rowid,run.accession,experiment.accession,sample.accession,study.accession,bioproject,study.title,study.alias,study.type,study.abstract,study.attributes,study.PMIDs,sample.description,sample.title,sample.alias,sample.centername,sample.attributes,GEOsample.title,GEOsample.dataprocessing,GEOsample.source,GEOsample.treatmentprotocol,GEOsample.extractprotocol,GEOsample.growthprotocol,GEOsample.characteristics,GEOsample.accession,experiment.title,experiment.alias,experiment.library_name,experiment.design_description,experiment.library_construction_protocol,experiment.attributes,experiment.library_strategy,experiment.library_source,experiment.library_selection,experiment.library_layout,experiment.platform,experiment.instrument_model,experiment.spot_descriptor,experiment.study_ref,run.title,run.attributes,run.filename,run.semantic_name,run.total_bases,run.total_spots,run.alias,run.read_lengths,run.base_counts,run.r1_length,run.r2_length,run.r3_length,run.r4_length,run.Acount,run.Ccount,run.Gcount,run.Tcount,run.Ncount,run.experiment,run.pool_member,submission.accession,submission.srasource,submission.bioprojectsource,seqdetective.n_mates,seqdetective.mapping_rate.mate1,seqdetective.mapping_rate.mate2,seqdetective.nofeature_rate.mate1,seqdetective.nofeature_rate.mate2,seqdetective.sparsity.mate1,seqdetective.sparsity.mate2,seqdetective.pos_strand_rate.mate1,seqdetective.pos_strand_rate.mate2,seqdetective.readlen.mate1,seqdetective.readlen.mate2,seqdetective.judgement.mate1,seqdetective.judgement.mate2,seqdetective.judgement.reason,platform_family,instrument_generation,read_bias,selection_class,prep_kit,sc_or_bulk,tech_class,technology,tech_variant,submission.bioprojectsource.country,earliest_date,devstage_curation,devstage_curation_coarse,tissue_curation,tissue_curation_coarse
26558,SRR26173859,SRX21885960,SRS18977085,SRP463130,PRJNA1020854,Molecular blueprints for spinal circuit modules controlling locomotor speed,GSE243993,Transcriptome Analysis,The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.,,pubmed:37919423,,V2a sample2 354 F17 R1,GSM7804200,,source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing,V2a sample2 354 F17 R1,The reads from each sequenced cell were mapped to the zebrafish reference genome “Danio rerio  Ensembl  GRCz11” using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis,Spinal cord,,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons,GSM7804200,GSM7804200: V2a sample2 354 F17 R1; Danio rerio; RNA Seq,GSM7804200 r1,GSM7804200,1,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP463130,,,SS2_18_354_F17_R1.fastq.gz,fastq,26979490.0,627430.0,GSM7804200 r1,0:43,A:7493119;C:5872644;G:6013311;T:7600416;N:0,43,,,,7493119,5872644,6013311,7600416,0,SRX21885960,SRS18977085,SRA1719948,"Neuroscience, Karolinaska Institutet","Neuroscience, Karolinaska Institutet",1,0.82979,,0.33034,,0.94253,,0.53995,,43,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Sweden,2023-09-25,Juvenile,Juvenile,Spinal Cord,Nervous System
26559,SRR26173860,SRX21885959,SRS18977083,SRP463130,PRJNA1020854,Molecular blueprints for spinal circuit modules controlling locomotor speed,GSE243993,Transcriptome Analysis,The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.,,pubmed:37919423,,V2a sample2 354 F16 R1,GSM7804199,,source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing,V2a sample2 354 F16 R1,The reads from each sequenced cell were mapped to the zebrafish reference genome “Danio rerio  Ensembl  GRCz11” using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis,Spinal cord,,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons,GSM7804199,GSM7804199: V2a sample2 354 F16 R1; Danio rerio; RNA Seq,GSM7804199 r1,GSM7804199,1,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP463130,,,SS2_18_354_F16_R1.fastq.gz,fastq,26312130.0,611910.0,GSM7804199 r1,0:43,A:7117249;C:5957278;G:6103577;T:7134026;N:0,43,,,,7117249,5957278,6103577,7134026,0,SRX21885959,SRS18977083,SRA1719948,"Neuroscience, Karolinaska Institutet","Neuroscience, Karolinaska Institutet",1,0.87071,,0.23579,,0.90678,,0.52226,,43,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Sweden,2023-09-25,Juvenile,Juvenile,Spinal Cord,Nervous System
26560,SRR26173861,SRX21885958,SRS18977084,SRP463130,PRJNA1020854,Molecular blueprints for spinal circuit modules controlling locomotor speed,GSE243993,Transcriptome Analysis,The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.,,pubmed:37919423,,V2a sample2 354 F15 R1,GSM7804198,,source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing,V2a sample2 354 F15 R1,The reads from each sequenced cell were mapped to the zebrafish reference genome “Danio rerio  Ensembl  GRCz11” using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis,Spinal cord,,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons,GSM7804198,GSM7804198: V2a sample2 354 F15 R1; Danio rerio; RNA Seq,GSM7804198 r1,GSM7804198,1,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP463130,,,SS2_18_354_F15_R1.fastq.gz,fastq,32073872.0,745904.0,GSM7804198 r1,0:43,A:8695962;C:7255833;G:7422516;T:8699561;N:0,43,,,,8695962,7255833,7422516,8699561,0,SRX21885958,SRS18977084,SRA1719948,"Neuroscience, Karolinaska Institutet","Neuroscience, Karolinaska Institutet",1,0.86262,,0.24391,,0.90881,,0.52511,,43,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Sweden,2023-09-25,Juvenile,Juvenile,Spinal Cord,Nervous System
26561,SRR26173862,SRX21885957,SRS18977081,SRP463130,PRJNA1020854,Molecular blueprints for spinal circuit modules controlling locomotor speed,GSE243993,Transcriptome Analysis,The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.,,pubmed:37919423,,V2a sample2 354 F14 R1,GSM7804197,,source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing,V2a sample2 354 F14 R1,The reads from each sequenced cell were mapped to the zebrafish reference genome “Danio rerio  Ensembl  GRCz11” using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis,Spinal cord,,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons,GSM7804197,GSM7804197: V2a sample2 354 F14 R1; Danio rerio; RNA Seq,GSM7804197 r1,GSM7804197,1,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP463130,,,SS2_18_354_F14_R1.fastq.gz,fastq,31158875.0,724625.0,GSM7804197 r1,0:43,A:8769852;C:6707813;G:6866255;T:8814955;N:0,43,,,,8769852,6707813,6866255,8814955,0,SRX21885957,SRS18977081,SRA1719948,"Neuroscience, Karolinaska Institutet","Neuroscience, Karolinaska Institutet",1,0.8739,,0.27254,,0.9246,,0.54185,,43,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Sweden,2023-09-25,Juvenile,Juvenile,Spinal Cord,Nervous System
26562,SRR26173863,SRX21885956,SRS18977082,SRP463130,PRJNA1020854,Molecular blueprints for spinal circuit modules controlling locomotor speed,GSE243993,Transcriptome Analysis,The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.,,pubmed:37919423,,V2a sample2 354 F13 R1,GSM7804196,,source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing,V2a sample2 354 F13 R1,The reads from each sequenced cell were mapped to the zebrafish reference genome “Danio rerio  Ensembl  GRCz11” using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis,Spinal cord,,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons,GSM7804196,GSM7804196: V2a sample2 354 F13 R1; Danio rerio; RNA Seq,GSM7804196 r1,GSM7804196,1,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP463130,,,SS2_18_354_F13_R1.fastq.gz,fastq,41289804.0,960228.0,GSM7804196 r1,0:43,A:11114918;C:9358398;G:9568761;T:11247727;N:0,43,,,,11114918,9358398,9568761,11247727,0,SRX21885956,SRS18977082,SRA1719948,"Neuroscience, Karolinaska Institutet","Neuroscience, Karolinaska Institutet",1,0.82861,,0.29409,,0.93235,,0.49485,,43,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Sweden,2023-09-25,Juvenile,Juvenile,Spinal Cord,Nervous System
26563,SRR26173864,SRX21885955,SRS18977079,SRP463130,PRJNA1020854,Molecular blueprints for spinal circuit modules controlling locomotor speed,GSE243993,Transcriptome Analysis,The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.,,pubmed:37919423,,V2a sample2 354 F12 R1,GSM7804195,,source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing,V2a sample2 354 F12 R1,The reads from each sequenced cell were mapped to the zebrafish reference genome “Danio rerio  Ensembl  GRCz11” using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis,Spinal cord,,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons,GSM7804195,GSM7804195: V2a sample2 354 F12 R1; Danio rerio; RNA Seq,GSM7804195 r1,GSM7804195,1,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP463130,,,SS2_18_354_F12_R1.fastq.gz,fastq,30569259.0,710913.0,GSM7804195 r1,0:43,A:8286806;C:6854804;G:7028453;T:8399196;N:0,43,,,,8286806,6854804,7028453,8399196,0,SRX21885955,SRS18977079,SRA1719948,"Neuroscience, Karolinaska Institutet","Neuroscience, Karolinaska Institutet",1,0.80426,,0.29136,,0.94123,,0.54305,,43,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Sweden,2023-09-25,Juvenile,Juvenile,Spinal Cord,Nervous System
26564,SRR26173865,SRX21885954,SRS18977080,SRP463130,PRJNA1020854,Molecular blueprints for spinal circuit modules controlling locomotor speed,GSE243993,Transcriptome Analysis,The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.,,pubmed:37919423,,V2a sample2 354 F11 R1,GSM7804194,,source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing,V2a sample2 354 F11 R1,The reads from each sequenced cell were mapped to the zebrafish reference genome “Danio rerio  Ensembl  GRCz11” using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis,Spinal cord,,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons,GSM7804194,GSM7804194: V2a sample2 354 F11 R1; Danio rerio; RNA Seq,GSM7804194 r1,GSM7804194,1,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP463130,,,SS2_18_354_F11_R1.fastq.gz,fastq,29626097.0,688979.0,GSM7804194 r1,0:43,A:8063765;C:6645347;G:6803778;T:8113207;N:0,43,,,,8063765,6645347,6803778,8113207,0,SRX21885954,SRS18977080,SRA1719948,"Neuroscience, Karolinaska Institutet","Neuroscience, Karolinaska Institutet",1,0.84972,,0.26423,,0.9234,,0.54087,,43,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Sweden,2023-09-25,Juvenile,Juvenile,Spinal Cord,Nervous System
26565,SRR26173866,SRX21885953,SRS18977078,SRP463130,PRJNA1020854,Molecular blueprints for spinal circuit modules controlling locomotor speed,GSE243993,Transcriptome Analysis,The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.,,pubmed:37919423,,V2a sample2 354 F10 R1,GSM7804193,,source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing,V2a sample2 354 F10 R1,The reads from each sequenced cell were mapped to the zebrafish reference genome “Danio rerio  Ensembl  GRCz11” using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis,Spinal cord,,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons,GSM7804193,GSM7804193: V2a sample2 354 F10 R1; Danio rerio; RNA Seq,GSM7804193 r1,GSM7804193,1,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP463130,,,SS2_18_354_F10_R1.fastq.gz,fastq,24594409.0,571963.0,GSM7804193 r1,0:43,A:6605642;C:5535165;G:5682586;T:6771016;N:0,43,,,,6605642,5535165,5682586,6771016,0,SRX21885953,SRS18977078,SRA1719948,"Neuroscience, Karolinaska Institutet","Neuroscience, Karolinaska Institutet",1,0.77683,,0.28872,,0.94633,,0.52513,,43,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Sweden,2023-09-25,Juvenile,Juvenile,Spinal Cord,Nervous System
26566,SRR26173867,SRX21885952,SRS18977077,SRP463130,PRJNA1020854,Molecular blueprints for spinal circuit modules controlling locomotor speed,GSE243993,Transcriptome Analysis,The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.,,pubmed:37919423,,V2a sample2 354 E9 R1,GSM7804168,,source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing,V2a sample2 354 E9 R1,The reads from each sequenced cell were mapped to the zebrafish reference genome “Danio rerio  Ensembl  GRCz11” using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis,Spinal cord,,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons,GSM7804168,GSM7804168: V2a sample2 354 E9 R1; Danio rerio; RNA Seq,GSM7804168 r1,GSM7804168,1,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP463130,,,SS2_18_354_E9_R1.fastq.gz,fastq,33259941.0,773487.0,GSM7804168 r1,0:43,A:9004615;C:7506729;G:7674909;T:9073688;N:0,43,,,,9004615,7506729,7674909,9073688,0,SRX21885952,SRS18977077,SRA1719948,"Neuroscience, Karolinaska Institutet","Neuroscience, Karolinaska Institutet",1,0.85528,,0.32094,,0.89217,,0.50224,,43,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Sweden,2023-09-25,Juvenile,Juvenile,Spinal Cord,Nervous System
26567,SRR26173868,SRX21885951,SRS18977076,SRP463130,PRJNA1020854,Molecular blueprints for spinal circuit modules controlling locomotor speed,GSE243993,Transcriptome Analysis,The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.,,pubmed:37919423,,V2a sample2 354 E8 R1,GSM7804167,,source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing,V2a sample2 354 E8 R1,The reads from each sequenced cell were mapped to the zebrafish reference genome “Danio rerio  Ensembl  GRCz11” using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis,Spinal cord,,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons,GSM7804167,GSM7804167: V2a sample2 354 E8 R1; Danio rerio; RNA Seq,GSM7804167 r1,GSM7804167,1,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP463130,,,SS2_18_354_E8_R1.fastq.gz,fastq,45348316.0,1054612.0,GSM7804167 r1,0:43,A:12143243;C:10459395;G:10612458;T:12133220;N:0,43,,,,12143243,10459395,10612458,12133220,0,SRX21885951,SRS18977076,SRA1719948,"Neuroscience, Karolinaska Institutet","Neuroscience, Karolinaska Institutet",1,0.8783,,0.19318,,0.88572,,0.49101,,43,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Sweden,2023-09-25,Juvenile,Juvenile,Spinal Cord,Nervous System
26568,SRR26173869,SRX21885950,SRS18977075,SRP463130,PRJNA1020854,Molecular blueprints for spinal circuit modules controlling locomotor speed,GSE243993,Transcriptome Analysis,The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.,,pubmed:37919423,,V2a sample2 354 E7 R1,GSM7804166,,source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing,V2a sample2 354 E7 R1,The reads from each sequenced cell were mapped to the zebrafish reference genome “Danio rerio  Ensembl  GRCz11” using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis,Spinal cord,,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons,GSM7804166,GSM7804166: V2a sample2 354 E7 R1; Danio rerio; RNA Seq,GSM7804166 r1,GSM7804166,1,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP463130,,,SS2_18_354_E7_R1.fastq.gz,fastq,30522002.0,709814.0,GSM7804166 r1,0:43,A:8167984;C:7033955;G:7127866;T:8192197;N:0,43,,,,8167984,7033955,7127866,8192197,0,SRX21885950,SRS18977075,SRA1719948,"Neuroscience, Karolinaska Institutet","Neuroscience, Karolinaska Institutet",1,0.87804,,0.20762,,0.88418,,0.51381,,43,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Sweden,2023-09-25,Juvenile,Juvenile,Spinal Cord,Nervous System
