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characteristic: INSDC center name

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characteristic: SRA accession

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characteristic: age (years)

characteristic: collection date

text: human

characteristic: common name

characteristic: description

text: organism-associated habitat

text: organism-associated habitat

text: mucus

text: Ulcerative Colitis

text: Lithuania

text: mucus

text: sigmoid colon

text: remission

text: male

characteristic: host sex

characteristic: host subject id

text: human-gut

characteristic: human gut environmental package

text: metagenome

text: PCR

characteristic: library screening strategy

text: ASA

characteristic: medication

text: CGTCTAGTAC

characteristic: multiplex identifiers

text: PMID: 22068912

characteristic: nucleic acid amplification

text: Qiagen Allprep DNA/RNA (PMID: 20522625)

characteristic: nucleic acid extraction

text: Homo sapiens

characteristic: pcr conditions

characteristic: pcr primers

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text: pyrosequencing

text: cDNA

characteristic: sequencing template

text: 16S rRNA

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characteristic: weight (kg)


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tag: attribute

characteristic: ENA-CHECKLIST

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text: The knowledge of species composition and functional aspects of the human microbiome is steadily increasing; but still limited information regarding its variation on a global scale is available. Due to the microbial involvement in inflammatory bowel diseases and their increase in global frequency; shared patterns across populations may hold important clinical relevance. In this study; we analyze a set of 89 mucosal biopsies sampled from individuals of German; Lithuanian and Indian origins; using bacterial community profiling of a roughly equal number of healthy controls; Crohn Disease and Ulcerative Colitis patients from each location. From each individual sample 16S rDNA and rRNA are analyzed as proxies for standing and active microbial community structure; respectively. We find pronounced regional as well as global disease patterns in the major phyla and patterns of diversity; which differ when investigated in the standing or active community. Geography appears to dominate patterns of beta diversity; with European samples being more similar to each other; which is more pronounced in the active microbial community. However; when geographic influence is accounted for; some universal patterns of disease become apparent. In particular; two genera belonging to the Clostridium leptum subgroup; Faecalibacteria and Papillibacter; display consistent patterns with respect to disease status and may thus serve as reliable ?microbiomarkers?. These analyses reveal the importance of the interaction of geography and disease in the interpretation of disease-associated changes in microbial communities and highlight the added value of analyzing communities on both the rDNA and rRNA level.

characteristic: description

text: organism-associated habitat

characteristic: environment (biome)

text: organism-associated habitat

characteristic: environment (feature)

text: mucus

characteristic: environment (material)

text: sex,sampling site,inflammatory bowel disease,clinical treatment,population,human gut metagenome,health trait

characteristic: experimental factor

text: Crohn's Disease

characteristic: gastrointestinal tract disorder

text: Lithuania

characteristic: geographic location (country and/or sea)

unit: DD

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: not provided

characteristic: height (cm)

text: mucus

characteristic: host body product

text: sigmoid colon

characteristic: host body site

text: remission

characteristic: host disease status

text: female

text: human-gut

text: metagenome

characteristic: investigation type

text: PCR

text: no medication

text: TCACGTACTA

text: PMID: 22068912

text: Qiagen Allprep DNA/RNA (PMID: 20522625)

text: Homo sapiens

characteristic: organism

text: initial denaturation: 98degC_0.5min;30cycles denaturation=98degC_9sec,annealing=55degC_0.5min,extension=72degC_0.5min;final extension:72degC_10min

text: BMRP

text: biopsy

text: Homo sapiens

text: pyrosequencing

characteristic: sequencing method

text: cDNA

text: 16S rRNA

text: Regional patterns of the standing and active human gut microbiome in health and inflammatory bowel diseases

characteristic: title

text: not provided


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

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characteristic: common name

characteristic: description

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text: organism-associated habitat

text: mucus

text: Healthy

text: Lithuania

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text: healthy

text: female

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text: metagenome

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characteristic: library screening strategy

text: no medication

characteristic: medication

text: TAGAGACGAG

characteristic: multiplex identifiers

text: PMID: 22068912

characteristic: nucleic acid amplification

text: Qiagen Allprep DNA/RNA (PMID: 20522625)

characteristic: nucleic acid extraction

text: Homo sapiens

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characteristic: ENA-LAST-UPDATE

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characteristic: INSDC center name

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characteristic: common name

characteristic: description

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characteristic: environment (biome)

text: organism-associated habitat

characteristic: environment (feature)

text: mucus

characteristic: environment (material)

characteristic: experimental factor

text: Healthy

characteristic: gastrointestinal tract disorder

text: Lithuania

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

characteristic: height (cm)

text: mucus

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characteristic: sequencing method

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text: 16S rRNA

characteristic: title


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characteristic: collection date

text: human

characteristic: common name

characteristic: description

text: organism-associated habitat

text: organism-associated habitat

text: mucus

text: Crohn's Disease

text: Lithuania

text: not provided

text: mucus

text: sigmoid colon

text: remission

text: not provided

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characteristic: host subject id

text: human-gut

characteristic: human gut environmental package

text: metagenome

text: PCR

characteristic: library screening strategy

text: no medication

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text: CGTCTAGTAC

characteristic: multiplex identifiers

text: PMID: 22068912

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characteristic: geographic location (longitude)

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characteristic: experimental factor

text: Crohn's Disease

characteristic: gastrointestinal tract disorder

text: Lithuania

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

characteristic: height (cm)

text: mucus

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text: sigmoid colon

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text: remission

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text: human-gut

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characteristic: investigation type

text: PCR

text: no medication

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text: Qiagen Allprep DNA/RNA (PMID: 20522625)

text: Homo sapiens

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characteristic: ENA-CHECKLIST

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characteristic: External Id

text: The Earlham Institute

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text: A single community dominates structure and function of a mixture of multiple methanogenic communities


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text: Zurich University of Applied Sciences

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tag: Namespace:Zurich University of Applied Sciences

unit: g

characteristic: amount or size of sample collected

characteristic: collection date

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characteristic: common name

text: Tomato leaves

characteristic: environment (material)

text: Switzerland

characteristic: geographic location (country and/or sea)

text: 47° 13‘ 4“ N

characteristic: geographic location (latitude)

text: 8° 40‘ 44“

characteristic: geographic location (longitude)

unit: week

characteristic: host age

text: Tomato

characteristic: host common name

text: artificially drop inoculated with spore and corresponding mock solution

characteristic: host taxid

text: metatranscriptome

text: Solanum lycopersicum

text: Phytophthora infestans (PI), Botrytis cinerea (BC), Oidium neolycopersici (ON)

characteristic: pathogene

text: leaf

characteristic: plant body site

text: plant-associated

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text: Transcriptome of Solanum lycopersicum

