characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

text: public

text: E-MTAB-115631647023036:G7-B001634-1_S271

text: ArrayExpress

text: ependymal cell

text: house mouse

text: adult

text: GFP-positive

characteristic: immunophenotype

text: Mus musculus

characteristic: organism

text: Mus musculus

text: spinal cord

text: Mus musculus

text: female

text: OK

characteristic: single cell well quality


status: PUBLIC

tag: attribute

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

tag: Namespace:Division of Cell and Developmental Biology, School of Life Sciences, University of Dundee

characteristic: Submitter Id

unit: day

characteristic: age

text: ArrayExpress

characteristic: broker name

text: ependymal cell

text: house mouse

characteristic: common name

text: Protocols: The ependymal cell layer from the thoracic spinal cord of FOXJ1-EGFP mice was microdissected and dissociated it into a cell suspension. GFP-positive DAPI-negative cells were then sorted into 384-well plates containing lysis buffer. GFP-positive DAPI-negative cells were sorted into lysis plates with a BD Influx Cell Sorter using 6 psi pressure and a 130 μm nozzle. Lysis plates were created by dispensing 0.4 μl lysis buffer (0.5 U Recombinant RNase Inhibitor (Takara Bio, 2313B), 0.0625% Triton X-100 (Sigma, 93443-100ML), 3.125 mM dNTP mix (Thermo Fisher, R0193), 3.125 μM Oligo-dT 30 VN (IDT, 5'AAGCAGTGGTATCAACGCAGAGTACT 30 VN-3') and 1:600,000 ERCC RNA spike-in mix (Thermo Fisher, 4456740)) into 384-well hard-shell PCR plates (Biorad HSP3901) using a Tempest liquid handler (Formulatrix). cDNA synthesis was performed using the Smart-seq2 protocol (Picelli et al., 2013, 2014). Briefly, 384-well plates containing single-cell lysates were thawed on ice followed by first strand synthesis. 0.6 μl of reaction mix (16.7 U/μl SMARTScribe TM Reverse Transcriptase (Takara Bio, 639538), 1.67 U/μl Recombinant RNase Inhibitor (Takara Bio, 2313B), 1.67X First-Strand Buffer (Takara Bio, 639538), 1.67 μM TSO (Exiqon, 5'-AAGCAGTGGTATCAACGCAGACTACATrGrG+G-3'), 8.33 mM DTT (Bioworld, 40420001-1), 1.67 M Betaine (Sigma, B0300-5VL), and 10 mM MgCl 2 (Sigma, M1028-10X1ML)) was added to each well using a Tempest liquid handler. Bulk wells received twice the amount of RT mix (1.2 μl). Reverse transcription was carried out by incubating wells on a ProFlex 2x384 thermal-cycler (Thermo Fisher) at 42°C for 90 min and stopped by heating at 70°C for 5 min. Subsequently, 1.6 μl of PCR mix (1.67X KAPA HiFi HotStart ReadyMix (Kapa Biosystems, KK2602), 0.17 μM IS PCR primer (IDT, 5'-AAGCAGTGGTATCAACGCAGAGT-3'), and 0.038U/μl Lambda Exonuclease (NEB, M0262L)) was added to each well with a Tempest liquid handler (Formulatrix). The amplified product was diluted with a ratio of 1 part cDNA to 10 parts 10mM Tris-HCl (Thermo Fisher, 15568025), and concentrations were measured with dye-fluorescence assay (Quant-iT dsDNA High Sensitivity kit; Thermo Fisher, Q33120) on a SpectraMax i3x microplate reader (Molecular Devices). These wells were reformatted to a new 384-well plate at a concentration of 0.3 ng/μl and final volume of 0.4 μl using an Echo 550 acoustic liquid dispenser (Labcyte). If the cell concentration was below 0.3 ng/μl, 0.4 μl of sample was transferred. Illumina sequencing libraries were prepared using the Nextera XT Library Sample Preparation kit (Illumina, FC-131-1096) (Darmanis et al., 2015; Schaum et al., 2018). Each well was mixed with 0.8 μl Nextera tagmentation DNA buffer (Illumina) and 0.4 μl Tn5 enzyme (Illumina), then tagmented at 55°C for 10 min. The reaction was stopped by adding 0.4 μl \Neutralize Tagment Buffer\ (Illumina) and spinning at room temperature (RT) in a centrifuge at 3220 xg for 5 min. Indexing PCR reactions were performed by adding 0.4 μl of 5 μM i5 indexing primer, 0.4 μl of 5 μM i7 indexing primer, and 1.2 μl of Nextera NPM mix (Illumina). PCR amplification was carried out on a ProFlex 2x384 thermal cycler using the following program: 1. 72°C for 3 minutes, 2. 95°C for 30 s, 3. 12 cycles of 95°C for 10 s, 55°C for 30 s, and 72°C for 1 min, and 4. 72°C for 5 min.

characteristic: description

text: adult

characteristic: developmental stage

characteristic: genotype

text: GFP-positive

characteristic: individual

text: Mus musculus

text: Mus musculus

text: spinal cord

characteristic: organism part

text: Mus musculus

text: female

characteristic: sex

text: OK

characteristic: strain

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Division of Cell and Developmental Biology, School of Life Sciences, University of Dundee

characteristic: INSDC center name

text: public

text: E-MTAB-115631647023036:G7-B001636-1_S139

text: ArrayExpress

text: ependymal cell

text: house mouse

text: adult

text: GFP-positive

characteristic: immunophenotype

text: Mus musculus

characteristic: organism

text: Mus musculus

text: spinal cord

text: Mus musculus

text: female

text: OK

characteristic: single cell well quality


characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-115631647023036:G8-B001633-1_S188

characteristic: Submitter Id

characteristic: age

text: ArrayExpress

characteristic: broker name

text: ependymal cell

text: house mouse

characteristic: common name

text: adult

text: GFP-positive

text: Mus musculus

text: Mus musculus

text: spinal cord

text: Mus musculus

text: female

text: OK


text: public

text: E-MTAB-115631647023036:G8-B001634-1_S272

text: ArrayExpress

text: ependymal cell

text: house mouse

characteristic: description

text: adult

characteristic: developmental stage

characteristic: genotype

text: GFP-positive

characteristic: individual

text: Mus musculus

text: Mus musculus

text: spinal cord

characteristic: organism part

text: Mus musculus

text: female

characteristic: sex

text: OK

characteristic: strain

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

text: public

text: ArrayExpress

text: ependymal cell

text: house mouse

text: adult

text: GFP-positive

characteristic: immunophenotype

text: Mus musculus

characteristic: organism

text: Mus musculus

text: spinal cord

text: Mus musculus

text: female

text: OK

characteristic: single cell well quality


characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-115631647023036:G8-B001636-1_S140

characteristic: Submitter Id

characteristic: age

text: ArrayExpress

characteristic: broker name

text: ependymal cell

text: house mouse

characteristic: common name

text: adult

text: GFP-positive

text: Mus musculus

text: Mus musculus

text: spinal cord

text: Mus musculus

text: female

text: OK


text: public

text: E-MTAB-115631647023036:G9-B001633-1_S189

text: ArrayExpress

text: ependymal cell

text: house mouse

characteristic: description

text: adult

characteristic: developmental stage

characteristic: genotype

text: GFP-positive

characteristic: individual

text: Mus musculus

text: Mus musculus

text: spinal cord

characteristic: organism part

text: Mus musculus

text: female

characteristic: sex

text: OK

characteristic: strain

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

text: public

text: E-MTAB-115631647023036:G9-B001634-1_S273

text: ArrayExpress

text: ependymal cell

text: house mouse

text: adult

text: GFP-positive

characteristic: immunophenotype

text: Mus musculus

characteristic: organism

text: Mus musculus

text: spinal cord

text: Mus musculus

text: female

text: OK

characteristic: single cell well quality


characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-115631647023036:G9-B001636-1_S141

characteristic: Submitter Id

characteristic: age

text: ArrayExpress

characteristic: broker name

text: ependymal cell

text: house mouse

characteristic: common name

text: adult

text: GFP-positive

text: Mus musculus

text: Mus musculus

text: spinal cord

text: Mus musculus

text: female

text: OK


text: public

text: E-MTAB-115631647023036:H1-B001633-1_S205

text: ArrayExpress

text: ependymal cell

text: house mouse

characteristic: description

text: adult

characteristic: developmental stage

characteristic: genotype

text: GFP-positive

characteristic: individual

text: Mus musculus

text: Mus musculus

text: spinal cord

characteristic: organism part

text: Mus musculus

text: female

characteristic: sex

text: OK

characteristic: strain

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

text: public

text: E-MTAB-115631647023036:H1-B001634-1_S289

text: ArrayExpress

text: ependymal cell

text: house mouse

text: adult

text: GFP-positive

characteristic: immunophenotype

text: Mus musculus

characteristic: organism

text: Mus musculus

text: spinal cord

text: Mus musculus

text: female

text: OK

characteristic: single cell well quality


characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-115631647023036:H1-B001636-1_S157

characteristic: Submitter Id

characteristic: age

text: ArrayExpress

characteristic: broker name

text: ependymal cell

text: house mouse

characteristic: common name

text: adult

text: GFP-positive

text: Mus musculus

text: Mus musculus

text: spinal cord

text: Mus musculus

text: female

text: OK


text: public

text: E-MTAB-115631647023036:H10-B001633-1_S214

text: ArrayExpress

text: ependymal cell

text: house mouse

characteristic: description

text: adult

characteristic: developmental stage

characteristic: genotype

text: GFP-positive

characteristic: individual

text: Mus musculus

text: Mus musculus

text: spinal cord

characteristic: organism part

text: Mus musculus

text: female

characteristic: sex

text: OK

characteristic: strain

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

text: public

text: E-MTAB-115631647023036:H10-B001634-1_S298

text: ArrayExpress

text: ependymal cell

text: house mouse

text: adult

text: GFP-positive

characteristic: immunophenotype

text: Mus musculus

characteristic: organism

text: Mus musculus

text: spinal cord

text: Mus musculus

text: female

text: OK

characteristic: single cell well quality


characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-115631647023036:H10-B001635-1_S82

characteristic: Submitter Id

characteristic: age

text: ArrayExpress

characteristic: broker name

text: ependymal cell

text: house mouse

characteristic: common name

text: adult

text: GFP-positive

text: Mus musculus

text: Mus musculus

text: spinal cord

text: Mus musculus

text: female

text: OK


text: public

text: E-MTAB-115631647023036:H10-B001636-1_S166

text: ArrayExpress

text: ependymal cell

text: house mouse

characteristic: description

text: adult

characteristic: developmental stage

characteristic: genotype

text: GFP-positive

characteristic: individual

text: Mus musculus

text: Mus musculus

text: spinal cord

characteristic: organism part

text: Mus musculus

text: female

characteristic: sex

text: OK

characteristic: strain

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

text: public

text: E-MTAB-115631647023036:H11-B001633-1_S215

text: ArrayExpress

text: ependymal cell

text: house mouse

text: adult

text: GFP-positive

characteristic: immunophenotype

text: Mus musculus

characteristic: organism

text: Mus musculus

text: spinal cord

text: Mus musculus

text: female

text: OK

characteristic: single cell well quality


characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-115631647023036:H11-B001634-1_S299