26569,SRR26173870,SRX21885949,SRS18977074,SRP463130,PRJNA1020854,Molecular blueprints for spinal circuit modules controlling locomotor speed,GSE243993,Transcriptome Analysis,The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.,,pubmed:37919423,,V2a sample2 354 E6 R1,GSM7804165,,source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing,V2a sample2 354 E6 R1,The reads from each sequenced cell were mapped to the zebrafish reference genome “Danio rerio  Ensembl  GRCz11” using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis,Spinal cord,,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons,GSM7804165,GSM7804165: V2a sample2 354 E6 R1; Danio rerio; RNA Seq,GSM7804165 r1,GSM7804165,1,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP463130,,,SS2_18_354_E6_R1.fastq.gz,fastq,39095858.0,909206.0,GSM7804165 r1,0:43,A:10597068;C:8804712;G:8974908;T:10719170;N:0,43,,,,10597068,8804712,8974908,10719170,0,SRX21885949,SRS18977074,SRA1719948,"Neuroscience, Karolinaska Institutet","Neuroscience, Karolinaska Institutet",1,0.8093,,0.38297,,0.91545,,0.56195,,43,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Sweden,2023-09-25,Juvenile,Juvenile,Spinal Cord,Nervous System
26570,SRR26173871,SRX21885948,SRS18977073,SRP463130,PRJNA1020854,Molecular blueprints for spinal circuit modules controlling locomotor speed,GSE243993,Transcriptome Analysis,The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.,,pubmed:37919423,,V2a sample2 354 E5 R1,GSM7804164,,source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing,V2a sample2 354 E5 R1,The reads from each sequenced cell were mapped to the zebrafish reference genome “Danio rerio  Ensembl  GRCz11” using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis,Spinal cord,,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons,GSM7804164,GSM7804164: V2a sample2 354 E5 R1; Danio rerio; RNA Seq,GSM7804164 r1,GSM7804164,1,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP463130,,,SS2_18_354_E5_R1.fastq.gz,fastq,33632880.0,782160.0,GSM7804164 r1,0:43,A:9099447;C:7602241;G:7747634;T:9183558;N:0,43,,,,9099447,7602241,7747634,9183558,0,SRX21885948,SRS18977073,SRA1719948,"Neuroscience, Karolinaska Institutet","Neuroscience, Karolinaska Institutet",1,0.83226,,0.28405,,0.90715,,0.52148,,43,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Sweden,2023-09-25,Juvenile,Juvenile,Spinal Cord,Nervous System
26571,SRR26173872,SRX21885947,SRS18977072,SRP463130,PRJNA1020854,Molecular blueprints for spinal circuit modules controlling locomotor speed,GSE243993,Transcriptome Analysis,The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.,,pubmed:37919423,,V2a sample2 354 E4 R1,GSM7804163,,source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing,V2a sample2 354 E4 R1,The reads from each sequenced cell were mapped to the zebrafish reference genome “Danio rerio  Ensembl  GRCz11” using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis,Spinal cord,,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons,GSM7804163,GSM7804163: V2a sample2 354 E4 R1; Danio rerio; RNA Seq,GSM7804163 r1,GSM7804163,1,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP463130,,,SS2_18_354_E4_R1.fastq.gz,fastq,10823057.0,251699.0,GSM7804163 r1,0:43,A:3014035;C:2419189;G:2487845;T:2901988;N:0,43,,,,3014035,2419189,2487845,2901988,0,SRX21885947,SRS18977072,SRA1719948,"Neuroscience, Karolinaska Institutet","Neuroscience, Karolinaska Institutet",1,0.85783,,0.26946,,0.91033,,0.52459,,43,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Sweden,2023-09-25,Juvenile,Juvenile,Spinal Cord,Nervous System
26572,SRR26173873,SRX21885946,SRS18977068,SRP463130,PRJNA1020854,Molecular blueprints for spinal circuit modules controlling locomotor speed,GSE243993,Transcriptome Analysis,The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.,,pubmed:37919423,,V2a sample2 354 E3 R1,GSM7804162,,source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing,V2a sample2 354 E3 R1,The reads from each sequenced cell were mapped to the zebrafish reference genome “Danio rerio  Ensembl  GRCz11” using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis,Spinal cord,,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons,GSM7804162,GSM7804162: V2a sample2 354 E3 R1; Danio rerio; RNA Seq,GSM7804162 r1,GSM7804162,1,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP463130,,,SS2_18_354_E3_R1.fastq.gz,fastq,49775381.0,1157567.0,GSM7804162 r1,0:43,A:13325978;C:11313973;G:11568082;T:13567348;N:0,43,,,,13325978,11313973,11568082,13567348,0,SRX21885946,SRS18977068,SRA1719948,"Neuroscience, Karolinaska Institutet","Neuroscience, Karolinaska Institutet",1,0.80873,,0.29504,,0.93791,,0.52789,,43,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Sweden,2023-09-25,Juvenile,Juvenile,Spinal Cord,Nervous System
26573,SRR26173874,SRX21885945,SRS18977070,SRP463130,PRJNA1020854,Molecular blueprints for spinal circuit modules controlling locomotor speed,GSE243993,Transcriptome Analysis,The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.,,pubmed:37919423,,V2a sample2 354 E2 R1,GSM7804161,,source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing,V2a sample2 354 E2 R1,The reads from each sequenced cell were mapped to the zebrafish reference genome “Danio rerio  Ensembl  GRCz11” using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis,Spinal cord,,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons,GSM7804161,GSM7804161: V2a sample2 354 E2 R1; Danio rerio; RNA Seq,GSM7804161 r1,GSM7804161,1,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP463130,,,SS2_18_354_E2_R1.fastq.gz,fastq,44072334.0,1024938.0,GSM7804161 r1,0:43,A:11780930;C:10068667;G:10185567;T:12037170;N:0,43,,,,11780930,10068667,10185567,12037170,0,SRX21885945,SRS18977070,SRA1719948,"Neuroscience, Karolinaska Institutet","Neuroscience, Karolinaska Institutet",1,0.78009,,0.2621,,0.943,,0.54719,,43,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Sweden,2023-09-25,Juvenile,Juvenile,Spinal Cord,Nervous System
26574,SRR26173875,SRX21885944,SRS18977071,SRP463130,PRJNA1020854,Molecular blueprints for spinal circuit modules controlling locomotor speed,GSE243993,Transcriptome Analysis,The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.,,pubmed:37919423,,V2a sample2 354 D1 R1,GSM7804136,,source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing,V2a sample2 354 D1 R1,The reads from each sequenced cell were mapped to the zebrafish reference genome “Danio rerio  Ensembl  GRCz11” using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis,Spinal cord,,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons,GSM7804136,GSM7804136: V2a sample2 354 D1 R1; Danio rerio; RNA Seq,GSM7804136 r1,GSM7804136,1,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP463130,,,SS2_18_354_D1_R1.fastq.gz,fastq,49923.0,1161.0,GSM7804136 r1,0:43,A:12799;C:11604;G:11134;T:14386;N:0,43,,,,12799,11604,11134,14386,0,SRX21885944,SRS18977071,SRA1719948,"Neuroscience, Karolinaska Institutet","Neuroscience, Karolinaska Institutet",1,0.5773,,0.18478,,0.99472,,0.51097,,43,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Sweden,2023-09-25,Juvenile,Juvenile,Spinal Cord,Nervous System
26575,SRR26173876,SRX21885943,SRS18977069,SRP463130,PRJNA1020854,Molecular blueprints for spinal circuit modules controlling locomotor speed,GSE243993,Transcriptome Analysis,The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.,,pubmed:37919423,,V2a sample2 354 C24 R1,GSM7804135,,source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing,V2a sample2 354 C24 R1,The reads from each sequenced cell were mapped to the zebrafish reference genome “Danio rerio  Ensembl  GRCz11” using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis,Spinal cord,,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons,GSM7804135,GSM7804135: V2a sample2 354 C24 R1; Danio rerio; RNA Seq,GSM7804135 r1,GSM7804135,1,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP463130,,,SS2_18_354_C24_R1.fastq.gz,fastq,30735540.0,714780.0,GSM7804135 r1,0:43,A:7999390;C:7036767;G:7190113;T:8509270;N:0,43,,,,7999390,7036767,7190113,8509270,0,SRX21885943,SRS18977069,SRA1719948,"Neuroscience, Karolinaska Institutet","Neuroscience, Karolinaska Institutet",1,0.48457,,0.16974,,0.99328,,0.82979,,43,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Sweden,2023-09-25,Juvenile,Juvenile,Spinal Cord,Nervous System
26576,SRR26173877,SRX21885942,SRS18977067,SRP463130,PRJNA1020854,Molecular blueprints for spinal circuit modules controlling locomotor speed,GSE243993,Transcriptome Analysis,The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.,,pubmed:37919423,,V2a sample2 354 C23 R1,GSM7804134,,source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing,V2a sample2 354 C23 R1,The reads from each sequenced cell were mapped to the zebrafish reference genome “Danio rerio  Ensembl  GRCz11” using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis,Spinal cord,,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons,GSM7804134,GSM7804134: V2a sample2 354 C23 R1; Danio rerio; RNA Seq,GSM7804134 r1,GSM7804134,1,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP463130,,,SS2_18_354_C23_R1.fastq.gz,fastq,24386031.0,567117.0,GSM7804134 r1,0:43,A:6620599;C:5230020;G:5371347;T:7164065;N:0,43,,,,6620599,5230020,5371347,7164065,0,SRX21885942,SRS18977067,SRA1719948,"Neuroscience, Karolinaska Institutet","Neuroscience, Karolinaska Institutet",1,0.55183,,0.13531,,0.99105,,0.54904,,43,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Sweden,2023-09-25,Juvenile,Juvenile,Spinal Cord,Nervous System
26577,SRR26173878,SRX21885941,SRS18977064,SRP463130,PRJNA1020854,Molecular blueprints for spinal circuit modules controlling locomotor speed,GSE243993,Transcriptome Analysis,The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.,,pubmed:37919423,,V2a sample2 354 C22 R1,GSM7804133,,source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing,V2a sample2 354 C22 R1,The reads from each sequenced cell were mapped to the zebrafish reference genome “Danio rerio  Ensembl  GRCz11” using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis,Spinal cord,,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons,GSM7804133,GSM7804133: V2a sample2 354 C22 R1; Danio rerio; RNA Seq,GSM7804133 r1,GSM7804133,1,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP463130,,,SS2_18_354_C22_R1.fastq.gz,fastq,35984550.0,836850.0,GSM7804133 r1,0:43,A:9917644;C:7959027;G:8126203;T:9981676;N:0,43,,,,9917644,7959027,8126203,9981676,0,SRX21885941,SRS18977064,SRA1719948,"Neuroscience, Karolinaska Institutet","Neuroscience, Karolinaska Institutet",1,0.85473,,0.2804,,0.91165,,0.52909,,43,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Sweden,2023-09-25,Juvenile,Juvenile,Spinal Cord,Nervous System
26578,SRR26173879,SRX21885940,SRS18977065,SRP463130,PRJNA1020854,Molecular blueprints for spinal circuit modules controlling locomotor speed,GSE243993,Transcriptome Analysis,The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.,,pubmed:37919423,,V2a sample2 354 C21 R1,GSM7804132,,source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing,V2a sample2 354 C21 R1,The reads from each sequenced cell were mapped to the zebrafish reference genome “Danio rerio  Ensembl  GRCz11” using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis,Spinal cord,,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons,GSM7804132,GSM7804132: V2a sample2 354 C21 R1; Danio rerio; RNA Seq,GSM7804132 r1,GSM7804132,1,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP463130,,,SS2_18_354_C21_R1.fastq.gz,fastq,32265738.0,750366.0,GSM7804132 r1,0:43,A:8963112;C:7046873;G:7192067;T:9063686;N:0,43,,,,8963112,7046873,7192067,9063686,0,SRX21885940,SRS18977065,SRA1719948,"Neuroscience, Karolinaska Institutet","Neuroscience, Karolinaska Institutet",1,0.8426,,0.36876,,0.91179,,0.58759,,43,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Sweden,2023-09-25,Juvenile,Juvenile,Spinal Cord,Nervous System
26579,SRR26173880,SRX21885939,SRS18977066,SRP463130,PRJNA1020854,Molecular blueprints for spinal circuit modules controlling locomotor speed,GSE243993,Transcriptome Analysis,The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.,,pubmed:37919423,,V2a sample2 354 C20 R1,GSM7804131,,source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing,V2a sample2 354 C20 R1,The reads from each sequenced cell were mapped to the zebrafish reference genome “Danio rerio  Ensembl  GRCz11” using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis,Spinal cord,,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons,GSM7804131,GSM7804131: V2a sample2 354 C20 R1; Danio rerio; RNA Seq,GSM7804131 r1,GSM7804131,1,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP463130,,,SS2_18_354_C20_R1.fastq.gz,fastq,33471157.0,778399.0,GSM7804131 r1,0:43,A:9073629;C:7510863;G:7675381;T:9211284;N:0,43,,,,9073629,7510863,7675381,9211284,0,SRX21885939,SRS18977066,SRA1719948,"Neuroscience, Karolinaska Institutet","Neuroscience, Karolinaska Institutet",1,0.82141,,0.28926,,0.93655,,0.49873,,43,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Sweden,2023-09-25,Juvenile,Juvenile,Spinal Cord,Nervous System
26580,SRR26173881,SRX21885938,SRS18977062,SRP463130,PRJNA1020854,Molecular blueprints for spinal circuit modules controlling locomotor speed,GSE243993,Transcriptome Analysis,The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.,,pubmed:37919423,,V2a sample2 354 C19 R1,GSM7804130,,source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing,V2a sample2 354 C19 R1,The reads from each sequenced cell were mapped to the zebrafish reference genome “Danio rerio  Ensembl  GRCz11” using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis,Spinal cord,,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons,GSM7804130,GSM7804130: V2a sample2 354 C19 R1; Danio rerio; RNA Seq,GSM7804130 r1,GSM7804130,1,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP463130,,,SS2_18_354_C19_R1.fastq.gz,fastq,30131304.0,700728.0,GSM7804130 r1,0:43,A:8036932;C:6893678;G:7034855;T:8165839;N:0,43,,,,8036932,6893678,7034855,8165839,0,SRX21885938,SRS18977062,SRA1719948,"Neuroscience, Karolinaska Institutet","Neuroscience, Karolinaska Institutet",1,0.80896,,0.25245,,0.94067,,0.54072,,43,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Sweden,2023-09-25,Juvenile,Juvenile,Spinal Cord,Nervous System
26581,SRR26173882,SRX21885937,SRS18977061,SRP463130,PRJNA1020854,Molecular blueprints for spinal circuit modules controlling locomotor speed,GSE243993,Transcriptome Analysis,The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.,,pubmed:37919423,,V2a sample2 354 C18 R1,GSM7804129,,source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing,V2a sample2 354 C18 R1,The reads from each sequenced cell were mapped to the zebrafish reference genome “Danio rerio  Ensembl  GRCz11” using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis,Spinal cord,,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons,GSM7804129,GSM7804129: V2a sample2 354 C18 R1; Danio rerio; RNA Seq,GSM7804129 r1,GSM7804129,1,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP463130,,,SS2_18_354_C18_R1.fastq.gz,fastq,31050429.0,722103.0,GSM7804129 r1,0:43,A:8363024;C:7088111;G:7227301;T:8371993;N:0,43,,,,8363024,7088111,7227301,8371993,0,SRX21885937,SRS18977061,SRA1719948,"Neuroscience, Karolinaska Institutet","Neuroscience, Karolinaska Institutet",1,0.87399,,0.20843,,0.89881,,0.49682,,43,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Sweden,2023-09-25,Juvenile,Juvenile,Spinal Cord,Nervous System
26582,SRR26173883,SRX21885936,SRS18977063,SRP463130,PRJNA1020854,Molecular blueprints for spinal circuit modules controlling locomotor speed,GSE243993,Transcriptome Analysis,The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.,,pubmed:37919423,,V2a sample2 354 B17 R1,GSM7804104,,source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing,V2a sample2 354 B17 R1,The reads from each sequenced cell were mapped to the zebrafish reference genome “Danio rerio  Ensembl  GRCz11” using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis,Spinal cord,,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons,GSM7804104,GSM7804104: V2a sample2 354 B17 R1; Danio rerio; RNA Seq,GSM7804104 r1,GSM7804104,1,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP463130,,,SS2_18_354_B17_R1.fastq.gz,fastq,47093729.0,1095203.0,GSM7804104 r1,0:43,A:13057598;C:10185883;G:10457076;T:13393172;N:0,43,,,,13057598,10185883,10457076,13393172,0,SRX21885936,SRS18977063,SRA1719948,"Neuroscience, Karolinaska Institutet","Neuroscience, Karolinaska Institutet",1,0.80343,,0.36098,,0.95059,,0.52562,,43,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Sweden,2023-09-25,Juvenile,Juvenile,Spinal Cord,Nervous System
