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text: microbial mat metagenome

characteristic: organism

characteristic: project name

text: microbial mat metagenome

text: sediment

text: Illumina

text: Sample from Västermanland County, Sala silver mine, Grisen, Johan/Liljeborg (3m further in) (Sweden), biofilm


characteristic: ENA-FIRST-PUBLIC

characteristic: External Id

text: UPPSALA UNIVERSITY

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: mine

text: mine

text: biofilm

characteristic: environment (material)

text: Sweden

characteristic: geographic location (country and/or sea)

characteristic: geographic location (depth)

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

text: metagenome

text: microbial mat metagenome

text: microbial mat metagenome

text: sediment

characteristic: sediment environmental package

text: Illumina

characteristic: sequencing method

characteristic: temperature

text: Sample from Västermanland County, Sala silver mine, Kanslern (Sweden), biofilm


characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

text: UPPSALA UNIVERSITY

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

text: mine

characteristic: environment (biome)

text: mine

text: biofilm

text: Sweden

characteristic: geographic location (longitude)

text: Västermanland County, Sala silver mine, Kanslern

characteristic: host description

text: metagenome

characteristic: investigation type

text: microbial mat metagenome

text: microbial mat metagenome

text: sediment

text: Illumina

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: External Id

text: UPPSALA UNIVERSITY

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: mine

text: mine

characteristic: environment (feature)

text: biofilm

characteristic: environment (material)

text: Sweden

characteristic: geographic location (country and/or sea)

characteristic: geographic location (depth)

characteristic: geographic location (elevation)

characteristic: geographic location (region and locality)

text: metagenome

text: microbial mat metagenome

characteristic: organism

characteristic: ph

characteristic: project name

text: microbial mat metagenome

text: sediment

text: Illumina

text: Sample from Västermanland County, Sala silver mine, Kanslern (black seap) (Sweden), biofilm


characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

text: UPPSALA UNIVERSITY

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

text: mine

characteristic: environment (biome)

text: mine

text: water

text: Sweden

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome

text: freshwater metagenome

text: freshwater metagenome

text: Illumina

characteristic: sequencing method

text: Sample from Västermanland County, Sala silver mine, Rödstjärten (Sweden), water

text: water

characteristic: water environmental package


characteristic: ENA-FIRST-PUBLIC

characteristic: External Id

text: UPPSALA UNIVERSITY

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: mine

text: mine

characteristic: environment (feature)

text: biofilm

characteristic: environment (material)

text: Sweden

characteristic: geographic location (country and/or sea)

characteristic: geographic location (depth)

characteristic: geographic location (elevation)

characteristic: host description

text: metagenome

characteristic: investigation type

text: microbial mat metagenome

text: Abundance, diversity and distribution of Legionellales in wet environments in Sweden

text: microbial mat metagenome

text: sediment

characteristic: sediment environmental package

text: Illumina

characteristic: temperature

text: Sample from Västermanland County, Sala silver mine, Victoria Salen (Sweden), biofilm

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

text: UPPSALA UNIVERSITY

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

text: mine

characteristic: environment (biome)

text: mine

text: water

text: Sweden

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

characteristic: geographic location (region and locality)

text: metagenome

text: freshwater metagenome

characteristic: organism

characteristic: ph

characteristic: project name

text: freshwater metagenome

text: Illumina

text: Sample from Västermanland County, Sala silver mine, Ribbings schakt (Sweden), water

text: water


characteristic: ENA-FIRST-PUBLIC

characteristic: External Id

text: IBENS

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: LoVo ATCC CCL-229

characteristic: cell line

text: Epithelial (colon adenocarcinoma)

