text: Teagasc

text: public

text: over 7

unit: day

characteristic: age

text: ArrayExpress

text: English grain aphid

characteristic: common name

text: Protocols: The maternal Grain Aphid was collected in 2017 from a wheat field in Carlow, Ireland, and removed from the colony and stored after producing nymphs. The aphid colony was reared on barley plants in an insect incubator at 20 °C and 16/8 h day-night circle. Genotyping of the original maternal aphid and aphids from following generations confirmed that the aphids were the partially resistant SA3 clonal lineage. 50 aphids were put onto a microscope glass plate into droplets of lysis buffer and were dissected with a sterilized scalpel at the beginning of the thorax. RNA was extracted using the GenElute™ Mammalian Total RNA Miniprep Kit (Sigma-Aldrich; Merck KGaA, Darmstadt, Germany). 50 aphids per sample were used to perform RNA extractions. Oligo dT Selection to enrich the mRNA; stranded specific mRNA libraries，second-strand cDNA synthesis with dUTP instead of dTTP

characteristic: description

text: adult

characteristic: developmental stage

text: wild type genotype

characteristic: genotype

characteristic: individual

text: Sitobion avenae

text: Sitobion avenae

text: body

characteristic: organism part

text: unwinged

characteristic: phenotype

text: Sitobion avenae

text: female

characteristic: sex

characteristic: title


status: PUBLIC

tag: attribute

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Teagasc

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: over 7

text: ArrayExpress

characteristic: broker name

text: English grain aphid

text: adult

text: wild type genotype

text: Sitobion avenae

characteristic: organism

text: Sitobion avenae

text: head

text: unwinged

text: Sitobion avenae

text: female

characteristic: strain


text: Teagasc

text: public

text: over 7

characteristic: age

text: ArrayExpress

text: English grain aphid

characteristic: common name

text: Protocols: The maternal Grain Aphid was collected in 2017 from a wheat field in Carlow, Ireland, and removed from the colony and stored after producing nymphs. The aphid colony was reared on barley plants in an insect incubator at 20 °C and 16/8 h day-night circle. Genotyping of the original maternal aphid and aphids from following generations confirmed that the aphids were the partially resistant SA3 clonal lineage. RNA was extracted using the GenElute™ Mammalian Total RNA Miniprep Kit (Sigma-Aldrich; Merck KGaA, Darmstadt, Germany). 50 aphids per sample were used to perform RNA extractions. Oligo dT Selection to enrich the mRNA; stranded specific mRNA libraries，second-strand cDNA synthesis with dUTP instead of dTTP

characteristic: description

text: adult

characteristic: developmental stage

text: wild type genotype

characteristic: genotype

characteristic: individual

text: Sitobion avenae

text: Sitobion avenae

text: whole organism

characteristic: organism part

text: unwinged

text: Sitobion avenae

text: female


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Teagasc

text: public

text: over 7

text: ArrayExpress

text: English grain aphid

text: adult

text: wild type genotype

text: Sitobion avenae

text: Sitobion avenae

text: whole organism

text: winged

characteristic: phenotype

text: Sitobion avenae

text: female

characteristic: sex

characteristic: title


text: Tromsoe University Museum

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

tag: Namespace:Tromsoe University Museum

characteristic: Submitter Id

text: Eie, Sigrid; Knaben, Gunvor

characteristic: collected by

characteristic: collection date

text: terrestrial biome

characteristic: environment (biome)

text: natural environment

characteristic: environment (feature)

text: plant matter

characteristic: environment (material)

text: USA

characteristic: geographic location (country and/or sea)

unit: DD

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: genome skimming

characteristic: investigation type

text: herbarium sample

characteristic: isolation and growth condition

text: Empetrum nigrum

text: herbarium sample

characteristic: plant developmental stage

text: soil

characteristic: plant growth medium

text: leaf (PO_0025034)

characteristic: plant structure

text: Empetrum nigrum

text: Tromsoe herbarium specimen TROM_V_135794

characteristic: source material identifiers

text: TROM_V_135794 herbarium sample of Empetrum nigrum


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Tromsoe University Museum

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: Eie, Sigrid; Knaben, Gunvor

text: terrestrial biome

text: natural environment

text: plant matter

text: USA

text: genome skimming

text: herbarium sample

text: Harrimanella stelleriana

characteristic: organism

text: herbarium sample

text: soil

text: leaf (PO_0025034)

text: Harrimanella stelleriana

text: Tromsoe herbarium specimen TROM_V_135813

text: TROM_V_135813 herbarium sample of Harrimanella stelleriana

characteristic: title


text: Tromsoe University Museum

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: Elven, Reidar

characteristic: collected by

characteristic: collection date

text: terrestrial biome

characteristic: environment (biome)

text: natural environment

characteristic: environment (feature)

text: plant matter

characteristic: environment (material)

text: Sweden

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: genome skimming

text: herbarium sample

text: Hottonia palustris

text: herbarium sample

text: soil

text: leaf (PO_0025034)

text: Hottonia palustris

text: Tromsoe herbarium specimen TROM_V_145592

text: TROM_V_145592 herbarium sample of Hottonia palustris


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Tromsoe University Museum

text: public

text: Gaarder, Geir; Rosok, Oystein

text: terrestrial biome

text: natural environment

text: plant matter

text: Norway

text: genome skimming

characteristic: investigation type

text: herbarium sample

characteristic: isolation and growth condition

text: Rhododendron lapponicum

text: herbarium sample

characteristic: plant developmental stage

text: soil

characteristic: plant growth medium

text: leaf (PO_0025034)

characteristic: plant structure

text: Rhododendron lapponicum

text: Tromsoe herbarium specimen TROM_V_651537

characteristic: source material identifiers

text: TROM_V_651537 herbarium sample of Rhododendron lapponicum


text: Tromsoe University Museum

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: Vagen, Inger

characteristic: collected by

characteristic: collection date

text: terrestrial biome

text: natural environment

text: plant matter

text: Norway

text: genome skimming

text: herbarium sample

text: Impatiens parviflora

characteristic: organism

text: herbarium sample

text: soil

text: leaf (PO_0025034)

text: Impatiens parviflora

text: Tromsoe herbarium specimen TROM_V_89843

text: TROM_V_89843 herbarium sample of Impatiens parviflora

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Tromsoe University Museum

text: public

text: Alm, Torbjorn

text: terrestrial biome

characteristic: environment (biome)

text: natural environment

characteristic: environment (feature)

text: plant matter

characteristic: environment (material)

text: Norway

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: genome skimming

text: herbarium sample

text: Vaccinium myrtillus

text: herbarium sample

text: soil

text: leaf (PO_0025034)

text: Vaccinium myrtillus

text: Tromsoe herbarium specimen TROM_V_961324

text: TROM_V_961324 herbarium sample of Vaccinium myrtillus


text: Tromsoe University Museum

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: Alm, Torbjorn; Gamst, Unni Bjerke

text: terrestrial biome

text: natural environment

text: plant matter

text: Norway

text: genome skimming

characteristic: investigation type

text: herbarium sample

characteristic: isolation and growth condition

text: Harrimanella hypnoides

text: herbarium sample

characteristic: plant developmental stage

text: soil

characteristic: plant growth medium

text: leaf (PO_0025034)

characteristic: plant structure

text: Harrimanella hypnoides

text: Tromsoe herbarium specimen TROM_V_962002

characteristic: source material identifiers

text: TROM_V_962002 herbarium sample of Harrimanella hypnoides


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Tromsoe University Museum

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: Alm, Torbjorn

characteristic: collected by

characteristic: collection date

text: terrestrial biome

text: natural environment

text: plant matter

text: Norway

text: genome skimming

text: herbarium sample

text: Trientalis europaea

characteristic: organism

text: herbarium sample

text: soil

text: leaf (PO_0025034)

text: Trientalis europaea

text: Tromsoe herbarium specimen TROM_V_964193

text: TROM_V_964193 herbarium sample of Trientalis europaea

characteristic: title


text: Tromsoe University Museum

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: Alm, Torbjorn

text: terrestrial biome

characteristic: environment (biome)

text: natural environment

characteristic: environment (feature)

text: plant matter

characteristic: environment (material)

