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characteristic: cell type

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text: Protocols: Mouse pNBSCs were derived from a mixed 129X1/SvJ background and are homozygous for Gt(ROSA)26Sortm4(ACTB-tdTomato,-EGFP)Luo (see also: https://www.jax.org/strain/007576). Induced Neural Border Stem cells were harvested by treatment with Accutase and washed twice with unsupplemented DMEM/ F12. Subsequently iNBSCs were stained for CD133/2 (293C3)-FITC (Miltenyi Biotec) and anti-CXCR4 (12G5)-PeCy5 (BioLegend) for 30 minutes at 4°C in basal medium and washed twice with DMEM/ F12. Cell sorting was carried out on a BD FACSAria™ III sorter (Becton Dickinson, San Jose, CA). The following sort parameters were used: 100µm nozzle; up to 800 events/second. Single cells were sorted into lysis buffer (2.86µl H2O, 1µl dT30VN (10µM), 1µl dNTPs, 0.1µl RNAse inhibitor, 0.04µl Triton X-100, 0.081µl of 1: 1 000 000 diluted stock of ERCC spike-ins (ThermoFisher)) in separate 96 wells and flash-frozen in liquid N2 until further processing. NBSC maintenance medium is composed of Adv. DMEM/ F12 Glutamax (for pNBSCs) and Neurobasal Medium (1:1) containing 64 µg/ml LAAP, N2 Supplement (1:100, Life Technologies), B27 without RA (1:50, Life Technologies), 18 µg/ml Albumax I (Life Technologies) and Glutamax (1:200, Life Technologies), referred to as ‘basal medium’, and 4 µM Chir99028, 5µM Alk5 Inhibitor II and 0.5 µM Purmorphamine. Once visible, distinct colonies were manually picked and cultured in NBSC maintenance medium on a layer of inactivated mouse embryonic fibroblasts (feeder) at 37°C in 5% O2 and 5% CO2. Single-cell RNA sequencing was performed following the Smart-seq2 protocol with adaptation as outlined below (Picelli et al. (2014). Full-length RNA-seq from single cells using Smart-seq2. Nature Protocols, 9(1), 171-181. http://doi.org/10.1038/nprot.2014.006).Plates containing single cells in lysis buffer were thawed on ice, incubated at 72°C for 3 minutes and reverse transcribed using the SmartScribe RT Kit (Takara Bio Clontech): 2µl Smart FS buffer, 0.5µl DTT, 0.1µl 100µM TSO, 1µl Smarc Scribe, 1.4µl H2O per cell. PCR preamplification and cDNA purification was performed as described in Picelli et al., applying 19 amplification cycles. For tagmentation 0.15-0.2 ng/µl cDNA was used per reaction: 1.25µl diluted sample, 2.5µl Tagment DNA buffer, and 1.25µl Amplification Tagment Mix. The reaction was neutralized with 1.25µL NT buffer. The adapter ligation was performed with 5µl of the neutralized tagmentation reaction, 3.75µl of Nextera PCR master mix and 1.25µl of Index-Primer 1 and Index-Primer 2 and amplified as decribed in the Smart-seq2 protocol. Finally, 192 reactions were were pooled (1µl per reaction) and purified according to the Smart-seq2 protocol.

text: embryonic day 8.5

characteristic: developmental stage

text: normal

characteristic: disease

characteristic: genotype

text: CAP-FEEDER

characteristic: growth condition

text: pNBSC C6

characteristic: individual

text: Mus musculus

text: Mus Musculus

text: hindbrain

characteristic: organism part

text: fail

characteristic: post analysis well quality

text: Mus musculus

text: OK, filtered

characteristic: single cell quality

characteristic: strain

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: HI-STEM gGmbH

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: embryonic neural border stem cell

