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
25237,SRR25721801,SRX21445937,SRS18680715,SRP456253,PRJNA1007646,Single cell analysis of Rohon Beard neurons implicates Fgf signaling in axon maintenance and cell survival [larva],GSE241296,Other,Peripheral sensory neurons are a critical part of the nervous system that transmit a multitude of sensory stimuli to the central nervous system. During larval and juvenile stages in zebrafish  this function is mediated by Rohon Beard somatosensory neurons RBs. RBs are optically accessible and amenable to experimental manipulation  making them a powerful system for mechanistic investigation of sensory neurons. Previous studies provided evidence that RBs fall into multiple subclasses; however  the number and molecular make up of these potential RB subtypes have not been well defined. Using a single cell RNA sequencing scRNA seq approach  we demonstrate that larval RBs in zebrafish fall into three  largely non overlapping classes of neurons. We also show that RBs are molecularly distinct from trigeminal neurons in zebrafish. Cross species transcriptional analysis indicates that one RB subclass is similar to a mammalian group of A fiber sensory neurons. Another RB subclass is predicted to sense multiple modalities  including mechanical stimulation and chemical irritants. We leveraged our scRNA seq data to determine that the fibroblast growth factor Fgf pathway is active in RBs. Pharmacological and genetic inhibition of this pathway led to defects in axon maintenance and RB cell death. Moreover  this phenotype can be phenocopied by treatment with an FDA approved Fgf inhibitor dovitinib  which is used in clinic and causes peripheral neuropathy. Importantly  dovitinib mediated axon loss can be suppressed by loss of Sarm1  a positive regulator of neuronal cell death and axonal injury. This offers a molecular target for future clinical intervention to fight neurotoxic effects of this drug. Overall design: About 150 dpf 7 dpf larva were euthanized in 0.02% tricaine  and individually decapitated behind the hindbrain. They were incubated with 20 mg/ml collagenase Life Sciences in a buffer containing 134 mM NaCl  2.9 mM KCl  1.2 mM MgCl2  2.1 mM CaCl2  and 10 mM Na HEPES pH 7.8 at 28 °C for 2 hr  with intermittent trituration using a p200 pipette aid at 0  0.5 hr and 1 hr of the incubation. To release spinal cords from remaining tissue  the final triturations were done using fire polished Pasteur pipettes with decreased opening sizes 300  200  100 µm respectively. Intact spinal cords were transferred to L15 media and washed 3 times with fresh media. The spinal cords were incubated with 0.25% trypsin solution in 1xPBS containing 1 mM EDTA at 28 °C for 25 min. The digestion was terminated by adding 500 µl stop solution L15 with 1% fetal bovine serum. The tissue was collected by spinning at 400 g for 3 min at 4°C  washed once with L15 and resuspended in 200 µl of L15 media. Spinal cord cells were dissociated by triturating the digested tissue with fire polished Pasteur pipettes with 80 100 µm opening. The solution was filtered through a 35 µm strainer into a siliconized collection tube. The suspension was examined on a microscope for cell count  Trypan blue staining based viability test and proportion of dispersed single cells. Samples with a viability above 70% were used for sequencing,,,,zebrafish larva  neurons and glia  scRNAseq,GSM7720759,,source name:zebrafish larva|cell type:neurons and glia|tissue:zebrafish larva|strain:mixed|age:7 dpf loc name:missing|collection date:missing,zebrafish larva  neurons and glia  scRNAseq,using Cell Ranger version 3.1.0; 10X Genomics  Pleasanton  CA. USA Assembly: ZebraFishGRCz11 Supplementary files format and content: Tab separated values files and matrix files,zebrafish larva,,About 150 dpf 7 dpf larva were euthanized in 0.02% tricaine  and individually decapitated behind the hindbrain. They were incubated with 20 mg/ml collagenase Life Sciences in a buffer containing 134 mM NaCl  2.9 mM KCl  1.2 mM MgCl2  2.1 mM CaCl2  and 10 mM Na HEPES pH 7.8 at 28 °C for 2 hr  with intermittent trituration using a p200 pipette aid at 0  0.5 hr and 1 hr of the incubation. To release spinal cords from remaining tissue  the final triturations were done using fire polished Pasteur pipettes with decreased opening sizes 300  200  100 μm respectively. Intact spinal cords were transferred to L15 media and washed 3 times with fresh media. The spinal cords were incubated with 0.25% trypsin solution in 1xPBS containing 1 mM EDTA at 28 °C for 25 min. The digestion was terminated by adding 500 μl stop solution L15 with 1% fetal bovine serum. The tissue was collected by spinning at 400 g for 3 min at 4°C  washed once with L15 and resuspended in 200 μl of L15 media. Spinal cord cells were dissociated by triturating the digested tissue with fire polished Pasteur pipettes with 80 100 μm opening. The solution was filtered through a 35 μm strainer into a siliconized collection tube. The suspension was examined on a microscope for cell count  Trypan blue staining based viability test and proportion of dispersed single cells. Samples with a viability above 70% were used for sequencing Library was performed according to the