text: Not applicable

characteristic: ArrayExpress-PHENOTYPE

text: male

characteristic: ArrayExpress-SEX

text: Human

characteristic: ArrayExpress-SPECIES

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Male

characteristic: GENDER

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: Not applicable

characteristic: PHENOTYPE

text: human

characteristic: common name

text: Homo sapiens

text: Homo sapiens


status: PUBLIC

tag: attribute

text: UTRECHT UNIVERSITY

text: public

characteristic: INSDC status

characteristic: SRA accession

tag: Namespace:UTRECHT UNIVERSITY

characteristic: Submitter Id

text: Nanopore sequencing of 16S06614-1

characteristic: description

text: Netherlands

characteristic: geographic location (country and/or sea)

text: human

text: Staphylococcus pseudintermedius

characteristic: organism

text: Staphylococcus pseudintermedius

text: Nanopore sequencing of 16S06614-1

characteristic: title


characteristic: ENA-CHECKLIST

text: UTRECHT UNIVERSITY

text: public

text: Nanopore sequencing of 16S06620-1

text: Netherlands

text: human

text: Staphylococcus pseudintermedius

text: Staphylococcus pseudintermedius

text: Nanopore sequencing of 16S06620-1


characteristic: ENA-FIRST-PUBLIC

text: UTRECHT UNIVERSITY

text: public

text: Nanopore sequencing of 17S01301-1

text: Netherlands

text: dog

text: Staphylococcus pseudintermedius

text: Staphylococcus pseudintermedius

text: Nanopore sequencing of 17S01301-1


characteristic: ENA-LAST-UPDATE

text: UTRECHT UNIVERSITY

text: public

text: Nanopore sequencing of 17S01307-1

text: Netherlands

text: dog

text: Staphylococcus pseudintermedius

text: Staphylococcus pseudintermedius

text: Nanopore sequencing of 17S01307-1


characteristic: External Id

text: UTRECHT UNIVERSITY

text: public

text: Nanopore sequencing of 17S01333-1

text: Netherlands

text: dog

text: Staphylococcus pseudintermedius

text: Staphylococcus pseudintermedius

text: Nanopore sequencing of 17S01333-1


text: UTRECHT UNIVERSITY

text: public

text: Nanopore sequencing of 18S02729-1

text: Netherlands

text: dog

text: Staphylococcus pseudintermedius

text: Staphylococcus pseudintermedius

text: Nanopore sequencing of 18S02729-1


text: UTRECHT UNIVERSITY

text: public

text: Nanopore sequencing of 18S02731-1

text: Netherlands

text: dog

text: Staphylococcus pseudintermedius

text: Staphylococcus pseudintermedius

text: Nanopore sequencing of 18S02731-1


text: UTRECHT UNIVERSITY

text: public

text: Nanopore sequencing of 18S02741-1

text: Netherlands

text: dog

text: Staphylococcus pseudintermedius

text: Staphylococcus pseudintermedius

text: Nanopore sequencing of 18S02741-1


text: UTRECHT UNIVERSITY

text: public

text: Nanopore sequencing of 18S02748-1

text: Netherlands

text: dog

text: Staphylococcus pseudintermedius

text: Staphylococcus pseudintermedius

text: Nanopore sequencing of 18S02748-1


text: UTRECHT UNIVERSITY

text: public

text: Nanopore sequencing of 18S02749-1

text: Netherlands

text: dog

text: Staphylococcus pseudintermedius

text: Staphylococcus pseudintermedius

text: Nanopore sequencing of 18S02749-1


text: UTRECHT UNIVERSITY

text: public

text: Nanopore sequencing of 18S02750-1

text: Netherlands

text: dog

text: Staphylococcus pseudintermedius

text: Staphylococcus pseudintermedius

text: Nanopore sequencing of 18S02750-1


text: UTRECHT UNIVERSITY

text: public

text: Nanopore sequencing of 18S02761-1

text: Netherlands

text: dog

text: Staphylococcus pseudintermedius

text: Staphylococcus pseudintermedius

text: Nanopore sequencing of 18S02761-1


text: UTRECHT UNIVERSITY

text: public

text: Nanopore sequencing of 18S02769-1

text: Netherlands

text: dog

text: Staphylococcus pseudintermedius

text: Staphylococcus pseudintermedius

text: Nanopore sequencing of 18S02769-1


text: UTRECHT UNIVERSITY

text: public

text: Nanopore sequencing of 18S02770-1

text: Netherlands

text: dog

text: Staphylococcus pseudintermedius

text: Staphylococcus pseudintermedius

text: Nanopore sequencing of 18S02770-1


text: UTRECHT UNIVERSITY

text: public

text: Nanopore sequencing of 18S02816-1

text: Netherlands

text: dog

text: Staphylococcus pseudintermedius

text: Staphylococcus pseudintermedius

text: Nanopore sequencing of 18S02816-1


text: UTRECHT UNIVERSITY

text: public

text: Nanopore sequencing of 18S02820-1

text: Netherlands

text: dog

text: Staphylococcus pseudintermedius

text: Staphylococcus pseudintermedius

text: Nanopore sequencing of 18S02820-1


text: UTRECHT UNIVERSITY

text: public

text: Nanopore sequencing of 18S02828-1

text: Netherlands

text: dog

text: Staphylococcus pseudintermedius

text: Staphylococcus pseudintermedius

text: Nanopore sequencing of 18S02828-1


text: UTRECHT UNIVERSITY

text: public

text: Nanopore sequencing of 18S02839-1

text: Netherlands

text: dog

text: Staphylococcus pseudintermedius

text: Staphylococcus pseudintermedius

text: Nanopore sequencing of 18S02839-1


text: UTRECHT UNIVERSITY

text: public

text: Nanopore sequencing of 18S03459-1

text: Netherlands

text: dog

text: Staphylococcus pseudintermedius

text: Staphylococcus pseudintermedius

text: Nanopore sequencing of 18S03459-1


text: UTRECHT UNIVERSITY

text: public

text: Nanopore sequencing of 18S03480-1

text: Netherlands

text: dog

text: Staphylococcus pseudintermedius

text: Staphylococcus pseudintermedius

text: Nanopore sequencing of 18S03480-1


text: UTRECHT UNIVERSITY

text: public

text: Nanopore sequencing of 208082803802-1

text: Netherlands

text: dog

text: Staphylococcus pseudintermedius

text: Staphylococcus pseudintermedius

text: Nanopore sequencing of 208082803802-1


text: UTRECHT UNIVERSITY

text: public

text: Nanopore sequencing of 208090903101-3

text: Netherlands

text: dog

text: Staphylococcus pseudintermedius

text: Staphylococcus pseudintermedius

text: Nanopore sequencing of 208090903101-3


text: UTRECHT UNIVERSITY

text: public

text: Nanopore sequencing of 209011300901-1

text: Netherlands

text: dog

text: Staphylococcus pseudintermedius

text: Staphylococcus pseudintermedius

text: Nanopore sequencing of 209011300901-1


text: UTRECHT UNIVERSITY

text: public

text: Nanopore sequencing of 211083101901-1

text: Netherlands

text: dog

text: Staphylococcus pseudintermedius

text: Staphylococcus pseudintermedius

text: Nanopore sequencing of 211083101901-1


text: UTRECHT UNIVERSITY

text: public

text: Nanopore sequencing of 213101701201-2

text: Netherlands

text: dog

text: Staphylococcus pseudintermedius

text: Staphylococcus pseudintermedius

text: Nanopore sequencing of 213101701201-2


E-MTAB-12856:Sample 1

text: UNIVERSITY OF MANCHESTER

text: public

text: E-MTAB-12856:Sample 1

tag: Namespace:UNIVERSITY OF MANCHESTER

text: ArrayExpress

characteristic: broker name

