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text: Arctic Ocean

characteristic: geographic location (country and/or sea)

characteristic: geographic location (depth)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Fram Strait

characteristic: geographic location (region and locality)

text: mimarks-survey

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text: PowerWater

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text: seawater metagenome

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text: Remote Access Sampler

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text: true

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text: marine biome [ENVO:00000447]

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text: E-MTAB-92751616585327:BMDM_aIL-10R_Isotype_PGE2_4h_A_bulk_RNA

tag: Namespace:San Raffaele Telethon Institute for Gene Therapy.

characteristic: Submitter Id

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text: Protocols: Bone marrow cells were collected from femurs and tibias in 50 mL PBS, filtered through a 70 µm cell strainer and centrifuged 450 x g for 5 minutes. Red blood cells were lysed using 0.2% NaCl solution, followed by 1.6% NaCl solution. Cells were filtered through a 70 µm cell strainer and centrifuged 450 x g for 5 minutes. 5 x 104 - 5 x 106 bone marrow cells were plated and cultured in Iscove’s Modified Dulbecco’s Medium (IMDM) supplemented with 10% Fetal Bovine Serum (FBS), 20% L929-conditioned medium containing M-CSF, antibiotics (penicillin G 100 U/ml and streptomycin sulfate 100 U/ml), 2 mM L-glutamine and 5 µM 2-mercaptoethanol. After six days of culture, adherent cells were >99% Cd11b+ F4/80+, as assessed by flow cytometry BMDMs or iMACs were stimulated for four hours with the indicated stimuli Total RNA was extracted using ReliaPrep RNA Cell Miniprep System and quantified using NanoDrop 8000. RNA-Seq libraries were generated using the Smart-seq2 method (Picelli et al., 2014). Five ng of RNA were retrotranscribed, cDNA was PCR-amplified (15 cycles) and purified with AMPure XP beads. After purification, the concentration was determined using Qubit 3.0 and size distribution was assessed using Agilent 4200 TapeStation system. Then, the tagmentation reaction was performed starting from 0.5 ng of cDNA for 30 minutes at 55°C and the enrichment PCR was carried out using 12 cycles. Libraries were then purified with AMPure XP beads, quantified using Qubit 3.0 and sequenced.

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text: E-MTAB-92751616585327:BMDM_aIL-10R_Isotype_PGE2_4h_B_bulk_RNA

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text: 6 to 10

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text: bone marrow macrophage

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text: Protocols: Bone marrow cells were collected from femurs and tibias in 50 mL PBS, filtered through a 70 µm cell strainer and centrifuged 450 x g for 5 minutes. Red blood cells were lysed using 0.2% NaCl solution, followed by 1.6% NaCl solution. Cells were filtered through a 70 µm cell strainer and centrifuged 450 x g for 5 minutes. 5 x 104 - 5 x 106 bone marrow cells were plated and cultured in Iscove’s Modified Dulbecco’s Medium (IMDM) supplemented with 10% Fetal Bovine Serum (FBS), 20% L929-conditioned medium containing M-CSF, antibiotics (penicillin G 100 U/ml and streptomycin sulfate 100 U/ml), 2 mM L-glutamine and 5 µM 2-mercaptoethanol. After six days of culture, adherent cells were >99% Cd11b+ F4/80+, as assessed by flow cytometry BMDMs or iMACs were stimulated for four hours with the indicated stimuli Total RNA was extracted using ReliaPrep RNA Cell Miniprep System and quantified using NanoDrop 8000. RNA-Seq libraries were generated using the Smart-seq2 method (Picelli et al., 2014). Five ng of RNA were retrotranscribed, cDNA was PCR-amplified (15 cycles) and purified with AMPure XP beads. After purification, the concentration was determined using Qubit 3.0 and size distribution was assessed using Agilent 4200 TapeStation system. Then, the tagmentation reaction was performed starting from 0.5 ng of cDNA for 30 minutes at 55°C and the enrichment PCR was carried out using 12 cycles. Libraries were then purified with AMPure XP beads, quantified using Qubit 3.0 and sequenced.