characteristic: Submitter Id

characteristic: age

text: ArrayExpress

characteristic: broker name

text: ependymal cell

text: house mouse

characteristic: common name

text: Protocols: The ependymal cell layer from the thoracic spinal cord of FOXJ1-EGFP mice was microdissected and dissociated it into a cell suspension. GFP-positive DAPI-negative cells were then sorted into 384-well plates containing lysis buffer. GFP-positive DAPI-negative cells were sorted into lysis plates with a BD Influx Cell Sorter using 6 psi pressure and a 130 μm nozzle. Lysis plates were created by dispensing 0.4 μl lysis buffer (0.5 U Recombinant RNase Inhibitor (Takara Bio, 2313B), 0.0625% Triton X-100 (Sigma, 93443-100ML), 3.125 mM dNTP mix (Thermo Fisher, R0193), 3.125 μM Oligo-dT 30 VN (IDT, 5'AAGCAGTGGTATCAACGCAGAGTACT 30 VN-3') and 1:600,000 ERCC RNA spike-in mix (Thermo Fisher, 4456740)) into 384-well hard-shell PCR plates (Biorad HSP3901) using a Tempest liquid handler (Formulatrix). cDNA synthesis was performed using the Smart-seq2 protocol (Picelli et al., 2013, 2014). Briefly, 384-well plates containing single-cell lysates were thawed on ice followed by first strand synthesis. 0.6 μl of reaction mix (16.7 U/μl SMARTScribe TM Reverse Transcriptase (Takara Bio, 639538), 1.67 U/μl Recombinant RNase Inhibitor (Takara Bio, 2313B), 1.67X First-Strand Buffer (Takara Bio, 639538), 1.67 μM TSO (Exiqon, 5'-AAGCAGTGGTATCAACGCAGACTACATrGrG+G-3'), 8.33 mM DTT (Bioworld, 40420001-1), 1.67 M Betaine (Sigma, B0300-5VL), and 10 mM MgCl 2 (Sigma, M1028-10X1ML)) was added to each well using a Tempest liquid handler. Bulk wells received twice the amount of RT mix (1.2 μl). Reverse transcription was carried out by incubating wells on a ProFlex 2x384 thermal-cycler (Thermo Fisher) at 42°C for 90 min and stopped by heating at 70°C for 5 min. Subsequently, 1.6 μl of PCR mix (1.67X KAPA HiFi HotStart ReadyMix (Kapa Biosystems, KK2602), 0.17 μM IS PCR primer (IDT, 5'-AAGCAGTGGTATCAACGCAGAGT-3'), and 0.038U/μl Lambda Exonuclease (NEB, M0262L)) was added to each well with a Tempest liquid handler (Formulatrix). The amplified product was diluted with a ratio of 1 part cDNA to 10 parts 10mM Tris-HCl (Thermo Fisher, 15568025), and concentrations were measured with dye-fluorescence assay (Quant-iT dsDNA High Sensitivity kit; Thermo Fisher, Q33120) on a SpectraMax i3x microplate reader (Molecular Devices). These wells were reformatted to a new 384-well plate at a concentration of 0.3 ng/μl and final volume of 0.4 μl using an Echo 550 acoustic liquid dispenser (Labcyte). If the cell concentration was below 0.3 ng/μl, 0.4 μl of sample was transferred. Illumina sequencing libraries were prepared using the Nextera XT Library Sample Preparation kit (Illumina, FC-131-1096) (Darmanis et al., 2015; Schaum et al., 2018). Each well was mixed with 0.8 μl Nextera tagmentation DNA buffer (Illumina) and 0.4 μl Tn5 enzyme (Illumina), then tagmented at 55°C for 10 min. The reaction was stopped by adding 0.4 μl \Neutralize Tagment Buffer\ (Illumina) and spinning at room temperature (RT) in a centrifuge at 3220 xg for 5 min. Indexing PCR reactions were performed by adding 0.4 μl of 5 μM i5 indexing primer, 0.4 μl of 5 μM i7 indexing primer, and 1.2 μl of Nextera NPM mix (Illumina). PCR amplification was carried out on a ProFlex 2x384 thermal cycler using the following program: 1. 72°C for 3 minutes, 2. 95°C for 30 s, 3. 12 cycles of 95°C for 10 s, 55°C for 30 s, and 72°C for 1 min, and 4. 72°C for 5 min.

text: adult

text: GFP-positive

text: Mus musculus

text: Mus musculus

text: spinal cord

text: Mus musculus

text: female

text: OK


text: Division of Cell and Developmental Biology, School of Life Sciences, University of Dundee

text: public

text: E-MTAB-115631647023036:H11-B001635-1_S83

text: ArrayExpress

text: ependymal cell

text: house mouse

characteristic: description

text: adult

characteristic: developmental stage

characteristic: genotype

text: GFP-positive

characteristic: individual

text: Mus musculus

text: Mus musculus

text: spinal cord

characteristic: organism part

text: Mus musculus

text: female

characteristic: sex

text: OK

characteristic: strain

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

text: public

text: E-MTAB-115631647023036:H11-B001636-1_S167

text: ArrayExpress

text: ependymal cell

text: house mouse

text: adult

text: GFP-positive

characteristic: immunophenotype

text: Mus musculus

characteristic: organism

text: Mus musculus

text: spinal cord

text: Mus musculus

text: female

text: OK

characteristic: single cell well quality


characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-115631647023036:H12-B001633-1_S216

characteristic: Submitter Id

characteristic: age

text: ArrayExpress

characteristic: broker name

text: ependymal cell

text: house mouse

characteristic: common name

text: adult

text: GFP-positive

text: Mus musculus

text: Mus musculus

text: spinal cord

text: Mus musculus

text: female

text: OK


text: public

text: E-MTAB-115631647023036:H12-B001634-1_S300

text: ArrayExpress

text: ependymal cell

text: house mouse

characteristic: description

text: adult

characteristic: developmental stage

characteristic: genotype

text: GFP-positive

characteristic: individual

text: Mus musculus

text: Mus musculus

text: spinal cord

characteristic: organism part

text: Mus musculus

text: female

characteristic: sex

text: OK

characteristic: strain

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

text: public

text: E-MTAB-115631647023036:H12-B001635-1_S84

text: ArrayExpress

text: ependymal cell

text: house mouse

text: adult

text: GFP-positive

characteristic: immunophenotype

text: Mus musculus

characteristic: organism

text: Mus musculus

text: spinal cord

text: Mus musculus

text: female

text: OK

characteristic: single cell well quality


characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-115631647023036:H12-B001636-1_S168

characteristic: Submitter Id

characteristic: age

text: ArrayExpress

characteristic: broker name

text: ependymal cell

text: house mouse

characteristic: common name

text: adult

text: GFP-positive

text: Mus musculus

text: Mus musculus

text: spinal cord

text: Mus musculus

text: female

text: OK


text: public

text: E-MTAB-115631647023036:H13-B001633-1_S217

text: ArrayExpress

text: ependymal cell

text: house mouse

characteristic: description

text: adult

characteristic: developmental stage

characteristic: genotype

text: GFP-positive

characteristic: individual

text: Mus musculus

text: Mus musculus

text: spinal cord

characteristic: organism part

text: Mus musculus

text: female

characteristic: sex

text: OK

characteristic: strain

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

text: public

text: ArrayExpress

text: ependymal cell

text: house mouse

text: adult

text: GFP-positive

characteristic: immunophenotype

text: Mus musculus

characteristic: organism

text: Mus musculus

text: spinal cord

text: Mus musculus

text: female

text: OK

characteristic: single cell well quality


characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-115631647023036:H13-B001635-1_S85

characteristic: Submitter Id

characteristic: age

text: ArrayExpress

characteristic: broker name

text: ependymal cell

text: house mouse

characteristic: common name

text: adult

text: GFP-positive

text: Mus musculus

text: Mus musculus

text: spinal cord

text: Mus musculus

text: female

text: OK


text: public

text: E-MTAB-115631647023036:H13-B001636-1_S169

text: ArrayExpress

text: ependymal cell

text: house mouse

characteristic: description

text: adult

characteristic: developmental stage

characteristic: genotype

text: GFP-positive

characteristic: individual

text: Mus musculus

text: Mus musculus

text: spinal cord

characteristic: organism part

text: Mus musculus

text: female

characteristic: sex

text: OK

characteristic: strain

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

text: public

text: E-MTAB-115631647023036:H14-B001633-1_S218

text: ArrayExpress

text: ependymal cell

text: house mouse

text: adult

text: GFP-positive

characteristic: immunophenotype

text: Mus musculus

characteristic: organism

text: Mus musculus

text: spinal cord

text: Mus musculus

text: female

text: OK

characteristic: single cell well quality


characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-115631647023036:H14-B001635-1_S86

characteristic: Submitter Id

characteristic: age

text: ArrayExpress

characteristic: broker name

text: ependymal cell

text: house mouse

characteristic: common name

text: adult

text: GFP-positive

text: Mus musculus

text: Mus musculus

text: spinal cord

text: Mus musculus

text: female

text: OK


text: public

text: E-MTAB-115631647023036:H14-B001636-1_S170

text: ArrayExpress

text: ependymal cell

text: house mouse

characteristic: description

text: adult

characteristic: developmental stage

characteristic: genotype

text: GFP-positive

characteristic: individual

text: Mus musculus

text: Mus musculus

text: spinal cord

characteristic: organism part

text: Mus musculus

text: female

characteristic: sex

text: OK

characteristic: strain

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

text: public

text: E-MTAB-115631647023036:H15-B001633-1_S219

text: ArrayExpress

text: ependymal cell

text: house mouse

text: adult

text: GFP-positive

characteristic: immunophenotype

text: Mus musculus

characteristic: organism

text: Mus musculus

text: spinal cord

text: Mus musculus

text: female

text: OK

characteristic: single cell well quality


characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-115631647023036:H15-B001635-1_S87