characteristic: cell type

text: human

characteristic: common name

text: LoVo cells were maintained in Kaign's modification of Ham's F12 medium (F12-K) supplemented with 10% (vol/vol) heat-inactivated foetal bovine serum (FBS). The culture medium was changed every 24-h, and kept for further use as ”conditioned medium”. LoVo cells were plated in 75 cm2 culture flasks 4 days before infection so that cell confluency was 80% on the day of infection. On the day of infection, non-infected cells were treated the same as infected cells except Listeria monocytogenes (Lm) was not added to the flask. Control flasks were centrifuged at 200 x g for 2 minutes, and incubated at 37°C and 5% CO2 for 30 min. After 30min, the media was removed and the cells were incubated in conditioned medium containing 25 µg/ml gentamicin, at 37°C until 2 hours post-infection. Cells were rinsed with 5 ml of ice-cold PBS(100µg/ml cycloheximide) twice. The PBS was thoroughly aspirated and the T75 flaks were submerged in a reservoir of liquid nitrogen for 10 s, and stored at -80°C until lysis. To proceed with lysis, flasks were transferred to dry ice and 200 µl of lysis buffer was added per flask [20 mM Tris-HCl pH 7.4, 150 mM NaCl, 5 mM MgCl2, 1 mM DTT, 1% Triton X-100, 100 µg/ml cycloheximide and 25 U/ml TurboDNase (ThermoFisher Scientific)]. Cells were scraped extensively to ensure lysis after which the lysate was incubated on ice for 10 minutes and then triturated with a 26-G needle ten times. Lysates were clarified by centrifugation for 10 min at 21,000 g at 4°C. The supernatants were recovered separated in two fractions: 350 µl was used for RNase footprinting for RiboSeq based on the original protocols of Ingolia and colleagues (Ingolia et al., 2012 doi:10.1038/nprot.2012.086), while 50 µl was directly used in RNA extraction using acid-phenol chloroform.

characteristic: description

text: Homo sapiens

text: Homo sapiens

text: Non-infected LoVo cells, Replicate 1


characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

text: IBENS

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: LoVo ATCC CCL-229

text: Epithelial (colon adenocarcinoma)

text: human

text: Homo sapiens

text: Homo sapiens

text: Non-infected LoVo cells, Replicate 2

characteristic: title


text: IBENS

text: public

text: LoVo ATCC CCL-229

text: Epithelial (colon adenocarcinoma)

text: human

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: Non-infected LoVo cells, Replicate 3


text: IBENS

text: public

text: LoVo ATCC CCL-229

text: Epithelial (colon adenocarcinoma)

text: human

text: LoVo cells were maintained in Kaign's modification of Ham's F12 medium (F12-K) supplemented with 10% (vol/vol) heat-inactivated foetal bovine serum (FBS). The culture medium was changed every 24-h, and kept for further use during the infection as ”conditioned medium”. Listeria monocytonenes (Lm, LL195 strain) was grown in Brain Heart Infusion medium (BHI) at 37°C to early saturation, washed in 37°C PBS and diluted in conditioned medium. LoVo cells were plated in 75 cm2 culture flasks 4 days before infection and, upon reaching 80% confluence, Lm was added at a multiplicity of infection (MOI) of 30 colony forming unit (CFU)/cell in conditioned medium. Flasks were then centrifuged at 200 x g for 2 minutes, and incubated at 37°C and 5% CO2 for 30 min. After 30min, the inoculum was removed and the cells were incubated in conditioned medium containing 25 µg/ml gentamicin, at 37°C until 2 hours post-infection. Cells were rinsed with 5 ml of ice-cold PBS(100µg/ml cycloheximide) twice. The PBS was thoroughly aspirated and the T75 flaks were submerged in a reservoir of liquid nitrogen for 10 s, and stored at -80°C until lysis. To proceed with lysis, flasks were transferred to dry ice and 200 µl of lysis buffer was added per flask [20 mM Tris-HCl pH 7.4, 150 mM NaCl, 5 mM MgCl2, 1 mM DTT, 1% Triton X-100, 100 µg/ml cycloheximide and 25 U/ml TurboDNase (ThermoFisher Scientific)]. Cells were scraped extensively to ensure lysis after which the lysate was incubated on ice for 10 minutes and then triturated with a 26-G needle ten times. Lysates were clarified by centrifugation for 10 min at 21,000 g at 4°C. The supernatants were recovered separated in two fractions: 350 µl was used for RNase footprinting for RiboSeq based on the original protocols of Ingolia and colleagues (Ingolia et al., 2012 doi:10.1038/nprot.2012.086), while 50 µl was directly used in RNA extraction using acid-phenol chloroform.

