubated at 37°C for 15 minutes to allow the Matrigel to solidify before adding LWRN growth media containing Thiazovivin (2.5 μmol/L), SB431542 (100 nmol/L), CHIR99021 (4 μmol/L), and Y27632 (10 μmol/L). After 24 hours, the media was replaced with LWRN growth media containing TZV (2.5 μmol/L), SB431542 (100 nmol/L), and CHIR99021 (4 μmol/L). After 3 days, cultures were maintained with LWRN growth media replaced every other day. Prior to transplantation, human intestinal organoids (HIOs) were mechanically dissociated from either alginate or Matrigel. HIOs were implanted under the kidney capsules of immunocompromised NOD-scid IL2Rg-null (NSG) mice (Jackson Laboratory strain no. 0005557) as previously described (Finkbeiner et al., 2015b). In summary, mice were anaesthetized using 2% isoflurane. A left-flank incision was used to expose the kidney after shaving and sterilization with isopropyl alcohol. HIOs cultured in alginate and Matrigel were surgically implanted beneath mouse kidney capsules using forceps. Mice were euthanized for retrieval of transplanted HIOs (tHIOs) after 10 weeks. RNA from each sample was isolated using MagMAX-96 Total RNA (AM1830; Applied Biosystems) RNA isolation kits and used as input for library generation with Takara SMARTer Stranded Total RNA Sample Prep Kit (634876; Takara Bio USA).

text: embryo

text: wild type genotype

characteristic: genotype

text: organoid culture in alginate gel

characteristic: growth condition

text: Homo sapiens

text: Homo sapiens

text: embryonic stem cell

characteristic: progenitor cell type

text: Homo sapiens


text: University of Michigan Medical School: Department of Internal Medicine, Division of Gastroenterology

text: public

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: intestinal epithelial cell

text: human

characteristic: common name

characteristic: description

text: embryo

text: wild type genotype

text: organoid culture in alginate gel

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: embryonic stem cell

text: Homo sapiens


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: ArrayExpress

text: intestinal epithelial cell

text: human

text: embryo

text: wild type genotype

text: organoid culture in matrigel

text: Homo sapiens

text: Homo sapiens

text: embryonic stem cell

text: Homo sapiens

characteristic: title


characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-7000:tHdE-CYST-Alginate-d5-tHIO-A-1

text: ArrayExpress

text: intestinal epithelial cell

text: human

text: embryo

characteristic: developmental stage

text: wild type genotype

text: organoid culture in alginate gel

text: Homo sapiens

text: Homo sapiens

text: embryonic stem cell

text: Homo sapiens

text: xenografted under NOD-scid/IL2Rg-null mouse kidney capsule for 10 weeks

characteristic: xenograft


characteristic: INSDC last update

text: public

text: E-MTAB-7000:tHdE-CYST-Alginate-d5-tHIO-B-1

text: ArrayExpress

characteristic: cell line

text: intestinal epithelial cell

characteristic: cell type

text: human

text: embryo

text: wild type genotype

characteristic: genotype

text: organoid culture in alginate gel

characteristic: growth condition

text: Homo sapiens

text: Homo sapiens

text: embryonic stem cell

characteristic: progenitor cell type

text: Homo sapiens


characteristic: ENA-CHECKLIST

text: public

text: E-MTAB-7000:tHdE-CYST-Alginate-d5-tHIO-C-1

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: intestinal epithelial cell

text: human

characteristic: common name

characteristic: description

text: embryo

text: wild type genotype

text: organoid culture in alginate gel

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: embryonic stem cell

text: Homo sapiens


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-7000:tHdE-CYST-Alginate-d5-tHIO-D-1

text: ArrayExpress

text: intestinal epithelial cell

text: human

text: embryo

text: wild type genotype

text: organoid culture in alginate gel

text: Homo sapiens

text: Homo sapiens

text: embryonic stem cell

text: Homo sapiens

characteristic: title


characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-7000:tHdE-CYST-Alginate-d5-tHIO-E-1

