E-MTAB-5446:Sample 2

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: Barton Group, Division of Computational Biology

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-5446:Sample 2

characteristic: Submitter Id

text: ArrayExpress

text: thale cress

characteristic: description

text: seedling

text: wild type genotype

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: Sample 2


E-MTAB-5446:Sample 3

status: PUBLIC

tag: attribute

characteristic: ENA-CHECKLIST

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-5446:Sample 3

tag: Namespace:Barton Group, Division of Computational Biology

unit: day

characteristic: age

text: ArrayExpress

characteristic: broker name

text: thale cress

characteristic: common name

text: Protocols: Seedlings were harvested after 14 days. WT A. thaliana Col-0 seeds were sown aseptically on MS10 plates, stratified for 2 days at 4 degrees C and then grown at a constant 21 degrees C under a 16-h light/8-h dark cycle for a further 14 days. Total RNA extraction with RNeasy Plant Mini Kit (Qiagen) then treated with TURBOTM DNase (Ambion). 4 μl of ERCC spike-ins at a 1:100 dilution were added to 1 μg/6 μl of total RNA. Illumina TruSeq Stranded Total RNA with Ribo-Zero Plant.

text: seedling

characteristic: developmental stage

characteristic: ecotype

characteristic: ercc spike-in mix

characteristic: experiment

text: wild type genotype

characteristic: genotype

text: Arabidopsis thaliana

characteristic: organism

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: Sample 3

characteristic: title


E-MTAB-5446:Sample 4

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-5446:Sample 4

text: ArrayExpress

text: thale cress

text: seedling

text: wild type genotype

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: Sample 4


E-MTAB-5446:Sample 5

characteristic: ENA-CHECKLIST

characteristic: External Id

characteristic: INSDC center name

text: public

text: E-MTAB-5446:Sample 5

characteristic: Submitter Id

text: ArrayExpress

text: thale cress

characteristic: description

text: seedling

text: wild type genotype

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: Sample 5


E-MTAB-5446:Sample 6

characteristic: INSDC first public

text: public

text: E-MTAB-5446:Sample 6

characteristic: age

text: ArrayExpress

characteristic: broker name

text: thale cress

characteristic: common name

text: seedling

characteristic: developmental stage

text: wild type genotype

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: Sample 6


E-MTAB-5446:Sample 7

text: public

text: E-MTAB-5446:Sample 7

text: ArrayExpress

text: thale cress

text: seedling

characteristic: ecotype

characteristic: ercc spike-in mix

characteristic: experiment

text: wild type genotype

characteristic: genotype

text: Arabidopsis thaliana

characteristic: organism

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: Sample 7


E-MTAB-5446:Sample 10

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-5446:Sample 10

text: ArrayExpress

text: thale cress

text: seedling

text: wild type genotype

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: Sample 10

characteristic: title


E-MTAB-5446:Sample 11

characteristic: ENA-CHECKLIST

characteristic: External Id

characteristic: INSDC center name

text: public

characteristic: SRA accession

text: E-MTAB-5446:Sample 11

characteristic: Submitter Id

text: ArrayExpress

text: thale cress

text: seedling

text: wild type genotype

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: Sample 11


E-MTAB-5446:Sample 12

characteristic: INSDC first public

text: public

text: E-MTAB-5446:Sample 12

characteristic: age

text: ArrayExpress

characteristic: broker name

text: thale cress

characteristic: common name

characteristic: description

text: seedling

text: wild type genotype

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: Sample 12


E-MTAB-5446:Sample 13

text: public

text: E-MTAB-5446:Sample 13

text: ArrayExpress

text: thale cress

text: seedling

characteristic: developmental stage

characteristic: ecotype

characteristic: ercc spike-in mix

characteristic: experiment

text: wild type genotype

characteristic: genotype

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: Sample 13


E-MTAB-5446:Sample 14

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-5446:Sample 14

text: ArrayExpress

text: thale cress

text: seedling

text: wild type genotype

text: Arabidopsis thaliana

characteristic: organism

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: Sample 14


E-MTAB-5446:Sample 8

characteristic: ENA-CHECKLIST

characteristic: External Id

characteristic: INSDC center name

text: public

characteristic: SRA accession

text: E-MTAB-5446:Sample 8

text: ArrayExpress

text: thale cress

text: seedling

text: wild type genotype

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: Sample 8

characteristic: title


E-MTAB-5446:Sample 9

characteristic: INSDC first public

text: public

text: E-MTAB-5446:Sample 9

characteristic: Submitter Id

characteristic: age

text: ArrayExpress

characteristic: broker name

text: thale cress

characteristic: common name

text: seedling

text: wild type genotype

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: Sample 9


E-MTAB-5446:Sample 15

text: public

text: E-MTAB-5446:Sample 15

text: ArrayExpress

text: thale cress

characteristic: description

text: seedling

characteristic: developmental stage

characteristic: ecotype

characteristic: ercc spike-in mix

characteristic: experiment

text: wild type genotype

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: Sample 15


E-MTAB-5446:Sample 16

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-5446:Sample 16

text: ArrayExpress

text: thale cress

text: seedling

text: wild type genotype

characteristic: genotype

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: Sample 16


E-MTAB-5446:Sample 17

characteristic: ENA-CHECKLIST

characteristic: External Id

characteristic: INSDC center name

text: public

characteristic: SRA accession

text: E-MTAB-5446:Sample 17

text: ArrayExpress

text: thale cress

text: seedling

text: wild type genotype

text: Arabidopsis thaliana

characteristic: organism

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: Sample 17


text: University Hospital Galway

characteristic: INSDC first public

text: public

tag: Namespace:University Hospital Galway

characteristic: Submitter Id

characteristic: collection date

text: Ireland

characteristic: geographic location (country and/or sea)

text: Homo sapiens

characteristic: host scientific name

characteristic: isolate

text: Human

characteristic: isolation source

text: Shigella sonnei

text: Shigella sonnei

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: University Hospital Galway

text: public

text: Ireland

text: Homo sapiens

text: Human

text: Shigella flexneri 2a

text: Shigella flexneri 2a


text: University Hospital Galway

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: Ireland

text: Homo sapiens

text: Human

text: Shigella flexneri 1c

text: Shigella flexneri 1c


characteristic: ENA-CHECKLIST

text: UCL

text: public

text: Div of Infection & Immunity, Farr Institute of Health Informatics Research, University College London, 222 Euston Road, London, NW1 2DA, United Kingdom

characteristic: collecting institution

text: PANGEA_HIV Project

characteristic: collector name

text: human

characteristic: common name

text: HIV Sample PANGEA Project

characteristic: description

text: Uganda

text: human

characteristic: host common name

text: Homo sapiens

text: restricted access

characteristic: host sex

characteristic: host subject id

text: Homo sapiens

text: Homo sapiens

text: HIV Sample PANGEA Project


characteristic: External Id

text: URMITE

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: Mycobacterium colombiense was isolated from a lymph node in 2014 in Marseille

text: Mycobacterium colombiense

characteristic: organism

text: Mycobacterium colombiense

characteristic: strain

text: Draft genome sequence of Mycobacterium colombiense


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: University College Dublin

characteristic: INSDC last update

text: public

tag: Namespace:University College Dublin

text: Thoroughbred

characteristic: breed

text: ArrayExpress

characteristic: broker name

characteristic: cohort

text: horse

text: Protocols: Percutaneous needle muscle biopsies (approx. 300mg) were obtained from the ventral compartment of the middle gluteal muscle from standing unsedated horses using a previously described method [53]and preserved in RNAlater (Thermo Fisher, Massachusetts, United States). Total RNA was extracted from approximately 70mg tissue, using a protocol combining TRIzol reagent (Thermo Fisher, Massachusetts, United States), DNase treatment (RNase free DNase) (Qiagen, Hilden, Germany) and RNeasy Mini-Kit (Qiagen). The study cohort comprised a subset of Thoroughbred horses, trained for Flat racing at a single training establishment under the management of a single trainer. The UR cohort comprised of yearling Thoroughbred horses (n = 51; 23 males and 28 females; 19.5±1.5 months old) in submaximal training prior to entering sprint training. The UE cohort consisted of the same group of horses undertaking their first or second ‘work day’ (WD, high-intensity sprint exercise simulating a race) on an all-weather gallop. The TR cohort consisted of horses at the end of the racing season following approximately six months of sprint training. All horses in this group had achieved “race fitness” with an average of 15.1±9.1 SD WDs (range 6-43). Table 1 summarises details of sampling and physiological measurements. Percutaneous needle muscle biopsies (approx. 300mg) were obtained from the ventral compartment of the middle gluteal muscle from standing unsedated horses using a previously described method [53]and preserved in RNAlater (Thermo Fisher, Massachusetts, United States). Total RNA was extracted from approximately 70mg tissue, using a protocol combining TRIzol reagent (Thermo Fisher, Massachusetts, United States), DNase treatment (RNase free DNase) (Qiagen, Hilden, Germany) and RNeasy Mini-Kit (Qiagen). RNA was quantified using a Nano Drop ND1000 spectrophotometer V 3.5.27 and RNA quality and purity were assessed using the 18S/28S ratio and RNA integrity number (RIN) on an Agilent Bioanalyser with the RNA 6000 Nano LabChip kit6 (Agilent, Cork, Ireland). The RNA isolated from UR, UE and TR samples had an average RIN of 8.1 (7.2-9.3), 8.2 (7-9.1) and 8.1 (5.4-8.6), respectively. Indexed, strand-specific Illumina sequencing libraries were prepared using the TruSeq Stranded mRNA Library Preparation Kit LT (Illumina, San Diego, United States).