text: Norway

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: genome skimming

text: herbarium sample

text: Vaccinium vitis-idaea

text: herbarium sample

text: soil

text: leaf (PO_0025034)

text: Vaccinium vitis-idaea

text: Tromsoe herbarium specimen TROM_V_965838

text: TROM_V_965838 herbarium sample of Vaccinium vitis-idaea


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Tromsoe University Museum

text: public

text: Osterkloft, Bernt-Gunnar

text: terrestrial biome

text: natural environment

text: plant matter

text: Norway

text: genome skimming

characteristic: investigation type

text: herbarium sample

characteristic: isolation and growth condition

text: Trientalis europaea

text: herbarium sample

characteristic: plant developmental stage

text: soil

characteristic: plant growth medium

text: leaf (PO_0025034)

characteristic: plant structure

text: Trientalis europaea

text: Tromsoe herbarium specimen TROM_V_96829

characteristic: source material identifiers

text: TROM_V_96829 herbarium sample of Trientalis europaea


characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

tag: Namespace:Novartis Institutes for BioMedical Research

characteristic: Submitter Id

text: 9 to 12

unit: week

characteristic: age

text: ArrayExpress

characteristic: broker name

text: Norway rat

characteristic: common name

text: Protocols: To induce hepatic fibrosis, Male Sprague Dawley rats (9-12 weeks of age and 380-420 g of weight upon arrival, supplied by Beijing Vital River laboratory animal Co., Ltd.) underwent surgery of bile duct ligation (BDL). The bile ducts of Sprague-Dawley rats were ligated after 12 hours of fasting and water deprivation. Rat liver samples were collected from three groups of rats at week 1, 2 and 5 after BDL surgery. Three control groups of rats underwent sham operation, including bile duct mobilization, but without BDL. Three biological replicates were used for each group. Frozen rat liver tissue (~ 2 mm cube) was lysed and homogenized using Trizol reagent in a Qiagen TissueLyser II. After phase separation of the homogenate, the upper aqueous phase was subject to total RNA purification using Qiagen RNeasy Mini spin column with extensive on-column DNase I digestion. Purified total RNA samples were analyzed by Agilent Bioanalyzer RNA 6000 Nano assay and quantified by Qubit RNA assay. For construction of sequencing libraries, 1 ug of total RNA (RIN > 8) was subject to Illumina TruSeq Stranded Total RNA Sample Prep kit with Ribo-Zero Gold. Libraries were analyzed by Bioanalyzer High Sensitivity DNA assay and quantified by Qubit DNA assay.

characteristic: description

text: adult

characteristic: developmental stage

text: liver fibrosis

characteristic: disease

text: wild type genotype

characteristic: genotype

characteristic: individual

text: bile duct ligation

characteristic: injury

text: not applicable

characteristic: isolate

text: Rattus norvegicus

characteristic: organism

text: Rattus norvegicus

text: liver

characteristic: organism part

characteristic: replicate

text: Rattus norvegicus

text: male

characteristic: sex

text: Sprague-Dawley

characteristic: strain

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Novartis Institutes for BioMedical Research

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: 9 to 12

text: ArrayExpress

text: Norway rat

text: adult

text: liver fibrosis

text: wild type genotype

text: bile duct ligation

text: not applicable

text: Rattus norvegicus

text: Rattus norvegicus

text: liver

text: Rattus norvegicus

text: male

text: Sprague-Dawley


text: public

text: 9 to 12

characteristic: age

text: ArrayExpress

characteristic: broker name

text: Norway rat

characteristic: common name

characteristic: description

text: adult

characteristic: developmental stage

text: normal

characteristic: disease

text: wild type genotype

characteristic: genotype

characteristic: individual

text: sham

characteristic: injury

text: not applicable

characteristic: isolate

text: Rattus norvegicus

text: Rattus norvegicus

text: liver

text: Rattus norvegicus

text: male

text: Sprague-Dawley


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: 9 to 12

text: ArrayExpress

text: Norway rat

characteristic: compound

text: Protocols: To induce hepatic fibrosis, Male Sprague Dawley rats (9-12 weeks of age and 380-420 g of weight upon arrival, supplied by Beijing Vital River laboratory animal Co., Ltd.) were treated with thioacetamide (TAA). Rat liver samples were collected from five groups of rats at week 1, 2, 4, 8 and 13 after TAA (300 mg/kg) administration three times per week while five control groups receive the same volume of 0.9% normal saline. Four biological replicates were used for each group. Frozen rat liver tissue (~ 2 mm cube) was lysed and homogenized using Trizol reagent in a Qiagen TissueLyser II. After phase separation of the homogenate, the upper aqueous phase was subject to total RNA purification using Qiagen RNeasy Mini spin column with extensive on-column DNase I digestion. Purified total RNA samples were analyzed by Agilent Bioanalyzer RNA 6000 Nano assay and quantified by Qubit RNA assay. For construction of sequencing libraries, 1 ug of total RNA (RIN > 8) was subject to Illumina TruSeq Stranded Total RNA Sample Prep kit with Ribo-Zero Gold. Libraries were analyzed by Bioanalyzer High Sensitivity DNA assay and quantified by Qubit DNA assay.

text: adult

text: normal

characteristic: dose

text: wild type genotype

text: not applicable

text: Rattus norvegicus

characteristic: organism

text: Rattus norvegicus

text: liver

characteristic: organism part

characteristic: replicate

text: Rattus norvegicus

text: male

characteristic: sex

text: Sprague-Dawley

characteristic: strain

characteristic: title


characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: 9 to 12

characteristic: age

text: ArrayExpress

characteristic: broker name

text: Norway rat

characteristic: common name

text: thioacetamide

characteristic: description

text: adult

characteristic: developmental stage

text: liver fibrosis

characteristic: disease

unit: milligram per kilogram

text: wild type genotype

text: not applicable

text: Rattus norvegicus

text: Rattus norvegicus

text: liver

text: Rattus norvegicus

text: male

text: Sprague-Dawley


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

tag: Namespace:Unit of Viral Infection and Immunity, National Center for Microbiology, Institute of Health Carlos III

text: adult

unit: year

text: ArrayExpress

text: peripheral blood mononuclear cell

characteristic: cell type

text: HIV-1 coinfection with hepatitis C virus (HCV)

characteristic: clinical history

text: human

text: Protocols: Peripheral venous blood samples were collected in EDTA tubes, and PBMCs were isolated within the first 4 hours after extraction, using a Ficoll-Paque gradient method. Total RNA including miRNAs were isolated from PBMCs with the miRNeasy Mini kit (Qiagen). Quality and integrity of the RNA were evaluated by the Bioanalyzer 2100 with Agilent RNA 6000 Nano kit (Agilent). Only those samples with RIN > 7.5 were sequenced. Small RNA libraries were constructed with Illumina’s TruSeq Small RNA kit v.4 (Illumina, ref. RS-200-0012). In brief, 1 microgram of total RNA was used, 3′ and 5′ adapters were sequentially ligated to the ends of RNA < 200 nt long, and reverse transcribed to generate cDNA (SuperScript II, ref. 18064-014, Invitrogen) with a specific primer (RNA RT Primer) complementary to the 3’ RNA adapter. The cDNA was further amplified by PCR (11 cycles) using a common primer complementary to the 3′ adapter, and a 5′ primer containing 1 of 48 index sequences. Libraries were size-selected using 6% Novex® TBE Gels (ref. EC6265BOX, Life Technologies). Fragments with insert sizes of 18 to 36 bp were cut from the gel, and DNA was purified, quantified and pooled for multiplexed sequencing. Final libraries were analyzed using Agilent DNA 1000 chip to estimate the quantity and check size distribution, and were then quantified by qPCR using the KAPA Library Quantification Kit (ref. KK4835, KapaBiosystems) prior to amplification with Illumina’s cBot.

text: adult

text: HIV-1 coinfection with hepatitis C Virus infection

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: blood

characteristic: organism part

text: Homo sapiens

text: female

text: HMH


text: Unit of Viral Infection and Immunity, National Center for Microbiology, Institute of Health Carlos III

