text: The Francis Crick Institute

text: public

text: ArrayExpress

text: epithelial cell

characteristic: cell type

text: human

characteristic: description

text: hepatocellular carcinoma

characteristic: disease

text: CRISPR/Cas9 mediated knockout with sgRNA pool 100-1

characteristic: genotype

text: Homo sapiens

text: Homo sapiens

text: liver

text: Homo sapiens


status: PUBLIC

tag: attribute

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: The Francis Crick Institute

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

tag: Namespace:The Francis Crick Institute

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

characteristic: cell line

text: epithelial cell

text: human

characteristic: common name

text: Protocols: HepG2 cells were cultured in Minimum Essential Media (MEM) with 10% FBS. All media was supplemented with 2mM L-glutamine, 100U/ml penicillin, and 100μg/ml streptomycin. sgRNA pools are described in the additional files associated with the submission Table_S1_sgrna_metadata.tsv and Table_S6_pools.tsv. HepG2 cells inducible for Cas9 expression were generated as previously described (Henser-Brownhill et al., 2017; 10.1080/15592294.2017.1395121). Cas9 induction was induced with 1ug/mL doxycycline 1 day prior to infection with the sgRNAs and sustained until cells were harvested for genomic DNA extraction. Transduced cells were selected with 4ug/mL blasticidin, starting 24h after the first infection, and genomic DNA was extracted 5 days after infection (Qiagen 69506). DNA libraries enriched for the targeted sites were generated using the SureSelect Target enrichment kit (Agilent) following the manufacturer’s instructions. Capture probes were designed to cover 2Kb regions centered on each target site.

text: hepatocellular carcinoma

text: CRISPR/Cas9 mediated knockout with sgRNA pool 100-2

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: liver

characteristic: organism part

text: Homo sapiens

characteristic: title


text: The Francis Crick Institute

text: public

text: ArrayExpress

text: epithelial cell

characteristic: cell type

text: human

characteristic: description

text: hepatocellular carcinoma

characteristic: disease

text: CRISPR/Cas9 mediated knockout with sgRNA pool 100-3

characteristic: genotype

text: Homo sapiens

text: Homo sapiens

text: liver

text: Homo sapiens


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: ILVO

text: public

text: MGRAST

characteristic: collection date

characteristic: collection time

text: Potting Soil with Chitin 1 merged Taxonomy ID:256318

text: terrestrial biome

characteristic: environment (biome)

text: rhizosphere

characteristic: environment (feature)

text: soil

characteristic: environment (material)

text: plant-associated

characteristic: environmental package

text: Belgium

characteristic: geographic location (country and/or sea)

unit: DD

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Merelbeke

characteristic: geographic location (region and locality)

text: metagenome

characteristic: investigation type

text: metagenome

text: plant-associated

characteristic: plant-associated environmental package

text: Lettuce_rhizosphere_chitin_pottingSoil_merged

characteristic: project name

text: Potting Soil with Chitin 1 merged

characteristic: sample name

text: metagenome

text: illumina

characteristic: sequencing method


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: ILVO

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: MGRAST

characteristic: broker name

text: Potting Soil 2 merged Taxonomy ID:256318

characteristic: description

text: terrestrial biome

text: rhizosphere

text: soil

text: plant-associated

text: Belgium

text: Merelbeke

text: metagenome

text: metagenome

characteristic: organism

text: plant-associated

text: Potting Soil 2 merged

text: metagenome

text: illumina

characteristic: title


characteristic: External Id

text: ILVO

text: public

text: MGRAST

characteristic: collection date

characteristic: collection time

text: Potting Soil 3 merged Taxonomy ID:256318

text: terrestrial biome

characteristic: environment (biome)

text: rhizosphere

characteristic: environment (feature)

text: soil

characteristic: environment (material)

text: plant-associated

characteristic: environmental package

text: Belgium

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Merelbeke

characteristic: geographic location (region and locality)

text: metagenome

characteristic: investigation type

text: metagenome

text: plant-associated

characteristic: plant-associated environmental package

text: Potting Soil 3 merged

text: metagenome

text: illumina


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: ILVO

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: MGRAST

characteristic: broker name

text: Potting Soil with Chitin 5 merged Taxonomy ID:256318

text: terrestrial biome

text: rhizosphere

text: soil

text: plant-associated

text: Belgium

text: Merelbeke

text: metagenome

text: metagenome

text: plant-associated

characteristic: project name

text: Potting Soil with Chitin 5 merged

characteristic: sample name

text: metagenome

text: illumina

characteristic: sequencing method


characteristic: External Id

text: ILVO

text: public

text: MGRAST

characteristic: collection date

characteristic: collection time

text: Potting Soil 4 merged Taxonomy ID:256318

characteristic: description

text: terrestrial biome

characteristic: environment (biome)

text: rhizosphere

characteristic: environment (feature)

text: soil

characteristic: environment (material)

text: plant-associated

characteristic: environmental package

text: Belgium

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Merelbeke

text: metagenome

text: metagenome

characteristic: organism

text: plant-associated

text: Potting Soil 4 merged

text: metagenome

text: illumina

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: ILVO

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: MGRAST

characteristic: broker name

text: Potting Soil with Chitin 4 merged Taxonomy ID:256318

text: terrestrial biome

text: rhizosphere

text: soil

text: plant-associated

text: Belgium

text: Merelbeke

characteristic: geographic location (region and locality)

text: metagenome

characteristic: investigation type

text: metagenome

text: plant-associated

characteristic: plant-associated environmental package

text: Potting Soil with Chitin 4 merged

text: metagenome

text: illumina


characteristic: External Id

text: ILVO

text: public

text: MGRAST

characteristic: collection date

characteristic: collection time

text: Potting Soil 5 merged Taxonomy ID:256318

characteristic: description

text: terrestrial biome

characteristic: environment (biome)

text: rhizosphere

characteristic: environment (feature)

text: soil

characteristic: environment (material)

text: plant-associated

characteristic: environmental package

text: Belgium

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

text: Merelbeke

text: metagenome

text: metagenome

text: plant-associated

characteristic: project name

text: Potting Soil 5 merged

characteristic: sample name

text: metagenome

text: illumina

characteristic: sequencing method


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: LMB

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: Vegetative

characteristic: cell type

text: Dictyostelium discoideum

characteristic: organism

text: Dictyostelium discoideum

text: HM597 consensus genome

characteristic: title


characteristic: External Id

text: LMB

text: public

text: Vegetative

text: Dictyostelium discoideum

text: Dictyostelium discoideum

text: HM598 consensus genome


text: LMB

text: public

text: Vegetative

text: Dictyostelium discoideum

text: Dictyostelium discoideum

text: WS2162 consensus genome


text: EMBL EBI

text: public

tag: Namespace:EMBL EBI

characteristic: collection date

text: bakery food

characteristic: environment (biome)

text: bread dough

characteristic: environment (feature)

text: food

characteristic: environment (material)

text: United Kingdom

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome

characteristic: investigation type

text: miscellaneous natural or artificial environment

characteristic: miscellaneous environmental package

text: food metagenome

text: Cambridge dough

text: food metagenome

text: Illumina MiSeq

text: bread dough sample from Cambridge bakery


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

tag: Namespace:Universite de Toulouse ; UPS ; LBCMCP ; 118 route de Narbonne, 31062, Toulouse, France;CNRS ; LBCMCP ; F-31062 Toulouse, France

text: ArrayExpress

characteristic: broker name

characteristic: cell line

text: human

characteristic: common name

text: Protocols: DIvA (AsiSI-ER-U20S) cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with antibiotics, 10% FCS (InVitrogenInvitrogen) with 1 µg/mL puromycin (DIvA cells) at 37°C under a humidified atmosphere with 5% CO2. For AsiSI-dependent DSB induction, cells were treated with 300 nM 4OHT (Sigma; H7904) for 4h For ChIP:Formaldehyde was added to the culture medium at a final concentration of 1% and crosslinking was allowed to proceed for 15 min at room temperature. Reaction was stopped by adding glycine (0.125M final concentration) and incubation for 5 minutes at room temperature. Cells were washed twice with PBS and harvested by scraping. Cell lysis was performed by incubation in cell lysis buffer (5 mM Pipes pH 8, 85 mM KCl, 0.5% IGEPAL® CA-630) followed by Dounce homogenization. Nuclei were harvested by centrifugation and incubated in nuclear lysis buffer: (50 mM Tris pH 8.1, 10 mM EDTA, 1% SDS) and sonicated 10 times for 10 s at a power setting of 5 and 50% duty cycle (Branson Sonifier 250). Samples were diluted 10 times in ChIP dilution buffer (16.7 mM Tris pH 8.1, 167 mM NaCl, 1.2 mM EDTA, 1.1% Triton X‐100, 0.01% SDS) and precleared using a mixture of protein A-agarose (Pierce) and protein G-sepharose (Sigma) previously blocked with BSA (Sigma). Precleared samples (10 to 200 μg) were incubated overnight at 4°C with indicated antibodies. Immune complexes were recovered by incubation with blocked protein A/protein G beads for 2 h at 4°C on a rotating wheel. Beads were washed once in dialysis buffer (50 mM Tris pH 8, 2 mM EDTA, 0.2% Sarkosyl), five times in wash buffer (100 mM Tris pH 8.8, 500 mM LiCl, 1% IGEPAL® CA-630, 1% NaDoc) and twice with TE (10mM Tris-HCl, pH 8, 1mM EDTA). Beads were resuspended in TE supplemented with 50µg/ml DNase-free RNase A (Abcam) and incubated for 30 minutes at 37°C. SDS (final concentration 0.5%) was added and crosslink was reversed by overnight incubation at 70°C. Following a 2 hours treatment with 200 µg/ml proteinase K (Roche) at 45°C, DNA was purified by phenol/chloroform extraction and recovered by ethanol precipitation in presence of 5 µg glycogen (Invitrogen). DNA pellet was resuspended in water. Prior to next-generation sequencing library preparation, samples from multiples ChIP experiments were pooled and sonicated for 5 cycles (30 seconds on, 30 seconds off, high setting) on a Bioruptor (Diagenode) then concentrated with a vacuum concentrator (Eppendorf). Libraries for H3K4me2, H4K20me1, H3K36me3, H3K79me2, H2Bub, H3K56ac, H4K16ac, H3K9me2, H4S1P, H3K36me2 and γH2AX were prepared BGI (Beijin Genomics Institute, Hong Kong) using proprietary protocols. Libraries for FK2 samples were prepared at GATC biotech (Konstanz, Germany) using proprietary protocols. Libraries for H2BK120ac, H2AZ, H1, MacroH2A, H4K20me3, 53BP1, H4K12ac, H2AZac and H3 were prepared atEMBL Genomics core facilities (Heidelberg, Germany) using NEBNext ChIP-Seq Library Prep kit (New England Biolabs). Libraries for BLESS were prepared using TruSeq Nano DNA LT Library Preparation Kit (Illumina).