text: Protocols: Bacterial cells were harvested by centrifugation at 13000 x g for 3 mins. Listeria monocytogenes were grown in MD10 media consisting of 49 mM K2HPO4, 11 mM NaH2PO4, 1.7 mM MgSO4, 187 µM ferric ammonium citrate, 9.3 mM NH4Cl, 49.5 mM glucose or glycerol, 2.96 µM thiamine‐HCl, 1.33 µM riboflavin, 2.05 µM biotin, 24 µM lipoic acid, 0.1 g l−1l‐cysteine and l‐leucine, 0.2 g l−1l‐arginine, l‐histidine, l‐methionine, l‐valine and l‐isoleucine. Additionally, the medium was supplemented with 0.1 % w/v case‐amino acids. For microaerobic growth (oxygen 5 %-6 % v/v, carbon dioxide 10 % v/v and nitrogen 85 % v/v) L. monocytogenes were grown in a VAIN incubator (Du scientific) in 6 well plates (Coster®) shaking at 140 rpm respectively at 37 C. Carbon source was glucose or glycerol. RNA extraction was carried out using Invitrogen’s Purelink RNA Extraction Kit and Lysing Matrix E tubes (MP Biomedicals). Prior to starting the extraction, fresh lysozyme solution (consisting of 10 mg/ml lysozyme, 10 mM Tris-HCl pH 8.0 and 0.1 mM EDTA,) and a solution of 10% SDS (w/v) were prepared in RNAse-free water and the kit lysis buffer was supplemented with 10 μl of 2-mercaptoethanol per 1 ml of lysis buffer. Bacterial cells were harvested by centrifugation at 13000 x g for 3 mins. The supernatant was discarded and 100 μl of lysozyme solution was added to the pellet for cell resuspension. Next, 0.5 μl of SDS solution (10% v/v) and 350 μl of lysis buffer was added and vortexed sequentially. The lysate, added to a Lysing Matrix E tube, was homogenised in a rotor stator homogeniser (FastPrep FP120, 6.5 speed) for 45 secs. The tube was centrifuged for 5 mins at 2600 x g followed by transfer of the supernatant to a microcentrifuge tube (RNAse-free) and addition of 250 μl of absolute ethanol (100% v/v) to the tube. The solution mixture was vortexed to remove precipitate. The sample was then transferred to a spin cartridge and centrifuged at 12000 x g for 15 secs allowing RNA to bind to the spin column. The subsequent flow-through was discarded and 700 μl of Wash Buffer 1 was added to the column. This was then centrifuged again for 15 secs at 12000 x g, followed by discarding both the flow through and the collection tube. The column was then placed in a new collection tube. Wash Buffer 2 (500 μl) was added to the column and centrifuged at 12000 x g for 15 secs, again discarding the subsequent flow-through. The wash step was repeated with Wash Buffer 2 and flow-through was discarded again. The column was centrifuged at 12000 x g to remove any residual wash buffer. The collection tube was discarded and the column was transferred to a RNAse-free recovery tube; 50 μl of RNAse-free water was carefully added to the column membrane. RNA was eluted in this 1.5 ml tube with 1 min incubation at room followed by centrifugation at 12000 x g for 2 mins. All further experiments involving RNA were performed on ice. The Nanodrop spectrophotometer (ND-1000) was used for RNA quantification using 1 μl of the sample. Additionally, the Super RNAse Inhibitor (Invitrogen) was added to the samples at 1U/μl to inhibit RNAse activity. Illumina Stranded Total RNA Prep, Ligation with Ribo-Zero Plus. In addition, Illumina ran Listeria monocytogenes fasta files through their in house in-silico analysis program which predicted we would need some additional probes to efficiently deplete the rRNA from this species. These were purchased from from Integrated DNA Technologies, Inc.(https://eu.idtdna.com/) and added during the probe hybridization step.

text: aerobic

characteristic: environmental stress

text: wild type genotype

characteristic: genotype

text: Listeria monocytogenes

text: Listeria monocytogenes

text: whole organism

characteristic: organism part

text: Listeria monocytogenes

text: EGD-e

characteristic: strain

text: Sample 1


E-MTAB-12856:Sample 2

text: UNIVERSITY OF MANCHESTER

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-12856:Sample 2

text: ArrayExpress

text: aerobic

text: wild type genotype

text: Listeria monocytogenes

text: Listeria monocytogenes

text: whole organism

text: Listeria monocytogenes

text: EGD-e

text: Sample 2


E-MTAB-12856:Sample 3

text: UNIVERSITY OF MANCHESTER

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-12856:Sample 3

characteristic: Submitter Id

text: ArrayExpress

text: microaerobic

text: wild type genotype

text: Listeria monocytogenes

text: Listeria monocytogenes

text: whole organism

text: Listeria monocytogenes

text: EGD-e

text: Sample 3


E-MTAB-12856:Sample 4

text: UNIVERSITY OF MANCHESTER

text: public

text: E-MTAB-12856:Sample 4

text: ArrayExpress

characteristic: description

text: microaerobic

text: wild type genotype

text: Listeria monocytogenes

characteristic: organism

text: Listeria monocytogenes

text: whole organism

text: Listeria monocytogenes

text: EGD-e

text: Sample 4


E-MTAB-12856:Sample 5

characteristic: ENA-CHECKLIST

text: UNIVERSITY OF MANCHESTER

text: public

text: E-MTAB-12856:Sample 5

text: ArrayExpress

text: aerobic

text: wild type genotype

text: Listeria monocytogenes

text: Listeria monocytogenes

text: whole organism

text: Listeria monocytogenes

text: EGD-e

text: Sample 5

characteristic: title


E-MTAB-12856:Sample 6

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: UNIVERSITY OF MANCHESTER

text: public

text: E-MTAB-12856:Sample 6

text: ArrayExpress

text: aerobic

text: wild type genotype

text: Listeria monocytogenes

text: Listeria monocytogenes

text: whole organism

text: Listeria monocytogenes

text: EGD-e

text: Sample 6


E-MTAB-12856:Sample 7

characteristic: External Id

text: UNIVERSITY OF MANCHESTER

text: public

text: E-MTAB-12856:Sample 7

text: ArrayExpress

characteristic: broker name

text: microaerobic

text: wild type genotype

text: Listeria monocytogenes

text: Listeria monocytogenes

text: whole organism

text: Listeria monocytogenes

text: EGD-e

text: Sample 7


E-MTAB-12856:Sample 8

text: UNIVERSITY OF MANCHESTER

text: public

text: E-MTAB-12856:Sample 8

text: ArrayExpress

text: microaerobic

characteristic: environmental stress

text: wild type genotype

characteristic: genotype

text: Listeria monocytogenes

text: Listeria monocytogenes

text: whole organism

text: Listeria monocytogenes

text: EGD-e

text: Sample 8


E-MTAB-12913:Sample 1

text: UNIVERSITY OF MANCHESTER

text: public

text: E-MTAB-12913:Sample 1

unit: week

characteristic: age

text: ArrayExpress

text: Shandong wt

characteristic: cultivar

text: Protocols: Total RNA of E. salsugineum leaves were extracted from plants subjected to high light stress (HL, 800 μmol m−2 s−1) at days 0, 3, 5 and 10 (n = 3) Seeds of Eutrema salsugineum (Shandong wt) were stratified at 4 °C for 2 d, and then germinated in a controlled-environment cabinet (E. J. Stiell) in an 8-h photoperiod (100 μmol m−2 s−1 provided by led tubes) at 22 °C/18 °C (day/night). 6-week-old Eutrema plants were used for the high light acclimation experiments. High light treatment was performed by placing the plants at 800 μmol m−2 s−1, in an 8-h photoperiod at 22 °C/18 °C (day/night). Total RNA of E. salsugineum leaves were extracted from plants subjected to high light stress (HL, 800 μmol m−2 s−1) at days 0, 3, 5 and 10 (n = 3), following the manufacturer's instructions of the Plant Spectrum Total RNA Kit (Sigma, MO, USA). Plant Spectrum Total RNA Kit (Sigma, MO, USA) Illumina stranded RNA kit