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: adult

text: ArrayExpress

text: peripheral blood mononuclear cell

text: human

text: adult

text: Homo sapiens

text: Homo sapiens

text: blood

text: Homo sapiens

text: female

characteristic: sex

text: HMB

characteristic: title


text: public

characteristic: SRA accession

characteristic: Submitter Id

text: adult

characteristic: age

text: ArrayExpress

characteristic: broker name

text: peripheral blood mononuclear cell

text: human

characteristic: common name

characteristic: description

text: adult

text: Homo sapiens

text: Homo sapiens

text: blood

text: Homo sapiens

text: female

text: HMC


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: adult

text: ArrayExpress

text: peripheral blood mononuclear cell

text: human

text: adult

characteristic: developmental stage

characteristic: disease

text: Homo sapiens

text: Homo sapiens

text: blood

text: Homo sapiens

text: female

text: HMN


characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: adult

text: ArrayExpress

text: peripheral blood mononuclear cell

characteristic: cell type

characteristic: clinical history

text: human

text: adult

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: blood

characteristic: organism part

text: Homo sapiens

text: female

text: HME


characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: adult

text: ArrayExpress

text: peripheral blood mononuclear cell

text: human

text: adult

text: Homo sapiens

text: Homo sapiens

text: blood

text: Homo sapiens

text: female

characteristic: sex

text: HMF

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: adult

characteristic: age

text: ArrayExpress

characteristic: broker name

text: peripheral blood mononuclear cell

text: human

characteristic: common name

characteristic: description

text: adult

text: Homo sapiens

text: Homo sapiens

text: blood

text: Homo sapiens

text: female

text: HML


characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: adult

text: ArrayExpress

text: peripheral blood mononuclear cell

text: human

text: adult

characteristic: developmental stage

characteristic: disease

text: Homo sapiens

text: Homo sapiens

text: blood

text: Homo sapiens

text: female

text: HMQ


characteristic: INSDC last update

text: public

characteristic: INSDC status

text: adult

text: ArrayExpress

text: peripheral blood mononuclear cell

characteristic: cell type

characteristic: clinical history

text: human

text: adult

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: blood

characteristic: organism part

text: Homo sapiens

text: female

text: HMM


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: adult

text: ArrayExpress

text: peripheral blood mononuclear cell

text: human

text: adult

text: Homo sapiens

text: Homo sapiens

text: blood

text: Homo sapiens

text: female

characteristic: sex

text: HMR

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: adult

characteristic: age

text: ArrayExpress

characteristic: broker name

text: peripheral blood mononuclear cell

text: human

characteristic: common name

characteristic: description

text: adult

text: Homo sapiens

text: Homo sapiens

text: blood

text: Homo sapiens

text: female

text: HMS


characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: adult

text: ArrayExpress

text: peripheral blood mononuclear cell

text: human

text: adult

characteristic: developmental stage

characteristic: disease

text: Homo sapiens

text: Homo sapiens

text: blood

text: Homo sapiens

text: male


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: adult

text: ArrayExpress

text: peripheral blood mononuclear cell

characteristic: cell type

characteristic: clinical history

text: human

text: adult

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: blood

characteristic: organism part

text: Homo sapiens

text: male

text: HVC


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: adult

text: ArrayExpress

text: peripheral blood mononuclear cell

text: human

text: adult

text: Homo sapiens

text: Homo sapiens

text: blood

text: Homo sapiens

text: male

characteristic: sex

text: HVG

characteristic: title


characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: adult

characteristic: age

text: ArrayExpress

characteristic: broker name

text: peripheral blood mononuclear cell

text: human

characteristic: common name

characteristic: description

text: adult

text: Homo sapiens

text: Homo sapiens

text: blood

text: Homo sapiens

text: male

text: HVL


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: adult

text: ArrayExpress

text: peripheral blood mononuclear cell

text: human

text: adult

characteristic: developmental stage

characteristic: disease

text: Homo sapiens

text: Homo sapiens

text: blood

text: Homo sapiens

text: male

text: HVM


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: adult

text: ArrayExpress

text: peripheral blood mononuclear cell

characteristic: cell type

characteristic: clinical history

text: human

text: adult

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: blood

characteristic: organism part

text: Homo sapiens

text: male

text: HVN


characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: adult

text: ArrayExpress

text: peripheral blood mononuclear cell

text: human

text: adult

text: Homo sapiens

text: Homo sapiens

text: blood

text: Homo sapiens

text: male

characteristic: sex

text: HVO

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: adult

characteristic: age

text: ArrayExpress

characteristic: broker name

text: peripheral blood mononuclear cell

text: human

characteristic: common name

characteristic: description

text: adult

text: Homo sapiens

text: Homo sapiens

text: blood

text: Homo sapiens

text: male

text: HVP


characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: adult

text: ArrayExpress

text: peripheral blood mononuclear cell

text: human

text: adult

characteristic: developmental stage

characteristic: disease

text: Homo sapiens

text: Homo sapiens

text: blood

text: Homo sapiens

text: male

text: HVR


characteristic: INSDC center name

characteristic: INSDC first public

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text: WVK


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text: public

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text: adult

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text: blood

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text: male

characteristic: sex

text: WVL

characteristic: title


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text: public

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text: WVM


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text: adult

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text: human

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characteristic: INSDC center name

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text: public

text: E-MTAB-99541623777143:T_N_aPDL1_9091_a_fibro_enriched_2

tag: Namespace:Division of Translational Cancer Research, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK)

text: 11 to 15

text: ArrayExpress

text: fibroblasts and mesenchymal tumor cells

characteristic: cell type

text: house mouse

text: Protocols: Fresh tumor samples were minced using a scalpel and enzymatically digested with the tumor dissociation kit (Miltenyi #130-096-730) in DMEM medium (Sigma, #D5796-500 mL) for 40 min at 37°C with agitation. The cell suspension was strained through a 100 μm strainer, spun down and resuspended in 2% FCS/PBS including RNase inhibitor (NEB, #M0314L,1:100). Debris removal solution (Miltenyi #130-109-398) was used to remove cell debris from the dissociated tissue. Then the dead cell removal kit (Miltenyi #130-090-101) was used to enrich for live cells. The cell suspension was spun down and then resuspended in PBS and blocked for non- antigen-specific binding for 10 min on ice with anti-mouse CD16/CD32 FC block (Biolegend, 1:100). Cells were stained with the following antibodies for FACS sorting: TER-119 BV421 (Biolegend, 1:100), CD45-AF647 (Biolegend, 1:20), CD31-AF647 (Biolegend, 1:20) and EPCAM-AF647 (Biolegend, 1:20) for 30 min on ice. Cell sorting was performed using the BD FACS Aria Fusion. The sorted cells from the TER-119- negative/CD45-/CD31-/EPCAM-positive fraction (for enrichment of immune, endothelial and epithelial tumor cells and exclusion of erythrocytes) as well as TER- 119-/CD45-/CD31-/EPCAM-negative fraction (for enrichment of fibroblasts/mesenchymal tumor cells and exclusion of erythrocytes). Sorted cells were collected in 2% FCS/PBS. The sorted cells were counted, diluted in 2% FCS/PBS and up to 20,000 cells were loaded per lane on a 10x Chromium chip to generate gel beads in emulsion (GEMs). Single cell GEM Generation, barcoding and library construction was performed by using 10x Chromium Single Cell 3’ v3 chemistry according to the manufacturer’s instructions. cDNA and generated libraries were checked for sample size and quality on an Agilent Tapestation 4200 using DNA HS 5000 tape.

