characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

text: public

text: E-MTAB-115631647023036:F16-B001636-1_S124

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


status: PUBLIC

tag: attribute

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-115631647023036:F17-B001633-1_S173

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

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:F17-B001634-1_S257

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:F17-B001635-1_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:F17-B001636-1_S125

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:F18-B001633-1_S174

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:F18-B001634-1_S258

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:F18-B001635-1_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:F18-B001636-1_S126

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:F19-B001633-1_S175

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:F19-B001634-1_S259

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:F19-B001635-1_S43

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:F19-B001636-1_S127

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:F2-B001633-1_S158

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:F2-B001634-1_S242

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:F2-B001636-1_S110

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:F20-B001633-1_S176

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:F20-B001634-1_S260

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:F20-B001635-1_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-115631647023036:F20-B001636-1_S128

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:F21-B001633-1_S177

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:F21-B001634-1_S261

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:F21-B001635-1_S45

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:F21-B001636-1_S129

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:F22-B001633-1_S178

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:F22-B001634-1_S262

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:F22-B001635-1_S46

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:F22-B001636-1_S130

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:F23-B001633-1_S179

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:F23-B001634-1_S263

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:F23-B001635-1_S47

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:F23-B001636-1_S131

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:F24-B001633-1_S33

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:F24-B001634-1_S34

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:F24-B001635-1_S35

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:F3-B001633-1_S159

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:F3-B001634-1_S243

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:F3-B001636-1_S111

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:F4-B001633-1_S160

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:F4-B001634-1_S244

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:F4-B001636-1_S112

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:F5-B001633-1_S161

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:F5-B001634-1_S245

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:F5-B001636-1_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-115631647023036:F6-B001633-1_S162

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:F6-B001634-1_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-115631647023036:F6-B001636-1_S114

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:F7-B001633-1_S163

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:F7-B001634-1_S247

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:F7-B001636-1_S115

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:F8-B001633-1_S164

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:F8-B001634-1_S248

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:F8-B001636-1_S116

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:F9-B001633-1_S165

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:F9-B001634-1_S249

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:F9-B001636-1_S117

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:G1-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:G1-B001634-1_S265

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:G1-B001636-1_S133

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:G10-B001633-1_S190

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:G10-B001634-1_S274

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:G10-B001635-1_S58

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:G10-B001636-1_S142

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:G11-B001633-1_S191

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:G11-B001634-1_S275

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:G11-B001635-1_S59

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:G11-B001636-1_S143

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:G12-B001633-1_S192

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:G12-B001634-1_S276

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:G12-B001635-1_S60

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:G12-B001636-1_S144

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:G13-B001633-1_S193

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:G13-B001634-1_S277

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:G13-B001635-1_S61

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:G13-B001636-1_S145

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:G14-B001633-1_S194

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:G14-B001634-1_S278

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:G14-B001635-1_S62

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:G14-B001636-1_S146

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:G15-B001633-1_S195

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:G15-B001634-1_S279

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:G15-B001635-1_S63

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:G15-B001636-1_S147

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:G16-B001633-1_S196

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:G16-B001634-1_S280

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:G16-B001635-1_S64

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:G16-B001636-1_S148

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:G17-B001633-1_S197

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:G17-B001634-1_S281

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:G17-B001635-1_S65

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:G17-B001636-1_S149

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:G18-B001633-1_S198

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:G18-B001634-1_S282

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:G18-B001635-1_S66

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:G18-B001636-1_S150

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:G19-B001633-1_S199

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:G19-B001634-1_S283

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:G19-B001635-1_S67

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:G19-B001636-1_S151

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:G2-B001633-1_S182

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:G2-B001634-1_S266

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:G2-B001636-1_S134

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:G20-B001633-1_S200

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:G20-B001635-1_S68

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:G20-B001636-1_S152

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:G21-B001633-1_S201

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:G21-B001635-1_S69

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:G21-B001636-1_S153

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:G22-B001633-1_S202

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:G22-B001634-1_S286

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:G22-B001635-1_S70

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:G22-B001636-1_S154

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:G23-B001633-1_S203

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:G23-B001635-1_S71

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:G23-B001636-1_S155

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:G24-B001633-1_S37

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:G24-B001634-1_S38

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:G24-B001635-1_S39

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:G24-B001636-1_S40

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:G3-B001633-1_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:G3-B001634-1_S267

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:G3-B001636-1_S135

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:G4-B001633-1_S184

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:G4-B001634-1_S268

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:G4-B001636-1_S136

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:G5-B001633-1_S185

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:G5-B001634-1_S269

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:G5-B001636-1_S137

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:G6-B001633-1_S186

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:G6-B001634-1_S270

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:G6-B001636-1_S138

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:G7-B001633-1_S187

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