text: adult

characteristic: developmental stage

text: wild type genotype

text: Eutrema salsugineum

text: Eutrema salsugineum

text: leaf

characteristic: organism part

text: Eutrema salsugineum

text: Sample 1


E-MTAB-12913:Sample 10

text: UNIVERSITY OF MANCHESTER

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-12913:Sample 10

text: ArrayExpress

text: Shandong wt

text: adult

text: wild type genotype

text: Eutrema salsugineum

text: Eutrema salsugineum

text: leaf

text: Eutrema salsugineum

text: Sample 10


E-MTAB-12913:Sample 11

text: UNIVERSITY OF MANCHESTER

text: public

characteristic: SRA accession

text: E-MTAB-12913:Sample 11

characteristic: Submitter Id

text: ArrayExpress

text: Shandong wt

characteristic: description

text: adult

text: wild type genotype

text: Eutrema salsugineum

characteristic: organism

text: Eutrema salsugineum

text: leaf

text: Eutrema salsugineum

text: Sample 11


E-MTAB-12913:Sample 12

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: UNIVERSITY OF MANCHESTER

text: public

text: E-MTAB-12913:Sample 12

text: ArrayExpress

text: Shandong wt

text: adult

text: wild type genotype

text: Eutrema salsugineum

text: Eutrema salsugineum

text: leaf

text: Eutrema salsugineum

text: Sample 12

characteristic: title


E-MTAB-12913:Sample 2

characteristic: External Id

text: UNIVERSITY OF MANCHESTER

text: public

text: E-MTAB-12913:Sample 2

text: ArrayExpress

characteristic: broker name

text: Shandong wt

text: adult

text: wild type genotype

characteristic: genotype

text: Eutrema salsugineum

text: Eutrema salsugineum

text: leaf

text: Eutrema salsugineum

text: Sample 2


E-MTAB-12913:Sample 3

text: UNIVERSITY OF MANCHESTER

text: public

text: E-MTAB-12913:Sample 3

characteristic: age

text: ArrayExpress

text: Shandong wt

characteristic: cultivar

text: adult

characteristic: developmental stage

text: wild type genotype

text: Eutrema salsugineum

text: Eutrema salsugineum

text: leaf

text: Eutrema salsugineum

text: Sample 3


E-MTAB-12913:Sample 4

text: UNIVERSITY OF MANCHESTER

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-12913:Sample 4

text: ArrayExpress

text: Shandong wt

text: adult

text: wild type genotype

text: Eutrema salsugineum

text: Eutrema salsugineum

text: leaf

characteristic: organism part

text: Eutrema salsugineum

text: Sample 4


E-MTAB-12913:Sample 5

text: UNIVERSITY OF MANCHESTER

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-12913:Sample 5

text: ArrayExpress

text: Shandong wt

text: adult

text: wild type genotype

text: Eutrema salsugineum

text: Eutrema salsugineum

text: leaf

text: Eutrema salsugineum

text: Sample 5


E-MTAB-12913:Sample 6

text: UNIVERSITY OF MANCHESTER

text: public

text: E-MTAB-12913:Sample 6

characteristic: Submitter Id

text: ArrayExpress

text: Shandong wt

characteristic: description

text: adult

text: wild type genotype

text: Eutrema salsugineum

characteristic: organism

text: Eutrema salsugineum

text: leaf

text: Eutrema salsugineum

text: Sample 6


E-MTAB-12913:Sample 7

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: UNIVERSITY OF MANCHESTER

text: public

text: E-MTAB-12913:Sample 7

text: ArrayExpress

text: Shandong wt

text: adult

text: wild type genotype

text: Eutrema salsugineum

text: Eutrema salsugineum

text: leaf

text: Eutrema salsugineum

text: Sample 7


E-MTAB-12913:Sample 8

characteristic: External Id

text: UNIVERSITY OF MANCHESTER

text: public

text: E-MTAB-12913:Sample 8

text: ArrayExpress

characteristic: broker name

text: Shandong wt

text: adult

text: wild type genotype

text: Eutrema salsugineum

text: Eutrema salsugineum

text: leaf

text: Eutrema salsugineum

text: Sample 8

characteristic: title


E-MTAB-12913:Sample 9

text: UNIVERSITY OF MANCHESTER

text: public

text: E-MTAB-12913:Sample 9

characteristic: age

text: ArrayExpress

text: Shandong wt

characteristic: cultivar

text: adult

text: wild type genotype

characteristic: genotype

text: Eutrema salsugineum

text: Eutrema salsugineum

text: leaf

text: Eutrema salsugineum

text: Sample 9


text: GEOMAR Helmholtz Centre for Ocean

characteristic: INSDC center name

characteristic: INSDC first public

text: public

tag: Namespace:GEOMAR Helmholtz Centre for Ocean

characteristic: collection date

text: Dysidea avara incubated with symbiont

text: Mediterranean Sea

characteristic: geographic location (country and/or sea)

text: Dysidea avara

text: Dysidea avara

text: Dysidea avara incubated with bacteria


text: GEOMAR Helmholtz Centre for Ocean

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: Dysidea avara incubated with bacterioplankton

text: Mediterranean Sea

text: Dysidea avara

text: Dysidea avara

text: Dysidea avara incubated with bacteria


text: GEOMAR Helmholtz Centre for Ocean

text: public

characteristic: Submitter Id

text: Aplysina aerophoba incubated with symbiont

characteristic: description

text: Mediterranean Sea

text: Aplysina aerophoba

characteristic: organism

text: Aplysina aerophoba

text: Aplysina aerophoba incubated with bacteria


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: GEOMAR Helmholtz Centre for Ocean

text: public

text: Aplysina aerophoba incubated with bacterioplankton

text: Mediterranean Sea

text: Aplysina aerophoba

text: Aplysina aerophoba


characteristic: External Id

text: public

tag: Namespace:Department of Earth and Environmental Sciences, LMU Muenchen

text: Target Captured Genomic Loci

text: Red Sea

characteristic: geographic location (region and locality)

text: J. van der Sprong; N.J. de Voogd

text: Chalinula aff. milnei GW4433

text: Chalinula aff. milnei GW4433

text: Sponge Body

characteristic: title


text: Department of Earth and Environmental Sciences, LMU Muenchen

text: public

text: Target Captured Genomic Loci

text: Red Sea

text: J. van der Sprong; N.J. de Voogd

text: Chalinula aff. milnei GW6134

text: Chalinula aff. milnei GW6134

text: Sponge Body


text: public

text: Target Captured Genomic Loci

text: Red Sea

text: J. van der Sprong; N.J. de Voogd

text: Callyspongia sp. GW4436

text: Callyspongia sp. GW4436

text: Sponge Body


text: public

text: Target Captured Genomic Loci

text: Red Sea

text: J. van der Sprong; N.J. de Voogd

text: Callyspongia sp. GW6059

text: Callyspongia sp. GW6059

text: Sponge Body


text: public

text: Target Captured Genomic Loci

text: Red Sea

text: J. van der Sprong; N.J. de Voogd

text: Amphimedon aff. jalae GW5936

text: Amphimedon aff. jalae GW5936

text: Sponge Body


text: public

text: Target Captured Genomic Loci

text: Red Sea

text: J. van der Sprong; N.J. de Voogd

text: Amphimedon aff. jalae GW5998

text: Amphimedon aff. jalae GW5998

text: Sponge Body


text: public

text: Target Captured Genomic Loci

text: Red Sea

text: J. van der Sprong; N.J. de Voogd

text: Petrosia aff. spheroida GW6015

text: Petrosia aff. spheroida GW6015

text: Sponge Body


text: public

text: Target Captured Genomic Loci

text: Red Sea

text: J. van der Sprong; N.J. de Voogd

text: Chalinula sp. GW3005

text: Chalinula sp. GW3005

text: Sponge Body


text: public

text: Target Captured Genomic Loci

text: Red Sea

text: J. van der Sprong; N.J. de Voogd

text: Chalinula sp. GW4226

text: Chalinula sp. GW4226

text: Sponge Body


text: public

text: Target Captured Genomic Loci

text: Red Sea

text: J. van der Sprong; N.J. de Voogd

text: Chalinula sp. GW4148

text: Chalinula sp. GW4148

text: Sponge Body


text: public

text: Target Captured Genomic Loci

text: Red Sea

text: J. van der Sprong; N.J. de Voogd

text: Chalinula sp. GW4285

text: Chalinula sp. GW4285

text: Sponge Body


text: public

text: Target Captured Genomic Loci

text: Red Sea

text: J. van der Sprong; N.J. de Voogd

text: Cladocroce sp. GW5878

text: Cladocroce sp. GW5878

text: Sponge Body


text: public

text: Target Captured Genomic Loci

text: Red Sea

text: J. van der Sprong; N.J. de Voogd

text: Haliclona sp. GW3018

text: Haliclona sp. GW3018

text: Sponge Body


text: public

text: Target Captured Genomic Loci

text: Red Sea

text: J. van der Sprong; N.J. de Voogd

text: Haliclona sp. GW3108

text: Haliclona sp. GW3108

text: Sponge Body


text: public

text: Target Captured Genomic Loci

text: Red Sea

text: J. van der Sprong; N.J. de Voogd

text: Amphimedon sp. GW5894

text: Amphimedon sp. GW5894

text: Sponge Body


text: public

text: Target Captured Genomic Loci

text: Red Sea

text: J. van der Sprong; N.J. de Voogd

text: Neopetrosia sp. GW3257

text: Neopetrosia sp. GW3257

text: Sponge Body


text: public

text: Target Captured Genomic Loci

text: Red Sea

text: J. van der Sprong; N.J. de Voogd

text: Arenosclera arabica

text: Arenosclera arabica

text: Sponge Body


text: public

text: Target Captured Genomic Loci

text: Red Sea

text: J. van der Sprong; N.J. de Voogd

text: Amphimedon dinae

text: Amphimedon dinae

text: Sponge Body


text: public

tag: Namespace:Botnar Research Centre Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences University of Oxford

unit: year

characteristic: age

text: ArrayExpress

characteristic: broker name

text: mononuclear cell

text: human

characteristic: common name

text: Protocols: 1M PBMC were cultured in 200 μl medium in non-tissue culture treated 96-well round bottom plates (Corning) and left unstimulated or treated with 200 ng/ml LPS (Enzo Bioscience) or anti-CD2/CD3/CD28-coated T-cell activation/expansion beads (Miltenyi Biotec) for 16 h before being prepared for sequencing. After cell culture, cells were harvested and washed in PBS with 0.1% BSA. 20,000 cells from each condition were put into a channel of Chromium Next GEM Chip K of 10x Genomics platform. 10x 5' v2 10x 5' v2

text: adult

characteristic: developmental stage

text: ankylosing spondylitis

characteristic: disease

text: wild type genotype

characteristic: genotype

characteristic: individual

text: Homo sapiens

text: Homo sapiens

text: blood

characteristic: organism part

text: Homo sapiens

text: female

characteristic: sex


text: Botnar Research Centre Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences University of Oxford

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: mononuclear cell

text: human

characteristic: description

text: adult

text: ankylosing spondylitis

text: wild type genotype

text: Homo sapiens

text: Homo sapiens

text: blood

text: Homo sapiens

text: female


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: ArrayExpress

text: mononuclear cell

text: human

text: adult

text: ankylosing spondylitis

text: wild type genotype

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: blood

text: Homo sapiens

text: male

characteristic: title


E-MTAB-12924:Sample 9

text: public

text: E-MTAB-12924:Sample 9

tag: Namespace:Laboratory of Stem Cell Biology and Pharmacology of Neurodegenerative Diseases Department of Biosciences University of Milan and Istituto Nazionale di Genetica Molecolare

text: ArrayExpress

characteristic: broker name

text: neuronal stem cell

text: human

characteristic: common name

text: Protocols: Additional protocol information can be found in the Addtional Files. The organoids were transferred in a dish to cut away the excess of Matrigel with a blade and then were processed by dissociation using Papain Dissociation System with DNase (Worthington, LK003150) following the manufacturer’s recommendations. The incubation time was adjusted, based on size, at 20 min in the orbital shaker at 37°C. Then the samples were centrifugate for 1min at 1000 rpm and resuspended in DMEM+Neurobasal containing N2 supplement (1:100, Gibco), B27 supplement (1:50, Gibco), and Rock Inhibitor Y-27632 (10µM, provided by CHDI Foundation, CHDI-00197406-0001-007). For the dissociation into single cell suspension, the samples were pipetted up and down first with 1000µl pipettes and following with glass pipettes of increasingly smaller tip diameter (fire-polished). The suspension was filtered with disposable filter of 20µm (Celltrics sysmex, 04-004-2325). The cells were counted with Countess Automated Cell Counter to check viability (higher than 90%) and concentration. The suspension was centrifugated for 1 min at 1000 rpm and resuspended at the concentration of 1x104 cells /µl in PBS containing 0.04% weight/volume BSA (Ambion, AM2616, 400 µg/ml). The Chromium Single Cell 3′ Library & Gel Bead Kit v2 (PN- 120237), Chromium Single Cell 3′ Chip kit v2 (PN-120236) and Chromium i7 Multiplex Kit (PN-120262) were used according to the manufacturer’s instructions in the Chromium Single Cell 3′ Reagents Kits V2 User Guide The Chromium Single Cell 3′ Library & Gel Bead Kit v2 (PN- 120237), Chromium Single Cell 3′ Chip kit v2 (PN-120236) and Chromium i7 Multiplex Kit (PN-120262) were used according to the manufacturer’s instructions in the Chromium Single Cell 3′ Reagents Kits V2 User Guide

text: normal

characteristic: disease

text: wild type genotype

characteristic: genotype

text: brain organoid single culture

characteristic: growth condition

text: Homo sapiens

text: Homo sapiens

text: inner cell mass

text: embryonic stem cell

characteristic: progenitor cell type

text: Homo sapiens

text: Sample 9


E-MTAB-12924:Sample 10

text: Laboratory of Stem Cell Biology and Pharmacology of Neurodegenerative Diseases Department of Biosciences University of Milan and Istituto Nazionale di Genetica Molecolare