text: house mouse

characteristic: common name

characteristic: description

text: embryonic day 8.5

text: normal

text: Gt(ROSA)26Sortm4(ACTB-tdTomato,-EGFP)Luo

text: CAP-FEEDER

text: pNBSC C6

text: Mus musculus

text: Mus Musculus

text: hindbrain

text: fail

text: Mus musculus

text: OK, filtered


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: HI-STEM gGmbH

text: public

text: ArrayExpress

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text: embryonic neural border stem cell

characteristic: cell type

text: house mouse

text: embryonic day 8.5

characteristic: developmental stage

text: normal

characteristic: disease

characteristic: genotype

text: CAP-FEEDER

characteristic: growth condition

text: pNBSC C10.5

text: Mus musculus

characteristic: organism

text: Mus Musculus

text: hindbrain

text: fail

text: Mus musculus

text: OK, filtered


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: HI-STEM gGmbH

characteristic: INSDC center name

text: public

text: ArrayExpress

text: embryonic neural border stem cell

text: house mouse

text: embryonic day 8.5

text: normal

text: CAP-FEEDER

text: pNBSC C6

characteristic: individual

text: Mus musculus

text: Mus Musculus

text: hindbrain

characteristic: organism part

text: pass

characteristic: post analysis well quality

text: Mus musculus

text: OK

characteristic: single cell quality

characteristic: strain

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: HI-STEM gGmbH

characteristic: INSDC first public

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text: public

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characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: embryonic neural border stem cell

text: house mouse

characteristic: common name

characteristic: description

text: embryonic day 8.5

text: normal

text: CAP-FEEDER

text: pNBSC C10.5

text: Mus musculus

text: Mus Musculus

text: hindbrain

text: pass

text: Mus musculus

text: OK


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: INRA (INRA Jouy en Josas)

text: public

tag: Namespace:INRA (INRA Jouy en Josas)

text: Streptococcus thermophilus

characteristic: organism

text: Streptococcus thermophilus

text: Streptococcus thermophilus N4L complete annotated genome


text: ACIB

characteristic: INSDC center name

text: public

text: tomato

text: Moneymaker seeds

text: Solanum lycopersicum

text: Solanum lycopersicum


text: ACIB

text: public

text: tomato

text: Hildares F1 seeds

text: Solanum lycopersicum

text: Solanum lycopersicum


text: ACIB

text: public

text: tomato

text: Loamy soil

text: Solanum lycopersicum

text: Solanum lycopersicum


text: ACIB

text: public

text: tomato

text: Sandy soil

text: Solanum lycopersicum

text: Solanum lycopersicum


text: ACIB

text: public

text: tomato

text: Rhizosphere moneymaker sandy soil

text: Solanum lycopersicum

text: Solanum lycopersicum


text: ACIB

text: public

text: tomato

text: Rhizosphere moneymaker loamy soil

text: Solanum lycopersicum

text: Solanum lycopersicum


text: ACIB

text: public

text: tomato

text: Rhizosphere hildares sandy soil

text: Solanum lycopersicum

text: Solanum lycopersicum


text: ACIB

text: public

text: tomato

text: Rhizosphere hildares loamy soil

text: Solanum lycopersicum

text: Solanum lycopersicum


text: ACIB

text: public

text: tomato

text: Root-Endosphere moneymaker sandy soil

text: Solanum lycopersicum

text: Solanum lycopersicum


text: ACIB

text: public

text: tomato

text: Root-Endosphere moneymaker loamy soil

text: Solanum lycopersicum

text: Solanum lycopersicum


text: ACIB

text: public

text: tomato

text: Root-Endosphere hildares sandy soil

text: Solanum lycopersicum

text: Solanum lycopersicum


text: ACIB

text: public

text: tomato

text: Root-Endosphere hildares loamy soil

text: Solanum lycopersicum

text: Solanum lycopersicum


text: ACIB

text: public

text: tomato

text: Seeds moneymaker loamy soil 2 gen

text: Solanum lycopersicum

text: Solanum lycopersicum


text: ACIB

text: public

text: tomato

text: Seeds moneymaker sandy soil 2 gen

text: Solanum lycopersicum

text: Solanum lycopersicum


text: TMU-RCCTM

text: public

characteristic: collection date

text: Control C002, Time1

text: dense settlement biome

characteristic: environment (biome)