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unit: °C

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text: Solanum lycopersicum

text: Illumina HiSeq

unit: ºC

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text: Tomato-pathgoen interaction RNA-seq

type: has member


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characteristic: Submitter Id

text: tomato

text: Tomato leaves

text: Switzerland

text: 47° 13‘ 4“ N

text: 8° 40‘ 44“

text: Tomato

characteristic: host disease status

text: metatranscriptome

characteristic: investigation type

text: Solanum lycopersicum

characteristic: organism

text: leaf

text: plant-associated

text: Transcriptome of Solanum lycopersicum

text: Solanum lycopersicum

text: Illumina HiSeq

characteristic: sequencing method

text: Tomato-pathgoen interaction RNA-seq

characteristic: title


text: Department of Zoology

text: public

tag: Namespace:Department of Zoology

text: western gorilla

characteristic: common name

text: Gorilla gorilla

text: Gorilla gorilla

text: ITS2 profile


text: public

tag: Namespace:Department of Biochemistry University of Cambridge UK

text: ArrayExpress

characteristic: broker name

text: fission yeast

text: Protocols: Cells were incubated with CHX at 100 ug/ul for 5 minutes before collection Cells were grown at 32C in EMM2 (Moreno et al. Methods Enzymology 194: 795). Cells were grown in EMM2 (Moreno et al. Methods Enzymology 194: 795) in the presence of 10 mM 3-AT for 60 minutes at 32C. This treatment mimics histidine starvation. Total RNA was extracted using a hot phenol extraction method as described in Lyne et al. (2003) BMC Genomics 4:27. Clean up and DNase treatment were performed on with Purelink RNA microcolumns (Life Technologies) following the manufacturer’s instructions. Samples were ribo-depleted using Ribo-Zero Gold rRNA Removal Kit Yeast (Illumina) with a 4 ug input. 30 ng of ribo-depleted RNA was used as starting material for the NEXTflex Rapid Directional qRNA-Seq Kit (Bioo Scientific).

characteristic: description

characteristic: genotype

text: Schizosaccharomyces pombe

text: Schizosaccharomyces pombe

text: rRNA-depleted total RNA

characteristic: rna source

text: Schizosaccharomyces pombe


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characteristic: External Id

text: Department of Biochemistry University of Cambridge UK

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text: ArrayExpress

text: fission yeast

text: Schizosaccharomyces pombe

text: Schizosaccharomyces pombe

text: rRNA-depleted total RNA

text: Schizosaccharomyces pombe


characteristic: INSDC center name

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characteristic: INSDC status

text: ArrayExpress

text: fission yeast

text: Protocols: Cells were incubated with CHX at 100 ug/ul for 5 minutes before collection Cells were grown at 32C in EMM2 (Moreno et al. Methods Enzymology 194: 795). Cells were grown in EMM2 (Moreno et al. Methods Enzymology 194: 795) in the presence of 10 mM 3-AT for 60 minutes at 32C. This treatment mimics histidine starvation. Between 3x10E8 and 12x10E8 cells were resuspended in 100 ul of lysis buffer (20 mM Tris-HCl pH 8.0, 140 mM KCl, 5 mM Mg2Cl, 1 % Triton X-100, 100 ug/ml cycloheximide) with 1 g of chilled glass beads (Biospec) and lysed using a Fastprep 24 bead-beater (MP Biomedicals) at level 6 for 13 seconds. The extract was diluted with 400 ul of lysis buffer and cleared by centrifugation in two steps at 4 degrees C at 16,000 g (5 minutes followed by 15 minutes). 600 A260 units of cell extract were digested with 750 units of RNase I (Life Technologies) for 45 minutes. Reactions were quenched with 600 units of SUPERaseIn (Life Technologies). Digested extracts in 500 ul were loaded onto a 14 ml linear 10-50% (w/v) sucrose gradient prepared with a Gradient Master (Biocomp), and separated by centrifugation for 160 min at 35,000 rpm in a SW 40Ti rotor (Beckman). The gradients were then fractionated by upward displacement with 55% (w/v) sucrose, and fractions containing monosomes selected for further processing. RNAs were then purified by phenol extraction, passed through amicon ultra 100 kDa columns (Millipore), and run on 15% TBE-urea gels (Life Technologies). Fragments of around 28 nucleotides were extracted from the gel. Gel purified RNA fragments were treated with 10 units of T4 PNK (Thermo Fisher) in a low pH buffer (700 mM Tris pH 7, 50 mM DTT, 100 mM MgCl2) for 30 min at 37C. ATP and buffer A (Thermo Fisher) were then added for an additional 30 min incubation. RNA fragments were column-purified (PureLink RNA micro-columns, Life Technologies). 100 ng were used as input for the NEXTflex Small RNA Sequencing Kit v2 (Bioo Scientific), following manufacturer’s protocol.

text: Schizosaccharomyces pombe

text: Schizosaccharomyces pombe

text: Ribosome protected fragments (RPF)

text: Schizosaccharomyces pombe


text: public

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: fission yeast

text: wild type genotype

text: Schizosaccharomyces pombe

text: Schizosaccharomyces pombe

text: Ribosome protected fragments (RPF)

text: Schizosaccharomyces pombe


text: public

text: ArrayExpress

text: fission yeast

text: Protocols: Cells were incubated with CHX at 100 ug/ul for 5 minutes before collection Cells were grown at 32C in EMM2 (Moreno et al. Methods Enzymology 194: 795). Total RNA was extracted using a hot phenol extraction method as described in Lyne et al. (2003) BMC Genomics 4:27. Clean up and DNase treatment were performed on with Purelink RNA microcolumns (Life Technologies) following the manufacturer’s instructions. Samples were ribo-depleted using Ribo-Zero Gold rRNA Removal Kit Yeast (Illumina) with a 4 ug input. 30 ng of ribo-depleted RNA was used as starting material for the NEXTflex Rapid Directional qRNA-Seq Kit (Bioo Scientific).

text: Schizosaccharomyces pombe

characteristic: organism

text: Schizosaccharomyces pombe

text: rRNA-depleted total RNA

text: Schizosaccharomyces pombe


text: public

text: ArrayExpress

text: fission yeast

text: Protocols: Cells were incubated with CHX at 100 ug/ul for 5 minutes before collection Cells were grown at 32C in EMM2 (Moreno et al. Methods Enzymology 194: 795). Between 3x10E8 and 12x10E8 cells were resuspended in 100 ul of lysis buffer (20 mM Tris-HCl pH 8.0, 140 mM KCl, 5 mM Mg2Cl, 1 % Triton X-100, 100 ug/ml cycloheximide) with 1 g of chilled glass beads (Biospec) and lysed using a Fastprep 24 bead-beater (MP Biomedicals) at level 6 for 13 seconds. The extract was diluted with 400 ul of lysis buffer and cleared by centrifugation in two steps at 4 degrees C at 16,000 g (5 minutes followed by 15 minutes). 600 A260 units of cell extract were digested with 750 units of RNase I (Life Technologies) for 45 minutes. Reactions were quenched with 600 units of SUPERaseIn (Life Technologies). Digested extracts in 500 ul were loaded onto a 14 ml linear 10-50% (w/v) sucrose gradient prepared with a Gradient Master (Biocomp), and separated by centrifugation for 160 min at 35,000 rpm in a SW 40Ti rotor (Beckman). The gradients were then fractionated by upward displacement with 55% (w/v) sucrose, and fractions containing monosomes selected for further processing. RNAs were then purified by phenol extraction, passed through amicon ultra 100 kDa columns (Millipore), and run on 15% TBE-urea gels (Life Technologies). Fragments of around 28 nucleotides were extracted from the gel. Gel purified RNA fragments were treated with 10 units of T4 PNK (Thermo Fisher) in a low pH buffer (700 mM Tris pH 7, 50 mM DTT, 100 mM MgCl2) for 30 min at 37C. ATP and buffer A (Thermo Fisher) were then added for an additional 30 min incubation. RNA fragments were column-purified (PureLink RNA micro-columns, Life Technologies). 100 ng were used as input for the NEXTflex Small RNA Sequencing Kit v2 (Bioo Scientific), following manufacturer’s protocol.