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-12924:Sample 10

text: ArrayExpress

text: neuronal stem cell

text: human

text: normal

text: wild type genotype

text: brain organoid single culture

text: Homo sapiens

text: Homo sapiens

text: inner cell mass

characteristic: organism part

text: embryonic stem cell

text: Homo sapiens

text: Sample 10


E-MTAB-12924:Sample 11

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-12924:Sample 11

characteristic: Submitter Id

text: ArrayExpress

text: neuronal stem cell

text: human

characteristic: description

text: normal

text: wild type genotype

text: brain organoid single culture

text: Homo sapiens

text: Homo sapiens

text: inner cell mass

text: embryonic stem cell

text: Homo sapiens

text: Sample 11


E-MTAB-12924:Sample 12

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: E-MTAB-12924:Sample 12

text: ArrayExpress

text: neuronal stem cell

text: human

text: Huntington disease

text: CRISPR/Cas9 modification of HD

text: brain organoid single culture

text: Homo sapiens

text: Homo sapiens

text: inner cell mass

text: embryonic stem cell

text: Homo sapiens

text: Sample 12


E-MTAB-12924:Sample 13

text: public

text: E-MTAB-12924:Sample 13

text: ArrayExpress

characteristic: broker name

text: neuronal stem cell

text: human

characteristic: common name

text: Huntington disease

text: CRISPR/Cas9 modification of HD

text: brain organoid single culture

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: inner cell mass

text: embryonic stem cell

text: Homo sapiens

text: Sample 13

characteristic: title


E-MTAB-12924:Sample 14

text: public

text: E-MTAB-12924:Sample 14

text: ArrayExpress

text: neuronal stem cell

text: human

text: Huntington disease

characteristic: disease

text: CRISPR/Cas9 modification of HD

characteristic: genotype

text: brain organoid single culture

characteristic: growth condition

text: Homo sapiens

text: Homo sapiens

text: inner cell mass

text: embryonic stem cell

characteristic: progenitor cell type

text: Homo sapiens

text: Sample 14


E-MTAB-12924:Sample 1

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-12924:Sample 1

text: ArrayExpress

text: neuronal stem cell

text: human

text: mixed Huntington disease and normal

text: mixed wild type genotype and CRISPR/Cas9 modification of HD

text: brain organoid co-culture

text: Homo sapiens

text: Homo sapiens

text: inner cell mass

characteristic: organism part

text: embryonic stem cell

text: Homo sapiens

text: Sample 1


E-MTAB-12924:Sample 2

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-12924:Sample 2

characteristic: Submitter Id

text: ArrayExpress

text: neuronal stem cell

text: human

characteristic: description

text: mixed Huntington disease and normal

text: brain organoid co-culture

text: Homo sapiens

text: Homo sapiens

text: inner cell mass

text: embryonic stem cell

text: Homo sapiens

text: Sample 2


E-MTAB-12924:Sample 4

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: E-MTAB-12924:Sample 4

text: ArrayExpress

text: neuronal stem cell

text: human

text: normal

text: wild type genotype

text: brain organoid monoculture

text: Homo sapiens

text: Homo sapiens

text: inner cell mass

text: embryonic stem cell

text: Homo sapiens

text: Sample 4


E-MTAB-12924:Sample 3

text: public

text: E-MTAB-12924:Sample 3

text: ArrayExpress

characteristic: broker name

text: neuronal stem cell

text: human

characteristic: common name

text: normal

text: wild type genotype

text: brain organoid monoculture

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: inner cell mass

text: embryonic stem cell

text: Homo sapiens

text: Sample 3

characteristic: title


E-MTAB-12924:Sample 6

text: public

text: E-MTAB-12924:Sample 6

text: ArrayExpress

text: neuronal stem cell

text: human

text: Huntington disease

characteristic: disease

text: CRISPR/Cas9 modification of HD

characteristic: genotype

text: brain organoid monoculture

characteristic: growth condition

text: Homo sapiens

text: Homo sapiens

text: inner cell mass

text: embryonic stem cell

characteristic: progenitor cell type

text: Homo sapiens

text: Sample 6


E-MTAB-12924:Sample 5

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-12924:Sample 5

text: ArrayExpress

text: neuronal stem cell

text: human

text: Huntington disease

text: CRISPR/Cas9 modification of HD

text: brain organoid monoculture

text: Homo sapiens

text: Homo sapiens

text: inner cell mass

characteristic: organism part

text: embryonic stem cell

text: Homo sapiens

text: Sample 5


E-MTAB-12924:Sample 8

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-12924:Sample 8

characteristic: Submitter Id

text: ArrayExpress

text: neuronal stem cell

text: human

characteristic: description

text: mixed Huntington disease and normal

text: brain organoid co-culture

text: Homo sapiens

text: Homo sapiens

text: inner cell mass

text: embryonic stem cell

text: Homo sapiens

text: Sample 8


E-MTAB-12924:Sample 7

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: E-MTAB-12924:Sample 7

text: ArrayExpress

text: neuronal stem cell

text: human

text: mixed Huntington disease and normal

text: brain organoid co-culture

text: Homo sapiens

text: Homo sapiens

text: inner cell mass

text: embryonic stem cell

text: Homo sapiens

text: Sample 7


text: public

tag: Namespace:Division of Virology,  Department of Pathology,  University of Cambridge

text: ArrayExpress

characteristic: broker name

text: astrocytoid

text: human

characteristic: common name

text: Protocols: Vero and U251 cells were grown on 100-mm dishes to 90% confluency and infected with ZIKV (PE243 or Dak84) at a multiplicity of infection (MOI) of 3. At 24 h p.i., cells were rinsed with 5 ml of ice-cold PBS, flash frozen in a dry ice/ethanol bath and lysed with 400 μl of lysis buffer [20 mM Tris-HCl pH 7.5, 150 mM NaCl, 5 mM MgCl2, 1 mM DTT, 1% Triton X-100, 100 μg/ml cycloheximide and 25 U/ml TURBO DNase (Life Technologies)]. Cells were scraped extensively to ensure lysis, collected and triturated ten times with a 26-G needle. Cell lysates were clarified by centrifugation at 13,000 g for 20 min at 4°C. The supernatants were recovered and stored in liquid nitrogen. RNA was extracted from the lysates by proteinase K digestion (enzyme from NEB, reaction at 42 degrees for 30 minutes) followed by hot acidic phenol: chloroform extraction and ethanol precipitation. The methodologies employed were based on the original protocols of Ingolia and colleagues (Ingolia et al., 2009; Ingolia et al., 2012), except library amplicons were constructed using a small RNA cloning strategy (Guo et al., 2010) adapted to Illumina smallRNA v2 to allow multiplexing. Ribosomal RNA was removed using Ribo-Zero Gold rRNA removal kit (Illumina), and the remaining RNA was fragmented by alkaline hydrolysis (45mM NaHCO3, 6mM Na2CO3, 1mM EDTA; 95 degrees, 15 minutes). Fragments of 25-35nt were selected by 15% denaturing urea gel purification, and library amplicons were constructed.