text: adult

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characteristic: description

text: adult

characteristic: developmental stage

text: normal

characteristic: disease

text: wild type genotype

characteristic: genotype

text: Mus musculus

characteristic: organism

text: Mus musculus

text: bone marrow

text: C

text: Mus musculus

text: female

text: Untreated


characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-92751616585327:BMDM_IFNa+IL-10_4h_A_bulk_RNA

text: 6 to 10

text: ArrayExpress

text: primary cell line

text: bone marrow macrophage

text: house mouse

text: adult

text: normal

text: wild type genotype

text: Mus musculus

text: Mus musculus

text: bone marrow

characteristic: organism part

text: A

characteristic: replicate

text: Mus musculus

text: female

characteristic: sex

characteristic: stimulus

characteristic: strain

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

characteristic: SRA accession

text: E-MTAB-92751616585327:BMDM_IFNa+IL-10_4h_B_bulk_RNA

characteristic: Submitter Id

text: 6 to 10

characteristic: age

text: ArrayExpress

characteristic: broker name

text: primary cell line

characteristic: cell line

text: bone marrow macrophage

characteristic: cell type

text: house mouse

text: adult

text: normal

text: wild type genotype

text: Mus musculus

text: Mus musculus

text: bone marrow

text: B

text: Mus musculus

text: female


characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-92751616585327:BMDM_IFNb_0h_LPS+PGE2_4h_A_bulk_RNA

text: 6 to 10

text: ArrayExpress

text: primary cell line

text: bone marrow macrophage

text: house mouse

characteristic: common name

text: Protocols: Bone marrow cells were collected from femurs and tibias in 50 mL PBS, filtered through a 70 µm cell strainer and centrifuged 450 x g for 5 minutes. Red blood cells were lysed using 0.2% NaCl solution, followed by 1.6% NaCl solution. Cells were filtered through a 70 µm cell strainer and centrifuged 450 x g for 5 minutes. 5 x 104 - 5 x 106 bone marrow cells were plated and cultured in Iscove’s Modified Dulbecco’s Medium (IMDM) supplemented with 10% Fetal Bovine Serum (FBS), 20% L929-conditioned medium containing M-CSF, antibiotics (penicillin G 100 U/ml and streptomycin sulfate 100 U/ml), 2 mM L-glutamine and 5 µM 2-mercaptoethanol. After six days of culture, adherent cells were >99% Cd11b+ F4/80+, as assessed by flow cytometry BMDMs or iMACs were stimulated for four hours with the indicated stimuli Total RNA was extracted using ReliaPrep RNA Cell Miniprep System and quantified using NanoDrop 8000. RNA-Seq libraries were generated using the Smart-seq2 method (Picelli et al., 2014). Five ng of RNA were retrotranscribed, cDNA was PCR-amplified (15 cycles) and purified with AMPure XP beads. After purification, the concentration was determined using Qubit 3.0 and size distribution was assessed using Agilent 4200 TapeStation system. Then, the tagmentation reaction was performed starting from 0.5 ng of cDNA for 30 minutes at 55°C and the enrichment PCR was carried out using 12 cycles. Libraries were then purified with AMPure XP beads, quantified using Qubit 3.0 and sequenced.

characteristic: description

text: adult

characteristic: developmental stage

text: normal

characteristic: disease

text: wild type genotype

characteristic: genotype

text: Mus musculus

characteristic: organism

text: Mus musculus

text: bone marrow

text: A

text: Mus musculus

text: female


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: San Raffaele Telethon Institute for Gene Therapy.

text: public

text: E-MTAB-92751616585327:BMDM_IFNb_0h_LPS+PGE2_4h_B_bulk_RNA

text: 6 to 10

text: ArrayExpress

text: primary cell line

text: bone marrow macrophage

text: house mouse

text: adult

text: normal

text: wild type genotype

text: Mus musculus

text: Mus musculus

text: bone marrow

characteristic: organism part

text: B

characteristic: replicate

text: Mus musculus

text: female

characteristic: sex

characteristic: stimulus

characteristic: strain

characteristic: title


characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-92751616585327:BMDM_IFNb_0h_LPS+PGE2_4h_C_bulk_RNA