characteristic: Submitter Id

characteristic: age

text: ArrayExpress

characteristic: broker name

text: ependymal cell

text: house mouse

characteristic: common name

text: adult

text: GFP-positive

text: Mus musculus

text: Mus musculus

text: spinal cord

text: Mus musculus

text: female

text: OK


text: public

text: E-MTAB-115631647023036:H15-B001636-1_S171

text: ArrayExpress

text: ependymal cell

text: house mouse

characteristic: description

text: adult

characteristic: developmental stage

characteristic: genotype

text: GFP-positive

characteristic: individual

text: Mus musculus

text: Mus musculus

text: spinal cord

characteristic: organism part

text: Mus musculus

text: female

characteristic: sex

text: OK

characteristic: strain

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

text: public

text: E-MTAB-115631647023036:H16-B001633-1_S220

text: ArrayExpress

text: ependymal cell

text: house mouse

text: Protocols: The ependymal cell layer from the thoracic spinal cord of FOXJ1-EGFP mice was microdissected and dissociated it into a cell suspension. GFP-positive DAPI-negative cells were then sorted into 384-well plates containing lysis buffer. GFP-positive DAPI-negative cells were sorted into lysis plates with a BD Influx Cell Sorter using 6 psi pressure and a 130 μm nozzle. Lysis plates were created by dispensing 0.4 μl lysis buffer (0.5 U Recombinant RNase Inhibitor (Takara Bio, 2313B), 0.0625% Triton X-100 (Sigma, 93443-100ML), 3.125 mM dNTP mix (Thermo Fisher, R0193), 3.125 μM Oligo-dT 30 VN (IDT, 5'AAGCAGTGGTATCAACGCAGAGTACT 30 VN-3') and 1:600,000 ERCC RNA spike-in mix (Thermo Fisher, 4456740)) into 384-well hard-shell PCR plates (Biorad HSP3901) using a Tempest liquid handler (Formulatrix). cDNA synthesis was performed using the Smart-seq2 protocol (Picelli et al., 2013, 2014). Briefly, 384-well plates containing single-cell lysates were thawed on ice followed by first strand synthesis. 0.6 μl of reaction mix (16.7 U/μl SMARTScribe TM Reverse Transcriptase (Takara Bio, 639538), 1.67 U/μl Recombinant RNase Inhibitor (Takara Bio, 2313B), 1.67X First-Strand Buffer (Takara Bio, 639538), 1.67 μM TSO (Exiqon, 5'-AAGCAGTGGTATCAACGCAGACTACATrGrG+G-3'), 8.33 mM DTT (Bioworld, 40420001-1), 1.67 M Betaine (Sigma, B0300-5VL), and 10 mM MgCl 2 (Sigma, M1028-10X1ML)) was added to each well using a Tempest liquid handler. Bulk wells received twice the amount of RT mix (1.2 μl). Reverse transcription was carried out by incubating wells on a ProFlex 2x384 thermal-cycler (Thermo Fisher) at 42°C for 90 min and stopped by heating at 70°C for 5 min. Subsequently, 1.6 μl of PCR mix (1.67X KAPA HiFi HotStart ReadyMix (Kapa Biosystems, KK2602), 0.17 μM IS PCR primer (IDT, 5'-AAGCAGTGGTATCAACGCAGAGT-3'), and 0.038U/μl Lambda Exonuclease (NEB, M0262L)) was added to each well with a Tempest liquid handler (Formulatrix). The amplified product was diluted with a ratio of 1 part cDNA to 10 parts 10mM Tris-HCl (Thermo Fisher, 15568025), and concentrations were measured with dye-fluorescence assay (Quant-iT dsDNA High Sensitivity kit; Thermo Fisher, Q33120) on a SpectraMax i3x microplate reader (Molecular Devices). These wells were reformatted to a new 384-well plate at a concentration of 0.3 ng/μl and final volume of 0.4 μl using an Echo 550 acoustic liquid dispenser (Labcyte). If the cell concentration was below 0.3 ng/μl, 0.4 μl of sample was transferred. Illumina sequencing libraries were prepared using the Nextera XT Library Sample Preparation kit (Illumina, FC-131-1096) (Darmanis et al., 2015; Schaum et al., 2018). Each well was mixed with 0.8 μl Nextera tagmentation DNA buffer (Illumina) and 0.4 μl Tn5 enzyme (Illumina), then tagmented at 55°C for 10 min. The reaction was stopped by adding 0.4 μl \Neutralize Tagment Buffer\ (Illumina) and spinning at room temperature (RT) in a centrifuge at 3220 xg for 5 min. Indexing PCR reactions were performed by adding 0.4 μl of 5 μM i5 indexing primer, 0.4 μl of 5 μM i7 indexing primer, and 1.2 μl of Nextera NPM mix (Illumina). PCR amplification was carried out on a ProFlex 2x384 thermal cycler using the following program: 1. 72°C for 3 minutes, 2. 95°C for 30 s, 3. 12 cycles of 95°C for 10 s, 55°C for 30 s, and 72°C for 1 min, and 4. 72°C for 5 min.

text: adult

text: GFP-positive

characteristic: immunophenotype

text: Mus musculus

characteristic: organism

text: Mus musculus

text: spinal cord

text: Mus musculus

text: female

text: OK

characteristic: single cell well quality


text: Division of Cell and Developmental Biology, School of Life Sciences, University of Dundee

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-115631647023036:H16-B001635-1_S88

characteristic: Submitter Id

characteristic: age

text: ArrayExpress

characteristic: broker name

text: ependymal cell

text: house mouse

characteristic: common name

text: adult

text: GFP-positive

text: Mus musculus

text: Mus musculus

text: spinal cord

text: Mus musculus

text: female

text: OK


text: public

text: E-MTAB-115631647023036:H16-B001636-1_S172

text: ArrayExpress

text: ependymal cell

text: house mouse

characteristic: description

text: adult

characteristic: developmental stage

characteristic: genotype

text: GFP-positive

characteristic: individual

text: Mus musculus

text: Mus musculus

text: spinal cord

characteristic: organism part

text: Mus musculus

text: female

characteristic: sex

text: OK

characteristic: strain

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

text: public

text: E-MTAB-115631647023036:H17-B001633-1_S221

text: ArrayExpress

text: ependymal cell

text: house mouse

text: adult

text: GFP-positive

characteristic: immunophenotype

text: Mus musculus

characteristic: organism

text: Mus musculus

text: spinal cord

text: Mus musculus

text: female

text: OK

characteristic: single cell well quality


characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-115631647023036:H17-B001635-1_S89

characteristic: Submitter Id

characteristic: age

text: ArrayExpress

characteristic: broker name

text: ependymal cell

text: house mouse

characteristic: common name

text: adult

text: GFP-positive

text: Mus musculus

text: Mus musculus

text: spinal cord

text: Mus musculus

text: female

text: OK


text: public

text: E-MTAB-115631647023036:H17-B001636-1_S173

text: ArrayExpress

text: ependymal cell

text: house mouse

characteristic: description

text: adult

characteristic: developmental stage

characteristic: genotype

text: GFP-positive

characteristic: individual

text: Mus musculus

text: Mus musculus

text: spinal cord

characteristic: organism part

text: Mus musculus

text: female

characteristic: sex

text: OK

characteristic: strain

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

text: public

text: E-MTAB-115631647023036:H18-B001633-1_S222

text: ArrayExpress

text: ependymal cell

text: house mouse

text: adult

text: GFP-positive

characteristic: immunophenotype

text: Mus musculus

characteristic: organism

text: Mus musculus

text: spinal cord

text: Mus musculus

text: female

text: OK

characteristic: single cell well quality


characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-115631647023036:H18-B001635-1_S90

characteristic: Submitter Id

characteristic: age

text: ArrayExpress

characteristic: broker name

text: ependymal cell

text: house mouse

characteristic: common name

text: adult

text: GFP-positive

text: Mus musculus

text: Mus musculus

text: spinal cord

text: Mus musculus

text: female

text: OK


text: public

text: E-MTAB-115631647023036:H18-B001636-1_S174

text: ArrayExpress

text: ependymal cell

text: house mouse

characteristic: description

text: adult

characteristic: developmental stage

characteristic: genotype

text: GFP-positive

characteristic: individual

text: Mus musculus

text: Mus musculus

text: spinal cord

characteristic: organism part

text: Mus musculus

text: female

characteristic: sex

text: OK

characteristic: strain

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

text: public

text: E-MTAB-115631647023036:H19-B001633-1_S223

text: ArrayExpress

text: ependymal cell

text: house mouse

text: adult

text: GFP-positive

characteristic: immunophenotype

text: Mus musculus

characteristic: organism

text: Mus musculus

text: spinal cord

text: Mus musculus

text: female

text: OK

characteristic: single cell well quality


characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: age

text: ArrayExpress

characteristic: broker name

text: ependymal cell

text: house mouse

characteristic: common name

text: adult

text: GFP-positive

text: Mus musculus

text: Mus musculus

text: spinal cord

text: Mus musculus

text: female

text: OK


text: public

text: E-MTAB-115631647023036:H19-B001635-1_S91

text: ArrayExpress

text: ependymal cell

text: house mouse

characteristic: description

text: adult

characteristic: developmental stage

characteristic: genotype

text: GFP-positive

characteristic: individual

text: Mus musculus

text: Mus musculus

text: spinal cord

characteristic: organism part

text: Mus musculus

text: female

characteristic: sex

text: OK

characteristic: strain

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

text: public

text: E-MTAB-115631647023036:H19-B001636-1_S175

text: ArrayExpress

text: ependymal cell

text: house mouse

text: adult

text: GFP-positive

characteristic: immunophenotype

text: Mus musculus

characteristic: organism

text: Mus musculus

text: spinal cord

text: Mus musculus

text: female

text: OK

characteristic: single cell well quality


characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-115631647023036:H2-B001633-1_S206

characteristic: Submitter Id

characteristic: age

text: ArrayExpress

characteristic: broker name

text: ependymal cell

text: house mouse

characteristic: common name

text: adult

text: GFP-positive

text: Mus musculus

text: Mus musculus

text: spinal cord

text: Mus musculus

text: female

text: OK


text: public

text: E-MTAB-115631647023036:H2-B001634-1_S290

text: ArrayExpress

text: ependymal cell

text: house mouse

characteristic: description

text: adult

characteristic: developmental stage

characteristic: genotype

text: GFP-positive

characteristic: individual

text: Mus musculus

text: Mus musculus

text: spinal cord

characteristic: organism part

text: Mus musculus

text: female

characteristic: sex

text: OK

characteristic: strain

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

text: public

text: E-MTAB-115631647023036:H2-B001636-1_S158

text: ArrayExpress

text: ependymal cell

text: house mouse

text: adult

text: GFP-positive

characteristic: immunophenotype

text: Mus musculus

characteristic: organism

text: Mus musculus

text: spinal cord

text: Mus musculus

text: female

text: OK

characteristic: single cell well quality


characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-115631647023036:H20-B001633-1_S224