text: adult

text: pancreatic ductal adenocarcinoma

text: TER-119- CD45- CD31- EPCAM-negative

characteristic: immunophenotype

characteristic: individual

text: Mus musculus

characteristic: organism

text: Mus musculus

text: neoplasm

characteristic: organism part

text: Mus musculus

text: transplanted with Ptf1aCre/+;LSL-KrasG12D/+ pancreatic ductal adenocarcinoma cells at 8-12 weeks

characteristic: stimulus

characteristic: strain


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Division of Translational Cancer Research, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK)

text: public

characteristic: SRA accession

text: E-MTAB-99541623777143:T_N_aPDL1_9091_b_immune_enriched_2

characteristic: Submitter Id

text: 11 to 15

characteristic: age

text: ArrayExpress

characteristic: broker name

text: immune, endothelial and epithelial tumor cells

text: house mouse

characteristic: common name

text: adult

text: pancreatic ductal adenocarcinoma

text: TER-119-negative CD45- CD31- EPCAM-positive

text: Mus musculus

text: Mus musculus

text: neoplasm

text: Mus musculus

characteristic: title


E-MTAB-10602:Sample 1

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-10602:Sample 1

tag: Namespace:Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf (UKE)

text: ArrayExpress

text: macrophage

text: human

text: Protocols: Human peripheral blood monocytes were isolated by centrifugation of heparinized blood in Ficoll. Monocytic cells were isolated with magnetic anti-CD14 antibody beads and an MS+ Separation Column (Miltenyi Biotec) according to the manufacturer’s instructions and seeded into 6-well plates at a density of 2 × 106 cells. Cells were cultured in RPMI containing 20% autologous serum at 37°C, 5% CO2, and 90% humidity. Medium was changed every 3-4 days. Cells were cultured in RPMI1640 containing 20 % autologous serum at 37 °C and 5 % CO2 atmosphere. The medium was changed every three days until cells were differentiated into macrophages after 7 days. Macrophages were used for infection 1-2 weeks after the isolation. On the day before the infection of primary human macrophages the cell medium was changed to RPMI1640 without antibiotics and serum and Yersinia precultures were grown overnight in LB medium with appropriate antibiotics at 27 °C and 200 x rpm. On the day of infection precultures were diluted 1:20 in fresh LB medium without antibiotics and incubated for 90 min at 37 °C and 200 x rpm to induce activation of the Yersinia T3SS machinery and Yop expression. Afterwards bacteria were pelleted by centrifugation for 10 min at 6000 x g and 4 °C and resuspended in 1 ml ice-cold PBS containing 1 mM MgCl2 and CaCl2. The optical density OD600 was adjusted to 3.6 and afterwards macrophages were infected at multiplicity-of-infection (MOI) of 100. Cell culture dishes were centrifuged for 2 min at RT and 200 x g to sediment bacteria on the cells and synchronize infection. Cells were incubated at 37 °C for 1.5h or 6h. Total RNA of ~1-2 x 106 human macrophages was isolated using RNeasy extraction kit (Qiagen, Germany) including DNAse treatment according to manufacturer’s instructions. RNA integrity of the isolated RNA was analysed with the RNA 6000 Nano Chip (Agilent Technologies, USA) on an Agilent 2100 Bioanalyzer (Agilent Technologies, USA). mRNA was extracted using the NEBNext Poly(A) mRNA Magnetic Isolation module (New England Biolabs, USA). RNA-seq libraries were generated using the NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs, USA) as per the manufacturer’s recommendations.

characteristic: description

text: DonorII

text: Yersinia enterocolitica WA314deltaYopMP

characteristic: infect

text: Homo sapiens

text: Homo sapiens

text: blood

text: Homo sapiens

text: Sample 1


E-MTAB-10602:Sample 2

text: Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf (UKE)

characteristic: INSDC first public

text: public

text: E-MTAB-10602:Sample 2

text: ArrayExpress

text: macrophage

characteristic: cell type

text: human

text: DonorIII

characteristic: individual

text: Yersinia enterocolitica WA314deltaYopMP

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: blood

characteristic: organism part

text: Homo sapiens

text: Sample 2


E-MTAB-10602:Sample 3

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

characteristic: SRA accession

text: E-MTAB-10602:Sample 3

characteristic: Submitter Id

text: ArrayExpress

text: macrophage

text: human

text: DonorII

text: Yersinia enterocolitica WA314deltaYopMP

text: Homo sapiens

text: Homo sapiens

text: blood

text: Homo sapiens

text: Sample 3


E-MTAB-10602:Sample 4

text: public

text: E-MTAB-10602:Sample 4

text: ArrayExpress

characteristic: broker name

text: macrophage

text: human

characteristic: common name

text: DonorIII

text: Yersinia enterocolitica WA314deltaYopMP

text: Homo sapiens

text: Homo sapiens

text: blood

text: Homo sapiens

text: Sample 4

characteristic: title


E-MTAB-10602:Sample 5

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

text: public

text: E-MTAB-10602:Sample 5

text: ArrayExpress

text: macrophage

text: human

text: DonorII

text: Yersinia enterocolitica WA314deltaYopP

text: Homo sapiens

text: Homo sapiens

text: blood

text: Homo sapiens

text: Sample 5


E-MTAB-10602:Sample 6

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-10602:Sample 6

text: ArrayExpress

text: macrophage

text: human

characteristic: description

text: DonorIII

text: Yersinia enterocolitica WA314deltaYopP

text: Homo sapiens

text: Homo sapiens

text: blood

text: Homo sapiens

text: Sample 6


text: Ugent

characteristic: INSDC first public

text: public

text: ArrayExpress

text: CLB-Bar

characteristic: cell line

text: human

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

text: neuroblastoma

characteristic: disease

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: female

characteristic: sex


characteristic: ENA-CHECKLIST

text: Ugent

text: public

text: ArrayExpress

text: CLB-Ge

text: human

text: neuroblastoma

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: Homo sapiens

text: male


E-MTAB-10605:D1 spheroid 21 weeks

characteristic: ENA-FIRST-PUBLIC

text: public

characteristic: SRA accession

text: E-MTAB-10605:D1 spheroid 21 weeks

tag: Namespace:Center for Molecular Biology of Heidelberg University (ZMBH)

text: ArrayExpress

text: iPSC D1

text: forebrain organoid cell

characteristic: cell type

text: human

text: Protocols: D1 spheroids were formed and cultured for 21 weeks under the conditions specified in the growth protocol. Subsequently, ca. 30 spheroids were frozen and single nuclei were extracted according to the protocol specified in the associated publication. Human iPSC lines D1 were cultured in mTeSR Plus medium (STEMCELL Technologies, Vancouver, Canada) according to the protocol provided by the manufacturer on Matrigel (Corning, Corning, NY, USA) coated cell culture plates. For forebrain organoid generation, the culture medium was supplemented with 10 µM ROCK inhibitor (Y-27632 dihydrochloride, Tocris, NY, USA) for 15 min followed by dissociation with Accutase (STEMCELL Technologies). 105 cells were transferred into each well of a low attachment conical bottom 96-well plate (ThermoFisher Scientific, Waltham MA, USA) and aggregated by centrifugation for 5 min at 75 x g. The next day, hiPSC aggregates were collected, taken up in neural induction medium (NIM: DMEM/F-12, 1 x GlutaMAX, 2 x B27 without Vitamin A, 1 x N2, β-Mercaptoethanol (#21985023, 1:1000) (ThermoFisher Scientific), Dorsomorphin dihydrochloride (500 nM, Tocris,), recombinant Noggin (5 ng/ml, R&D Systems, Minneapolis, MN, USA), SB431542 (10 µM, Tocris,), Normocin (1:1000, Invivogen, San Diego, CA, USA)) and transferred into non-coated 35 mm plastic dishes (#627102, Greiner, Kremsmünster, Austria). On day two in NIM, FGF-2 (10 ng/ml, Peprotech, Rocky Hill, NJ, USA) was added to the culture medium. After seven days in NIM, flee-floating organoids were moved into neural medium (NM: Neurobasal (ThermoFisher Scientific), 1 x GlutaMAX, 1 x B27 without vitamin A, Normocin) supplemented with FGF-2 (10 ng/ml) and EGF (10 ng/ml, Peprotech) for two weeks. In order to ensure forebrain fate adoption, IWP-2 (2 µM, Sigma Aldrich, St. Louis, MO, USA) and Cyclopamine (1 µM, Merck, Darmstadt, Germany) were included in the media for the first 21 days. From day 21 to 35 NM was supplemented with BDNF (10 ng/ml) and NT-3 (10 ng/ml, both Peprotech). From day 35 onwards organoids were kept in maintenance medium (MM: BrainPhys (STEMCELL Technologies), 1 x GlutaMAX, 1 x B27 without Vitamin A, Normocin). Nucleic acids were processed using the 10x Chromium Single Cell 3’ v3.1 Gene Expression Kit according to the manufacturer's instructions Libraries were constructed using the 10x Chromium Single Cell 3’ v3.1 Gene Expression Kit according to the manufacturer's instructions

