text: public

tag: Namespace:Cell Signal Unit, Okinawa Institute of Science and Technology Graduate University

characteristic: age

text: ArrayExpress

characteristic: broker name

text: house mouse

characteristic: common name

text: Protocols: Liver was isolated from C57BL/6J wild-type mice at 8 weeks of age Mice were maintained on a 12 hr light / dark cycle in a temperature-controlled (22ºC) barrier facility with free access to water and a normal diet (NCD, CA-1, CLEA Japan, Inc.). Liver was solubilized in TNE buffer for 30 min at 4ºC. 150 mg of protein lysate was incubated with 180 µg of antibodies against Cnot3 (Takahashi et al., 2015), Ago2 (018-22021; Wako), and BRF1 (Cell Signaling) for 1 hr at 4ºC, and then incubated with 1.2 mL of Dynabeads (Invitrogen) for 2 hr at 4ºC. mRNAs in immune complexes were isolated using Isogen II (Nippongene). 100 ng of total RNA was used for RNA-seq library preparation with TruSeq Stranded mRNA Library Prep Kit for NeoPrep (NP-202-1001; Illumina), according to the manufacturer’s protocol with minor modification and optimization as follows. Custom dual index adaptors were ligated at the 5’ and 3’-end of library, and PCR was performed 11 cycles.

text: normal diet

characteristic: diet

text: normal

characteristic: disease

text: wild type genotype

characteristic: genotype

text: Mus musculus

text: Mus musculus

text: liver

characteristic: organism part

text: wild type phenotype

text: Mus musculus

text: male

characteristic: sex

characteristic: strain


status: PUBLIC

tag: attribute

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Cell Signal Unit, Okinawa Institute of Science and Technology Graduate University

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

unit: week

text: ArrayExpress

text: house mouse

characteristic: description

text: normal diet

text: normal

text: wild type genotype

text: Mus musculus

characteristic: organism

text: Mus musculus

text: liver

text: wild type phenotype

characteristic: phenotype

text: Mus musculus

text: male

characteristic: title


text: public

text: E-MTAB-6941:Liver_Input_ControlIgG_Cnot3_1

characteristic: age

text: ArrayExpress

characteristic: broker name

text: house mouse

characteristic: common name

text: normal diet

characteristic: diet

text: normal

characteristic: disease

text: wild type genotype

characteristic: genotype

text: Mus musculus

text: Mus musculus

text: liver

characteristic: organism part

text: wild type phenotype

text: Mus musculus

text: male


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

text: public

text: E-MTAB-6941:Liver_Input_ControlIgG_Cnot3_2

text: ArrayExpress

text: house mouse

text: normal diet

text: normal

text: wild type genotype

text: Mus musculus

text: Mus musculus

text: liver

text: wild type phenotype

text: Mus musculus

text: male

characteristic: sex

characteristic: strain


characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-6941:Liver_Input_ControlIgG_Cnot3_3

characteristic: Submitter Id

text: ArrayExpress

text: house mouse

characteristic: description

text: normal diet

text: normal

text: wild type genotype

text: Mus musculus

characteristic: organism

text: Mus musculus

text: liver

text: wild type phenotype

text: Mus musculus

text: male


text: Innstituto de Biomedicina de Valencia

text: public

tag: Namespace:Innstituto de Biomedicina de Valencia

text: WGS of Mycobacterium tuberculosis isolates from Mozambique

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis

characteristic: title


text: IFREMER

text: public

text: Oysters contamination

text: Norovirus 02/2010/Nanjing

text: Norovirus 02/2010/Nanjing

text: bioacc-exp


text: UNIVERSITY OF CAMBRIDGE

text: public

tag: Namespace:UNIVERSITY OF CAMBRIDGE

text: Euglena gracilis

text: Euglena gracilis

text: Z

text: Euglena gracilis gDNA 150PE


text: UNIVERSITY OF CAMBRIDGE

text: public

text: Euglena gracilis

text: Euglena gracilis

text: Z

text: Euglena gracilis DNA


text: public

tag: Namespace:Faculty of Medicine, Goethe-University Frankfurt

text: ArrayExpress

characteristic: broker name

text: macrophage

characteristic: cell type

text: human

characteristic: common name

text: Protocols: Primary human macrophages from anonymous adult donors were provided as buffy coats were acquired from Blutspendedienst Frankfurt for PBMCs isolation. We used PBMCs from 6 donors (1 - 6) and the sample name indicates whether its a pool of donors 1-3 or 4-6. Macrophages were differentiated from PBMC using AB+ serum for 7 days. Macrophages were transfected with control or miR-375 overexpression mimic (MISSION® microRNA Mimic hsa-miR 375 from Sigma # HMI0537-5NMOL. For control tranfection we used MISSION® miRNA, Negative Control 2 Sequence from *C. elegans* also from Sigma # HMC0003-5NMOL) for 48h then stimulated with MCF-7 apoptotic conditioning medium. After the stimulation, cells were washed and scrapped in PBS, centrifuged and pellet was lysed in PLB lysis buffer (5 mM MgCl2, 100 mM KCl, 10 mM Hepes, pH7.0 and 0.5% Nonidet P-40; freshly added 1 mM DTT, 100 U/ml RNase OUT (Invitrogen, Carlsbad, USA) and 1× complete mini EDTA free protease inhibitor cocktail (Roche, Basel, Switzerland)) and incubated on ice for 5 min Anti-pan-Ago IgG 2A8 (10 µg, Abcam) or IgG1 isotype control (ImmunoTools) were coupled to protein G Dynabeads (ThermoFisher Scientific) in 500 µL NT2 buffer overnight rotating at 4°C, followed by three washing steps with NT2 buffer. Thawed cell lysates were centrifuged for 30 min at 17,000g and 4°C and added 1:10 to NT2 buffer. The lysate was equally distributed to two tubes containing pan-Ago-IgG- or IgG1- coated beads and incubated overnight rotating at 4°C. The next day, beads were collected at the magnetic part and washed five times with 1 mL NT2 buffer. Protein-RNA complexes were eluted from the beads by incubation with 50 µL glycine (pH 2.3) for 15 min at room temperature and the obtained solution was neutralized using 5 µL Tris-HCL (pH 8.0). Proteins were digested by adding 3 µL of proteinase K (Sigma-Aldrich) and incubation for 10 min at 55°C. Thereafter, 350 µL PeqGold RNA Pure solution (Peqlab Biotechnologie) were added and RNA was purified using miRNeasy Mini Kit (Qiagen) without on-column DNase I digestion according to the manufacturers recommendations. Purified RNA of Ago and IgG IP fractions was quantified using NanoDrop spectrometer and quality was assessed by Agilent capillary electrophoresis using RNA picoChips. 10 ng of RNA was DNaseI (Qiagen) treated and rRNA depleted by RiboZero (Epicentre). Then, sequencing libraries were generated with the SMARTer Stranded Total RNA Sample Prep Kit (Takara Clontech). Enrichment and size distribution of the libraries were quality-assessed by Agilent capillary electrophoresis on a DNA high sensitivity chip (Agilent). For sequencing, all 12 samples were pooled to generate a final concentration of 5nM per lane.