manufacter’s instructions single cell 3’ v3 protocol  10x Genomics.,,cell type:neurons and glia|tissue:zebrafish larva|strain:mixed|age:7 dpf,GSM7720759,GSM7720759: zebrafish larva  neurons and glia  scRNAseq; Danio rerio; RNA Seq,GSM7720759 r1,GSM7720759,1,About 150 dpf 7 dpf larva were euthanized in 0.02% tricaine  and individually decapitated behind the hindbrain. They were incubated with 20 mg/ml collagenase Life Sciences in a buffer containing 134 mM NaCl  2.9 mM KCl  1.2 mM MgCl2  2.1 mM CaCl2  and 10 mM Na HEPES pH 7.8 at 28 °C for 2 hr  with intermittent trituration using a p200 pipette aid at 0  0.5 hr and 1 hr of the incubation. To release spinal cords from remaining tissue  the final triturations were done using fire polished Pasteur pipettes with decreased opening sizes 300  200  100 μm respectively. Intact spinal cords were transferred to L15 media and washed 3 times with fresh media. The spinal cords were incubated with 0.25% trypsin solution in 1xPBS containing 1 mM EDTA at 28 °C for 25 min. The digestion was terminated by adding 500 μl stop solution L15 with 1% fetal bovine serum. The tissue was collected by spinning at 400 g for 3 min at 4°C  washed once with L15 and resuspended in 200 μl of L15 media. Spinal cord cells were dissociated by triturating the digested tissue with fire polished Pasteur pipettes with 80 100 μm opening. The solution was filtered through a 35 μm strainer into a siliconized collection tube. The suspension was examined on a microscope for cell count  Trypan blue staining based viability test and proportion of dispersed single cells. Samples with a viability above 70% were used for sequencing Library was performed according to the manufacter's instructions single cell three prime v3 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP456253,,loader:fastq load.py,CEL210928PB_HW1008_SAIG_D7_S1_L002_I1_001.fastq.gz CEL210928PB_HW1008_SAIG_D7_S1_L002_I2_001.fastq.gz CEL210928PB_HW1008_SAIG_D7_S1_L002_R1_001.fastq.gz CEL210928PB_HW1008_SAIG_D7_S1_L002_R2_001.fastq.gz,fastq fastq fastq fastq,55936355640.0,254256162.0,GSM7720759 r1,0:10 1:10 2:100 3:100,A:13207297968;C:10496996981;G:10989402500;T:16156355819;N:1179132,10,10,100,100,13207297968,10496996981,10989402500,16156355819,1179132,SRX21445937,SRS18680715,SRA1696793,Oregon Health and Science Univ,Oregon Health and Science Univ,2,0.0,0.81961,0.0,0.19165,1.0,0.8508,,0.59575,100,100,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-08-21,Larval,Larval,Multi-tissue,Multi-system
25238,SRR25721802,SRX21445937,SRS18680715,SRP456253,PRJNA1007646,Single cell analysis of Rohon Beard neurons implicates Fgf signaling in axon maintenance and cell survival [larva],GSE241296,Other,Peripheral sensory neurons are a critical part of the nervous system that transmit a multitude of sensory stimuli to the central nervous system. During larval and juvenile stages in zebrafish  this function is mediated by Rohon Beard somatosensory neurons RBs. RBs are optically accessible and amenable to experimental manipulation  making them a powerful system for mechanistic investigation of sensory neurons. Previous studies provided evidence that RBs fall into multiple subclasses; however  the number and molecular make up of these potential RB subtypes have not been well defined. Using a single cell RNA sequencing scRNA seq approach  we demonstrate that larval RBs in zebrafish fall into three  largely non overlapping classes of neurons. We also show that RBs are molecularly distinct from trigeminal neurons in zebrafish. Cross species transcriptional analysis indicates that one RB subclass is similar to a mammalian group of A fiber sensory neurons. Another RB subclass is predicted to sense multiple modalities  including mechanical stimulation and chemical irritants. We leveraged our scRNA seq data to determine that the fibroblast growth factor Fgf pathway is active in RBs. Pharmacological and genetic inhibition of this pathway led to defects in axon maintenance and RB cell death. Moreover  this phenotype can be phenocopied by treatment with an FDA approved Fgf inhibitor dovitinib  which is used in clinic and causes peripheral neuropathy. Importantly  dovitinib mediated axon loss can be suppressed by loss of Sarm1  a positive regulator of neuronal cell death and axonal injury. This offers a molecular target for future clinical intervention to fight neurotoxic effects of this drug. Overall design: About 150 dpf 7 dpf larva were euthanized in 0.02% tricaine  and individually decapitated behind the hindbrain. They were incubated with 20 mg/ml collagenase Life Sciences in a buffer containing 134 mM NaCl  2.9 mM KCl  1.2 mM MgCl2  2.1 mM CaCl2  and 10 mM Na HEPES pH 7.8 at 28 °C for 2 hr  with intermittent trituration using a p200 pipette aid at 0  0.5 hr and 1 hr of the incubation. To release spinal cords from remaining tissue  the final triturations were done using fire polished Pasteur pipettes with decreased opening sizes 300  200  100 µm respectively. Intact spinal cords were transferred to L15 media and washed 3 times with fresh media. The spinal cords were incubated with 0.25% trypsin solution in 1xPBS containing 1 mM EDTA at 28 °C for 25 min. The digestion was terminated by adding 500 µl stop solution L15 