26583,SRR26173884,SRX21885935,SRS18977060,SRP463130,PRJNA1020854,Molecular blueprints for spinal circuit modules controlling locomotor speed,GSE243993,Transcriptome Analysis,The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.,,pubmed:37919423,,V2a sample2 354 B16 R1,GSM7804103,,source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing,V2a sample2 354 B16 R1,The reads from each sequenced cell were mapped to the zebrafish reference genome “Danio rerio  Ensembl  GRCz11” using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis,Spinal cord,,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons,GSM7804103,GSM7804103: V2a sample2 354 B16 R1; Danio rerio; RNA Seq,GSM7804103 r1,GSM7804103,1,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP463130,,,SS2_18_354_B16_R1.fastq.gz,fastq,34160791.0,794437.0,GSM7804103 r1,0:43,A:9178469;C:7729053;G:7901331;T:9351938;N:0,43,,,,9178469,7729053,7901331,9351938,0,SRX21885935,SRS18977060,SRA1719948,"Neuroscience, Karolinaska Institutet","Neuroscience, Karolinaska Institutet",1,0.79028,,0.25695,,0.94627,,0.51668,,43,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Sweden,2023-09-25,Juvenile,Juvenile,Spinal Cord,Nervous System
26584,SRR26173885,SRX21885934,SRS18977059,SRP463130,PRJNA1020854,Molecular blueprints for spinal circuit modules controlling locomotor speed,GSE243993,Transcriptome Analysis,The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.,,pubmed:37919423,,V2a sample2 354 B15 R1,GSM7804102,,source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing,V2a sample2 354 B15 R1,The reads from each sequenced cell were mapped to the zebrafish reference genome “Danio rerio  Ensembl  GRCz11” using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis,Spinal cord,,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons,GSM7804102,GSM7804102: V2a sample2 354 B15 R1; Danio rerio; RNA Seq,GSM7804102 r1,GSM7804102,1,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP463130,,,SS2_18_354_B15_R1.fastq.gz,fastq,29152495.0,677965.0,GSM7804102 r1,0:43,A:7966546;C:6516464;G:6675123;T:7994362;N:0,43,,,,7966546,6516464,6675123,7994362,0,SRX21885934,SRS18977059,SRA1719948,"Neuroscience, Karolinaska Institutet","Neuroscience, Karolinaska Institutet",1,0.83832,,0.25969,,0.92673,,0.51661,,43,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Sweden,2023-09-25,Juvenile,Juvenile,Spinal Cord,Nervous System
26585,SRR26173886,SRX21885933,SRS18977057,SRP463130,PRJNA1020854,Molecular blueprints for spinal circuit modules controlling locomotor speed,GSE243993,Transcriptome Analysis,The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.,,pubmed:37919423,,V2a sample2 354 B14 R1,GSM7804101,,source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing,V2a sample2 354 B14 R1,The reads from each sequenced cell were mapped to the zebrafish reference genome “Danio rerio  Ensembl  GRCz11” using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis,Spinal cord,,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons,GSM7804101,GSM7804101: V2a sample2 354 B14 R1; Danio rerio; RNA Seq,GSM7804101 r1,GSM7804101,1,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP463130,,,SS2_18_354_B14_R1.fastq.gz,fastq,23811379.0,553753.0,GSM7804101 r1,0:43,A:6532691;C:5215122;G:5353003;T:6710563;N:0,43,,,,6532691,5215122,5353003,6710563,0,SRX21885933,SRS18977057,SRA1719948,"Neuroscience, Karolinaska Institutet","Neuroscience, Karolinaska Institutet",1,0.74067,,0.3282,,0.95272,,0.49582,,43,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Sweden,2023-09-25,Juvenile,Juvenile,Spinal Cord,Nervous System
26586,SRR26173887,SRX21885932,SRS18977058,SRP463130,PRJNA1020854,Molecular blueprints for spinal circuit modules controlling locomotor speed,GSE243993,Transcriptome Analysis,The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.,,pubmed:37919423,,V2a sample2 354 B13 R1,GSM7804100,,source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing,V2a sample2 354 B13 R1,The reads from each sequenced cell were mapped to the zebrafish reference genome “Danio rerio  Ensembl  GRCz11” using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis,Spinal cord,,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons,GSM7804100,GSM7804100: V2a sample2 354 B13 R1; Danio rerio; RNA Seq,GSM7804100 r1,GSM7804100,1,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP463130,,,SS2_18_354_B13_R1.fastq.gz,fastq,18141356.0,421892.0,GSM7804100 r1,0:43,A:4926550;C:4092334;G:4186281;T:4936191;N:0,43,,,,4926550,4092334,4186281,4936191,0,SRX21885932,SRS18977058,SRA1719948,"Neuroscience, Karolinaska Institutet","Neuroscience, Karolinaska Institutet",1,0.87463,,0.22642,,0.89826,,0.50541,,43,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Sweden,2023-09-25,Juvenile,Juvenile,Spinal Cord,Nervous System
26587,SRR26173888,SRX21885931,SRS18977056,SRP463130,PRJNA1020854,Molecular blueprints for spinal circuit modules controlling locomotor speed,GSE243993,Transcriptome Analysis,The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.,,pubmed:37919423,,V2a sample2 354 B12 R1,GSM7804099,,source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing,V2a sample2 354 B12 R1,The reads from each sequenced cell were mapped to the zebrafish reference genome “Danio rerio  Ensembl  GRCz11” using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis,Spinal cord,,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons,GSM7804099,GSM7804099: V2a sample2 354 B12 R1; Danio rerio; RNA Seq,GSM7804099 r1,GSM7804099,1,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP463130,,,SS2_18_354_B12_R1.fastq.gz,fastq,34932039.0,812373.0,GSM7804099 r1,0:43,A:9555191;C:7704451;G:7897587;T:9774810;N:0,43,,,,9555191,7704451,7897587,9774810,0,SRX21885931,SRS18977056,SRA1719948,"Neuroscience, Karolinaska Institutet","Neuroscience, Karolinaska Institutet",1,0.80402,,0.30224,,0.93592,,0.53659,,43,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Sweden,2023-09-25,Juvenile,Juvenile,Spinal Cord,Nervous System
26588,SRR26173889,SRX21885930,SRS18977055,SRP463130,PRJNA1020854,Molecular blueprints for spinal circuit modules controlling locomotor speed,GSE243993,Transcriptome Analysis,The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.,,pubmed:37919423,,V2a sample2 354 B11 R1,GSM7804098,,source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing,V2a sample2 354 B11 R1,The reads from each sequenced cell were mapped to the zebrafish reference genome “Danio rerio  Ensembl  GRCz11” using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis,Spinal cord,,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons,GSM7804098,GSM7804098: V2a sample2 354 B11 R1; Danio rerio; RNA Seq,GSM7804098 r1,GSM7804098,1,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP463130,,,SS2_18_354_B11_R1.fastq.gz,fastq,35987087.0,836909.0,GSM7804098 r1,0:43,A:9801738;C:8047161;G:8248020;T:9890168;N:0,43,,,,9801738,8047161,8248020,9890168,0,SRX21885930,SRS18977055,SRA1719948,"Neuroscience, Karolinaska Institutet","Neuroscience, Karolinaska Institutet",1,0.81805,,0.24526,,0.92092,,0.54523,,43,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Sweden,2023-09-25,Juvenile,Juvenile,Spinal Cord,Nervous System
26589,SRR26173890,SRX21885929,SRS18977054,SRP463130,PRJNA1020854,Molecular blueprints for spinal circuit modules controlling locomotor speed,GSE243993,Transcriptome Analysis,The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.,,pubmed:37919423,,V2a sample2 354 B10 R1,GSM7804097,,source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing,V2a sample2 354 B10 R1,The reads from each sequenced cell were mapped to the zebrafish reference genome “Danio rerio  Ensembl  GRCz11” using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis,Spinal cord,,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons,GSM7804097,GSM7804097: V2a sample2 354 B10 R1; Danio rerio; RNA Seq,GSM7804097 r1,GSM7804097,1,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP463130,,,SS2_18_354_B10_R1.fastq.gz,fastq,33252846.0,773322.0,GSM7804097 r1,0:43,A:8996915;C:7433025;G:7633859;T:9189047;N:0,43,,,,8996915,7433025,7633859,9189047,0,SRX21885929,SRS18977054,SRA1719948,"Neuroscience, Karolinaska Institutet","Neuroscience, Karolinaska Institutet",1,0.78892,,0.28622,,0.94237,,0.53023,,43,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Sweden,2023-09-25,Juvenile,Juvenile,Spinal Cord,Nervous System
26590,SRR26173891,SRX21885928,SRS18977053,SRP463130,PRJNA1020854,Molecular blueprints for spinal circuit modules controlling locomotor speed,GSE243993,Transcriptome Analysis,The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.,,pubmed:37919423,,V2a sample2 354 A9 R1,GSM7804072,,source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing,V2a sample2 354 A9 R1,The reads from each sequenced cell were mapped to the zebrafish reference genome “Danio rerio  Ensembl  GRCz11” using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis,Spinal cord,,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons,GSM7804072,GSM7804072: V2a sample2 354 A9 R1; Danio rerio; RNA Seq,GSM7804072 r1,GSM7804072,1,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP463130,,,SS2_18_354_A9_R1.fastq.gz,fastq,23658600.0,550200.0,GSM7804072 r1,0:43,A:6447300;C:5342358;G:5472128;T:6396814;N:0,43,,,,6447300,5342358,5472128,6396814,0,SRX21885928,SRS18977053,SRA1719948,"Neuroscience, Karolinaska Institutet","Neuroscience, Karolinaska Institutet",1,0.86727,,0.23136,,0.8996,,0.52692,,43,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Sweden,2023-09-25,Juvenile,Juvenile,Spinal Cord,Nervous System
26591,SRR26173892,SRX21885927,SRS18977051,SRP463130,PRJNA1020854,Molecular blueprints for spinal circuit modules controlling locomotor speed,GSE243993,Transcriptome Analysis,The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.,,pubmed:37919423,,V2a sample2 354 A8 R1,GSM7804071,,source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing,V2a sample2 354 A8 R1,The reads from each sequenced cell were mapped to the zebrafish reference genome “Danio rerio  Ensembl  GRCz11” using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis,Spinal cord,,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons,GSM7804071,GSM7804071: V2a sample2 354 A8 R1; Danio rerio; RNA Seq,GSM7804071 r1,GSM7804071,1,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP463130,,,SS2_18_354_A8_R1.fastq.gz,fastq,18645187.0,433609.0,GSM7804071 r1,0:43,A:5151340;C:4145072;G:4243308;T:5105467;N:0,43,,,,5151340,4145072,4243308,5105467,0,SRX21885927,SRS18977051,SRA1719948,"Neuroscience, Karolinaska Institutet","Neuroscience, Karolinaska Institutet",1,0.86561,,0.28633,,0.89438,,0.53463,,43,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Sweden,2023-09-25,Juvenile,Juvenile,Spinal Cord,Nervous System
26592,SRR26173893,SRX21885926,SRS18977052,SRP463130,PRJNA1020854,Molecular blueprints for spinal circuit modules controlling locomotor speed,GSE243993,Transcriptome Analysis,The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.,,pubmed:37919423,,V2a sample2 354 A7 R1,GSM7804070,,source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing,V2a sample2 354 A7 R1,The reads from each sequenced cell were mapped to the zebrafish reference genome “Danio rerio  Ensembl  GRCz11” using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis,Spinal cord,,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons,GSM7804070,GSM7804070: V2a sample2 354 A7 R1; Danio rerio; RNA Seq,GSM7804070 r1,GSM7804070,1,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP463130,,,SS2_18_354_A7_R1.fastq.gz,fastq,42340466.0,984662.0,GSM7804070 r1,0:43,A:11373539;C:9660020;G:9840242;T:11466665;N:0,43,,,,11373539,9660020,9840242,11466665,0,SRX21885926,SRS18977052,SRA1719948,"Neuroscience, Karolinaska Institutet","Neuroscience, Karolinaska Institutet",1,0.81646,,0.24599,,0.93833,,0.57817,,43,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Sweden,2023-09-25,Juvenile,Juvenile,Spinal Cord,Nervous System
26593,SRR26173894,SRX21885925,SRS18977050,SRP463130,PRJNA1020854,Molecular blueprints for spinal circuit modules controlling locomotor speed,GSE243993,Transcriptome Analysis,The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.,,pubmed:37919423,,V2a sample2 354 A6 R1,GSM7804069,,source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing,V2a sample2 354 A6 R1,The reads from each sequenced cell were mapped to the zebrafish reference genome “Danio rerio  Ensembl  GRCz11” using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis,Spinal cord,,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons,GSM7804069,GSM7804069: V2a sample2 354 A6 R1; Danio rerio; RNA Seq,GSM7804069 r1,GSM7804069,1,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP463130,,,SS2_18_354_A6_R1.fastq.gz,fastq,23486858.0,546206.0,GSM7804069 r1,0:43,A:6654369;C:4998242;G:5115579;T:6718668;N:0,43,,,,6654369,4998242,5115579,6718668,0,SRX21885925,SRS18977050,SRA1719948,"Neuroscience, Karolinaska Institutet","Neuroscience, Karolinaska Institutet",1,0.84122,,0.57245,,0.77794,,0.53266,,43,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Sweden,2023-09-25,Juvenile,Juvenile,Spinal Cord,Nervous System
26594,SRR26173895,SRX21885924,SRS18977048,SRP463130,PRJNA1020854,Molecular blueprints for spinal circuit modules controlling locomotor speed,GSE243993,Transcriptome Analysis,The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.,,pubmed:37919423,,V2a sample2 354 A5 R1,GSM7804068,,source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing,V2a sample2 354 A5 R1,The reads from each sequenced cell were mapped to the zebrafish reference genome “Danio rerio  Ensembl  GRCz11” using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis,Spinal cord,,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons,GSM7804068,GSM7804068: V2a sample2 354 A5 R1; Danio rerio; RNA Seq,GSM7804068 r1,GSM7804068,1,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP463130,,,SS2_18_354_A5_R1.fastq.gz,fastq,46876450.0,1090150.0,GSM7804068 r1,0:43,A:12599291;C:10693086;G:10940020;T:12644053;N:0,43,,,,12599291,10693086,10940020,12644053,0,SRX21885924,SRS18977048,SRA1719948,"Neuroscience, Karolinaska Institutet","Neuroscience, Karolinaska Institutet",1,0.86707,,0.22085,,0.89412,,0.51257,,43,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Sweden,2023-09-25,Juvenile,Juvenile,Spinal Cord,Nervous System
26595,SRR26173896,SRX21885923,SRS18977049,SRP463130,PRJNA1020854,Molecular blueprints for spinal circuit modules controlling locomotor speed,GSE243993,Transcriptome Analysis,The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.,,pubmed:37919423,,V2a sample2 354 A4 R1,GSM7804067,,source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing,V2a sample2 354 A4 R1,The reads from each sequenced cell were mapped to the zebrafish reference genome “Danio rerio  Ensembl  GRCz11” using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis,Spinal cord,,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons,GSM7804067,GSM7804067: V2a sample2 354 A4 R1; Danio rerio; RNA Seq,GSM7804067 r1,GSM7804067,1,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP463130,,,SS2_18_354_A4_R1.fastq.gz,fastq,43487233.0,1011331.0,GSM7804067 r1,0:43,A:11900913;C:9677048;G:9921622;T:11987650;N:0,43,,,,11900913,9677048,9921622,11987650,0,SRX21885923,SRS18977049,SRA1719948,"Neuroscience, Karolinaska Institutet","Neuroscience, Karolinaska Institutet",1,0.8409,,0.27122,,0.91165,,0.55221,,43,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Sweden,2023-09-25,Juvenile,Juvenile,Spinal Cord,Nervous System