characteristic: description

text: AsiSI-ER expression

characteristic: genotype

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: female

characteristic: sex


characteristic: External Id

text: Universite de Toulouse ; UPS ; LBCMCP ; 118 route de Narbonne, 31062, Toulouse, France;CNRS ; LBCMCP ; F-31062 Toulouse, France

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: human

text: AsiSI-ER expression

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: Homo sapiens

text: female

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: ArrayExpress

text: human

text: Protocols: DIvA (AsiSI-ER-U20S) cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with antibiotics, 10% FCS (InVitrogenInvitrogen) with 1 µg/mL puromycin (DIvA cells) at 37°C under a humidified atmosphere with 5% CO2. For ChIP:Formaldehyde was added to the culture medium at a final concentration of 1% and crosslinking was allowed to proceed for 15 min at room temperature. Reaction was stopped by adding glycine (0.125M final concentration) and incubation for 5 minutes at room temperature. Cells were washed twice with PBS and harvested by scraping. Cell lysis was performed by incubation in cell lysis buffer (5 mM Pipes pH 8, 85 mM KCl, 0.5% IGEPAL® CA-630) followed by Dounce homogenization. Nuclei were harvested by centrifugation and incubated in nuclear lysis buffer: (50 mM Tris pH 8.1, 10 mM EDTA, 1% SDS) and sonicated 10 times for 10 s at a power setting of 5 and 50% duty cycle (Branson Sonifier 250). Samples were diluted 10 times in ChIP dilution buffer (16.7 mM Tris pH 8.1, 167 mM NaCl, 1.2 mM EDTA, 1.1% Triton X‐100, 0.01% SDS) and precleared using a mixture of protein A-agarose (Pierce) and protein G-sepharose (Sigma) previously blocked with BSA (Sigma). Precleared samples (10 to 200 μg) were incubated overnight at 4°C with indicated antibodies. Immune complexes were recovered by incubation with blocked protein A/protein G beads for 2 h at 4°C on a rotating wheel. Beads were washed once in dialysis buffer (50 mM Tris pH 8, 2 mM EDTA, 0.2% Sarkosyl), five times in wash buffer (100 mM Tris pH 8.8, 500 mM LiCl, 1% IGEPAL® CA-630, 1% NaDoc) and twice with TE (10mM Tris-HCl, pH 8, 1mM EDTA). Beads were resuspended in TE supplemented with 50µg/ml DNase-free RNase A (Abcam) and incubated for 30 minutes at 37°C. SDS (final concentration 0.5%) was added and crosslink was reversed by overnight incubation at 70°C. Following a 2 hours treatment with 200 µg/ml proteinase K (Roche) at 45°C, DNA was purified by phenol/chloroform extraction and recovered by ethanol precipitation in presence of 5 µg glycogen (Invitrogen). DNA pellet was resuspended in water. Prior to next-generation sequencing library preparation, samples from multiples ChIP experiments were pooled and sonicated for 5 cycles (30 seconds on, 30 seconds off, high setting) on a Bioruptor (Diagenode) then concentrated with a vacuum concentrator (Eppendorf). Libraries for H3K4me2, H4K20me1, H3K36me3, H3K79me2, H2Bub, H3K56ac, H4K16ac, H3K9me2, H4S1P, H3K36me2 and γH2AX were prepared BGI (Beijin Genomics Institute, Hong Kong) using proprietary protocols. Libraries for FK2 samples were prepared at GATC biotech (Konstanz, Germany) using proprietary protocols. Libraries for H2BK120ac, H2AZ, H1, MacroH2A, H4K20me3, 53BP1, H4K12ac, H2AZac and H3 were prepared atEMBL Genomics core facilities (Heidelberg, Germany) using NEBNext ChIP-Seq Library Prep kit (New England Biolabs). Libraries for BLESS were prepared using TruSeq Nano DNA LT Library Preparation Kit (Illumina).

text: AsiSI-ER expression

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: female


characteristic: ENA-LAST-UPDATE

text: UNIVERSITY OF BIRMINGHAM

characteristic: INSDC center name

text: public

tag: Namespace:UNIVERSITY OF BIRMINGHAM

text: Escherichia coli 042

text: Escherichia coli 042

text: Biological replicate of EAEC 042 transcriptome


text: UNIVERSITY OF BIRMINGHAM

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: Escherichia coli 042

text: Escherichia coli 042

text: Biological replicate of EAEC 042 aggR mutant transcriptome


text: UNIVERSITY OF CAMBRIDGE

text: public

tag: Namespace:UNIVERSITY OF CAMBRIDGE

text: 3 nt deletion transposon indel library in phosphotriesterase S6 background

text: E. coli

characteristic: lab host

text: Escherichia coli

text: Escherichia coli


text: UNIVERSITY OF CAMBRIDGE

text: public

text: 6 nt deletion transposon indel library in phosphotriesterase S6 background

text: E. coli

text: Escherichia coli

text: Escherichia coli


text: UNIVERSITY OF CAMBRIDGE

text: public

text: 9 nt deletion transposon indel library in phosphotriesterase S6 background

text: E. coli

text: Escherichia coli

text: Escherichia coli


text: UNIVERSITY OF CAMBRIDGE

text: public

text: 3 nt insertion transposon indel library in phosphotriesterase S6 background

text: E. coli

text: Escherichia coli

text: Escherichia coli


text: UNIVERSITY OF CAMBRIDGE

text: public

text: 6 nt insertion transposon indel library in phosphotriesterase S6 background

text: E. coli

text: Escherichia coli

text: Escherichia coli


text: UNIVERSITY OF CAMBRIDGE

text: public

text: 9 nt insertion transposon indel library in phosphotriesterase S6 background

text: E. coli

text: Escherichia coli

text: Escherichia coli


text: UNIVERSITY OF CAMBRIDGE

text: public

text: 3 nt exchange transposon indel library in phosphotriesterase S6 background

text: E. coli

text: Escherichia coli

text: Escherichia coli


text: LMU

text: public

characteristic: collection date

text: skin metagenome

characteristic: common name

text: 16S amplicon sequencing of microbial communities from Antarctic fur seal skin

text: skin environment

characteristic: environment (biome)

text: beach

characteristic: environment (feature)

text: skin environment

characteristic: environment (material)

text: South Georgia and the South Sandwich Islands

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: skin

characteristic: host body habitat

text: antarctic fur seal

characteristic: host common name

text: adult

characteristic: host life stage

text: female

characteristic: host sex

characteristic: host subject id

characteristic: host taxid

text: host-associated

characteristic: host-associated environmental package

text: metagenome

characteristic: investigation type

text: skin metagenome

characteristic: project name

text: DNA extraction from microbial biomass on a sterile swab and amplification of V3-4 region of SSU rRNA

characteristic: sample collection device or method

text: skin metagenome

text: Illumina

characteristic: sequencing method

text: Skin metagenome sample from Antarctic fur seal


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: LMU

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: skin metagenome

characteristic: common name

characteristic: description

text: skin environment

characteristic: environment (biome)

text: beach

text: skin environment

text: skin

text: antarctic fur seal

text: pup

text: female

text: host-associated

text: metagenome

text: skin metagenome

characteristic: organism

text: skin metagenome

text: Illumina

characteristic: title


text: LMU

text: public

text: skin metagenome

text: skin environment

text: beach

characteristic: environment (feature)

text: skin environment

characteristic: environment (material)

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: skin

characteristic: host body habitat

text: antarctic fur seal

characteristic: host common name

text: pup

characteristic: host life stage

text: male

characteristic: host sex

characteristic: host subject id

characteristic: host taxid

text: host-associated

characteristic: host-associated environmental package

text: metagenome

characteristic: investigation type

text: skin metagenome

characteristic: project name

characteristic: sample collection device or method

text: skin metagenome

text: Illumina

characteristic: sequencing method


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Institut de la Mer de Villefranche