with 1% fetal bovine serum. The tissue was collected by spinning at 400 g for 3 min at 4°C  washed once with L15 and resuspended in 200 µl of L15 media. Spinal cord cells were dissociated by triturating the digested tissue with fire polished Pasteur pipettes with 80 100 µm opening. The solution was filtered through a 35 µm strainer into a siliconized collection tube. The suspension was examined on a microscope for cell count  Trypan blue staining based viability test and proportion of dispersed single cells. Samples with a viability above 70% were used for sequencing,,,,zebrafish larva  neurons and glia  scRNAseq,GSM7720759,,source name:zebrafish larva|cell type:neurons and glia|tissue:zebrafish larva|strain:mixed|age:7 dpf loc name:missing|collection date:missing,zebrafish larva  neurons and glia  scRNAseq,using Cell Ranger version 3.1.0; 10X Genomics  Pleasanton  CA. USA Assembly: ZebraFishGRCz11 Supplementary files format and content: Tab separated values files and matrix files,zebrafish larva,,About 150 dpf 7 dpf larva were euthanized in 0.02% tricaine  and individually decapitated behind the hindbrain. They were incubated with 20 mg/ml collagenase Life Sciences in a buffer containing 134 mM NaCl  2.9 mM KCl  1.2 mM MgCl2  2.1 mM CaCl2  and 10 mM Na HEPES pH 7.8 at 28 °C for 2 hr  with intermittent trituration using a p200 pipette aid at 0  0.5 hr and 1 hr of the incubation. To release spinal cords from remaining tissue  the final triturations were done using fire polished Pasteur pipettes with decreased opening sizes 300  200  100 μm respectively. Intact spinal cords were transferred to L15 media and washed 3 times with fresh media. The spinal cords were incubated with 0.25% trypsin solution in 1xPBS containing 1 mM EDTA at 28 °C for 25 min. The digestion was terminated by adding 500 μl stop solution L15 with 1% fetal bovine serum. The tissue was collected by spinning at 400 g for 3 min at 4°C  washed once with L15 and resuspended in 200 μl of L15 media. Spinal cord cells were dissociated by triturating the digested tissue with fire polished Pasteur pipettes with 80 100 μm opening. The solution was filtered through a 35 μm strainer into a siliconized collection tube. The suspension was examined on a microscope for cell count  Trypan blue staining based viability test and proportion of dispersed single cells. Samples with a viability above 70% were used for sequencing Library was performed according to the manufacter’s instructions single cell 3’ v3 protocol  10x Genomics.,,cell type:neurons and glia|tissue:zebrafish larva|strain:mixed|age:7 dpf,GSM7720759,GSM7720759: zebrafish larva  neurons and glia  scRNAseq; Danio rerio; RNA Seq,GSM7720759 r1,GSM7720759,1,About 150 dpf 7 dpf larva were euthanized in 0.02% tricaine  and individually decapitated behind the hindbrain. They were incubated with 20 mg/ml collagenase Life Sciences in a buffer containing 134 mM NaCl  2.9 mM KCl  1.2 mM MgCl2  2.1 mM CaCl2  and 10 mM Na HEPES pH 7.8 at 28 °C for 2 hr  with intermittent trituration using a p200 pipette aid at 0  0.5 hr and 1 hr of the incubation. To release spinal cords from remaining tissue  the final triturations were done using fire polished Pasteur pipettes with decreased opening sizes 300  200  100 μm respectively. Intact spinal cords were transferred to L15 media and washed 3 times with fresh media. The spinal cords were incubated with 0.25% trypsin solution in 1xPBS containing 1 mM EDTA at 28 °C for 25 min. The digestion was terminated by adding 500 μl stop solution L15 with 1% fetal bovine serum. The tissue was collected by spinning at 400 g for 3 min at 4°C  washed once with L15 and resuspended in 200 μl of L15 media. Spinal cord cells were dissociated by triturating the digested tissue with fire polished Pasteur pipettes with 80 100 μm opening. The solution was filtered through a 35 μm strainer into a siliconized collection tube. The suspension was examined on a microscope for cell count  Trypan blue staining based viability test and proportion of dispersed single cells. Samples with a viability above 70% were used for sequencing Library was performed according to the manufacter's instructions single cell three prime v3 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP456253,,loader:fastq load.py,CEL210928PB_HW1008_SAIG_D7_S1_L001_I1_001.fastq.gz CEL210928PB_HW1008_SAIG_D7_S1_L001_I2_001.fastq.gz CEL210928PB_HW1008_SAIG_D7_S1_L001_R1_001.fastq.gz CEL210928PB_HW1008_SAIG_D7_S1_L001_R2_001.fastq.gz,fastq fastq fastq fastq,54474841080.0,247612914.0,GSM7720759 r2,0:10 1:10 2:100 3:100,A:12887048507;C:10210716068;G:10683375130;T:15740176261;N:1266834,10,10,100,100,12887048507,10210716068,10683375130,15740176261,1266834,SRX21445937,SRS18680715,SRA1696793,Oregon Health and Science Univ,Oregon Health and Science Univ,2,0.0,0.82189,0.0,0.19349,1.0,0.85025,,0.6092,100,100,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-08-21,Larval,Larval,Multi-tissue,Multi-system