text: forebrain organoid culture

characteristic: growth condition

text: Homo sapiens

text: Homo sapiens

text: induced pluripotent stem cell

characteristic: progenitor cell type

characteristic: sampling time point

text: Homo sapiens

text: D1 spheroid 21 weeks


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

tag: Namespace:Institute for molecular and tumor biology Bioinformatics Core facility Philipps University  Marburg Germany

characteristic: Submitter Id

text: 75 to 80

characteristic: age

text: ArrayExpress

characteristic: broker name

text: macrophage

text: human

characteristic: common name

text: Protocols: Ascites or omentum was collected from patients with high-grade serous ovarian carcinoma undergoing primary surgery at the University Hospital in Marburg. Informed consent was obtained from all patients according to the protocols approved by the local ethical committee RNA-extraction with TriFast (1ml) according the manufacturer protocol. RNA is dissolved in RNase-free water (with RNase-Inhibitor Superase-IN 1:20). DNase digestion with DNA-free™ Kit (invitrogen, ThermoFisher scientific) followed. The integrity and purity of RNA was determined using the Experion RNA StdSens Illumina TruSeq stranded mRNA according to manufactures' instructions

text: adult

characteristic: developmental stage

text: high grade ovarian serous adenocarcinoma

characteristic: individual

text: Illumina TruSeq Stranded mRNA

characteristic: nucleic acid library construction protocol

text: Homo sapiens

text: Homo sapiens

text: ascites fluid

characteristic: organism part

text: Homo sapiens

text: female

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Institute for molecular and tumor biology Bioinformatics Core facility Philipps University Marburg Germany

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: 70 to 75

text: ArrayExpress

text: macrophage

text: human

characteristic: description

text: adult

characteristic: disease

text: Illumina TruSeq Stranded mRNA

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: ascites fluid

text: Homo sapiens

text: female

characteristic: sex


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: 60 to 65

characteristic: age

text: ArrayExpress

characteristic: broker name

text: tumor cell

characteristic: cell type

text: human

text: adult

text: Illumina TruSeq Stranded mRNA

text: Homo sapiens

text: Homo sapiens

text: ascites fluid

text: Homo sapiens

text: female


characteristic: ENA-CHECKLIST

text: public

text: 70 to 75

text: ArrayExpress

text: tumor cell

text: human

characteristic: common name

text: adult

characteristic: developmental stage

characteristic: individual

text: Illumina TruSeq Stranded mRNA

characteristic: nucleic acid library construction protocol

text: Homo sapiens

text: Homo sapiens

text: ascites fluid

characteristic: organism part

text: Homo sapiens

text: female

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: 60 to 65

text: ArrayExpress

text: macrophage

text: human

characteristic: description

text: adult

characteristic: disease

text: Illumina TruSeq Stranded mRNA

text: Homo sapiens

text: Homo sapiens

text: ascites fluid

text: Homo sapiens

text: female


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: 50 to 55

characteristic: age

text: ArrayExpress

text: macrophage

text: human

text: adult

text: Illumina TruSeq Stranded mRNA

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: ascites fluid

text: Homo sapiens

text: female

characteristic: sex


characteristic: ENA-CHECKLIST

text: public

text: 50 to 55

text: ArrayExpress

characteristic: broker name

text: cancer associated fibroblast

characteristic: cell type

text: human

characteristic: common name

text: Protocols: Ascites or omentum was collected from patients with high-grade serous ovarian carcinoma undergoing primary surgery at the University Hospital in Marburg. Informed consent was obtained from all patients according to the protocols approved by the local ethical committee Cells were extracted ex-vivo and sequenced without culture. Cells were cultured in OCMI+50%Asc and dissolved in TriFast. RNA-extraction with TriFast (1ml) according the manufacturer protocol. RNA is dissolved in RNase-free water (with RNase-Inhibitor Superase-IN 1:20). DNase digestion with DNA-free™ Kit (invitrogen, ThermoFisher scientific) followed. The integrity and purity of RNA was determined using the Experion RNA StdSens Lexogen Quantseq according to manufacturer's instructions.

text: adult

characteristic: developmental stage

characteristic: individual

text: Lexogen Quantseq

characteristic: nucleic acid library construction protocol

text: Homo sapiens

text: Homo sapiens

text: omentum

text: Homo sapiens

text: female


characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: 50 to 55

text: ArrayExpress

text: macrophage

text: human

text: Protocols: Ascites or omentum was collected from patients with high-grade serous ovarian carcinoma undergoing primary surgery at the University Hospital in Marburg. Informed consent was obtained from all patients according to the protocols approved by the local ethical committee Metastasized omentum was digested with Trypsin for 2h, followed by overnight digestion with Collagenase (2,5μg/ml)/Hyaluronidase (50μg/ml). Isolated cells were cryopreserved. TAMs were isolated from Cryo using a CD14-MACS selection and dissolved in TriFast. Purity was determined via flow cytometry. Cells were extracted ex-vivo and sequenced without culture. RNA-extraction with TriFast (1ml) according the manufacturer protocol. RNA is dissolved in RNase-free water (with RNase-Inhibitor Superase-IN 1:20). DNase digestion with DNA-free™ Kit (invitrogen, ThermoFisher scientific) followed. The integrity and purity of RNA was determined using the Experion RNA StdSens Illumina TruSeq stranded mRNA according to manufactures' instructions

text: adult

text: Illumina TruSeq Stranded mRNA

text: Homo sapiens

text: Homo sapiens

text: omentum

characteristic: organism part

text: Homo sapiens

text: female

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: 70 to 75

characteristic: age

text: ArrayExpress

text: macrophage

text: human

characteristic: description

text: adult

characteristic: disease

text: Illumina TruSeq Stranded mRNA

text: Homo sapiens

text: Homo sapiens

text: omentum

text: Homo sapiens

text: female


characteristic: ENA-CHECKLIST

text: public

text: 70 to 75

text: ArrayExpress

characteristic: broker name

text: tumor cell

characteristic: cell type

text: human

characteristic: common name

text: Protocols: Ascites or omentum was collected from patients with high-grade serous ovarian carcinoma undergoing primary surgery at the University Hospital in Marburg. Informed consent was obtained from all patients according to the protocols approved by the local ethical committee Metastasized omentum was digested with Trypsin for 2h. Isolated cells were cryopreserved. Tumor cells were isolated from Cryo using a CD45-MACS depletion, followed by MACS-Depletion using Anti-Fibroblast beads and dissolved in TriFast. Purity was determined via flow cytometry. Cells were extracted ex-vivo and sequenced without culture. RNA-extraction with TriFast (1ml) according the manufacturer protocol. RNA is dissolved in RNase-free water (with RNase-Inhibitor Superase-IN 1:20). DNase digestion with DNA-free™ Kit (invitrogen, ThermoFisher scientific) followed. The integrity and purity of RNA was determined using the Experion RNA StdSens Illumina TruSeq stranded mRNA according to manufactures' instructions