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

tag: Namespace:Institut de la Mer de Villefranche

characteristic: Submitter Id

text: Biological replicate 1

characteristic: description

text: Early gastrula

characteristic: dev stage

text: Laboratoire de Biologie du Developpement de Villefranche-sur-mer, Sorbonne Université, CNRS, France

characteristic: lab host

text: Clytia hemisphaerica

characteristic: organism

text: Clytia hemisphaerica

text: Z4B * Z10

characteristic: strain

text: Early gastrula - 1

characteristic: title


text: Homo sapiens

characteristic: ArrayExpress-SPECIES

text: SC

text: public

text: human

characteristic: common name

text: Homo sapiens

text: Homo sapiens

characteristic: subject id


E-MTAB-7099:Sample 1

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: Institut Pasteur

text: public

text: E-MTAB-7099:Sample 1

tag: Namespace:Institut Pasteur

text: ArrayExpress

characteristic: broker name

text: Protocols: Bacteria grown to OD= 0.8 were quickly centrifuged and directly used or frozen in a dry ice/ethanol and stored at -80 °C Bacteria were cultured to late-exponential phase (OD 0.8) in Todd-Hewitt broth with yeast extract (THY) supplemented or not with 15 mM MgCl2. For each condition triplicate cultures were obtained. Bacterial pellets were resuspended in 400 µl 10% glucose, 60 mM EDTA, 12.5 mM Tris pH 7.6. Bacteria cell walls were broken by using two cycles in FastPrep (FastPrep FP120 homogenizer- speed: 6, time:30 s) at 4 \C, separated by 1 min., in the presence of 0.4 g of 200-300 µM glass beads and 500 µl acid phenol pH 4.5. After centrifugation the aquaeous phase was extracted once with 1 ml trizol and 100µl phenol:chloroform:isoamyl alcohol (25:24:1 volume ratio) and once with 200 μl chloroform:isoamyl alcohol and RNA was precipitated by isopropanol. Traces of DNA were removed by using the Turbo DNA-free kit(Life Technologies) according to manufacturer’s instructionq. RNA quality was controled on Agilent 2100 Bioanalyzer with RNA 6000 nanochip and only RNA with RNA Integrity Number (RIN) higher than 9 was used.8 µg total RNA from each RNA sample was depleted in rRNA by using the MICROBExpress bacterial mRNA enrichment kit and rRNA depletion was controled on Agilent Bioanalyzer. For differential RNA-seq experiments, depleted RNAs from each of the 6 samples were mixed. Depleted RNA samples were divided into two subsamples (hereby TAP+ and TAP-) containing the equivalent of 7.5 μ g of total RNA. The TAP+ subsample was pretreated with 10 U of Tobacco Acid Phosphatase (Tebu-Bio), the other steps being strictly run in parallel for the two subsamples. TAP treatment was followed by ligation with an excess of 5′ adapter (Illumina TruSeq Small RNA kit) and by reverse transcription using a random primer (RPO primer: 5′ CCTTGGCACCCGAGAATTCCANNNNNN- 3′ ). The first strand cDNA/RNA hybrids were then run on a 2% Low Range Agarose (Biorad). cDNAs ranging from 120 to 250 bp were extracted from a gel slice by using the Qiaquick gel extraction kit (Qiagen) and PCR amplified for 14 cycles using the Illumina primer RP1, and one of the indexed primers (Illumina TruSeq Small RNA kit). The resulting PCR products were purified with Agencourt AMPure Beads XP (Beckman)

text: wild type genotype

characteristic: genotype

text: mixed pool of bacteria grown in THY with or without 15 mM MgCl2

characteristic: growth condition

text: Streptococcus pyogenes

text: Streptococcus pyogenes

text: Streptococcus pyogenes

text: Sample 1


E-MTAB-7099:Sample 2

characteristic: External Id

text: Institut Pasteur

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-7099:Sample 2

text: ArrayExpress

text: wild type genotype

text: Streptococcus pyogenes

text: Streptococcus pyogenes

text: Streptococcus pyogenes

text: Sample 2


text: LMB

text: public

characteristic: Submitter Id

text: Vegetative

characteristic: cell type

text: Dictyostelium discoideum

characteristic: organism

text: Dictyostelium discoideum


Q1 2014

text: BASF

text: public

text: Q1 2014

characteristic: collection date

text: Injection water

characteristic: description

text: water

characteristic: environment (biome)

text: water

characteristic: environment (feature)

text: water

characteristic: environment (material)

text: Germany

characteristic: geographic location (country and/or sea)

unit: m

characteristic: geographic location (depth)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome

characteristic: investigation type

text: oil field metagenome

text: MEOR

characteristic: project name

text: oil field metagenome

characteristic: sequencing method

text: MEOR

characteristic: title

text: water

characteristic: water environmental package


With nitrate d7

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: BASF

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: With nitrate d7

characteristic: Submitter Id

text: Injection water

text: water

text: water

text: water

text: Germany

text: metagenome

text: oil field metagenome

text: MEOR

text: oil field metagenome

text: MEOR

text: water


With nitrate d18

text: BASF

text: public

text: With nitrate d18

characteristic: collection date

text: Injection water

characteristic: description

text: water

characteristic: environment (biome)

text: water

characteristic: environment (feature)

text: water

characteristic: environment (material)

text: Germany

characteristic: geographic location (country and/or sea)

characteristic: geographic location (depth)

characteristic: geographic location (latitude)

text: metagenome

text: oil field metagenome

characteristic: organism

text: MEOR

text: oil field metagenome

text: MEOR

text: water


With nitrate d160

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: BASF

text: public

text: With nitrate d160

text: Injection water

text: water

text: water

text: water

text: Germany

characteristic: geographic location (longitude)

text: metagenome

characteristic: investigation type

text: oil field metagenome

text: MEOR

characteristic: project name

text: oil field metagenome

characteristic: sequencing method

text: MEOR

characteristic: title

text: water

characteristic: water environmental package


Q2 2014

characteristic: External Id

text: BASF

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: Q2 2014

characteristic: Submitter Id

characteristic: collection date

text: Injection water

characteristic: description

text: water

text: water

text: water

text: Germany

text: metagenome

text: oil field metagenome

text: MEOR

text: oil field metagenome

text: MEOR

text: water


Q3 2014

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: BASF

text: public

text: Q3 2014

text: Injection water

text: water

characteristic: environment (biome)

text: water

characteristic: environment (feature)

text: water

characteristic: environment (material)

text: Germany

characteristic: geographic location (country and/or sea)

characteristic: geographic location (depth)

characteristic: geographic location (latitude)

text: metagenome

text: oil field metagenome

characteristic: organism

text: MEOR

text: oil field metagenome

text: MEOR

text: water


Q4 2014

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: BASF

characteristic: INSDC center name

text: public

text: Q4 2014

text: Injection water

text: water

text: water

text: water

text: Germany

characteristic: geographic location (longitude)

text: metagenome

characteristic: investigation type

text: oil field metagenome

text: MEOR

characteristic: project name

text: oil field metagenome

characteristic: sequencing method

text: MEOR

characteristic: title

text: water

characteristic: water environmental package


Q1 2015

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: BASF

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: Q1 2015

characteristic: Submitter Id

characteristic: collection date

text: Injection water

characteristic: description

text: water

text: water

text: water

text: Germany

text: metagenome

text: oil field metagenome

text: MEOR

text: oil field metagenome

text: MEOR

text: water


Q1.1 2015

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: BASF

text: public

text: Q1.1 2015

text: Injection water

text: water

characteristic: environment (biome)

text: water

characteristic: environment (feature)

text: water

characteristic: environment (material)

text: Germany

characteristic: geographic location (country and/or sea)

characteristic: geographic location (depth)

characteristic: geographic location (latitude)

text: metagenome

text: oil field metagenome

characteristic: organism

text: MEOR

text: oil field metagenome

text: MEOR

text: water


Q2 2015

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: BASF

characteristic: INSDC center name

text: public

text: Q2 2015

text: Injection water

text: water

text: water

text: water

text: Germany

characteristic: geographic location (longitude)

text: metagenome

characteristic: investigation type

text: oil field metagenome

text: MEOR

characteristic: project name

text: oil field metagenome

characteristic: sequencing method

text: MEOR

characteristic: title

text: water

characteristic: water environmental package


Without nitrate d4

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: BASF

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: Without nitrate d4

characteristic: Submitter Id

characteristic: collection date

text: Injection water

characteristic: description

text: water

text: water

text: water

text: Germany

text: metagenome

text: oil field metagenome

text: MEOR

text: oil field metagenome

text: MEOR

text: water


Without nitrate d10

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: BASF

text: public

text: Without nitrate d10

text: Injection water

text: water

characteristic: environment (biome)

text: water

characteristic: environment (feature)

text: water

characteristic: environment (material)

text: Germany

characteristic: geographic location (country and/or sea)

characteristic: geographic location (depth)

characteristic: geographic location (latitude)

text: metagenome

text: oil field metagenome

characteristic: organism

text: MEOR

text: oil field metagenome

text: MEOR

text: water


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: YANGZHOU UNIVERSITY

characteristic: INSDC center name

text: public

tag: Namespace:YANGZHOU UNIVERSITY

text: China

text: diseased

characteristic: host health state

text: Gallus gallus domesticus

characteristic: host scientific name

characteristic: isolate

text: Salmonella enterica subsp. enterica serovar Pullorum

text: Salmonella enterica subsp. enterica serovar Gallinarum biovar Pullorum

characteristic: title


text: YANGZHOU UNIVERSITY

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

text: China

text: diseased

text: Gallus gallus domesticus

text: liver

characteristic: isolation source


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: YANGZHOU UNIVERSITY

text: public

text: China

characteristic: geographic location (country and/or sea)

text: diseased

text: Gallus gallus domesticus

text: caecum


characteristic: ENA-LAST-UPDATE

text: YANGZHOU UNIVERSITY

text: public

text: China

text: diseased

text: Gallus gallus domesticus

text: ovary

characteristic: organism


characteristic: External Id

text: YANGZHOU UNIVERSITY

characteristic: INSDC center name

text: public

text: China

text: diseased

text: Gallus gallus domesticus

text: wind egg


text: YANGZHOU UNIVERSITY

text: public

text: Denmark

text: diseased

characteristic: host health state

text: Gallus gallus domesticus

characteristic: host scientific name


text: YANGZHOU UNIVERSITY

text: public

text: United Kingdom

text: diseased

text: Gallus gallus domesticus

characteristic: isolate

characteristic: title


text: YANGZHOU UNIVERSITY

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: Denmark

text: diseased

text: Gallus gallus domesticus

text: I ex


text: YANGZHOU UNIVERSITY

text: public

characteristic: INSDC status

characteristic: SRA accession

text: United Kingdom

text: diseased

text: Gallus gallus domesticus

text: liver


text: YANGZHOU UNIVERSITY

text: public

characteristic: Submitter Id

characteristic: collection date

text: Brazil

text: diseased

text: Gallus gallus domesticus


characteristic: ENA-CHECKLIST

text: YANGZHOU UNIVERSITY

text: public

text: China

text: diseased

text: Gallus gallus domesticus

text: yolk sac

characteristic: isolation source


characteristic: ENA-FIRST-PUBLIC

text: YANGZHOU UNIVERSITY

text: public

text: United Kingdom

characteristic: geographic location (country and/or sea)

text: diseased

text: Gallus gallus domesticus

text: viscera


characteristic: ENA-LAST-UPDATE

text: CNGB

text: public

text: CNSA

characteristic: broker name

characteristic: description

text: Netherlands : Maastricht

characteristic: geographic location

text: human

characteristic: host

text: 50.85 N 5.69 E

characteristic: latitude and longitude

text: human gut metagenome

characteristic: organism

characteristic: sample name

text: human gut metagenome

text: human gut metagenome


characteristic: External Id

text: University of Gothenburg

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

tag: Namespace:University of Gothenburg

text: MGRAST

characteristic: collection time

text: asia

characteristic: continent

text: Metagenomics3_1 Taxonomy ID:556182

text: small lake biome

characteristic: environment (biome)

text: lake

characteristic: environment (feature)

text: sediment

characteristic: environment (material)

text: sediment

characteristic: environmental package

text: India

characteristic: geographic location (depth)