28707,SRR26588119,SRX22289209,SRS19340293,SRP469198,PRJNA1033661,scRNAseq of skeletal tissue during zebrafish craniofacial development,GSE246579,Transcriptome Analysis,We used scRNAseq to characterize differentiation of cell populations during zebrafish craniofacial development. We focused critical stages during suture formation  and compared wildtype fish to mutants lacking the transcription factor sp7  that display striking abnormalities in skull and suture formation. Overall design: Dissociated cells were isolated from heads of wildtype and sp7 mutant zebrafish at  5.8 mm SL 2 wpf and 7 mm SL 3wpf. To enrich for skeletal tissues  brain and eyes were removed before dissociation. To aid in dissection and transcript analysis  fish carried two transgenes   117BMPER: egfp and sp7: mcherry. Cells were analyzed by scRNAseq.,,,,WT 5.8 mm,GSM7871949,,source name:craniofacial skeletal tissues|tissue:craniofacial skeletal tissues|genotype:WT|geo loc name:missing|collection date:missing,WT 5.8 mm,Demultiplexing  barcoded processing  gene counting  and aggregation were performed using Cell Ranger software version 3.1.0 10X Genomics Assembly: danRer11 Supplementary files format and content: Tab separated values files and matrix files,craniofacial skeletal tissues,,Fish were euthanized and transferred to ice cold PBS. In <2 min  we cut off the head just above the pectoral fins  and removed the eyes and brain to enrich for musculoskeletal tissue.The remaining skull was rinsed 2X in PBS  and transferred to a dissociation buffer containing 0.25% trypsin EDTA and 10mg/mL collagenase at 30°. Alternating between pipetting and incubation at 30°  the tissue was fully dissociated  again in <2 min. Digestion was stopped by addition of DMEM w/ 10% BSA. post centrifugation at 700g for 5min  cells were resuspended in PBS  centrifuged again to wash  and the final pellet resuspended in 100μL of FACS buffer 1x PBS  2% BSA and 1mM EDTA. Single cells were isolated by filtration through a 40μm nylon mesh. Cells were loaded onto 10X Genomics microfluidic chips and processed for scRNAseq according to manufacturer's instructions.,,tissue:craniofacial skeletal tissues|genotype:WT,GSM7871949,GSM7871949: WT 5.8 mm; Danio rerio; RNA Seq,GSM7871949 r1,GSM7871949,1,Fish were euthanized and transferred to ice cold PBS. In <2 min  we cut off the head just above the pectoral fins  and removed the eyes and brain to enrich for musculoskeletal tissue.The remaining skull was rinsed 2X in PBS  and transferred to a dissociation buffer containing 0.25% trypsin EDTA and 10mg/mL collagenase at 30°. Alternating between pipetting and incubation at 30°  the tissue was fully dissociated  again in <2 min. Digestion was stopped by addition of DMEM w/ 10% BSA. post centrifugation at 700g for 5min  cells were resuspended in PBS  centrifuged again to wash  and the final pellet resuspended in 100μL of FACS buffer 1x PBS  2% BSA and 1mM EDTA. Single cells were isolated by filtration through a 40μm nylon mesh. Cells were loaded onto 10X Genomics microfluidic chips and processed for scRNAseq according to manufacturer's instructions.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP469198,,loader:fastq load.py,FS_WT0628_S3_L001_R2_001.fastq.gz FS_WT0628_S3_L001_R1_001.fastq.gz FS_WT0628_S3_L001_I1_001.fastq.gz,fastq fastq fastq,3515731348.0,27682924.0,GSM7871949 r1,0:8 1:28 2:91,A:723968955;C:551528974;G:650193733;T:593113624;N:340798,8,28,91,,723968955,551528974,650193733,593113624,340798,SRX22289209,SRS19340293,SRA1742079,Boston University,Boston University,1,0.8674,,0.17534,,0.84098,,0.62971,,91,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-10-30,Undetermined,Undetermined,Multi-tissue,Multi-system
28708,SRR26588120,SRX22289209,SRS19340293,SRP469198,PRJNA1033661,scRNAseq of skeletal tissue during zebrafish craniofacial development,GSE246579,Transcriptome Analysis,We used scRNAseq to characterize differentiation of cell populations during zebrafish craniofacial development. We focused critical stages during suture formation  and compared wildtype fish to mutants lacking the transcription factor sp7  that display striking abnormalities in skull and suture formation. Overall design: Dissociated cells were isolated from heads of wildtype and sp7 mutant zebrafish at  5.8 mm SL 2 wpf and 7 mm SL 3wpf. To enrich for skeletal tissues  brain and eyes were removed before dissociation. To aid in dissection and transcript analysis  fish carried two transgenes   117BMPER: egfp and sp7: mcherry. Cells were analyzed by scRNAseq.,,,,WT 5.8 mm,GSM7871949,,source name:craniofacial skeletal tissues|tissue:craniofacial skeletal tissues|genotype:WT|geo loc name:missing|collection date:missing,WT 5.8 mm,Demultiplexing  barcoded processing  gene counting  and aggregation were performed using Cell Ranger software version 3.1.0 10X Genomics Assembly: danRer11 Supplementary files format and content: Tab separated values files and matrix files,craniofacial skeletal tissues,,Fish were euthanized and transferred to ice cold PBS. In <2 min  we cut off the head just above the pectoral fins  and removed the eyes and brain to enrich for musculoskeletal tissue.The remaining skull was rinsed 2X in PBS  and transferred to a dissociation buffer containing 0.25% trypsin EDTA and 10mg/mL collagenase at 30°. Alternating between pipetting and incubation at 30°  the tissue was fully dissociated  again in <2 min. Digestion was stopped by addition of DMEM w/ 10% BSA. post centrifugation at 700g for 5min  cells were resuspended in PBS  centrifuged