characteristic: Submitter Id

characteristic: age

text: ArrayExpress

characteristic: broker name

text: ependymal cell

text: house mouse

characteristic: common name

text: adult

text: GFP-positive

text: Mus musculus

text: Mus musculus

text: spinal cord

text: Mus musculus

text: female

text: OK


text: public

text: E-MTAB-115631647023036:H20-B001635-1_S92

text: ArrayExpress

text: ependymal cell

text: house mouse

text: Protocols: The ependymal cell layer from the thoracic spinal cord of FOXJ1-EGFP mice was microdissected and dissociated it into a cell suspension. GFP-positive DAPI-negative cells were then sorted into 384-well plates containing lysis buffer. GFP-positive DAPI-negative cells were sorted into lysis plates with a BD Influx Cell Sorter using 6 psi pressure and a 130 μm nozzle. Lysis plates were created by dispensing 0.4 μl lysis buffer (0.5 U Recombinant RNase Inhibitor (Takara Bio, 2313B), 0.0625% Triton X-100 (Sigma, 93443-100ML), 3.125 mM dNTP mix (Thermo Fisher, R0193), 3.125 μM Oligo-dT 30 VN (IDT, 5'AAGCAGTGGTATCAACGCAGAGTACT 30 VN-3') and 1:600,000 ERCC RNA spike-in mix (Thermo Fisher, 4456740)) into 384-well hard-shell PCR plates (Biorad HSP3901) using a Tempest liquid handler (Formulatrix). cDNA synthesis was performed using the Smart-seq2 protocol (Picelli et al., 2013, 2014). Briefly, 384-well plates containing single-cell lysates were thawed on ice followed by first strand synthesis. 0.6 μl of reaction mix (16.7 U/μl SMARTScribe TM Reverse Transcriptase (Takara Bio, 639538), 1.67 U/μl Recombinant RNase Inhibitor (Takara Bio, 2313B), 1.67X First-Strand Buffer (Takara Bio, 639538), 1.67 μM TSO (Exiqon, 5'-AAGCAGTGGTATCAACGCAGACTACATrGrG+G-3'), 8.33 mM DTT (Bioworld, 40420001-1), 1.67 M Betaine (Sigma, B0300-5VL), and 10 mM MgCl 2 (Sigma, M1028-10X1ML)) was added to each well using a Tempest liquid handler. Bulk wells received twice the amount of RT mix (1.2 μl). Reverse transcription was carried out by incubating wells on a ProFlex 2x384 thermal-cycler (Thermo Fisher) at 42°C for 90 min and stopped by heating at 70°C for 5 min. Subsequently, 1.6 μl of PCR mix (1.67X KAPA HiFi HotStart ReadyMix (Kapa Biosystems, KK2602), 0.17 μM IS PCR primer (IDT, 5'-AAGCAGTGGTATCAACGCAGAGT-3'), and 0.038U/μl Lambda Exonuclease (NEB, M0262L)) was added to each well with a Tempest liquid handler (Formulatrix). The amplified product was diluted with a ratio of 1 part cDNA to 10 parts 10mM Tris-HCl (Thermo Fisher, 15568025), and concentrations were measured with dye-fluorescence assay (Quant-iT dsDNA High Sensitivity kit; Thermo Fisher, Q33120) on a SpectraMax i3x microplate reader (Molecular Devices). These wells were reformatted to a new 384-well plate at a concentration of 0.3 ng/μl and final volume of 0.4 μl using an Echo 550 acoustic liquid dispenser (Labcyte). If the cell concentration was below 0.3 ng/μl, 0.4 μl of sample was transferred. Illumina sequencing libraries were prepared using the Nextera XT Library Sample Preparation kit (Illumina, FC-131-1096) (Darmanis et al., 2015; Schaum et al., 2018). Each well was mixed with 0.8 μl Nextera tagmentation DNA buffer (Illumina) and 0.4 μl Tn5 enzyme (Illumina), then tagmented at 55°C for 10 min. The reaction was stopped by adding 0.4 μl \Neutralize Tagment Buffer\ (Illumina) and spinning at room temperature (RT) in a centrifuge at 3220 xg for 5 min. Indexing PCR reactions were performed by adding 0.4 μl of 5 μM i5 indexing primer, 0.4 μl of 5 μM i7 indexing primer, and 1.2 μl of Nextera NPM mix (Illumina). PCR amplification was carried out on a ProFlex 2x384 thermal cycler using the following program: 1. 72°C for 3 minutes, 2. 95°C for 30 s, 3. 12 cycles of 95°C for 10 s, 55°C for 30 s, and 72°C for 1 min, and 4. 72°C for 5 min.

characteristic: description

text: adult

characteristic: developmental stage

characteristic: genotype

text: GFP-positive

characteristic: individual

text: Mus musculus

text: Mus musculus

text: spinal cord

characteristic: organism part

text: Mus musculus

text: female

characteristic: sex

text: OK

characteristic: strain

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Division of Cell and Developmental Biology, School of Life Sciences, University of Dundee

characteristic: INSDC center name

text: public

text: E-MTAB-115631647023036:H20-B001636-1_S176

text: ArrayExpress

text: ependymal cell

text: house mouse

text: adult

text: GFP-positive

characteristic: immunophenotype

text: Mus musculus

characteristic: organism

text: Mus musculus

text: spinal cord

text: Mus musculus

text: female

text: OK

characteristic: single cell well quality


characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-115631647023036:H21-B001633-1_S225

characteristic: Submitter Id

characteristic: age

text: ArrayExpress

characteristic: broker name

text: ependymal cell

text: house mouse

characteristic: common name

text: adult

text: GFP-positive

text: Mus musculus

text: Mus musculus

text: spinal cord

text: Mus musculus

text: female

text: OK


text: public

text: E-MTAB-115631647023036:H21-B001635-1_S93

text: ArrayExpress

text: ependymal cell

text: house mouse

characteristic: description

text: adult

characteristic: developmental stage

characteristic: genotype

text: GFP-positive

characteristic: individual

text: Mus musculus

text: Mus musculus

text: spinal cord

characteristic: organism part

text: Mus musculus

text: female

characteristic: sex

text: OK

characteristic: strain

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

text: public

text: E-MTAB-115631647023036:H21-B001636-1_S177

text: ArrayExpress

text: ependymal cell

text: house mouse

text: adult

text: GFP-positive

characteristic: immunophenotype

text: Mus musculus

characteristic: organism

text: Mus musculus

text: spinal cord

text: Mus musculus

text: female

text: OK

characteristic: single cell well quality


characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-115631647023036:H22-B001633-1_S226

characteristic: Submitter Id

characteristic: age

text: ArrayExpress

characteristic: broker name

text: ependymal cell

text: house mouse

characteristic: common name

text: adult

text: GFP-positive

text: Mus musculus

text: Mus musculus

text: spinal cord

text: Mus musculus

text: female

text: OK


text: public

text: E-MTAB-115631647023036:H22-B001634-1_S10

text: ArrayExpress

text: ependymal cell

text: house mouse

characteristic: description

text: adult

characteristic: developmental stage

characteristic: genotype

text: GFP-positive

characteristic: individual

text: Mus musculus

text: Mus musculus

text: spinal cord

characteristic: organism part

text: Mus musculus

text: female

characteristic: sex

text: OK

characteristic: strain

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

text: public

text: E-MTAB-115631647023036:H22-B001635-1_S94

text: ArrayExpress

text: ependymal cell

text: house mouse

text: adult

text: GFP-positive

characteristic: immunophenotype

text: Mus musculus

characteristic: organism

text: Mus musculus

text: spinal cord

text: Mus musculus

text: female

text: OK

characteristic: single cell well quality


characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-115631647023036:H22-B001636-1_S178

characteristic: Submitter Id

characteristic: age

text: ArrayExpress

characteristic: broker name

text: ependymal cell

text: house mouse

characteristic: common name

text: adult

text: GFP-positive

text: Mus musculus

text: Mus musculus

text: spinal cord

text: Mus musculus

text: female

text: OK


text: public

text: E-MTAB-115631647023036:H23-B001633-1_S227

text: ArrayExpress

text: ependymal cell

text: house mouse

characteristic: description

text: adult

characteristic: developmental stage

characteristic: genotype

text: GFP-positive

characteristic: individual

text: Mus musculus

text: Mus musculus

text: spinal cord

characteristic: organism part

text: Mus musculus

text: female

characteristic: sex

text: OK

characteristic: strain

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

text: public

text: E-MTAB-115631647023036:H23-B001634-1_S11

text: ArrayExpress

text: ependymal cell

text: house mouse

text: adult

text: GFP-positive

characteristic: immunophenotype

text: Mus musculus

characteristic: organism

text: Mus musculus

text: spinal cord

text: Mus musculus

text: female

text: OK

characteristic: single cell well quality


characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-115631647023036:H23-B001635-1_S95

characteristic: Submitter Id

characteristic: age

text: ArrayExpress

characteristic: broker name

text: ependymal cell

text: house mouse

characteristic: common name

text: adult

text: GFP-positive

text: Mus musculus

text: Mus musculus

text: spinal cord

text: Mus musculus

text: female

text: OK


text: public

text: E-MTAB-115631647023036:H23-B001636-1_S179

text: ArrayExpress

text: ependymal cell

text: house mouse

characteristic: description

text: adult

characteristic: developmental stage

characteristic: genotype

text: GFP-positive

characteristic: individual

text: Mus musculus

text: Mus musculus

text: spinal cord

characteristic: organism part

text: Mus musculus

text: female

characteristic: sex

text: OK

characteristic: strain

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

text: public

text: E-MTAB-115631647023036:H24-B001633-1_S181

text: ArrayExpress

text: ependymal cell

text: house mouse

text: adult

text: GFP-positive

characteristic: immunophenotype

text: Mus musculus

characteristic: organism

text: Mus musculus

text: spinal cord

text: Mus musculus

text: female

text: OK

characteristic: single cell well quality


characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-115631647023036:H24-B001633-1_S41

characteristic: Submitter Id

characteristic: age

text: ArrayExpress

characteristic: broker name

text: ependymal cell

text: house mouse

characteristic: common name

text: adult

text: GFP-positive

text: Mus musculus

text: Mus musculus

text: spinal cord

text: Mus musculus

text: female

text: OK


text: public

text: E-MTAB-115631647023036:H24-B001634-1_S42

text: ArrayExpress

text: ependymal cell

text: house mouse

characteristic: description

text: adult

characteristic: developmental stage

characteristic: genotype

text: GFP-positive

characteristic: individual

text: Mus musculus

text: Mus musculus

text: spinal cord

characteristic: organism part

text: Mus musculus

text: female

characteristic: sex

text: OK

characteristic: strain

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

text: public

text: E-MTAB-115631647023036:H24-B001635-1_S43

text: ArrayExpress

text: ependymal cell

text: house mouse

text: Protocols: The ependymal cell layer from the thoracic spinal cord of FOXJ1-EGFP mice was microdissected and dissociated it into a cell suspension. GFP-positive DAPI-negative cells were then sorted into 384-well plates containing lysis buffer. GFP-positive DAPI-negative cells were sorted into lysis plates with a BD Influx Cell Sorter using 6 psi pressure and a 130 μm nozzle. Lysis plates were created by dispensing 0.4 μl lysis buffer (0.5 U Recombinant RNase Inhibitor (Takara Bio, 2313B), 0.0625% Triton X-100 (Sigma, 93443-100ML), 3.125 mM dNTP mix (Thermo Fisher, R0193), 3.125 μM Oligo-dT 30 VN (IDT, 5'AAGCAGTGGTATCAACGCAGAGTACT 30 VN-3') and 1:600,000 ERCC RNA spike-in mix (Thermo Fisher, 4456740)) into 384-well hard-shell PCR plates (Biorad HSP3901) using a Tempest liquid handler (Formulatrix). cDNA synthesis was performed using the Smart-seq2 protocol (Picelli et al., 2013, 2014). Briefly, 384-well plates containing single-cell lysates were thawed on ice followed by first strand synthesis. 0.6 μl of reaction mix (16.7 U/μl SMARTScribe TM Reverse Transcriptase (Takara Bio, 639538), 1.67 U/μl Recombinant RNase Inhibitor (Takara Bio, 2313B), 1.67X First-Strand Buffer (Takara Bio, 639538), 1.67 μM TSO (Exiqon, 5'-AAGCAGTGGTATCAACGCAGACTACATrGrG+G-3'), 8.33 mM DTT (Bioworld, 40420001-1), 1.67 M Betaine (Sigma, B0300-5VL), and 10 mM MgCl 2 (Sigma, M1028-10X1ML)) was added to each well using a Tempest liquid handler. Bulk wells received twice the amount of RT mix (1.2 μl). Reverse transcription was carried out by incubating wells on a ProFlex 2x384 thermal-cycler (Thermo Fisher) at 42°C for 90 min and stopped by heating at 70°C for 5 min. Subsequently, 1.6 μl of PCR mix (1.67X KAPA HiFi HotStart ReadyMix (Kapa Biosystems, KK2602), 0.17 μM IS PCR primer (IDT, 5'-AAGCAGTGGTATCAACGCAGAGT-3'), and 0.038U/μl Lambda Exonuclease (NEB, M0262L)) was added to each well with a Tempest liquid handler (Formulatrix). The amplified product was diluted with a ratio of 1 part cDNA to 10 parts 10mM Tris-HCl (Thermo Fisher, 15568025), and concentrations were measured with dye-fluorescence assay (Quant-iT dsDNA High Sensitivity kit; Thermo Fisher, Q33120) on a SpectraMax i3x microplate reader (Molecular Devices). These wells were reformatted to a new 384-well plate at a concentration of 0.3 ng/μl and final volume of 0.4 μl using an Echo 550 acoustic liquid dispenser (Labcyte). If the cell concentration was below 0.3 ng/μl, 0.4 μl of sample was transferred. Illumina sequencing libraries were prepared using the Nextera XT Library Sample Preparation kit (Illumina, FC-131-1096) (Darmanis et al., 2015; Schaum et al., 2018). Each well was mixed with 0.8 μl Nextera tagmentation DNA buffer (Illumina) and 0.4 μl Tn5 enzyme (Illumina), then tagmented at 55°C for 10 min. The reaction was stopped by adding 0.4 μl \Neutralize Tagment Buffer\ (Illumina) and spinning at room temperature (RT) in a centrifuge at 3220 xg for 5 min. Indexing PCR reactions were performed by adding 0.4 μl of 5 μM i5 indexing primer, 0.4 μl of 5 μM i7 indexing primer, and 1.2 μl of Nextera NPM mix (Illumina). PCR amplification was carried out on a ProFlex 2x384 thermal cycler using the following program: 1. 72°C for 3 minutes, 2. 95°C for 30 s, 3. 12 cycles of 95°C for 10 s, 55°C for 30 s, and 72°C for 1 min, and 4. 72°C for 5 min.