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Hyderabad

characteristic: geographic location (region and locality)

text: metagenome

characteristic: investigation type

text: freshwater sediment

characteristic: mgrast id

text: freshwater sediment metagenome

characteristic: project name

text: freshwater sediment metagenome

text: sediment

characteristic: sediment environmental package

text: illumina

characteristic: sequencing method

text: Metagenomics3_1 Taxonomy ID:556182

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: University of Gothenburg

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: MGRAST

characteristic: broker name

characteristic: collection date

characteristic: collection time

text: asia

text: Metagenomics1_1 Taxonomy ID:556182

characteristic: description

text: small river biome

text: river

text: sediment

text: sediment

text: India

characteristic: geographic location (country and/or sea)

text: Hyderabad

text: metagenome

text: freshwater sediment

text: freshwater sediment metagenome

characteristic: organism

characteristic: sample name

text: freshwater sediment metagenome

text: sediment

text: illumina

text: Metagenomics1_1 Taxonomy ID:556182


characteristic: ENA-CHECKLIST

text: University of Gothenburg

text: public

text: MGRAST

text: asia

characteristic: continent

text: JL28_1 Taxonomy ID:556182

text: small river biome

characteristic: environment (biome)

text: river

characteristic: environment (feature)

text: sediment

characteristic: environment (material)

text: sediment

characteristic: environmental package

text: India

characteristic: geographic location (depth)

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Hyderabad

characteristic: geographic location (region and locality)

text: metagenome

characteristic: investigation type

text: freshwater sediment

characteristic: mgrast id

text: freshwater sediment metagenome

characteristic: project name

text: freshwater sediment metagenome

text: sediment

characteristic: sediment environmental package

text: illumina

characteristic: sequencing method

text: JL28_1 Taxonomy ID:556182

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: University of Gothenburg

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: MGRAST

characteristic: broker name

characteristic: collection date

characteristic: collection time

text: asia

text: JL28_2 Taxonomy ID:556182

characteristic: description

text: small river biome

text: river

text: sediment

text: sediment

text: India

characteristic: geographic location (country and/or sea)

text: Hyderabad

text: metagenome

text: freshwater sediment

text: freshwater sediment metagenome

characteristic: organism

characteristic: sample name

text: freshwater sediment metagenome

text: sediment

text: illumina

text: JL28_2 Taxonomy ID:556182


characteristic: ENA-CHECKLIST

text: University of Gothenburg

text: public

text: MGRAST

text: asia

characteristic: continent

text: JL33_2 Taxonomy ID:556182

text: small lake biome

characteristic: environment (biome)

text: lake

characteristic: environment (feature)

text: sediment

characteristic: environment (material)

text: sediment

characteristic: environmental package

text: India

characteristic: geographic location (depth)

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Hyderabad

characteristic: geographic location (region and locality)

text: metagenome

characteristic: investigation type

text: freshwater sediment

characteristic: mgrast id

text: freshwater sediment metagenome

characteristic: project name

text: freshwater sediment metagenome

text: sediment

characteristic: sediment environmental package

text: illumina

characteristic: sequencing method

text: JL33_2 Taxonomy ID:556182

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: University of Gothenburg

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: MGRAST

characteristic: broker name

characteristic: collection date

characteristic: collection time

text: asia

text: JL30_1 Taxonomy ID:556182

characteristic: description

text: small river biome

text: river

text: sediment

text: sediment

text: India

characteristic: geographic location (country and/or sea)

text: Hyderabad

text: metagenome

text: freshwater sediment

text: freshwater sediment metagenome

characteristic: organism

characteristic: sample name

text: freshwater sediment metagenome

text: sediment

text: illumina

text: JL30_1 Taxonomy ID:556182


characteristic: ENA-CHECKLIST

text: University of Gothenburg

text: public

text: MGRAST

text: asia

characteristic: continent

text: Metagenomics1_2 Taxonomy ID:556182

text: small river biome

characteristic: environment (biome)

text: river

characteristic: environment (feature)

text: sediment

characteristic: environment (material)

text: sediment

characteristic: environmental package

text: India

characteristic: geographic location (depth)

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Hyderabad

characteristic: geographic location (region and locality)

text: metagenome

characteristic: investigation type

text: freshwater sediment

characteristic: mgrast id

text: freshwater sediment metagenome

characteristic: project name

text: freshwater sediment metagenome

text: sediment

characteristic: sediment environmental package

text: illumina

characteristic: sequencing method

text: Metagenomics1_2 Taxonomy ID:556182

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: University of Gothenburg

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: MGRAST

characteristic: broker name

characteristic: collection date

characteristic: collection time

text: asia

text: JL32_1 Taxonomy ID:556182

characteristic: description

text: small river biome

text: river

text: sediment

text: sediment

text: India

characteristic: geographic location (country and/or sea)

text: Hyderabad

text: metagenome

text: freshwater sediment

text: freshwater sediment metagenome

characteristic: organism

characteristic: sample name

text: freshwater sediment metagenome

text: sediment

text: illumina

text: JL32_1 Taxonomy ID:556182


characteristic: ENA-CHECKLIST

text: University of Gothenburg

text: public

text: MGRAST

text: asia

characteristic: continent

text: JL29_1 Taxonomy ID:556182

text: small river biome

characteristic: environment (biome)

text: river

characteristic: environment (feature)

text: sediment

characteristic: environment (material)

text: sediment

characteristic: environmental package

text: India

characteristic: geographic location (depth)

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Hyderabad

characteristic: geographic location (region and locality)

text: metagenome

characteristic: investigation type

text: freshwater sediment

characteristic: mgrast id

text: freshwater sediment metagenome

characteristic: project name

text: freshwater sediment metagenome

text: sediment

characteristic: sediment environmental package

text: illumina

characteristic: sequencing method

text: JL29_1 Taxonomy ID:556182

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: University of Gothenburg

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: MGRAST

characteristic: broker name

characteristic: collection date

characteristic: collection time

text: asia

text: JL29_2 Taxonomy ID:556182

characteristic: description

text: small river biome

text: river

text: sediment

text: sediment

text: India

characteristic: geographic location (country and/or sea)

text: Hyderabad

text: metagenome

text: freshwater sediment

text: freshwater sediment metagenome

characteristic: organism

characteristic: sample name

text: freshwater sediment metagenome

text: sediment

text: illumina

text: JL29_2 Taxonomy ID:556182


characteristic: ENA-CHECKLIST

text: University of Gothenburg

text: public

text: MGRAST

text: asia

characteristic: continent

text: JL31_2 Taxonomy ID:556182

text: small river biome

characteristic: environment (biome)

text: river

characteristic: environment (feature)

text: sediment

characteristic: environment (material)

text: sediment

characteristic: environmental package

text: India

characteristic: geographic location (depth)

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Hyderabad

characteristic: geographic location (region and locality)

text: metagenome

characteristic: investigation type

text: freshwater sediment

characteristic: mgrast id

text: freshwater sediment metagenome

characteristic: project name

text: freshwater sediment metagenome

text: sediment

characteristic: sediment environmental package

text: illumina

characteristic: sequencing method

text: JL31_2 Taxonomy ID:556182

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: University of Gothenburg

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: MGRAST

characteristic: broker name

characteristic: collection date

characteristic: collection time

text: asia

text: JL33_1 Taxonomy ID:556182

characteristic: description

text: small lake biome

text: lake

text: sediment

text: sediment

text: India

characteristic: geographic location (country and/or sea)

text: Hyderabad

text: metagenome

text: freshwater sediment

text: freshwater sediment metagenome

characteristic: organism

characteristic: sample name

text: freshwater sediment metagenome

text: sediment

text: illumina

text: JL33_1 Taxonomy ID:556182


characteristic: ENA-CHECKLIST

text: University of Gothenburg

text: public

text: MGRAST

text: asia

characteristic: continent

text: Metagenomics4_1 Taxonomy ID:556182

text: small lake biome

characteristic: environment (biome)

text: lake

characteristic: environment (feature)

text: sediment

characteristic: environment (material)

text: sediment

characteristic: environmental package

text: India

characteristic: geographic location (depth)

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Hyderabad

characteristic: geographic location (region and locality)

text: metagenome

characteristic: investigation type

text: freshwater sediment

characteristic: mgrast id

text: freshwater sediment metagenome

characteristic: project name

text: freshwater sediment metagenome

text: sediment

characteristic: sediment environmental package

text: illumina

characteristic: sequencing method

text: Metagenomics4_1 Taxonomy ID:556182

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: University of Gothenburg

characteristic: INSDC center name

characteristic: INSDC first public

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text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: MGRAST

characteristic: broker name

characteristic: collection date

characteristic: collection time

text: asia

text: JL30_2 Taxonomy ID:556182

characteristic: description

text: small river biome

text: river

text: sediment

text: sediment

text: India

characteristic: geographic location (country and/or sea)

text: Hyderabad

text: metagenome

text: freshwater sediment

text: freshwater sediment metagenome

characteristic: organism

characteristic: sample name

text: freshwater sediment metagenome

text: sediment

text: illumina

text: JL30_2 Taxonomy ID:556182


characteristic: ENA-CHECKLIST

text: University of Gothenburg

text: public

text: MGRAST

text: asia

characteristic: continent

text: JL27_2 Taxonomy ID:556182

text: small river biome

characteristic: environment (biome)

text: river

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text: sediment

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text: sediment

characteristic: environmental package

text: India

characteristic: geographic location (depth)