text: adult

characteristic: developmental stage

text: wild type genotype

characteristic: genotype

text: non-conditioned media

characteristic: growth condition

text: pool of donors 1 to 3

characteristic: indivudal

text: Homo sapiens

text: Homo sapiens

text: blood

text: wild type phenotype

characteristic: phenotype

text: peripheral blood mononuclear cell

characteristic: progenitor cell type

text: Homo sapiens


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Faculty of Medicine, Goethe-University Frankfurt

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: ArrayExpress

text: macrophage

text: human

text: adult

text: wild type genotype

text: MCF-7 conditioned media

text: pool of donors 1 to 3

text: Homo sapiens

text: Homo sapiens

text: blood

characteristic: organism part

text: wild type phenotype

text: peripheral blood mononuclear cell

text: Homo sapiens


characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: macrophage

text: human

characteristic: description

text: adult

text: wild type genotype

text: non-conditioned media

text: pool of donors 1 to 3

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: blood

text: miR-375 overexpression

text: peripheral blood mononuclear cell

text: Homo sapiens

text: miR-375 mimic

characteristic: stimulus

characteristic: title


text: public

text: ArrayExpress

characteristic: broker name

text: macrophage

characteristic: cell type

text: human

characteristic: common name

text: adult

characteristic: developmental stage

text: wild type genotype

characteristic: genotype

text: MCF-7 conditioned media

characteristic: growth condition

text: pool of donors 1 to 3

characteristic: indivudal

text: Homo sapiens

text: Homo sapiens

text: blood

text: miR-375 overexpression

characteristic: phenotype

text: peripheral blood mononuclear cell

text: Homo sapiens

text: miR-375 mimic


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: ArrayExpress

text: macrophage

text: human

text: adult

text: wild type genotype

text: non-conditioned media

text: pool of donors 4 to 6

text: Homo sapiens

text: Homo sapiens

text: blood

characteristic: organism part

text: wild type phenotype

text: peripheral blood mononuclear cell

characteristic: progenitor cell type

text: Homo sapiens


characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: macrophage

text: human

characteristic: description

text: adult

text: wild type genotype

text: MCF-7 conditioned media

text: pool of donors 4 to 6

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: blood

text: wild type phenotype

text: peripheral blood mononuclear cell

text: Homo sapiens

characteristic: title


text: public

text: ArrayExpress

characteristic: broker name

text: macrophage

characteristic: cell type

text: human

characteristic: common name

text: adult

characteristic: developmental stage

text: wild type genotype

characteristic: genotype

text: non-conditioned media

characteristic: growth condition

text: pool of donors 4 to 6

characteristic: indivudal

text: Homo sapiens

text: Homo sapiens

text: blood

text: miR-375 overexpression

text: peripheral blood mononuclear cell

text: Homo sapiens

text: miR-375 mimic

characteristic: stimulus


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: ArrayExpress

text: macrophage

text: human

text: adult

text: wild type genotype

text: MCF-7 conditioned media

text: pool of donors 4 to 6

text: Homo sapiens

text: Homo sapiens

text: blood

characteristic: organism part

text: miR-375 overexpression

characteristic: phenotype

text: peripheral blood mononuclear cell

text: Homo sapiens

text: miR-375 mimic


characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: macrophage

text: human

characteristic: description

text: adult

text: wild type genotype

text: non-conditioned media

text: pool of donors 1 to 3

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: blood

text: wild type phenotype

text: peripheral blood mononuclear cell

characteristic: progenitor cell type

text: Homo sapiens

characteristic: title


text: UOM

text: public

text: ArrayExpress

characteristic: broker name

characteristic: cell line

text: epithelial cell

characteristic: cell type

text: human

characteristic: common name

text: Protocols: The cells were generated by infecting cells with 2nd generation lentiviruses. The genes are under Tet-on control. 2d and 4d indicates either doxycycline induction for 2 or 4 days. Het1A, Het1A-HNF4A and Het1A-GATA6 cells were cultured in DMEM (+10% FBS and 1% PenStrep) with 100ng/mL doxycycline for 2 or 4 days. Cells were trypsinised and counted. 50000 cells were taken forward for Tn5 reaction. 50000 cells were lysed in ATAC lysis buffer and Tn5 reactions were performed as described in Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position. 2013. Jason D. Buenrostro, Paul G. Giresi, Lisa C. Zaba, Howard Y. Chang and William J. Greenleaf. doi:10.1038/nmeth.2688 Libraries were constructed by amplifying transposed DNA with Illumina Nextera adapters.