text: Schizosaccharomyces pombe

text: Schizosaccharomyces pombe

text: Ribosome protected fragments (RPF)

text: Schizosaccharomyces pombe

characteristic: title


text: public

text: ArrayExpress

text: fission yeast

characteristic: common name

text: wild type genotype

text: Schizosaccharomyces pombe

text: Schizosaccharomyces pombe

text: Ribosome protected fragments (RPF)

text: Schizosaccharomyces pombe


text: public

text: ArrayExpress

characteristic: broker name

text: fission yeast

text: Protocols: Cells were incubated with CHX at 100 ug/ul for 5 minutes before collection Cells were grown at 32C in EMM2 (Moreno et al. Methods Enzymology 194: 795). 30 ng of ribo-depleted RNA was used as starting material for the NEXTflex Rapid Directional qRNA-Seq Kit (Bioo Scientific).

text: wild type genotype

text: Schizosaccharomyces pombe

text: Schizosaccharomyces pombe

text: rRNA-depleted total RNA

text: Schizosaccharomyces pombe


text: public

text: ArrayExpress

text: fission yeast

text: Protocols: Cells were grown at 32C in EMM2 (Moreno et al. Methods Enzymology 194: 795). 30 ng of ribo-depleted RNA was used as starting material for the NEXTflex Rapid Directional qRNA-Seq Kit (Bioo Scientific).

characteristic: description

text: wild type genotype

text: Schizosaccharomyces pombe

text: Schizosaccharomyces pombe

text: rRNA-depleted total RNA

text: Schizosaccharomyces pombe


text: public

text: ArrayExpress

text: fission yeast

text: Protocols: Cells were grown at 32C in EMM2 (Moreno et al. Methods Enzymology 194: 795). Between 3x10E8 and 12x10E8 cells were resuspended in 100 ul of lysis buffer (20 mM Tris-HCl pH 8.0, 140 mM KCl, 5 mM Mg2Cl, 1 % Triton X-100, 100 ug/ml cycloheximide) with 1 g of chilled glass beads (Biospec) and lysed using a Fastprep 24 bead-beater (MP Biomedicals) at level 6 for 13 seconds. The extract was diluted with 400 ul of lysis buffer and cleared by centrifugation in two steps at 4 degrees C at 16,000 g (5 minutes followed by 15 minutes). 600 A260 units of cell extract were digested with 750 units of RNase I (Life Technologies) for 45 minutes. Reactions were quenched with 600 units of SUPERaseIn (Life Technologies). Digested extracts in 500 ul were loaded onto a 14 ml linear 10-50% (w/v) sucrose gradient prepared with a Gradient Master (Biocomp), and separated by centrifugation for 160 min at 35,000 rpm in a SW 40Ti rotor (Beckman). The gradients were then fractionated by upward displacement with 55% (w/v) sucrose, and fractions containing monosomes selected for further processing. RNAs were then purified by phenol extraction, passed through amicon ultra 100 kDa columns (Millipore), and run on 15% TBE-urea gels (Life Technologies). Fragments of around 28 nucleotides were extracted from the gel. Gel purified RNA fragments were treated with 10 units of T4 PNK (Thermo Fisher) in a low pH buffer (700 mM Tris pH 7, 50 mM DTT, 100 mM MgCl2) for 30 min at 37C. ATP and buffer A (Thermo Fisher) were then added for an additional 30 min incubation. RNA fragments were column-purified (PureLink RNA micro-columns, Life Technologies). 100 ng were used as input for the NEXTflex Small RNA Sequencing Kit v2 (Bioo Scientific), following manufacturer’s protocol.

text: wild type genotype

characteristic: genotype

text: Schizosaccharomyces pombe

text: Schizosaccharomyces pombe

text: Ribosome protected fragments (RPF)

text: Schizosaccharomyces pombe


text: public

text: ArrayExpress

text: fission yeast

text: wild type genotype

text: Schizosaccharomyces pombe

text: Schizosaccharomyces pombe

text: rRNA-depleted total RNA

characteristic: rna source

text: Schizosaccharomyces pombe


characteristic: ENA-CHECKLIST

text: public

text: ArrayExpress

text: fission yeast

text: Protocols: Cells were incubated with CHX at 100 ug/ul for 5 minutes before collection Cells were grown at 32C in EMM2 (Moreno et al. Methods Enzymology 194: 795). Cells were grown in EMM2 (Moreno et al. Methods Enzymology 194: 795) in the presence of 10 mM 3-AT for 60 minutes at 32C. This treatment mimics histidine starvation. Between 3x10E8 and 12x10E8 cells were resuspended in 100 ul of lysis buffer (20 mM Tris-HCl pH 8.0, 140 mM KCl, 5 mM Mg2Cl, 1 % Triton X-100, 100 ug/ml cycloheximide) with 1 g of chilled glass beads (Biospec) and lysed using a Fastprep 24 bead-beater (MP Biomedicals) at level 6 for 13 seconds. The extract was diluted with 400 ul of lysis buffer and cleared by centrifugation in two steps at 4 degrees C at 16,000 g (5 minutes followed by 15 minutes). 600 A260 units of cell extract were digested with 750 units of RNase I (Life Technologies) for 45 minutes. Reactions were quenched with 600 units of SUPERaseIn (Life Technologies). Digested extracts in 500 ul were loaded onto a 14 ml linear 10-50% (w/v) sucrose gradient prepared with a Gradient Master (Biocomp), and separated by centrifugation for 160 min at 35,000 rpm in a SW 40Ti rotor (Beckman). The gradients were then fractionated by upward displacement with 55% (w/v) sucrose, and fractions containing monosomes selected for further processing. RNAs were then purified by phenol extraction, passed through amicon ultra 100 kDa columns (Millipore), and run on 15% TBE-urea gels (Life Technologies). Fragments of around 28 nucleotides were extracted from the gel. RNA samples were purified using Purelink RNA microcolumns (Life Technologies) as described by the manufacturer, except that the samples were initially passed through the column in the presence of 70% ethanol (to favour binding of small RNAs). Samples were then treated with poly nucleotide kinase (PNK, Fermentas) and polyadenylated using 12 units of poly-(A) polymerase (NEB) at 37C for 45 minutes. Reverse transcription reactions were performed using custom primers containing an anchored oligo(dT), 4 nucleotides of known sequence used for multiplexing, and 5 random nucleotides that serve as unique molecular identifiers. Reverse transcription products were gel-purified and circularised using CircLigase II (Epicentre), and amplified by PCR with custom library primers for 12 or 15 cycles