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

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text: Hyderabad

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text: metagenome

characteristic: investigation type

text: freshwater sediment

characteristic: mgrast id

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characteristic: project name

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text: illumina

characteristic: sequencing method

text: JL27_2 Taxonomy ID:556182

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: University of Gothenburg

characteristic: INSDC center name

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characteristic: SRA accession

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text: MGRAST

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text: asia

text: Metagenomics2_2 Taxonomy ID:556182

characteristic: description

text: small river biome

text: river

text: sediment

text: sediment

text: India

characteristic: geographic location (country and/or sea)

text: Hyderabad

text: metagenome

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text: freshwater sediment metagenome

characteristic: organism

characteristic: sample name

text: freshwater sediment metagenome

text: sediment

text: illumina

text: Metagenomics2_2 Taxonomy ID:556182


characteristic: ENA-CHECKLIST

text: University of Gothenburg

text: public

text: MGRAST

text: asia

characteristic: continent

text: JL31_1 Taxonomy ID:556182

text: small river biome

characteristic: environment (biome)

text: river

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text: sediment

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text: sediment

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characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Hyderabad

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text: illumina

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text: JL31_1 Taxonomy ID:556182

characteristic: title


characteristic: ENA-CHECKLIST

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text: University of Gothenburg

characteristic: INSDC center name

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text: public

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characteristic: Submitter Id

text: MGRAST

characteristic: broker name

characteristic: collection date

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text: asia

text: Metagenomics2_1 Taxonomy ID:556182

characteristic: description

text: small river biome

text: river

text: sediment

text: sediment

text: India

characteristic: geographic location (country and/or sea)

text: Hyderabad

text: metagenome

text: freshwater sediment

text: freshwater sediment metagenome

characteristic: organism

characteristic: sample name

text: freshwater sediment metagenome

text: sediment

text: illumina

text: Metagenomics2_1 Taxonomy ID:556182


characteristic: ENA-CHECKLIST

text: University of Gothenburg

text: public

text: MGRAST

text: asia

characteristic: continent

text: Metagenomics4_2 Taxonomy ID:556182

text: small lake biome

characteristic: environment (biome)

text: lake

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text: sediment

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text: sediment

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text: India

characteristic: geographic location (depth)

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Hyderabad

characteristic: geographic location (region and locality)

text: metagenome

characteristic: investigation type

text: freshwater sediment

characteristic: mgrast id

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text: sediment

characteristic: sediment environmental package

text: illumina

characteristic: sequencing method

text: Metagenomics4_2 Taxonomy ID:556182

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: University of Gothenburg

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: MGRAST

characteristic: broker name

characteristic: collection date

characteristic: collection time

text: asia

text: JL32_2 Taxonomy ID:556182

characteristic: description

text: small river biome

text: river

text: sediment

text: sediment

text: India

characteristic: geographic location (country and/or sea)

text: Hyderabad

text: metagenome

text: freshwater sediment

text: freshwater sediment metagenome

characteristic: organism

characteristic: sample name

text: freshwater sediment metagenome

text: sediment

text: illumina

text: JL32_2 Taxonomy ID:556182


characteristic: ENA-CHECKLIST

text: University of Gothenburg

text: public

text: MGRAST

text: asia

characteristic: continent

text: JL27_1 Taxonomy ID:556182

text: small river biome

characteristic: environment (biome)

text: river

characteristic: environment (feature)

text: sediment

characteristic: environment (material)

text: sediment

characteristic: environmental package

text: India

characteristic: geographic location (depth)

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Hyderabad

characteristic: geographic location (region and locality)

text: metagenome

characteristic: investigation type

text: freshwater sediment

characteristic: mgrast id

text: freshwater sediment metagenome

characteristic: project name

text: freshwater sediment metagenome

text: sediment

characteristic: sediment environmental package

text: illumina

characteristic: sequencing method

text: JL27_1 Taxonomy ID:556182

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: University of Gothenburg

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: MGRAST

characteristic: broker name

characteristic: collection date

characteristic: collection time

text: asia

text: Metagenomics3_2 Taxonomy ID:556182

characteristic: description

text: small lake biome

text: lake

text: sediment

text: sediment

text: India

characteristic: geographic location (country and/or sea)

text: Hyderabad

text: metagenome

text: freshwater sediment

text: freshwater sediment metagenome

characteristic: organism

characteristic: sample name

text: freshwater sediment metagenome

text: sediment

text: illumina

text: Metagenomics3_2 Taxonomy ID:556182


characteristic: ENA-CHECKLIST

text: CNGB

text: public

text: CNSA

text: Netherlands : Maastricht

characteristic: geographic location

text: human

characteristic: host

text: 50.85 N 5.69 E

characteristic: latitude and longitude

text: human gut metagenome

text: human gut metagenome

text: human gut metagenome

characteristic: title


E-MTAB-7101:Sample 1

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: IP

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-7101:Sample 1

text: ArrayExpress

text: Protocols: Bacteria grown to OD= 0.8 were quickly centrifuged and directly used or frozen in a dry ice/ethanol bath and stored at -80 °C. Bacteria were cultured to late-exponential phase (OD 0.8) in Todd-Hewitt broth with yeast extract (THY) supplemented or not with 15 mM MgCl2. For each condition triplicate cultures were obtained Bacterial pellets were resuspended in 400 µl 10% glucose, 60 mM EDTA, 12.5 mM Tris pH 7.6. Bacteria cell walls were broken by using two cycles in FastPrep (FastPrep FP120 homogenizer- speed: 6, time:30 s) at 4 \C, separated by 1 min., in the presence of 0.4 g of 200-300 µM glass beads and 500 µl acid phenol pH 4.5. After centrifugation the aquaeous phase was extracted once with 1 ml trizol and 100µl phenol:chloroform:isoamyl alcohol (25:24:1 volume ratio) and once with 200 μl chloroform:isoamyl alcohol and RNA was precipitated by isopropanol.Traces of DNA were removed by using the Turbo DNA-free kit(Life Technologies) according to manufacturer’s instructionq. RNA quality was controled on Agilent 2100 Bioanalyzer with RNA 6000 nanochip and only RNA with RNA Integrity Number (RIN) higher than 9 was used.8 µg total RNA from each RNA sample was depleted in rRNA by using the MICROBExpress bacterial mRNA enrichment kit and rRNA depletion was controled on Agilent Bioanalyzer. For each of the strand-specific RNA-seq library preparation, depleted RNA corresponding to 1 µg of total RNA was used. RNA was treated with TAP (Tebu-Bio), fragmented using the RNA fragmentation Reagent kit(Ambion). Dephosphorylation of the fragmented RNA by using the antarctic phosphatase (Biolabs), and rephosphorylation with the T4 polynucleotide kinase (Biolabs) were followed by a purification step through RNeasy MinElute Cleanup columns (Qiagen). The RNA was then successively ligated to the 3′ RNA adapter (Illumina TruSeq Small RNA kit) by using truncated T4 RNA ligase 2 (Biolabs) and to the 5′ RNA adapter (Illumina TruSeq Small RNA kit) with T4 RNA ligase (Biolabs). RNA ligated to the two adapters was reverse-transcribed with the Superscript II Reverse Transcriptase (Life Technologies) and the RNA reverse transcription primer (Illumina TruSeq Small RNA kit). The resulting cDNAs were amplified for 13 PCR cycles with Phusion Taq polymerase using the RP1 primer and one of the indexed PCR primers (Illumina TruSeq Small RNA kit).