text: normal

characteristic: disease

characteristic: genotype

text: Homo sapiens

text: Homo sapiens

text: esophagus

text: doxycyclin mediated overexpression of GATA6

text: Homo sapiens


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UOM

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: ArrayExpress

text: epithelial cell

text: human

text: normal

text: Homo sapiens

text: Homo sapiens

text: esophagus

text: doxycyclin mediated overexpression of HNF4A

text: Homo sapiens


text: UOM

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: epithelial cell

text: human

text: normal

text: wild type genotype

text: Homo sapiens

text: Homo sapiens

text: esophagus

characteristic: organism part

text: wild type phenotype

characteristic: phenotype

text: Homo sapiens


text: GSC

text: public

text: M extorquens 4

characteristic: clone

text: Methylobacterium extorquens

characteristic: organism

text: Methylobacterium extorquens

characteristic: title


text: GSC

text: public

text: M extorquens 10

text: Methylobacterium extorquens

text: Methylobacterium extorquens


text: GSC

text: public

text: M extorquens 16

text: Methylobacterium extorquens

text: Methylobacterium extorquens


text: GSC

text: public

text: M extorquens 35

text: Methylobacterium extorquens

text: Methylobacterium extorquens


text: GSC

text: public

text: M extorquens 36

text: Methylobacterium extorquens

text: Methylobacterium extorquens


text: GSC

text: public

text: M extorquens 38

text: Methylobacterium extorquens

text: Methylobacterium extorquens


text: GSC

text: public

text: M. extorquens TK0001 Ã©voluÃ© Ã 10% MeOH isolat 1 : MEM 10.1

text: Methylobacterium extorquens

text: Methylobacterium extorquens


text: GSC

text: public

text: M. extorquens TK0001 Ã©voluÃ© Ã 10% MeOH isolat 2 : MEM 10.2

text: Methylobacterium extorquens

text: Methylobacterium extorquens


text: GSC

text: public

text: M. extorquens TK0001 Ã©voluÃ© Ã 10% MeOH isolat 3 : MEM10.3

text: Methylobacterium extorquens

text: Methylobacterium extorquens


text: GSC

text: public

text: M. extorquens TK0001 Ã©voluÃ© Ã 10% MeOH isolat 4 : MEM10.4

text: Methylobacterium extorquens

text: Methylobacterium extorquens


text: GSC

text: public

text: M. extorquens TK0001 Ã©voluÃ© Ã 10% MeOH isolat 5 : MEM10.5

text: Methylobacterium extorquens

text: Methylobacterium extorquens


text: GSC

text: public

text: M. extorquens TK0001 Ã©voluÃ© Ã 10% MeOH isolat 6 : MEM10.6

text: Methylobacterium extorquens

text: Methylobacterium extorquens


text: Streptococcus suis

characteristic: ArrayExpress-Species

text: SC

text: public

text: Streptococcus suis

characteristic: common name

text: Streptococcus suis

text: Streptococcus suis


text: Streptococcus suis

characteristic: ArrayExpress-SPECIES

characteristic: ENA-CHECKLIST

text: SC

text: public

text: Streptococcus suis

text: Streptococcus suis

text: Streptococcus suis


Euglena gracilis genome assembly

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: UNIVERSITY OF CAMBRIDGE

text: public

text: Euglena gracilis genome assembly

text: Euglena gracilis

text: Euglena gracilis

text: Z

characteristic: strain

text: Euglena gracilis genome assembly


characteristic: External Id

text: UNIVERSITY OF EXETER

characteristic: INSDC center name

characteristic: INSDC first public

text: public

tag: Namespace:UNIVERSITY OF EXETER

text: alb1 mutant in Guy11 background generated by CRISPR

characteristic: description

text: Magnaporthe oryzae

text: Magnaporthe oryzae

text: alb1_3 genomic DNA


text: UNIVERSITY OF EXETER

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: Magnaporthe oryzae

text: Magnaporthe oryzae

text: alb1_6 genomic DNA


text: UNIVERSITY OF EXETER

text: public

text: Control, from untransformed regenerated Guy11 protoplast

text: Magnaporthe oryzae

characteristic: organism

text: Magnaporthe oryzae

text: R1 genomic DNA


text: UNIVERSITY OF EXETER

text: public

text: Magnaporthe oryzae

text: Magnaporthe oryzae

text: R2 genomic DNA

characteristic: title


text: Auckland University of Technology

text: public

tag: Namespace:Auckland University of Technology

text: 16S rRNA gene amplicon of environmental DNA extracted from aerosol samples collected in McMurdo Dry Valleys, Antarctica

text: Yes

characteristic: environmental sample

text: Antarctica

characteristic: geographic location (country and/or sea)

text: McMurdo Dry Valleys

characteristic: geographic location (region and locality)

text: Aerosol

characteristic: isolation source

text: uncultured prokaryote

text: uncultured prokaryote

text: Valley


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Auckland University of Technology

text: public

text: Yes

text: Antarctica

text: McMurdo Dry Valleys

text: Aerosol

text: uncultured prokaryote

text: uncultured prokaryote

text: Bull Pass


characteristic: ENA-LAST-UPDATE

text: Auckland University of Technology

text: public

text: Yes

text: Antarctica

text: McMurdo Dry Valleys

text: Aerosol

text: uncultured prokaryote

text: uncultured prokaryote

text: Ridge


characteristic: External Id

text: Auckland University of Technology

text: public

text: Yes

text: Antarctica

text: McMurdo Dry Valleys

text: Aerosol

text: uncultured prokaryote

text: uncultured prokaryote

text: BullPass


text: Auckland University of Technology

characteristic: INSDC center name

text: public

text: Yes

text: Antarctica

text: McMurdo Dry Valleys

text: Aerosol

text: uncultured prokaryote

text: uncultured prokaryote

text: Helicopter


text: Auckland University of Technology

characteristic: INSDC first public

text: public

text: 16S rRNA gene amplicon of environmental DNA extracted from soil samples collected in McMurdo Dry Valleys, Antarctica

text: Yes

text: Antarctica

text: McMurdo Dry Valleys

text: Soil

text: uncultured prokaryote

text: uncultured prokaryote

text: Valley


text: Auckland University of Technology

text: public

characteristic: description

text: Yes

text: Antarctica

text: McMurdo Dry Valleys

text: Soil

text: uncultured prokaryote

text: uncultured prokaryote

text: BullPass


text: Auckland University of Technology

characteristic: INSDC last update

text: public

text: Yes

text: Antarctica

text: McMurdo Dry Valleys

text: Soil

text: uncultured prokaryote

text: uncultured prokaryote

text: Bull Pass


text: Auckland University of Technology

text: public

characteristic: INSDC status

text: 16S rRNA gene amplicon of environmental DNA extracted from aerosol samples collected in Glen Eden, Auckland, New Zealand