text: wild type genotype

text: Schizosaccharomyces pombe

text: Schizosaccharomyces pombe

text: Ribosome protected fragments (RPF)

text: Schizosaccharomyces pombe


characteristic: ENA-FIRST-PUBLIC

text: public

text: ArrayExpress

text: fission yeast

text: Protocols: Cells were incubated with CHX at 100 ug/ul for 5 minutes before collection Cells were grown at 32C in EMM2 (Moreno et al. Methods Enzymology 194: 795). Between 3x10E8 and 12x10E8 cells were resuspended in 100 ul of lysis buffer (20 mM Tris-HCl pH 8.0, 140 mM KCl, 5 mM Mg2Cl, 1 % Triton X-100, 100 ug/ml cycloheximide) with 1 g of chilled glass beads (Biospec) and lysed using a Fastprep 24 bead-beater (MP Biomedicals) at level 6 for 13 seconds. The extract was diluted with 400 ul of lysis buffer and cleared by centrifugation in two steps at 4 degrees C at 16,000 g (5 minutes followed by 15 minutes). 600 A260 units of cell extract were digested with 750 units of RNase I (Life Technologies) for 45 minutes. Reactions were quenched with 600 units of SUPERaseIn (Life Technologies). Digested extracts in 500 ul were loaded onto a 14 ml linear 10-50% (w/v) sucrose gradient prepared with a Gradient Master (Biocomp), and separated by centrifugation for 160 min at 35,000 rpm in a SW 40Ti rotor (Beckman). The gradients were then fractionated by upward displacement with 55% (w/v) sucrose, and fractions containing monosomes selected for further processing. RNAs were then purified by phenol extraction, passed through amicon ultra 100 kDa columns (Millipore), and run on 15% TBE-urea gels (Life Technologies). Fragments of around 28 nucleotides were extracted from the gel. Gel purified RNA fragments were treated with 10 units of T4 PNK (Thermo Fisher) in a low pH buffer (700 mM Tris pH 7, 50 mM DTT, 100 mM MgCl2) for 30 min at 37C. ATP and buffer A (Thermo Fisher) were then added for an additional 30 min incubation. RNA fragments were column-purified (PureLink RNA micro-columns, Life Technologies). 100 ng were used as input for the NEXTflex Small RNA Sequencing Kit v2 (Bioo Scientific), following manufacturer’s protocol. RNA samples were purified using Purelink RNA microcolumns (Life Technologies) as described by the manufacturer, except that the samples were initially passed through the column in the presence of 70% ethanol (to favour binding of small RNAs). Samples were then treated with poly nucleotide kinase (PNK, Fermentas) and polyadenylated using 12 units of poly-(A) polymerase (NEB) at 37C for 45 minutes. Reverse transcription reactions were performed using custom primers containing an anchored oligo(dT), 4 nucleotides of known sequence used for multiplexing, and 5 random nucleotides that serve as unique molecular identifiers. Reverse transcription products were gel-purified and circularised using CircLigase II (Epicentre), and amplified by PCR with custom library primers for 12 or 15 cycles

text: wild type genotype

text: Schizosaccharomyces pombe

text: Schizosaccharomyces pombe

text: Ribosome protected fragments (RPF)

text: Schizosaccharomyces pombe


characteristic: ENA-LAST-UPDATE

text: public

text: ArrayExpress

text: fission yeast

text: wild type genotype

text: Schizosaccharomyces pombe

text: Schizosaccharomyces pombe

text: rRNA-depleted total RNA

text: Schizosaccharomyces pombe


characteristic: External Id

text: public

text: ArrayExpress

text: fission yeast

text: Protocols: Cells were incubated with CHX at 100 ug/ul for 5 minutes before collection Cells were grown at 32C in EMM2 (Moreno et al. Methods Enzymology 194: 795). Between 3x10E8 and 12x10E8 cells were resuspended in 100 ul of lysis buffer (20 mM Tris-HCl pH 8.0, 140 mM KCl, 5 mM Mg2Cl, 1 % Triton X-100, 100 ug/ml cycloheximide) with 1 g of chilled glass beads (Biospec) and lysed using a Fastprep 24 bead-beater (MP Biomedicals) at level 6 for 13 seconds. The extract was diluted with 400 ul of lysis buffer and cleared by centrifugation in two steps at 4 degrees C at 16,000 g (5 minutes followed by 15 minutes). 600 A260 units of cell extract were digested with 750 units of RNase I (Life Technologies) for 45 minutes. Reactions were quenched with 600 units of SUPERaseIn (Life Technologies). Digested extracts in 500 ul were loaded onto a 14 ml linear 10-50% (w/v) sucrose gradient prepared with a Gradient Master (Biocomp), and separated by centrifugation for 160 min at 35,000 rpm in a SW 40Ti rotor (Beckman). The gradients were then fractionated by upward displacement with 55% (w/v) sucrose, and fractions containing monosomes selected for further processing. RNAs were then purified by phenol extraction, passed through amicon ultra 100 kDa columns (Millipore), and run on 15% TBE-urea gels (Life Technologies). Fragments of around 28 nucleotides were extracted from the gel. RNA samples were purified using Purelink RNA microcolumns (Life Technologies) as described by the manufacturer, except that the samples were initially passed through the column in the presence of 70% ethanol (to favour binding of small RNAs). Samples were then treated with poly nucleotide kinase (PNK, Fermentas) and polyadenylated using 12 units of poly-(A) polymerase (NEB) at 37C for 45 minutes. Reverse transcription reactions were performed using custom primers containing an anchored oligo(dT), 4 nucleotides of known sequence used for multiplexing, and 5 random nucleotides that serve as unique molecular identifiers. Reverse transcription products were gel-purified and circularised using CircLigase II (Epicentre), and amplified by PCR with custom library primers for 12 or 15 cycles

text: wild type genotype

text: Schizosaccharomyces pombe

text: Schizosaccharomyces pombe

text: Ribosome protected fragments (RPF)

text: Schizosaccharomyces pombe


characteristic: INSDC center name

text: public

tag: Namespace:CHINESE ACADEMY OF AGRICULTURAL SCIENCES

characteristic: collection date

text: foxtail millet

characteristic: estimated size

text: China

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Field

characteristic: isolation and growth condition

characteristic: number of replicons

text: Setaria italica

text: 4 leaves

characteristic: plant developmental stage

text: field

characteristic: plant growth medium

text: all above ground

characteristic: plant structure

text: healthy

characteristic: sample health state

text: Setaria italica

text: Drought Setaria RNAseq


text: CHINESE ACADEMY OF AGRICULTURAL SCIENCES

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: foxtail millet

characteristic: common name

text: China

text: Field

text: Setaria italica

characteristic: organism

text: 4 leaves

text: field

text: all above ground

text: healthy

text: Setaria italica

text: Drought Setaria RNAseq

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

text: public

characteristic: collection date

text: Germany

characteristic: country

text: Pseudomonas aeruginosa

text: Pseudomonas aeruginosa


text: IMEDEA

text: public

text: Salinas de Trinidad

characteristic: description

text: Sediment

characteristic: environment (biome)

text: Sediment

characteristic: environment (feature)

text: Sediment

characteristic: environment (material)

text: Spain

characteristic: geographic location (country and/or sea)

unit: m

characteristic: geographic location (depth)