text: adult

characteristic: developmental stage

text: glioblastoma

text: wild type genotype

text: ZIKV Dak84

characteristic: infect

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: parietal lobe

text: Homo sapiens

characteristic: title


text: Division of Virology, Department of Pathology, University of Cambridge

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: ArrayExpress

text: Vero

text: fibroblast

text: adult

text: normal

characteristic: disease

text: wild type genotype

characteristic: genotype

text: ZIKV Dak84

text: Chlorocebus sabaeus

text: Chlorocebus sabaeus

text: kidney

text: Chlorocebus sabaeus


characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: ArrayExpress

text: astrocytoid

text: human

text: adult

text: glioblastoma

text: wild type genotype

text: ZIKV PE243

text: Homo sapiens

text: Homo sapiens

text: parietal lobe

characteristic: organism part

text: Homo sapiens


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

characteristic: Submitter Id

text: ArrayExpress

text: Vero

text: fibroblast

characteristic: description

text: adult

text: normal

text: wild type genotype

text: ZIKV PE243

text: Chlorocebus sabaeus

text: Chlorocebus sabaeus

text: kidney

text: Chlorocebus sabaeus


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Ugent

text: public

text: ArrayExpress

characteristic: broker name

text: house mouse

characteristic: common name

text: Protocols: DNAse treated total RNA samples dissolved in nuclease free water Promega Total RNA Isolation Kit Eukaryotic Transcriptome Library

text: neuroblastoma

text: TH-MYCN, ALK-F1178S

text: Mus musculus

text: Mus musculus

text: neoplasm

text: Mus musculus

characteristic: strain


text: Furtwangen University

characteristic: INSDC center name

text: public

tag: Namespace:Furtwangen University

text: Human body [FMAID:305853]

characteristic: broad-scale environmental context

characteristic: collection date

text: Scalp [UBERON:0000403]

characteristic: environmental medium

text: Germany

characteristic: geographic location (country and/or sea)

unit: DD

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: male

characteristic: host sex

text: Scalp [UBERON:0000403]

characteristic: local environmental context

text: human metagenome

characteristic: organism

characteristic: project name

text: human metagenome

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: Furtwangen University

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: Human body [FMAID:305853]

characteristic: description

text: Scalp [UBERON:0000403]

text: Germany

text: female

text: Scalp [UBERON:0000403]

text: human metagenome

text: human metagenome


characteristic: External Id

text: UNIST

characteristic: INSDC center name

text: public

text: Norway rat

characteristic: common name

text: Female 6week sample 5 left Substantia nigra

text: Rattus norvegicus

text: Rattus norvegicus


text: UNIST

text: public

text: Norway rat

text: Female 6week sample 5 right Substantia nigra

text: Rattus norvegicus

text: Rattus norvegicus


text: UNIST

text: public

text: Norway rat

text: Female 6week sample 6 left Substantia nigra

text: Rattus norvegicus

text: Rattus norvegicus


text: UNIST

text: public

text: Norway rat

text: Female 6week sample 6 right Substantia nigra

text: Rattus norvegicus

text: Rattus norvegicus


text: UNIST

text: public

text: Norway rat

text: Female 6week sample 7 left Substantia nigra

text: Rattus norvegicus

text: Rattus norvegicus


text: UNIST

text: public

text: Norway rat

text: Female 6week sample 7 right Substantia nigra

text: Rattus norvegicus

text: Rattus norvegicus


text: UNIST

text: public

text: Norway rat

text: Female 6week sample 8 left Substantia nigra

text: Rattus norvegicus

text: Rattus norvegicus


text: UNIST

text: public

text: Norway rat

text: Female 6week sample 8 right Substantia nigra

text: Rattus norvegicus

text: Rattus norvegicus


text: UNIST

text: public

text: Norway rat

text: Female 6week sample 9 left Substantia nigra

text: Rattus norvegicus

text: Rattus norvegicus


text: UNIST

text: public

text: Norway rat

text: Female 6week sample 9 right Substantia nigra

text: Rattus norvegicus

text: Rattus norvegicus


text: Anopheles dirus

characteristic: ArrayExpress-SPECIES

text: SC

text: public

text: Anopheles dirus

text: Anopheles dirus

text: Anopheles dirus


text: public

tag: Namespace:Latvian Biomedical Research and Study Centre

text: post-eradication

text: human gut metagenome

text: human gut metagenome


E-MTAB-12968:African like_RNA

text: public

text: E-MTAB-12968:African like_RNA

text: ArrayExpress

characteristic: broker name

text: Vero

text: fibroblast

text: Protocols: Vero cells were grown on 100-mm dishes to 90% confluency and infected with different ZIKV mutants (American WT, African-like, uORF1-KO and uORF2-PTC1) at a multiplicity of infection (MOI) of 3. At 24 h p.i., cells were rinsed with 5 ml of ice-cold PBS, flash frozen in a dry ice/ethanol bath and lysed with 400 μl of lysis buffer [20 mM Tris-HCl pH 7.5, 150 mM NaCl, 5 mM MgCl2, 1 mM DTT, 1% Triton X-100, 100 μg/ml cycloheximide and 25 U/ml TURBO DNase (Life Technologies)]. Cells were scraped extensively to ensure lysis, collected and triturated ten times with a 26-G needle. Cell lysates were clarified by centrifugation at 13,000 g for 20 min at 4°C. The supernatants were recovered and stored in liquid nitrogen. RNA was extracted from the lysates by proteinase K digestion (enzyme from NEB, reaction at 42 degrees for 30 minutes) followed by hot acidic phenol: chloroform extraction and ethanol precipitation. The methodologies employed were based on the original protocols of Ingolia and colleagues (Ingolia et al., 2009; Ingolia et al., 2012), except library amplicons were constructed using a small RNA cloning strategy (Guo et al., 2010) adapted to Illumina smallRNA v2 to allow multiplexing. Ribosomal RNA was removed using Ribo-Zero Gold rRNA removal kit (Illumina), and the remaining RNA was fragmented by alkaline hydrolysis (45mM NaHCO3, 6mM Na2CO3, 1mM EDTA; 95 degrees, 15 minutes). Fragments of 25-35nt were selected by 15% denaturing urea gel purification, and library amplicons were constructed.

text: normal

characteristic: disease

text: wild type genotype

characteristic: genotype

text: ZIKV African like

characteristic: infect

text: Chlorocebus sabaeus

text: Chlorocebus sabaeus

text: kidney

characteristic: organism part

text: Chlorocebus sabaeus

text: African like_RNA


E-MTAB-12968:American WT_RNA

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: E-MTAB-12968:American WT_RNA

text: ArrayExpress

text: Vero

text: fibroblast

text: normal

text: wild type genotype

text: ZIKV American WT

text: Chlorocebus sabaeus

characteristic: organism

text: Chlorocebus sabaeus

text: kidney

text: Chlorocebus sabaeus

text: American WT_RNA

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: ArrayExpress

text: Vero

text: fibroblast

text: normal

text: wild type genotype

text: ZIKV uORF1-KO

text: Chlorocebus sabaeus

text: Chlorocebus sabaeus

text: kidney

text: Chlorocebus sabaeus


characteristic: External Id

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: Vero

text: fibroblast

characteristic: description

text: normal

text: wild type genotype

text: ZIKV uORF2-PTC1

text: Chlorocebus sabaeus

text: Chlorocebus sabaeus

text: kidney

text: Chlorocebus sabaeus


E-MTAB-12969:African like_Ribo

characteristic: INSDC center name

text: public

text: E-MTAB-12969:African like_Ribo

text: ArrayExpress

characteristic: broker name

text: Vero

text: fibroblast

text: Protocols: Vero cells were grown on 100-mm dishes to 90% confluency and infected with different ZIKV mutants (American WT, African-like, uORF1-KO and uORF2-PTC1) at a multiplicity of infection (MOI) of 3. At 24 h p.i., cells were rinsed with 5 ml of ice-cold PBS, flash frozen in a dry ice/ethanol bath and lysed with 400 μl of lysis buffer [20 mM Tris-HCl pH 7.5, 150 mM NaCl, 5 mM MgCl2, 1 mM DTT, 1% Triton X-100, 100 μg/ml cycloheximide and 25 U/ml TURBO DNase (Life Technologies)]. Cells were scraped extensively to ensure lysis, collected and triturated ten times with a 26-G needle. Cell lysates were clarified by centrifugation at 13,000 g for 20 min at 4°C. The supernatants were recovered and stored in liquid nitrogen. RNase I was added to the lysates for 45 minutes at room temperature, following which ribosomes and ribosome-protected fragments of RNA were purified by centrifugation through a sucrose cushion. RNA was extracted from the purified ribosomes by proteinase K digestion (enzyme from NEB, reaction at 42 degrees for 30 minutes) followed by hot acidic phenol: chloroform extraction and ethanol precipitation. The methodologies employed were based on the original protocols of Ingolia and colleagues (Ingolia et al., 2009; Ingolia et al., 2012), except library amplicons were constructed using a small RNA cloning strategy (Guo et al., 2010) adapted to Illumina smallRNA v2 to allow multiplexing. Ribosomal RNA was removed using Ribo-Zero Gold rRNA removal kit (Illumina), and remaining RNA was purified by 15% denaturing urea gel purification to select fragments of 25-35nt, and library amplicons were constructed.