characteristic: Submitter Id

text: 6 to 10

characteristic: age

text: ArrayExpress

characteristic: broker name

text: primary cell line

characteristic: cell line

text: bone marrow macrophage

characteristic: cell type

text: house mouse

text: adult

text: normal

text: wild type genotype

text: Mus musculus

text: Mus musculus

text: bone marrow

text: C

text: Mus musculus

text: female


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: E-MTAB-92751616585327:BMDM_IFNb_0h_UT_A_bulk_RNA

text: 6 to 10

text: ArrayExpress

text: primary cell line

text: bone marrow macrophage

text: house mouse

characteristic: common name

characteristic: description

text: adult

characteristic: developmental stage

text: normal

characteristic: disease

text: wild type genotype

characteristic: genotype

text: Mus musculus

characteristic: organism

text: Mus musculus

text: bone marrow

text: A

text: Mus musculus

text: female

text: Untreated


characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-92751616585327:BMDM_IFNb_0h_UT_B_bulk_RNA

text: 6 to 10

text: ArrayExpress

text: primary cell line

text: bone marrow macrophage

text: house mouse

text: adult

text: normal

text: wild type genotype

text: Mus musculus

text: Mus musculus

text: bone marrow

characteristic: organism part

text: B

characteristic: replicate

text: Mus musculus

text: female

characteristic: sex

text: Untreated

characteristic: stimulus

characteristic: strain

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

characteristic: SRA accession

text: E-MTAB-92751616585327:BMDM_IFNb_0h_UT_C_bulk_RNA

characteristic: Submitter Id

text: 6 to 10

characteristic: age

text: ArrayExpress

characteristic: broker name

text: primary cell line

characteristic: cell line

text: bone marrow macrophage

characteristic: cell type

text: house mouse

text: adult

text: normal

text: wild type genotype

text: Mus musculus

text: Mus musculus

text: bone marrow

text: C

text: Mus musculus

text: female

text: Untreated


characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-92751616585327:BMDM_IFNb_3h_LPS+PGE2_4h_A_bulk_RNA

text: 6 to 10

text: ArrayExpress

text: primary cell line

text: bone marrow macrophage

text: house mouse

characteristic: common name

characteristic: description

text: adult

characteristic: developmental stage

text: normal

characteristic: disease

text: wild type genotype

characteristic: genotype

text: Mus musculus

characteristic: organism

text: Mus musculus

text: bone marrow

text: A

text: Mus musculus

text: female


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: E-MTAB-92751616585327:BMDM_IFNb_3h_LPS+PGE2_4h_B_bulk_RNA

text: 6 to 10

text: ArrayExpress

text: primary cell line

text: bone marrow macrophage

text: house mouse

text: adult

text: normal

text: wild type genotype

text: Mus musculus

text: Mus musculus

text: bone marrow

characteristic: organism part

text: B

characteristic: replicate

text: Mus musculus

text: female

characteristic: sex

characteristic: stimulus

characteristic: strain

characteristic: title


characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-92751616585327:BMDM_IFNb_3h_LPS+PGE2_4h_C_bulk_RNA