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome

characteristic: investigation type

text: sediment bacterium 15-27

text: Biogeographical patterns of bacterial and archaeal communities of distant hypersaline environments

characteristic: project name

text: sediment bacterium 15-27

text: sediment

characteristic: sediment environmental package

characteristic: sequencing method


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: IMEDEA

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: S´Avall

text: Sediment

text: Sediment

text: Sediment

text: Spain

text: metagenome

text: sediment bacterium 15-27

characteristic: organism

text: sediment bacterium 15-27

text: sediment

characteristic: title


text: IMEDEA

characteristic: INSDC center name

text: public

characteristic: collection date

text: Campos

characteristic: description

text: Sediment

characteristic: environment (biome)

text: Sediment

characteristic: environment (feature)

text: Sediment

characteristic: environment (material)

text: Spain

characteristic: geographic location (country and/or sea)

characteristic: geographic location (depth)

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

text: metagenome

text: sediment bacterium 15-27

text: sediment bacterium 15-27

text: sediment


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: IMEDEA

characteristic: INSDC first public

text: public

text: Formentera

text: Sediment

text: Sediment

text: Sediment

text: Spain

characteristic: geographic location (longitude)

text: metagenome

characteristic: investigation type

text: sediment bacterium 15-27

characteristic: project name

text: sediment bacterium 15-27

text: sediment

characteristic: sediment environmental package

characteristic: sequencing method


text: IMEDEA

characteristic: INSDC center name

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

text: Ibiza

characteristic: description

text: Sediment

characteristic: environment (biome)

text: Sediment

text: Sediment

text: Spain

text: metagenome

text: sediment bacterium 15-27

characteristic: organism

text: sediment bacterium 15-27

text: sediment

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: IMEDEA

text: public

text: Fuerteventura

text: Sediment

text: Sediment

characteristic: environment (feature)

text: Sediment

characteristic: environment (material)

text: Spain

characteristic: geographic location (country and/or sea)

characteristic: geographic location (depth)

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

text: metagenome

text: sediment bacterium 15-27

text: sediment bacterium 15-27

text: sediment


text: IMEDEA

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: Lanzarote

text: Sediment

text: Sediment

text: Sediment

text: Spain

characteristic: geographic location (longitude)

text: metagenome

characteristic: investigation type

text: sediment bacterium 15-27

characteristic: project name

text: sediment bacterium 15-27

text: sediment

characteristic: sediment environmental package

characteristic: sequencing method


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: IMEDEA

text: public

characteristic: Submitter Id

characteristic: collection date

text: Peña Hueca

characteristic: description

text: Sediment

characteristic: environment (biome)

text: Sediment

text: Sediment

text: Spain

text: metagenome

text: sediment bacterium 15-27

characteristic: organism

text: sediment bacterium 15-27

text: sediment

characteristic: title


text: IMEDEA

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: Peña Hueca

text: Brines

text: Brines

characteristic: environment (feature)

text: Brines

characteristic: environment (material)

text: Spain

characteristic: geographic location (country and/or sea)

characteristic: geographic location (depth)

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

text: metagenome

text: sediment bacterium 15-27

text: sediment bacterium 15-27

text: sediment


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: IMEDEA

text: public

characteristic: SRA accession

text: Boyeruca

text: Sediment

text: Sediment

text: Sediment

text: Chile

characteristic: geographic location (longitude)

text: metagenome

characteristic: investigation type

text: sediment bacterium 15-27

characteristic: project name

text: sediment bacterium 15-27

text: sediment

characteristic: sediment environmental package

characteristic: sequencing method


text: IMEDEA

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: Submitter Id

characteristic: collection date

text: Santa Pola

characteristic: description

text: Sediment

characteristic: environment (biome)

text: Sediment

text: Sediment

text: Spain

text: metagenome

text: sediment bacterium 15-27

characteristic: organism

text: sediment bacterium 15-27

text: sediment

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: IMEDEA

text: public

text: Salar Pocitos

text: Sediment

text: Sediment

characteristic: environment (feature)

text: Sediment

characteristic: environment (material)

text: Argentina

characteristic: geographic location (country and/or sea)

characteristic: geographic location (depth)

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

text: metagenome

text: sediment bacterium 15-27

text: sediment bacterium 15-27

text: sediment


text: IMEDEA

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: Tolar Grande

text: Sediment

text: Sediment

text: Sediment

text: Argentina

characteristic: geographic location (longitude)

text: metagenome

characteristic: investigation type

text: sediment bacterium 15-27

characteristic: project name

text: sediment bacterium 15-27

text: sediment

characteristic: sediment environmental package

characteristic: sequencing method


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: IMEDEA

text: public

characteristic: Submitter Id

characteristic: collection date

text: Salar de COIPA

characteristic: description

text: Sediment

characteristic: environment (biome)

text: Sediment

text: Sediment

text: Argentina

text: metagenome

text: sediment bacterium 15-27

characteristic: organism

text: sediment bacterium 15-27

text: sediment

characteristic: title


text: IMEDEA

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: Salar de Llullialliaco

text: Sediment

text: Sediment

characteristic: environment (feature)

text: Sediment

characteristic: environment (material)

text: Argentina

characteristic: geographic location (country and/or sea)

characteristic: geographic location (depth)

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

text: metagenome

text: sediment bacterium 15-27

text: sediment bacterium 15-27

text: sediment


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: IMEDEA

text: public

characteristic: SRA accession

text: Laguna Santa María

text: Sediment

text: Sediment

text: Sediment

text: Argentina

characteristic: geographic location (longitude)

text: metagenome

characteristic: investigation type

text: sediment bacterium 15-27

characteristic: project name

text: sediment bacterium 15-27

text: sediment

characteristic: sediment environmental package

characteristic: sequencing method


text: IMEDEA

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: Submitter Id

characteristic: collection date

text: Ojo Naranja Antofalla

characteristic: description

text: Sediment

characteristic: environment (biome)

text: Sediment

text: Sediment

text: Argentina

text: metagenome

text: sediment bacterium 15-27

characteristic: organism

text: sediment bacterium 15-27

text: sediment

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: IMEDEA

text: public

text: Laguna Diamante

text: Sediment

text: Sediment

characteristic: environment (feature)

text: Sediment

characteristic: environment (material)

text: Argentina

characteristic: geographic location (country and/or sea)

characteristic: geographic location (depth)