text: Equus caballus

text: Equus caballus

text: gluteus medius

characteristic: organism part

text: Equus caballus

characteristic: title


characteristic: ENA-CHECKLIST

text: CEBITEC

text: public

characteristic: INSDC status

characteristic: collection date

text: Mito-plasmid of Pichia pastoris JPS664 (follow up on ERS1026218)

characteristic: description

text: fermenter

characteristic: environment (biome)

text: fermenter

characteristic: environment (feature)

text: fermenter

characteristic: environment (material)

text: Germany

characteristic: geographic location (country and/or sea)

unit: m

characteristic: geographic location (depth)

characteristic: geographic location (elevation)

unit: DD

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: mimarks-survey

characteristic: investigation type

text: Komagataella pastoris

text: Mito-plasmid

characteristic: project name

text: Komagataella pastoris

text: Illumina MiSeq

characteristic: sequencing method

text: soil

characteristic: soil environmental package

text: Mito-plasmid of Pichia pastoris JPS664


text: Klebsiellla pneumoniae

characteristic: ArrayExpress-Species

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: Klebsiellla pneumoniae

characteristic: common name

text: Klebsiella pneumoniae

characteristic: organism

text: Klebsiella pneumoniae

characteristic: title


characteristic: ENA-CHECKLIST

text: UCL

text: public

characteristic: INSDC status

characteristic: collecting institution

characteristic: collection date

text: PANGEA_HIV Project

characteristic: collector name

text: human

text: HIV Sample PANGEA Project

characteristic: description

text: South Africa

characteristic: geographic location (country and/or sea)

text: human

characteristic: host common name

text: Homo sapiens

characteristic: host scientific name

text: restricted access

characteristic: host sex

characteristic: host subject id

characteristic: isolate

text: Homo sapiens

text: Homo sapiens

text: HIV Sample PANGEA Project


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UCL

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: SRA accession

text: PANGEA_HIV Project

text: human

text: HIV Sample PANGEA Project

text: Botswana

text: human

text: Homo sapiens

text: restricted access

text: Homo sapiens

text: Homo sapiens

text: HIV Sample PANGEA Project


text: Acinetobacter baumanii

characteristic: ArrayExpress-Species

characteristic: ENA-CHECKLIST

text: SC

text: public

characteristic: INSDC status

characteristic: Submitter Id

text: Acinetobacter baumanii

characteristic: common name

text: Acinetobacter baumannii

characteristic: organism

text: Acinetobacter baumannii

characteristic: title


text: Klebsiella pneumoniae

text: SC

text: public

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae


text: Enterobacter cloacae

text: SC

text: public

text: Enterobacter cloacae

text: Enterobacter cloacae

text: Enterobacter cloacae


text: Pseudomonas fluorescens

text: SC

text: public

text: Pseudomonas fluorescens

text: Pseudomonas fluorescens

text: Pseudomonas fluorescens


text: Pseudomonas aeruginosa

text: SC

text: public

text: Pseudomonas aeruginosa

text: Pseudomonas aeruginosa

text: Pseudomonas aeruginosa


text: Acinetobacter baumannii

text: SC

text: public

text: Acinetobacter baumannii

text: Acinetobacter baumannii

text: Acinetobacter baumannii


text: Enterococcus faecium

text: SC

text: public

text: Enterococcus faecium

text: Enterococcus faecium

text: Enterococcus faecium


Donor 1 bone marrow sample 1

text: LUND UNIVERSITY

text: public

text: Donor 1 bone marrow sample 1

tag: Namespace:LUND UNIVERSITY

text: human

text: Sequences of IGHV-encoding genes (amplified by 5' Biomed2 primers and 3' CH1 primers) as found in cells of paired samples of human bone marrow and peripheral blood

characteristic: description

text: Homo sapiens

text: Homo sapiens

text: IGHV-encoding sequences derived from human bone marrow and peripheral blood


Donor 1 bone marrow sample 2

text: LUND UNIVERSITY

text: public

text: Donor 1 bone marrow sample 2

text: human

text: Homo sapiens

text: Homo sapiens


Donor 2 bone marrow sample 1

text: LUND UNIVERSITY

text: public

text: Donor 2 bone marrow sample 1

text: human

text: Homo sapiens

text: Homo sapiens


Donor 2 bone marrow sample 2

text: LUND UNIVERSITY

text: public

text: Donor 2 bone marrow sample 2

text: human

text: Homo sapiens

text: Homo sapiens


Donor 3 bone marrow sample 1

text: LUND UNIVERSITY

text: public

text: Donor 3 bone marrow sample 1

text: human

text: Homo sapiens

text: Homo sapiens


Donor 3 bone marrow sample 2

text: LUND UNIVERSITY

text: public

text: Donor 3 bone marrow sample 2

text: human

text: Homo sapiens

text: Homo sapiens


Donor 1 peripheral blood sample 1

text: LUND UNIVERSITY

text: public

text: Donor 1 peripheral blood sample 1

text: human

text: Homo sapiens

text: Homo sapiens


Donor 1 peripheral blood sample 2

text: LUND UNIVERSITY

text: public

text: Donor 1 peripheral blood sample 2

text: human

text: Homo sapiens

text: Homo sapiens


Donor 2 peripheral blood sample 1

text: LUND UNIVERSITY

text: public

text: Donor 2 peripheral blood sample 1

text: human

text: Homo sapiens

text: Homo sapiens


Donor 2 peripheral blood sample 2

text: LUND UNIVERSITY

text: public

text: Donor 2 peripheral blood sample 2

text: human

text: Homo sapiens

text: Homo sapiens


Donor 3 peripheral blood sample 1

text: LUND UNIVERSITY

text: public

text: Donor 3 peripheral blood sample 1

text: human

text: Homo sapiens

text: Homo sapiens


Donor 3 peripheral blood sample 2

text: LUND UNIVERSITY

text: public

text: Donor 3 peripheral blood sample 2

text: human

text: Homo sapiens

text: Homo sapiens


Donor 4 bone marrow sample 1

text: LUND UNIVERSITY

text: public

text: Donor 4 bone marrow sample 1

text: human

text: Homo sapiens

text: Homo sapiens


Donor 4 bone marrow sample 2

text: LUND UNIVERSITY

text: public

text: Donor 4 bone marrow sample 2

text: human

text: Homo sapiens

text: Homo sapiens


Donor 5 bone marrow sample 1

text: LUND UNIVERSITY

text: public

text: Donor 5 bone marrow sample 1

text: human

text: Homo sapiens

text: Homo sapiens


Donor 5 bone marrow sample 2

text: LUND UNIVERSITY

text: public

text: Donor 5 bone marrow sample 2

text: human

text: Homo sapiens

text: Homo sapiens


Donor 6 bone marrow sample 1

text: LUND UNIVERSITY

text: public

text: Donor 6 bone marrow sample 1

text: human

text: Homo sapiens

text: Homo sapiens


Donor 6 bone marrow sample 2

text: LUND UNIVERSITY

text: public

text: Donor 6 bone marrow sample 2

text: human

text: Homo sapiens

text: Homo sapiens


Donor 4 peripheral blood sample 1

text: LUND UNIVERSITY

text: public

text: Donor 4 peripheral blood sample 1

text: human

text: Homo sapiens

text: Homo sapiens


Donor 4 peripheral blood sample 2

text: LUND UNIVERSITY

text: public

text: Donor 4 peripheral blood sample 2

text: human

text: Homo sapiens

text: Homo sapiens


Donor 5 peripheral blood sample 1

text: LUND UNIVERSITY

text: public

text: Donor 5 peripheral blood sample 1

text: human

text: Homo sapiens

text: Homo sapiens


Donor 5 peripheral blood sample 2

text: LUND UNIVERSITY

text: public

text: Donor 5 peripheral blood sample 2

text: human

text: Homo sapiens

text: Homo sapiens


Donor 6 peripheral blood sample 1

text: LUND UNIVERSITY

text: public

text: Donor 6 peripheral blood sample 1

text: human

text: Homo sapiens

text: Homo sapiens


Donor 6 peripheral blood sample 2

text: LUND UNIVERSITY

text: public

text: Donor 6 peripheral blood sample 2

text: human

text: Homo sapiens

text: Homo sapiens


text: AUSTRALIAN NATIONAL UNIVERSITY

text: public

text: Lampropholis coggeri

text: Lampropholis coggeri

text: lamcogg all bams


text: UNIMI

text: public

text: Acinetobacter baumannii

text: Acinetobacter baumannii


MGTN

text: UNIMI

text: public

text: MGTN

text: Acinetobacter baumannii

text: Acinetobacter baumannii

text: MGTN


MONUR

text: UNIMI

text: public

text: MONUR

text: Acinetobacter baumannii

text: Acinetobacter baumannii

text: MONUR


text: University Hospital Galway

text: public

characteristic: collection date

text: Ireland

characteristic: geographic location (country and/or sea)

text: Homo sapiens

characteristic: host scientific name

text: Human

characteristic: isolation source

text: Shigella sonnei

text: Shigella sonnei


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: University Hospital Galway

text: public

text: Ireland

text: Homo sapiens

characteristic: isolate

text: Human

text: Shigella flexneri 1c

text: Shigella flexneri 1c


text: University Hospital Galway

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: SRA accession

text: Ireland

text: Homo sapiens

text: Human

text: Shigella flexneri

text: Shigella flexneri


characteristic: ENA-CHECKLIST

text: public

characteristic: INSDC status

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

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: house mouse

text: Protocols: A total of four stages of murine cardiac development (embryonic day 12, embryonic day 18, post-partum day 2, 4 weeks) were utilized in this study. Female mice at day 12 and 18 of pregnancy were sacrificed followed by the excision of the embryos. For embryonic day 12 the whole heart was removed for each embryo. At embryonic day 18, the left ventricle was excised from the embryos. The left ventricle of post-partum day 2 pups were removed following decapitation. 4 week old mice were sacrificed after which the left ventricle was isolated. We also included 20 week old mice which had undergone ischemia/reperfusion injury or sham treatment. Total RNA was isolated by the Trizol RNA isolation protocol. Libraries were generated strictly NEXTflex™ Illumina RNA-Seq Library Prep v2 kit recommendations (Bioo Life Science).