again to wash  and the final pellet resuspended in 100μL of FACS buffer 1x PBS  2% BSA and 1mM EDTA. Single cells were isolated by filtration through a 40μm nylon mesh. Cells were loaded onto 10X Genomics microfluidic chips and processed for scRNAseq according to manufacturer's instructions.,,tissue:craniofacial skeletal tissues|genotype:WT,GSM7871949,GSM7871949: WT 5.8 mm; Danio rerio; RNA Seq,GSM7871949 r1,GSM7871949,1,Fish were euthanized and transferred to ice cold PBS. In <2 min  we cut off the head just above the pectoral fins  and removed the eyes and brain to enrich for musculoskeletal tissue.The remaining skull was rinsed 2X in PBS  and transferred to a dissociation buffer containing 0.25% trypsin EDTA and 10mg/mL collagenase at 30°. Alternating between pipetting and incubation at 30°  the tissue was fully dissociated  again in <2 min. Digestion was stopped by addition of DMEM w/ 10% BSA. post centrifugation at 700g for 5min  cells were resuspended in PBS  centrifuged again to wash  and the final pellet resuspended in 100μL of FACS buffer 1x PBS  2% BSA and 1mM EDTA. Single cells were isolated by filtration through a 40μm nylon mesh. Cells were loaded onto 10X Genomics microfluidic chips and processed for scRNAseq according to manufacturer's instructions.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP469198,,loader:fastq load.py,FS_WT0628_S3_L002_R2_001.fastq.gz FS_WT0628_S3_L002_R1_001.fastq.gz FS_WT0628_S3_L002_I1_001.fastq.gz,fastq fastq fastq,3453128095.0,27189985.0,GSM7871949 r2,0:8 1:28 2:91,A:711376907;C:541911169;G:638181451;T:582510928;N:308180,8,28,91,,711376907,541911169,638181451,582510928,308180,SRX22289209,SRS19340293,SRA1742079,Boston University,Boston University,1,0.86684,,0.17663,,0.84108,,0.64294,,91,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-10-30,Undetermined,Undetermined,Multi-tissue,Multi-system
28709,SRR26588121,SRX22289209,SRS19340293,SRP469198,PRJNA1033661,scRNAseq of skeletal tissue during zebrafish craniofacial development,GSE246579,Transcriptome Analysis,We used scRNAseq to characterize differentiation of cell populations during zebrafish craniofacial development. We focused critical stages during suture formation  and compared wildtype fish to mutants lacking the transcription factor sp7  that display striking abnormalities in skull and suture formation. Overall design: Dissociated cells were isolated from heads of wildtype and sp7 mutant zebrafish at  5.8 mm SL 2 wpf and 7 mm SL 3wpf. To enrich for skeletal tissues  brain and eyes were removed before dissociation. To aid in dissection and transcript analysis  fish carried two transgenes   117BMPER: egfp and sp7: mcherry. Cells were analyzed by scRNAseq.,,,,WT 5.8 mm,GSM7871949,,source name:craniofacial skeletal tissues|tissue:craniofacial skeletal tissues|genotype:WT|geo loc name:missing|collection date:missing,WT 5.8 mm,Demultiplexing  barcoded processing  gene counting  and aggregation were performed using Cell Ranger software version 3.1.0 10X Genomics Assembly: danRer11 Supplementary files format and content: Tab separated values files and matrix files,craniofacial skeletal tissues,,Fish were euthanized and transferred to ice cold PBS. In <2 min  we cut off the head just above the pectoral fins  and removed the eyes and brain to enrich for musculoskeletal tissue.The remaining skull was rinsed 2X in PBS  and transferred to a dissociation buffer containing 0.25% trypsin EDTA and 10mg/mL collagenase at 30°. Alternating between pipetting and incubation at 30°  the tissue was fully dissociated  again in <2 min. Digestion was stopped by addition of DMEM w/ 10% BSA. post centrifugation at 700g for 5min  cells were resuspended in PBS  centrifuged again to wash  and the final pellet resuspended in 100μL of FACS buffer 1x PBS  2% BSA and 1mM EDTA. Single cells were isolated by filtration through a 40μm nylon mesh. Cells were loaded onto 10X Genomics microfluidic chips and processed for scRNAseq according to manufacturer's instructions.,,tissue:craniofacial skeletal tissues|genotype:WT,GSM7871949,GSM7871949: WT 5.8 mm; Danio rerio; RNA Seq,GSM7871949 r1,GSM7871949,1,Fish were euthanized and transferred to ice cold PBS. In <2 min  we cut off the head just above the pectoral fins  and removed the eyes and brain to enrich for musculoskeletal tissue.The remaining skull was rinsed 2X in PBS  and transferred to a dissociation buffer containing 0.25% trypsin EDTA and 10mg/mL collagenase at 30°. Alternating between pipetting and incubation at 30°  the tissue was fully dissociated  again in <2 min. Digestion was stopped by addition of DMEM w/ 10% BSA. post centrifugation at 700g for 5min  cells were resuspended in PBS  centrifuged again to wash  and the final pellet resuspended in 100μL of FACS buffer 1x PBS  2% BSA and 1mM EDTA. Single cells were isolated by filtration through a 40μm nylon mesh. Cells were loaded onto 10X Genomics microfluidic chips and processed for scRNAseq according to manufacturer's instructions.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP469198,,loader:fastq load.py,FS_WT0628_S3_L003_R2_001.fastq.gz FS_WT0628_S3_L003_R1_001.fastq.gz FS_WT0628_S3_L003_I1_001.fastq.gz,fastq fastq fastq,3525654366.0,27761058.0,GSM7871949 r3,0:8 1:28 2:91,A:725811733;C:554304351;G:651619754;T:593988032;N:532408,8,28,91,,725811733,554304351,651619754,593988032,532408,SRX22289209,SRS19340293,SRA1742079,Boston University,Boston University,1,0.86621,,0.17459,,0.83936,,0.63657,,91,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-10-30,Undetermined,Undetermined,Multi-tissue,Multi-system