text: wild type genotype

characteristic: genotype

text: THY broth

characteristic: growth condition

text: Streptococcus pyogenes

text: Streptococcus pyogenes

text: Streptococcus pyogenes

characteristic: strain

text: Sample 1


E-MTAB-7101:Sample 2

text: IP

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-7101:Sample 2

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

characteristic: description

text: wild type genotype

text: THY broth

text: Streptococcus pyogenes

text: Streptococcus pyogenes

text: Streptococcus pyogenes

text: Sample 2


E-MTAB-7101:Sample 3

characteristic: ENA-CHECKLIST

text: IP

text: public

text: E-MTAB-7101:Sample 3

text: ArrayExpress

text: wild type genotype

text: THY broth

text: Streptococcus pyogenes

characteristic: organism

text: Streptococcus pyogenes

text: Streptococcus pyogenes

text: Sample 3


E-MTAB-7101:Sample 4

text: IP

text: public

text: E-MTAB-7101:Sample 4

text: ArrayExpress

text: wild type genotype

text: THY broth

text: Streptococcus pyogenes

text: Streptococcus pyogenes

text: Streptococcus pyogenes

text: Sample 4

characteristic: title


E-MTAB-7101:Sample 5

characteristic: ENA-FIRST-PUBLIC

text: IP

text: public

text: E-MTAB-7101:Sample 5

text: ArrayExpress

text: wild type genotype

text: THY broth

text: Streptococcus pyogenes

text: Streptococcus pyogenes

text: Streptococcus pyogenes

text: Sample 5


E-MTAB-7101:Sample 6

characteristic: ENA-LAST-UPDATE

text: IP

text: public

text: E-MTAB-7101:Sample 6

text: ArrayExpress

text: wild type genotype

text: THY broth

text: Streptococcus pyogenes

text: Streptococcus pyogenes

text: Streptococcus pyogenes

text: Sample 6


E-MTAB-7101:Sample 10

characteristic: External Id

text: IP

text: public

text: E-MTAB-7101:Sample 10

text: ArrayExpress

text: wild type genotype

text: THY broth

text: Streptococcus pyogenes

text: Streptococcus pyogenes

text: Streptococcus pyogenes

text: Sample 10


E-MTAB-7101:Sample 11

text: IP

characteristic: INSDC center name

text: public

text: E-MTAB-7101:Sample 11

text: ArrayExpress

text: wild type genotype

text: THY broth

text: Streptococcus pyogenes

text: Streptococcus pyogenes

text: Streptococcus pyogenes

text: Sample 11


E-MTAB-7101:Sample 12

text: IP

characteristic: INSDC first public

text: public

text: E-MTAB-7101:Sample 12

text: ArrayExpress

text: wild type genotype

text: THY broth

text: Streptococcus pyogenes

text: Streptococcus pyogenes

text: Streptococcus pyogenes

text: Sample 12


E-MTAB-7101:Sample 7

text: IP

text: public

text: E-MTAB-7101:Sample 7

text: ArrayExpress

text: wild type genotype

characteristic: genotype

text: THY broth

text: Streptococcus pyogenes

text: Streptococcus pyogenes

text: Streptococcus pyogenes

text: Sample 7


E-MTAB-7101:Sample 8

text: IP

text: public

text: E-MTAB-7101:Sample 8

text: ArrayExpress

text: wild type genotype

text: THY broth

characteristic: growth condition

text: Streptococcus pyogenes

text: Streptococcus pyogenes

text: Streptococcus pyogenes

text: Sample 8


E-MTAB-7101:Sample 9

text: IP

text: public

text: E-MTAB-7101:Sample 9

text: ArrayExpress

text: wild type genotype

text: THY broth

text: Streptococcus pyogenes

text: Streptococcus pyogenes

text: Streptococcus pyogenes

characteristic: strain

text: Sample 9


text: WELLCOME TRUST SANGER INSTITUTE

characteristic: INSDC last update

text: public

tag: Namespace:WELLCOME TRUST SANGER INSTITUTE

text: ArrayExpress

text: CD4-positive helper T cell

characteristic: cell type

text: house mouse

characteristic: common name

text: Protocols: 20 million cells from each sample were crosslinked in 1% HCHO (prepared in 1X DPBS) at room temperature for 10 minutes, and HCHO was quenched by the addition of glycine at a final concentration of 0.125 M. Cells were pelleted at 4°C at 2000 x g, washed with ice-cold 1X DPBS twice, and snapped frozen in liquid nitrogen. The cell pellets were stored in -80°C until the experiments were performed. ChIPmentation was performed according to the version 1.0 of the published protocol (Schmidl et al., 2015b) with some modifications at the ChIP stage. Briefly, cell pellets were thawed on ice, and lysed in 300 l ChIP Lysis Buffer I (50 mM HEPES.KOH, pH 7.5, 140 mM NaCl, 1 mM EDTA, pH 8.0, 10% Glycerol, 0.5% NP-40, 0.25% Triton X-100) on ice for 10 minutes. Then cells were pelleted at 4°C at 2000 x g for 5 minutes, and washed by 300 l ChIP Lysis Buffer II (10 mM Tris.Cl, pH 8.0, 200 mM NaCl, 1 mM EDTA, pH 8.0, 0.5 mM EGTA, pH 8.0), and pelleted again at 4°C at 2000 x g for 5 minutes. Nuclei were resuspended in 300 l ChIP Lysis Buffer III (10 mM Tris.Cl, pH 8.0, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% Sodium Deoxycholate, 0.5% N-Lauryolsarcosine). Chromatin was sonicated using Bioruptor Pico (Diagenode) with 30 seconds ON/30 seconds OFF for 5 cycles. 30 l 10% Triton X-100 were added into each sonicated chromatin, and insoluble chromatin was pelleted at 16,100 x g at 4°C for 10 minutes. 1 l supernatant was taken as input control. The rest of the supernatant was incubated with 10 l Protein A Dynabeads (Invitrogen) pre-bound with 1 g XBP1 antibody (XBP1 (M-186)X - Santa cruz), in a rotating platform in a cold room overnight. Each immunoprecipitation (IP) was washed with 500 l RIPA Buffer (50 mM HEPES.KOH, pH 7.5, 500 mM LiCl, 1 mM EDTA, 1% NP-40, 0.7% Sodium Deoxycholate, check components) for 3 times. Then, each IP was washed with 500 l 10 mM Tris, pH 8.0 twice, and resuspended in 30 l tagmentation reaction mix (10 mM Tris.Cl, pH 8.0, 5 mM Mg2Cl, 1 l TDE1 (Nextera)). Then, the tagmentation reaction was put on a thermomixer at 37°C for 10 minutes at 800 rpm shaking. After the tagmentation reaction, each IP was washed sequentially with 500 l RIPA Buffer twice, and 1X TE NaCl (10 mM Tris.Cl, pH 8.0, 1 mM EDTA, pH 8.0, 50 mM NaCl) once. Elution and reverse-crosslinking was done by resuspending the beads with 100 l ChIP Elution Buffer (50 mM Tris.Cl, pH 8.0, 10 mM EDTA, pH 8.0, 1% SDS) on a thermomixer at 65°C overnight, 1,400 rpm. DNA was purified by MinElute PCR Purification Kit (QIAGEN, cat no. 28004 and eluted in 12.5 l Buffer EB (QIAGEN kit, cat no 28004), which yielded ~10 l ChIPed DNA. ChIPed DNA before amplification was purified using Qiagen MinElute PCR purification kit. After library amplification, DNA was purified using AmpureXP beads with a 0.5X upper cutoff and 1.2X lower cutoff. The library preparation reactions contained the following: 10 l purified DNA (from above), 2.5 l PCR Primer Cocktails (Nextera DNA Library Preparation Kit, Illumina Cat no. FC-121-1030), 2.5 l N5xx (Nextera Index Kit , Illumina cat no.FC-121-1012), 2.5 l N7xx (Nextera index kit , Illumina cat no. FC-121-1012), 7.5 l NPM PCR Master Mix (Nextera DNA Library Preparation Kit, Illumina Cat no. FC-121-1030) PCR was set up as follows: 72°C, 5 mins; 98°C, 2 mins; [98°C, 10 secs, 63°C, 30 secs, 72°C, 20 secs] x 12; 10°C hold

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: interleukin-4 (10 nanogram per milliter for 5 days)

characteristic: stimulus


text: Baker Institute, Cornell University

text: public

characteristic: INSDC status

characteristic: SRA accession

tag: Namespace:Baker Institute, Cornell University

characteristic: Submitter Id

text: Beagle

characteristic: breed

text: ArrayExpress

characteristic: broker name

text: mammary stem cell

text: dog

text: Protocols: Cells were cultured for 24 h prior to a 4 h treatment with vehicle (DMSO) or DMBA. Total RNA was extracted with TRIzol reagent following the recommendations of the manufacturer. The quality of total RNA was evaluated using the Agilent 2100 bioanalyzer (Agilent, Palo Alto, CA, USA) with the RNA 6000 Nano LabChip kit. RNA-seq libraries were prepared with the NEBNext Ultra Directional RNA Library Prep Kit (New England Biolabs) using 500 ng total RNA followed by polyA+ enrichment.

text: adult

characteristic: developmental stage

characteristic: individual

text: Canis lupus familiaris

text: Canis lupus familiaris

text: mammary gland

characteristic: organism part

text: Canis lupus familiaris

text: female

characteristic: sex

text: DM-DMSO


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Baker Institute, Cornell University

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: Beagle

text: ArrayExpress

text: mammary stem cell

text: dog

characteristic: description

text: adult

text: Canis lupus familiaris

characteristic: organism

text: Canis lupus familiaris

text: mammary gland

text: Canis lupus familiaris

text: female

text: DN-DMSO

characteristic: title


text: Baker Institute, Cornell University

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: Beagle

text: ArrayExpress

text: mammary stem cell

characteristic: cell type

text: dog

characteristic: common name

text: adult

text: Canis lupus familiaris

text: Canis lupus familiaris

text: mammary gland

text: Canis lupus familiaris

text: female

text: DQ-DMSO


text: Baker Institute, Cornell University

text: public

characteristic: Submitter Id

text: Thoroughbred

characteristic: breed

text: ArrayExpress

characteristic: broker name

text: mammary stem cell

text: horse

text: adult

characteristic: developmental stage

characteristic: individual

text: Equus caballus

text: Equus caballus

text: mammary gland

text: Equus caballus

text: female

text: HB-DMSO


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: Baker Institute, Cornell University

text: public

text: Thoroughbred

text: ArrayExpress

text: mammary stem cell

text: horse

text: adult

text: Equus caballus

text: Equus caballus

text: mammary gland

characteristic: organism part

text: Equus caballus

text: female

characteristic: sex

text: HF-DMSO


characteristic: External Id

text: Baker Institute, Cornell University

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: Thoroughbred

text: ArrayExpress

text: mammary stem cell

text: horse

characteristic: description

text: adult

text: Equus caballus

characteristic: organism

text: Equus caballus

text: mammary gland

text: Equus caballus

text: female

text: HN-DMSO


text: Baker Institute, Cornell University

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: Beagle

text: ArrayExpress

text: mammary stem cell

characteristic: cell type

text: dog

text: adult

text: Canis lupus familiaris

text: Canis lupus familiaris

text: mammary gland

text: Canis lupus familiaris

text: female

text: DM-DMBA

characteristic: title


text: Baker Institute, Cornell University

text: public

characteristic: Submitter Id

text: Beagle

characteristic: breed

text: ArrayExpress

characteristic: broker name

text: mammary stem cell

text: dog

characteristic: common name

text: adult

characteristic: developmental stage

text: Canis lupus familiaris

text: Canis lupus familiaris

text: mammary gland

text: Canis lupus familiaris

text: female

text: DN-DMBA


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: Baker Institute, Cornell University