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

text: metagenome

text: sediment bacterium 15-27

text: sediment bacterium 15-27

text: sediment


text: IMEDEA

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: Campos

text: Brines

text: Brines

text: Brines

text: Spain

characteristic: geographic location (longitude)

text: metagenome

characteristic: investigation type

text: sediment bacterium 15-27

characteristic: project name

text: sediment bacterium 15-27

text: sediment

characteristic: sediment environmental package

characteristic: sequencing method


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: IMEDEA

text: public

characteristic: Submitter Id

characteristic: collection date

text: Laguna Cabe

characteristic: description

text: Sediments

characteristic: environment (biome)

text: Sediment

text: Sediment

text: Argentina

text: metagenome

text: sediment bacterium 15-27

characteristic: organism

text: sediment bacterium 15-27

text: sediment

characteristic: title


text: IMEDEA

characteristic: INSDC center name

characteristic: INSDC first public

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text: public

characteristic: INSDC status

text: Salar de Pocitos

text: Brines

text: Brines

characteristic: environment (feature)

text: Brines

characteristic: environment (material)

text: Argentina

characteristic: geographic location (country and/or sea)

characteristic: geographic location (depth)

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

text: metagenome

text: sediment bacterium 15-27

text: sediment bacterium 15-27

text: sediment


characteristic: ENA-CHECKLIST

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characteristic: title


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characteristic: title


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characteristic: environment (feature)

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characteristic: geographic location (country and/or sea)

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characteristic: ENA-CHECKLIST

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text: Sediment

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characteristic: ENA-CHECKLIST

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text: Sediment

text: Sediment

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text: Salar de COIPA

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text: Sediment

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text: sediment bacterium 15-27

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characteristic: ENA-CHECKLIST

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text: Sediment

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text: Argentina

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text: Sediment

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characteristic: geographic location (longitude)

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text: Ojo Naranja Antofalla

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characteristic: environment (biome)

text: Sediment

text: Sediment

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characteristic: environment (feature)

text: Sediment

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text: Argentina

characteristic: geographic location (country and/or sea)

characteristic: geographic location (depth)

characteristic: geographic location (elevation)

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characteristic: ENA-CHECKLIST

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text: Sediment

text: Sediment

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characteristic: geographic location (longitude)

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text: sediment bacterium 15-27

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text: Spain

characteristic: geographic location (country and/or sea)

characteristic: geographic location (depth)

characteristic: geographic location (elevation)

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text: sediment bacterium 15-27

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text: IMEDEA

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characteristic: geographic location (longitude)

text: metagenome

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text: sediment bacterium 15-27

characteristic: project name

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characteristic: ENA-CHECKLIST

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characteristic: collection date

text: Laguna Santa María

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text: sediment bacterium 15-27

characteristic: organism

text: sediment bacterium 15-27

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text: Ojo Naranja Antofalla

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characteristic: environment (feature)

text: Brines

characteristic: environment (material)

text: Argentina

characteristic: geographic location (country and/or sea)

characteristic: geographic location (depth)

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

text: metagenome

text: sediment bacterium 15-27

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text: sediment


characteristic: ENA-CHECKLIST

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text: Ojo Seco

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text: Argentina

characteristic: geographic location (longitude)

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text: sediment bacterium 15-27

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characteristic: collection date

text: Ojo Blanco

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text: Brines

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text: Argentina

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text: sediment bacterium 15-27

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text: Laguna Diamante

text: Brines

text: Brines

characteristic: environment (feature)

text: Brines

characteristic: environment (material)

text: Argentina

characteristic: geographic location (country and/or sea)

characteristic: geographic location (depth)

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

text: metagenome

text: sediment bacterium 15-27

text: sediment bacterium 15-27

text: sediment


text: IMEDEA

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text: Laguna Cabe

text: Brines

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text: Argentina

characteristic: geographic location (longitude)

text: metagenome

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text: sediment bacterium 15-27

characteristic: project name

text: sediment bacterium 15-27

text: sediment

characteristic: sediment environmental package

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characteristic: ENA-CHECKLIST

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characteristic: External Id

text: IMEDEA

text: public

characteristic: Submitter Id

characteristic: collection date

text: Laguna Negra, Tinogasta-Catamarca

characteristic: description

text: Sediment

characteristic: environment (biome)

text: Sediment

text: Sediment

text: Argentina

text: metagenome

text: sediment bacterium 15-27

characteristic: organism

text: sediment bacterium 15-27

text: sediment

characteristic: title


status: KILLED

text: Not supplied

characteristic: ArrayExpress-PHENOTYPE

text: Homo sapiens

characteristic: ArrayExpress-SPECIES

text: SC

characteristic: INSDC center name

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characteristic: INSDC last update

text: killed

characteristic: INSDC status

text: Not supplied

characteristic: PHENOTYPE

text: human

characteristic: common name

text: Homo sapiens

text: Homo sapiens


characteristic: ENA-CHECKLIST

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text: CRI-FEM

text: public

characteristic: SRA accession

text: Potentilla micrantha illumina genome sequencing

text: Serbia

characteristic: geographic location (country and/or sea)

text: Potentilla micrantha

text: Potentilla micrantha

text: young leaf

characteristic: tissue type

text: Potentilla micrantha genome sequencing


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UNIVERSITY HOHENHEIM

text: public

tag: Namespace:UNIVERSITY HOHENHEIM

characteristic: Submitter Id

text: ceca digesta

characteristic: description

text: chicken gut metagenome

text: chicken gut metagenome

text: Sample


text: Mycobacterium abscessus

text: SC

text: public

text: Mycobacterium abscessus

text: Mycobacterium abscessus

characteristic: organism

text: Mycobacterium abscessus

characteristic: subject id

characteristic: title


text: gut metagenome

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text: SC

characteristic: INSDC center name

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text: public

text: gut metagenome

text: gut metagenome

text: gut metagenome


text: West Liberty University

characteristic: INSDC last update

text: public

characteristic: INSDC status

tag: Namespace:West Liberty University

characteristic: collection date

text: uncultured prokaryote

text: Namibian Upwelling nitrifiers 10m

text: Seawater

characteristic: environment (biome)

text: Seawater

characteristic: environment (feature)

text: Seawater

characteristic: environment (material)

text: Namibia

characteristic: geographic location (depth)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: mimarks-survey

characteristic: investigation type

text: uncultured prokaryote

text: Namibian Upwelling nitrifiers

characteristic: project name

text: uncultured prokaryote

text: Illumina MiSeq

characteristic: sequencing method

text: water

characteristic: water environmental package


characteristic: ENA-CHECKLIST

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characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: West Liberty University

text: public

characteristic: SRA accession

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text: uncultured prokaryote

characteristic: common name

text: Namibian Upwelling nitrifiers25m

characteristic: description

text: Seawater

text: Seawater

text: Seawater

text: Namibia

characteristic: geographic location (country and/or sea)

text: mimarks-survey

text: uncultured prokaryote

characteristic: organism

text: Namibian Upwelling nitrifiers

text: uncultured prokaryote

text: Illumina MiSeq

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text: West Liberty University

characteristic: INSDC center name

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characteristic: INSDC last update