text: Yes

text: New Zealand

text: Glen Eden, Auckland

text: Aerosol

text: uncultured prokaryote

text: uncultured prokaryote

text: Glen Eden


text: Auckland University of Technology

text: public

characteristic: SRA accession

text: ITS1 region amplicon of environmental DNA extracted from aerosol samples collected in McMurdo Dry Valleys, Antarctica

text: Yes

text: Antarctica

text: McMurdo Dry Valleys

text: Aerosol

text: uncultured fungus

text: uncultured fungus

text: Valley


text: Auckland University of Technology

text: public

characteristic: Submitter Id

text: Yes

text: Antarctica

text: McMurdo Dry Valleys

text: Aerosol

text: uncultured fungus

text: uncultured fungus

text: Bull Pass


text: Auckland University of Technology

text: public

text: Yes

text: Antarctica

text: McMurdo Dry Valleys

text: Aerosol

text: uncultured fungus

characteristic: organism

text: uncultured fungus

text: Ridge


text: Auckland University of Technology

text: public

text: Yes

text: Antarctica

text: McMurdo Dry Valleys

text: Aerosol

text: uncultured fungus

text: uncultured fungus

text: Helicopter

characteristic: title


text: Auckland University of Technology

text: public

text: ITS1 region amplicon of environmental DNA extracted from soil samples collected in McMurdo Dry Valleys, Antarctica

text: Yes

characteristic: environmental sample

text: Antarctica

text: McMurdo Dry Valleys

text: Soil

text: uncultured fungus

text: uncultured fungus

text: Valley


text: Auckland University of Technology

text: public

text: Yes

text: Antarctica

characteristic: geographic location (country and/or sea)

text: McMurdo Dry Valleys

text: Soil

text: uncultured fungus

text: uncultured fungus

text: BullPass


text: Auckland University of Technology

text: public

text: ITS1 region amplicon of environmental DNA extracted from aerosol samples collected in Glen Eden, Auckland, New Zealand

text: Yes

text: New Zealand

text: Glen Eden, Auckland

characteristic: geographic location (region and locality)

text: Aerosol

text: uncultured fungus

text: uncultured fungus

text: Glen Eden


text: UNIVERSITY OF CAMBRIDGE

text: public

text: Euglena gracilis gDNA 300PE

text: Euglena gracilis

text: Euglena gracilis

text: Z

characteristic: strain

text: Euglena gracilis gDNA 300PE


characteristic: ENA-CHECKLIST

text: Wellcome Trust Sanger Institute

text: public

tag: Namespace:Wellcome Trust Sanger Institute

text: 3 to 4

unit: month

characteristic: age

text: ArrayExpress

characteristic: broker name

text: adipocyte progenitor cell

characteristic: cell type

text: house mouse

characteristic: common name

text: Protocols: Epididymal fat pads from 4 adult male Wt1-GFP mice (3-4 months old) were dissected and made into a single cell suspension. SVF (stromal vascular fraction) was suspended in PBS (5% FCS) and filtered (40 uM) before staining with surface antibodies for FACS isolation. The Lineage panel of antibodies was purchased from BD (559971), CD31 (eBioscience, 46-0311-80, 1:100), IgM (eBioscience, 25-5790-81, 1:100), and CD34 (BioLegend, 119311, 1:50). For multicolour analysis and sorting, colour compensation samples were produced by singly staining SVF cells with one antibody of each of the combined fluorochromes as well as by FMO (Fluorochrome Minus One) controls. Single cell FACS sorting in 384 well plates was performed using a FACS Flow Cytometer (BD Aria II). Single adipocyte precursor cells were sorted in 384 well plates, directly into lysis buffer containing ERCC92 RNA mixture 1 at a dilution of 1:10^6 (ThermoFisher). Single cell cDNA was generated by the SMARTSeq2 protocol. Multiplexed single-cell libraries were prepared for high throughput sequencing using the Nextera XT protocol (Illumina).

text: adult

characteristic: developmental stage

characteristic: genotype

characteristic: individual

text: Mus musculus

text: Mus musculus

text: epididymal fat pad

characteristic: organism part

text: fail

characteristic: post analysis well quality

text: Mus musculus

text: male

characteristic: sex

text: no cell

characteristic: single cell well quality

characteristic: stain


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Wellcome Trust Sanger Institute

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: 3 to 4

text: ArrayExpress

text: adipocyte progenitor cell

text: house mouse

characteristic: description

text: adult

text: Mus musculus

characteristic: organism

text: Mus musculus

text: epididymal fat pad

characteristic: phenotype

text: fail

text: Mus musculus

text: male

text: OK

characteristic: title


characteristic: ENA-CHECKLIST

text: Wellcome Trust Sanger Institute

text: public

text: 3 to 4

characteristic: age

text: ArrayExpress

characteristic: broker name

text: adipocyte progenitor cell

characteristic: cell type

text: house mouse

characteristic: common name

text: adult

characteristic: developmental stage

characteristic: genotype

characteristic: individual

text: Mus musculus

text: Mus musculus

text: epididymal fat pad

characteristic: organism part

text: pass

characteristic: post analysis well quality

text: Mus musculus

text: male

text: OK


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UNIVERSITY OF CAMBRIDGE

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: Euglena gracilis 40 kbp PE

text: Euglena gracilis

text: Euglena gracilis

text: Z

characteristic: strain

text: Euglena gracilis 40 kbp PE


characteristic: ENA-CHECKLIST

text: UNIVERSITY OF CAMBRIDGE

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: Euglena gracilis PacBio - Peter Myler