text: public

text: Beagle

text: ArrayExpress

text: mammary stem cell

text: dog

text: adult

characteristic: individual

text: Canis lupus familiaris

text: Canis lupus familiaris

text: mammary gland

characteristic: organism part

text: Canis lupus familiaris

text: female

text: DQ-DMBA


characteristic: External Id

text: Baker Institute, Cornell University

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: Thoroughbred

text: ArrayExpress

text: mammary stem cell

text: horse

characteristic: description

text: adult

text: Equus caballus

text: Equus caballus

text: mammary gland

text: Equus caballus

text: female

characteristic: sex

text: HB-DMBA


text: Baker Institute, Cornell University

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: Thoroughbred

text: ArrayExpress

text: mammary stem cell

characteristic: cell type

text: horse

text: adult

text: Equus caballus

characteristic: organism

text: Equus caballus

text: mammary gland

text: Equus caballus

text: female

text: HF-DMBA


text: Baker Institute, Cornell University

text: public

characteristic: Submitter Id

text: Thoroughbred

characteristic: breed

text: ArrayExpress

characteristic: broker name

text: mammary stem cell

text: horse

characteristic: common name

text: adult

text: Equus caballus

text: Equus caballus

text: mammary gland

text: Equus caballus

text: female

text: HN-DMBA

characteristic: title


text: Plasmodium falciparum

characteristic: ArrayExpress-SPECIES

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: SC

text: public

text: malaria parasite P. falciparum

text: Plasmodium falciparum

text: Plasmodium falciparum

characteristic: subject id


characteristic: External Id

text: CNGB

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: age

text: CNSA

text: Norway rat

characteristic: description

text: Rattus norvegicus

text: IR

characteristic: sample name

text: Rattus norvegicus

text: female

text: Wistar rats

characteristic: strain

text: hypothalamus

characteristic: tissue


text: CNGB

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: CNSA

text: Xiaofen Fu

characteristic: collected by

characteristic: collection date

text: China: Beijing

characteristic: geographic location

text: Fermentation medium

characteristic: isolation source

text: Kluyveromyces marxianus

characteristic: organism

text: Pure culture

characteristic: sample type

text: Kluyveromyces marxianus


text: Streptococcus pneumoniae

characteristic: ArrayExpress-SPECIES

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

characteristic: INSDC center name

text: public

text: Streptococcus pneumoniae

characteristic: common name

text: Streptococcus pneumoniae

text: Streptococcus pneumoniae

characteristic: subject id

text: RMV1 tvr::cat rpsL*

characteristic: title


text: Streptococcus pneumoniae

text: SC

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: Streptococcus pneumoniae

text: Streptococcus pneumoniae

text: Streptococcus pneumoniae


text: Streptococcus pneumoniae

text: SC

text: public

characteristic: Submitter Id

text: Streptococcus pneumoniae

text: Streptococcus pneumoniae

text: Streptococcus pneumoniae

text: R6I-7.5d passage


text: Hopital Henri Mondor APHP

text: public

tag: Namespace:Hopital Henri Mondor APHP

text: 01/01/2018 - 01/03/2018

characteristic: collection date

text: Escherichia coli

text: Colistin-resistant E. coli

characteristic: description

text: France

characteristic: geographic location (country and/or sea)

text: Paris

characteristic: geographic location (region and locality)

characteristic: isolate

text: Rectal swab

characteristic: isolation source

text: Escherichia coli

text: Escherichia coli

text: Colistin resistance in human faecal Escherichia coli as the result of two distinct evolutionary pathways in France


text: Plasmodium vivax

characteristic: ArrayExpress-SPECIES

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: SC

text: public

text: malaria parasite P. vivax

text: Plasmodium vivax

characteristic: organism

text: Plasmodium vivax


Heterodera sacchari RNAseq1

characteristic: External Id

text: The James Hutton Institute

characteristic: INSDC center name

text: public

text: Heterodera sacchari RNAseq1

tag: Namespace:The James Hutton Institute

text: Whole nematode

characteristic: cell type

text: somnath pokhare

characteristic: collected by

text: Transcriptome analysis of the sugarcane cyst nematode Heterodera sacchari shows signatures of adaptation to a monocot host: Heterodera sacchari, the sugar cane cyst nematode, is a serious pathogen of rice crops but is relatively neglected compared to other nematodes. To address this we have sequenced the transcriptome of invasive stage and parasitic stage nematodes. Analysis of effectors from this transcriptome revealed signatures of adaptation to parasitism of monocots, including loss of GH53 cell wall degrading enzymes.

text: J2 and femal 15 day post infection

characteristic: dev stage

text: Oryza sativa

characteristic: host scientific name

text: Heterodera sacchari

text: Heterodera sacchari

characteristic: title


text: Friedrich-Loeffler-Institute

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald - Insel Riems, Germany

characteristic: collecting institution

text: Leonie Forth

characteristic: collector name

text: Giant squirrel respirovirus

characteristic: common name

text: A novel squirrel respirovirus with putative zoonotic potential

characteristic: description

text: Sri Lanka

text: Sri Lankan Giant Squirrel

characteristic: host common name

text: diseased

characteristic: host health state

text: Ratufa macroura

text: female

characteristic: host sex

characteristic: host subject id

text: Giant squirrel respirovirus

text: Giant squirrel respirovirus


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Medical Univeristy of Graz

characteristic: INSDC center name

text: public

tag: Namespace:Medical Univeristy of Graz

characteristic: collection date

text: plant leaf

characteristic: environment (biome)

text: Leaves

characteristic: environment (feature)

text: plant

characteristic: environment (material)

text: Austria

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome

characteristic: investigation type

text: Chlorophytum comosum

characteristic: organism

text: plant-associated

characteristic: plant-associated environmental package

text: Biostimulants

characteristic: project name

text: Chlorophytum comosum

text: Illumina

characteristic: sequencing method


characteristic: ENA-CHECKLIST

text: Medical Univeristy of Graz

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: indoor

characteristic: common name

characteristic: description

text: plant environment

text: Surfaces

text: glass

text: Austria

text: metagenome

text: indoor metagenome

text: plant-associated

text: Biostimulants

text: indoor metagenome

text: Illumina

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Medical Univeristy of Graz

characteristic: INSDC center name

text: public

characteristic: collection date

text: indoor

text: plant control

characteristic: environment (biome)

text: Control

characteristic: environment (feature)

text: textile

characteristic: environment (material)

text: Austria

characteristic: geographic location (country and/or sea)

text: metagenome

text: indoor metagenome

text: plant-associated

text: Biostimulants

text: indoor metagenome

text: Illumina


characteristic: ENA-CHECKLIST

text: Medical Univeristy of Graz

characteristic: INSDC first public

text: public

text: indoor

text: plant soil

text: Soil

text: soil

text: Austria

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome

characteristic: investigation type

text: indoor metagenome

characteristic: organism

text: plant-associated

characteristic: plant-associated environmental package

text: Biostimulants

characteristic: project name

text: indoor metagenome

text: Illumina

characteristic: sequencing method


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: Medical Univeristy of Graz

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: indoor

characteristic: common name

characteristic: description

text: plant control

text: Control

text: reagent

text: Austria

text: metagenome

text: indoor metagenome

text: plant-associated

text: Biostimulants

text: indoor metagenome

text: Illumina

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: External Id

text: Medical Univeristy of Graz

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: collection date

text: indoor

text: biostimulant

characteristic: environment (biome)

text: Product

characteristic: environment (feature)

text: vermicompost

characteristic: environment (material)

text: Austria

characteristic: geographic location (country and/or sea)

text: metagenome

text: indoor metagenome

text: plant-associated

text: Biostimulants

text: indoor metagenome

text: Illumina


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: Medical Univeristy of Graz

text: public

text: indoor

text: plant air

text: Air

text: air

text: Austria

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome

characteristic: investigation type

text: indoor metagenome

characteristic: organism

text: plant-associated

characteristic: plant-associated environmental package

text: Biostimulants

characteristic: project name

text: indoor metagenome

text: Illumina

characteristic: sequencing method


characteristic: ENA-CHECKLIST

characteristic: External Id

text: Medical Univeristy of Graz

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: indoor

characteristic: common name

characteristic: description

text: plant surfaces

text: Surfaces

text: glass

text: Austria

text: metagenome

text: indoor metagenome

text: plant-associated

text: Biostimulants

text: indoor metagenome

text: Illumina

characteristic: title


E-MTAB-7097:Sample 10

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-7097:Sample 10

tag: Namespace:Institute of Immunobiology, Kantonsspital St. Gallen

text: 6 to 8

unit: week

characteristic: age

text: ArrayExpress

characteristic: broker name

text: reticular cell

characteristic: cell type

text: house mouse

text: Protocols: EYFP+ cells from Ccl19-iEYFP fetal spleens (mean yield = 1150 cells, n = 5), adult Ccl19-iEYFP (mean yield = 4100 cells, n = 7) and Ccl19-iEYFP Ltbrfl/fl (mean yield = 3500 cells, n = 9) spleens were sorted with a Bio-Rad S3 cell sorter and were collected in 200 µl Eppendorf tubes containing 100 μl of RNAlater reagent (Qiagen) to preserve the RNA after sorting. Likewise, reticular cell populations were sorted based on the defined markers sets, i.e. PDPN+ TRCs (mean yield = 670 cells, n = 4), CD35+ FDCs (mean yield = 950 cells, n = 3), MAdCAM-1+ MRCs (mean yield = 1010 cells, n = 2), Sca-1+ PRCs (mean yield = 1525 cells, n = 3). RNA extraction was performed using Quick-RNA Mini-Prep (Zymo Research). Reverse transcription and cDNA library generation was done using the Ovation SoLo RNA-Seq System (NuGEN) as described by the manufacturer. cDNA libraries were quantified by KAPA library Quantification kit (KAPA Biosystems) and Agilent Tape station in the Functional Genomics Center Zurich, Zurich, Switzerland.