text: ArrayExpress

characteristic: cell line

text: intestinal epithelial cell

text: human

text: embryo

characteristic: developmental stage

text: wild type genotype

text: organoid culture in alginate gel

text: Homo sapiens

text: Homo sapiens

text: embryonic stem cell

text: Homo sapiens

characteristic: xenograft


characteristic: ENA-CHECKLIST

text: public

text: E-MTAB-7000:tHdE-CYST-Matrigel-d5-tHIO-A-1

characteristic: Submitter Id

text: ArrayExpress

text: intestinal epithelial cell

characteristic: cell type

text: human

text: embryo

text: wild type genotype

characteristic: genotype

text: organoid culture in matrigel

characteristic: growth condition

text: Homo sapiens

text: Homo sapiens

text: embryonic stem cell

characteristic: progenitor cell type

text: Homo sapiens


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: public

text: E-MTAB-7000:tHdE-CYST-Matrigel-d5-tHIO-B-1

text: ArrayExpress

characteristic: broker name

text: intestinal epithelial cell

text: human

characteristic: common name

characteristic: description

text: embryo

text: wild type genotype

text: organoid culture in matrigel

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: embryonic stem cell

text: Homo sapiens


characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-7000:tHdE-CYST-Matrigel-d5-tHIO-D-1

text: ArrayExpress

text: intestinal epithelial cell

text: human

text: embryo

text: wild type genotype

text: organoid culture in matrigel

text: Homo sapiens

text: Homo sapiens

text: embryonic stem cell

text: Homo sapiens

characteristic: title


characteristic: ENA-CHECKLIST

text: public

characteristic: SRA accession

text: E-MTAB-7000:tHdE-CYST-Matrigel-d5-tHIO-E-2

characteristic: Submitter Id

text: ArrayExpress

characteristic: cell line

text: intestinal epithelial cell

text: human

text: embryo

characteristic: developmental stage

text: wild type genotype

text: organoid culture in matrigel

text: Homo sapiens

text: Homo sapiens

text: embryonic stem cell

text: Homo sapiens

characteristic: xenograft


text: Enterococcus faecium

characteristic: ArrayExpress-SPECIES

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: SC

text: public

text: Enterococcus faecium

text: Enterococcus faecium

text: Enterococcus faecium

characteristic: subject id


text: Staphylococcus aureus

text: SC

text: public

text: Staphylococcus aureus

characteristic: common name

text: Staphylococcus aureus

characteristic: organism

text: Staphylococcus aureus


characteristic: External Id

characteristic: INSDC center name

text: public

tag: Namespace:National Center for Microbiology - Institute of Health Carlos III

characteristic: collection date

text: Spain

characteristic: geographic location (country and/or sea)

text: diseased

characteristic: host health state

text: Homo sapiens

characteristic: host scientific name

characteristic: isolate

text: human faeces

characteristic: isolation source

text: Escherichia coli

text: Escherichia coli

characteristic: serovar

characteristic: strain

text: CNM-2741/17 whole genome sequencing


tag: attribute

characteristic: ENA-CHECKLIST

text: National Center for Microbiology - Institute of Health Carlos III

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: Spain

text: diseased

text: Homo sapiens

text: human faeces

text: Escherichia coli

text: Escherichia coli

text: CNM-2368/11 whole genome sequencing

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: Italy

text: diseased

text: Homo sapiens

text: human faeces

text: Escherichia coli

characteristic: organism

text: Escherichia coli

text: ED703 whole genome sequencing


T5 pA

text: UNIVERSITY OF GOTHENBURG

characteristic: INSDC center name

text: public

text: T5 pA

tag: Namespace:UNIVERSITY OF GOTHENBURG

text: A circular, single-stranded DNA molecule of ∼4,300 nucleotides.