text: Listeria monocytogenes LL195, 2 h

characteristic: experimental factor: infection

text: Homo sapiens

text: Homo sapiens

text: LoVo cells 2h after infection by Listeria monocytogenes strain LL195 - Replicate 1


characteristic: ENA-FIRST-PUBLIC

text: IBENS

text: public

text: LoVo ATCC CCL-229

text: Epithelial (colon adenocarcinoma)

text: human

text: Listeria monocytogenes LL195, 2 h

text: Homo sapiens

text: Homo sapiens

text: LoVo cells 2h after infection by Listeria monocytogenes strain LL195 - Replicate 2


characteristic: External Id

text: IBENS

text: public

text: LoVo ATCC CCL-229

text: Epithelial (colon adenocarcinoma)

text: human

text: Listeria monocytogenes LL195, 2 h

text: Homo sapiens

text: Homo sapiens

text: LoVo cells 2h after infection by Listeria monocytogenes strain LL195 - Replicate 3


text: IBENS

characteristic: INSDC center name

text: public

text: LoVo ATCC CCL-229

text: Epithelial (colon adenocarcinoma)

text: human

text: LoVo cells were maintained in Kaign's modification of Ham's F12 medium (F12-K) supplemented with 10% (vol/vol) heat-inactivated foetal bovine serum (FBS). The culture medium was changed every 24-h, and kept for further use during the infection as ”conditioned medium”. Listeria monocytonenes (Lm, LL195 strain) was grown in Brain Heart Infusion medium (BHI) at 37°C to early saturation, washed in 37°C PBS and diluted in conditioned medium. LoVo cells were plated in 75 cm2 culture flasks 4 days before infection and, upon reaching 80% confluence, Lm was added at a multiplicity of infection (MOI) of 30 colony forming unit (CFU)/cell in conditioned medium. Flasks were then centrifuged at 200 x g for 2 minutes, and incubated at 37°C and 5% CO2 for 30 min. After 30min, the inoculum was removed and the cells were incubated in conditioned medium containing 25 µg/ml gentamicin, at 37°C until 5 hours post-infection. Cells were rinsed with 5 ml of ice-cold PBS(100µg/ml cycloheximide) twice. The PBS was thoroughly aspirated and the T75 flaks were submerged in a reservoir of liquid nitrogen for 10 s, and stored at -80°C until lysis. To proceed with lysis, flasks were transferred to dry ice and 200 µl of lysis buffer was added per flask [20 mM Tris-HCl pH 7.4, 150 mM NaCl, 5 mM MgCl2, 1 mM DTT, 1% Triton X-100, 100 µg/ml cycloheximide and 25 U/ml TurboDNase (ThermoFisher Scientific)]. Cells were scraped extensively to ensure lysis after which the lysate was incubated on ice for 10 minutes and then triturated with a 26-G needle ten times. Lysates were clarified by centrifugation for 10 min at 21,000 g at 4°C. The supernatants were recovered separated in two fractions: 350 µl was used for RNase footprinting for RiboSeq based on the original protocols of Ingolia and colleagues (Ingolia et al., 2012 doi:10.1038/nprot.2012.086), while 50 µl was directly used in RNA extraction using acid-phenol chloroform.