28710,SRR26588122,SRX22289209,SRS19340293,SRP469198,PRJNA1033661,scRNAseq of skeletal tissue during zebrafish craniofacial development,GSE246579,Transcriptome Analysis,We used scRNAseq to characterize differentiation of cell populations during zebrafish craniofacial development. We focused critical stages during suture formation  and compared wildtype fish to mutants lacking the transcription factor sp7  that display striking abnormalities in skull and suture formation. Overall design: Dissociated cells were isolated from heads of wildtype and sp7 mutant zebrafish at  5.8 mm SL 2 wpf and 7 mm SL 3wpf. To enrich for skeletal tissues  brain and eyes were removed before dissociation. To aid in dissection and transcript analysis  fish carried two transgenes   117BMPER: egfp and sp7: mcherry. Cells were analyzed by scRNAseq.,,,,WT 5.8 mm,GSM7871949,,source name:craniofacial skeletal tissues|tissue:craniofacial skeletal tissues|genotype:WT|geo loc name:missing|collection date:missing,WT 5.8 mm,Demultiplexing  barcoded processing  gene counting  and aggregation were performed using Cell Ranger software version 3.1.0 10X Genomics Assembly: danRer11 Supplementary files format and content: Tab separated values files and matrix files,craniofacial skeletal tissues,,Fish were euthanized and transferred to ice cold PBS. In <2 min  we cut off the head just above the pectoral fins  and removed the eyes and brain to enrich for musculoskeletal tissue.The remaining skull was rinsed 2X in PBS  and transferred to a dissociation buffer containing 0.25% trypsin EDTA and 10mg/mL collagenase at 30°. Alternating between pipetting and incubation at 30°  the tissue was fully dissociated  again in <2 min. Digestion was stopped by addition of DMEM w/ 10% BSA. post centrifugation at 700g for 5min  cells were resuspended in PBS  centrifuged again to wash  and the final pellet resuspended in 100μL of FACS buffer 1x PBS  2% BSA and 1mM EDTA. Single cells were isolated by filtration through a 40μm nylon mesh. Cells were loaded onto 10X Genomics microfluidic chips and processed for scRNAseq according to manufacturer's instructions.,,tissue:craniofacial skeletal tissues|genotype:WT,GSM7871949,GSM7871949: WT 5.8 mm; Danio rerio; RNA Seq,GSM7871949 r1,GSM7871949,1,Fish were euthanized and transferred to ice cold PBS. In <2 min  we cut off the head just above the pectoral fins  and removed the eyes and brain to enrich for musculoskeletal tissue.The remaining skull was rinsed 2X in PBS  and transferred to a dissociation buffer containing 0.25% trypsin EDTA and 10mg/mL collagenase at 30°. Alternating between pipetting and incubation at 30°  the tissue was fully dissociated  again in <2 min. Digestion was stopped by addition of DMEM w/ 10% BSA. post centrifugation at 700g for 5min  cells were resuspended in PBS  centrifuged again to wash  and the final pellet resuspended in 100μL of FACS buffer 1x PBS  2% BSA and 1mM EDTA. Single cells were isolated by filtration through a 40μm nylon mesh. Cells were loaded onto 10X Genomics microfluidic chips and processed for scRNAseq according to manufacturer's instructions.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP469198,,loader:fastq load.py,FS_WT0628_S3_L004_R2_001.fastq.gz FS_WT0628_S3_L004_R1_001.fastq.gz FS_WT0628_S3_L004_I1_001.fastq.gz,fastq fastq fastq,3476431706.0,27373478.0,GSM7871949 r4,0:8 1:28 2:91,A:715940083;C:546111535;G:642639757;T:585816460;N:478663,8,28,91,,715940083,546111535,642639757,585816460,478663,SRX22289209,SRS19340293,SRA1742079,Boston University,Boston University,1,0.86857,,0.17561,,0.84094,,0.63847,,91,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-10-30,Undetermined,Undetermined,Multi-tissue,Multi-system
28711,SRR26588123,SRX22289208,SRS19340290,SRP469198,PRJNA1033661,scRNAseq of skeletal tissue during zebrafish craniofacial development,GSE246579,Transcriptome Analysis,We used scRNAseq to characterize differentiation of cell populations during zebrafish craniofacial development. We focused critical stages during suture formation  and compared wildtype fish to mutants lacking the transcription factor sp7  that display striking abnormalities in skull and suture formation. Overall design: Dissociated cells were isolated from heads of wildtype and sp7 mutant zebrafish at  5.8 mm SL 2 wpf and 7 mm SL 3wpf. To enrich for skeletal tissues  brain and eyes were removed before dissociation. To aid in dissection and transcript analysis  fish carried two transgenes   117BMPER: egfp and sp7: mcherry. Cells were analyzed by scRNAseq.,,,,WT 7.0 mm,GSM7871948,,source name:craniofacial skeletal tissues|tissue:craniofacial skeletal tissues|genotype:WT|geo loc name:missing|collection date:missing,WT 7.0 mm,Demultiplexing  barcoded processing  gene counting  and aggregation were performed using Cell Ranger software version 3.1.0 10X Genomics Assembly: danRer11 Supplementary files format and content: Tab