text: normal

text: wild type genotype

text: ZIKV African like

text: Chlorocebus sabaeus

text: Chlorocebus sabaeus

text: kidney

text: Chlorocebus sabaeus

text: African like_Ribo


E-MTAB-12969:American WT_Ribo

text: public

text: E-MTAB-12969:American WT_Ribo

text: ArrayExpress

text: Vero

text: fibroblast

text: normal

characteristic: disease

text: wild type genotype

characteristic: genotype

text: ZIKV American WT

text: Chlorocebus sabaeus

text: Chlorocebus sabaeus

text: kidney

text: Chlorocebus sabaeus

text: American WT_Ribo


text: public

text: ArrayExpress

text: Vero

text: fibroblast

text: normal

text: wild type genotype

text: ZIKV uORF1-KO

characteristic: infect

text: Chlorocebus sabaeus

text: Chlorocebus sabaeus

text: kidney

characteristic: organism part

text: Chlorocebus sabaeus


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: ArrayExpress

text: Vero

text: fibroblast

text: normal

text: wild type genotype

text: ZIKV uORF2-PTC1

text: Chlorocebus sabaeus

text: Chlorocebus sabaeus

text: kidney

text: Chlorocebus sabaeus


text: public

text: ArrayExpress

text: Vero

text: fibroblast

text: Protocols: Vero and U251 cells were grown on 100-mm dishes to 90% confluency and infected with ZIKV (PE243 or Dak84) at a multiplicity of infection (MOI) of 3. At 24 h p.i., cells were rinsed with 5 ml of ice-cold PBS, flash frozen in a dry ice/ethanol bath and lysed with 400 μl of lysis buffer [20 mM Tris-HCl pH 7.5, 150 mM NaCl, 5 mM MgCl2, 1 mM DTT, 1% Triton X-100, 100 μg/ml cycloheximide and 25 U/ml TURBO DNase (Life Technologies)]. Cells were scraped extensively to ensure lysis, collected and triturated ten times with a 26-G needle. Cell lysates were clarified by centrifugation at 13,000 g for 20 min at 4°C. The supernatants were recovered and stored in liquid nitrogen. RNase I was added to the lysates for 45 minutes at room temperature, following which ribosomes and ribosome-protected fragments of RNA were purified by centrifugation through a sucrose cushion. RNA was extracted from the purified ribosomes by proteinase K digestion (enzyme from NEB, reaction at 42 degrees for 30 minutes) followed by hot acidic phenol: chloroform extraction and ethanol precipitation. The methodologies employed were based on the original protocols of Ingolia and colleagues (Ingolia et al., 2009; Ingolia et al., 2012), except library amplicons were constructed using a small RNA cloning strategy (Guo et al., 2010) adapted to Illumina smallRNA v2 to allow multiplexing. Ribosomal RNA was removed using Ribo-Zero Gold rRNA removal kit (Illumina), and remaining RNA was purified by 15% denaturing urea gel purification to select fragments of 25-35nt, and library amplicons were constructed.

text: adult

characteristic: developmental stage

text: normal

text: wild type genotype

text: ZIKV Dak84

text: Chlorocebus sabaeus

characteristic: organism

text: Chlorocebus sabaeus

text: kidney

text: Chlorocebus sabaeus

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: ArrayExpress

text: Vero

text: fibroblast

text: adult

text: normal

text: wild type genotype

text: ZIKV PE243

text: Chlorocebus sabaeus

text: Chlorocebus sabaeus

text: kidney

text: Chlorocebus sabaeus


characteristic: External Id

text: public

characteristic: INSDC status

characteristic: SRA accession

text: ArrayExpress

text: astrocytoid

text: human

characteristic: common name

text: adult

text: glioblastoma

text: wild type genotype

text: ZIKV Dak84

text: Homo sapiens

text: Homo sapiens

text: parietal lobe

text: Homo sapiens


characteristic: INSDC center name

text: public

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: astrocytoid

text: human

characteristic: description

text: adult

text: glioblastoma

text: wild type genotype

text: ZIKV PE243

text: Homo sapiens

text: Homo sapiens

text: parietal lobe

text: Homo sapiens


text: public

text: ArrayExpress

text: Vero

text: fibroblast

text: Protocols: Vero cells were grown on 100-mm dishes to 90% confluency and infected with the American/Asian Zika virus (ZIKV)strain, PE243, at a multiplicity of infection (MOI) of 3. At 24 h p.i., cells were rinsed with 5 ml of ice-cold PBS, flash frozen in a dry ice/ethanol bath and lysed with 400 μl of lysis buffer [20 mM Tris-HCl pH 7.5, 150 mM NaCl, 5 mM MgCl2, 1 mM DTT, 1% Triton X-100, 100 μg/ml cycloheximide and 25 U/ml TURBO DNase (Life Technologies)]. Cells were scraped extensively to ensure lysis, collected and triturated ten times with a 26-G needle. Cell lysates were clarified by centrifugation at 13,000 g for 20 min at 4°C. The supernatants were spontaneously immortalised cell line recovered and stored in liquid nitrogen. RNase I was added to the lysates for 45 minutes at room temperature, following which ribosomes and ribosome-protected fragments of RNA were purified by centrifugation through a sucrose cushion. RNA was extracted from the purified ribosomes by proteinase K digestion (enzyme from NEB, reaction at 42 degrees for 30 minutes) followed by hot acidic phenol: chloroform extraction and ethanol precipitation. The methodologies employed were based on the original protocols of Ingolia and colleagues (Ingolia et al., 2009; Ingolia et al., 2012), except library amplicons were constructed using a small RNA cloning strategy (Guo et al., 2010) adapted to Illumina smallRNA v2 to allow multiplexing. Ribosomal RNA was removed using Ribo-Zero Gold rRNA removal kit (Illumina), and remaining RNA was purified by 15% denaturing urea gel purification to select fragments of 25-35nt, and library amplicons were constructed.

text: adult

text: normal

characteristic: disease

text: wild type genotype

characteristic: genotype

text: ZIKV PE243

characteristic: infect

text: Chlorocebus sabaeus

text: Chlorocebus sabaeus

text: kidney

characteristic: organism part

text: Chlorocebus sabaeus


name: E-MTAB-12988:Sample 4: DNA barcodes of micro-beads in ID-coded droplets (without cells)

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: THE UNIVERSITY OF TOKYO

text: public

tag: Namespace:THE UNIVERSITY OF TOKYO

text: ArrayExpress

text: synthetic construct

text: Protocols: Micro-particles functionalized both by DNA barcodes and fluorescent molecules were synthesized and used for the study. Synthetic DNA oligonucleotides bearing barcodes sequences provided in protocol 13 were used in the study. DNA-barcoded microbeads were resuspended in a buffer containing 0.75% (w/v) agarose (Sigma Aldrich, ultra-low gelling temperature). Monodisperse droplets were generated by flowing the beads suspension and HFE7500 oil supplemented with 2% 008-fluorosurfactant (RAN Biotechnologies) into a droplet generation chip. After droplet generation, water-in-oil hydrogel droplets were cooled at 4 °C at 500 rpm shaking. To the droplets, medium-based buffer solution and perfluoro octanol (final volume: 20% in oil, v/v) were slowly added, and hydrogel droplets were extracted into the aqueous layer, which was further washed with 20% perfluorooctanol in HFE7200, and hexane supplemented with Span 80. The resulting hydrogel droplets were firstly subjected to microscopic imaging and then “single-droplet” sequencing, where the whole nucleic acid components in a hydrogel droplet were processed as single-cell components in the droplet-based single-cell RNA sequencing library preparation. Cell lysis and RNA extraction using polyT-functionalized DNA-barcoded beads for droplet-based single cell RNA sequencing (drop-seq) Reverse transcription and cDNA preparation using polyT-functionalized DNA-barcoded beads for droplet-based single cell RNA sequencing (drop-seq)

text: DNA barcoding

characteristic: library construction

text: synthetic construct

characteristic: organism

text: synthetic construct

text: synthetic construct


name: E-MTAB-12988:Sample 7: Single-cell RNA-seq data of HEK293 cells (fixed) in hydrogel droplets

characteristic: ENA-LAST-UPDATE

text: THE UNIVERSITY OF TOKYO

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: ArrayExpress

text: human

text: Protocols: HEK293 cells were purchased from JCRB CellBank (JCRB9068); K562 cells were purchased from JCRB CellBank (JCRB0019). Murine NIH/3T3 cells (spiked only in sample 1) were purchased from JCRB CellBank (JCRB0615). K562 cells were grown in RPMI1640 medium (Sigma-Aldrich) supplemented with 10%FBS (Sigma-Aldrich) and 1x Antibiotic Antimycotic (Thermo Fisher Scientific). HEK293 cells were grown in Minimum Essential Medium Eagle (Sigma-Aldrich) supplemented with 10% Horse serum (Thermo Fisher Scientific) and 1x Antibiotic Antimycotic to reach 60-80% confluence. NIH/3T3 cells (used to estimate the rate of doublet errors during NGS library preparation, Fig. S5a) were grown in Dulbecco’s Modified Eagles’ Medium low glucose (Sigma-Aldrich) supplemented with 10% Newborn Calf serum (Thermo Fisher Scientific) and 1x Antibiotic Antimycotic to reach 60-80% confluence. Cell pellets were resuspended in a buffer containing 0.75% (w/v) agarose (Sigma Aldrich, ultra-low gelling temperature) and the suspension was passed through pluriStrainer (20 μm). Monodisperse droplets were generated by flowing the beads suspension and HFE7500 oil supplemented with 2% 008-fluorosurfactant (RAN Biotechnologies) into a droplet generation chip. After droplet generation, water-in-oil hydrogel droplets were cooled at 4 °C at 500 rpm shaking. To the droplets, medium-based buffer solution and perfluoro octanol (final volume: 20% in oil, v/v) were slowly added, and hydrogel droplets were extracted into the aqueous layer, which was further washed with 20% perfluorooctanol in HFE7200, and hexane supplemented with Span 80. The resulting hydrogel droplets were firstly subjected to microscopic imaging and then “single-droplet” sequencing, where the whole nucleic acid components in a hydrogel droplet were processed as single-cell components in the droplet-based single-cell RNA sequencing library preparation. Cell lysis and RNA extraction using polyT-functionalized DNA-barcoded beads for droplet-based single cell RNA sequencing (drop-seq) Reverse transcription and cDNA preparation using polyT-functionalized DNA-barcoded beads for droplet-based single cell RNA sequencing (drop-seq)

text: embryo

characteristic: developmental stage

text: normal

text: gene expression profiling

text: Homo sapiens

text: Homo sapiens

text: kidney

text: Homo sapiens

characteristic: title


name: E-MTAB-12988:Sample 5: Single-cell RNA-seq data of K562 cells (fixed) in hydrogel droplets