text: adult

text: GFP-positive

characteristic: immunophenotype

text: Mus musculus

characteristic: organism

text: Mus musculus

text: spinal cord

text: Mus musculus

text: female

text: OK

characteristic: single cell well quality


text: Division of Cell and Developmental Biology, School of Life Sciences, University of Dundee

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-115631647023036:H24-B001635-ARA-KGS_BB001635_340370-1_S183

characteristic: Submitter Id

characteristic: age

text: ArrayExpress

characteristic: broker name

text: ependymal cell

text: house mouse

characteristic: common name

text: adult

text: GFP-positive

text: Mus musculus

text: Mus musculus

text: spinal cord

text: Mus musculus

text: female

text: OK


text: public

text: E-MTAB-115631647023036:H24-B001636-1_S44

text: ArrayExpress

text: ependymal cell

text: house mouse

characteristic: description

text: adult

characteristic: developmental stage

characteristic: genotype

text: GFP-positive

characteristic: individual

text: Mus musculus

text: Mus musculus

text: spinal cord

characteristic: organism part

text: Mus musculus

text: female

characteristic: sex

text: OK

characteristic: strain

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

text: public

text: E-MTAB-115631647023157:H3-B001633-1_S207

text: ArrayExpress

text: ependymal cell

text: house mouse

text: adult

text: GFP-positive

characteristic: immunophenotype

text: Mus musculus

characteristic: organism

text: Mus musculus

text: spinal cord

text: Mus musculus

text: female

text: OK

characteristic: single cell well quality


characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-115631647023157:H3-B001634-1_S291

characteristic: Submitter Id

characteristic: age

text: ArrayExpress

characteristic: broker name

text: ependymal cell

text: house mouse

characteristic: common name

text: adult

text: GFP-positive

text: Mus musculus

text: Mus musculus

text: spinal cord

text: Mus musculus

text: female

text: OK


text: public

text: ArrayExpress

text: ependymal cell

text: house mouse

characteristic: description

text: adult

characteristic: developmental stage

characteristic: genotype

text: GFP-positive

characteristic: individual

text: Mus musculus

text: Mus musculus

text: spinal cord

characteristic: organism part

text: Mus musculus

text: female

characteristic: sex

text: OK

characteristic: strain

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

text: public

text: E-MTAB-115631647023157:H3-B001636-1_S159

text: ArrayExpress

text: ependymal cell

text: house mouse

text: adult

text: GFP-positive

characteristic: immunophenotype

text: Mus musculus

characteristic: organism

text: Mus musculus

text: spinal cord

text: Mus musculus

text: female

text: OK

characteristic: single cell well quality


characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-115631647023157:H4-B001633-1_S208

characteristic: Submitter Id

characteristic: age

text: ArrayExpress

characteristic: broker name

text: ependymal cell

text: house mouse

characteristic: common name

text: adult

text: GFP-positive

text: Mus musculus

text: Mus musculus

text: spinal cord

text: Mus musculus

text: female

text: OK


text: public

text: E-MTAB-115631647023157:H4-B001634-1_S292

text: ArrayExpress

text: ependymal cell

text: house mouse

characteristic: description

text: adult

characteristic: developmental stage

characteristic: genotype

text: GFP-positive

characteristic: individual

text: Mus musculus

text: Mus musculus

text: spinal cord

characteristic: organism part

text: Mus musculus

text: female

characteristic: sex

text: OK

characteristic: strain

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

text: public

text: E-MTAB-115631647023157:H4-B001636-1_S160

text: ArrayExpress

text: ependymal cell

text: house mouse

text: adult

text: GFP-positive

characteristic: immunophenotype

text: Mus musculus

characteristic: organism

text: Mus musculus

text: spinal cord

text: Mus musculus

text: female

text: OK

characteristic: single cell well quality


characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-115631647023157:H5-B001633-1_S209

characteristic: Submitter Id

characteristic: age

text: ArrayExpress

characteristic: broker name

text: ependymal cell

text: house mouse

characteristic: common name

text: adult

text: GFP-positive

text: Mus musculus

text: Mus musculus

text: spinal cord

text: Mus musculus

text: female

text: OK


text: public

text: E-MTAB-115631647023157:H5-B001634-1_S293

text: ArrayExpress

text: ependymal cell

text: house mouse

characteristic: description

text: adult

characteristic: developmental stage

characteristic: genotype

text: GFP-positive

characteristic: individual

text: Mus musculus

text: Mus musculus

text: spinal cord

characteristic: organism part

text: Mus musculus

text: female

characteristic: sex

text: OK

characteristic: strain

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

text: public

text: E-MTAB-115631647023157:H5-B001636-1_S161

text: ArrayExpress

text: ependymal cell

text: house mouse

text: adult

text: GFP-positive

characteristic: immunophenotype

text: Mus musculus

characteristic: organism

text: Mus musculus

text: spinal cord

text: Mus musculus

text: female

text: OK

characteristic: single cell well quality


characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-115631647023157:H6-B001633-1_S210

characteristic: Submitter Id

characteristic: age

text: ArrayExpress

characteristic: broker name

text: ependymal cell

text: house mouse

characteristic: common name

text: adult

text: GFP-positive

text: Mus musculus

text: Mus musculus

text: spinal cord

text: Mus musculus

text: female

text: OK


text: public

text: E-MTAB-115631647023157:H6-B001634-1_S294

text: ArrayExpress

text: ependymal cell

text: house mouse

characteristic: description

text: adult

characteristic: developmental stage

characteristic: genotype

text: GFP-positive

characteristic: individual

text: Mus musculus

text: Mus musculus

text: spinal cord

characteristic: organism part

text: Mus musculus

text: female

characteristic: sex

text: OK

characteristic: strain

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

text: public

text: E-MTAB-115631647023157:H6-B001636-1_S162

text: ArrayExpress

text: ependymal cell

text: house mouse

text: adult

text: GFP-positive

characteristic: immunophenotype

text: Mus musculus

characteristic: organism

text: Mus musculus

text: spinal cord

text: Mus musculus

text: female

text: OK

characteristic: single cell well quality


characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-115631647023157:H7-B001633-1_S211

characteristic: Submitter Id

characteristic: age

text: ArrayExpress

characteristic: broker name

text: ependymal cell

text: house mouse

characteristic: common name

text: adult

text: GFP-positive

text: Mus musculus

text: Mus musculus

text: spinal cord

text: Mus musculus

text: female

text: OK


text: public

text: E-MTAB-115631647023157:H7-B001634-1_S295

text: ArrayExpress

text: ependymal cell

text: house mouse

text: Protocols: The ependymal cell layer from the thoracic spinal cord of FOXJ1-EGFP mice was microdissected and dissociated it into a cell suspension. GFP-positive DAPI-negative cells were then sorted into 384-well plates containing lysis buffer. GFP-positive DAPI-negative cells were sorted into lysis plates with a BD Influx Cell Sorter using 6 psi pressure and a 130 μm nozzle. Lysis plates were created by dispensing 0.4 μl lysis buffer (0.5 U Recombinant RNase Inhibitor (Takara Bio, 2313B), 0.0625% Triton X-100 (Sigma, 93443-100ML), 3.125 mM dNTP mix (Thermo Fisher, R0193), 3.125 μM Oligo-dT 30 VN (IDT, 5'AAGCAGTGGTATCAACGCAGAGTACT 30 VN-3') and 1:600,000 ERCC RNA spike-in mix (Thermo Fisher, 4456740)) into 384-well hard-shell PCR plates (Biorad HSP3901) using a Tempest liquid handler (Formulatrix). cDNA synthesis was performed using the Smart-seq2 protocol (Picelli et al., 2013, 2014). Briefly, 384-well plates containing single-cell lysates were thawed on ice followed by first strand synthesis. 0.6 μl of reaction mix (16.7 U/μl SMARTScribe TM Reverse Transcriptase (Takara Bio, 639538), 1.67 U/μl Recombinant RNase Inhibitor (Takara Bio, 2313B), 1.67X First-Strand Buffer (Takara Bio, 639538), 1.67 μM TSO (Exiqon, 5'-AAGCAGTGGTATCAACGCAGACTACATrGrG+G-3'), 8.33 mM DTT (Bioworld, 40420001-1), 1.67 M Betaine (Sigma, B0300-5VL), and 10 mM MgCl 2 (Sigma, M1028-10X1ML)) was added to each well using a Tempest liquid handler. Bulk wells received twice the amount of RT mix (1.2 μl). Reverse transcription was carried out by incubating wells on a ProFlex 2x384 thermal-cycler (Thermo Fisher) at 42°C for 90 min and stopped by heating at 70°C for 5 min. Subsequently, 1.6 μl of PCR mix (1.67X KAPA HiFi HotStart ReadyMix (Kapa Biosystems, KK2602), 0.17 μM IS PCR primer (IDT, 5'-AAGCAGTGGTATCAACGCAGAGT-3'), and 0.038U/μl Lambda Exonuclease (NEB, M0262L)) was added to each well with a Tempest liquid handler (Formulatrix). The amplified product was diluted with a ratio of 1 part cDNA to 10 parts 10mM Tris-HCl (Thermo Fisher, 15568025), and concentrations were measured with dye-fluorescence assay (Quant-iT dsDNA High Sensitivity kit; Thermo Fisher, Q33120) on a SpectraMax i3x microplate reader (Molecular Devices). These wells were reformatted to a new 384-well plate at a concentration of 0.3 ng/μl and final volume of 0.4 μl using an Echo 550 acoustic liquid dispenser (Labcyte). If the cell concentration was below 0.3 ng/μl, 0.4 μl of sample was transferred. Illumina sequencing libraries were prepared using the Nextera XT Library Sample Preparation kit (Illumina, FC-131-1096) (Darmanis et al., 2015; Schaum et al., 2018). Each well was mixed with 0.8 μl Nextera tagmentation DNA buffer (Illumina) and 0.4 μl Tn5 enzyme (Illumina), then tagmented at 55°C for 10 min. The reaction was stopped by adding 0.4 μl \Neutralize Tagment Buffer\ (Illumina) and spinning at room temperature (RT) in a centrifuge at 3220 xg for 5 min. Indexing PCR reactions were performed by adding 0.4 μl of 5 μM i5 indexing primer, 0.4 μl of 5 μM i7 indexing primer, and 1.2 μl of Nextera NPM mix (Illumina). PCR amplification was carried out on a ProFlex 2x384 thermal cycler using the following program: 1. 72°C for 3 minutes, 2. 95°C for 30 s, 3. 12 cycles of 95°C for 10 s, 55°C for 30 s, and 72°C for 1 min, and 4. 72°C for 5 min.