26596,SRR26173897,SRX21885922,SRS18977047,SRP463130,PRJNA1020854,Molecular blueprints for spinal circuit modules controlling locomotor speed,GSE243993,Transcriptome Analysis,The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.,,pubmed:37919423,,V2a sample2 354 A3 R1,GSM7804066,,source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing,V2a sample2 354 A3 R1,The reads from each sequenced cell were mapped to the zebrafish reference genome “Danio rerio  Ensembl  GRCz11” using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis,Spinal cord,,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons,GSM7804066,GSM7804066: V2a sample2 354 A3 R1; Danio rerio; RNA Seq,GSM7804066 r1,GSM7804066,1,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP463130,,,SS2_18_354_A3_R1.fastq.gz,fastq,44287248.0,1029936.0,GSM7804066 r1,0:43,A:12065729;C:9907516;G:10143806;T:12170197;N:0,43,,,,12065729,9907516,10143806,12170197,0,SRX21885922,SRS18977047,SRA1719948,"Neuroscience, Karolinaska Institutet","Neuroscience, Karolinaska Institutet",1,0.80982,,0.29232,,0.93675,,0.5661,,43,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Sweden,2023-09-25,Juvenile,Juvenile,Spinal Cord,Nervous System
26597,SRR26173898,SRX21885921,SRS18977046,SRP463130,PRJNA1020854,Molecular blueprints for spinal circuit modules controlling locomotor speed,GSE243993,Transcriptome Analysis,The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.,,pubmed:37919423,,V2a sample2 354 A2 R1,GSM7804065,,source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing,V2a sample2 354 A2 R1,The reads from each sequenced cell were mapped to the zebrafish reference genome “Danio rerio  Ensembl  GRCz11” using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis,Spinal cord,,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons,GSM7804065,GSM7804065: V2a sample2 354 A2 R1; Danio rerio; RNA Seq,GSM7804065 r1,GSM7804065,1,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP463130,,,SS2_18_354_A2_R1.fastq.gz,fastq,39822515.0,926105.0,GSM7804065 r1,0:43,A:10662390;C:9155016;G:9361757;T:10643352;N:0,43,,,,10662390,9155016,9361757,10643352,0,SRX21885921,SRS18977046,SRA1719948,"Neuroscience, Karolinaska Institutet","Neuroscience, Karolinaska Institutet",1,0.88377,,0.19244,,0.88627,,0.52412,,43,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Sweden,2023-09-25,Juvenile,Juvenile,Spinal Cord,Nervous System
26598,SRR26173899,SRX21885920,SRS18977044,SRP463130,PRJNA1020854,Molecular blueprints for spinal circuit modules controlling locomotor speed,GSE243993,Transcriptome Analysis,The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.,,pubmed:37919423,,V2a sample1 353 P1 R1,GSM7804040,,source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing,V2a sample1 353 P1 R1,The reads from each sequenced cell were mapped to the zebrafish reference genome “Danio rerio  Ensembl  GRCz11” using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis,Spinal cord,,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons,GSM7804040,GSM7804040: V2a sample1 353 P1 R1; Danio rerio; RNA Seq,GSM7804040 r1,GSM7804040,1,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP463130,,,SS2_18_353_P1_R1.fastq.gz,fastq,35622877.0,828439.0,GSM7804040 r1,0:43,A:10094838;C:7580955;G:7760837;T:10186247;N:0,43,,,,10094838,7580955,7760837,10186247,0,SRX21885920,SRS18977044,SRA1719948,"Neuroscience, Karolinaska Institutet","Neuroscience, Karolinaska Institutet",1,0.82753,,0.38743,,0.94085,,0.70753,,43,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Sweden,2023-09-25,Juvenile,Juvenile,Spinal Cord,Nervous System
26599,SRR26173900,SRX21885919,SRS18977045,SRP463130,PRJNA1020854,Molecular blueprints for spinal circuit modules controlling locomotor speed,GSE243993,Transcriptome Analysis,The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.,,pubmed:37919423,,V2a sample1 353 O24 R1,GSM7804039,,source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing,V2a sample1 353 O24 R1,The reads from each sequenced cell were mapped to the zebrafish reference genome “Danio rerio  Ensembl  GRCz11” using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis,Spinal cord,,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons,GSM7804039,GSM7804039: V2a sample1 353 O24 R1; Danio rerio; RNA Seq,GSM7804039 r1,GSM7804039,1,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP463130,,,SS2_18_353_O24_R1.fastq.gz,fastq,25162482.0,585174.0,GSM7804039 r1,0:43,A:6589034;C:5708817;G:5862315;T:7002316;N:0,43,,,,6589034,5708817,5862315,7002316,0,SRX21885919,SRS18977045,SRA1719948,"Neuroscience, Karolinaska Institutet","Neuroscience, Karolinaska Institutet",1,0.50646,,0.15797,,0.99086,,0.48626,,43,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Sweden,2023-09-25,Juvenile,Juvenile,Spinal Cord,Nervous System
26600,SRR26173901,SRX21885918,SRS18977043,SRP463130,PRJNA1020854,Molecular blueprints for spinal circuit modules controlling locomotor speed,GSE243993,Transcriptome Analysis,The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.,,pubmed:37919423,,V2a sample1 353 O23 R1,GSM7804038,,source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing,V2a sample1 353 O23 R1,The reads from each sequenced cell were mapped to the zebrafish reference genome “Danio rerio  Ensembl  GRCz11” using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis,Spinal cord,,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons,GSM7804038,GSM7804038: V2a sample1 353 O23 R1; Danio rerio; RNA Seq,GSM7804038 r1,GSM7804038,1,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP463130,,,SS2_18_353_O23_R1.fastq.gz,fastq,21378396.0,497172.0,GSM7804038 r1,0:43,A:5419690;C:4870276;G:5019946;T:6068484;N:0,43,,,,5419690,4870276,5019946,6068484,0,SRX21885918,SRS18977043,SRA1719948,"Neuroscience, Karolinaska Institutet","Neuroscience, Karolinaska Institutet",1,0.4177,,0.18826,,0.99344,,0.78066,,43,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Sweden,2023-09-25,Juvenile,Juvenile,Spinal Cord,Nervous System
26601,SRR26173902,SRX21885917,SRS18977042,SRP463130,PRJNA1020854,Molecular blueprints for spinal circuit modules controlling locomotor speed,GSE243993,Transcriptome Analysis,The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.,,pubmed:37919423,,V2a sample1 353 O22 R1,GSM7804037,,source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing,V2a sample1 353 O22 R1,The reads from each sequenced cell were mapped to the zebrafish reference genome “Danio rerio  Ensembl  GRCz11” using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis,Spinal cord,,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons,GSM7804037,GSM7804037: V2a sample1 353 O22 R1; Danio rerio; RNA Seq,GSM7804037 r1,GSM7804037,1,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP463130,,,SS2_18_353_O22_R1.fastq.gz,fastq,30321665.0,705155.0,GSM7804037 r1,0:43,A:8123534;C:6839326;G:6921711;T:8437094;N:0,43,,,,8123534,6839326,6921711,8437094,0,SRX21885917,SRS18977042,SRA1719948,"Neuroscience, Karolinaska Institutet","Neuroscience, Karolinaska Institutet",1,0.76574,,0.24445,,0.94014,,0.51811,,43,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Sweden,2023-09-25,Juvenile,Juvenile,Spinal Cord,Nervous System
26602,SRR26173903,SRX21885916,SRS18977041,SRP463130,PRJNA1020854,Molecular blueprints for spinal circuit modules controlling locomotor speed,GSE243993,Transcriptome Analysis,The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.,,pubmed:37919423,,V2a sample1 353 O21 R1,GSM7804036,,source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing,V2a sample1 353 O21 R1,The reads from each sequenced cell were mapped to the zebrafish reference genome “Danio rerio  Ensembl  GRCz11” using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis,Spinal cord,,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons,GSM7804036,GSM7804036: V2a sample1 353 O21 R1; Danio rerio; RNA Seq,GSM7804036 r1,GSM7804036,1,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP463130,,,SS2_18_353_O21_R1.fastq.gz,fastq,24544916.0,570812.0,GSM7804036 r1,0:43,A:6528543;C:5656479;G:5771413;T:6588481;N:0,43,,,,6528543,5656479,5771413,6588481,0,SRX21885916,SRS18977041,SRA1719948,"Neuroscience, Karolinaska Institutet","Neuroscience, Karolinaska Institutet",1,0.87756,,0.17329,,0.88124,,0.51427,,43,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Sweden,2023-09-25,Juvenile,Juvenile,Spinal Cord,Nervous System
26603,SRR26173904,SRX21885915,SRS18977040,SRP463130,PRJNA1020854,Molecular blueprints for spinal circuit modules controlling locomotor speed,GSE243993,Transcriptome Analysis,The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.,,pubmed:37919423,,V2a sample1 353 O20 R1,GSM7804035,,source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing,V2a sample1 353 O20 R1,The reads from each sequenced cell were mapped to the zebrafish reference genome “Danio rerio  Ensembl  GRCz11” using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis,Spinal cord,,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons,GSM7804035,GSM7804035: V2a sample1 353 O20 R1; Danio rerio; RNA Seq,GSM7804035 r1,GSM7804035,1,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP463130,,,SS2_18_353_O20_R1.fastq.gz,fastq,27471324.0,638868.0,GSM7804035 r1,0:43,A:7349212;C:6154048;G:6323796;T:7644268;N:0,43,,,,7349212,6154048,6323796,7644268,0,SRX21885915,SRS18977040,SRA1719948,"Neuroscience, Karolinaska Institutet","Neuroscience, Karolinaska Institutet",1,0.7529,,0.26778,,0.94635,,0.5148,,43,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Sweden,2023-09-25,Juvenile,Juvenile,Spinal Cord,Nervous System
26604,SRR26173905,SRX21885914,SRS18977039,SRP463130,PRJNA1020854,Molecular blueprints for spinal circuit modules controlling locomotor speed,GSE243993,Transcriptome Analysis,The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.,,pubmed:37919423,,V2a sample1 353 O19 R1,GSM7804034,,source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing,V2a sample1 353 O19 R1,The reads from each sequenced cell were mapped to the zebrafish reference genome “Danio rerio  Ensembl  GRCz11” using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis,Spinal cord,,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons,GSM7804034,GSM7804034: V2a sample1 353 O19 R1; Danio rerio; RNA Seq,GSM7804034 r1,GSM7804034,1,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP463130,,,SS2_18_353_O19_R1.fastq.gz,fastq,24908137.0,579259.0,GSM7804034 r1,0:43,A:6706594;C:5634956;G:5764632;T:6801955;N:0,43,,,,6706594,5634956,5764632,6801955,0,SRX21885914,SRS18977039,SRA1719948,"Neuroscience, Karolinaska Institutet","Neuroscience, Karolinaska Institutet",1,0.8525,,0.23739,,0.90694,,0.5194,,43,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Sweden,2023-09-25,Juvenile,Juvenile,Spinal Cord,Nervous System
26605,SRR26173906,SRX21885913,SRS18977038,SRP463130,PRJNA1020854,Molecular blueprints for spinal circuit modules controlling locomotor speed,GSE243993,Transcriptome Analysis,The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.,,pubmed:37919423,,V2a sample1 353 O18 R1,GSM7804033,,source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing,V2a sample1 353 O18 R1,The reads from each sequenced cell were mapped to the zebrafish reference genome “Danio rerio  Ensembl  GRCz11” using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis,Spinal cord,,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons,GSM7804033,GSM7804033: V2a sample1 353 O18 R1; Danio rerio; RNA Seq,GSM7804033 r1,GSM7804033,1,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP463130,,,SS2_18_353_O18_R1.fastq.gz,fastq,23328790.0,542530.0,GSM7804033 r1,0:43,A:6296932;C:5290824;G:5423100;T:6317934;N:0,43,,,,6296932,5290824,5423100,6317934,0,SRX21885913,SRS18977038,SRA1719948,"Neuroscience, Karolinaska Institutet","Neuroscience, Karolinaska Institutet",1,0.87485,,0.19256,,0.88422,,0.46891,,43,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Sweden,2023-09-25,Juvenile,Juvenile,Spinal Cord,Nervous System
26606,SRR26173907,SRX21885912,SRS18977037,SRP463130,PRJNA1020854,Molecular blueprints for spinal circuit modules controlling locomotor speed,GSE243993,Transcriptome Analysis,The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.,,pubmed:37919423,,V2a sample1 353 N17 R1,GSM7804008,,source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing,V2a sample1 353 N17 R1,The reads from each sequenced cell were mapped to the zebrafish reference genome “Danio rerio  Ensembl  GRCz11” using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis,Spinal cord,,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons,GSM7804008,GSM7804008: V2a sample1 353 N17 R1; Danio rerio; RNA Seq,GSM7804008 r1,GSM7804008,1,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP463130,,,SS2_18_353_N17_R1.fastq.gz,fastq,20379592.0,473944.0,GSM7804008 r1,0:43,A:5592768;C:4503044;G:4602811;T:5680969;N:0,43,,,,5592768,4503044,4602811,5680969,0,SRX21885912,SRS18977037,SRA1719948,"Neuroscience, Karolinaska Institutet","Neuroscience, Karolinaska Institutet",1,0.84619,,0.24373,,0.94095,,0.4423,,43,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Sweden,2023-09-25,Juvenile,Juvenile,Spinal Cord,Nervous System
26607,SRR26173908,SRX21885911,SRS18977035,SRP463130,PRJNA1020854,Molecular blueprints for spinal circuit modules controlling locomotor speed,GSE243993,Transcriptome Analysis,The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.,,pubmed:37919423,,V2a sample1 353 N16 R1,GSM7804007,,source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing,V2a sample1 353 N16 R1,The reads from each sequenced cell were mapped to the zebrafish reference genome “Danio rerio  Ensembl  GRCz11” using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis,Spinal cord,,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons,GSM7804007,GSM7804007: V2a sample1 353 N16 R1; Danio rerio; RNA Seq,GSM7804007 r1,GSM7804007,1,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP463130,,,SS2_18_353_N16_R1.fastq.gz,fastq,14151343.0,329101.0,GSM7804007 r1,0:43,A:3796916;C:3223155;G:3290919;T:3840353;N:0,43,,,,3796916,3223155,3290919,3840353,0,SRX21885911,SRS18977035,SRA1719948,"Neuroscience, Karolinaska Institutet","Neuroscience, Karolinaska Institutet",1,0.85097,,0.21705,,0.93097,,0.52334,,43,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Sweden,2023-09-25,Juvenile,Juvenile,Spinal Cord,Nervous System
26608,SRR26173909,SRX21885910,SRS18977036,SRP463130,PRJNA1020854,Molecular blueprints for spinal circuit modules controlling locomotor speed,GSE243993,Transcriptome Analysis,The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.,,pubmed:37919423,,V2a sample1 353 N15 R1,GSM7804006,,source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing,V2a sample1 353 N15 R1,The reads from each sequenced cell were mapped to the zebrafish reference genome “Danio rerio  Ensembl  GRCz11” using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis,Spinal cord,,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons,GSM7804006,GSM7804006: V2a sample1 353 N15 R1; Danio rerio; RNA Seq,GSM7804006 r1,GSM7804006,1,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP463130,,,SS2_18_353_N15_R1.fastq.gz,fastq,16536209.0,384563.0,GSM7804006 r1,0:43,A:4473687;C:3744698;G:3838620;T:4479204;N:0,43,,,,4473687,3744698,3838620,4479204,0,SRX21885910,SRS18977036,SRA1719948,"Neuroscience, Karolinaska Institutet","Neuroscience, Karolinaska Institutet",1,0.88744,,0.19834,,0.89966,,0.5281,,43,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Sweden,2023-09-25,Juvenile,Juvenile,Spinal Cord,Nervous System