characteristic: description

text: Euglena gracilis

characteristic: organism

text: Euglena gracilis

text: Z

text: Euglena gracilis PacBio - Puri/Dave

characteristic: title


text: UNIVERSITY OF CAMBRIDGE

text: public

text: Euglena gracilis PacBio - Peter Myler

text: Euglena gracilis

text: Euglena gracilis

text: Z

text: Euglena gracilis PacBio - Peter Myler


text: UNIVERSITY OF CALGARY

text: public

tag: Namespace:UNIVERSITY OF CALGARY

text: Moredun Research Institute

characteristic: collecting institution

characteristic: collection date

text: Charlotte Burgess

characteristic: collector name

text: Beta-tubulin isotype-1 from mixed nematode species population

characteristic: dev stage

text: United Kingdom

characteristic: geographic location (country and/or sea)

text: Sheep

characteristic: host common name

characteristic: isolate

text: nematode metagenome

text: nematode metagenome


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: University of Milan-Bicocca

characteristic: INSDC center name

characteristic: INSDC first public

text: public

tag: Namespace:University of Milan-Bicocca

text: meadow

characteristic: environment (biome)

text: pollen

characteristic: environment (feature)

text: pollen

characteristic: environment (material)

text: Yes

characteristic: environmental sample

text: Czech Republic

text: 48�49'30.52 N

unit: DD

characteristic: geographic location (latitude)

text: 14�19'4.02 E

characteristic: geographic location (longitude)

text: embryophyte clone 100r6

text: S2F and S3R

characteristic: pcr primers

text: embryophyte clone 100r6

text: nuclear internal transcribed spacer 2 region (ITS2).

characteristic: target gene

characteristic: target subfragment

text: foraging Bomben metabarcoding


characteristic: ENA-CHECKLIST

text: UNIVERSITY OF BASEL

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

tag: Namespace:UNIVERSITY OF BASEL

characteristic: Submitter Id

text: human

characteristic: common name

characteristic: description

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: Candidate circulating-tumor cell from GBM patient

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UNIVERSITY OF BASEL

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: Deep sequencing of a primary tumor sample from GBM patient


text: Strongylocentrotus droebachiensis

characteristic: HOST TAXON NAME

text: UNIVERSITY OF BIRMINGHAM

text: public

tag: Namespace:UNIVERSITY OF BIRMINGHAM

text: Vibrio splendidus

text: Body surface lesions

text: Vibrio splendidus

text: Vibrio splendidus


text: Strongylocentrotus droebachiensis

text: UNIVERSITY OF BIRMINGHAM

text: public

text: Vibrio sp. NFH.MB010

text: Body surface lesions

text: Vibrio sp. NFH.MB010

text: Vibrio sp. NFH.MB010


text: Plasmodium falciparum

characteristic: ArrayExpress-SPECIES

text: SC

text: public

text: malaria parasite P. falciparum

text: Plasmodium falciparum

text: Plasmodium falciparum

characteristic: subject id


characteristic: ENA-CHECKLIST

text: UNIVERSITY OF OSLO

text: public

tag: Namespace:UNIVERSITY OF OSLO

text: Gammarus setosus

characteristic: bio material

text: Ralf Stefan Neumann

characteristic: collected by

characteristic: collection date

text: Mixed stages

characteristic: dev stage

text: From culture grown in MAP medium (18.6g/l Difco marine broth 2216, 20g/l Bacto peptone, 10g/l NaCl) at 12 degrees celcius

characteristic: isolation source

text: University of Oslo, Institute of Biosciences, EVOGENE

characteristic: lab host

text: Sphaeroforma arctica JP610

text: Sphaeroforma arctica JP610

text: Sphaeroforma arctica small RNA


text: UNIVERSITY OF OSLO

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: mixed

text: Gammarus setosus

characteristic: host scientific name

text: Sphaeroforma arctica JP610

characteristic: organism

text: Sphaeroforma arctica JP610

text: Small RNA sequencing of Sphaeroforma arctica


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

tag: Namespace:Latvian Biomedical Research and Study Centre

text: metagenome

text: metagenome

text: Human gut microbiome - fecal sample

characteristic: title


characteristic: ENA-CHECKLIST

text: Latvian Biomedical Research and Study Centre

text: public

text: metagenome

text: metagenome

text: Human gut microbiome - fecal sample


text: EMBL-EBI

text: public

unit: day

characteristic: age

text: ArrayExpress

characteristic: broker name

text: house mouse

characteristic: common name

text: Protocols: To assay the robustness of the meiotic cell division process, we profiled germ cells of the trans-chromosomal mouse model (Tc1) (containing Tc(HSA21)1TybEmcf genotype) that carries a copy of the human chromosome 21. The Tc0 genotype is the same as Tc1 but did not inherit the human chromosome 21. So these are littermates of Tc1 that were breed with F1 animals (129S8 x C57BL/6J) but lost the chromosome. Spermatogenic cell populations were isolated from adult mouse testes as described in Ernst et al. (2016). In brief, the albuginea was removed and tissue was incubated in dissociation buffer containing 25mg/ml Collagenase A, 25mg/ml Dispase II and 2.5mg/ml DNase I for 30 minutes at 37C. Enzymatic digestion was quenched with Dulbecco’s Modified Eagle Medium (DMEM, Gibco) supplemented with 10% Fetal calf serum (FCS, 10270106, Gibco). Mouse testes were enzymatically dissociated and 34 ul of single-cell suspension at a concentration of ~297.000 cells/ml was loaded into one channel of the ChromiumTM Single Cell A Chip (10X Genomics®), aiming for a recovery of 4000-5000 cells. Single-cell barcoding, cDNA synthesis and library preparation were performed following manufacturer’s instructions according to Chromium Single Cell 3′ Library & Gel Bead Kit v2, 16 rxns (Product Code: 120237)

characteristic: description

characteristic: individual

text: Mus musculus

text: Mus musculus

text: testis

characteristic: organism part

text: Mus musculus

text: male

characteristic: sex

characteristic: strain


text: EMBL-EBI

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: house mouse

text: Mus musculus

text: Mus musculus

text: testis

text: Mus musculus

text: male

text: 129S2/SvPas x (129S8 x C57BL/6J)