separated values files and matrix files,craniofacial skeletal tissues,,Fish were euthanized and transferred to ice cold PBS. In <2 min  we cut off the head just above the pectoral fins  and removed the eyes and brain to enrich for musculoskeletal tissue.The remaining skull was rinsed 2X in PBS  and transferred to a dissociation buffer containing 0.25% trypsin EDTA and 10mg/mL collagenase at 30°. Alternating between pipetting and incubation at 30°  the tissue was fully dissociated  again in <2 min. Digestion was stopped by addition of DMEM w/ 10% BSA. post centrifugation at 700g for 5min  cells were resuspended in PBS  centrifuged again to wash  and the final pellet resuspended in 100μL of FACS buffer 1x PBS  2% BSA and 1mM EDTA. Single cells were isolated by filtration through a 40μm nylon mesh. Cells were loaded onto 10X Genomics microfluidic chips and processed for scRNAseq according to manufacturer's instructions.,,tissue:craniofacial skeletal tissues|genotype:WT,GSM7871948,GSM7871948: WT 7.0 mm; Danio rerio; RNA Seq,GSM7871948 r1,GSM7871948,1,Fish were euthanized and transferred to ice cold PBS. In <2 min  we cut off the head just above the pectoral fins  and removed the eyes and brain to enrich for musculoskeletal tissue.The remaining skull was rinsed 2X in PBS  and transferred to a dissociation buffer containing 0.25% trypsin EDTA and 10mg/mL collagenase at 30°. Alternating between pipetting and incubation at 30°  the tissue was fully dissociated  again in <2 min. Digestion was stopped by addition of DMEM w/ 10% BSA. post centrifugation at 700g for 5min  cells were resuspended in PBS  centrifuged again to wash  and the final pellet resuspended in 100μL of FACS buffer 1x PBS  2% BSA and 1mM EDTA. Single cells were isolated by filtration through a 40μm nylon mesh. Cells were loaded onto 10X Genomics microfluidic chips and processed for scRNAseq according to manufacturer's instructions.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP469198,,loader:fastq load.py,FS_WT0621_S1_L001_R2_001.fastq.gz FS_WT0621_S1_L001_R1_001.fastq.gz FS_WT0621_S1_L001_I1_001.fastq.gz,fastq fastq fastq,4296091865.0,33827495.0,GSM7871948 r1,0:8 1:28 2:91,A:873692918;C:671758488;G:778592608;T:753844494;N:413537,8,28,91,,873692918,671758488,778592608,753844494,413537,SRX22289208,SRS19340290,SRA1742079,Boston University,Boston University,1,0.88226,,0.23142,,0.80811,,0.58869,,91,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-10-30,Undetermined,Undetermined,Multi-tissue,Multi-system
28712,SRR26588124,SRX22289208,SRS19340290,SRP469198,PRJNA1033661,scRNAseq of skeletal tissue during zebrafish craniofacial development,GSE246579,Transcriptome Analysis,We used scRNAseq to characterize differentiation of cell populations during zebrafish craniofacial development. We focused critical stages during suture formation  and compared wildtype fish to mutants lacking the transcription factor sp7  that display striking abnormalities in skull and suture formation. Overall design: Dissociated cells were isolated from heads of wildtype and sp7 mutant zebrafish at  5.8 mm SL 2 wpf and 7 mm SL 3wpf. To enrich for skeletal tissues  brain and eyes were removed before dissociation. To aid in dissection and transcript analysis  fish carried two transgenes   117BMPER: egfp and sp7: mcherry. Cells were analyzed by scRNAseq.,,,,WT 7.0 mm,GSM7871948,,source name:craniofacial skeletal tissues|tissue:craniofacial skeletal tissues|genotype:WT|geo loc name:missing|collection date:missing,WT 7.0 mm,Demultiplexing  barcoded processing  gene counting  and aggregation were performed using Cell Ranger software version 3.1.0 10X Genomics Assembly: danRer11 Supplementary files format and content: Tab separated values files and matrix files,craniofacial skeletal tissues,,Fish were euthanized and transferred to ice cold PBS. In <2 min  we cut off the head just above the pectoral fins  and removed the eyes and brain to enrich for musculoskeletal tissue.The remaining skull was rinsed 2X in PBS  and transferred to a dissociation buffer containing 0.25% trypsin EDTA and 10mg/mL collagenase at 30°. Alternating between pipetting and incubation at 30°  the tissue was fully dissociated  again in <2 min. Digestion was stopped by addition of DMEM w/ 10% BSA. post centrifugation at 700g for 5min  cells were resuspended in PBS  centrifuged again to wash  and the final pellet resuspended in 100μL of FACS buffer 1x PBS  2% BSA and 1mM EDTA. Single cells were isolated by filtration through a 40μm nylon mesh. Cells were loaded onto 10X Genomics microfluidic chips and processed for scRNAseq according to manufacturer's instructions.,,tissue:craniofacial skeletal tissues|genotype:WT,GSM7871948,GSM7871948: WT 7.0 mm; Danio rerio; RNA Seq,GSM7871948 r1,GSM7871948,1,Fish were euthanized and transferred to ice cold PBS. In <2 min  we cut off the head just above the pectoral fins  and removed the eyes and brain to enrich for musculoskeletal tissue.The remaining skull was rinsed 2X in PBS  and transferred to a dissociation buffer containing 0.25% trypsin EDTA and 10mg/mL collagenase at 30°. Alternating between pipetting and incubation at 30°  the tissue was fully dissociated  again in <2 min. Digestion was stopped by addition of DMEM w/ 10% BSA. post centrifugation at 700g for 5min  cells were resuspended in PBS  centrifuged again to wash  and the final pellet resuspended in 100μL of FACS buffer 1x PBS  2% BSA and 1mM EDTA. Single cells were isolated by filtration through a 40μm nylon mesh. Cells were loaded onto 10X Genomics microfluidic chips and processed for scRNAseq according to manufacturer's instructions.