text: Listeria monocytogenes LL195, 5 h

text: Homo sapiens

text: Homo sapiens

text: LoVo cells 5h after infection by Listeria monocytogenes strain LL195 - Replicate 1


text: IBENS

characteristic: INSDC first public

text: public

text: LoVo ATCC CCL-229

text: Epithelial (colon adenocarcinoma)

text: human

text: Listeria monocytogenes LL195, 5 h

text: Homo sapiens

text: Homo sapiens

text: LoVo cells 5h after infection by Listeria monocytogenes strain LL195 - Replicate 2


text: IBENS

text: public

text: LoVo ATCC CCL-229

characteristic: cell line

text: Epithelial (colon adenocarcinoma)

text: human

text: Listeria monocytogenes LL195, 5 h

text: Homo sapiens

text: Homo sapiens

text: LoVo cells 5h after infection by Listeria monocytogenes strain LL195 - Replicate 3


text: IBENS

text: public

text: LoVo ATCC CCL-229

text: Epithelial (colon adenocarcinoma)

characteristic: cell type

text: human

text: LoVo cells were maintained in Kaign's modification of Ham's F12 medium (F12-K) supplemented with 10% (vol/vol) heat-inactivated foetal bovine serum (FBS). The culture medium was changed every 24-h, and kept for further use during the infection as ”conditioned medium”. Listeria monocytonenes (Lm, LL195 strain) was grown in Brain Heart Infusion medium (BHI) at 37°C to early saturation, washed in 37°C PBS and diluted in conditioned medium. LoVo cells were plated in 75 cm2 culture flasks 4 days before infection and, upon reaching 80% confluence, Lm was added at a multiplicity of infection (MOI) of 30 colony forming unit (CFU)/cell in conditioned medium. Flasks were then centrifuged at 200 x g for 2 minutes, and incubated at 37°C and 5% CO2 for 30 min. After 30min, the inoculum was removed and the cells were incubated in conditioned medium containing 25 µg/ml gentamicin, at 37°C until 10 hours post-infection. Cells were rinsed with 5 ml of ice-cold PBS(100µg/ml cycloheximide) twice. The PBS was thoroughly aspirated and the T75 flaks were submerged in a reservoir of liquid nitrogen for 10 s, and stored at -80°C until lysis. To proceed with lysis, flasks were transferred to dry ice and 200 µl of lysis buffer was added per flask [20 mM Tris-HCl pH 7.4, 150 mM NaCl, 5 mM MgCl2, 1 mM DTT, 1% Triton X-100, 100 µg/ml cycloheximide and 25 U/ml TurboDNase (ThermoFisher Scientific)]. Cells were scraped extensively to ensure lysis after which the lysate was incubated on ice for 10 minutes and then triturated with a 26-G needle ten times. Lysates were clarified by centrifugation for 10 min at 21,000 g at 4°C. The supernatants were recovered separated in two fractions: 350 µl was used for RNase footprinting for RiboSeq based on the original protocols of Ingolia and colleagues (Ingolia et al., 2012 doi:10.1038/nprot.2012.086), while 50 µl was directly used in RNA extraction using acid-phenol chloroform.

text: Listeria monocytogenes LL195, 10 h

text: Homo sapiens

text: Homo sapiens

text: LoVo cells 10h after infection by Listeria monocytogenes strain LL195 - Replicate 1


text: IBENS

text: public

text: LoVo ATCC CCL-229

text: Epithelial (colon adenocarcinoma)

text: human

characteristic: common name

text: Listeria monocytogenes LL195, 10 h

text: Homo sapiens

text: Homo sapiens

text: LoVo cells 10h after infection by Listeria monocytogenes strain LL195 - Replicate 2


text: IBENS

text: public

text: LoVo ATCC CCL-229

text: Epithelial (colon adenocarcinoma)

text: human

characteristic: description

text: Listeria monocytogenes LL195, 10 h

text: Homo sapiens

text: Homo sapiens

text: LoVo cells 10h after infection by Listeria monocytogenes strain LL195 - Replicate 3