26609,SRR26173910,SRX21885909,SRS18977034,SRP463130,PRJNA1020854,Molecular blueprints for spinal circuit modules controlling locomotor speed,GSE243993,Transcriptome Analysis,The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.,,pubmed:37919423,,V2a sample1 353 N14 R1,GSM7804005,,source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing,V2a sample1 353 N14 R1,The reads from each sequenced cell were mapped to the zebrafish reference genome “Danio rerio  Ensembl  GRCz11” using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis,Spinal cord,,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons,GSM7804005,GSM7804005: V2a sample1 353 N14 R1; Danio rerio; RNA Seq,GSM7804005 r1,GSM7804005,1,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP463130,,,SS2_18_353_N14_R1.fastq.gz,fastq,16039215.0,373005.0,GSM7804005 r1,0:43,A:4355837;C:3605999;G:3695364;T:4382015;N:0,43,,,,4355837,3605999,3695364,4382015,0,SRX21885909,SRS18977034,SRA1719948,"Neuroscience, Karolinaska Institutet","Neuroscience, Karolinaska Institutet",1,0.86632,,0.22226,,0.90268,,0.5092,,43,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Sweden,2023-09-25,Juvenile,Juvenile,Spinal Cord,Nervous System
26610,SRR26173911,SRX21885908,SRS18977033,SRP463130,PRJNA1020854,Molecular blueprints for spinal circuit modules controlling locomotor speed,GSE243993,Transcriptome Analysis,The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.,,pubmed:37919423,,V2a sample1 353 N13 R1,GSM7804004,,source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing,V2a sample1 353 N13 R1,The reads from each sequenced cell were mapped to the zebrafish reference genome “Danio rerio  Ensembl  GRCz11” using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis,Spinal cord,,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons,GSM7804004,GSM7804004: V2a sample1 353 N13 R1; Danio rerio; RNA Seq,GSM7804004 r1,GSM7804004,1,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP463130,,,SS2_18_353_N13_R1.fastq.gz,fastq,15280910.0,355370.0,GSM7804004 r1,0:43,A:4072742;C:3469231;G:3555056;T:4183881;N:0,43,,,,4072742,3469231,3555056,4183881,0,SRX21885908,SRS18977033,SRA1719948,"Neuroscience, Karolinaska Institutet","Neuroscience, Karolinaska Institutet",1,0.73874,,0.31529,,0.95988,,0.5442,,43,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Sweden,2023-09-25,Juvenile,Juvenile,Spinal Cord,Nervous System
26611,SRR26173912,SRX21885907,SRS18977032,SRP463130,PRJNA1020854,Molecular blueprints for spinal circuit modules controlling locomotor speed,GSE243993,Transcriptome Analysis,The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.,,pubmed:37919423,,V2a sample1 353 N12 R1,GSM7804003,,source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing,V2a sample1 353 N12 R1,The reads from each sequenced cell were mapped to the zebrafish reference genome “Danio rerio  Ensembl  GRCz11” using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis,Spinal cord,,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons,GSM7804003,GSM7804003: V2a sample1 353 N12 R1; Danio rerio; RNA Seq,GSM7804003 r1,GSM7804003,1,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP463130,,,SS2_18_353_N12_R1.fastq.gz,fastq,10529926.0,244882.0,GSM7804003 r1,0:43,A:2835885;C:2354590;G:2390746;T:2948705;N:0,43,,,,2835885,2354590,2390746,2948705,0,SRX21885907,SRS18977032,SRA1719948,"Neuroscience, Karolinaska Institutet","Neuroscience, Karolinaska Institutet",1,0.74571,,0.36729,,0.9443,,0.77069,,43,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Sweden,2023-09-25,Juvenile,Juvenile,Spinal Cord,Nervous System
26612,SRR26173913,SRX21885906,SRS18977030,SRP463130,PRJNA1020854,Molecular blueprints for spinal circuit modules controlling locomotor speed,GSE243993,Transcriptome Analysis,The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.,,pubmed:37919423,,V2a sample1 353 N11 R1,GSM7804002,,source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing,V2a sample1 353 N11 R1,The reads from each sequenced cell were mapped to the zebrafish reference genome “Danio rerio  Ensembl  GRCz11” using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis,Spinal cord,,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons,GSM7804002,GSM7804002: V2a sample1 353 N11 R1; Danio rerio; RNA Seq,GSM7804002 r1,GSM7804002,1,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP463130,,,SS2_18_353_N11_R1.fastq.gz,fastq,21706271.0,504797.0,GSM7804002 r1,0:43,A:5853146;C:4922477;G:5009970;T:5920678;N:0,43,,,,5853146,4922477,5009970,5920678,0,SRX21885906,SRS18977030,SRA1719948,"Neuroscience, Karolinaska Institutet","Neuroscience, Karolinaska Institutet",1,0.8394,,0.23984,,0.93468,,0.51881,,43,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Sweden,2023-09-25,Juvenile,Juvenile,Spinal Cord,Nervous System
26613,SRR26173914,SRX21885905,SRS18977031,SRP463130,PRJNA1020854,Molecular blueprints for spinal circuit modules controlling locomotor speed,GSE243993,Transcriptome Analysis,The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.,,pubmed:37919423,,V2a sample1 353 N10 R1,GSM7804001,,source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing,V2a sample1 353 N10 R1,The reads from each sequenced cell were mapped to the zebrafish reference genome “Danio rerio  Ensembl  GRCz11” using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis,Spinal cord,,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons,GSM7804001,GSM7804001: V2a sample1 353 N10 R1; Danio rerio; RNA Seq,GSM7804001 r1,GSM7804001,1,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP463130,,,SS2_18_353_N10_R1.fastq.gz,fastq,22772585.0,529595.0,GSM7804001 r1,0:43,A:6225918;C:5071489;G:5184079;T:6291099;N:0,43,,,,6225918,5071489,5184079,6291099,0,SRX21885905,SRS18977031,SRA1719948,"Neuroscience, Karolinaska Institutet","Neuroscience, Karolinaska Institutet",1,0.83486,,0.27703,,0.92433,,0.54887,,43,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Sweden,2023-09-25,Juvenile,Juvenile,Spinal Cord,Nervous System
26614,SRR26173915,SRX21885904,SRS18977029,SRP463130,PRJNA1020854,Molecular blueprints for spinal circuit modules controlling locomotor speed,GSE243993,Transcriptome Analysis,The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.,,pubmed:37919423,,V2a sample1 353 M9 R1,GSM7803976,,source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing,V2a sample1 353 M9 R1,The reads from each sequenced cell were mapped to the zebrafish reference genome “Danio rerio  Ensembl  GRCz11” using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis,Spinal cord,,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons,GSM7803976,GSM7803976: V2a sample1 353 M9 R1; Danio rerio; RNA Seq,GSM7803976 r1,GSM7803976,1,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP463130,,,SS2_18_353_M9_R1.fastq.gz,fastq,19698730.0,458110.0,GSM7803976 r1,0:43,A:5282525;C:4494162;G:4591316;T:5330727;N:0,43,,,,5282525,4494162,4591316,5330727,0,SRX21885904,SRS18977029,SRA1719948,"Neuroscience, Karolinaska Institutet","Neuroscience, Karolinaska Institutet",1,0.8598,,0.23744,,0.90871,,0.52081,,43,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Sweden,2023-09-25,Juvenile,Juvenile,Spinal Cord,Nervous System
26615,SRR26173916,SRX21885903,SRS18977028,SRP463130,PRJNA1020854,Molecular blueprints for spinal circuit modules controlling locomotor speed,GSE243993,Transcriptome Analysis,The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.,,pubmed:37919423,,V2a sample1 353 M8 R1,GSM7803975,,source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing,V2a sample1 353 M8 R1,The reads from each sequenced cell were mapped to the zebrafish reference genome “Danio rerio  Ensembl  GRCz11” using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis,Spinal cord,,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons,GSM7803975,GSM7803975: V2a sample1 353 M8 R1; Danio rerio; RNA Seq,GSM7803975 r1,GSM7803975,1,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP463130,,,SS2_18_353_M8_R1.fastq.gz,fastq,19646485.0,456895.0,GSM7803975 r1,0:43,A:5214519;C:4539724;G:4616920;T:5275322;N:0,43,,,,5214519,4539724,4616920,5275322,0,SRX21885903,SRS18977028,SRA1719948,"Neuroscience, Karolinaska Institutet","Neuroscience, Karolinaska Institutet",1,0.82407,,0.22367,,0.94298,,0.50209,,43,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Sweden,2023-09-25,Juvenile,Juvenile,Spinal Cord,Nervous System
26616,SRR26173917,SRX21885902,SRS18977025,SRP463130,PRJNA1020854,Molecular blueprints for spinal circuit modules controlling locomotor speed,GSE243993,Transcriptome Analysis,The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.,,pubmed:37919423,,V2a sample1 353 M7 R1,GSM7803974,,source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing,V2a sample1 353 M7 R1,The reads from each sequenced cell were mapped to the zebrafish reference genome “Danio rerio  Ensembl  GRCz11” using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis,Spinal cord,,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons,GSM7803974,GSM7803974: V2a sample1 353 M7 R1; Danio rerio; RNA Seq,GSM7803974 r1,GSM7803974,1,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP463130,,,SS2_18_353_M7_R1.fastq.gz,fastq,7333994.0,170558.0,GSM7803974 r1,0:43,A:1958042;C:1671444;G:1690497;T:2014011;N:0,43,,,,1958042,1671444,1690497,2014011,0,SRX21885902,SRS18977025,SRA1719948,"Neuroscience, Karolinaska Institutet","Neuroscience, Karolinaska Institutet",1,0.77392,,0.29548,,0.95114,,0.51367,,43,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Sweden,2023-09-25,Juvenile,Juvenile,Spinal Cord,Nervous System
26617,SRR26173918,SRX21885901,SRS18977027,SRP463130,PRJNA1020854,Molecular blueprints for spinal circuit modules controlling locomotor speed,GSE243993,Transcriptome Analysis,The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.,,pubmed:37919423,,V2a sample1 353 M6 R1,GSM7803973,,source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing,V2a sample1 353 M6 R1,The reads from each sequenced cell were mapped to the zebrafish reference genome “Danio rerio  Ensembl  GRCz11” using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis,Spinal cord,,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons,GSM7803973,GSM7803973: V2a sample1 353 M6 R1; Danio rerio; RNA Seq,GSM7803973 r1,GSM7803973,1,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP463130,,,SS2_18_353_M6_R1.fastq.gz,fastq,23546413.0,547591.0,GSM7803973 r1,0:43,A:6369803;C:5317401;G:5430197;T:6429012;N:0,43,,,,6369803,5317401,5430197,6429012,0,SRX21885901,SRS18977027,SRA1719948,"Neuroscience, Karolinaska Institutet","Neuroscience, Karolinaska Institutet",1,0.85602,,0.25223,,0.92654,,0.5306,,43,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Sweden,2023-09-25,Juvenile,Juvenile,Spinal Cord,Nervous System
26618,SRR26173919,SRX21885900,SRS18977026,SRP463130,PRJNA1020854,Molecular blueprints for spinal circuit modules controlling locomotor speed,GSE243993,Transcriptome Analysis,The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.,,pubmed:37919423,,V2a sample1 353 M5 R1,GSM7803972,,source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing,V2a sample1 353 M5 R1,The reads from each sequenced cell were mapped to the zebrafish reference genome “Danio rerio  Ensembl  GRCz11” using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis,Spinal cord,,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons,GSM7803972,GSM7803972: V2a sample1 353 M5 R1; Danio rerio; RNA Seq,GSM7803972 r1,GSM7803972,1,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP463130,,,SS2_18_353_M5_R1.fastq.gz,fastq,32919424.0,765568.0,GSM7803972 r1,0:43,A:8685316;C:7623131;G:7771679;T:8839298;N:0,43,,,,8685316,7623131,7771679,8839298,0,SRX21885900,SRS18977026,SRA1719948,"Neuroscience, Karolinaska Institutet","Neuroscience, Karolinaska Institutet",1,0.80691,,0.23128,,0.95404,,0.45556,,43,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Sweden,2023-09-25,Juvenile,Juvenile,Spinal Cord,Nervous System
26619,SRR26173920,SRX21885899,SRS18977024,SRP463130,PRJNA1020854,Molecular blueprints for spinal circuit modules controlling locomotor speed,GSE243993,Transcriptome Analysis,The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.,,pubmed:37919423,,V2a sample1 353 M4 R1,GSM7803971,,source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing,V2a sample1 353 M4 R1,The reads from each sequenced cell were mapped to the zebrafish reference genome “Danio rerio  Ensembl  GRCz11” using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis,Spinal cord,,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons,GSM7803971,GSM7803971: V2a sample1 353 M4 R1; Danio rerio; RNA Seq,GSM7803971 r1,GSM7803971,1,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP463130,,,SS2_18_353_M4_R1.fastq.gz,fastq,27743858.0,645206.0,GSM7803971 r1,0:43,A:7502879;C:6275733;G:6399007;T:7566239;N:0,43,,,,7502879,6275733,6399007,7566239,0,SRX21885899,SRS18977024,SRA1719948,"Neuroscience, Karolinaska Institutet","Neuroscience, Karolinaska Institutet",1,0.84534,,0.24169,,0.92131,,0.52033,,43,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Sweden,2023-09-25,Juvenile,Juvenile,Spinal Cord,Nervous System
26620,SRR26173921,SRX21885898,SRS18977023,SRP463130,PRJNA1020854,Molecular blueprints for spinal circuit modules controlling locomotor speed,GSE243993,Transcriptome Analysis,The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.,,pubmed:37919423,,V2a sample1 353 M3 R1,GSM7803970,,source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing,V2a sample1 353 M3 R1,The reads from each sequenced cell were mapped to the zebrafish reference genome “Danio rerio  Ensembl  GRCz11” using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis,Spinal cord,,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons,GSM7803970,GSM7803970: V2a sample1 353 M3 R1; Danio rerio; RNA Seq,GSM7803970 r1,GSM7803970,1,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP463130,,,SS2_18_353_M3_R1.fastq.gz,fastq,31646753.0,735971.0,GSM7803970 r1,0:43,A:8540660;C:7169606;G:7344972;T:8591515;N:0,43,,,,8540660,7169606,7344972,8591515,0,SRX21885898,SRS18977023,SRA1719948,"Neuroscience, Karolinaska Institutet","Neuroscience, Karolinaska Institutet",1,0.86607,,0.22984,,0.90905,,0.52816,,43,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Sweden,2023-09-25,Juvenile,Juvenile,Spinal Cord,Nervous System
26621,SRR26173922,SRX21885897,SRS18977019,SRP463130,PRJNA1020854,Molecular blueprints for spinal circuit modules controlling locomotor speed,GSE243993,Transcriptome Analysis,The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.,,pubmed:37919423,,V2a sample1 353 M2 R1,GSM7803969,,source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing,V2a sample1 353 M2 R1,The reads from each sequenced cell were mapped to the zebrafish reference genome “Danio rerio  Ensembl  GRCz11” using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis,Spinal cord,,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons,GSM7803969,GSM7803969: V2a sample1 353 M2 R1; Danio rerio; RNA Seq,GSM7803969 r1,GSM7803969,1,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP463130,,,SS2_18_353_M2_R1.fastq.gz,fastq,18262487.0,424709.0,GSM7803969 r1,0:43,A:4905794;C:4167223;G:4257561;T:4931909;N:0,43,,,,4905794,4167223,4257561,4931909,0,SRX21885897,SRS18977019,SRA1719948,"Neuroscience, Karolinaska Institutet","Neuroscience, Karolinaska Institutet",1,0.87727,,0.19789,,0.88327,,0.51404,,43,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Sweden,2023-09-25,Juvenile,Juvenile,Spinal Cord,Nervous System