text: adult

characteristic: developmental stage

text: Illumina TruSeq Stranded mRNA

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: omentum

text: Homo sapiens

text: female

characteristic: sex


characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: 85 to 90

text: ArrayExpress

text: macrophage

text: human

text: adult

characteristic: individual

text: Illumina TruSeq Stranded mRNA

characteristic: nucleic acid library construction protocol

text: Homo sapiens

text: Homo sapiens

text: ascites fluid

text: Homo sapiens

text: female


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: 85 to 90

characteristic: age

text: ArrayExpress

text: tumor cell

text: human

text: adult

text: Illumina TruSeq Stranded mRNA

text: Homo sapiens

text: Homo sapiens

text: ascites fluid

characteristic: organism part

text: Homo sapiens

text: female

characteristic: title


characteristic: ENA-CHECKLIST

text: public

text: 85 to 90

text: ArrayExpress

characteristic: broker name

text: tumor cell

characteristic: cell type

text: human

characteristic: common name

characteristic: description

text: adult

characteristic: developmental stage

characteristic: disease

text: Illumina TruSeq Stranded mRNA

text: Homo sapiens

text: Homo sapiens

text: omentum

text: Homo sapiens

text: female


characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: 65 to 70

text: ArrayExpress

text: macrophage

text: human

text: adult

text: Illumina TruSeq Stranded mRNA

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: ascites fluid

text: Homo sapiens

text: female

characteristic: sex


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: 65 to 70

characteristic: age

text: ArrayExpress

text: tumor cell

text: human

text: adult

characteristic: individual

text: Illumina TruSeq Stranded mRNA

characteristic: nucleic acid library construction protocol

text: Homo sapiens

text: Homo sapiens

text: ascites fluid

text: Homo sapiens

text: female


characteristic: ENA-CHECKLIST

text: public

text: 65 to 70

text: ArrayExpress

characteristic: broker name

text: macrophage

characteristic: cell type

text: human

characteristic: common name

characteristic: description

text: adult

text: Illumina TruSeq Stranded mRNA

text: Homo sapiens

text: Homo sapiens

text: omentum

characteristic: organism part

text: Homo sapiens

text: female

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: 65 to 70

text: ArrayExpress

text: tumor cell

text: human

text: adult

characteristic: developmental stage

characteristic: disease

text: Illumina TruSeq Stranded mRNA

text: Homo sapiens

text: Homo sapiens

text: omentum

text: Homo sapiens

text: female


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: 65 to 70

characteristic: age

text: ArrayExpress

text: human peritoneal mesothelial cell

text: human

text: Protocols: Ascites or omentum was collected from patients with high-grade serous ovarian carcinoma undergoing primary surgery at the University Hospital in Marburg. Informed consent was obtained from all patients according to the protocols approved by the local ethical committee Metastasized omentum was digested with Trypsin for 30 min. Isolated cells were cryopreserved. Tumor cells were isolated from Cryo using a CD45/EpCAM-MACS depletion and dissolved in TriFast. Purity was determined via flow cytometry. Cells were extracted ex-vivo and sequenced without culture. RNA-extraction with TriFast (1ml) according the manufacturer protocol. RNA is dissolved in RNase-free water (with RNase-Inhibitor Superase-IN 1:20). DNase digestion with DNA-free™ Kit (invitrogen, ThermoFisher scientific) followed. The integrity and purity of RNA was determined using the Experion RNA StdSens Illumina TruSeq stranded mRNA according to manufactures' instructions

text: adult

text: Illumina TruSeq Stranded mRNA

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: omentum

text: Homo sapiens

text: female

characteristic: sex


characteristic: ENA-CHECKLIST

text: public

text: 50 to 55

text: ArrayExpress

characteristic: broker name

text: tumor cell

characteristic: cell type

text: human

characteristic: common name

characteristic: description

text: adult

characteristic: individual

text: Illumina TruSeq Stranded mRNA

characteristic: nucleic acid library construction protocol

text: Homo sapiens

text: Homo sapiens

text: ascites fluid

text: Homo sapiens

text: female


characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: 50 to 55

text: ArrayExpress

text: tumor cell

text: human

text: adult

text: Illumina TruSeq Stranded mRNA

text: Homo sapiens

text: Homo sapiens

text: omentum

characteristic: organism part

text: Homo sapiens

text: female

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: 55 to 60

characteristic: age

text: ArrayExpress

text: adipocyte

text: human

text: Protocols: Ascites or omentum was collected from patients with high-grade serous ovarian carcinoma undergoing primary surgery at the University Hospital in Marburg. Informed consent was obtained from all patients according to the protocols approved by the local ethical committee Tumor-free\ omental tissue was digested with Collagenase (370U/ml), freshly added to adipocyte digestion buffer (5mM D-Glucose, 1.5% BSA in PBS)for 1h at 37°C (rotating). After centrifugation and washing (with PBS), 250 μl adipocytes were dissolved in 2 ml TriFast (ex vivo). Purity was tested via immunofluorescence. No EpCAM+ or CD45+ cells were visible. Cells were extracted ex-vivo and sequenced without culture. RNA-extraction with TriFast (1ml) according the manufacturer protocol. RNA is dissolved in RNase-free water (with RNase-Inhibitor Superase-IN 1:20). DNase digestion with DNA-free™ Kit (invitrogen, ThermoFisher scientific) followed. The integrity and purity of RNA was determined using the Experion RNA StdSens Illumina TruSeq stranded mRNA according to manufactures' instructions