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UNIVERSITY OF EXETER

text: public

text: Genomic DNA from CP665 background 4136-1-2

text: Magnaporthe oryzae

characteristic: organism

text: Magnaporthe oryzae

text: CP665 Genomic DNA


characteristic: ENA-CHECKLIST

text: UNIVERSITY OF EXETER

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: Genomic DNA from CP750 background 4091-5-8

text: Magnaporthe oryzae

text: Magnaporthe oryzae

text: CP750 Genomic DNA

characteristic: title


text: UNIVERSITY OF EXETER

text: public

text: Genomic DNA from CP751 background 4091-5-8

characteristic: description

text: Magnaporthe oryzae

text: Magnaporthe oryzae

text: CP751 Genomic DNA


text: UNIVERSITY OF EXETER

text: public

text: Genomic DNA from CP777 background 4091-5-8

text: Magnaporthe oryzae

text: Magnaporthe oryzae

text: CP777 Genomic DNA


text: UNIVERSITY OF EXETER

text: public

text: Genomic DNA from CP778 background 4091-5-8

text: Magnaporthe oryzae

text: Magnaporthe oryzae

text: CP778 Genomic DNA


text: UNIVERSITY OF EXETER

text: public

text: Genomic DNA from CP785 background 4091-5-8

text: Magnaporthe oryzae

text: Magnaporthe oryzae

text: CP785 Genomic DNA


text: UNIVERSITY OF EXETER

text: public

text: Genomic DNA from CP786 background 4091-5-8

text: Magnaporthe oryzae

text: Magnaporthe oryzae

text: CP786 Genomic DNA


text: UNIVERSITY OF EXETER

text: public

text: Genomic DNA from CP788 background 4091-5-8

text: Magnaporthe oryzae

text: Magnaporthe oryzae

text: CP788 Genomic DNA


text: UNIVERSITY OF EXETER

text: public

text: Genomic DNA from CP789 background 4091-5-8

text: Magnaporthe oryzae

text: Magnaporthe oryzae

text: CP789 Genomic DNA


text: UNIVERSITY OF EXETER

text: public

text: Genomic DNA from CP790 background 4091-5-8

text: Magnaporthe oryzae

text: Magnaporthe oryzae

text: CP790 Genomic DNA


text: UNIVERSITY OF EXETER

text: public

text: Genomic DNA from CP824 background 4091-5-8

text: Magnaporthe oryzae

text: Magnaporthe oryzae

text: CP824 Genomic DNA


text: UNIVERSITY OF EXETER

text: public

text: Genomic DNA from CP892 background 4379-R-16

text: Magnaporthe oryzae

text: Magnaporthe oryzae

text: CP892 Genomic DNA


text: UNIVERSITY OF EXETER

text: public

text: rsy1 mutant in Guy11 background generated by CRISPR

text: Magnaporthe oryzae

text: Magnaporthe oryzae

text: rsy1_12 genomic DNA


text: UNIVERSITY OF EXETER

text: public

text: Magnaporthe oryzae

text: Magnaporthe oryzae

text: rsy1_3 genomic DNA


E-MTAB-6854:Nulliparous 1

text: University of Cambridge

text: public

text: E-MTAB-6854:Nulliparous 1

tag: Namespace:University of Cambridge

characteristic: age

text: ArrayExpress

characteristic: broker name

text: mammary epithelial cell

characteristic: cell type

text: house mouse

characteristic: common name

text: Protocols: Tissues were harvested at gestation day 14.5 (G), lactation day 6 (L) and day 11 post natural weaning of the pups (PI). Tissue from NP females was harvested at 8 weeks of age. Two individual mice per developmental time point were used in the study. Lymph node divested mammary glands (excluding the cervical pair) were dissected from the mice and mechanically dissociated. The finely minced tissue was transferred to a digestion mix consisting of DMEM/F12 (Gibco) + 10 mM HEPES (Gibco) + collagenase (Roche) + 200 U ml-1 hyaluronidase (Sigma) + gentamicin (Gibco) and incubated for 3 hours at 37° C. Next, single cell suspensions were incubated in HF medium (Hank’s balanced salt solution (Gibco) + 1% foetal bovine serum, Gibco) + 10% normal rat serum (Sigma) for 20 min on ice to pre-block before antibody staining. All antibody incubations were performed for 10 min on ice in HF media. Mammary cells were stained with the following primary antibodies: CD31-biotin (eBioscience, clone 390); CD45-biotin (eBioscience, clone 30F11); Ter119-biotin (eBioscience, clone Ter119) and EpCAM-PE (Biolegend, clone G8.8). Cells were then stained with streptavidin-PE-CF594 (BD-Biosciences). Propidium Iodide (PI, ; Sigma) was used to detect dead cells. Cells were filtered through a cell strainer (Partec) before sorting. Sorting of cells was done using a SH800Z sorter (SONY). Single-stained control cells were used to perform compensation manually and unstained cells were used to set gates. Chip alignment and sorting calibration was performed with automatic setup beads (SONY) immediately prior to sorting. Doublets, dead cells and contaminating haematopoietic, endothelial and stromal cells were gated out and EpCAM positive cells were sorted in LoBind microcentrifuges tubes (Eppendorf) with HF. After sorting cells were spun down and resuspended in of HF. Samples were manually counted using an improved Neubauer chamber and the cell concentration was normalized by addition of HF. Equal numbers of cells per sample were processed for scRNA library preparation. Samples were processed for scRNA library preparation within 9 hours from tissue isolation. For droplet-based scRNA-seq, sorted cells were encapsulated into droplets, and libraries were prepared using the ChromiumTM Single Cell 3’ Reagent Kits v2 according to manufacturer’s protocol (10x Genomics). For droplet-based scRNA-seq, sorted cells were encapsulated into droplets, and libraries were prepared using the ChromiumTM Single Cell 3’ Reagent Kits v2 according to manufacturer’s protocol (10x Genomics).