26622,SRR26173923,SRX21885896,SRS18977022,SRP463130,PRJNA1020854,Molecular blueprints for spinal circuit modules controlling locomotor speed,GSE243993,Transcriptome Analysis,The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.,,pubmed:37919423,,V2a sample1 353 L1 R1,GSM7803944,,source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing,V2a sample1 353 L1 R1,The reads from each sequenced cell were mapped to the zebrafish reference genome “Danio rerio  Ensembl  GRCz11” using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis,Spinal cord,,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons,GSM7803944,GSM7803944: V2a sample1 353 L1 R1; Danio rerio; RNA Seq,GSM7803944 r1,GSM7803944,1,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP463130,,,SS2_18_353_L1_R1.fastq.gz,fastq,39261064.0,913048.0,GSM7803944 r1,0:43,A:10675714;C:8831605;G:9068828;T:10684917;N:0,43,,,,10675714,8831605,9068828,10684917,0,SRX21885896,SRS18977022,SRA1719948,"Neuroscience, Karolinaska Institutet","Neuroscience, Karolinaska Institutet",1,0.87519,,0.20246,,0.89696,,0.53416,,43,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Sweden,2023-09-25,Juvenile,Juvenile,Spinal Cord,Nervous System
26623,SRR26173924,SRX21885895,SRS18977020,SRP463130,PRJNA1020854,Molecular blueprints for spinal circuit modules controlling locomotor speed,GSE243993,Transcriptome Analysis,The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.,,pubmed:37919423,,V2a sample1 353 K24 R1,GSM7803943,,source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing,V2a sample1 353 K24 R1,The reads from each sequenced cell were mapped to the zebrafish reference genome “Danio rerio  Ensembl  GRCz11” using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis,Spinal cord,,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons,GSM7803943,GSM7803943: V2a sample1 353 K24 R1; Danio rerio; RNA Seq,GSM7803943 r1,GSM7803943,1,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP463130,,,SS2_18_353_K24_R1.fastq.gz,fastq,10877753.0,252971.0,GSM7803943 r1,0:43,A:2828581;C:2427642;G:2504205;T:3117325;N:0,43,,,,2828581,2427642,2504205,3117325,0,SRX21885895,SRS18977020,SRA1719948,"Neuroscience, Karolinaska Institutet","Neuroscience, Karolinaska Institutet",1,0.43358,,0.14805,,0.96483,,0.89489,,43,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Sweden,2023-09-25,Juvenile,Juvenile,Spinal Cord,Nervous System
26624,SRR26173925,SRX21885894,SRS18977021,SRP463130,PRJNA1020854,Molecular blueprints for spinal circuit modules controlling locomotor speed,GSE243993,Transcriptome Analysis,The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.,,pubmed:37919423,,V2a sample1 353 K23 R1,GSM7803942,,source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing,V2a sample1 353 K23 R1,The reads from each sequenced cell were mapped to the zebrafish reference genome “Danio rerio  Ensembl  GRCz11” using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis,Spinal cord,,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons,GSM7803942,GSM7803942: V2a sample1 353 K23 R1; Danio rerio; RNA Seq,GSM7803942 r1,GSM7803942,1,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP463130,,,SS2_18_353_K23_R1.fastq.gz,fastq,11967287.0,278309.0,GSM7803942 r1,0:43,A:3236216;C:2487815;G:2583125;T:3660131;N:0,43,,,,3236216,2487815,2583125,3660131,0,SRX21885894,SRS18977021,SRA1719948,"Neuroscience, Karolinaska Institutet","Neuroscience, Karolinaska Institutet",1,0.45352,,0.10712,,0.99249,,0.66514,,43,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Sweden,2023-09-25,Juvenile,Juvenile,Spinal Cord,Nervous System
26625,SRR26173926,SRX21885893,SRS18977016,SRP463130,PRJNA1020854,Molecular blueprints for spinal circuit modules controlling locomotor speed,GSE243993,Transcriptome Analysis,The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.,,pubmed:37919423,,V2a sample1 353 K22 R1,GSM7803941,,source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing,V2a sample1 353 K22 R1,The reads from each sequenced cell were mapped to the zebrafish reference genome “Danio rerio  Ensembl  GRCz11” using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis,Spinal cord,,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons,GSM7803941,GSM7803941: V2a sample1 353 K22 R1; Danio rerio; RNA Seq,GSM7803941 r1,GSM7803941,1,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP463130,,,SS2_18_353_K22_R1.fastq.gz,fastq,27851702.0,647714.0,GSM7803941 r1,0:43,A:7549377;C:6154745;G:6313649;T:7833931;N:0,43,,,,7549377,6154745,6313649,7833931,0,SRX21885893,SRS18977016,SRA1719948,"Neuroscience, Karolinaska Institutet","Neuroscience, Karolinaska Institutet",1,0.75496,,0.26752,,0.9472,,0.55385,,43,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Sweden,2023-09-25,Juvenile,Juvenile,Spinal Cord,Nervous System
26626,SRR26173927,SRX21885892,SRS18977017,SRP463130,PRJNA1020854,Molecular blueprints for spinal circuit modules controlling locomotor speed,GSE243993,Transcriptome Analysis,The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.,,pubmed:37919423,,V2a sample1 353 K21 R1,GSM7803940,,source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing,V2a sample1 353 K21 R1,The reads from each sequenced cell were mapped to the zebrafish reference genome “Danio rerio  Ensembl  GRCz11” using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis,Spinal cord,,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons,GSM7803940,GSM7803940: V2a sample1 353 K21 R1; Danio rerio; RNA Seq,GSM7803940 r1,GSM7803940,1,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP463130,,,SS2_18_353_K21_R1.fastq.gz,fastq,25669151.0,596957.0,GSM7803940 r1,0:43,A:6873604;C:5886019;G:6019889;T:6889639;N:0,43,,,,6873604,5886019,6019889,6889639,0,SRX21885892,SRS18977017,SRA1719948,"Neuroscience, Karolinaska Institutet","Neuroscience, Karolinaska Institutet",1,0.88089,,0.15861,,0.87988,,0.53381,,43,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Sweden,2023-09-25,Juvenile,Juvenile,Spinal Cord,Nervous System
26627,SRR26173928,SRX21885891,SRS18977018,SRP463130,PRJNA1020854,Molecular blueprints for spinal circuit modules controlling locomotor speed,GSE243993,Transcriptome Analysis,The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.,,pubmed:37919423,,V2a sample1 353 K20 R1,GSM7803939,,source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing,V2a sample1 353 K20 R1,The reads from each sequenced cell were mapped to the zebrafish reference genome “Danio rerio  Ensembl  GRCz11” using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis,Spinal cord,,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons,GSM7803939,GSM7803939: V2a sample1 353 K20 R1; Danio rerio; RNA Seq,GSM7803939 r1,GSM7803939,1,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP463130,,,SS2_18_353_K20_R1.fastq.gz,fastq,21481940.0,499580.0,GSM7803939 r1,0:43,A:5797700;C:4860618;G:4983240;T:5840382;N:0,43,,,,5797700,4860618,4983240,5840382,0,SRX21885891,SRS18977018,SRA1719948,"Neuroscience, Karolinaska Institutet","Neuroscience, Karolinaska Institutet",1,0.86105,,0.23237,,0.90134,,0.52076,,43,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Sweden,2023-09-25,Juvenile,Juvenile,Spinal Cord,Nervous System
26628,SRR26173929,SRX21885890,SRS18977014,SRP463130,PRJNA1020854,Molecular blueprints for spinal circuit modules controlling locomotor speed,GSE243993,Transcriptome Analysis,The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.,,pubmed:37919423,,V2a sample1 353 K19 R1,GSM7803938,,source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing,V2a sample1 353 K19 R1,The reads from each sequenced cell were mapped to the zebrafish reference genome “Danio rerio  Ensembl  GRCz11” using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis,Spinal cord,,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons,GSM7803938,GSM7803938: V2a sample1 353 K19 R1; Danio rerio; RNA Seq,GSM7803938 r1,GSM7803938,1,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP463130,,,SS2_18_353_K19_R1.fastq.gz,fastq,23007709.0,535063.0,GSM7803938 r1,0:43,A:6158988;C:5204570;G:5321940;T:6322211;N:0,43,,,,6158988,5204570,5321940,6322211,0,SRX21885890,SRS18977014,SRA1719948,"Neuroscience, Karolinaska Institutet","Neuroscience, Karolinaska Institutet",1,0.78733,,0.25377,,0.94556,,0.53829,,43,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Sweden,2023-09-25,Juvenile,Juvenile,Spinal Cord,Nervous System
26629,SRR26173930,SRX21885889,SRS18977015,SRP463130,PRJNA1020854,Molecular blueprints for spinal circuit modules controlling locomotor speed,GSE243993,Transcriptome Analysis,The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.,,pubmed:37919423,,V2a sample1 353 K18 R1,GSM7803937,,source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing,V2a sample1 353 K18 R1,The reads from each sequenced cell were mapped to the zebrafish reference genome “Danio rerio  Ensembl  GRCz11” using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis,Spinal cord,,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons,GSM7803937,GSM7803937: V2a sample1 353 K18 R1; Danio rerio; RNA Seq,GSM7803937 r1,GSM7803937,1,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP463130,,,SS2_18_353_K18_R1.fastq.gz,fastq,25088565.0,583455.0,GSM7803937 r1,0:43,A:6762035;C:5659600;G:5805722;T:6861208;N:0,43,,,,6762035,5659600,5805722,6861208,0,SRX21885889,SRS18977015,SRA1719948,"Neuroscience, Karolinaska Institutet","Neuroscience, Karolinaska Institutet",1,0.83379,,0.22893,,0.9251,,0.51495,,43,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Sweden,2023-09-25,Juvenile,Juvenile,Spinal Cord,Nervous System
26630,SRR26173931,SRX21885888,SRS18977011,SRP463130,PRJNA1020854,Molecular blueprints for spinal circuit modules controlling locomotor speed,GSE243993,Transcriptome Analysis,The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.,,pubmed:37919423,,V2a sample1 353 J17 R1,GSM7803912,,source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing,V2a sample1 353 J17 R1,The reads from each sequenced cell were mapped to the zebrafish reference genome “Danio rerio  Ensembl  GRCz11” using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis,Spinal cord,,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons,GSM7803912,GSM7803912: V2a sample1 353 J17 R1; Danio rerio; RNA Seq,GSM7803912 r1,GSM7803912,1,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP463130,,,SS2_18_353_J17_R1.fastq.gz,fastq,24235359.0,563613.0,GSM7803912 r1,0:43,A:6687906;C:5244266;G:5377965;T:6925222;N:0,43,,,,6687906,5244266,5377965,6925222,0,SRX21885888,SRS18977011,SRA1719948,"Neuroscience, Karolinaska Institutet","Neuroscience, Karolinaska Institutet",1,0.80212,,0.29984,,0.94769,,0.57954,,43,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Sweden,2023-09-25,Juvenile,Juvenile,Spinal Cord,Nervous System
26631,SRR26173932,SRX21885887,SRS18977013,SRP463130,PRJNA1020854,Molecular blueprints for spinal circuit modules controlling locomotor speed,GSE243993,Transcriptome Analysis,The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.,,pubmed:37919423,,V2a sample1 353 J16 R1,GSM7803911,,source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing,V2a sample1 353 J16 R1,The reads from each sequenced cell were mapped to the zebrafish reference genome “Danio rerio  Ensembl  GRCz11” using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis,Spinal cord,,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons,GSM7803911,GSM7803911: V2a sample1 353 J16 R1; Danio rerio; RNA Seq,GSM7803911 r1,GSM7803911,1,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP463130,,,SS2_18_353_J16_R1.fastq.gz,fastq,27111973.0,630511.0,GSM7803911 r1,0:43,A:7217001;C:6181115;G:6340909;T:7372948;N:0,43,,,,7217001,6181115,6340909,7372948,0,SRX21885887,SRS18977013,SRA1719948,"Neuroscience, Karolinaska Institutet","Neuroscience, Karolinaska Institutet",1,0.71684,,0.26529,,0.94491,,0.50602,,43,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Sweden,2023-09-25,Juvenile,Juvenile,Spinal Cord,Nervous System
26632,SRR26173933,SRX21885886,SRS18977010,SRP463130,PRJNA1020854,Molecular blueprints for spinal circuit modules controlling locomotor speed,GSE243993,Transcriptome Analysis,The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.,,pubmed:37919423,,V2a sample1 353 J15 R1,GSM7803910,,source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing,V2a sample1 353 J15 R1,The reads from each sequenced cell were mapped to the zebrafish reference genome “Danio rerio  Ensembl  GRCz11” using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis,Spinal cord,,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons,GSM7803910,GSM7803910: V2a sample1 353 J15 R1; Danio rerio; RNA Seq,GSM7803910 r1,GSM7803910,1,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP463130,,,SS2_18_353_J15_R1.fastq.gz,fastq,23290391.0,541637.0,GSM7803910 r1,0:43,A:6290890;C:5279983;G:5398604;T:6320914;N:0,43,,,,6290890,5279983,5398604,6320914,0,SRX21885886,SRS18977010,SRA1719948,"Neuroscience, Karolinaska Institutet","Neuroscience, Karolinaska Institutet",1,0.85285,,0.2328,,0.92214,,0.51744,,43,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Sweden,2023-09-25,Juvenile,Juvenile,Spinal Cord,Nervous System
26633,SRR26173934,SRX21885885,SRS18977012,SRP463130,PRJNA1020854,Molecular blueprints for spinal circuit modules controlling locomotor speed,GSE243993,Transcriptome Analysis,The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.,,pubmed:37919423,,V2a sample1 353 J14 R1,GSM7803909,,source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing,V2a sample1 353 J14 R1,The reads from each sequenced cell were mapped to the zebrafish reference genome “Danio rerio  Ensembl  GRCz11” using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis,Spinal cord,,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons,GSM7803909,GSM7803909: V2a sample1 353 J14 R1; Danio rerio; RNA Seq,GSM7803909 r1,GSM7803909,1,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP463130,,,SS2_18_353_J14_R1.fastq.gz,fastq,22177637.0,515759.0,GSM7803909 r1,0:43,A:5946858;C:4992625;G:5124052;T:6114102;N:0,43,,,,5946858,4992625,5124052,6114102,0,SRX21885885,SRS18977012,SRA1719948,"Neuroscience, Karolinaska Institutet","Neuroscience, Karolinaska Institutet",1,0.75767,,0.28218,,0.95394,,0.44926,,43,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Sweden,2023-09-25,Juvenile,Juvenile,Spinal Cord,Nervous System
26634,SRR26173935,SRX21885884,SRS18977009,SRP463130,PRJNA1020854,Molecular blueprints for spinal circuit modules controlling locomotor speed,GSE243993,Transcriptome Analysis,The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.,,pubmed:37919423,,V2a sample1 353 J13 R1,GSM7803908,,source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing,V2a sample1 353 J13 R1,The reads from each sequenced cell were mapped to the zebrafish reference genome “Danio rerio  Ensembl  GRCz11” using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis,Spinal cord,,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons,GSM7803908,GSM7803908: V2a sample1 353 J13 R1; Danio rerio; RNA Seq,GSM7803908 r1,GSM7803908,1,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP463130,,,SS2_18_353_J13_R1.fastq.gz,fastq,25862479.0,601453.0,GSM7803908 r1,0:43,A:6973520;C:5810960;G:5943676;T:7134323;N:0,43,,,,6973520,5810960,5943676,7134323,0,SRX21885884,SRS18977009,SRA1719948,"Neuroscience, Karolinaska Institutet","Neuroscience, Karolinaska Institutet",1,0.81395,,0.28506,,0.92801,,0.50957,,43,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Sweden,2023-09-25,Juvenile,Juvenile,Spinal Cord,Nervous System