text: embryonic day 12.5

characteristic: developmental stage

text: Mus musculus

text: Mus musculus

text: heart

characteristic: organism part

text: Mus musculus

type: has member


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

text: public

text: ArrayExpress

text: house mouse

characteristic: common name

characteristic: description

text: embryonic day 12.5

text: Mus musculus

characteristic: organism

text: Mus musculus

text: heart

text: Mus musculus

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: public

text: ArrayExpress

text: house mouse

text: embryonic day 18.5

text: Mus musculus

text: Mus musculus

text: left ventricle

text: Mus musculus


characteristic: External Id

text: public

text: ArrayExpress

text: house mouse

text: postnatal week 20

text: Mus musculus

text: Mus musculus

text: left ventricle

text: Mus musculus


characteristic: INSDC center name

text: public

text: ArrayExpress

text: house mouse

text: postnatal day 2

text: Mus musculus

text: Mus musculus

text: left ventricle

text: Mus musculus


characteristic: INSDC first public

text: public

text: ArrayExpress

text: house mouse

text: postnatal week 4

text: Mus musculus

text: Mus musculus

text: left ventricle

text: Mus musculus


E-MTAB-5412:Sample 1

characteristic: INSDC last update

text: public

text: E-MTAB-5412:Sample 1

tag: Namespace:Institute of Experimental Immunology University of Zurich

text: ArrayExpress

text: granulocyte-macrophage colony-stimulating factor induced inflammatory monocyte-derived cell

characteristic: cell type

text: house mouse

text: Protocols: Cell isolation by cell sorting from indicated organs 4 weeks of tamoxifen chow pellets, Harlan Teklad CRD TAM400/CreER RNeasy Plus Micro kit (Qiagen) TruSeq Stranded mRNA Sample Prep Kit (Illumina, Inc, California, USA), libraries were normalized to 10nM in Tris-Cl 10 mM, pH8.5 with 0.1% Tween 20

text: GM-CSFind x CD4-CrERT2

characteristic: genotype

text: Mus musculus

text: Mus musculus

text: central nervous system

text: Mus musculus

characteristic: strain

text: Sample 1

text: Tamoxifen treated

characteristic: treatment


E-MTAB-5412:Sample 10

characteristic: ENA-CHECKLIST

text: Institute of Experimental Immunology University of Zurich

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-5412:Sample 10

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: house mouse

text: GM-CSFind x CD4-CrERT2

text: Mus musculus

text: Mus musculus

text: liver

text: Mus musculus

text: Sample 10

text: Tamoxifen treated


E-MTAB-5412:Sample 11

text: public

text: E-MTAB-5412:Sample 11

text: ArrayExpress

text: house mouse

characteristic: common name

characteristic: description

text: GM-CSFind x CD4-CrERT2

text: Mus musculus

characteristic: organism

text: Mus musculus

text: liver

characteristic: organism part

text: Mus musculus

text: Sample 11

text: Tamoxifen treated


E-MTAB-5412:Sample 12

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: E-MTAB-5412:Sample 12

text: ArrayExpress

text: house mouse

text: GM-CSFind x CD4-CrERT2

text: Mus musculus

text: Mus musculus

text: liver

text: Mus musculus

text: Sample 12

characteristic: title

text: Tamoxifen treated


E-MTAB-5412:Sample 13

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-5412:Sample 13

text: ArrayExpress

characteristic: cell type

text: house mouse

text: GM-CSFind x CD4-CrERT2

text: Mus musculus

text: Mus musculus

text: kidney

text: Mus musculus

text: Sample 13

text: Tamoxifen treated


E-MTAB-5412:Sample 14

characteristic: ENA-CHECKLIST

text: public

text: E-MTAB-5412:Sample 14

text: ArrayExpress

text: house mouse

text: GM-CSFind x CD4-CrERT2

characteristic: genotype

text: Mus musculus

text: Mus musculus

text: kidney

text: Mus musculus

characteristic: strain

text: Sample 14

text: Tamoxifen treated

characteristic: treatment


E-MTAB-5412:Sample 15

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-5412:Sample 15

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: house mouse

text: GM-CSFind x CD4-CrERT2

text: Mus musculus

text: Mus musculus

text: kidney

text: Mus musculus

text: Sample 15

text: Tamoxifen treated


E-MTAB-5412:Sample 2

text: public

text: E-MTAB-5412:Sample 2

text: ArrayExpress

text: house mouse

characteristic: common name

characteristic: description

text: GM-CSFind x CD4-CrERT2

text: Mus musculus

characteristic: organism

text: Mus musculus

text: central nervous system

characteristic: organism part

text: Mus musculus

text: Sample 2

text: Tamoxifen treated


E-MTAB-5412:Sample 3

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: E-MTAB-5412:Sample 3

text: ArrayExpress

text: house mouse

text: GM-CSFind x CD4-CrERT2

text: Mus musculus

text: Mus musculus

text: central nervous system

text: Mus musculus

text: Sample 3

characteristic: title

text: Tamoxifen treated


E-MTAB-5412:Sample 4

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-5412:Sample 4

text: ArrayExpress

characteristic: cell type

text: house mouse

text: GM-CSFind x CD4-CrERT2

text: Mus musculus

text: Mus musculus

text: central nervous system

text: Mus musculus

text: Sample 4

text: Tamoxifen treated


E-MTAB-5412:Sample 5

characteristic: ENA-CHECKLIST

text: public

text: E-MTAB-5412:Sample 5

text: ArrayExpress

text: house mouse

text: GM-CSFind x CD4-CrERT2

characteristic: genotype

text: Mus musculus

text: Mus musculus

text: spleen

text: Mus musculus

characteristic: strain

text: Sample 5

text: Tamoxifen treated

characteristic: treatment


E-MTAB-5412:Sample 6

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-5412:Sample 6

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: house mouse

text: GM-CSFind x CD4-CrERT2

text: Mus musculus

text: Mus musculus

text: spleen

text: Mus musculus

text: Sample 6

text: Tamoxifen treated


E-MTAB-5412:Sample 7

text: public

text: E-MTAB-5412:Sample 7

text: ArrayExpress

text: house mouse

characteristic: common name

characteristic: description

text: GM-CSFind x CD4-CrERT2

text: Mus musculus

characteristic: organism

text: Mus musculus

text: lung

characteristic: organism part

text: Mus musculus

text: Sample 7

text: Tamoxifen treated


E-MTAB-5412:Sample 8

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: E-MTAB-5412:Sample 8

text: ArrayExpress

text: house mouse

text: GM-CSFind x CD4-CrERT2

text: Mus musculus

text: Mus musculus

text: lung

text: Mus musculus

text: Sample 8

characteristic: title

text: Tamoxifen treated


E-MTAB-5412:Sample 9

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-5412:Sample 9

text: ArrayExpress

characteristic: cell type

text: house mouse

text: GM-CSFind x CD4-CrERT2

text: Mus musculus

text: Mus musculus

text: lung

text: Mus musculus

text: Sample 9

text: Tamoxifen treated


characteristic: ENA-CHECKLIST

text: public

tag: Namespace:Institute of Molecular Life Sciences, University of Zurich

text: ArrayExpress

text: Protocols: C. elegans CPEB homolog mutants and wild-type N2 were metabolically labelled at lysine and arginine amino acids by feeding light (Lys0 and Arg0) labelled bacteria using SILAC protocol, as previously described [Subasic et al. 2015]. Samples were harvested after two generations at different developmental stages (fog-1 and cpb-2 at L3; cpb-3 at L4; and N2 at L3, L4 and YA) in biological triplicates. RNA extraction was done using TRIzol reagent (15596-026; Life Technologies) in accordance with the manufacturer’s protocol and further purified by using DNA-free kit (AM1906; Ambion). Random primed cDNA library was generated from each sample by GATC Biotech as per their \InView Transcriptome Explore\ package.

text: L3 larva

characteristic: developmental stage

text: cpb-2(ok1772) II

characteristic: genotype

text: 20 C

characteristic: growth condition

text: Caenorhabditis elegans

text: Caenorhabditis elegans

text: Caenorhabditis elegans

characteristic: strain

text: SILAC labelled (light; Lys0, Arg0)

characteristic: treatment


text: Institute of Molecular Life Sciences, University of Zurich

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

characteristic: description

text: L3 larva

text: cpb-2(ok1772) II

text: 20 C

text: Caenorhabditis elegans

text: Caenorhabditis elegans

text: Caenorhabditis elegans

text: SILAC labelled (light; Lys0, Arg0)


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: ArrayExpress

text: L4 larva

text: cpb-3(op234) I

text: 20 C

text: Caenorhabditis elegans

characteristic: organism

text: Caenorhabditis elegans

text: Caenorhabditis elegans

text: SILAC labelled (light; Lys0, Arg0)


text: UFP

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: collection date

text: Amazon

characteristic: environment (biome)

text: Reservoir

characteristic: environment (feature)

text: water

characteristic: environment (material)

text: Brazil

characteristic: geographic location (country and/or sea)

characteristic: geographic location (depth)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome

characteristic: investigation type

text: metagenome

text: Curua Una

characteristic: project name

text: metagenome

text: Semiconduction

characteristic: sequencing method

characteristic: title

text: water

characteristic: water environmental package


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UFP

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: Amazon

text: Reservoir

text: water

text: Brazil

text: metagenome

text: metagenome

characteristic: organism

text: Curua Una

text: metagenome

text: Semiconduction

text: water


text: Saolta

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: IRL

characteristic: collection date

characteristic: description

text: Klebsiella

characteristic: genus

text: Ireland

characteristic: geographic location (country and/or sea)

text: Homo sapiens

characteristic: host

text: Homo sapiens

characteristic: host scientific name

characteristic: isolate

text: Human

characteristic: isolation source

text: urinary tract

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

type: AMR curated data - CABBAGE

value: ampicillin

value: EUCAST

value: broth dilution

value: Vitek

value: resistant

value: Klebsiella pneumoniae

value: tobramycin

value: amikacin

value: cefpodoxime

value: cefoxitin

value: piperacillin-tazobactam

value: amoxicillin-clavulanic acid

value: cefotaxime

value: meropenem

value: tigecycline

value: ertapenem

value: gentamicin


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: Saolta

text: public

text: IRL

text: Klebsiella

text: Ireland

text: Homo sapiens

text: Homo sapiens

text: Human

text: gastrointestinal system

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

characteristic: title

value: susceptible

value: cefpodoxime-clavulanic acid

value: intermediate

value: ampicillin


characteristic: External Id

text: Saolta

text: public

characteristic: INSDC status

text: IRL

characteristic: SRA accession

characteristic: Submitter Id

text: Klebsiella

text: Ireland

text: Homo sapiens

text: Homo sapiens

text: Human

text: urinary tract

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

value: EUCAST

value: broth dilution

value: Vitek

value: resistant


text: Saolta

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: IRL

text: Klebsiella

text: Ireland

text: Homo sapiens

text: Homo sapiens

text: Human

text: gastrointestinal system

text: Klebsiella pneumoniae

characteristic: organism

text: Klebsiella pneumoniae

value: Klebsiella pneumoniae

value: cefpodoxime

value: tobramycin


text: Saolta

text: public

text: IRL

characteristic: collection date

characteristic: description

text: Klebsiella

characteristic: genus

text: Ireland

characteristic: geographic location (country and/or sea)