text: adult

characteristic: developmental stage

characteristic: disease

text: Illumina TruSeq Stranded mRNA

text: Homo sapiens

text: Homo sapiens

text: omentum

text: Homo sapiens

text: female


characteristic: ENA-CHECKLIST

text: public

text: 55 to 60

text: ArrayExpress

characteristic: broker name

text: cancer associated fibroblast

characteristic: cell type

text: human

characteristic: common name

characteristic: description

text: adult

text: Lexogen Quantseq

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: omentum

text: Homo sapiens

text: female

characteristic: sex


characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: 50 to 55

text: ArrayExpress

text: macrophage

text: human

text: adult

characteristic: individual

text: Illumina TruSeq Stranded mRNA

characteristic: nucleic acid library construction protocol

text: Homo sapiens

text: Homo sapiens

text: ascites fluid

text: Homo sapiens

text: female


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: 50 to 55

characteristic: age

text: ArrayExpress

text: cancer associated fibroblast

text: human

text: adult

text: Lexogen Quantseq

text: Homo sapiens

text: Homo sapiens

text: omentum

characteristic: organism part

text: Homo sapiens

text: female

characteristic: title


characteristic: ENA-CHECKLIST

text: public

text: 50 to 55

text: ArrayExpress

characteristic: broker name

text: macrophage

characteristic: cell type

text: human

characteristic: common name

characteristic: description

text: adult

characteristic: developmental stage

characteristic: disease

text: Illumina TruSeq Stranded mRNA

text: Homo sapiens

text: Homo sapiens

text: omentum

text: Homo sapiens

text: female


characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: 85 to 90

text: ArrayExpress

text: cancer associated fibroblast

text: human

text: adult

text: Lexogen Quantseq

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: omentum

text: Homo sapiens

text: female

characteristic: sex


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: 85 to 90

characteristic: age

text: ArrayExpress

text: adipocyte

text: human

text: adult

characteristic: individual

text: Illumina TruSeq Stranded mRNA

characteristic: nucleic acid library construction protocol

text: Homo sapiens

text: Homo sapiens

text: omentum

text: Homo sapiens

text: female


characteristic: ENA-CHECKLIST

text: public

text: 60 to 65

text: ArrayExpress

characteristic: broker name

text: cancer associated fibroblast

characteristic: cell type

text: human

characteristic: common name

characteristic: description

text: adult

text: Lexogen Quantseq

text: Homo sapiens

text: Homo sapiens

text: omentum

characteristic: organism part

text: Homo sapiens

text: female

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: 60 to 65

text: ArrayExpress

text: human peritoneal mesothelial cell

text: human

text: adult

characteristic: developmental stage

characteristic: disease

text: Illumina TruSeq Stranded mRNA

text: Homo sapiens

text: Homo sapiens

text: omentum

text: Homo sapiens

text: female


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: 65 to 70

characteristic: age

text: ArrayExpress

text: cancer associated fibroblast

text: human

text: adult

text: Lexogen Quantseq

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: omentum

text: Homo sapiens

text: female

characteristic: sex


characteristic: ENA-CHECKLIST

text: public

text: 75 to 80

text: ArrayExpress

characteristic: broker name

text: human peritoneal mesothelial cell

characteristic: cell type

text: human

characteristic: common name

characteristic: description

text: adult

characteristic: individual

text: Illumina TruSeq Stranded mRNA

characteristic: nucleic acid library construction protocol

text: Homo sapiens

text: Homo sapiens

text: omentum

text: Homo sapiens

text: female


characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: 60 to 65

text: ArrayExpress

text: adipocyte

text: human

text: adult

text: Illumina TruSeq Stranded mRNA

text: Homo sapiens

text: Homo sapiens

text: omentum

characteristic: organism part

text: Homo sapiens

text: female

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: 55 to 60

characteristic: age

text: ArrayExpress

text: human peritoneal mesothelial cell

text: human

text: adult

characteristic: developmental stage

characteristic: disease

text: Illumina TruSeq Stranded mRNA

text: Homo sapiens

text: Homo sapiens

text: omentum

text: Homo sapiens

text: female


characteristic: ENA-CHECKLIST

text: public

text: 65 to 70

text: ArrayExpress

characteristic: broker name

text: adipocyte

characteristic: cell type

text: human

characteristic: common name

characteristic: description

text: adult

text: Illumina TruSeq Stranded mRNA

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: omentum

text: Homo sapiens

text: female

characteristic: sex


characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: 65 to 70

text: ArrayExpress

text: human peritoneal mesothelial cell

text: human

text: adult

characteristic: individual

text: Illumina TruSeq Stranded mRNA

characteristic: nucleic acid library construction protocol

text: Homo sapiens

text: Homo sapiens

text: omentum

text: Homo sapiens

text: female


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: 70 to 75

characteristic: age

text: ArrayExpress

text: macrophage

text: human

text: adult

text: Illumina TruSeq Stranded mRNA

text: Homo sapiens

text: Homo sapiens

text: ascites fluid

characteristic: organism part

text: Homo sapiens

text: female

characteristic: title


characteristic: ENA-CHECKLIST

text: public

text: 70 to 75

text: ArrayExpress

characteristic: broker name

text: macrophage

characteristic: cell type

text: human

characteristic: common name

characteristic: description

text: adult

characteristic: developmental stage

characteristic: disease

text: Illumina TruSeq Stranded mRNA

text: Homo sapiens

text: Homo sapiens

text: omentum

text: Homo sapiens

text: female


characteristic: ENA-FIRST-PUBLIC

text: Ugent

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: ArrayExpress

text: house mouse

text: neuroblastoma

text: TH-MYCN, ALKAL2

characteristic: genotype

text: Mus musculus

characteristic: organism

text: Mus musculus

text: tumour

text: Mus musculus

text: male

characteristic: sex

characteristic: strain


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Ugent

text: public

characteristic: SRA accession

characteristic: Submitter Id

characteristic: age

text: ArrayExpress

text: house mouse

text: neuroblastoma

text: TH-MYCN, ALK-F1178S

characteristic: individual

text: Mus musculus

text: Mus musculus

text: tumour

characteristic: organism part

text: Mus musculus

text: female

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Ugent

text: public

text: ArrayExpress

characteristic: broker name

text: house mouse

characteristic: common name

characteristic: description

text: neuroblastoma

characteristic: disease

text: TH-MYCN, ALK-F1178S

text: Mus musculus

text: Mus musculus

text: tumour

text: Mus musculus

text: male


text: EMBL

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: ArrayExpress

text: Esg1-tdTomato reporter mESC line

characteristic: cell line

text: mouse embryonic stem cell

characteristic: cell type

text: house mouse

text: Protocols: Esg1-tdTomato or p53-tdTomato reporter ESC line containing inducible dCas9::KRAB or dCas9::GFP control and target-specific gRNA have bee treated with DOX (100 ng/ml) for 7 days to impose epigenetic silencing of the reporter. Memory of the silenced state has been assayed after 4 or 7 days of DOX washout. This protocol has been optimised from Skene and Henikoff, Elife, 2017 to detect interaction between DNA and histone modifications. Briefly, fresh cells are harvested, permeabilised, bound to concanavallin magnetic beads and incubated with the antibody for the modification of interest. Samples were then incubated with pA-MNase to cut the DNA side of the bound antibody and the DNA fragments were eluted and subjected to size selection. Finally DNA library was generated with NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB #E7645S).

text: gene knock in

characteristic: genetic modification

text: WT ESC with Esg1-tdTomato reporter

characteristic: genotype

text: Mus musculus

characteristic: organism

text: Mus musculus

text: Mus musculus

text: DOX treatment

characteristic: treatment

characteristic: treatment time


characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMBL

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: Esg1-tdTomato reporter mESC line

text: mouse embryonic stem cell

text: house mouse

text: gene knock in

text: WT ESC with Esg1-tdTomato reporter and dCas9::KRAB

text: Mus musculus

text: Mus musculus

text: Mus musculus

characteristic: title

text: DOX treatment


characteristic: ENA-FIRST-PUBLIC

text: EMBL

characteristic: INSDC center name

text: public

text: ArrayExpress

characteristic: broker name

text: Esg1-tdTomato reporter mESC line

text: mouse embryonic stem cell

text: house mouse

characteristic: common name

characteristic: description

text: gene knock in

text: WT ESC with Esg1-tdTomato reporter and dCas9::GFP

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: DOX treatment


text: EMBL

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: ArrayExpress

text: Esg1-tdTomato reporter mESC line

characteristic: cell line

text: mouse embryonic stem cell

characteristic: cell type

text: house mouse

text: gene knock in

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: DOX washout


text: EMBL

text: public

text: ArrayExpress

text: Esg1-tdTomato reporter mESC line

text: mouse embryonic stem cell

text: house mouse

text: gene knock in

characteristic: genetic modification

characteristic: genotype

text: Mus musculus

characteristic: organism

text: Mus musculus

text: Mus musculus

text: DOX washout

characteristic: treatment

characteristic: treatment time


characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMBL

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: Esg1-tdTomato reporter mESC line

text: mouse embryonic stem cell

text: house mouse

text: gene knock in

text: WT ESC with Esg1-tdTomato reporter

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: minus DOX


text: Acinetobacter baumannii

characteristic: ArrayExpress-SPECIES

characteristic: ENA-FIRST-PUBLIC

text: SC

characteristic: INSDC center name

text: public

text: Acinetobacter baumannii

characteristic: common name

text: Acinetobacter baumannii

text: Acinetobacter baumannii

characteristic: subject id

characteristic: title


text: Pseudomonas aeruginosa

text: SC

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: Pseudomonas aeruginosa

text: Pseudomonas aeruginosa

text: Pseudomonas aeruginosa


text: public

tag: Namespace:Laboratory of genomics and metagenomics, Institute of Microbiology, University Hospital Centre and University of Lausanne, Switzerland

text: Switzerland

characteristic: geographic location (country and/or sea)

text: Escherichia coli

characteristic: organism

text: Escherichia coli

text: Escherichia coli K-12 substr. MG1655

characteristic: strain

text: Escherichia coli WT_untr


characteristic: ENA-CHECKLIST

text: Laboratory of genomics and metagenomics, Institute of Microbiology, University Hospital Centre and University of Lausanne, Switzerland