characteristic: description

text: synthetic construct

text: synthetic construct

text: pBluescript SK(+) vector DNA, phagemid excised from lambda ZAP


T5 pWT

text: UNIVERSITY OF GOTHENBURG

text: public

text: T5 pWT

text: A circular, single-stranded DNA molecule of ∼4,300 nucleotides inclusing two ∼600 bp regions of the huamn mtDNA H-strand designated as 8470-CR and 13447-CR in reference to the location in the human mitochondria genome.

text: synthetic construct

text: synthetic construct

text: pBluescript SK(+) vector DNA, phagemid excised from lambda ZAP with human mitochondria fragment


T5 A467T/T521I+P587L

text: UNIVERSITY OF GOTHENBURG

text: public

text: T5 A467T/T521I+P587L

text: synthetic construct

text: synthetic construct


T1 pA

text: UNIVERSITY OF GOTHENBURG

text: public

text: T1 pA

text: synthetic construct

text: synthetic construct


T1 pWT

text: UNIVERSITY OF GOTHENBURG

text: public

text: T1 pWT

text: synthetic construct

text: synthetic construct


T1 A467T/T521I+P587L

text: UNIVERSITY OF GOTHENBURG

text: public

text: T1 A467T/T521I+P587L

text: synthetic construct

text: synthetic construct


name: E-MTAB-58751531847201:B-cells from a DLBCL patient

text: Postdoctoral Fellow

text: public

tag: Namespace:Postdoctoral Fellow

text: ArrayExpress

characteristic: broker name

text: primary cell

characteristic: cell line

text: B-lymphoblast

characteristic: cell type

text: human

characteristic: common name

text: Protocols: 1.We followed the general protocol for in situ Hi-C as described in (Rao et al., 2014) which we adapted for use on low cell numbers. Mainly, differences were related to adjustments on the volume of the reactions, a shortening of the digestion step, a removal of biotin from the un-ligated fragments, and an alternative strategy for size-selection during library preparation. mESC OB2 cells were cultured as described in (Osunkoya et al., 1968)), FACS-sorted, selected for positive GFP expression and collected on PBS. Cells were then pelleted (300 g, 40C for 10 min) and resuspended in 1 ml PBS. For the human samples, PBMCs were crosslinked and MACS-sorted to isolate CD20+ B-cells to get the Hi-C libraries. Samples from a healthy donor and cancer patient processing. Patient and Control samples processing. Peripheral blood mononuclear cells (PBMCs) were obtained either from a blood extraction from a healthy donor or from a lymph node biopsy from a DLBCL patient. The patient sample came from the Department of Clinical Pathology at the Robert-Bosch-Hospital in Stuttgart (Germany) and its informed consent for retrospective analysis was approved by the ethics committee of the Medical Faculty, Eberhard-Karls-University and University Hospital Tübingen (reference no. 159/2011BO2). PBMCs from the control came from a donor from the Department of Medicine A, Hematology, Oncology and Pneumology, University Hospital Muenster in Muenster (Germany). Control PBMCs were isolated from the in-between layer by density gradient centrifugation with Biocoll (Biochrom AG, Germany) and were then frozen at -80°C for preservation. The patient sample came from a biopsy of a lymph node. Briefly, the biopsy was immediately cut into pieces, homogenized and re-suspended generating a cell suspension that was then frozen and kept at -80°C, as previously described at Staiger et al., 2017. Once the samples were thawed, cells were cross-linked in a 1% formaldehyde and quenched with 2.5M Glycine solution and proceed with the Low-C protocol as described for the rest of the samples. B-cells were then isolated by MACS-sorting (Yan et al., 2009) using a positive selection kit (Miltenyi Biotec, 130-091-104). Briefly, CD20+ cells were labelled using magnetic