text: Homo sapiens

text: Homo sapiens

text: Human

text: gastrointestinal system

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

value: amoxicillin-clavulanic acid

value: amikacin

value: piperacillin-tazobactam

value: cefoxitin


text: Saolta

text: public

text: IRL

text: Klebsiella

text: Ireland

text: Homo sapiens

characteristic: host

text: Homo sapiens

characteristic: host scientific name

characteristic: isolate

text: Human

characteristic: isolation source

text: central nervous system

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

value: tigecycline

value: meropenem

value: ertapenem

value: cefotaxime


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: Saolta

text: public

text: IRL

text: Klebsiella

text: Ireland

text: Homo sapiens

text: Homo sapiens

text: Human

text: gastrointestinal system

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

characteristic: title

value: intermediate

value: cefpodoxime-clavulanic acid

value: gentamicin

value: susceptible


characteristic: External Id

text: Saolta

text: public

characteristic: INSDC status

text: IRL

characteristic: SRA accession

characteristic: Submitter Id

text: Klebsiella

text: Ireland

text: Homo sapiens

text: Homo sapiens

text: Human

text: respiratory tract

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

value: EUCAST

value: broth dilution

value: Vitek

value: ampicillin


text: FREIE UNIVERSIT*T BERLIN

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

tag: Namespace:FREIE UNIVERSIT*T BERLIN

text: Soil collected in microcosms with gap soil placed in gap microhabitat . This sterile soil was initially inoculated with alive gap soil

text: Semiarid

characteristic: environment (biome)

text: Dry valley

characteristic: environment (feature)

text: Soil

characteristic: environment (material)

text: Spain

characteristic: geographic location (depth)

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: mimarks-survey

characteristic: investigation type

text: Soil metagenome

characteristic: organism

text: Disentangling facilitation drivers: The role of soil microorganisms. (Retama-gap)

characteristic: project name

text: Soil metagenome

text: Pyrosequencing

characteristic: sequencing method

text: soil

characteristic: soil environmental package

text: Alive gap soil placed in gap microhabitat


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: FREIE UNIVERSIT*T BERLIN

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: collection date

text: Soil collected in microcosms with gap soil placed in gap microhabitat. This sterile soil was initially inoculated with alive gap soil

characteristic: description

text: Semiarid

text: Dry valley

text: Soil

text: Spain

characteristic: geographic location (country and/or sea)

text: mimarks-survey

text: Soil metagenome

text: Soil metagenome

text: Pyrosequencing

text: soil

characteristic: title


text: FREIE UNIVERSIT*T BERLIN

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: Submitter Id

text: Soil collected in microcosms with gap soil placed in gap microhabitat. This sterile soil was initially inoculated with sterile gap soil

text: Semiarid

characteristic: environment (biome)

text: Dry valley

characteristic: environment (feature)

text: Soil

characteristic: environment (material)

text: Spain

characteristic: geographic location (depth)

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

text: mimarks-survey

text: Soil metagenome

text: Soil metagenome

text: Pyrosequencing

text: soil

text: Sterile gap soil placed in gap microhabitat


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: FREIE UNIVERSIT*T BERLIN

text: public

text: Soil collected in microcosms with large Retama soil placed under large Retama shrubs. This sterile soil was initially inoculated with alive large Retama soil

text: Semiarid

text: Dry valley

text: Soil

text: Spain

characteristic: geographic location (longitude)

text: mimarks-survey

characteristic: investigation type

text: Soil metagenome

characteristic: organism

characteristic: project name

text: Soil metagenome

text: Pyrosequencing

characteristic: sequencing method

text: soil

characteristic: soil environmental package

text: Alive Retama soil placed in Retama microhabitat


text: FREIE UNIVERSIT*T BERLIN

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

text: Soil collected in microcosms with large Retama soil placed under large Retama shrubs. This sterile soil was initially inoculated with sterile large Retama soil

characteristic: description

text: Semiarid

text: Dry valley

text: Soil

text: Spain

characteristic: geographic location (country and/or sea)

text: mimarks-survey

text: Soil metagenome

text: Soil metagenome

text: Pyrosequencing

text: soil

text: Sterile Retama soil placed in Retama microhabitat

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UNIVERSITY OF ABERDEEN

text: public

tag: Namespace:UNIVERSITY OF ABERDEEN

text: Campylobacter jejuni

text: Campylobacter jejuni

text: iCaMPS-4 study chicken isolate


text: Genoscope CEA

text: public

tag: Namespace:Genoscope CEA

text: Planktothrix sp. PCC 11201

characteristic: organism

text: Planktothrix sp. PCC 11201

text: Prokaryotic genome sequencing


name: E-MTAB-5444:CFBP 1430 T6-d1d3 mutant in vitro (M9 sucrose)

text: public

tag: Namespace:Zurich University of Applied Sciences (ZHAW) School of Life Sciences and Facility Management Institute of Natural Resource Sciences Environmental Genomics and Systems Biology Research Group

text: ArrayExpress

characteristic: broker name

text: Protocols: Growth at 28°C with continuous shaking to the mid-log phase in liquid minimal M9 medium (Difco) supplemented with sucrose (0.4 g l-1). RNA was extracted using the NucleoSpin RNA II kit (Macherey Nagel) following manufacturer's instructions. Total RNA samples were treated with DNase I (Thermo Scientific). Quality and concentration was determined using the Bioanalyzer 2100 (Agilent). Samples were pooled to the required amount for further processing. For the cDNA bacterial transcripts from the in planta RNA extract, first the polyA+ RNA was removed by oligo(dT) chromatography. The polyA- RNAs or RNA extracts from pure bacterial cultures were then treated with Terminator exonuclease (TEX) in order to enrich for bacterial transcripts carrying 5'-triphosphate. The terminator resistant transcripts were fragmented by ultrasound treatment (4 pulses of 30 s at 4°C) and then poly(A) tails were added to the 3' ends of the RNA fragments using poly(A) polymerase. The polyadenylated RNA fragments were further treated with RNA 5' polyphosphatase to remove 5'triphosphate groups from the 5' fragments After ligation of a RNA oligonucleotide to the 5' monophosphate of the RNA fragments, first-strand cDNA was synthesized using an oligo(dT)-linker primer and M-MLV H- reverse transcriptase. Finally, the cDNA was PCR amplified using a high fidelity DNA polymerase and 15 cycles. The cDNAs were purified using the Agencourt AMPure XP kit (Beckman Coulter Genomics) and analyzed by capillary electrophoresis.

text: T6-d1d3 mutant

characteristic: genotype

text: logarithmic growth phase in vitro

characteristic: growth condition

text: Erwinia amylovora

text: Erwinia amylovora

text: Erwinia amylovora

text: CFBP 1430

characteristic: strain


name: E-MTAB-5444:CFBP 1430 WT in vitro (M9 sucrose)

text: Zurich University of Applied Sciences (ZHAW) School of Life Sciences and Facility Management Institute of Natural Resource Sciences Environmental Genomics and Systems Biology Research Group

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: ArrayExpress

text: wild type genotype

text: logarithmic growth phase in vitro

text: Erwinia amylovora

text: Erwinia amylovora

text: Erwinia amylovora

text: CFBP 1430

text: CFBP 1430 WT in vitro (M9 sucrose)


text: UPSC

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: Siberian spruce

characteristic: common name

text: Cultivated from germplasm collected in Tomsk Oblast in Russia

text: Picea obovata

text: Picea obovata

text: Picea obovata cultivated at Mustila Arboretum Finland


text: CBSFAX

text: public

text: Halobacillus sp. CR3

text: Halobacillus sp. CR3

text: genome assembly of Halobacillus sp. CR3

characteristic: title


characteristic: ENA-CHECKLIST

text: CBSFAX

text: public

text: Salicola sp. SBJ9

text: Salicola sp. SBJ9

text: genome assembly of Salicola sp. SBJ9


characteristic: ENA-FIRST-PUBLIC

text: public

tag: Namespace:Pontificia Universidad Catolica de Chile

characteristic: collection date

text: human

text: Fecal sample microbiota

characteristic: description

text: fecal

characteristic: environment (biome)

text: human gut

characteristic: environment (feature)

text: DNA

characteristic: environment (material)

text: Chile

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: human-gut

characteristic: human gut environmental package

text: metagenome

characteristic: investigation type

text: Homo sapiens

text: zebrafish inoculation

characteristic: project name

text: Homo sapiens

text: Miseq

characteristic: sequencing method

text: Fecal sample


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Pontificia Universidad Catolica de Chile