26635,SRR26173936,SRX21885883,SRS18977008,SRP463130,PRJNA1020854,Molecular blueprints for spinal circuit modules controlling locomotor speed,GSE243993,Transcriptome Analysis,The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.,,pubmed:37919423,,V2a sample1 353 J12 R1,GSM7803907,,source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing,V2a sample1 353 J12 R1,The reads from each sequenced cell were mapped to the zebrafish reference genome “Danio rerio  Ensembl  GRCz11” using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis,Spinal cord,,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons,GSM7803907,GSM7803907: V2a sample1 353 J12 R1; Danio rerio; RNA Seq,GSM7803907 r1,GSM7803907,1,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP463130,,,SS2_18_353_J12_R1.fastq.gz,fastq,21381621.0,497247.0,GSM7803907 r1,0:43,A:5870837;C:4668159;G:4791244;T:6051381;N:0,43,,,,5870837,4668159,4791244,6051381,0,SRX21885883,SRS18977008,SRA1719948,"Neuroscience, Karolinaska Institutet","Neuroscience, Karolinaska Institutet",1,0.7505,,0.43605,,0.95639,,0.84845,,43,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Sweden,2023-09-25,Juvenile,Juvenile,Spinal Cord,Nervous System
26636,SRR26173937,SRX21885882,SRS18977006,SRP463130,PRJNA1020854,Molecular blueprints for spinal circuit modules controlling locomotor speed,GSE243993,Transcriptome Analysis,The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.,,pubmed:37919423,,V2a sample1 353 J11 R1,GSM7803906,,source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing,V2a sample1 353 J11 R1,The reads from each sequenced cell were mapped to the zebrafish reference genome “Danio rerio  Ensembl  GRCz11” using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis,Spinal cord,,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons,GSM7803906,GSM7803906: V2a sample1 353 J11 R1; Danio rerio; RNA Seq,GSM7803906 r1,GSM7803906,1,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP463130,,,SS2_18_353_J11_R1.fastq.gz,fastq,23749287.0,552309.0,GSM7803906 r1,0:43,A:6394024;C:5405641;G:5544581;T:6405041;N:0,43,,,,6394024,5405641,5544581,6405041,0,SRX21885882,SRS18977006,SRA1719948,"Neuroscience, Karolinaska Institutet","Neuroscience, Karolinaska Institutet",1,0.88044,,0.20802,,0.89327,,0.49819,,43,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Sweden,2023-09-25,Juvenile,Juvenile,Spinal Cord,Nervous System
26637,SRR26173938,SRX21885881,SRS18977005,SRP463130,PRJNA1020854,Molecular blueprints for spinal circuit modules controlling locomotor speed,GSE243993,Transcriptome Analysis,The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.,,pubmed:37919423,,V2a sample1 353 J10 R1,GSM7803905,,source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing,V2a sample1 353 J10 R1,The reads from each sequenced cell were mapped to the zebrafish reference genome “Danio rerio  Ensembl  GRCz11” using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis,Spinal cord,,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons,GSM7803905,GSM7803905: V2a sample1 353 J10 R1; Danio rerio; RNA Seq,GSM7803905 r1,GSM7803905,1,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP463130,,,SS2_18_353_J10_R1.fastq.gz,fastq,29176145.0,678515.0,GSM7803905 r1,0:43,A:7791607;C:6552866;G:6732705;T:8098967;N:0,43,,,,7791607,6552866,6732705,8098967,0,SRX21885881,SRS18977005,SRA1719948,"Neuroscience, Karolinaska Institutet","Neuroscience, Karolinaska Institutet",1,0.71479,,0.31461,,0.95937,,0.54763,,43,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Sweden,2023-09-25,Juvenile,Juvenile,Spinal Cord,Nervous System
26638,SRR26173939,SRX21885880,SRS18977007,SRP463130,PRJNA1020854,Molecular blueprints for spinal circuit modules controlling locomotor speed,GSE243993,Transcriptome Analysis,The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.,,pubmed:37919423,,V2a sample1 353 I9 R1,GSM7803880,,source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing,V2a sample1 353 I9 R1,The reads from each sequenced cell were mapped to the zebrafish reference genome “Danio rerio  Ensembl  GRCz11” using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis,Spinal cord,,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons,GSM7803880,GSM7803880: V2a sample1 353 I9 R1; Danio rerio; RNA Seq,GSM7803880 r1,GSM7803880,1,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP463130,,,SS2_18_353_I9_R1.fastq.gz,fastq,24090707.0,560249.0,GSM7803880 r1,0:43,A:6543882;C:5415516;G:5557789;T:6573520;N:0,43,,,,6543882,5415516,5557789,6573520,0,SRX21885880,SRS18977007,SRA1719948,"Neuroscience, Karolinaska Institutet","Neuroscience, Karolinaska Institutet",1,0.85372,,0.22772,,0.90094,,0.53266,,43,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Sweden,2023-09-25,Juvenile,Juvenile,Spinal Cord,Nervous System
26639,SRR26173940,SRX21885879,SRS18977004,SRP463130,PRJNA1020854,Molecular blueprints for spinal circuit modules controlling locomotor speed,GSE243993,Transcriptome Analysis,The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.,,pubmed:37919423,,V2a sample1 353 I8 R1,GSM7803879,,source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing,V2a sample1 353 I8 R1,The reads from each sequenced cell were mapped to the zebrafish reference genome “Danio rerio  Ensembl  GRCz11” using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis,Spinal cord,,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons,GSM7803879,GSM7803879: V2a sample1 353 I8 R1; Danio rerio; RNA Seq,GSM7803879 r1,GSM7803879,1,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP463130,,,SS2_18_353_I8_R1.fastq.gz,fastq,20394255.0,474285.0,GSM7803879 r1,0:43,A:5480008;C:4590753;G:4698367;T:5625127;N:0,43,,,,5480008,4590753,4698367,5625127,0,SRX21885879,SRS18977004,SRA1719948,"Neuroscience, Karolinaska Institutet","Neuroscience, Karolinaska Institutet",1,0.74576,,0.3214,,0.95806,,0.50252,,43,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Sweden,2023-09-25,Juvenile,Juvenile,Spinal Cord,Nervous System
26640,SRR26173941,SRX21885878,SRS18977003,SRP463130,PRJNA1020854,Molecular blueprints for spinal circuit modules controlling locomotor speed,GSE243993,Transcriptome Analysis,The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.,,pubmed:37919423,,V2a sample1 353 I7 R1,GSM7803878,,source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing,V2a sample1 353 I7 R1,The reads from each sequenced cell were mapped to the zebrafish reference genome “Danio rerio  Ensembl  GRCz11” using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis,Spinal cord,,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons,GSM7803878,GSM7803878: V2a sample1 353 I7 R1; Danio rerio; RNA Seq,GSM7803878 r1,GSM7803878,1,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP463130,,,SS2_18_353_I7_R1.fastq.gz,fastq,20725011.0,481977.0,GSM7803878 r1,0:43,A:5625880;C:4647001;G:4774993;T:5677137;N:0,43,,,,5625880,4647001,4774993,5677137,0,SRX21885878,SRS18977003,SRA1719948,"Neuroscience, Karolinaska Institutet","Neuroscience, Karolinaska Institutet",1,0.85618,,0.25757,,0.90479,,0.5166,,43,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Sweden,2023-09-25,Juvenile,Juvenile,Spinal Cord,Nervous System
26641,SRR26173942,SRX21885877,SRS18977002,SRP463130,PRJNA1020854,Molecular blueprints for spinal circuit modules controlling locomotor speed,GSE243993,Transcriptome Analysis,The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.,,pubmed:37919423,,V2a sample1 353 I6 R1,GSM7803877,,source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing,V2a sample1 353 I6 R1,The reads from each sequenced cell were mapped to the zebrafish reference genome “Danio rerio  Ensembl  GRCz11” using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis,Spinal cord,,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons,GSM7803877,GSM7803877: V2a sample1 353 I6 R1; Danio rerio; RNA Seq,GSM7803877 r1,GSM7803877,1,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP463130,,,SS2_18_353_I6_R1.fastq.gz,fastq,30081467.0,699569.0,GSM7803877 r1,0:43,A:8235100;C:6659013;G:6834239;T:8353115;N:0,43,,,,8235100,6659013,6834239,8353115,0,SRX21885877,SRS18977002,SRA1719948,"Neuroscience, Karolinaska Institutet","Neuroscience, Karolinaska Institutet",1,0.82589,,0.32845,,0.92417,,0.52161,,43,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Sweden,2023-09-25,Juvenile,Juvenile,Spinal Cord,Nervous System
26642,SRR26173943,SRX21885876,SRS18977001,SRP463130,PRJNA1020854,Molecular blueprints for spinal circuit modules controlling locomotor speed,GSE243993,Transcriptome Analysis,The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.,,pubmed:37919423,,V2a sample1 353 I5 R1,GSM7803876,,source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing,V2a sample1 353 I5 R1,The reads from each sequenced cell were mapped to the zebrafish reference genome “Danio rerio  Ensembl  GRCz11” using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis,Spinal cord,,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons,GSM7803876,GSM7803876: V2a sample1 353 I5 R1; Danio rerio; RNA Seq,GSM7803876 r1,GSM7803876,1,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP463130,,,SS2_18_353_I5_R1.fastq.gz,fastq,34927911.0,812277.0,GSM7803876 r1,0:43,A:9434960;C:7894430;G:8106720;T:9491801;N:0,43,,,,9434960,7894430,8106720,9491801,0,SRX21885876,SRS18977001,SRA1719948,"Neuroscience, Karolinaska Institutet","Neuroscience, Karolinaska Institutet",1,0.86691,,0.23833,,0.90429,,0.52495,,43,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Sweden,2023-09-25,Juvenile,Juvenile,Spinal Cord,Nervous System
26643,SRR26173944,SRX21885875,SRS18977000,SRP463130,PRJNA1020854,Molecular blueprints for spinal circuit modules controlling locomotor speed,GSE243993,Transcriptome Analysis,The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.,,pubmed:37919423,,V2a sample1 353 I4 R1,GSM7803875,,source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing,V2a sample1 353 I4 R1,The reads from each sequenced cell were mapped to the zebrafish reference genome “Danio rerio  Ensembl  GRCz11” using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis,Spinal cord,,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons,GSM7803875,GSM7803875: V2a sample1 353 I4 R1; Danio rerio; RNA Seq,GSM7803875 r1,GSM7803875,1,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP463130,,,SS2_18_353_I4_R1.fastq.gz,fastq,41615099.0,967793.0,GSM7803875 r1,0:43,A:11232545;C:9389292;G:9644531;T:11348731;N:0,43,,,,11232545,9389292,9644531,11348731,0,SRX21885875,SRS18977000,SRA1719948,"Neuroscience, Karolinaska Institutet","Neuroscience, Karolinaska Institutet",1,0.84939,,0.24066,,0.90337,,0.50767,,43,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Sweden,2023-09-25,Juvenile,Juvenile,Spinal Cord,Nervous System
26644,SRR26173945,SRX21885874,SRS18976999,SRP463130,PRJNA1020854,Molecular blueprints for spinal circuit modules controlling locomotor speed,GSE243993,Transcriptome Analysis,The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.,,pubmed:37919423,,V2a sample1 353 I3 R1,GSM7803874,,source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing,V2a sample1 353 I3 R1,The reads from each sequenced cell were mapped to the zebrafish reference genome “Danio rerio  Ensembl  GRCz11” using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis,Spinal cord,,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons,GSM7803874,GSM7803874: V2a sample1 353 I3 R1; Danio rerio; RNA Seq,GSM7803874 r1,GSM7803874,1,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP463130,,,SS2_18_353_I3_R1.fastq.gz,fastq,34316150.0,798050.0,GSM7803874 r1,0:43,A:9271155;C:7644902;G:7871948;T:9528145;N:0,43,,,,9271155,7644902,7871948,9528145,0,SRX21885874,SRS18976999,SRA1719948,"Neuroscience, Karolinaska Institutet","Neuroscience, Karolinaska Institutet",1,0.76458,,0.30549,,0.95649,,0.53971,,43,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Sweden,2023-09-25,Juvenile,Juvenile,Spinal Cord,Nervous System
26645,SRR26173772,SRX21885873,SRS18976998,SRP463130,PRJNA1020854,Molecular blueprints for spinal circuit modules controlling locomotor speed,GSE243993,Transcriptome Analysis,The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.,,pubmed:37919423,,V2a sample2 354 L20 R1,GSM7804347,,source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing,V2a sample2 354 L20 R1,The reads from each sequenced cell were mapped to the zebrafish reference genome “Danio rerio  Ensembl  GRCz11” using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis,Spinal cord,,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons,GSM7804347,GSM7804347: V2a sample2 354 L20 R1; Danio rerio; RNA Seq,GSM7804347 r1,GSM7804347,1,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP463130,,,SS2_18_354_L20_R1.fastq.gz,fastq,29370161.0,683027.0,GSM7804347 r1,0:43,A:8415585;C:6114838;G:6265996;T:8573742;N:0,43,,,,8415585,6114838,6265996,8573742,0,SRX21885873,SRS18976998,SRA1719948,"Neuroscience, Karolinaska Institutet","Neuroscience, Karolinaska Institutet",1,0.85077,,0.37188,,0.96952,,0.55266,,43,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Sweden,2023-09-25,Juvenile,Juvenile,Spinal Cord,Nervous System
26646,SRR26173773,SRX21885872,SRS18976996,SRP463130,PRJNA1020854,Molecular blueprints for spinal circuit modules controlling locomotor speed,GSE243993,Transcriptome Analysis,The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.,,pubmed:37919423,,V2a sample2 354 L19 R1,GSM7804346,,source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing,V2a sample2 354 L19 R1,The reads from each sequenced cell were mapped to the zebrafish reference genome “Danio rerio  Ensembl  GRCz11” using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis,Spinal cord,,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons,GSM7804346,GSM7804346: V2a sample2 354 L19 R1; Danio rerio; RNA Seq,GSM7804346 r1,GSM7804346,1,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP463130,,,SS2_18_354_L19_R1.fastq.gz,fastq,31064189.0,722423.0,GSM7804346 r1,0:43,A:8761668;C:6650054;G:6796322;T:8856145;N:0,43,,,,8761668,6650054,6796322,8856145,0,SRX21885872,SRS18976996,SRA1719948,"Neuroscience, Karolinaska Institutet","Neuroscience, Karolinaska Institutet",1,0.84784,,0.4328,,0.91865,,0.54701,,43,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Sweden,2023-09-25,Juvenile,Juvenile,Spinal Cord,Nervous System
26647,SRR26173774,SRX21885871,SRS18976997,SRP463130,PRJNA1020854,Molecular blueprints for spinal circuit modules controlling locomotor speed,GSE243993,Transcriptome Analysis,The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.,,pubmed:37919423,,V2a sample2 354 L18 R1,GSM7804345,,source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing,V2a sample2 354 L18 R1,The reads from each sequenced cell were mapped to the zebrafish reference genome “Danio rerio  Ensembl  GRCz11” using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis,Spinal cord,,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons,GSM7804345,GSM7804345: V2a sample2 354 L18 R1; Danio rerio; RNA Seq,GSM7804345 r1,GSM7804345,1,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP463130,,,SS2_18_354_L18_R1.fastq.gz,fastq,30281460.0,704220.0,GSM7804345 r1,0:43,A:8479926;C:6562726;G:6732082;T:8506726;N:0,43,,,,8479926,6562726,6732082,8506726,0,SRX21885871,SRS18976997,SRA1719948,"Neuroscience, Karolinaska Institutet","Neuroscience, Karolinaska Institutet",1,0.86278,,0.35585,,0.9133,,0.52905,,43,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Sweden,2023-09-25,Juvenile,Juvenile,Spinal Cord,Nervous System