coated CD20 MicroBeads, the cell suspension was loaded onto a MACS LS column (Miltenyi Biotec, 130-041-306) and placed on a magnetic field generated by a MACS Separator. The CD20+ cells were retained into the column while the flow through (unlabelled cells) was eliminated. Then the column was removed from the MACS Separator, the magnetically retained CD20+ cells were then eluted and collected into a 15 ml Falcon tube. 2. mESC OB2 cells were cultured as described in (Osunkoya et al., 1968)), FACS-sorted, selected for positive GFP expression and collected on PBS. Cells were then pelleted (300 g, 40C for 10 min) and resuspended in 1 ml PBS. 3.Cross-linking. Cells were then cross-linked in a 1% final concentration (v/v) of 37% Formaldehyde (VWR International GmbH) and vigorously shaken prior to 10 min room temperature incubation with gentle rotation (20 rpm). The reaction was quenched for 5 min at room temperature with gentle rotation (20 rpm) by adding 2.5M Glycine solution (Applichem) to a final concentration of 0.2M. Cells were pelleted twice (300 g, 4°C for 5 min) and resuspended on 1 ml of cold 1X PBS. After these washes, cells were finally resuspended in 50 ml, quantified on a Neubauer’s chamber and aliquoted at different cell concentrations (5x106, 106, 105, 5x104, 2.5x104, 104 and 103 cells). 5. DNA shearing. DNA was precipitated by adding 630 μL (5M to 100k samples) or 315 μL (50k to 1k samples) of the Phenol-Chloroform-Isoamyl alcohol mix (25:24:1; Sigma-Aldrich). Samples were spun (5 min at 17000 g, 4°C). The supernatant was then mixed to 63 μL (5M to 100k samples) or 31.5 μL (50k to 1k samples) of 3M sodium acetate pH5.2, 2 μL GlycoBlue (Life Technologies) and 1008 μL (5M to 100k samples) or 504 μL (50k to 1k samples) pure ethanol, followed by 15 min incubation at -80°C. Samples were then spun at 17000 g, 4°C for at least 30 min. The supernatant was then discarded and the pellet was washed twice with ice-cold 70% ethanol (800 μL for 5M to 100k samples or 400 μL for 50k to 1k samples). All ethanol traces were removed, the pellet was then air-dried for no longer than 5 min and dissolved in 30 μL (5M to 100k samples) or 15 μL (50k to 1k samples) of Tris pH 8.0 (Applichem) and incubated for 5 min at 37°C without rotation. RNA was digested by adding 1 μL RNAse (Applichem) to each sample and the mix was incubated for 15 min at 37°C. Biotin from unligated fragments was removed by adding 10 μL (5M to 100k samples) or 5 μL (50k to 1k samples) of 10X NEB2 buffer (New England Biolabs), 1mM of a dNTPs mix (2.5 μL for the 5M to 100k samples or 1.25 μL for the 50k to 1k samples), 20mg/ml BSA (0.5 μL for 5M to 100k samples or 0.25 μL for 50k to 1k samples), nuclease-free water (up to 100 μL or 50 μL, respectively) and 3U/μL T4 DNA polymerase (5 μL or 3 μL, respectively; New England Biolabs). Samples were mixed by gentle pipetting up and down and incubated at 20°C for 4h with no rotation. Samples were brought to a 120 μL volume with nuclease-free water and DNA was then sheared using a Covaris S220 instrument (2 cycles, each 50 sec long; 10% duty; 4 intensity; 200 cycles/burst). 4. Lysis. Cells were pelleted (13,000 g, 4°C for 5 min) and gently resuspended in 500 μL (5M and 1M samples), 250 μL (100k, 50k, 25k and 10k samples), or 125 μL (1k sample) of ice-cold in situ Hi-C lysis buffer (10 mM Tris-Cl pH 8.0, 10 mM NaCl, 0.2% IGEPAL CA-630 (Sigma-Aldrich), cOmplete Ultra protease inhibitors (Roche)). Following 15 min incubation on ice, cells were spun down (1000 g, 4°C for 5 min) and the pellet was resuspended in 250 μL (5M and 1M samples), 125 μL (100k, 50K, 25k and 10k samples) or 62.5 μL (1k sample) of ice-cold in situ Hi-C lysis buffer. Lysed cells were then flash-frozen in