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: human

text: Fecal sample microbiota

text: fecal

text: human gut

text: DNA

text: Chile

text: human-gut

text: metagenome

text: Homo sapiens

characteristic: organism

text: zebrafish inoculation

text: Homo sapiens

text: Miseq

text: Fecal sample2


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

characteristic: collection date

text: human

characteristic: common name

text: Fecal sample microbiota

characteristic: description

text: fecal

characteristic: environment (biome)

text: human gut

characteristic: environment (feature)

text: DNA

characteristic: environment (material)

text: Chile

text: human-gut

text: metagenome

text: Homo sapiens

text: zebrafish inoculation

text: Homo sapiens

text: Miseq

text: Inoculum

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: human

text: Fecal sample microbiota

text: fecal

text: human gut

text: DNA

text: Chile

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: human-gut

characteristic: human gut environmental package

text: metagenome

characteristic: investigation type

text: Homo sapiens

text: zebrafish inoculation

characteristic: project name

text: Homo sapiens

text: Miseq

characteristic: sequencing method


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: human

text: Fecal sample microbiota

text: fecal

text: human gut

text: DNA

text: Chile

text: human-gut

text: metagenome

text: Homo sapiens

characteristic: organism

text: zebrafish inoculation

text: Homo sapiens

text: Miseq

text: NN medium


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

characteristic: collection date

text: human

characteristic: common name

text: Fecal sample microbiota

characteristic: description

text: fecal

characteristic: environment (biome)

text: human gut

characteristic: environment (feature)

text: DNA

characteristic: environment (material)

text: Chile

text: human-gut

text: metagenome

text: Homo sapiens

text: zebrafish inoculation

text: Homo sapiens

text: Miseq

text: Rumen medium

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: human

text: Fecal sample microbiota

text: fecal

text: human gut

text: DNA

text: Chile

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: human-gut

characteristic: human gut environmental package

text: metagenome

characteristic: investigation type

text: Homo sapiens

text: zebrafish inoculation

characteristic: project name

text: Homo sapiens

text: Miseq

characteristic: sequencing method

text: inoculate larvae1


characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: human

text: Fecal sample microbiota

text: fecal

text: human gut

text: DNA

text: Chile

text: human-gut

text: metagenome

text: Homo sapiens

characteristic: organism

text: zebrafish inoculation

text: Homo sapiens

text: Miseq

text: control larvae


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

characteristic: collection date

text: human

characteristic: common name

text: Fecal sample microbiota

characteristic: description

text: fecal

characteristic: environment (biome)

text: human gut

characteristic: environment (feature)

text: DNA

characteristic: environment (material)

text: Chile

text: human-gut

text: metagenome

text: Homo sapiens

text: zebrafish inoculation

text: Homo sapiens

text: Miseq

text: inoculate larvae2

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: human

text: Fecal sample microbiota

text: fecal

text: human gut

text: DNA

text: Chile

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: human-gut

characteristic: human gut environmental package

text: metagenome

characteristic: investigation type

text: Homo sapiens

text: zebrafish inoculation

characteristic: project name

text: Homo sapiens

text: Miseq

characteristic: sequencing method

text: negative control


text: Klebsiella pneumoniae

characteristic: ArrayExpress-Species

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

characteristic: organism

text: Klebsiella pneumoniae


text: Enterobacter cloacae

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

text: public

text: Enterobacter cloacae

characteristic: common name

text: Enterobacter cloacae

text: Enterobacter cloacae

characteristic: title


E-MTAB-5105:Sample 1

text: public

text: E-MTAB-5105:Sample 1

tag: Namespace:Department of Biomedical Sciences, University of Barcelona

text: ArrayExpress

characteristic: broker name

text: MEF cell line

characteristic: cell line

text: house mouse

text: Protocols: For these experiments mouse embryonic fibroblasts (MEFs) from p27WT and p27-/- animals were used. Cells were cultured in Dulbecco's modified Eagle Medium (DMEM) supplemented with 10% fetal bovine serum (Biological Industries), 2 mM L-Glutamine (Merck), 1% nonessential amino acids (Biological Industries), 1 mM pyruvic acid (Sigma), 50 U/ml penicillin and 50 μg/ml streptomycin (Biological Industries). Prior to synchronization cells were cultured up to 90% confluence and to make them quiescent they were maintained for 72h in the medium in the absence of serum. Cell synchronization was monitored by flow cytometry of propidium iodide-stained cells. DNA was extracted from samples by ChIP-seq. Quiescent MEFs were used for ChIP with anti-p27 antibodies (Santa Cruz SC528). Briefly, cells were lysed and chromatin from cross-linked cells was sonicated. Chromatin was incubated with 5 µg of anti-p27 in RIPA buffer (50 mM Tris−HCl pH 7.5, 150 mM NaCl, 1% NP-40, 0.5% Sodium deoxycholate, 0.1% SDS, 1 mM EDTA, 1 mM DTT, 1 mM PMSF, 0.1 mM Na3VO4, 0.5 μg/μl aprotinin, 10 μg/μl leupeptin) adding 20 µl of Magna ChIP Protein A magnetic beads (Millipore). Samples were incubated in rotation overnight at 4ºC. Beads were washed with low salt buffer, high salt buffer, LiCl buffer and TE buffer. Subsequent elution and purification of the immunoprecipitated DNA-proteins complexes was performed using the IPure kit (Diagenode) according to manufacturer’s protocol. After DNA isolation, ChIP samples, together with the input, were sequenced. Libraries were prepared using the NEBNext® ChIP-Seq Library Prep Reagent Set for Illumina® kit (ref. E6200S) according to the manufacturer's protocol. Briefly, 10 ng of input and ChIP enriched DNA were subjected to end repair, addition of “A” bases to 3′ ends and ligation of PE adapters. All purification steps were performed using Qiagen PCR purification columns (refs. 50928106 and 50928006). Library size selection was done with 2% low-range agarose gels. Library amplification was performed by PCR on the size selected fragments. Final libraries were analyzed using Agilent DNA 1000 chip to estimate the quantity and check size distribution, and were then quantified by qPCR using the KAPA Library Quantification Kit (ref. KK4835, KapaBiosystems) prior to amplification with Illumina’s cBot. Sequencing was done on the HiSeq2000, Single Read, 50 nts. Libraries were prepared using the NEBNext® ChIP-Seq Library Prep Reagent Set for Illumina® kit (ref. E6200S) according to the manufacturer's protocol. Briefly, 10 ng of input and ChIP enriched DNA were subjected to end repair, addition of “A” bases to 3′ ends and ligation of PE adapters. All purification steps were performed using Qiagen PCR purification columns (refs. 50928106 and 50928006). Library size selection was done with 2% low-range agarose gels. Library amplification was performed by PCR on the size selected fragments.

characteristic: description

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Sample 1


E-MTAB-5105:Sample 2

text: Department of Biomedical Sciences, University of Barcelona

text: public

text: E-MTAB-5105:Sample 2

text: ArrayExpress

text: MEF cell line

text: house mouse

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Sample 2


text: Animal Breeding and Genomics Centre

text: public

tag: Namespace:Animal Breeding and Genomics Centre

text: transcription profiling by high throughput sequencing

characteristic: assay type

text: pig

characteristic: extraction protocol

text: Sus scrofa

characteristic: sample descriptor

text: RNAlater, frozen

characteristic: sample storage

text: fresh

characteristic: sample storage processing

text: 30 minutes

characteristic: sampling to preparation interval

text: Sus scrofa

text: Duroc liver RNA-seq


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Animal Breeding and Genomics Centre

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: pig

text: Sus scrofa

text: RNAlater, frozen

text: fresh

text: 30 minutes

text: Sus scrofa

text: Duroc spleen RNA-seq


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Animal Breeding and Genomics Centre

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: pig

characteristic: common name

text: Sus scrofa

characteristic: organism

text: RNAlater, frozen

text: fresh

text: 30 minutes

text: Sus scrofa

text: Duroc testis RNA-seq


text: Animal Breeding and Genomics Centre

text: public

characteristic: assay type

text: pig

characteristic: extraction protocol

text: Sus scrofa

text: RNAlater, frozen

text: fresh

text: 30 minutes

text: Sus scrofa

text: Duroc brain frontal lobe RNA-seq

characteristic: title


text: Animal Breeding and Genomics Centre

text: public

text: pig

text: Sus scrofa

characteristic: sample descriptor

text: RNAlater, frozen

characteristic: sample storage

text: fresh

characteristic: sample storage processing

text: 30 minutes

text: Sus scrofa

text: Duroc muscle RNA-seq


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Animal Breeding and Genomics Centre

text: public

text: pig

text: Sus scrofa

text: RNAlater, frozen

text: fresh

text: 30 minutes

characteristic: sampling to preparation interval

text: Sus scrofa

text: Pietrain liver RNA-seq


text: Animal Breeding and Genomics Centre

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: pig

text: Sus scrofa

text: RNAlater, frozen

text: fresh

text: 30 minutes

text: Sus scrofa

text: Pietrain spleen RNA-seq


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Animal Breeding and Genomics Centre

text: public

characteristic: INSDC status

text: pig

text: Sus scrofa

text: RNAlater, frozen

text: fresh

text: 30 minutes

text: Sus scrofa

text: Pietrain testis RNA-seq


text: Animal Breeding and Genomics Centre

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: pig

characteristic: common name

text: Sus scrofa

text: RNAlater, frozen

text: fresh

text: 30 minutes

text: Sus scrofa

text: Pietrain brain frontal lobe RNA-seq


text: Animal Breeding and Genomics Centre

text: public

characteristic: assay type

text: pig

characteristic: extraction protocol

text: Sus scrofa

characteristic: organism

text: RNAlater, frozen

text: fresh

text: 30 minutes

text: Sus scrofa

text: Pietrain muscle RNA-seq


text: Animal Breeding and Genomics Centre

text: public

text: pig

text: Sus scrofa

characteristic: sample descriptor

text: RNAlater, frozen

characteristic: sample storage

text: fresh

text: 30 minutes

text: Sus scrofa

text: Large white liver RNA-seq

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Animal Breeding and Genomics Centre

text: public

text: pig

text: Sus scrofa

text: RNAlater, frozen

text: fresh

characteristic: sample storage processing

text: 30 minutes

text: Sus scrofa

text: Large white spleen RNA-seq


text: Animal Breeding and Genomics Centre

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: pig

text: Sus scrofa

text: RNAlater, frozen

text: fresh

text: 30 minutes

characteristic: sampling to preparation interval

text: Sus scrofa

text: Large white testis RNA-seq


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Animal Breeding and Genomics Centre

characteristic: INSDC last update

text: public

text: pig

text: Sus scrofa

text: RNAlater, frozen

text: fresh

text: 30 minutes

text: Sus scrofa

text: Large white brain frontal lobe RNA-seq


text: Animal Breeding and Genomics Centre

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: pig

text: Sus scrofa

text: RNAlater, frozen

text: fresh

text: 30 minutes

text: Sus scrofa

text: Large white muscle RNA-seq


text: Animal Breeding and Genomics Centre

text: public

characteristic: assay type

text: pig

characteristic: common name

characteristic: extraction protocol

text: Sus scrofa

text: RNAlater, frozen

text: fresh

text: 30 minutes

text: Sus scrofa

text: Large white olfactory lobe RNA-seq


text: Animal Breeding and Genomics Centre

text: public

text: pig

text: Sus scrofa

characteristic: organism

characteristic: sample descriptor

text: RNAlater, frozen

characteristic: sample storage

text: fresh

text: 30 minutes

text: Sus scrofa

text: Large white lung RNA-seq


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Animal Breeding and Genomics Centre

text: public

text: pig

text: Sus scrofa

text: not provided

text: RNAlater, frozen

text: fresh

text: 30 minutes

text: Sus scrofa

text: Large white lymphe node RNA-seq

characteristic: title


text: University Hospital Galway

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: collection date

text: Ireland

characteristic: geographic location (country and/or sea)

text: Homo sapiens

characteristic: host scientific name

characteristic: isolate

text: Human

characteristic: isolation source

text: Salmonella enterica subsp. enterica serovar Enteritidis

text: Enteritidis

characteristic: serovar

text: Subsp. I

characteristic: sub species


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: University Hospital Galway