text: human-associated habitat

characteristic: environment (feature)

text: feces

characteristic: environment (material)

text: Taiwan

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: human-gut

characteristic: human gut environmental package

text: metagenome

characteristic: investigation type

text: human gut metagenome

text: DEHP affects gut microbiota of human neonates

characteristic: project name

text: human gut metagenome

text: Illumina MiSeq

characteristic: sequencing method

characteristic: target gene

characteristic: target subfragment

text: human gut metagenome


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text: TMU-RCCTM

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text: public

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text: Control C002, Time2

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text: dense settlement biome

text: human-associated habitat

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text: Taiwan

text: human-gut

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text: human gut metagenome

characteristic: title


characteristic: External Id

text: TMU-RCCTM

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text: Control C002, Time3

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text: feces

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text: Taiwan

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: human-gut

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text: human gut metagenome

characteristic: organism

text: human gut metagenome

text: Illumina MiSeq

text: human gut metagenome


characteristic: ENA-CHECKLIST

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text: TMU-RCCTM

characteristic: INSDC first public

text: public

text: Control C004, Time1

text: dense settlement biome

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text: Taiwan

text: human-gut

characteristic: human gut environmental package

text: metagenome

characteristic: investigation type

text: human gut metagenome

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text: human gut metagenome

text: Illumina MiSeq

characteristic: sequencing method

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characteristic: target subfragment

text: human gut metagenome


characteristic: External Id

text: TMU-RCCTM

characteristic: INSDC center name

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text: public

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text: human-associated habitat

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text: human gut metagenome

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text: Taiwan

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text: human-gut

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text: human gut metagenome

text: Illumina MiSeq

text: human gut metagenome


characteristic: External Id

text: TMU-RCCTM

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text: public

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text: Control C006, Time1

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text: Taiwan

text: human-gut

characteristic: human gut environmental package

text: metagenome

characteristic: investigation type

text: human gut metagenome

characteristic: project name

text: human gut metagenome

text: Illumina MiSeq

characteristic: sequencing method

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text: human gut metagenome


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text: TMU-RCCTM

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text: public

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text: Control C006, Time2

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text: human-associated habitat

text: feces

text: Taiwan

text: human-gut

text: metagenome

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text: human gut metagenome

text: Illumina MiSeq

text: human gut metagenome

characteristic: title


characteristic: External Id

text: TMU-RCCTM

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text: public

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text: Control C006, Time3

text: dense settlement biome

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text: feces

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text: Taiwan

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: human-gut

text: metagenome

text: human gut metagenome

characteristic: organism

text: human gut metagenome

text: Illumina MiSeq

text: human gut metagenome


characteristic: ENA-CHECKLIST

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text: TMU-RCCTM

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text: Taiwan

text: human-gut

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text: metagenome

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text: human gut metagenome

characteristic: project name

text: human gut metagenome

text: Illumina MiSeq

characteristic: sequencing method

characteristic: target gene

characteristic: target subfragment

text: human gut metagenome


characteristic: External Id

text: TMU-RCCTM

characteristic: INSDC center name

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text: public

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text: Control C007, Time2

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text: dense settlement biome

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text: human-associated habitat

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text: human gut metagenome

characteristic: title


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text: human-gut

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text: human gut metagenome

text: Illumina MiSeq

text: human gut metagenome


characteristic: External Id

text: TMU-RCCTM

characteristic: INSDC center name

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text: public

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text: Control C009, Time1

text: dense settlement biome

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text: Taiwan

text: human-gut

characteristic: human gut environmental package

text: metagenome

characteristic: investigation type

text: human gut metagenome

characteristic: project name

text: human gut metagenome

text: Illumina MiSeq

characteristic: sequencing method

characteristic: target gene

characteristic: target subfragment

text: human gut metagenome