characteristic: description

text: adult

characteristic: developmental stage

characteristic: genotype

text: GFP-positive

characteristic: individual

text: Mus musculus

text: Mus musculus

text: spinal cord

characteristic: organism part

text: Mus musculus

text: female

characteristic: sex

text: OK

characteristic: strain

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Division of Cell and Developmental Biology, School of Life Sciences, University of Dundee

characteristic: INSDC center name

text: public

text: E-MTAB-115631647023157:H7-B001636-1_S163

text: ArrayExpress

text: ependymal cell

text: house mouse

text: adult

text: GFP-positive

characteristic: immunophenotype

text: Mus musculus

characteristic: organism

text: Mus musculus

text: spinal cord

text: Mus musculus

text: female

text: OK

characteristic: single cell well quality


characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-115631647023157:H8-B001633-1_S212

characteristic: Submitter Id

characteristic: age

text: ArrayExpress

characteristic: broker name

text: ependymal cell

text: house mouse

characteristic: common name

text: adult

text: GFP-positive

text: Mus musculus

text: Mus musculus

text: spinal cord

text: Mus musculus

text: female

text: OK


text: public

text: E-MTAB-115631647023157:H8-B001634-1_S296

text: ArrayExpress

text: ependymal cell

text: house mouse

characteristic: description

text: adult

characteristic: developmental stage

characteristic: genotype

text: GFP-positive

characteristic: individual

text: Mus musculus

text: Mus musculus

text: spinal cord

characteristic: organism part

text: Mus musculus

text: female

characteristic: sex

text: OK

characteristic: strain

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

text: public

text: E-MTAB-115631647023157:H8-B001636-1_S164

text: ArrayExpress

text: ependymal cell

text: house mouse

text: adult

text: GFP-positive

characteristic: immunophenotype

text: Mus musculus

characteristic: organism

text: Mus musculus

text: spinal cord

text: Mus musculus

text: female

text: OK

characteristic: single cell well quality


characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-115631647023157:H9-B001633-1_S213

characteristic: Submitter Id

characteristic: age

text: ArrayExpress

characteristic: broker name

text: ependymal cell

text: house mouse

characteristic: common name

text: adult

text: GFP-positive

text: Mus musculus

text: Mus musculus

text: spinal cord

text: Mus musculus

text: female

text: OK


text: public

text: E-MTAB-115631647023157:H9-B001634-1_S297

text: ArrayExpress

text: ependymal cell

text: house mouse

characteristic: description

text: adult

characteristic: developmental stage

characteristic: genotype

text: GFP-positive

characteristic: individual

text: Mus musculus

text: Mus musculus

text: spinal cord

characteristic: organism part

text: Mus musculus

text: female

characteristic: sex

text: OK

characteristic: strain

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

text: public

text: ArrayExpress

text: ependymal cell

text: house mouse

text: adult

text: GFP-positive

characteristic: immunophenotype

text: Mus musculus

characteristic: organism

text: Mus musculus

text: spinal cord

text: Mus musculus

text: female

text: OK

characteristic: single cell well quality


characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-115631647023157:H9-B001636-1_S165

characteristic: Submitter Id

characteristic: age

text: ArrayExpress

characteristic: broker name

text: ependymal cell

text: house mouse

characteristic: common name

text: adult

text: GFP-positive

text: Mus musculus

text: Mus musculus

text: spinal cord

text: Mus musculus

text: female

text: OK


text: public

text: E-MTAB-115631647023157:I1-B001633-1_S229

text: ArrayExpress

text: ependymal cell

text: house mouse

characteristic: description

text: adult

characteristic: developmental stage

characteristic: genotype

text: GFP-positive

characteristic: individual

text: Mus musculus

text: Mus musculus

text: spinal cord

characteristic: organism part

text: Mus musculus

text: female

characteristic: sex

text: OK

characteristic: strain

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

text: public

text: E-MTAB-115631647023157:I1-B001636-1_S181

text: ArrayExpress

text: ependymal cell

text: house mouse

text: adult

text: GFP-positive

characteristic: immunophenotype

text: Mus musculus

characteristic: organism

text: Mus musculus

text: spinal cord

text: Mus musculus

text: female

text: OK

characteristic: single cell well quality


characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-115631647023157:I10-B001633-1_S238

characteristic: Submitter Id

characteristic: age

text: ArrayExpress

characteristic: broker name

text: ependymal cell

text: house mouse

characteristic: common name

text: adult

text: GFP-positive

text: Mus musculus

text: Mus musculus

text: spinal cord

text: Mus musculus

text: female

text: OK


text: public

text: E-MTAB-115631647023157:I10-B001634-1_S22

text: ArrayExpress

text: ependymal cell

text: house mouse

characteristic: description

text: adult

characteristic: developmental stage

characteristic: genotype

text: GFP-positive

characteristic: individual

text: Mus musculus

text: Mus musculus

text: spinal cord

characteristic: organism part

text: Mus musculus

text: female

characteristic: sex

text: OK

characteristic: strain

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

text: public

text: E-MTAB-115631647023157:I10-B001635-1_S106

text: ArrayExpress

text: ependymal cell

text: house mouse

text: adult

text: GFP-positive

characteristic: immunophenotype

text: Mus musculus

characteristic: organism

text: Mus musculus

text: spinal cord

text: Mus musculus

text: female

text: OK

characteristic: single cell well quality


characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-115631647023157:I10-B001636-1_S190

characteristic: Submitter Id

characteristic: age

text: ArrayExpress

characteristic: broker name

text: ependymal cell

text: house mouse

characteristic: common name

text: adult

text: GFP-positive

text: Mus musculus

text: Mus musculus

text: spinal cord

text: Mus musculus

text: female

text: OK


text: public

text: E-MTAB-115631647023157:I11-B001633-1_S239

text: ArrayExpress

text: ependymal cell

text: house mouse

characteristic: description

text: adult

characteristic: developmental stage

characteristic: genotype

text: GFP-positive

characteristic: individual

text: Mus musculus

text: Mus musculus

text: spinal cord

characteristic: organism part

text: Mus musculus

text: female

characteristic: sex

text: OK

characteristic: strain

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

text: public

text: E-MTAB-115631647023157:I11-B001634-1_S23

text: ArrayExpress

text: ependymal cell

text: house mouse

text: adult

text: GFP-positive

characteristic: immunophenotype

text: Mus musculus

characteristic: organism

text: Mus musculus

text: spinal cord

text: Mus musculus

text: female

text: OK

characteristic: single cell well quality


characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-115631647023157:I11-B001635-1_S107

characteristic: Submitter Id

characteristic: age

text: ArrayExpress

characteristic: broker name

text: ependymal cell

text: house mouse

characteristic: common name

text: Protocols: The ependymal cell layer from the thoracic spinal cord of FOXJ1-EGFP mice was microdissected and dissociated it into a cell suspension. GFP-positive DAPI-negative cells were then sorted into 384-well plates containing lysis buffer. GFP-positive DAPI-negative cells were sorted into lysis plates with a BD Influx Cell Sorter using 6 psi pressure and a 130 μm nozzle. Lysis plates were created by dispensing 0.4 μl lysis buffer (0.5 U Recombinant RNase Inhibitor (Takara Bio, 2313B), 0.0625% Triton X-100 (Sigma, 93443-100ML), 3.125 mM dNTP mix (Thermo Fisher, R0193), 3.125 μM Oligo-dT 30 VN (IDT, 5'AAGCAGTGGTATCAACGCAGAGTACT 30 VN-3') and 1:600,000 ERCC RNA spike-in mix (Thermo Fisher, 4456740)) into 384-well hard-shell PCR plates (Biorad HSP3901) using a Tempest liquid handler (Formulatrix). cDNA synthesis was performed using the Smart-seq2 protocol (Picelli et al., 2013, 2014). Briefly, 384-well plates containing single-cell lysates were thawed on ice followed by first strand synthesis. 0.6 μl of reaction mix (16.7 U/μl SMARTScribe TM Reverse Transcriptase (Takara Bio, 639538), 1.67 U/μl Recombinant RNase Inhibitor (Takara Bio, 2313B), 1.67X First-Strand Buffer (Takara Bio, 639538), 1.67 μM TSO (Exiqon, 5'-AAGCAGTGGTATCAACGCAGACTACATrGrG+G-3'), 8.33 mM DTT (Bioworld, 40420001-1), 1.67 M Betaine (Sigma, B0300-5VL), and 10 mM MgCl 2 (Sigma, M1028-10X1ML)) was added to each well using a Tempest liquid handler. Bulk wells received twice the amount of RT mix (1.2 μl). Reverse transcription was carried out by incubating wells on a ProFlex 2x384 thermal-cycler (Thermo Fisher) at 42°C for 90 min and stopped by heating at 70°C for 5 min. Subsequently, 1.6 μl of PCR mix (1.67X KAPA HiFi HotStart ReadyMix (Kapa Biosystems, KK2602), 0.17 μM IS PCR primer (IDT, 5'-AAGCAGTGGTATCAACGCAGAGT-3'), and 0.038U/μl Lambda Exonuclease (NEB, M0262L)) was added to each well with a Tempest liquid handler (Formulatrix). The amplified product was diluted with a ratio of 1 part cDNA to 10 parts 10mM Tris-HCl (Thermo Fisher, 15568025), and concentrations were measured with dye-fluorescence assay (Quant-iT dsDNA High Sensitivity kit; Thermo Fisher, Q33120) on a SpectraMax i3x microplate reader (Molecular Devices). These wells were reformatted to a new 384-well plate at a concentration of 0.3 ng/μl and final volume of 0.4 μl using an Echo 550 acoustic liquid dispenser (Labcyte). If the cell concentration was below 0.3 ng/μl, 0.4 μl of sample was transferred. Illumina sequencing libraries were prepared using the Nextera XT Library Sample Preparation kit (Illumina, FC-131-1096) (Darmanis et al., 2015; Schaum et al., 2018). Each well was mixed with 0.8 μl Nextera tagmentation DNA buffer (Illumina) and 0.4 μl Tn5 enzyme (Illumina), then tagmented at 55°C for 10 min. The reaction was stopped by adding 0.4 μl \Neutralize Tagment Buffer\ (Illumina) and spinning at room temperature (RT) in a centrifuge at 3220 xg for 5 min. Indexing PCR reactions were performed by adding 0.4 μl of 5 μM i5 indexing primer, 0.4 μl of 5 μM i7 indexing primer, and 1.2 μl of Nextera NPM mix (Illumina). PCR amplification was carried out on a ProFlex 2x384 thermal cycler using the following program: 1. 72°C for 3 minutes, 2. 95°C for 30 s, 3. 12 cycles of 95°C for 10 s, 55°C for 30 s, and 72°C for 1 min, and 4. 72°C for 5 min.