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: Ireland

text: Homo sapiens

text: Human

text: Salmonella enterica subsp. enterica serovar Typhimurium

text: Typhimurium

text: Subsp. I


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: University Hospital Galway

text: public

text: Ireland

text: Homo sapiens

text: Human

text: Salmonella enterica subsp. enterica serovar Paratyphi A

characteristic: organism

text: Paratyphi A

text: Subsp. I


text: University Hospital Galway

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: Ireland

text: Homo sapiens

text: Human

text: Salmonella enterica subsp. enterica serovar Saintpaul

text: Saintpaul

text: Subsp. I

characteristic: title


text: University Hospital Galway

text: public

characteristic: collection date

text: Ireland

characteristic: geographic location (country and/or sea)

text: Homo sapiens

characteristic: host scientific name

text: Human

text: Salmonella enterica subsp. enterica serovar Manhattan

text: Manhattan

text: Subsp. I


text: University Hospital Galway

text: public

text: Ireland

text: Homo sapiens

characteristic: isolate

text: Human

characteristic: isolation source

text: Salmonella enterica subsp. enterica serovar Infantis

text: Infantis

characteristic: serovar

text: Subsp. I


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: University Hospital Galway

text: public

text: Ireland

text: Homo sapiens

text: Human

text: Salmonella enterica subsp. enterica serovar Typhimurium var. monophasic 4,[5],12:i:-

text: Subsp. I

characteristic: sub species


text: IMB,Faculty of Health science

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

tag: Namespace:IMB,Faculty of Health science

text: human

characteristic: common name

text: Homo sapiens

text: Homo sapiens


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: UNIVERSITY OF ABERDEEN

text: public

characteristic: Submitter Id

text: Campylobacter coli

characteristic: organism

text: Campylobacter coli

text: iCaMPS-4 study chicken isolate


text: University Hospital Galway

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: collection date

text: Ireland

text: Homo sapiens

text: Human

text: Salmonella enterica subsp. Enterica

text: Salmonella enterica subsp. Enterica

text: Unnamed

text: Subsp. I

characteristic: title


text: University Hospital Galway

text: public

text: Ireland

characteristic: geographic location (country and/or sea)

text: Homo sapiens

characteristic: host scientific name

characteristic: isolate

text: Human

characteristic: isolation source

text: Salmonella enterica subsp. enterica serovar Panama

text: Panama

text: Subsp. I


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: University Hospital Galway

text: public

text: Ireland

text: Homo sapiens

text: Human

text: Salmonella enterica subsp. enterica serovar Brandenburg

text: Brandenburg

characteristic: serovar

text: Subsp. I

characteristic: sub species


text: University Hospital Galway

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: Ireland

text: Homo sapiens

text: Human

text: Salmonella enterica subsp. houtenae serovar 44:z4,z23:-

text: IV 44:z4,z23

text: Subsp. IV


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: University Hospital Galway

text: public

characteristic: Submitter Id

text: Ireland

text: Homo sapiens

text: Human

text: Salmonella enterica subsp. enterica serovar Stanley

text: Stanley

text: Subsp. I


text: University Hospital Galway

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: Ireland

text: Homo sapiens

text: Human

text: Salmonella enterica subsp. enterica serovar Newport

characteristic: organism

text: Newport

text: Subsp. I


text: public

tag: Namespace:DST/NRF Centre of Excellence for Biomedical TB research, SAMRC Centre for TB Research

characteristic: collection date

text: South Africa

characteristic: geographic location (country and/or sea)

text: not provided

characteristic: host health state

text: Panthera leo

text: Various

text: Lion

text: Mycobacterium bovis

text: Mycobacterium bovis

text: Mycobacterium bovis isolates from various animal hosts in South Africa

characteristic: title


tag: attribute

characteristic: ENA-LAST-UPDATE

text: DST/NRF Centre of Excellence for Biomedical TB research, SAMRC Centre for TB Research

text: public

text: South Africa

text: not provided

text: Syncerus caffer

characteristic: host scientific name

text: Various

characteristic: isolate

text: Buffalo

characteristic: isolation source

text: Mycobacterium bovis

text: Mycobacterium bovis


characteristic: External Id

characteristic: INSDC last update

text: public

text: South Africa

text: not provided

text: Tragelaphus strepsiceros

text: Various

text: Kudu

text: Mycobacterium bovis

text: Mycobacterium bovis


150(3) BovisKNP

text: public

characteristic: INSDC status

characteristic: SRA accession

text: 150(3) BovisKNP

text: South Africa

text: not provided

text: Syncerus caffer

text: Various

text: Buffalo

text: Mycobacterium bovis

text: Mycobacterium bovis


3912 (B)

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: 3912 (B)

text: South Africa

text: not provided

text: Bos taurus

text: Various

text: Cattle

text: Mycobacterium bovis

text: Mycobacterium bovis


440(5) BovisKNP

characteristic: INSDC center name

text: public

text: 440(5) BovisKNP

characteristic: Submitter Id

text: South Africa

text: not provided

text: Syncerus caffer

text: Various

text: Buffalo

text: Mycobacterium bovis

text: Mycobacterium bovis


659(A) BovisKNP

characteristic: INSDC first public

text: public

text: 659(A) BovisKNP

text: South Africa

text: not provided

text: Syncerus caffer

text: Various

text: Buffalo

text: Mycobacterium bovis

characteristic: organism

text: Mycobacterium bovis


text: public

characteristic: collection date

text: South Africa

characteristic: geographic location (country and/or sea)

text: not provided

text: Bos taurus

text: Various

text: Cattle

text: Mycobacterium bovis

text: Mycobacterium bovis


Bovis 1595-F(24)

text: public

text: Bovis 1595-F(24)

text: South Africa

text: not provided

characteristic: host health state

text: Panthera leo

text: Various

text: Lion

text: Mycobacterium bovis

text: Mycobacterium bovis

characteristic: title


Bovis1199 B(19)

characteristic: ENA-LAST-UPDATE

text: public

text: Bovis1199 B(19)

text: South Africa

text: not provided

text: Panthera leo

characteristic: host scientific name

text: Various

text: Lion

text: Mycobacterium bovis

text: Mycobacterium bovis


text: FFUL

text: public

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis clinical isolate


text: UNIVERSITY OF ABERDEEN

text: public

text: Campylobacter jejuni

text: Campylobacter jejuni

text: iCaMPS-4 study clinical/human isolate


text: UNIVERSITY OF ABERDEEN

text: public

text: Campylobacter coli

text: Campylobacter coli

text: iCaMPS-4 study clinical/human isolate


characteristic: #sampleid

text: Georgia State University

text: public

tag: Namespace:Georgia State University

text: CGGTAGTTGATC

characteristic: barcodesequence

text: house mouse

characteristic: common name

characteristic: day

text: Dietary emulsifiers directly alter human microbiota composition and gene expression ex vivo potentiating intestinal inflammation

characteristic: description

characteristic: dob

text: Water

characteristic: emulsifier

text: terrestrial biome

characteristic: environment (biome)

text: animal-associated habitat

characteristic: environment (feature)

text: feces

characteristic: environment (material)

characteristic: genotype

text: USA

text: 33.7490�_�� N

characteristic: geographic location (latitude)

text: 84.3880�_�� W

characteristic: geographic location (longitude)

text: host-associated

characteristic: host-associated environmental package

text: mimarks-survey

characteristic: investigation type

text: Mus musculus

text: SHIMETransplant

characteristic: project name

text: Mus musculus

text: Illumina MiSeq

characteristic: sequencing method

text: male

characteristic: sex

characteristic: vessel


characteristic: #sampleid

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Georgia State University

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: TGAAAGCGGCGA

characteristic: barcodesequence

characteristic: collection date

text: house mouse

characteristic: common name

text: Water

text: terrestrial biome

text: animal-associated habitat

text: feces

text: USA

characteristic: geographic location (country and/or sea)

text: 33.7490�_�� N

text: 84.3880�_�� W

text: host-associated

text: mimarks-survey

text: Mus musculus

characteristic: organism

text: SHIMETransplant

text: Mus musculus

text: Illumina MiSeq

text: male

characteristic: title


characteristic: #sampleid

text: Georgia State University

text: public

text: GGTTACGGTTAC

text: house mouse

characteristic: day

characteristic: description

characteristic: dob

text: Water

characteristic: emulsifier

text: terrestrial biome

characteristic: environment (biome)

text: animal-associated habitat

characteristic: environment (feature)

text: feces

characteristic: environment (material)

characteristic: genotype

text: USA

text: 33.7490�_�� N

characteristic: geographic location (latitude)

text: 84.3880�_�� W

characteristic: geographic location (longitude)

text: host-associated

characteristic: host-associated environmental package

text: mimarks-survey

characteristic: investigation type

text: Mus musculus

text: SHIMETransplant

characteristic: project name

text: Mus musculus

text: Illumina MiSeq

characteristic: sequencing method

text: male

characteristic: sex

characteristic: vessel


characteristic: #sampleid

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Georgia State University

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: ACATCAGGTCAC

characteristic: barcodesequence

characteristic: collection date

text: house mouse

characteristic: common name

text: Water

text: terrestrial biome

text: animal-associated habitat

text: feces

text: USA

characteristic: geographic location (country and/or sea)