text: wild type genotype

characteristic: genotype

text: Nulliparous 1

characteristic: individual

text: Mus musculus

text: Mus musculus

text: mammary gland

text: EpCAM-positive

characteristic: phenotype

text: nulliparous

characteristic: sampling time point

text: Mus musculus

text: female

text: Nulliparous 1


E-MTAB-6854:Gestation 2

characteristic: ENA-FIRST-PUBLIC

text: University of Cambridge

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-6854:Gestation 2

characteristic: Submitter Id

text: ArrayExpress

text: mammary epithelial cell

text: house mouse

text: wild type genotype

text: Gestation 2

text: Mus musculus

text: Mus musculus

text: mammary gland

characteristic: organism part

text: EpCAM-positive

text: gestation

text: Mus musculus

text: female

characteristic: sex

characteristic: strain

text: Gestation 2


E-MTAB-6854:Post-Involution 2

characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: University of Cambridge

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-6854:Post-Involution 2

text: ArrayExpress

text: mammary epithelial cell

text: house mouse

characteristic: description

text: wild type genotype

text: Post-Involution 2

text: Mus musculus

characteristic: organism

text: Mus musculus

text: mammary gland

text: EpCAM-positive

text: post-involution

text: Mus musculus

text: female

text: Post-Involution 2

characteristic: title


E-MTAB-6854:Gestation 1

text: University of Cambridge

text: public

text: E-MTAB-6854:Gestation 1

characteristic: age

text: ArrayExpress

characteristic: broker name

text: mammary epithelial cell

characteristic: cell type

text: house mouse

characteristic: common name

text: wild type genotype

characteristic: genotype

text: Gestation 1

characteristic: individual

text: Mus musculus

text: Mus musculus

text: mammary gland

text: EpCAM-positive

characteristic: phenotype

text: gestation

characteristic: sampling time point

text: Mus musculus

text: female

text: Gestation 1


E-MTAB-6854:Lactation 2

characteristic: ENA-FIRST-PUBLIC

text: University of Cambridge

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-6854:Lactation 2

characteristic: Submitter Id

text: ArrayExpress

text: mammary epithelial cell

text: house mouse

text: wild type genotype

text: Lactation 2

text: Mus musculus

text: Mus musculus

text: mammary gland

characteristic: organism part

text: EpCAM-positive

text: lactation

text: Mus musculus

text: female

characteristic: sex

characteristic: strain

text: Lactation 2


E-MTAB-6854:Lactation 1

characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: University of Cambridge

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-6854:Lactation 1

text: ArrayExpress

text: mammary epithelial cell

text: house mouse

characteristic: description

text: wild type genotype

text: Lactation 1

text: Mus musculus

characteristic: organism

text: Mus musculus

text: mammary gland

text: EpCAM-positive

text: lactation

text: Mus musculus

text: female

text: Lactation 1

characteristic: title


E-MTAB-6854:Nulliparous 2

text: University of Cambridge

text: public

text: E-MTAB-6854:Nulliparous 2

characteristic: age

text: ArrayExpress

characteristic: broker name

text: mammary epithelial cell

characteristic: cell type

text: house mouse

characteristic: common name

text: wild type genotype

characteristic: genotype

text: Nulliparous 2

characteristic: individual

text: Mus musculus

text: Mus musculus

text: mammary gland

text: EpCAM-positive

characteristic: phenotype

text: nulliparous

characteristic: sampling time point

text: Mus musculus

text: female

text: Nulliparous 2


E-MTAB-6854:Post-Involution 1

characteristic: ENA-FIRST-PUBLIC

text: University of Cambridge

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-6854:Post-Involution 1

characteristic: Submitter Id

text: ArrayExpress

text: mammary epithelial cell

text: house mouse

text: wild type genotype

text: Post-Involution 1

text: Mus musculus

text: Mus musculus

text: mammary gland

characteristic: organism part

text: EpCAM-positive

text: post-involution

text: Mus musculus

text: female

characteristic: sex

characteristic: strain

text: Post-Involution 1


text: healthy

characteristic: ArrayExpress-PHENOTYPE

text: Homo sapiens

characteristic: ArrayExpress-SPECIES

characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: human

text: Homo sapiens

characteristic: organism

text: healthy

text: Homo sapiens

characteristic: subject id

characteristic: title


text: wildtype

text: Mus musculus

characteristic: ENA-FIRST-PUBLIC

text: SC

characteristic: INSDC last update

text: public

text: house mouse

characteristic: common name

text: Mus musculus

text: wildtype

characteristic: phenotype

text: Mus musculus


text: HI-STEM gGmbH

text: public

characteristic: INSDC status

characteristic: SRA accession

tag: Namespace:HI-STEM gGmbH

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: induced neural border stem cell