characteristic: External Id

text: THE UNIVERSITY OF TOKYO

characteristic: INSDC center name

text: public

characteristic: INSDC status

characteristic: SRA accession

text: ArrayExpress

text: human

characteristic: common name

text: adult

text: normal

text: gene expression profiling

text: Homo sapiens

text: Homo sapiens

text: bone marrow

text: Homo sapiens


name: E-MTAB-12988:Sample 1: Single-cell RNA-seq data of ID-coded droplets (with single cells)

text: THE UNIVERSITY OF TOKYO

text: public

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: mixed K562 and HEK293

text: human

text: Protocols: HEK293 cells were purchased from JCRB CellBank (JCRB9068); K562 cells were purchased from JCRB CellBank (JCRB0019). Murine NIH/3T3 cells (spiked only in Sample 1) were purchased from JCRB CellBank (JCRB0615). Micro-particles functionalized both by DNA barcodes and fluorescent molecules were synthesized and used for ID-coding. HEK293 cells were purchased from JCRB CellBank (JCRB9068); K562 cells were purchased from JCRB CellBank (JCRB0019). Murine NIH/3T3 cells (spiked only in sample 1) were purchased from JCRB CellBank (JCRB0615). K562 cells were grown in RPMI1640 medium (Sigma-Aldrich) supplemented with 10%FBS (Sigma-Aldrich) and 1x Antibiotic Antimycotic (Thermo Fisher Scientific). HEK293 cells were grown in Minimum Essential Medium Eagle (Sigma-Aldrich) supplemented with 10% Horse serum (Thermo Fisher Scientific) and 1x Antibiotic Antimycotic to reach 60-80% confluence. NIH/3T3 cells (used to estimate the rate of doublet errors during NGS library preparation, Fig. S5a) were grown in Dulbecco’s Modified Eagles’ Medium low glucose (Sigma-Aldrich) supplemented with 10% Newborn Calf serum (Thermo Fisher Scientific) and 1x Antibiotic Antimycotic to reach 60-80% confluence. Cell pellets were resuspended in a buffer containing 0.75% (w/v) agarose (Sigma Aldrich, ultra-low gelling temperature). The suspension was passed through pluriStrainer (20 μm), mixed with pellets of DNA-barcoded microbeads. Monodisperse droplets were generated by flowing the beads suspension and HFE7500 oil supplemented with 2% 008-fluorosurfactant (RAN Biotechnologies) into a droplet generation chip. After droplet generation, water-in-oil hydrogel droplets were cooled at 4 °C at 500 rpm shaking. To the droplets, medium-based buffer solution and perfluoro octanol (final volume: 20% in oil, v/v) were slowly added, and hydrogel droplets were extracted into the aqueous layer, which was further washed with 20% perfluorooctanol in HFE7200, and hexane supplemented with Span 80. The resulting hydrogel droplets were firstly subjected to microscopic imaging and then “single-droplet” sequencing, where the whole nucleic acid components in a hydrogel droplet were processed as single-cell components in the droplet-based single-cell RNA sequencing library preparation. Cell lysis and RNA extraction using polyT-functionalized DNA-barcoded beads for droplet-based single cell RNA sequencing (drop-seq) Reverse transcription and cDNA preparation using polyT-functionalized DNA-barcoded beads for droplet-based single cell RNA sequencing (drop-seq)

characteristic: description

text: mixed adult and embryo

text: normal

characteristic: disease

text: gene expression profiling

text: Homo sapiens

text: Homo sapiens

text: mixed bone marrow and kidney

text: Homo sapiens


name: E-MTAB-12988:Sample 1: DNA barcodes of micro-beads in ID-coded droplets (with single cells)

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: THE UNIVERSITY OF TOKYO

text: public

text: ArrayExpress

text: mixed K562 and HEK293

text: mixed adult and embryo

text: normal

text: DNA barcoding

text: synthetic construct

text: synthetic construct

text: mixed bone marrow and kidney

characteristic: organism part

text: synthetic construct


name: E-MTAB-12988:Sample 8: Single-cell RNA-seq data of HEK293 cells in hydrogel droplets

characteristic: ENA-LAST-UPDATE

text: THE UNIVERSITY OF TOKYO

text: public

text: ArrayExpress

text: human

text: embryo

text: normal

text: gene expression profiling

characteristic: library construction

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: kidney

text: Homo sapiens


name: E-MTAB-12988:Sample 6: Single-cell RNA-seq data of K562 cells in hydrogel droplets

text: THE UNIVERSITY OF TOKYO

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: ArrayExpress

text: human

text: adult

characteristic: developmental stage

text: normal

text: gene expression profiling

text: Homo sapiens

text: Homo sapiens

text: bone marrow

text: Homo sapiens


name: E-MTAB-12988:Sample 9: DNA barcodes of micro-beads

characteristic: External Id

text: THE UNIVERSITY OF TOKYO

characteristic: INSDC center name

text: public

text: ArrayExpress

text: synthetic construct

text: DNA barcoding

text: synthetic construct

text: synthetic construct

text: synthetic construct

text: Sample 9: DNA barcodes of micro-beads

characteristic: title


name: E-MTAB-12988:Sample 3: DNA barcodes of micro-beads in ID-coded droplets (without cells)

text: THE UNIVERSITY OF TOKYO

text: public

characteristic: INSDC status

characteristic: SRA accession

text: ArrayExpress

text: synthetic construct

text: DNA barcoding

text: synthetic construct

text: synthetic construct

text: synthetic construct


name: E-MTAB-12988:Sample 2: DNA barcodes of micro-beads in ID-coded droplets (with single cells)

text: THE UNIVERSITY OF TOKYO

text: public

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: mixed K562 and HEK293

text: human

characteristic: common name

text: mixed adult and embryo

text: normal

text: DNA barcoding

text: Homo sapiens

text: Homo sapiens

text: mixed bone marrow and kidney

text: Homo sapiens


name: E-MTAB-12988:Sample 2: Single-cell RNA-seq data of ID-coded droplets (with single cells)

characteristic: ENA-CHECKLIST

text: THE UNIVERSITY OF TOKYO

text: public

text: ArrayExpress

text: mixed K562 and HEK293

text: human

characteristic: description

text: mixed adult and embryo

text: normal

characteristic: disease

text: gene expression profiling

text: Homo sapiens

text: Homo sapiens

text: mixed bone marrow and kidney

text: Homo sapiens


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: public

tag: Namespace:College of Health, Medicine and Life Sciences, Division of Biosciences, Brunel University London

text: ArrayExpress

text: mammary epithelial cell

text: human

text: Protocols: Cells were detached by addition of trypsin. Cells suspensions were quenched with medium and centrifuged at 400 x g for 5 minutes to pellet for subsequent extraction. Cells were cultured in DMEM/F12 with 5% horse serum and 100 U/ml penicillin/streptomycin, supplemented with 20 ng/ml human epithelial growth factor (HeGF), 500 ng/ml hydrocortisone, 100 ng/ml cholera toxin, and 10 ug/ml insulin. Doxycycline was added to the culturing medium at 2 ug/ml. Total RNA was extracted using Monarch Total RNA Miniprep Kit according to manufacturer's instructions (New England Biolabs, Hitchin, UK). Library construction was performed by Novogene UK (Cambridge, UK). A minimum of 1 ug (20 ng/μl) of high-quality total RNA (using Monarch Total RNA Miniprep Kit according to manufacturer's instructions, New England Biolabs, Hitchin, UK) was supplied for sequencing. Novogene UK constructed cDNA libraries by purification of messenger RNA using poly-A enrichment. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, PCR amplification, and purification.

text: adult

text: pINDUCER21 (ORF-EG)

characteristic: genotype

text: Homo sapiens

text: Homo sapiens

text: breast

characteristic: organism part

text: Homo sapiens


text: College of Health, Medicine and Life Sciences, Division of Biosciences, Brunel University London

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: ArrayExpress

text: mammary epithelial cell

text: human

text: adult

text: pINDUCER21 (ORF-EG)

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: breast

text: Homo sapiens


characteristic: External Id

characteristic: INSDC center name

text: public

text: ArrayExpress

text: mammary epithelial cell

text: human

text: adult

characteristic: developmental stage

text: Homo sapiens

text: Homo sapiens

text: breast

text: Homo sapiens


text: public

characteristic: INSDC status

characteristic: SRA accession

text: ArrayExpress

text: secretory cell

text: human

text: Protocols: Cells were detached by addition of trypsin. Cells suspensions were quenched with medium and centrifuged at 400 x g for 5 minutes to pellet for subsequent extraction. Total RNA was extracted using RNeasy Mini Kit (QIAGEN). Library construction was performed by Novogene UK (Cambridge, UK). A minimum of 1 ug (20 ng/μl) of high-quality total RNA (using Monarch Total RNA Miniprep Kit according to manufacturer's instructions, New England Biolabs, Hitchin, UK) was supplied for sequencing. Novogene UK constructed cDNA libraries by purification of messenger RNA using poly-A enrichment. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, PCR amplification, and purification.