text: 33.7490�_�� N

text: 84.3880�_�� W

text: host-associated

text: mimarks-survey

text: Mus musculus

characteristic: organism

text: SHIMETransplant

text: Mus musculus

text: Illumina MiSeq

text: male

characteristic: title


characteristic: #sampleid

text: Georgia State University

text: public

text: GTTGATACGATG

text: house mouse

characteristic: day

characteristic: description

characteristic: dob

text: Water

characteristic: emulsifier

text: terrestrial biome

characteristic: environment (biome)

text: animal-associated habitat

characteristic: environment (feature)

text: feces

characteristic: environment (material)

characteristic: genotype

text: USA

text: 33.7490�_�� N

characteristic: geographic location (latitude)

text: 84.3880�_�� W

characteristic: geographic location (longitude)

text: host-associated

characteristic: host-associated environmental package

text: mimarks-survey

characteristic: investigation type

text: Mus musculus

text: SHIMETransplant

characteristic: project name

text: Mus musculus

text: Illumina MiSeq

characteristic: sequencing method

text: male

characteristic: sex

characteristic: vessel


characteristic: #sampleid

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Georgia State University

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: CAGACACTTCCG

characteristic: barcodesequence

characteristic: collection date

text: house mouse

characteristic: common name

text: terrestrial biome

text: animal-associated habitat

text: feces

text: USA

characteristic: geographic location (country and/or sea)

text: 33.7490�_�� N

text: 84.3880�_�� W

text: host-associated

text: mimarks-survey

text: Mus musculus

characteristic: organism

text: SHIMETransplant

text: Mus musculus

text: Illumina MiSeq

text: male

characteristic: title


characteristic: #sampleid

text: Georgia State University

text: public

text: TCACCATCCGAG

text: house mouse

characteristic: day

characteristic: description

characteristic: dob

characteristic: emulsifier

text: terrestrial biome

characteristic: environment (biome)

text: animal-associated habitat

characteristic: environment (feature)

text: feces

characteristic: environment (material)

characteristic: genotype

text: USA

text: 33.7490�_�� N

characteristic: geographic location (latitude)

text: 84.3880�_�� W

characteristic: geographic location (longitude)

text: host-associated

characteristic: host-associated environmental package

text: mimarks-survey

characteristic: investigation type

text: Mus musculus

text: SHIMETransplant

characteristic: project name

text: Mus musculus

text: Illumina MiSeq

characteristic: sequencing method

text: male

characteristic: sex

characteristic: vessel


characteristic: #sampleid

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Georgia State University

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: ACCCACCACTAG

characteristic: barcodesequence

characteristic: collection date

text: house mouse

characteristic: common name

text: terrestrial biome

text: animal-associated habitat

text: feces

text: USA

characteristic: geographic location (country and/or sea)

text: 33.7490�_�� N

text: 84.3880�_�� W

text: host-associated

text: mimarks-survey

text: Mus musculus

characteristic: organism

text: SHIMETransplant

text: Mus musculus

text: Illumina MiSeq

text: male

characteristic: title


characteristic: #sampleid

text: Georgia State University

text: public

text: CAGAAGGTGTGG

text: house mouse

characteristic: day

characteristic: description

characteristic: dob

characteristic: emulsifier

text: terrestrial biome

characteristic: environment (biome)

text: animal-associated habitat

characteristic: environment (feature)

text: feces

characteristic: environment (material)

characteristic: genotype

text: USA

text: 33.7490�_�� N

characteristic: geographic location (latitude)

text: 84.3880�_�� W

characteristic: geographic location (longitude)

text: host-associated

characteristic: host-associated environmental package

text: mimarks-survey

characteristic: investigation type

text: Mus musculus

text: SHIMETransplant

characteristic: project name

text: Mus musculus

text: Illumina MiSeq

characteristic: sequencing method

text: male

characteristic: sex

characteristic: vessel


characteristic: #sampleid

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Georgia State University

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: GAAGCTTGAATC

characteristic: barcodesequence

characteristic: collection date

text: house mouse

characteristic: common name

text: terrestrial biome

text: animal-associated habitat

text: feces

text: USA

characteristic: geographic location (country and/or sea)

text: 33.7490�_�� N

text: 84.3880�_�� W

text: host-associated

text: mimarks-survey

text: Mus musculus

characteristic: organism

text: SHIMETransplant

text: Mus musculus

text: Illumina MiSeq

text: male

characteristic: title


characteristic: #sampleid

text: Georgia State University

text: public

text: ACTAGGATCAGT

text: house mouse

characteristic: day

characteristic: description

characteristic: dob

text: CMC

characteristic: emulsifier

text: terrestrial biome

characteristic: environment (biome)

text: animal-associated habitat

characteristic: environment (feature)

text: feces

characteristic: environment (material)

characteristic: genotype

text: USA

text: 33.7490�_�� N

characteristic: geographic location (latitude)

text: 84.3880�_�� W

characteristic: geographic location (longitude)

text: host-associated

characteristic: host-associated environmental package

text: mimarks-survey

characteristic: investigation type

text: Mus musculus

text: SHIMETransplant

characteristic: project name

text: Mus musculus

text: Illumina MiSeq

characteristic: sequencing method

text: male

characteristic: sex

characteristic: vessel


characteristic: #sampleid

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Georgia State University

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: GCTCCTTAGAAG

characteristic: barcodesequence

characteristic: collection date

text: house mouse

characteristic: common name

text: CMC

text: terrestrial biome

text: animal-associated habitat

text: feces

text: USA

characteristic: geographic location (country and/or sea)

text: 33.7490�_�� N

text: 84.3880�_�� W

text: host-associated

text: mimarks-survey

text: Mus musculus

characteristic: organism

text: SHIMETransplant

text: Mus musculus

text: Illumina MiSeq

text: male

characteristic: title


characteristic: #sampleid

text: Georgia State University

text: public

text: TCCCATTCCCAT

text: house mouse

characteristic: day

characteristic: description

characteristic: dob

text: CMC

characteristic: emulsifier

text: terrestrial biome

characteristic: environment (biome)

text: animal-associated habitat

characteristic: environment (feature)

text: feces

characteristic: environment (material)

characteristic: genotype

text: USA

text: 33.7490�_�� N

characteristic: geographic location (latitude)

text: 84.3880�_�� W

characteristic: geographic location (longitude)

text: host-associated

characteristic: host-associated environmental package

text: mimarks-survey

characteristic: investigation type

text: Mus musculus

text: SHIMETransplant

characteristic: project name

text: Mus musculus

text: Illumina MiSeq

characteristic: sequencing method

text: male

characteristic: sex

characteristic: vessel


characteristic: #sampleid

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Georgia State University

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: TGGCGTCATTCG

characteristic: barcodesequence

characteristic: collection date

text: house mouse

characteristic: common name

text: CMC

text: terrestrial biome

text: animal-associated habitat

text: feces

text: USA

characteristic: geographic location (country and/or sea)

text: 33.7490�_�� N

text: 84.3880�_�� W

text: host-associated

text: mimarks-survey

text: Mus musculus

characteristic: organism

text: SHIMETransplant

text: Mus musculus

text: Illumina MiSeq

text: male

characteristic: title


characteristic: #sampleid

text: Georgia State University

text: public

text: AATCCTCGGAGT

text: house mouse

characteristic: day

characteristic: description

characteristic: dob

text: CMC

characteristic: emulsifier

text: terrestrial biome

characteristic: environment (biome)

text: animal-associated habitat

characteristic: environment (feature)

text: feces

characteristic: environment (material)

characteristic: genotype

text: USA

text: 33.7490�_�� N

characteristic: geographic location (latitude)

text: 84.3880�_�� W

characteristic: geographic location (longitude)

text: host-associated

characteristic: host-associated environmental package

text: mimarks-survey

characteristic: investigation type

text: Mus musculus

text: SHIMETransplant

characteristic: project name

text: Mus musculus

text: Illumina MiSeq

characteristic: sequencing method

text: male

characteristic: sex

characteristic: vessel


characteristic: #sampleid

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Georgia State University

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: CTGGACGCATTA

characteristic: barcodesequence

characteristic: collection date

text: house mouse

characteristic: common name

text: Water

text: terrestrial biome

text: animal-associated habitat

text: feces

text: USA

characteristic: geographic location (country and/or sea)

text: 33.7490�_�� N

text: 84.3880�_�� W

text: host-associated

text: mimarks-survey

text: Mus musculus

characteristic: organism

text: SHIMETransplant

text: Mus musculus

text: Illumina MiSeq

text: male

characteristic: title


characteristic: #sampleid

text: Georgia State University

text: public

text: ACCGATTAGGTA

text: house mouse

characteristic: day

characteristic: description

characteristic: dob

text: Water

characteristic: emulsifier

text: terrestrial biome

characteristic: environment (biome)

text: animal-associated habitat

characteristic: environment (feature)

text: feces

characteristic: environment (material)

characteristic: genotype

text: USA

text: 33.7490�_�� N

characteristic: geographic location (latitude)

text: 84.3880�_�� W

characteristic: geographic location (longitude)

text: host-associated

characteristic: host-associated environmental package

text: mimarks-survey

characteristic: investigation type

text: Mus musculus

text: SHIMETransplant

characteristic: project name

text: Mus musculus

text: Illumina MiSeq

characteristic: sequencing method

text: male

characteristic: sex

characteristic: vessel


characteristic: #sampleid

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Georgia State University

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: ATGTGCTGCTCG

characteristic: barcodesequence

characteristic: collection date

text: house mouse

characteristic: common name

text: Water

text: terrestrial biome

text: animal-associated habitat

text: feces

text: USA

characteristic: geographic location (country and/or sea)

text: 33.7490�_�� N

text: 84.3880�_�� W

text: host-associated

text: mimarks-survey

text: Mus musculus

characteristic: organism

text: SHIMETransplant

text: Mus musculus

text: Illumina MiSeq

text: male

characteristic: title


characteristic: #sampleid

text: Georgia State University

text: public

text: TACGTACGAAAC

text: house mouse

characteristic: day

characteristic: description

characteristic: dob

text: Water

characteristic: emulsifier

text: terrestrial biome

characteristic: environment (biome)