text: public

text: Switzerland

text: Escherichia coli

text: Escherichia coli

text: Escherichia coli K-12 substr. MG1655

text: Escherichia coli WT_TAT


characteristic: ENA-LAST-UPDATE

text: public

text: Switzerland

text: Escherichia coli

text: Escherichia coli

text: Escherichia coli K-12 substr. MG1655

text: Escherichia coli WT_sucrose


characteristic: External Id

text: public

text: Switzerland

text: Escherichia coli

text: Escherichia coli

text: Escherichia coli K-12 substr. MG1655

text: Escherichia coli EnvZ_untreated


text: public

characteristic: SRA accession

text: Switzerland

text: Escherichia coli

text: Escherichia coli

text: Escherichia coli K-12 substr. MG1655

text: Escherichia coli EnvZ_TAT


text: public

characteristic: Submitter Id

text: Switzerland

text: Escherichia coli

text: Escherichia coli

text: Escherichia coli K-12 substr. MG1655

text: Escherichia coli EnvZ_sucrose


text: public

text: Illumina MiSeq

characteristic: INSTRUMENT

text: PCR

text: GENOMIC

text: Tn-seq

text: ILLUMINA

characteristic: PLATFORM

text: Switzerland

text: Pseudomonas aeruginosa

text: Pseudomonas aeruginosa

text: Pseudomonas aeruginosa PA14_BM2


characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC center name

text: public

text: Illumina MiSeq

text: PCR

text: GENOMIC

text: Tn-seq

text: ILLUMINA

text: Switzerland

text: Pseudomonas aeruginosa

text: Pseudomonas aeruginosa

text: Pseudomonas aeruginosa PA14_RasGAP


text: Goethe University Frankfurt

text: public

tag: Namespace:Goethe University Frankfurt

text: ArrayExpress

characteristic: broker name

characteristic: cell line

text: astrocyte

characteristic: cell type

text: human

characteristic: common name

text: Protocols: T98G cells were cultured in DMEM, high glucose supplemented with 10% fetal calf serum, sodium pyruvate (1 mM), penicillin (100 U/mL), and streptomycin (100 μg/mL) at 37 °C and 5% CO2 and seeded in 12-well plates (1.0×10^5 cells/well) for gene expression analysis. 24 h after seeding, medium was changed to reduced serum medium containing DMEM high glucose supplemented with 1% charcoal-stripped FCS, sodium pyruvate (1 mM), penicillin (100 U/mL) and streptomycin (100 μg/mL)right before transfection. Knockdown was mediated by transient transfection using the RNAiMAX reagent (Invitrogen) according to the manufacturer’s protocol with 30 nM of Nurr1 targeting esiRNA (Cat# EHU008731) or non-targeting control siRNA (Cat# SIC001, both Sigma Aldrich). After further 24 h, medium was changed again to reduced serum medium supplemented as described above now additionally containing 0.1% DMSO and the test compound simvastatin (10 µM) or 0.1% DMSO alone as control. Additionally, LPS (1 µg/mL) was added simultaneously to induce inflammation in one treatment arm. Each treatment condition was set up in three independent biological repeats (n=3). After 12 h incubation, cells were harvested (trypsin+EDTA), washed twice with cold phosphate buffered saline and then directly used for RNA extraction. RNA was extracted by the E.Z.N.A.® Total RNA Kit I (R6834-02, Omega Bio-Tek Inc., Norcross, GA, USA) according to the manufacturer's protocol. A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (New England Biolabs (NEB), Ipswich, MA, U.S.A.) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μL USER Enzyme (NEB, USA) was used with size-selected, adaptorligated cDNA at 37 °C for 15 min followed by 5 min at 95°C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using PE Cluster Kit cBot-HS (Illumina) according to the manufacturer’s instructions.

characteristic: description

text: glioblastoma multiforme

characteristic: disease

text: Homo sapiens

text: Homo sapiens

text: brain

characteristic: organism part

text: Homo sapiens


E-MTAB-10675:Sample 1

text: Sorbonne-universite

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-10675:Sample 1

text: ArrayExpress

text: Protocols: After cross-linking, the cells were collected by centrifugation. C. glabrata cells were grown in Yeast extract Peptone Glycerol (YPGly) medium, containing 2% glycerol, 1% yeast extract 1% bactopeptone. Chromatine immunoprecipitation was performed as described in Lelandais et al., Methods in Mol Biol 2016, except that after the cross-linf reversal step, DNA was purified using the Dyagenode High Pure kit, following the supplier's recommendations. The libraries were prepared with the MicroPlex v2 kit from Diagenode using the supplier's recommendations. The libraries were verified quantified and verified using the fragment analyzer and the Qubit devices.

text: Candida glabrata

characteristic: organism

text: [Candida] glabrata

text: [Candida] glabrata

text: Sample 1

characteristic: title


E-MTAB-10675:Sample 2

characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Sorbonne-universite

text: public

characteristic: SRA accession

text: E-MTAB-10675:Sample 2

characteristic: Submitter Id

text: ArrayExpress

text: Candida glabrata

text: [Candida] glabrata

text: [Candida] glabrata

text: Sample 2


E-MTAB-10675:Sample 3

characteristic: ENA-FIRST-PUBLIC

text: Sorbonne-universite

characteristic: INSDC center name

text: public

text: E-MTAB-10675:Sample 3

text: ArrayExpress

characteristic: broker name

text: Candida glabrata

text: [Candida] glabrata

text: [Candida] glabrata

text: Sample 3


E-MTAB-10675:Sample 4

text: Sorbonne-universite

text: public

text: E-MTAB-10675:Sample 4

text: ArrayExpress

text: Candida glabrata

text: [Candida] glabrata

text: [Candida] glabrata

text: Sample 4


E-MTAB-10675:Sample 5

text: Sorbonne-universite

text: public

text: E-MTAB-10675:Sample 5

text: ArrayExpress

text: Candida glabrata

text: [Candida] glabrata

text: [Candida] glabrata

text: Sample 5


status: KILLED

text: BCM

text: killed

characteristic: age

text: ArrayExpress

text: oenocyte

characteristic: cell type

text: fruit fly

characteristic: common name

text: Protocols: Adult fly tissues were dissected, nuclei were extracted using dounce homogenizer, and individual nuclei were collected into 384-well plates using FACS sorter (SONY SH800), each well with one nucleus; all samples are nuclei for single-nucleus sequencing. ERCC RNA Spike-In Mix (Thermo Fisher, 4456740) was used at a concentration of 1:600000 no nucleic acid extraction required; samples were directly processed for reverse transcription using Smart-seq2 protocol smart-seq2 protocol from Picelli et al., 2014, Nature Protocols

text: adult

characteristic: developmental stage

text: PromE800-GAL4; UAS-unc84GFP

characteristic: genotype

text: Drosophila melanogaster

text: Drosophila melanogaster

text: abdominal segment element

text: pass

characteristic: post analysis single cell quality

text: Drosophila melanogaster

text: male

characteristic: sex

characteristic: single cell identifier

text: OK

characteristic: single cell well quality

characteristic: strain


characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

text: BCM

characteristic: INSDC first public

characteristic: INSDC last update

text: killed

characteristic: INSDC status

text: E-MTAB-10628:FCA_P45_female_oenocyte_D21

text: ArrayExpress

text: oenocyte

text: fruit fly

characteristic: description

text: adult

text: PromE800-GAL4; UAS-unc84GFP

text: Drosophila melanogaster

characteristic: organism

text: Drosophila melanogaster

text: abdominal segment element

characteristic: organism part

text: pass

text: Drosophila melanogaster

text: female

text: OK

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: External Id

text: BCM

characteristic: INSDC center name

text: killed

characteristic: SRA accession

characteristic: Submitter Id

characteristic: age

text: ArrayExpress

characteristic: broker name

text: Akh secreting cell

characteristic: cell type

text: fruit fly

characteristic: common name

text: adult

text: Akh-GAL4; UAS-unc84GFP

text: Drosophila melanogaster

text: Drosophila melanogaster

text: thorax

text: pass

text: Drosophila melanogaster

text: female

text: OK


characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

text: BCM

text: killed

text: ArrayExpress

text: Akh secreting cell

text: fruit fly

text: adult

characteristic: developmental stage

text: Akh-GAL4; UAS-unc84GFP

characteristic: genotype

text: Drosophila melanogaster

text: Drosophila melanogaster

text: thorax

text: pass

characteristic: post analysis single cell quality

text: Drosophila melanogaster

text: male

characteristic: sex

characteristic: single cell identifier

text: OK

characteristic: single cell well quality

characteristic: strain


characteristic: ENA-FIRST-PUBLIC

characteristic: External Id

text: BCM

characteristic: INSDC first public

characteristic: INSDC last update

text: killed

characteristic: INSDC status

text: E-MTAB-106281624976556:FCA_P27_male_antenna_D21

text: ArrayExpress

text: fruit fly

characteristic: description

text: adult

text: wild type genotype

text: Drosophila melanogaster

characteristic: organism

text: Drosophila melanogaster

text: antenna

characteristic: organism part

text: pass

text: Drosophila melanogaster

text: male

text: OK

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

text: BCM

characteristic: INSDC center name

text: killed

characteristic: SRA accession

text: E-MTAB-106281624976556:FCA_P29_female_antenna_A1

characteristic: Submitter Id

characteristic: age

text: ArrayExpress

characteristic: broker name

text: fruit fly

characteristic: common name

text: adult

text: wild type genotype

text: Drosophila melanogaster

text: Drosophila melanogaster

text: antenna

text: pass

text: Drosophila melanogaster

text: female

text: OK


characteristic: ENA-FIRST-PUBLIC

text: BCM

text: killed

text: E-MTAB-106281624976556:FCA_P11_male_bodywall_D21

text: ArrayExpress

text: fruit fly

text: adult

characteristic: developmental stage

text: wild type genotype

characteristic: genotype

text: Drosophila melanogaster

text: Drosophila melanogaster

text: body wall

text: pass

characteristic: post analysis single cell quality

text: Drosophila melanogaster

text: male

characteristic: sex

characteristic: single cell identifier

text: OK

characteristic: single cell well quality

characteristic: strain