characteristic: Submitter Id

text: 6 to 10

characteristic: age

text: ArrayExpress

characteristic: broker name

text: primary cell line

characteristic: cell line

text: bone marrow macrophage

characteristic: cell type

text: house mouse

text: adult

text: normal

text: wild type genotype

text: Mus musculus

text: Mus musculus

text: bone marrow

text: C

text: Mus musculus

text: female


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: IRTA

text: public

text: plum

characteristic: common name

text: Prunus salicina var. cordata

characteristic: organism

text: Prunus salicina var. cordata

text: Plum cultivar


text: public

text: E-MTAB-92521616586090:BMDM_IL-10_4h_A_ATAC

text: 6 to 12

text: ArrayExpress

text: primary cell line

text: bone marrow macrophage

text: house mouse

text: Protocols: Bone marrow cells were collected from femurs and tibias in 50 mL PBS, filtered through a 70 µm cell strainer and centrifuged 450 x g for 5 minutes. Red blood cells were lysed using 0.2% NaCl solution, followed by 1.6% NaCl solution. Cells were filtered through a 70 µm cell strainer and centrifuged 450 x g for 5 minutes. 5 x 104 - 5 x 106 bone marrow cells were plated and cultured in Iscove’s Modified Dulbecco’s Medium (IMDM) supplemented with 10% Fetal Bovine Serum (FBS), 20% L929-conditioned medium containing M-CSF, antibiotics (penicillin G 100 U/ml and streptomycin sulfate 100 U/ml), 2 mM L-glutamine and 5 µM 2-mercaptoethanol. After six days of culture, adherent cells were >99% Cd11b+ F4/80+, as assessed by flow cytometry, and were stimulated as described. BMDMs or iMACs were stimulated for 2 hours at indicated condition 50,000 cells were collected and centrifuged at 450xg for 5 minutes. Then, the transposition reaction was performed using digitonin 1%, Tn5 transposase and TD Buffer for 45 minutes at 37°C. Immediately following transposition, the reaction was stopped using a solution of 900 mM NaCl and 300 mM EDTA, 5% SDS and Proteinase K for 30 minutes at 40°C. Transposed DNA fragments were purified using AMPure XP beads, barcoded with Illumina Nextera dual indexes and PCR amplified with KAPA HiFi PCR Kit. Then, the concentration of the library was determined using Qubit 3.0 and size distribution was assessed using Agilent 4200 TapeStation system.

characteristic: description

text: adult

characteristic: developmental stage

text: normal

characteristic: disease

text: wild type genotype

characteristic: genotype

text: Mus musculus

text: Mus musculus

text: bone marrow

characteristic: organism part

text: A

characteristic: replicate

text: Mus musculus

text: female

characteristic: sex

characteristic: stimulus

characteristic: strain

characteristic: title


characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-92521616586090:BMDM_IL-10_4h_B_ATAC

characteristic: Submitter Id

text: 6 to 12

characteristic: age

text: ArrayExpress

characteristic: broker name

text: primary cell line

characteristic: cell line

text: bone marrow macrophage

characteristic: cell type

text: house mouse

text: adult

text: normal

text: wild type genotype

text: Mus musculus

text: Mus musculus

text: bone marrow

text: B

text: Mus musculus

text: female


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: E-MTAB-92521616586090:BMDM_IL-10_4h_C_ATAC

text: 6 to 12

text: ArrayExpress

text: primary cell line

text: bone marrow macrophage

text: house mouse

characteristic: common name

characteristic: description

text: adult

characteristic: developmental stage

text: normal

characteristic: disease

text: wild type genotype

characteristic: genotype

text: Mus musculus

characteristic: organism

text: Mus musculus

text: bone marrow

text: C

text: Mus musculus

text: female


characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-92521616586090:BMDM_LPS+IL-10_4h_A_ATAC

text: 6 to 12

text: ArrayExpress

text: primary cell line

text: bone marrow macrophage

text: house mouse

text: adult

text: normal

text: wild type genotype

text: Mus musculus

text: Mus musculus

text: bone marrow

characteristic: organism part

text: A

characteristic: replicate

text: Mus musculus

text: female

characteristic: sex

characteristic: stimulus

characteristic: strain

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

characteristic: SRA accession

text: E-MTAB-92521616586090:BMDM_LPS+IL-10_4h_B_ATAC

characteristic: Submitter Id

text: 6 to 12

characteristic: age

text: ArrayExpress

characteristic: broker name

text: primary cell line

characteristic: cell line

text: bone marrow macrophage

characteristic: cell type

text: house mouse

text: adult

text: normal

text: wild type genotype

text: Mus musculus

text: Mus musculus

text: bone marrow

text: B

text: Mus musculus

text: female


characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-92521616586090:BMDM_LPS+IL-10_4h_C_ATAC

text: 6 to 12

text: ArrayExpress

text: primary cell line

text: bone marrow macrophage

text: house mouse

characteristic: common name

characteristic: description

text: adult

characteristic: developmental stage

text: normal

characteristic: disease

text: wild type genotype

characteristic: genotype

text: Mus musculus

characteristic: organism

text: Mus musculus

text: bone marrow

text: C

text: Mus musculus

text: female


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: INRA Tours

text: public

tag: Namespace:INRA Tours

characteristic: collection date

text: Isolate from bovine fecal sample

text: France

characteristic: geographic location (country and/or sea)