characteristic: ENA-CHECKLIST

text: DKFZ

text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: Human Keratinocytes immortalized by HPV16 Folate Control


characteristic: ENA-LAST-UPDATE

text: DKFZ

text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: Human Keratinocytes immortalized by HPV16 Folate Repleted


text: EMBL

characteristic: INSDC last update

text: public

characteristic: collection date

characteristic: environment (biome)

text: soil [ENVO:00001998]

characteristic: environment (feature)

text: soil [ENVO:00001998]

characteristic: environment (material)

text: Estonia

characteristic: geographic location (country and/or sea)

characteristic: geographic location (depth)

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome

characteristic: investigation type

text: soil metagenome

text: 16S metabarcoding data of global soil samples

characteristic: project name

text: soil metagenome

text: Illumina

characteristic: sequencing method

text: soil

characteristic: soil environmental package

text: soil sample


characteristic: ENA-FIRST-PUBLIC

characteristic: External Id

text: EMBL

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: Mediterrean

text: soil [ENVO:00001998]

text: soil [ENVO:00001998]

text: Australia

text: metagenome

text: soil metagenome

characteristic: organism

text: soil metagenome

text: Illumina

text: soil

text: soil sample

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

text: EMBL

characteristic: INSDC last update

text: public

characteristic: collection date

text: Savannas

characteristic: environment (biome)

text: soil [ENVO:00001998]

characteristic: environment (feature)

text: soil [ENVO:00001998]

characteristic: environment (material)

text: Australia

characteristic: geographic location (country and/or sea)

characteristic: geographic location (depth)

text: metagenome

text: soil metagenome

text: soil metagenome

text: Illumina

text: soil

text: soil sample


characteristic: ENA-FIRST-PUBLIC

characteristic: External Id

text: EMBL

text: public

text: soil [ENVO:00001998]

text: soil [ENVO:00001998]

text: India

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome

characteristic: investigation type

text: soil metagenome

characteristic: project name

text: soil metagenome

text: Illumina

characteristic: sequencing method

text: soil

characteristic: soil environmental package

text: soil sample


characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

text: EMBL

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: soil [ENVO:00001998]

text: soil [ENVO:00001998]

text: Italy

text: metagenome

text: soil metagenome

characteristic: organism

text: soil metagenome

text: Illumina

text: soil

text: soil sample

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: External Id

text: EMBL

characteristic: INSDC last update

text: public

characteristic: collection date

characteristic: environment (biome)

text: soil [ENVO:00001998]

characteristic: environment (feature)

text: soil [ENVO:00001998]

characteristic: environment (material)

text: Madagascar

characteristic: geographic location (country and/or sea)

characteristic: geographic location (depth)

text: metagenome

text: soil metagenome

text: soil metagenome

text: Illumina

text: soil

text: soil sample


characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

text: EMBL

text: public

text: soil [ENVO:00001998]

text: soil [ENVO:00001998]

text: Russia

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome

characteristic: investigation type

text: soil metagenome

characteristic: project name

text: soil metagenome

text: Illumina

characteristic: sequencing method

text: soil

characteristic: soil environmental package

text: soil sample


characteristic: ENA-FIRST-PUBLIC

characteristic: External Id

text: EMBL

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: soil [ENVO:00001998]

text: soil [ENVO:00001998]

text: Mexico

text: metagenome

text: soil metagenome

characteristic: organism

text: soil metagenome

text: Illumina

text: soil

text: soil sample

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

text: EMBL

characteristic: INSDC last update

text: public

characteristic: collection date

text: Mediterrean

characteristic: environment (biome)

text: soil [ENVO:00001998]

characteristic: environment (feature)

text: soil [ENVO:00001998]

characteristic: environment (material)

text: Iran

characteristic: geographic location (country and/or sea)

characteristic: geographic location (depth)

text: metagenome

text: soil metagenome

text: soil metagenome

text: Illumina

text: soil

text: soil sample