liquid Nitrogen and stored at -80°C. Restriction enzyme digestion. Frozen aliquots for different cell concentrations were placed on ice to thaw, spun (13,000 g for 5 min at 4°C) and resuspended in 500 μL (5M and 1M samples), 250 μL (100k sample), 125 μL (50K, 25k and 10k samples), or 62.5 μL (1k sample) lysis buffer. Following yet another spin (13,000 g for 5 min at 4°C), cells were gently resuspended in 500 μL (5M and 1M samples), 250 μL (100k sample), 125 μL (50K, 25k and 10k samples) or 62.5 μL (1k sample) ice-cold 10x NEB2 buffer (New England Biolabs). Then, nuclei were spun once more for 5 min at 13,000 g at 4°C before being permeabilised by resuspending them in 50 μL (5M, 1M and 100k samples), 25 μL (50K, 25k, 10k) or 12.5 μL (1k sample) of 0.4% SDS and incubating for 10 min at 65°C without agitation. The SDS (Applichem) was then quenched by adding 25 μL (5M, 1M and 100k samples) or 12.5 μL (50k, 25k, 10k and 1k samples) of 10% Triton X-100 (Applichem) and 145 μL or 72.5 μL of nuclease-free water, respectively, and incubating at 37°C for 45 min with rotation (650 rpm). Chromatin digestion was performed as follows: i) for HindIII digested samples, by adding 500U of New England Biolabs HindIII-HF (5M and 100k samples) in 25 μL of 10x NEB2 buffer; and ii) for MboI (New England Biolabs) digested samples, by adding 100U (1M and 100k samples), 50U (50k, 25k and 10k samples), or 25U (1k sample) of MboI in 20 μL (5M, 1M and 100k samples), 35 μL (50k, 25k and 10k samples) or 42.5 μL (1k sample) of 10x NEB2.1 buffer (New England Biolabs), respectively. All digestions were performed at 37°C with gentle rotation for a period of 90 min by adding the restriction enzyme in two instalments, the second one after 45 min. After digestion, only MboI samples were heat-inactivated for 20 min at 62°C. Marking of DNA ends. The overhangs generated by the restriction enzyme cuts were filled-in by adding a mix of biotin-14-CTP (0.4 mM stock; 18.75 μL for the 5M to 100k samples or 10 μL for the 50k to 1k samples; Life Technologies), 10mM dATP (whichever was not supplied in biotinylated form), dGTP and dTTP (10 mM stocks; 0.75 μL of each dinucleotide for the 5M to 100k samples or 0.5 μL for the 50k to 1k samples), and 5U/μL DNA polymerase I Klenow (5M to 100k samples or 4 μL for the 50k to 1k samples; New England Biolabs), followed by a 90 min incubation at 37°C with gentle rotation (20 rpm). Proximity ligation. The resulting DNA fragments were then ligated by adding a master mix containing nuclease-free water (657 μL for the 5M to 100k samples or 328.5 μL for the 50k to 1k samples), 10X T4 DNA ligase buffer (120 μL for the 5M to 100k samples or 60 μL for the 50k to 1k samples; Thermo Fisher Scientific), 10% Triton X-100 (100 μL for the 5M to 100k samples or 50 μL for the 50k to 1k samples), 20mg/ml BSA (12 μL for the 5M to 100k samples or 6 μL for the 50k to 1k samples; New England Biolabs) and 5 Weiss U/μL T4 DNA ligase (5 μL for the 5M to 100k samples or 3.5 μL for the 50k to 1k samples in two instalments; Thermo Fisher Scientific). Samples were mixed by inversion and incubated at 20°C with gentle rotation (20 rpm) for 4 h. Crosslink reversal. Nuclei were then spun (2500 g for 5 min at room temperature) and resuspended in 500 μL (5M to 100k samples) or 250 μL (50k to 1k samples) extraction buffer to revert the crosslinking. To digest the proteins 20 μL (5M to 100k samples) or 10 μL (50k to 1k samples) of 20mg/ml proteinase K (Applichem) were added followed by 30 min incubation at 55°C with shaking (1000 rpm). Subsequently, 130 μL (5M to 100k samples) or 65 μL (50k to 1k) of 5M sodium chloride was added to the samples, which were then incubated overnight at 65°C with shaking (1000 rpm).