text: diseased

characteristic: host health state

text: Bos taurus

characteristic: host scientific name

characteristic: isolate

text: Bovine fecal sample

characteristic: isolation source

text: Mycobacterium avium subsp. paratuberculosis

characteristic: strain

characteristic: title


text: INRAE Tours

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

tag: Namespace:INRAE Tours

characteristic: Submitter Id

text: Isolate from bovine fecal sample

characteristic: description

text: France

text: diseased

text: Bos taurus

text: Bovine fecal sample


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: INRA Tours

text: public

text: Isolate from bovine fecal sample

text: France

text: diseased

text: Bos taurus

text: 17-2306 _1

text: Bovine fecal sample

characteristic: organism


characteristic: External Id

text: INRA Tours

text: public

characteristic: collection date

text: Isolate from bovine fecal sample

text: France

characteristic: geographic location (country and/or sea)

text: diseased

characteristic: host health state

text: Bos taurus

text: 17-3070 _2

text: Bovine fecal sample


text: Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research

text: public

text: 51302:7589bbc3-6243-4bcc-bf3b-17f6476dbff5

text: GFBIO

characteristic: broker name

text: Stomach content sample of Salp variable region V4 Standard protocol

text: ocean biome [ENVO:01000048]

characteristic: environment (biome)

text: marine pelagic feature [ENVO:01000044]

characteristic: environment (feature)

text: sea water [ENVO:00002149

characteristic: environment (material)

text: water

characteristic: environmental package

text: Southern Ocean

characteristic: geographic location (depth)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Antactic Peninsula

characteristic: geographic location (region and locality)

text: mimarks-survey

characteristic: investigation type

text: Salpa thompsoni

text: Population Shift and Ecosystem Response - Krill vs. Salps (POSER); funded by the Ministry for Science and Culture of Lower Saxony (MWK)

characteristic: project name

characteristic: sample description

text: Salpa thompsoni

text: Illumina MiSeq

characteristic: sequencing method

text: true

characteristic: submitted to INSDC

text: water

characteristic: water environmental package


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: 51301:7589bbc3-6243-4bcc-bf3b-17f6476dbff5

characteristic: Submitter Id

text: GFBIO

characteristic: collection date

characteristic: description

text: ocean biome [ENVO:01000048]

text: marine pelagic feature [ENVO:01000044]

text: sea water [ENVO:00002149

text: water

text: Southern Ocean

characteristic: geographic location (country and/or sea)

text: Antactic Peninsula

text: mimarks-survey

text: Salpa thompsoni

characteristic: organism

text: Salpa thompsoni

text: Illumina MiSeq

text: true

characteristic: title

text: water


text: public

text: 51300:7589bbc3-6243-4bcc-bf3b-17f6476dbff5

text: GFBIO

characteristic: broker name

text: ocean biome [ENVO:01000048]

characteristic: environment (biome)

text: marine pelagic feature [ENVO:01000044]

characteristic: environment (feature)

text: sea water [ENVO:00002149

characteristic: environment (material)

text: water

characteristic: environmental package

text: Southern Ocean

characteristic: geographic location (depth)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Antactic Peninsula

characteristic: geographic location (region and locality)

text: mimarks-survey

characteristic: investigation type

text: Salpa thompsoni

characteristic: project name

characteristic: sample description

text: Salpa thompsoni

text: Illumina MiSeq

characteristic: sequencing method

text: true

characteristic: submitted to INSDC

text: water


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: 51299:7589bbc3-6243-4bcc-bf3b-17f6476dbff5

characteristic: Submitter Id

text: GFBIO

characteristic: collection date

characteristic: description

text: ocean biome [ENVO:01000048]

text: marine pelagic feature [ENVO:01000044]

text: sea water [ENVO:00002149

text: water

text: Southern Ocean

characteristic: geographic location (country and/or sea)

text: Antactic Peninsula

text: mimarks-survey

text: Salpa thompsoni

text: Salpa thompsoni

text: Illumina MiSeq

text: true

text: water

characteristic: water environmental package