text: adult

text: GFP-positive

text: Mus musculus

text: Mus musculus

text: spinal cord

text: Mus musculus

text: female

text: OK


text: Division of Cell and Developmental Biology, School of Life Sciences, University of Dundee

text: public

text: E-MTAB-115631647023157:I11-B001636-1_S191

text: ArrayExpress

text: ependymal cell

text: house mouse

characteristic: description

text: adult

characteristic: developmental stage

characteristic: genotype

text: GFP-positive

characteristic: individual

text: Mus musculus

text: Mus musculus

text: spinal cord

characteristic: organism part

text: Mus musculus

text: female

characteristic: sex

text: OK

characteristic: strain

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

text: public

text: E-MTAB-115631647023157:I12-B001633-1_S240

text: ArrayExpress

text: ependymal cell

text: house mouse

text: adult

text: GFP-positive

characteristic: immunophenotype

text: Mus musculus

characteristic: organism

text: Mus musculus

text: spinal cord

text: Mus musculus

text: female

text: OK

characteristic: single cell well quality


characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-115631647023157:I12-B001634-1_S24

characteristic: Submitter Id

characteristic: age

text: ArrayExpress

characteristic: broker name

text: ependymal cell

text: house mouse

characteristic: common name

text: adult

text: GFP-positive

text: Mus musculus

text: Mus musculus

text: spinal cord

text: Mus musculus

text: female

text: OK


text: public

text: E-MTAB-115631647023157:I12-B001635-1_S108

text: ArrayExpress

text: ependymal cell

text: house mouse

characteristic: description

text: adult

characteristic: developmental stage

characteristic: genotype

text: GFP-positive

characteristic: individual

text: Mus musculus

text: Mus musculus

text: spinal cord

characteristic: organism part

text: Mus musculus

text: female

characteristic: sex

text: OK

characteristic: strain

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

text: public

text: E-MTAB-115631647023157:I12-B001636-1_S192

text: ArrayExpress

text: ependymal cell

text: house mouse

text: adult

text: GFP-positive

characteristic: immunophenotype

text: Mus musculus

characteristic: organism

text: Mus musculus

text: spinal cord

text: Mus musculus

text: female

text: OK

characteristic: single cell well quality


characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-115631647023157:I13-B001633-1_S241

characteristic: Submitter Id

characteristic: age

text: ArrayExpress

characteristic: broker name

text: ependymal cell

text: house mouse

characteristic: common name

text: adult

text: GFP-positive

text: Mus musculus

text: Mus musculus

text: spinal cord

text: Mus musculus

text: female

text: OK


text: public

text: E-MTAB-115631647023157:I13-B001634-1_S25

text: ArrayExpress

text: ependymal cell

text: house mouse

characteristic: description

text: adult

characteristic: developmental stage

characteristic: genotype

text: GFP-positive

characteristic: individual

text: Mus musculus

text: Mus musculus

text: spinal cord

characteristic: organism part

text: Mus musculus

text: female

characteristic: sex

text: OK

characteristic: strain

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

text: public

text: E-MTAB-115631647023157:I13-B001635-1_S109

text: ArrayExpress

text: ependymal cell

text: house mouse

text: adult

text: GFP-positive

characteristic: immunophenotype

text: Mus musculus

characteristic: organism

text: Mus musculus

text: spinal cord

text: Mus musculus

text: female

text: OK

characteristic: single cell well quality


characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-115631647023157:I13-B001636-1_S193

characteristic: Submitter Id

characteristic: age

text: ArrayExpress

characteristic: broker name

text: ependymal cell

text: house mouse

characteristic: common name

text: adult

text: GFP-positive

text: Mus musculus

text: Mus musculus

text: spinal cord

text: Mus musculus

text: female

text: OK


text: public

text: E-MTAB-115631647023157:I14-B001633-1_S242

text: ArrayExpress

text: ependymal cell

text: house mouse

characteristic: description

text: adult

characteristic: developmental stage

characteristic: genotype

text: GFP-positive

characteristic: individual

text: Mus musculus

text: Mus musculus

text: spinal cord

characteristic: organism part

text: Mus musculus

text: female

characteristic: sex

text: OK

characteristic: strain

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

text: public

text: E-MTAB-115631647023157:I14-B001634-1_S26

text: ArrayExpress

text: ependymal cell

text: house mouse

text: adult

text: GFP-positive

characteristic: immunophenotype

text: Mus musculus

characteristic: organism

text: Mus musculus

text: spinal cord

text: Mus musculus

text: female

text: OK

characteristic: single cell well quality


characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-115631647023157:I14-B001635-1_S110

characteristic: Submitter Id

characteristic: age

text: ArrayExpress

characteristic: broker name

text: ependymal cell

text: house mouse

characteristic: common name

text: adult

text: GFP-positive

text: Mus musculus

text: Mus musculus

text: spinal cord

text: Mus musculus

text: female

text: OK


text: public

text: E-MTAB-115631647023157:I14-B001636-1_S194

text: ArrayExpress

text: ependymal cell

text: house mouse

characteristic: description

text: adult

characteristic: developmental stage

characteristic: genotype

text: GFP-positive

characteristic: individual

text: Mus musculus

text: Mus musculus

text: spinal cord

characteristic: organism part

text: Mus musculus

text: female

characteristic: sex

text: OK

characteristic: strain

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

text: public

text: E-MTAB-115631647023157:I15-B001633-1_S243

text: ArrayExpress

text: ependymal cell

text: house mouse

text: adult

text: GFP-positive

characteristic: immunophenotype

text: Mus musculus

characteristic: organism

text: Mus musculus

text: spinal cord

text: Mus musculus

text: female

text: OK

characteristic: single cell well quality


characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-115631647023157:I15-B001634-1_S27

characteristic: Submitter Id

characteristic: age

text: ArrayExpress

characteristic: broker name

text: ependymal cell

text: house mouse

characteristic: common name

text: adult

text: GFP-positive

text: Mus musculus

text: Mus musculus

text: spinal cord

text: Mus musculus

text: female

text: OK


text: public

text: E-MTAB-115631647023157:I15-B001635-1_S111

text: ArrayExpress

text: ependymal cell

text: house mouse

text: Protocols: The ependymal cell layer from the thoracic spinal cord of FOXJ1-EGFP mice was microdissected and dissociated it into a cell suspension. GFP-positive DAPI-negative cells were then sorted into 384-well plates containing lysis buffer. GFP-positive DAPI-negative cells were sorted into lysis plates with a BD Influx Cell Sorter using 6 psi pressure and a 130 μm nozzle. Lysis plates were created by dispensing 0.4 μl lysis buffer (0.5 U Recombinant RNase Inhibitor (Takara Bio, 2313B), 0.0625% Triton X-100 (Sigma, 93443-100ML), 3.125 mM dNTP mix (Thermo Fisher, R0193), 3.125 μM Oligo-dT 30 VN (IDT, 5'AAGCAGTGGTATCAACGCAGAGTACT 30 VN-3') and 1:600,000 ERCC RNA spike-in mix (Thermo Fisher, 4456740)) into 384-well hard-shell PCR plates (Biorad HSP3901) using a Tempest liquid handler (Formulatrix). cDNA synthesis was performed using the Smart-seq2 protocol (Picelli et al., 2013, 2014). Briefly, 384-well plates containing single-cell lysates were thawed on ice followed by first strand synthesis. 0.6 μl of reaction mix (16.7 U/μl SMARTScribe TM Reverse Transcriptase (Takara Bio, 639538), 1.67 U/μl Recombinant RNase Inhibitor (Takara Bio, 2313B), 1.67X First-Strand Buffer (Takara Bio, 639538), 1.67 μM TSO (Exiqon, 5'-AAGCAGTGGTATCAACGCAGACTACATrGrG+G-3'), 8.33 mM DTT (Bioworld, 40420001-1), 1.67 M Betaine (Sigma, B0300-5VL), and 10 mM MgCl 2 (Sigma, M1028-10X1ML)) was added to each well using a Tempest liquid handler. Bulk wells received twice the amount of RT mix (1.2 μl). Reverse transcription was carried out by incubating wells on a ProFlex 2x384 thermal-cycler (Thermo Fisher) at 42°C for 90 min and stopped by heating at 70°C for 5 min. Subsequently, 1.6 μl of PCR mix (1.67X KAPA HiFi HotStart ReadyMix (Kapa Biosystems, KK2602), 0.17 μM IS PCR primer (IDT, 5'-AAGCAGTGGTATCAACGCAGAGT-3'), and 0.038U/μl Lambda Exonuclease (NEB, M0262L)) was added to each well with a Tempest liquid handler (Formulatrix). The amplified product was diluted with a ratio of 1 part cDNA to 10 parts 10mM Tris-HCl (Thermo Fisher, 15568025), and concentrations were measured with dye-fluorescence assay (Quant-iT dsDNA High Sensitivity kit; Thermo Fisher, Q33120) on a SpectraMax i3x microplate reader (Molecular Devices). These wells were reformatted to a new 384-well plate at a concentration of 0.3 ng/μl and final volume of 0.4 μl using an Echo 550 acoustic liquid dispenser (Labcyte). If the cell concentration was below 0.3 ng/μl, 0.4 μl of sample was transferred. Illumina sequencing libraries were prepared using the Nextera XT Library Sample Preparation kit (Illumina, FC-131-1096) (Darmanis et al., 2015; Schaum et al., 2018). Each well was mixed with 0.8 μl Nextera tagmentation DNA buffer (Illumina) and 0.4 μl Tn5 enzyme (Illumina), then tagmented at 55°C for 10 min. The reaction was stopped by adding 0.4 μl \Neutralize Tagment Buffer\ (Illumina) and spinning at room temperature (RT) in a centrifuge at 3220 xg for 5 min. Indexing PCR reactions were performed by adding 0.4 μl of 5 μM i5 indexing primer, 0.4 μl of 5 μM i7 indexing primer, and 1.2 μl of Nextera NPM mix (Illumina). PCR amplification was carried out on a ProFlex 2x384 thermal cycler using the following program: 1. 72°C for 3 minutes, 2. 95°C for 30 s, 3. 12 cycles of 95°C for 10 s, 55°C for 30 s, and 72°C for 1 min, and 4. 72°C for 5 min.