text: animal-associated habitat

characteristic: environment (feature)

text: feces

characteristic: environment (material)

characteristic: genotype

text: USA

text: 33.7490�_�� N

characteristic: geographic location (latitude)

text: 84.3880�_�� W

characteristic: geographic location (longitude)

text: host-associated

characteristic: host-associated environmental package

text: mimarks-survey

characteristic: investigation type

text: Mus musculus

text: SHIMETransplant

characteristic: project name

text: Mus musculus

text: Illumina MiSeq

characteristic: sequencing method

text: male

characteristic: sex

characteristic: vessel


characteristic: #sampleid

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Georgia State University

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: ATCACATTCTCC

characteristic: barcodesequence

characteristic: collection date

text: house mouse

characteristic: common name

text: Water

text: terrestrial biome

text: animal-associated habitat

text: feces

text: USA

characteristic: geographic location (country and/or sea)

text: 33.7490�_�� N

text: 84.3880�_�� W

text: host-associated

text: mimarks-survey

text: Mus musculus

characteristic: organism

text: SHIMETransplant

text: Mus musculus

text: Illumina MiSeq

text: male

characteristic: title


characteristic: #sampleid

text: Georgia State University

text: public

text: AGCCTGGTACCT

text: house mouse

characteristic: day

characteristic: description

characteristic: dob

characteristic: emulsifier

text: terrestrial biome

characteristic: environment (biome)

text: animal-associated habitat

characteristic: environment (feature)

text: feces

characteristic: environment (material)

characteristic: genotype

text: USA

text: 33.7490�_�� N

characteristic: geographic location (latitude)

text: 84.3880�_�� W

characteristic: geographic location (longitude)

text: host-associated

characteristic: host-associated environmental package

text: mimarks-survey

characteristic: investigation type

text: Mus musculus

text: SHIMETransplant

characteristic: project name

text: Mus musculus

text: Illumina MiSeq

characteristic: sequencing method

text: male

characteristic: sex

characteristic: vessel


characteristic: #sampleid

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Georgia State University

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: GCTAAAGTCGTA

characteristic: barcodesequence

characteristic: collection date

text: house mouse

characteristic: common name

text: terrestrial biome

text: animal-associated habitat

text: feces

text: USA

characteristic: geographic location (country and/or sea)

text: 33.7490�_�� N

text: 84.3880�_�� W

text: host-associated

text: mimarks-survey

text: Mus musculus

characteristic: organism

text: SHIMETransplant

text: Mus musculus

text: Illumina MiSeq

text: male

characteristic: title


characteristic: #sampleid

text: Georgia State University

text: public

text: TCTCAGCGCGTA

text: house mouse

characteristic: day

characteristic: description

characteristic: dob

characteristic: emulsifier

text: terrestrial biome

characteristic: environment (biome)

text: animal-associated habitat

characteristic: environment (feature)

text: feces

characteristic: environment (material)

characteristic: genotype

text: USA

text: 33.7490�_�� N

characteristic: geographic location (latitude)

text: 84.3880�_�� W

characteristic: geographic location (longitude)

text: host-associated

characteristic: host-associated environmental package

text: mimarks-survey

characteristic: investigation type

text: Mus musculus

text: SHIMETransplant

characteristic: project name

text: Mus musculus

text: Illumina MiSeq

characteristic: sequencing method

text: male

characteristic: sex

characteristic: vessel


characteristic: #sampleid

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Georgia State University

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: GGACGTTAACTA

characteristic: barcodesequence

characteristic: collection date

text: house mouse

characteristic: common name

text: terrestrial biome

text: animal-associated habitat

text: feces

text: USA

characteristic: geographic location (country and/or sea)

text: 33.7490�_�� N

text: 84.3880�_�� W

text: host-associated

text: mimarks-survey

text: Mus musculus

characteristic: organism

text: SHIMETransplant

text: Mus musculus

text: Illumina MiSeq

text: male

characteristic: title


characteristic: #sampleid

text: Georgia State University

text: public

text: TATTCAGCGGAC

text: house mouse

characteristic: day

characteristic: description

characteristic: dob

characteristic: emulsifier

text: terrestrial biome

characteristic: environment (biome)

text: animal-associated habitat

characteristic: environment (feature)

text: feces

characteristic: environment (material)

characteristic: genotype

text: USA

text: 33.7490�_�� N

characteristic: geographic location (latitude)

text: 84.3880�_�� W

characteristic: geographic location (longitude)

text: host-associated

characteristic: host-associated environmental package

text: mimarks-survey

characteristic: investigation type

text: Mus musculus

text: SHIMETransplant

characteristic: project name

text: Mus musculus

text: Illumina MiSeq

characteristic: sequencing method

text: male

characteristic: sex

characteristic: vessel


characteristic: #sampleid

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Georgia State University

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: GTTCCGGATTAG

characteristic: barcodesequence

characteristic: collection date

text: house mouse

characteristic: common name

text: CMC

text: terrestrial biome

text: animal-associated habitat

text: feces

text: USA

characteristic: geographic location (country and/or sea)

text: 33.7490�_�� N

text: 84.3880�_�� W

text: host-associated

text: mimarks-survey

text: Mus musculus

characteristic: organism

text: SHIMETransplant

text: Mus musculus

text: Illumina MiSeq

text: male

characteristic: title


characteristic: #sampleid

text: Georgia State University

text: public

text: GCGTGTAATTAG

text: house mouse

characteristic: day

characteristic: description

characteristic: dob

text: CMC

characteristic: emulsifier

text: terrestrial biome

characteristic: environment (biome)

text: animal-associated habitat

characteristic: environment (feature)

text: feces

characteristic: environment (material)

characteristic: genotype

text: USA

text: 33.7490�_�� N

characteristic: geographic location (latitude)

text: 84.3880�_�� W

characteristic: geographic location (longitude)

text: host-associated

characteristic: host-associated environmental package

text: mimarks-survey

characteristic: investigation type

text: Mus musculus

text: SHIMETransplant

characteristic: project name

text: Mus musculus

text: Illumina MiSeq

characteristic: sequencing method

text: male

characteristic: sex

characteristic: vessel


characteristic: #sampleid

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Georgia State University

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: TAGCAGTTGCGT

characteristic: barcodesequence

characteristic: collection date

text: house mouse

characteristic: common name

text: CMC

text: terrestrial biome

text: animal-associated habitat

text: feces

text: USA

characteristic: geographic location (country and/or sea)

text: 33.7490�_�� N

text: 84.3880�_�� W

text: host-associated

text: mimarks-survey

text: Mus musculus

characteristic: organism

text: SHIMETransplant

text: Mus musculus

text: Illumina MiSeq

text: male

characteristic: title


characteristic: #sampleid

text: Georgia State University

text: public

text: CACGCTATTGGA

text: house mouse

characteristic: day

characteristic: description

characteristic: dob

text: CMC

characteristic: emulsifier

text: terrestrial biome

characteristic: environment (biome)

text: animal-associated habitat

characteristic: environment (feature)

text: feces

characteristic: environment (material)

characteristic: genotype

text: USA

text: 33.7490�_�� N

characteristic: geographic location (latitude)

text: 84.3880�_�� W

characteristic: geographic location (longitude)

text: host-associated

characteristic: host-associated environmental package

text: mimarks-survey

characteristic: investigation type

text: Mus musculus

text: SHIMETransplant

characteristic: project name

text: Mus musculus

text: Illumina MiSeq

characteristic: sequencing method

text: male

characteristic: sex

characteristic: vessel


characteristic: #sampleid

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Georgia State University

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: ACCTATGGTGAA

characteristic: barcodesequence

characteristic: collection date

text: house mouse

characteristic: common name

text: CMC

text: terrestrial biome

text: animal-associated habitat

text: feces

text: USA

characteristic: geographic location (country and/or sea)

text: 33.7490�_�� N

text: 84.3880�_�� W

text: host-associated

text: mimarks-survey

text: Mus musculus

characteristic: organism

text: SHIMETransplant

text: Mus musculus

text: Illumina MiSeq

text: male

characteristic: title


text: CEBITEC

text: public

text: Mitoplasmid of Pichia pastoris JPS664

characteristic: description

text: Fermenter

characteristic: environment (biome)

text: Fermenter

characteristic: environment (feature)

text: Fermenter

characteristic: environment (material)

text: Germany

characteristic: geographic location (depth)

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: mimarks-survey

characteristic: investigation type

text: Komagataella pastoris

characteristic: project name

text: Komagataella pastoris

text: Illumina MiSeq

characteristic: sequencing method

text: soil

characteristic: soil environmental package

text: Mitoplasmid of Pichia pastoris JPS664


E-MTAB-5383:Sample 1

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Sun Yat-sen University, China

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-5383:Sample 1

tag: Namespace:Sun Yat-sen University, China

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: human

text: Protocols: RNA substrates were made by in vitro transcription using SP6 or T7 RNA polymerase and DNA templates ,and biotinylated at 3’ end using a biotinylation Kit. Biotinylated RNAs were first bound to the streptavidin beads, and then incubated with Hela NE in the polyadenylation condition for 20 minutes, after biotin-streptavidine binding, washing, pull-down sample were heated in 1XSSC buffer for elution, as suggested by the manual of the Dynalbeads M280. The eluted samples were further subject to RNA purification for RNA-seq. Strand-specific RNA-seq libraries were prepared following the described protocol (Hunt, A. G, 2015) with the RNA-biotin based pull-down sample, and single-end squenceing (SE50) was carried out in Illumina Genome Analyzer II platform.

text: wild type genotype

characteristic: genotype

text: Homo sapiens

text: Homo sapiens

text: SV40 late pre-mRNA

characteristic: polyA site RNA substrate

text: Homo sapiens

text: Sample 1


E-MTAB-5383:Sample 2

text: Sun Yat-sen University, China

text: public

text: E-MTAB-5383:Sample 2

text: ArrayExpress

text: human

characteristic: common name

characteristic: description

text: U to C mutation in conserved cis-element AAUAAA

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: SV40 late pre-mRNA

text: Homo sapiens

text: Sample 2

characteristic: title