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characteristic: collection date

text: uncultured prokaryote

text: Namibian Upwelling nitrifiers 100m

text: Seawater

characteristic: environment (biome)

text: Seawater

characteristic: environment (feature)

text: Seawater

characteristic: environment (material)

text: Namibia

characteristic: geographic location (depth)

characteristic: geographic location (latitude)

text: mimarks-survey

text: uncultured prokaryote

text: Namibian Upwelling nitrifiers

text: uncultured prokaryote

text: Illumina MiSeq

text: water


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: West Liberty University

text: public

characteristic: SRA accession

text: uncultured prokaryote

text: Namibian Upwelling nitrifiers 130m

text: Seawater

text: Seawater

text: Seawater

text: Namibia

characteristic: geographic location (longitude)

text: mimarks-survey

characteristic: investigation type

text: uncultured prokaryote

text: Namibian Upwelling nitrifiers

characteristic: project name

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text: West Liberty University

characteristic: INSDC center name

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characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: Submitter Id

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characteristic: common name

text: Namibian Upwelling nitrifiers 250m

characteristic: description

text: Seawater

text: Seawater

text: Seawater

text: Namibia

characteristic: geographic location (country and/or sea)

text: mimarks-survey

text: uncultured prokaryote

characteristic: organism

text: Namibian Upwelling nitrifiers

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text: Illumina MiSeq

characteristic: title

text: water


characteristic: ENA-CHECKLIST

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characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Life Sciences Research Unit

text: public

tag: Namespace:Life Sciences Research Unit

characteristic: cell type

text: house mouse

text: ChIP DNA for undifferentiated ST2 cells - day0

text: Life Sciences Research Unit, University of Luxembourg

characteristic: lab host

text: Mus musculus

text: Mus musculus

text: male

characteristic: sex


text: TUM

characteristic: INSDC center name

text: public

characteristic: SRA accession

characteristic: collection date

text: house mouse

text: Caecal content of one 18-week-old mouse fed a control experimental diet for 8 weeks and subjected to an oral glucose tolerance test after a fasting period of 6 h

text: CD

characteristic: diet

text: Caecum

characteristic: environment (biome)

text: Caecal content

characteristic: environment (feature)

text: Caecal content

characteristic: environment (material)

text: specific pathogen-free

characteristic: facility

text: male

characteristic: gender

characteristic: genetic background

text: Germany

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: host-associated

characteristic: host-associated environmental package

text: metagenome

characteristic: investigation type

text: Mus musculus

characteristic: project name

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text: Illumina

characteristic: sequencing method

text: OGTT

characteristic: status


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characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: TUM

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characteristic: INSDC last update

text: public

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text: house mouse

characteristic: common name

text: Caecal content of one 18-week-old mouse fed a control experimental diet supplemented with 0.2 % (w/w) primary bile acids for 8 weeks and fasted for 6 h prior to sampling

characteristic: description

text: BA

text: Caecum

text: Caecal content

text: Caecal content

text: specific pathogen-free

text: male

text: Germany

characteristic: geographic location (country and/or sea)

text: host-associated

text: metagenome

text: Mus musculus

characteristic: organism

text: Mus musculus

text: Illumina

text: fasted

characteristic: title


text: TUM

text: public

characteristic: SRA accession

characteristic: collection date

text: house mouse

text: Caecal content of one 18-week-old mouse fed a control experimental diet for 8 weeks and fasted for 6 h prior to sampling

text: CD

characteristic: diet

text: Caecum

characteristic: environment (biome)

text: Caecal content

characteristic: environment (feature)

text: Caecal content

characteristic: environment (material)

text: specific pathogen-free

characteristic: facility

text: male

characteristic: gender

characteristic: genetic background

text: Germany

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: host-associated

characteristic: host-associated environmental package

text: metagenome

characteristic: investigation type

text: Mus musculus

characteristic: project name

text: Mus musculus

text: Illumina

text: fasted


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: TUM

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: Submitter Id

text: house mouse

characteristic: common name

text: Caecal content of one 18-week-old mouse fed a a control experimental diet supplemented with 0.2 % (w/w) primary bile acids and subjected to an oral glucose tolerance test after a fasting period of 6 h

characteristic: description

text: BA

text: Caecum

text: Caecal content

text: Caecal content

text: specific pathogen-free

text: male

text: Germany

characteristic: geographic location (country and/or sea)

text: host-associated

text: metagenome

text: Mus musculus

text: Mus musculus

text: Illumina

characteristic: sequencing method

text: OGTT

characteristic: status


text: TUM

text: public

characteristic: SRA accession

characteristic: collection date

text: house mouse

text: Caecal content of one 18-week-old mouse fed a lard-based high-fat diet (48% energy from fat) for 8 weeks and fasted for a 6 h prior to sampling

text: LHB

characteristic: diet

text: Caecum

characteristic: environment (biome)

text: Caecal content

characteristic: environment (feature)

text: Caecal content

characteristic: environment (material)

text: specific pathogen-free

characteristic: facility

text: male

characteristic: gender

characteristic: genetic background

text: Germany

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: host-associated

characteristic: host-associated environmental package

text: metagenome

text: Mus musculus

characteristic: organism

text: Mus musculus

text: Illumina

text: fasted

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: TUM

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: Submitter Id

text: house mouse

characteristic: common name

text: Caecal content of one 18-week-old mouse fed a palm oil-based high-fat diet (48% energy from fat) for 8 weeks and subjected to an oral glucose tolerance test after a fasting period of 6 h

characteristic: description

text: PHB

text: Caecum

text: Caecal content

text: Caecal content

text: specific pathogen-free

text: male

text: Germany

characteristic: geographic location (country and/or sea)

text: host-associated

text: metagenome

characteristic: investigation type

text: Mus musculus

characteristic: project name

text: Mus musculus

text: Illumina

text: OGTT


text: TUM

text: public

characteristic: SRA accession

characteristic: collection date

text: house mouse

text: Caecal content of one 18-week-old mouse fed a palm oil-based high-fat diet (48% energy from fat) for 8 weeks and fasted for a 6 h prior to sampling

text: PHB

characteristic: diet

text: Caecum

characteristic: environment (biome)

text: Caecal content

characteristic: environment (feature)

text: Caecal content

characteristic: environment (material)

text: specific pathogen-free

characteristic: facility

text: male

characteristic: gender

characteristic: genetic background

text: Germany

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: host-associated

characteristic: host-associated environmental package

text: metagenome

text: Mus musculus

text: Mus musculus

text: Illumina

characteristic: sequencing method

text: fasted

characteristic: status


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: TUM

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: Submitter Id

text: house mouse

characteristic: common name

text: Caecal content of one 18-week-old mouse fed a lard-based high-fat diet (48% energy from fat) for 8 weeks and subjected to an oral glucose tolerance test after a fasting period of 6 h