characteristic: description

text: adult

characteristic: developmental stage

characteristic: genotype

text: GFP-positive

characteristic: individual

text: Mus musculus

text: Mus musculus

text: spinal cord

characteristic: organism part

text: Mus musculus

text: female

characteristic: sex

text: OK

characteristic: strain

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Division of Cell and Developmental Biology, School of Life Sciences, University of Dundee

characteristic: INSDC center name

text: public

text: E-MTAB-115631647023157:I15-B001636-1_S195

text: ArrayExpress

text: ependymal cell

text: house mouse

text: adult

text: GFP-positive

characteristic: immunophenotype

text: Mus musculus

characteristic: organism

text: Mus musculus

text: spinal cord

text: Mus musculus

text: female

text: OK

characteristic: single cell well quality


characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-115631647023157:I16-B001633-1_S244

characteristic: Submitter Id

characteristic: age

text: ArrayExpress

characteristic: broker name

text: ependymal cell

text: house mouse

characteristic: common name

text: adult

text: GFP-positive

text: Mus musculus

text: Mus musculus

text: spinal cord

text: Mus musculus

text: female

text: OK


text: public

text: E-MTAB-115631647023157:I16-B001634-1_S28

text: ArrayExpress

text: ependymal cell

text: house mouse

characteristic: description

text: adult

characteristic: developmental stage

characteristic: genotype

text: GFP-positive

characteristic: individual

text: Mus musculus

text: Mus musculus

text: spinal cord

characteristic: organism part

text: Mus musculus

text: female

characteristic: sex

text: OK

characteristic: strain

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

text: public

text: E-MTAB-115631647023157:I16-B001635-1_S112

text: ArrayExpress

text: ependymal cell

text: house mouse

text: adult

text: GFP-positive

characteristic: immunophenotype

text: Mus musculus

characteristic: organism

text: Mus musculus

text: spinal cord

text: Mus musculus

text: female

text: OK

characteristic: single cell well quality


characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-115631647023157:I16-B001636-1_S196

characteristic: Submitter Id

characteristic: age

text: ArrayExpress

characteristic: broker name

text: ependymal cell

text: house mouse

characteristic: common name

text: adult

text: GFP-positive

text: Mus musculus

text: Mus musculus

text: spinal cord

text: Mus musculus

text: female

text: OK


text: public

text: E-MTAB-115631647023157:I17-B001633-1_S245

text: ArrayExpress

text: ependymal cell

text: house mouse

characteristic: description

text: adult

characteristic: developmental stage

characteristic: genotype

text: GFP-positive

characteristic: individual

text: Mus musculus

text: Mus musculus

text: spinal cord

characteristic: organism part

text: Mus musculus

text: female

characteristic: sex

text: OK

characteristic: strain

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

text: public

text: E-MTAB-115631647023157:I17-B001634-1_S29

text: ArrayExpress

text: ependymal cell

text: house mouse

text: adult

text: GFP-positive

characteristic: immunophenotype

text: Mus musculus

characteristic: organism

text: Mus musculus

text: spinal cord

text: Mus musculus

text: female

text: OK

characteristic: single cell well quality


characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-115631647023157:I17-B001635-1_S113

characteristic: Submitter Id

characteristic: age

text: ArrayExpress

characteristic: broker name

text: ependymal cell

text: house mouse

characteristic: common name

text: adult

text: GFP-positive

text: Mus musculus

text: Mus musculus

text: spinal cord

text: Mus musculus

text: female

text: OK


text: public

text: E-MTAB-115631647023157:I17-B001636-1_S197

text: ArrayExpress

text: ependymal cell

text: house mouse

characteristic: description

text: adult

characteristic: developmental stage

characteristic: genotype

text: GFP-positive

characteristic: individual

text: Mus musculus

text: Mus musculus

text: spinal cord

characteristic: organism part

text: Mus musculus

text: female

characteristic: sex

text: OK

characteristic: strain

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

text: public

text: E-MTAB-115631647023157:I18-B001633-1_S246

text: ArrayExpress

text: ependymal cell

text: house mouse

text: adult

text: GFP-positive

characteristic: immunophenotype

text: Mus musculus

characteristic: organism

text: Mus musculus

text: spinal cord

text: Mus musculus

text: female

text: OK

characteristic: single cell well quality


characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-115631647023157:I18-B001634-1_S30

characteristic: Submitter Id

characteristic: age

text: ArrayExpress

characteristic: broker name

text: ependymal cell

text: house mouse

characteristic: common name

text: adult

text: GFP-positive

text: Mus musculus

text: Mus musculus

text: spinal cord

text: Mus musculus

text: female

text: OK


text: public

text: E-MTAB-115631647023157:I18-B001635-1_S114

text: ArrayExpress

text: ependymal cell

text: house mouse

characteristic: description

text: adult

characteristic: developmental stage

characteristic: genotype

text: GFP-positive

characteristic: individual

text: Mus musculus

text: Mus musculus

text: spinal cord

characteristic: organism part

text: Mus musculus

text: female

characteristic: sex

text: OK

characteristic: strain

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

text: public

text: E-MTAB-115631647023157:I18-B001636-1_S198

text: ArrayExpress

text: ependymal cell

text: house mouse

text: adult

text: GFP-positive

characteristic: immunophenotype

text: Mus musculus

characteristic: organism

text: Mus musculus

text: spinal cord

text: Mus musculus

text: female

text: OK

characteristic: single cell well quality


characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-115631647023157:I19-B001633-1_S247

characteristic: Submitter Id

characteristic: age

text: ArrayExpress

characteristic: broker name

text: ependymal cell

text: house mouse

characteristic: common name

text: adult

text: GFP-positive

text: Mus musculus

text: Mus musculus

text: spinal cord

text: Mus musculus

text: female

text: OK


text: public

text: E-MTAB-115631647023157:I19-B001634-1_S31

text: ArrayExpress

text: ependymal cell

text: house mouse

characteristic: description

text: adult

characteristic: developmental stage

characteristic: genotype

text: GFP-positive

characteristic: individual

text: Mus musculus

text: Mus musculus

text: spinal cord

characteristic: organism part

text: Mus musculus

text: female

characteristic: sex

text: OK

characteristic: strain

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

text: public

text: E-MTAB-115631647023157:I19-B001635-1_S115

text: ArrayExpress

text: ependymal cell

text: house mouse

text: Protocols: The ependymal cell layer from the thoracic spinal cord of FOXJ1-EGFP mice was microdissected and dissociated it into a cell suspension. GFP-positive DAPI-negative cells were then sorted into 384-well plates containing lysis buffer. GFP-positive DAPI-negative cells were sorted into lysis plates with a BD Influx Cell Sorter using 6 psi pressure and a 130 μm nozzle. Lysis plates were created by dispensing 0.4 μl lysis buffer (0.5 U Recombinant RNase Inhibitor (Takara Bio, 2313B), 0.0625% Triton X-100 (Sigma, 93443-100ML), 3.125 mM dNTP mix (Thermo Fisher, R0193), 3.125 μM Oligo-dT 30 VN (IDT, 5'AAGCAGTGGTATCAACGCAGAGTACT 30 VN-3') and 1:600,000 ERCC RNA spike-in mix (Thermo Fisher, 4456740)) into 384-well hard-shell PCR plates (Biorad HSP3901) using a Tempest liquid handler (Formulatrix). cDNA synthesis was performed using the Smart-seq2 protocol (Picelli et al., 2013, 2014). Briefly, 384-well plates containing single-cell lysates were thawed on ice followed by first strand synthesis. 0.6 μl of reaction mix (16.7 U/μl SMARTScribe TM Reverse Transcriptase (Takara Bio, 639538), 1.67 U/μl Recombinant RNase Inhibitor (Takara Bio, 2313B), 1.67X First-Strand Buffer (Takara Bio, 639538), 1.67 μM TSO (Exiqon, 5'-AAGCAGTGGTATCAACGCAGACTACATrGrG+G-3'), 8.33 mM DTT (Bioworld, 40420001-1), 1.67 M Betaine (Sigma, B0300-5VL), and 10 mM MgCl 2 (Sigma, M1028-10X1ML)) was added to each well using a Tempest liquid handler. Bulk wells received twice the amount of RT mix (1.2 μl). Reverse transcription was carried out by incubating wells on a ProFlex 2x384 thermal-cycler (Thermo Fisher) at 42°C for 90 min and stopped by heating at 70°C for 5 min. Subsequently, 1.6 μl of PCR mix (1.67X KAPA HiFi HotStart ReadyMix (Kapa Biosystems, KK2602), 0.17 μM IS PCR primer (IDT, 5'-AAGCAGTGGTATCAACGCAGAGT-3'), and 0.038U/μl Lambda Exonuclease (NEB, M0262L)) was added to each well with a Tempest liquid handler (Formulatrix). The amplified product was diluted with a ratio of 1 part cDNA to 10 parts 10mM Tris-HCl (Thermo Fisher, 15568025), and concentrations were measured with dye-fluorescence assay (Quant-iT dsDNA High Sensitivity kit; Thermo Fisher, Q33120) on a SpectraMax i3x microplate reader (Molecular Devices). These wells were reformatted to a new 384-well plate at a concentration of 0.3 ng/μl and final volume of 0.4 μl using an Echo 550 acoustic liquid dispenser (Labcyte). If the cell concentration was below 0.3 ng/μl, 0.4 μl of sample was transferred. Illumina sequencing libraries were prepared using the Nextera XT Library Sample Preparation kit (Illumina, FC-131-1096) (Darmanis et al., 2015; Schaum et al., 2018). Each well was mixed with 0.8 μl Nextera tagmentation DNA buffer (Illumina) and 0.4 μl Tn5 enzyme (Illumina), then tagmented at 55°C for 10 min. The reaction was stopped by adding 0.4 μl \Neutralize Tagment Buffer\ (Illumina) and spinning at room temperature (RT) in a centrifuge at 3220 xg for 5 min. Indexing PCR reactions were performed by adding 0.4 μl of 5 μM i5 indexing primer, 0.4 μl of 5 μM i7 indexing primer, and 1.2 μl of Nextera NPM mix (Illumina). PCR amplification was carried out on a ProFlex 2x384 thermal cycler using the following program: 1. 72°C for 3 minutes, 2. 95°C for 30 s, 3. 12 cycles of 95°C for 10 s, 55°C for 30 s, and 72°C for 1 min, and 4. 72°C for 5 min.

text: adult

text: GFP-positive

characteristic: immunophenotype

text: Mus musculus

characteristic: organism

text: Mus musculus

text: spinal cord

text: Mus musculus

text: female

text: OK

characteristic: single cell well quality


text: Division of Cell and Developmental Biology, School of Life Sciences, University of Dundee

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-115631647023157:I19-B001636-1_S199

characteristic: Submitter Id

characteristic: age

text: ArrayExpress

characteristic: broker name

text: ependymal cell

text: house mouse

characteristic: common name

text: adult

text: GFP-positive

text: Mus musculus

text: Mus musculus

text: spinal cord

text: Mus musculus

text: female

text: OK


text: public

text: E-MTAB-115631647023157:I2-B001633-1_S230

text: ArrayExpress

text: ependymal cell

text: house mouse

characteristic: description

text: adult

characteristic: developmental stage

characteristic: genotype

text: GFP-positive

characteristic: individual

text: Mus musculus

text: Mus musculus

text: spinal cord

characteristic: organism part

text: Mus musculus

text: female

characteristic: sex

text: OK

characteristic: strain

characteristic: title