characteristic: cell type

text: human

text: Protocols: Adult dermal fibroblasts (ADFs) were derived from the skin biopsies of a healthy male donor (Age 24) as described in Meyer et al. 2015 ( Meyer, S., Wörsdörfer, P., Günther, K., Thier, M., Edenhofer, F., 2015. Derivation of Adult Human Fibroblasts and their Direct Conversion into Expandable Neural Progenitor Cells. J Vis Exp e52831-e52831. doi:10.3791/52831). ADFs were expanded until passage 4 and frozen in 90% Serum/ 10% DMSO prior to use. All culture were grown at 37°C in 5% CO2 and 20% O2. Peripheral blood mononuclear cells (PBMCs) were derived from a healthy male donors (Age 26) and isolated using the Ficoll gradient procedure. PBMCs were used either directly or frozen in 90% Serum Replacement/ 10% DMSO as previously described (for details see Sommer, A.G., Rozelle, S.S., Sullivan, S., Mills, J.A., Park, S.-M., Smith, B.W., Iyer, A.M., French, D.L., Kotton, D.N., Gadue, P., Murphy, G.J., Mostoslavsky, G., 2012. Generation of human induced pluripotent stem cells from peripheral blood using the STEMCCA lentiviral vector. J Vis Exp e4327-e4327. doi:10.3791/4327). Cells were derived from informed consent from all donors and handled in accordance with Ethics Committee II of Heidelberg University approval no. 2009-350N-MA. To reprogramme cells we used the pHAGE2-Vector (pHAGE2-TetO-BKSZ and pHAGE2-TetO-BKSZ-flox) in combination with the transactivator m2RTTA (Addgene plasmid #20342) for the overexpression of the transgene cassette. ADF2 were transduced with pHAGE2-TetO-BKSZ + m2RTTA; PBMC1 were transduced with pHAGE2-TetO-BKSZ-flox and m2RTTA. Induced Neural Border Stem cells were harvested by treatment with Accutase and washed twice with unsupplemented DMEM/ F12. After surface staining for 30 minutes at 4°C, 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 ERCC spike-ins) in separate 96 wells and flash-frozen in liquid N2 until further processing. NBSC maintenance: NBSC maintenance medium is composed of DMEM/ F-12 Glutamax (for iNBSCs) or 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. NBSCs were cultured in NBSC maintenance medium on a layer of inactivated mouse embryonic fibroblasts (feeder) at 37°C in 5% O2 and 5% CO2. iNBSC lines were routinely split after 4-5 days by treatment with Accutase (Life Technologies) and transferred onto fresh feeders. Conversion into iNBSCs: Lentiviral supernatants containing BKSZ-flox and m2RTTA were mixed in a ratio of 2:1, supplemented with 5 µg/ml polybrene (Sigma) and used freshly for transduction of 8x10**5/ 6 Well primary ADF and pancreas fibroblasts. For reprogramming of PBMCs the lentiviral supernatant was concentrated via ultracentrifugation and PBMCs were transduced in QBSF-60 Stem Cell Medium (Quality Biological) containing 50 μg/ml Ascorbic Acid (Sigma), 50 ng/ml SCF (R&D Systems), 10 ng/ml IL-3 (R&D Systems), 2 U/ml EPO (R&D Systems), 40 ng/ml IGF-1 (Peprotech), 1 μM Dexamethasone (Sigma) and 5 µg/ml polybrene (for details see {Sommer:2012db}). The other day 2x10**5 transduced PBMCs were transferred onto one well of a 6 Well plate, coated with inactivated MEFs and reprogramming was initiated one day thereafter.For reprogramming transduced cells were cultured in DMEM/F-12 Glutamax (Life Technologies) containing 64 µg/ml L-Ascorbic acid 2-phosphate (LAAP, Sigma), ITS-X (1:100, Life Technologies), NEAA (1:100, Life Technologies), 2% FCS, 8% Serum Replacement (Life Technologies) supplemented with 4 µM Chir99021 (Sigma), 5 µM Alk5 Inhibitor II (Enzolifesciences), 0.5 µM Purmorphamine (Sigma), 5µM Tranylcypromine (Sigma) and 1µg/ml Doxycycline (Sigma) and incubated at 37°C in 5% O2 and 5% CO2. During reprogramming medium was changed every other day. When first colonies became visible or latest after 19 days, medium was changed to NBSC maintenance medium. 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.

characteristic: description

text: adult

characteristic: developmental stage

text: normal

characteristic: disease

text: pHAGE2-TetO-BKSZ; m2RTTA

characteristic: genotype

text: CAP-FEEDER

characteristic: growth condition

characteristic: individual

text: Homo sapiens

text: Homo sapiens

text: dermis

characteristic: organism part

text: pass

characteristic: post analysis well quality

text: fibroblast of dermis

characteristic: progenitor cell type

text: Homo sapiens

text: male

characteristic: single cell identifier


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

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

text: ArrayExpress

text: induced neural border stem cell

text: human

characteristic: common name

text: adult

text: normal

text: pHAGE2-TetO-BKSZ; m2RTTA

text: CAP-FEEDER

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: dermis

text: fail

text: fibroblast of dermis

text: Homo sapiens

text: male

characteristic: sex

characteristic: title


text: HI-STEM gGmbH

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: induced neural border stem cell

characteristic: cell type

text: human

characteristic: description

text: adult

characteristic: developmental stage

text: normal

characteristic: disease

text: pHAGE2-TetO-BKSZ-flox; m2RTTA

characteristic: genotype

text: CAP-FEEDER

characteristic: growth condition

text: Homo sapiens

text: Homo sapiens

text: blood

text: pass

text: peripheral blood mononuclear cell

text: Homo sapiens

text: male


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: HI-STEM gGmbH

characteristic: INSDC center name

text: public

text: ArrayExpress

text: induced neural border stem cell

text: human

text: adult

text: normal

text: pHAGE2-TetO-BKSZ-flox; m2RTTA

text: CAP-FEEDER

characteristic: individual

text: Homo sapiens

text: Homo sapiens

text: blood

characteristic: organism part

text: fail

characteristic: post analysis well quality

text: peripheral blood mononuclear cell

characteristic: progenitor cell type

text: Homo sapiens

text: male

characteristic: single cell identifier


text: wildtype

characteristic: ArrayExpress-PHENOTYPE

text: Mus musculus

characteristic: ArrayExpress-SPECIES

text: SC

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: house mouse

characteristic: common name

text: Mus musculus

characteristic: organism

text: wildtype

characteristic: phenotype

text: Mus musculus

characteristic: subject id

characteristic: title


text: wildtype

text: Homo sapiens

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

characteristic: INSDC center name

text: public

text: human

text: Homo sapiens

text: wildtype

text: Homo sapiens


text: Fondation Merieux

text: public

text: BGD

tag: Namespace:Fondation Merieux

characteristic: collection date

text: S. Typhi In Bangladesh

characteristic: description

text: Salmonella

characteristic: genus

text: Bangladesh

characteristic: geographic location (country and/or sea)

text: Homo sapiens

characteristic: host

text: diseased

characteristic: host health state

text: human

characteristic: host scientific name

characteristic: isolate

text: Human

characteristic: isolation source

text: Salmonella enterica subsp. enterica serovar Typhi

type: AMR curated data - CABBAGE

value: chloramphenicol

value: resistant

value: Salmonella enterica

value: ciprofloxacin

value: trimethoprim-sulfamethoxazole

value: ampicillin


text: Fondation Merieux

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: BGD

characteristic: SRA accession

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