text: adult

text: adenoid cystic carcinoma

text: wild type genotype

text: Homo sapiens

text: Homo sapiens

text: salivary gland

text: Homo sapiens

characteristic: title


text: public

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: human

characteristic: common name

text: adult

text: normal

text: wild type genotype

text: Homo sapiens

text: Homo sapiens

text: salivary gland

text: Homo sapiens


E-MTAB-12976:ACCX11 input 1

characteristic: ENA-CHECKLIST

text: public

text: E-MTAB-12976:ACCX11 input 1

text: ArrayExpress

text: secretory cell

text: human

text: Protocols: 5x10^6 cultured cells were used for immunoprecipitation. To crosslink proteins to DNA, 540 µl of 37% formaldehyde was added to cells in 20 ml culturing medium and incubated for 10 minutes at room temperature. 2 ml of 10X glycine was added and incubated for 5 min at room temperature. Cells were pelleted at 500 x g at 4 degrees for 5 minutes and washes in ice-cold PBS + proteinase inhibitors. Chromatin extraction, digestion, and digestion was performed using SimpleChIP Enzymatic Chromatin IP Kit (Cell Signaling) according to manufacturer's instructions. Chromatin was digested using micrococcal nuclease (MNase) prior to chromatin immunoprecipitation (ChIP) with anti-MYB antibody (recombinant anti-MYB phosphoS11, Abcam). Following ChIP, chromatin was eluted from from Antibody/Protein G Magnetic Beads and reverse crosslinked. DNA was purified by the use of spin columns. Library construction was performed by Novogene UK (Cambridge, UK). Purified DNA (extracted and digested using SimpleChIP Enzymatic Chromatin IP Kit, Cell Signaling) was supplied for sequencing. Novogene UK constructed DNA libraries as follows: DNA fragments were repaired, A-tailed, and further ligated using Illumina adapter. The final DNA library was obtained by size selection and PCR amplification.

characteristic: description

text: adult

text: adenoid cystic carcinoma

characteristic: disease

text: wild type genotype

text: Homo sapiens

text: Homo sapiens

text: salivary gland

text: Homo sapiens

text: ACCX11 input 1


E-MTAB-12976:ACCX11 input 2

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: public

text: E-MTAB-12976:ACCX11 input 2

text: ArrayExpress

text: secretory cell

text: human

text: adult

text: adenoid cystic carcinoma

text: wild type genotype

characteristic: genotype

text: Homo sapiens

text: Homo sapiens

text: salivary gland

text: Homo sapiens

text: ACCX11 input 2


E-MTAB-12976:ACCX11 input 3

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-12976:ACCX11 input 3

text: ArrayExpress

text: secretory cell

text: human

text: adult

text: adenoid cystic carcinoma

text: wild type genotype

text: Homo sapiens

text: Homo sapiens

text: salivary gland

characteristic: organism part

text: Homo sapiens

text: ACCX11 input 3


E-MTAB-12976:ACCX11 MYB 1

characteristic: External Id

characteristic: INSDC center name

text: public

text: E-MTAB-12976:ACCX11 MYB 1

text: ArrayExpress

text: secretory cell

text: human

text: adult

text: adenoid cystic carcinoma

text: wild type genotype

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: salivary gland

text: Homo sapiens

text: ACCX11 MYB 1


E-MTAB-12976:ACCX11 MYB 2

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-12976:ACCX11 MYB 2

text: ArrayExpress

text: secretory cell

text: human

text: adult

characteristic: developmental stage

text: adenoid cystic carcinoma

text: wild type genotype

text: Homo sapiens

text: Homo sapiens

text: salivary gland

text: Homo sapiens

text: ACCX11 MYB 2


E-MTAB-12976:ACCX11 MYB 3

text: public

text: E-MTAB-12976:ACCX11 MYB 3

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: secretory cell

text: human

text: adult

text: adenoid cystic carcinoma

text: wild type genotype

text: Homo sapiens

text: Homo sapiens

text: salivary gland

text: Homo sapiens

text: ACCX11 MYB 3

characteristic: title


characteristic: ENA-CHECKLIST

text: public

tag: Namespace:Addis Ababa Science and Technology University

text: AH_DDME210007524 soil sample from AH station

characteristic: description

text: Grassland

characteristic: environment (biome)

text: Wastes

characteristic: environment (feature)

text: Soil

characteristic: environment (material)

text: Ethiopia

characteristic: geographic location (country and/or sea)

unit: m

characteristic: geographic location (depth)

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome

characteristic: investigation type

text: metagenome

characteristic: project name

text: metagenome

text: Illumina HiSeq 1500

characteristic: sequencing method

text: soil

characteristic: soil environmental package


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Addis Ababa Science and Technology 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: CP_DDME210007523 soil sample from CP station

text: Grassland

text: Wastes

text: Soil

text: Ethiopia

text: metagenome

text: metagenome

characteristic: organism

text: metagenome

text: Illumina HiSeq 1500

text: soil


characteristic: ENA-CHECKLIST

text: public

text: EP_DDME210007522 soil sample from EP station

characteristic: description

text: Grassland

characteristic: environment (biome)

text: Wastes

characteristic: environment (feature)

text: Soil

characteristic: environment (material)

text: Ethiopia

characteristic: geographic location (country and/or sea)

characteristic: geographic location (depth)

characteristic: geographic location (elevation)

text: metagenome

text: metagenome

text: metagenome

text: Illumina HiSeq 1500

text: soil

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: TB_DDME210007521 soil sample from TB station

text: Grassland

text: Wastes

text: Soil

text: Ethiopia

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome

characteristic: investigation type

text: metagenome

characteristic: project name

text: metagenome

text: Illumina HiSeq 1500

characteristic: sequencing method

text: soil

characteristic: soil environmental package


characteristic: ENA-CHECKLIST

text: IZSLER

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: Sequencing of a Listeria monocytogenes strain isolated from a loggerhead sea turtle

characteristic: description

text: Italy

text: diseased

characteristic: host health state

text: Caretta caretta

characteristic: host scientific name

characteristic: isolate

text: tissue

text: Listeria monocytogenes

characteristic: organism

text: Listeria monocytogenes


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: VTT

text: public

text: water

text: deep subsurface

characteristic: environment (biome)

text: crystalline bedrock

characteristic: environment (feature)

text: groundwater

characteristic: environment (material)

text: Finland

characteristic: geographic location (country and/or sea)

characteristic: geographic location (depth)

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

characteristic: investigation type

text: microbial mat/biofilm

characteristic: microbial mat/biofilm environmental package

text: uncultured bacterium

text: uncultured bacterium

text: IonTorrent

characteristic: title


characteristic: ENA-CHECKLIST

text: VTT

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: biofilm

characteristic: description

text: deep subsurface

text: crystalline bedrock

text: steel

text: Finland

text: microbial mat/biofilm

text: uncultured bacterium

characteristic: project name

text: uncultured bacterium

text: IonTorrent

characteristic: sequencing method


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: VTT

text: public

text: water

text: deep subsurface

characteristic: environment (biome)

text: crystalline bedrock

characteristic: environment (feature)

text: groundwater

characteristic: environment (material)

text: Finland

characteristic: geographic location (country and/or sea)

characteristic: geographic location (depth)

characteristic: geographic location (elevation)

text: microbial mat/biofilm

text: uncultured archaeon

characteristic: organism

text: uncultured archaeon

text: IonTorrent


characteristic: ENA-CHECKLIST

text: VTT

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: biofilm

text: deep subsurface

text: crystalline bedrock

text: steel

text: Finland

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

characteristic: investigation type

text: microbial mat/biofilm

characteristic: microbial mat/biofilm environmental package

text: uncultured archaeon

text: uncultured archaeon

text: IonTorrent

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: VTT

text: public

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

text: water

characteristic: description

text: deep subsurface

characteristic: environment (biome)

text: crystalline bedrock

text: groundwater

text: Finland

text: eukaryote

text: microbial mat/biofilm

text: uncultured fungus

characteristic: project name

text: uncultured fungus

text: IonTorrent

characteristic: sequencing method


characteristic: ENA-CHECKLIST

text: VTT

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: biofilm

text: deep subsurface

text: crystalline bedrock

characteristic: environment (feature)

text: steel

characteristic: environment (material)

text: Finland

characteristic: geographic location (country and/or sea)

characteristic: geographic location (depth)

characteristic: geographic location (elevation)

text: eukaryote

text: microbial mat/biofilm

text: uncultured fungus

characteristic: organism

text: uncultured fungus

text: IonTorrent


text: Homo sapiens

characteristic: ArrayExpress-SPECIES

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

text: public

characteristic: INSDC status

characteristic: SRA accession

text: human

characteristic: common name

text: Homo sapiens

text: Homo sapiens

characteristic: title


characteristic: ENA-CHECKLIST

text: GENGS-CBMSO

characteristic: INSDC center name

text: public

characteristic: Submitter Id

text: GENGS-CBMSO

characteristic: broker name

text: fruit fly

text: WT Naive A01

characteristic: description

text: Drosophila melanogaster

text: Drosophila melanogaster

text: WT Naive A01


text: GENGS-CBMSO

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: GENGS-CBMSO

text: fruit fly

text: WT Naive A02

text: Drosophila melanogaster

text: Drosophila melanogaster

text: WT Naive A02


text: GENGS-CBMSO

text: public

text: GENGS-CBMSO

text: fruit fly

text: WT Naive A03

text: Drosophila melanogaster

text: Drosophila melanogaster

text: WT Naive A03


text: GENGS-CBMSO

text: public

text: GENGS-CBMSO

text: fruit fly

text: WT Naive A04

text: Drosophila melanogaster

text: Drosophila melanogaster

text: WT Naive A04


text: GENGS-CBMSO

text: public

text: GENGS-CBMSO

text: fruit fly

text: WT Naive A05

text: Drosophila melanogaster

text: Drosophila melanogaster

text: WT Naive A05


text: GENGS-CBMSO

text: public

text: GENGS-CBMSO

text: fruit fly

text: WT Naive A06

text: Drosophila melanogaster

text: Drosophila melanogaster

text: WT Naive A06


text: GENGS-CBMSO

text: public

text: GENGS-CBMSO

text: fruit fly

text: WT Naive A07

text: Drosophila melanogaster

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