characteristic: description

text: LHB

text: Caecum

text: Caecal content

text: Caecal content

text: specific pathogen-free

text: male

text: Germany

characteristic: geographic location (country and/or sea)

text: host-associated

text: metagenome

text: Mus musculus

characteristic: organism

text: Mus musculus

text: Illumina

text: OGTT

characteristic: title


E-MTAB-5803:Sample 1

text: public

characteristic: SRA accession

text: E-MTAB-5803:Sample 1

tag: Namespace:Centre for Trophoblast Research, University of Cambridge

text: 8 to 12

characteristic: age

text: ArrayExpress

characteristic: broker name

text: group 2 innate lymphoid cell

characteristic: cell type

text: house mouse

text: Protocols: Single cell suspensions from Virgin and pregnant uteri were stained with CD127 (A7R34), ICOS (C398.4A), ST2 (RMST2-33), NK1.1 (PK136), CD3 (17A2), CD19 (6D5), GR-1 (RB6-8C5), TER-119 (TER-119), CD11c (HL3), CD8a (53-6.7), CD90.2 (53-2.1), CD45 (30-F11), CD11b (M1/70). All antibodies were purchased from Biolegend or BD bioscience. Viable cells were discriminated by using fixable viability dye ef450 from BD bioscience After sorting, uILC2 pellet were collected into fresh TRI Reagent (Sigma). RNA extraction was carried out by following TRI Reagent manufacture instructions. Transparent part containing mRNA was then purified with RNAeasy mini kit (Quiagen), gDNA contamination was eliminated with Turbo DNAse (Ambion) and we then clean up ILC2 mRNA with RNAeasy micro kit (Quiagen). C57BL/6 (B6) WT mice were used at 8-12 weeks. Single cell suspensions from Virgin and pregnant uteri were stained with CD127 (A7R34), ICOS (C398.4A), ST2 (RMST2-33), NK1.1 (PK136), CD3 (17A2), CD19 (6D5), GR-1 (RB6-8C5), TER-119 (TER-119), CD11c (HL3), CD8a (53-6.7), CD90.2 (53-2.1), CD45 (30-F11), CD11b (M1/70). Viable cells were discriminated by using fixable viability dye ef450 from BD bioscience. Live, single cells, CD45+ve CD11b-ve NK1.1-ve, CD3-ve, CD19-ve, GR-1-ve, Ter119-ve, CD11c-ve, CD8a-ve, ST2+ve, CD90+ve were sorted with BD FACSAria III into PBS 2% FCS. After sorting, uILC2 pellet were collected into fresh TRI Reagent (Sigma). RNA extraction was carried out by following TRI Reagent manufacture instructions. Transparent part containing mRNA was then purified with RNAeasy mini kit (Quiagen), gDNA contamination was eliminated with Turbo DNAse (Ambion) and we then clean up ILC2 mRNA with RNAeasy micro kit (Quiagen).

text: virgin

characteristic: developmental stage

text: wild type genotype

characteristic: genotype

characteristic: individual

text: Mus musculus

text: Mus musculus

text: uterus

characteristic: organism part

text: Mus musculus

text: female

characteristic: sex

characteristic: strain

text: Sample 1


E-MTAB-5803:Sample 2

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Centre for Trophoblast Research, University of Cambridge

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-5803:Sample 2

text: 8 to 12

text: ArrayExpress

text: group 2 innate lymphoid cell

text: house mouse

text: virgin

text: wild type genotype

text: Mus musculus

text: Mus musculus

text: uterus

text: Mus musculus

text: female

text: Sample 2


E-MTAB-5803:Sample 3

text: public

characteristic: SRA accession

text: E-MTAB-5803:Sample 3

characteristic: Submitter Id

text: 8 to 12

characteristic: age

text: ArrayExpress

text: group 2 innate lymphoid cell

text: house mouse

characteristic: common name

characteristic: description

text: virgin

text: wild type genotype

text: Mus musculus

characteristic: organism

text: Mus musculus

text: uterus

text: Mus musculus

text: female

text: Sample 3

characteristic: title


E-MTAB-5803:Sample 4

text: public

text: E-MTAB-5803:Sample 4

text: 8 to 12

text: ArrayExpress

characteristic: broker name

text: group 2 innate lymphoid cell

characteristic: cell type

text: house mouse

text: gravid adult at embryonic day 9.5

characteristic: developmental stage

text: wild type genotype

characteristic: genotype

characteristic: individual

text: Mus musculus

text: Mus musculus

text: uterus

characteristic: organism part

text: Mus musculus

text: female

characteristic: sex

text: Sample 4


E-MTAB-5803:Sample 5

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-5803:Sample 5

text: 8 to 12

text: ArrayExpress

text: group 2 innate lymphoid cell

text: house mouse

text: gravid adult at embryonic day 9.5

text: wild type genotype

text: Mus musculus

text: Mus musculus

text: uterus

text: Mus musculus

text: female

characteristic: strain

text: Sample 5


E-MTAB-5803:Sample 6

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-5803:Sample 6

characteristic: Submitter Id

text: 8 to 12

characteristic: age

text: ArrayExpress

text: group 2 innate lymphoid cell

text: house mouse

characteristic: common name

characteristic: description

text: gravid adult at embryonic day 9.5

text: wild type genotype

text: Mus musculus

text: Mus musculus

text: uterus

text: Mus musculus

text: female

text: Sample 6


E-MTAB-5803:Sample 7

text: public

text: E-MTAB-5803:Sample 7

text: 8 to 12

text: ArrayExpress

characteristic: broker name

text: group 2 innate lymphoid cell

characteristic: cell type

text: house mouse

text: gravid adult at embryonic day 18.5

characteristic: developmental stage

text: wild type genotype

characteristic: genotype

characteristic: individual

text: Mus musculus

characteristic: organism

text: Mus musculus

text: uterus

text: Mus musculus

text: female

text: Sample 7

characteristic: title


E-MTAB-5803:Sample 8

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

text: public

text: E-MTAB-5803:Sample 8

text: 8 to 12

text: ArrayExpress

text: group 2 innate lymphoid cell

text: house mouse

text: gravid adult at embryonic day 18.5

text: wild type genotype

text: Mus musculus

text: Mus musculus

text: uterus

characteristic: organism part

text: Mus musculus

text: female

characteristic: sex

text: Sample 8


E-MTAB-5803:Sample 9

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-5803:Sample 9

characteristic: Submitter Id

text: 8 to 12

characteristic: age

text: ArrayExpress

text: group 2 innate lymphoid cell

text: house mouse

text: gravid adult at embryonic day 18.5

text: wild type genotype

text: Mus musculus

text: Mus musculus

text: uterus

text: Mus musculus

text: female

characteristic: strain

text: Sample 9