text: diffuse large B-cell lymphoma

characteristic: disease

text: wild type genotype

characteristic: genotype

text: Homo sapiens

text: Homo sapiens

text: lymph node

characteristic: organism part

characteristic: phenotype

text: Homo sapiens

text: B-cells from a DLBCL patient


name: E-MTAB-58751531847201:B-cells from healthy donor

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text: Postdoctoral Fellow

characteristic: INSDC first public

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text: public

characteristic: INSDC status

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text: ArrayExpress

text: primary cell

text: B-lymphoblast

text: human

text: normal

text: wild type genotype

text: Homo sapiens

text: Homo sapiens

text: blood

text: Homo sapiens

text: B-cells from healthy donor


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UNIVERSITY OF SZEGED

text: public

tag: Namespace:UNIVERSITY OF SZEGED

characteristic: Submitter Id

text: fall armyworm

text: Spodoptera frugiperda

text: Spodoptera frugiperda

characteristic: title


text: UNIVERSITY OF SZEGED

characteristic: INSDC center name

text: public

characteristic: description

text: Autographa californica multiple nucleopolyhedrovirus

characteristic: organism


text: NORTHUMBRIA UNIVERSITY, NEWCASTLE

text: public

unit: g

characteristic: amount or size of sample collected

characteristic: collection date

text: Severely preterm infant

characteristic: environment (biome)

text: Gastrointestinal tract

characteristic: environment (feature)

text: Sequencing negative ctrl

characteristic: environment (material)

text: United Kingdom

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Newcastle upon Tyne, Tyne & Wear

characteristic: geographic location (region and locality)

text: human-associated

characteristic: human associated environmental package

text: mimarks-survey

characteristic: investigation type

text: human gut metagenome

text: 515F and 806R (Caporaso et al., 2011)

characteristic: pcr primers

text: SERVIS research Project

characteristic: project name

text: Northumbria University

characteristic: sample storage location

unit: °C

characteristic: sample storage temperature

characteristic: sample volume or weight for DNA extraction

text: human gut metagenome

text: Illumina Sequencing by synthesis

characteristic: sequencing method

text: 16s rRNA gene

characteristic: target gene

text: V4 region

characteristic: target subfragment

text: Sequencing negative ctrl


BLANKa

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text: Severely preterm infant

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text: 515F and 806R (Caporaso et al., 2011)

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text: Sequencing negative ctrl

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text: United Kingdom

characteristic: geographic location (country and/or sea)

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text: Newcastle upon Tyne, Tyne & Wear

characteristic: geographic location (region and locality)

text: human-associated

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text: Northumbria University

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text: Sequencing negative ctrl


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text: Severely preterm infant

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text: Breast milk

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text: Breast milk

characteristic: host body product

text: human-associated

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text: human gut metagenome

characteristic: organism

text: 515F and 806R (Caporaso et al., 2011)

text: Prophylactic probiotics & antifungals. Intubated with nasogastric feeding tube and endotracheal airway tube

characteristic: perturbation

text: SERVIS research Project

text: Run-off from nasogastric feeding tube

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text: Northumbria University

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characteristic: target subfragment

text: Breast milk sample collected from significantly preterm neonates


characteristic: ENA-CHECKLIST

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text: NORTHUMBRIA UNIVERSITY, NEWCASTLE

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text: Kit negative ctrl (BM)