26648,SRR26173775,SRX21885870,SRS18976994,SRP463130,PRJNA1020854,Molecular blueprints for spinal circuit modules controlling locomotor speed,GSE243993,Transcriptome Analysis,The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.,,pubmed:37919423,,V2a sample2 354 K17 R1,GSM7804320,,source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing,V2a sample2 354 K17 R1,The reads from each sequenced cell were mapped to the zebrafish reference genome “Danio rerio  Ensembl  GRCz11” using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis,Spinal cord,,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons,GSM7804320,GSM7804320: V2a sample2 354 K17 R1; Danio rerio; RNA Seq,GSM7804320 r1,GSM7804320,1,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP463130,,,SS2_18_354_K17_R1.fastq.gz,fastq,33586999.0,781093.0,GSM7804320 r1,0:43,A:9198057;C:7484755;G:7655890;T:9248297;N:0,43,,,,9198057,7484755,7655890,9248297,0,SRX21885870,SRS18976994,SRA1719948,"Neuroscience, Karolinaska Institutet","Neuroscience, Karolinaska Institutet",1,0.85328,,0.25956,,0.91013,,0.52033,,43,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Sweden,2023-09-25,Juvenile,Juvenile,Spinal Cord,Nervous System
26649,SRR26173776,SRX21885869,SRS18976995,SRP463130,PRJNA1020854,Molecular blueprints for spinal circuit modules controlling locomotor speed,GSE243993,Transcriptome Analysis,The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.,,pubmed:37919423,,V2a sample2 354 K16 R1,GSM7804319,,source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing,V2a sample2 354 K16 R1,The reads from each sequenced cell were mapped to the zebrafish reference genome “Danio rerio  Ensembl  GRCz11” using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis,Spinal cord,,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons,GSM7804319,GSM7804319: V2a sample2 354 K16 R1; Danio rerio; RNA Seq,GSM7804319 r1,GSM7804319,1,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP463130,,,SS2_18_354_K16_R1.fastq.gz,fastq,34942961.0,812627.0,GSM7804319 r1,0:43,A:9884091;C:7477031;G:7622507;T:9959332;N:0,43,,,,9884091,7477031,7622507,9959332,0,SRX21885869,SRS18976995,SRA1719948,"Neuroscience, Karolinaska Institutet","Neuroscience, Karolinaska Institutet",1,0.87105,,0.25941,,0.9344,,0.48083,,43,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Sweden,2023-09-25,Juvenile,Juvenile,Spinal Cord,Nervous System
26650,SRR26173777,SRX21885868,SRS18976993,SRP463130,PRJNA1020854,Molecular blueprints for spinal circuit modules controlling locomotor speed,GSE243993,Transcriptome Analysis,The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.,,pubmed:37919423,,V2a sample2 354 K15 R1,GSM7804318,,source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing,V2a sample2 354 K15 R1,The reads from each sequenced cell were mapped to the zebrafish reference genome “Danio rerio  Ensembl  GRCz11” using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis,Spinal cord,,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons,GSM7804318,GSM7804318: V2a sample2 354 K15 R1; Danio rerio; RNA Seq,GSM7804318 r1,GSM7804318,1,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP463130,,,SS2_18_354_K15_R1.fastq.gz,fastq,32995577.0,767339.0,GSM7804318 r1,0:43,A:8890551;C:7526324;G:7638992;T:8939710;N:0,43,,,,8890551,7526324,7638992,8939710,0,SRX21885868,SRS18976993,SRA1719948,"Neuroscience, Karolinaska Institutet","Neuroscience, Karolinaska Institutet",1,0.73421,,0.24037,,0.92281,,0.5232,,43,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Sweden,2023-09-25,Juvenile,Juvenile,Spinal Cord,Nervous System
26651,SRR26173778,SRX21885867,SRS18976991,SRP463130,PRJNA1020854,Molecular blueprints for spinal circuit modules controlling locomotor speed,GSE243993,Transcriptome Analysis,The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.,,pubmed:37919423,,V2a sample2 354 K14 R1,GSM7804317,,source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing,V2a sample2 354 K14 R1,The reads from each sequenced cell were mapped to the zebrafish reference genome “Danio rerio  Ensembl  GRCz11” using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis,Spinal cord,,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons,GSM7804317,GSM7804317: V2a sample2 354 K14 R1; Danio rerio; RNA Seq,GSM7804317 r1,GSM7804317,1,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP463130,,,SS2_18_354_K14_R1.fastq.gz,fastq,34918709.0,812063.0,GSM7804317 r1,0:43,A:9702093;C:7610097;G:7779557;T:9826962;N:0,43,,,,9702093,7610097,7779557,9826962,0,SRX21885867,SRS18976991,SRA1719948,"Neuroscience, Karolinaska Institutet","Neuroscience, Karolinaska Institutet",1,0.84054,,0.28341,,0.95844,,0.52971,,43,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Sweden,2023-09-25,Juvenile,Juvenile,Spinal Cord,Nervous System
26652,SRR26173779,SRX21885866,SRS18976992,SRP463130,PRJNA1020854,Molecular blueprints for spinal circuit modules controlling locomotor speed,GSE243993,Transcriptome Analysis,The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.,,pubmed:37919423,,V2a sample2 354 K13 R1,GSM7804316,,source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing,V2a sample2 354 K13 R1,The reads from each sequenced cell were mapped to the zebrafish reference genome “Danio rerio  Ensembl  GRCz11” using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis,Spinal cord,,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons,GSM7804316,GSM7804316: V2a sample2 354 K13 R1; Danio rerio; RNA Seq,GSM7804316 r1,GSM7804316,1,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP463130,,,SS2_18_354_K13_R1.fastq.gz,fastq,34277278.0,797146.0,GSM7804316 r1,0:43,A:9378683;C:7633762;G:7740014;T:9524819;N:0,43,,,,9378683,7633762,7740014,9524819,0,SRX21885866,SRS18976992,SRA1719948,"Neuroscience, Karolinaska Institutet","Neuroscience, Karolinaska Institutet",1,0.81082,,0.32096,,0.92908,,0.53117,,43,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Sweden,2023-09-25,Juvenile,Juvenile,Spinal Cord,Nervous System
26653,SRR26173780,SRX21885865,SRS18976990,SRP463130,PRJNA1020854,Molecular blueprints for spinal circuit modules controlling locomotor speed,GSE243993,Transcriptome Analysis,The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.,,pubmed:37919423,,V2a sample2 354 K12 R1,GSM7804315,,source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing,V2a sample2 354 K12 R1,The reads from each sequenced cell were mapped to the zebrafish reference genome “Danio rerio  Ensembl  GRCz11” using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis,Spinal cord,,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons,GSM7804315,GSM7804315: V2a sample2 354 K12 R1; Danio rerio; RNA Seq,GSM7804315 r1,GSM7804315,1,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP463130,,,SS2_18_354_K12_R1.fastq.gz,fastq,28040429.0,652103.0,GSM7804315 r1,0:43,A:7699772;C:6248721;G:6390568;T:7701368;N:0,43,,,,7699772,6248721,6390568,7701368,0,SRX21885865,SRS18976990,SRA1719948,"Neuroscience, Karolinaska Institutet","Neuroscience, Karolinaska Institutet",1,0.88142,,0.22865,,0.88051,,0.50605,,43,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Sweden,2023-09-25,Juvenile,Juvenile,Spinal Cord,Nervous System
26654,SRR26173781,SRX21885864,SRS18976988,SRP463130,PRJNA1020854,Molecular blueprints for spinal circuit modules controlling locomotor speed,GSE243993,Transcriptome Analysis,The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.,,pubmed:37919423,,V2a sample2 354 K11 R1,GSM7804314,,source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing,V2a sample2 354 K11 R1,The reads from each sequenced cell were mapped to the zebrafish reference genome “Danio rerio  Ensembl  GRCz11” using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis,Spinal cord,,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons,GSM7804314,GSM7804314: V2a sample2 354 K11 R1; Danio rerio; RNA Seq,GSM7804314 r1,GSM7804314,1,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP463130,,,SS2_18_354_K11_R1.fastq.gz,fastq,37066516.0,862012.0,GSM7804314 r1,0:43,A:10269237;C:8130071;G:8315363;T:10351845;N:0,43,,,,10269237,8130071,8315363,10351845,0,SRX21885864,SRS18976988,SRA1719948,"Neuroscience, Karolinaska Institutet","Neuroscience, Karolinaska Institutet",1,0.85469,,0.39595,,0.87758,,0.52563,,43,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Sweden,2023-09-25,Juvenile,Juvenile,Spinal Cord,Nervous System
26655,SRR26173782,SRX21885863,SRS18976989,SRP463130,PRJNA1020854,Molecular blueprints for spinal circuit modules controlling locomotor speed,GSE243993,Transcriptome Analysis,The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.,,pubmed:37919423,,V2a sample2 354 K10 R1,GSM7804313,,source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing,V2a sample2 354 K10 R1,The reads from each sequenced cell were mapped to the zebrafish reference genome “Danio rerio  Ensembl  GRCz11” using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis,Spinal cord,,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons,GSM7804313,GSM7804313: V2a sample2 354 K10 R1; Danio rerio; RNA Seq,GSM7804313 r1,GSM7804313,1,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP463130,,,SS2_18_354_K10_R1.fastq.gz,fastq,37245912.0,866184.0,GSM7804313 r1,0:43,A:10047107;C:8317880;G:8544201;T:10336724;N:0,43,,,,10047107,8317880,8544201,10336724,0,SRX21885863,SRS18976989,SRA1719948,"Neuroscience, Karolinaska Institutet","Neuroscience, Karolinaska Institutet",1,0.7613,,0.27366,,0.94448,,0.478,,43,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Sweden,2023-09-25,Juvenile,Juvenile,Spinal Cord,Nervous System
26656,SRR26173783,SRX21885862,SRS18976986,SRP463130,PRJNA1020854,Molecular blueprints for spinal circuit modules controlling locomotor speed,GSE243993,Transcriptome Analysis,The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.,,pubmed:37919423,,V2a sample2 354 J9 R1,GSM7804288,,source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing,V2a sample2 354 J9 R1,The reads from each sequenced cell were mapped to the zebrafish reference genome “Danio rerio  Ensembl  GRCz11” using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis,Spinal cord,,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons,GSM7804288,GSM7804288: V2a sample2 354 J9 R1; Danio rerio; RNA Seq,GSM7804288 r1,GSM7804288,1,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP463130,,,SS2_18_354_J9_R1.fastq.gz,fastq,28946955.0,673185.0,GSM7804288 r1,0:43,A:8009792;C:6401754;G:6532512;T:8002897;N:0,43,,,,8009792,6401754,6532512,8002897,0,SRX21885862,SRS18976986,SRA1719948,"Neuroscience, Karolinaska Institutet","Neuroscience, Karolinaska Institutet",1,0.86909,,0.25536,,0.90881,,0.53939,,43,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Sweden,2023-09-25,Juvenile,Juvenile,Spinal Cord,Nervous System
26657,SRR26173784,SRX21885861,SRS18976984,SRP463130,PRJNA1020854,Molecular blueprints for spinal circuit modules controlling locomotor speed,GSE243993,Transcriptome Analysis,The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules  yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Locomotion is a motor behavior characterized by sudden changes in speed and strength enabled by the coordinated recruitment of different motoneuron subtypes. Here we use adult zebrafish to link the molecular diversity of motoneurons and the rhythm generating V2a interneurons with their modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of motoneurons and V2a interneurons reflects their functional segregation into slow  intermediate or fast subtypes. Furthermore  we reveal shared molecular signatures between V2a interneurons and motoneurons of the three speed circuit modules. Overall  by characterizing how the molecular diversity of motoneurons and V2a interneurons relates to their function  connectivity and behavior  our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general. Overall design: To determine whether the functional subtypes of motoneurons and V2a Chx10+ interneurons are molecularly distinct  we performed single cell RNA sequencing respectively on adult islet1a:GFP and chx10:GFP transgenic zebrafish using SmartSeq2.,,pubmed:37919423,,V2a sample2 354 J8 R1,GSM7804287,,source name:Spinal cord|tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons|geo loc name:missing|collection date:missing,V2a sample2 354 J8 R1,The reads from each sequenced cell were mapped to the zebrafish reference genome “Danio rerio  Ensembl  GRCz11” using STAR version 2.5.3a. The resulting bam files were filtered to keep only uniquely mapped reads. Most of the following analysis was performed in R version 4.0.5  R core team  2022 using the Seurat package version 4.0.2. Assembly: GRCz11 Supplementary files format and content: .csv files with gene count matrixes; .txt and .csv metadata files and .rds files containing R objects from Seurat analysis,Spinal cord,,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,tissue:Spinal cord|cell line:Chx10:GFP|cell type:V2a interneurons,GSM7804287,GSM7804287: V2a sample2 354 J8 R1; Danio rerio; RNA Seq,GSM7804287 r1,GSM7804287,1,Adult animals 7 wpf of either sex were deeply anesthetized in a slush of frozen extracellular solution containing in mM: 134 NaCl  2.9 KCl  2.1 CaCl2  1.2 MgCl2  10 HEPES and 10 glucose  with pH of 7.8 adjusted with NaOH and osmolarity of 290 mOsm. The spinal cord was quickly dissected in the slush of frozen extracellular solution and collected. Two samples were prepared from the Tgislet1a:GFP line  and two samples were prepared from the Tgchx10:GFP line. For each sample  6 to 10 intact isolated spinal cords were incubated in 1 ml of DMEM F12 medium Thermo Fisher  #11039021  osmolarity adjusted to 280 280 mOsm containing papain 10 U/ml Worthington biochem  #LK003178 on a heated shaker at 37°C for 15 min. DMEM/F 12 1 ml  280 290 mOsm was added to stop the enzymatic reaction. The sample was centrifuged at 300 g at 4°C for 5 min  and then re suspended in 0.5 ml of DMEM/F 12 280 290 mOsm post removal of the supernatant. Following mechanical trituration using fire polished Pasteur pipettes  the cell suspension was filtered through a cell 16 strainer 40 μm. The sample was kept at room temperature for 20 min post the addition of 0 1 ml of the nuclear DNA stain DRAQ5 Thermo Fisher  #65 0880 92. Using fluorescence activated cell sorting FACs  cells positive for GFP and DRAQ5 in each sample were sorted into a 384 wells plate containing a mild hypotonic lysis buffer 0.2% Triton X 100  2 U/ml RNase inhibitor and immediately snap frozen on ice  then stored at  80°C. Smart Seq2,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP463130,,,SS2_18_354_J8_R1.fastq.gz,fastq,23315589.0,542223.0,GSM7804287 r1,0:43,A:6435989;C:5190350;G:5284504;T:6404746;N:0,43,,,,6435989,5190350,5284504,6404746,0,SRX21885861,SRS18976984,SRA1719948,"Neuroscience, Karolinaska Institutet","Neuroscience, Karolinaska Institutet",1,0.88805,,0.20444,,0.87708,,0.53025,,43,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Sweden,2023-09-25,Juvenile,Juvenile,Spinal Cord,Nervous System