text: adult

characteristic: developmental stage

characteristic: genotype

text: Mus musculus

text: Mus musculus

text: white pulp of spleen

characteristic: organism part

text: Mus musculus

text: mixed

characteristic: sex

characteristic: strain

text: Sample 10


E-MTAB-7097:Sample 11

characteristic: ENA-CHECKLIST

characteristic: External Id

text: Institute of Immunobiology, Kantonsspital St. Gallen

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-7097:Sample 11

text: 6 to 8

text: ArrayExpress

text: reticular cell

text: house mouse

text: adult

text: Mus musculus

characteristic: organism

text: Mus musculus

text: white pulp of spleen

text: Mus musculus

text: mixed

text: Sample 11


E-MTAB-7097:Sample 12

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: public

text: E-MTAB-7097:Sample 12

characteristic: Submitter Id

text: 6 to 8

text: ArrayExpress

text: reticular cell

text: house mouse

characteristic: common name

characteristic: description

text: adult

text: Mus musculus

text: Mus musculus

text: white pulp of spleen

text: Mus musculus

text: mixed

text: Sample 12

characteristic: title


E-MTAB-7097:Sample 13

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-7097:Sample 13

text: 6 to 8

characteristic: age

text: ArrayExpress

characteristic: broker name

text: reticular cell

characteristic: cell type

text: house mouse

text: adult

characteristic: developmental stage

text: Mus musculus

text: Mus musculus

text: white pulp of spleen

text: Mus musculus

text: mixed

text: Sample 13


E-MTAB-7097:Sample 14

characteristic: ENA-CHECKLIST

characteristic: External Id

text: public

text: E-MTAB-7097:Sample 14

text: 6 to 8

text: ArrayExpress

text: reticular cell

text: house mouse

text: adult

characteristic: genotype

text: Mus musculus

text: Mus musculus

text: white pulp of spleen

characteristic: organism part

text: Mus musculus

text: mixed

characteristic: sex

characteristic: strain

text: Sample 14


E-MTAB-7097:Sample 15

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-7097:Sample 15

text: 6 to 8

text: ArrayExpress

text: reticular cell

text: house mouse

text: adult

text: Mus musculus

characteristic: organism

text: Mus musculus

text: white pulp of spleen

text: Mus musculus

text: mixed

text: Sample 15


E-MTAB-7097:Sample 16

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-7097:Sample 16

characteristic: Submitter Id

text: 6 to 8

text: ArrayExpress

text: reticular cell

text: house mouse

characteristic: common name

characteristic: description

text: adult

text: Mus musculus

text: Mus musculus

text: white pulp of spleen

text: Mus musculus

text: mixed

text: Sample 16

characteristic: title


E-MTAB-7097:Sample 17

characteristic: ENA-CHECKLIST

characteristic: External Id

text: public

text: E-MTAB-7097:Sample 17

text: 6 to 8

characteristic: age

text: ArrayExpress

characteristic: broker name

text: reticular cell

characteristic: cell type

text: house mouse

text: adult

characteristic: developmental stage

text: Mus musculus

text: Mus musculus

text: white pulp of spleen

text: Mus musculus

text: mixed

text: Sample 17


E-MTAB-7097:Sample 18

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: public

text: E-MTAB-7097:Sample 18

text: 6 to 8

text: ArrayExpress

text: reticular cell

text: house mouse

text: adult

characteristic: genotype

text: Mus musculus

text: Mus musculus

text: white pulp of spleen

characteristic: organism part

text: Mus musculus

text: mixed

characteristic: sex

characteristic: strain

text: Sample 18


E-MTAB-7097:Sample 19

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-7097:Sample 19

text: 6 to 8

text: ArrayExpress

text: reticular cell

text: house mouse

text: adult

text: Mus musculus

characteristic: organism

text: Mus musculus

text: white pulp of spleen

text: Mus musculus

text: mixed

text: Sample 19


E-MTAB-7097:Sample 20

characteristic: ENA-CHECKLIST

characteristic: External Id

text: public

text: E-MTAB-7097:Sample 20

characteristic: Submitter Id

text: 6 to 8

text: ArrayExpress

text: reticular cell

text: house mouse

characteristic: common name

characteristic: description

text: adult

text: Mus musculus

text: Mus musculus

text: white pulp of spleen

text: Mus musculus

text: mixed

text: Sample 20

characteristic: title


E-MTAB-7097:Sample 21

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: public

text: E-MTAB-7097:Sample 21

text: 6 to 8

characteristic: age

text: ArrayExpress

characteristic: broker name

text: reticular cell

characteristic: cell type

text: house mouse

text: adult

characteristic: developmental stage

text: Mus musculus

text: Mus musculus

text: white pulp of spleen

text: Mus musculus

text: mixed

text: Sample 21


E-MTAB-7097:Sample 22

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-7097:Sample 22

text: 6 to 8

text: ArrayExpress

text: reticular cell

text: house mouse

text: adult

characteristic: genotype

text: Mus musculus

text: Mus musculus

text: white pulp of spleen

characteristic: organism part

text: Mus musculus

text: mixed

characteristic: sex

characteristic: strain

text: Sample 22


E-MTAB-7097:Sample 23

characteristic: ENA-CHECKLIST

characteristic: External Id

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-7097:Sample 23

text: 6 to 8

text: ArrayExpress

text: reticular cell

text: house mouse

text: adult

text: Mus musculus

characteristic: organism

text: Mus musculus

text: white pulp of spleen

text: Mus musculus

text: mixed

text: Sample 23


E-MTAB-7097:Sample 24

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: public

text: E-MTAB-7097:Sample 24

characteristic: Submitter Id

text: 6 to 8

text: ArrayExpress

text: reticular cell

text: house mouse

characteristic: common name

characteristic: description

text: adult

text: Mus musculus

text: Mus musculus

text: white pulp of spleen

text: Mus musculus

text: mixed

text: Sample 24

characteristic: title


E-MTAB-7097:Sample 25

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-7097:Sample 25

text: 6 to 8

characteristic: age

text: ArrayExpress

characteristic: broker name

text: reticular cell

characteristic: cell type

text: house mouse

text: adult

characteristic: developmental stage

text: Mus musculus

text: Mus musculus

text: white pulp of spleen

text: Mus musculus

text: mixed

text: Sample 25


E-MTAB-7097:Sample 26

characteristic: ENA-CHECKLIST

characteristic: External Id

text: public

text: E-MTAB-7097:Sample 26

text: 6 to 8

text: ArrayExpress

text: reticular cell

text: house mouse

text: adult

characteristic: genotype

text: Mus musculus

text: Mus musculus

text: white pulp of spleen

characteristic: organism part

text: Mus musculus

text: mixed

characteristic: sex

characteristic: strain

text: Sample 26


E-MTAB-7097:Sample 27

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-7097:Sample 27

text: 6 to 8

text: ArrayExpress

text: reticular cell

text: house mouse

text: adult

text: Mus musculus

characteristic: organism

text: Mus musculus

text: white pulp of spleen

text: Mus musculus

text: mixed

text: Sample 27


E-MTAB-7097:Sample 28

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-7097:Sample 28

characteristic: Submitter Id

text: 6 to 8

text: ArrayExpress

text: reticular cell

text: house mouse

characteristic: common name

characteristic: description

text: adult

text: Mus musculus

text: Mus musculus

text: white pulp of spleen

text: Mus musculus

text: mixed

text: Sample 28

characteristic: title


E-MTAB-7097:Sample 29

characteristic: ENA-CHECKLIST

characteristic: External Id

text: public

text: E-MTAB-7097:Sample 29

text: 6 to 8

characteristic: age

text: ArrayExpress

characteristic: broker name

text: reticular cell

characteristic: cell type

text: house mouse

text: adult

characteristic: developmental stage

text: Mus musculus

text: Mus musculus

text: white pulp of spleen

text: Mus musculus

text: mixed

text: Sample 29


E-MTAB-7097:Sample 30

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: public

text: E-MTAB-7097:Sample 30

text: 6 to 8

text: ArrayExpress

text: reticular cell

text: house mouse

text: adult

characteristic: genotype

text: Mus musculus

text: Mus musculus

text: white pulp of spleen

characteristic: organism part

text: Mus musculus

text: mixed

characteristic: sex

characteristic: strain

text: Sample 30


E-MTAB-7097:Sample 31

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-7097:Sample 31

text: 6 to 8

text: ArrayExpress

text: reticular cell

text: house mouse

text: adult

text: Mus musculus

characteristic: organism

text: Mus musculus

text: white pulp of spleen

text: Mus musculus

text: mixed

text: Sample 31


E-MTAB-7097:Sample 32

characteristic: ENA-CHECKLIST

characteristic: External Id

text: public

text: E-MTAB-7097:Sample 32

characteristic: Submitter Id

text: 6 to 8

text: ArrayExpress

text: reticular cell

text: house mouse

characteristic: common name

characteristic: description

text: adult

text: Mus musculus

text: Mus musculus

text: white pulp of spleen

text: Mus musculus

text: mixed

text: Sample 32

characteristic: title


E-MTAB-7097:Sample 33

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: public

text: E-MTAB-7097:Sample 33

text: 6 to 8

characteristic: age

text: ArrayExpress

characteristic: broker name

text: reticular cell

characteristic: cell type

text: house mouse

text: adult

characteristic: developmental stage

text: Mus musculus

text: Mus musculus

text: white pulp of spleen

text: Mus musculus

text: mixed

text: Sample 33


E-MTAB-7097:Sample 6

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-7097:Sample 6

text: 6 to 8

text: ArrayExpress

text: reticular cell

text: house mouse

text: adult

characteristic: genotype

text: Mus musculus

text: Mus musculus

text: white pulp of spleen

characteristic: organism part

text: Mus musculus

text: mixed

characteristic: sex

characteristic: strain

text: Sample 6


E-MTAB-7097:Sample 7

characteristic: ENA-CHECKLIST

characteristic: External Id

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-7097:Sample 7

text: 6 to 8

text: ArrayExpress

text: reticular cell

text: house mouse

text: adult

text: Mus musculus

characteristic: organism

text: Mus musculus

text: white pulp of spleen

text: Mus musculus

text: mixed

text: Sample 7


E-MTAB-7097:Sample 8

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: public

text: E-MTAB-7097:Sample 8

characteristic: Submitter Id

text: 6 to 8

text: ArrayExpress

text: reticular cell

text: house mouse

characteristic: common name

characteristic: description

text: adult

text: Mus musculus

text: Mus musculus

text: white pulp of spleen

text: Mus musculus

text: mixed

text: Sample 8

characteristic: title


E-MTAB-7097:Sample 9

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-7097:Sample 9

text: 6 to 8

characteristic: age

text: ArrayExpress

characteristic: broker name

text: reticular cell

characteristic: cell type

text: house mouse

text: adult

characteristic: developmental stage

text: Mus musculus

text: Mus musculus

text: white pulp of spleen

text: Mus musculus

text: mixed

text: Sample 9