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text: United Kingdom

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Newcastle upon Tyne, Tyne & Wear

characteristic: geographic location (region and locality)

text: Breast milk

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text: 515F and 806R (Caporaso et al., 2011)

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text: Kit negative ctrl (BM)


text: NORTHUMBRIA UNIVERSITY, NEWCASTLE

text: public

text: Severely preterm infant

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characteristic: environment (feature)

text: Endotracheal catheter secretion

characteristic: environment (material)

text: United Kingdom

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Newcastle upon Tyne, Tyne & Wear

characteristic: geographic location (region and locality)

text: Mucus

characteristic: host body product

text: human-associated

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text: mimarks-survey

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text: human gut metagenome

text: 515F and 806R (Caporaso et al., 2011)

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text: Flushed catheter lumen

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text: 16s rRNA gene

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text: V4 region

text: Endotracheal catheter secretion sample collected from significantly preterm neonates


characteristic: ENA-CHECKLIST

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text: United Kingdom

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text: 515F and 806R (Caporaso et al., 2011)

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text: Northumbria University

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text: Kit negative ctrl (endo)

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characteristic: ENA-CHECKLIST

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text: NORTHUMBRIA UNIVERSITY, NEWCASTLE

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text: Stool

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characteristic: geographic location (country and/or sea)

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text: Newcastle upon Tyne, Tyne & Wear

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text: Stool

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text: human-associated

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text: mimarks-survey

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text: human gut metagenome

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text: Sterile glass pots on ward

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text: Northumbria University

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characteristic: sample storage temperature

characteristic: sample volume or weight for DNA extraction

text: human gut metagenome

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characteristic: sequencing method

text: 16s rRNA gene

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text: V4 region

text: Stool sample collected from significantly preterm neonates


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text: NORTHUMBRIA UNIVERSITY, NEWCASTLE

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text: Severely preterm infant

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text: Gastrointestinal tract

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text: Kit negative ctrl (stool)

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text: United Kingdom

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characteristic: organism

text: 515F and 806R (Caporaso et al., 2011)

text: SERVIS research Project

text: Northumbria University

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text: 16s rRNA gene

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characteristic: target subfragment

text: Kit negative ctrl (stool)

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characteristic: ENA-CHECKLIST

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text: NORTHUMBRIA UNIVERSITY, NEWCASTLE

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text: Kit negative ctrl (oral)

text: United Kingdom

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Newcastle upon Tyne, Tyne & Wear

characteristic: geographic location (region and locality)

text: human-associated

characteristic: human associated environmental package

text: mimarks-survey

characteristic: investigation type

text: human gut metagenome

text: 515F and 806R (Caporaso et al., 2011)

characteristic: pcr primers

text: SERVIS research Project

characteristic: project name

text: Northumbria University

characteristic: sample storage location

characteristic: sample storage temperature

characteristic: sample volume or weight for DNA extraction

text: human gut metagenome

text: Illumina Sequencing by synthesis

characteristic: sequencing method

text: 16s rRNA gene

characteristic: target gene

text: V4 region

text: Kit negative ctrl (oral)


NEG

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: NORTHUMBRIA UNIVERSITY, NEWCASTLE

characteristic: INSDC center name

characteristic: INSDC first public

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text: NEG

characteristic: Submitter Id

characteristic: amount or size of sample collected

characteristic: collection date

text: Severely preterm infant

characteristic: environment (biome)

text: Gastrointestinal tract

characteristic: environment (feature)

text: Sequencing negative ctrl

characteristic: environment (material)

text: United Kingdom

text: Newcastle upon Tyne, Tyne & Wear

text: human-associated

text: mimarks-survey

text: human gut metagenome

characteristic: organism

text: 515F and 806R (Caporaso et al., 2011)

text: SERVIS research Project

text: Northumbria University

text: human gut metagenome

text: Illumina Sequencing by synthesis

text: 16s rRNA gene

text: V4 region

characteristic: target subfragment

text: Sequencing negative ctrl