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP469198,,loader:fastq load.py,FS_WT0621_S1_L002_R2_001.fastq.gz FS_WT0621_S1_L002_R1_001.fastq.gz FS_WT0621_S1_L002_I1_001.fastq.gz,fastq fastq fastq,4219879546.0,33227398.0,GSM7871948 r2,0:8 1:28 2:91,A:858665689;C:660231321;G:764062561;T:740359496;N:374151,8,28,91,,858665689,660231321,764062561,740359496,374151,SRX22289208,SRS19340290,SRA1742079,Boston University,Boston University,1,0.8833,,0.23028,,0.80734,,0.5998,,91,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-10-30,Undetermined,Undetermined,Multi-tissue,Multi-system
28713,SRR26588125,SRX22289208,SRS19340290,SRP469198,PRJNA1033661,scRNAseq of skeletal tissue during zebrafish craniofacial development,GSE246579,Transcriptome Analysis,We used scRNAseq to characterize differentiation of cell populations during zebrafish craniofacial development. We focused critical stages during suture formation  and compared wildtype fish to mutants lacking the transcription factor sp7  that display striking abnormalities in skull and suture formation. Overall design: Dissociated cells were isolated from heads of wildtype and sp7 mutant zebrafish at  5.8 mm SL 2 wpf and 7 mm SL 3wpf. To enrich for skeletal tissues  brain and eyes were removed before dissociation. To aid in dissection and transcript analysis  fish carried two transgenes   117BMPER: egfp and sp7: mcherry. Cells were analyzed by scRNAseq.,,,,WT 7.0 mm,GSM7871948,,source name:craniofacial skeletal tissues|tissue:craniofacial skeletal tissues|genotype:WT|geo loc name:missing|collection date:missing,WT 7.0 mm,Demultiplexing  barcoded processing  gene counting  and aggregation were performed using Cell Ranger software version 3.1.0 10X Genomics Assembly: danRer11 Supplementary files format and content: Tab separated values files and matrix files,craniofacial skeletal tissues,,Fish were euthanized and transferred to ice cold PBS. In <2 min  we cut off the head just above the pectoral fins  and removed the eyes and brain to enrich for musculoskeletal tissue.The remaining skull was rinsed 2X in PBS  and transferred to a dissociation buffer containing 0.25% trypsin EDTA and 10mg/mL collagenase at 30°. Alternating between pipetting and incubation at 30°  the tissue was fully dissociated  again in <2 min. Digestion was stopped by addition of DMEM w/ 10% BSA. post centrifugation at 700g for 5min  cells were resuspended in PBS  centrifuged again to wash  and the final pellet resuspended in 100μL of FACS buffer 1x PBS  2% BSA and 1mM EDTA. Single cells were isolated by filtration through a 40μm nylon mesh. Cells were loaded onto 10X Genomics microfluidic chips and processed for scRNAseq according to manufacturer's instructions.,,tissue:craniofacial skeletal tissues|genotype:WT,GSM7871948,GSM7871948: WT 7.0 mm; Danio rerio; RNA Seq,GSM7871948 r1,GSM7871948,1,Fish were euthanized and transferred to ice cold PBS. In <2 min  we cut off the head just above the pectoral fins  and removed the eyes and brain to enrich for musculoskeletal tissue.The remaining skull was rinsed 2X in PBS  and transferred to a dissociation buffer containing 0.25% trypsin EDTA and 10mg/mL collagenase at 30°. Alternating between pipetting and incubation at 30°  the tissue was fully dissociated  again in <2 min. Digestion was stopped by addition of DMEM w/ 10% BSA. post centrifugation at 700g for 5min  cells were resuspended in PBS  centrifuged again to wash  and the final pellet resuspended in 100μL of FACS buffer 1x PBS  2% BSA and 1mM EDTA. Single cells were isolated by filtration through a 40μm nylon mesh. Cells were loaded onto 10X Genomics microfluidic chips and processed for scRNAseq according to manufacturer's instructions.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP469198,,loader:fastq load.py,FS_WT0621_S1_L003_R2_001.fastq.gz FS_WT0621_S1_L003_R1_001.fastq.gz FS_WT0621_S1_L003_I1_001.fastq.gz,fastq fastq fastq,4341378795.0,34184085.0,GSM7871948 r3,0:8 1:28 2:91,A:882850653;C:681021491;G:786172206;T:760063970;N:643415,8,28,91,,882850653,681021491,786172206,760063970,643415,SRX22289208,SRS19340290,SRA1742079,Boston University,Boston University,1,0.88158,,0.23138,,0.80921,,0.5997,,91,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-10-30,Undetermined,Undetermined,Multi-tissue,Multi-system
28714,SRR26588126,SRX22289208,SRS19340290,SRP469198,PRJNA1033661,scRNAseq of skeletal tissue during zebrafish craniofacial development,GSE246579,Transcriptome Analysis,We used scRNAseq to characterize differentiation of cell populations during zebrafish craniofacial development. We focused critical stages during suture formation  and compared wildtype fish to mutants lacking the transcription factor sp7  that display striking abnormalities in skull and suture formation. Overall design: Dissociated cells were isolated from heads of wildtype and sp7 mutant zebrafish at  5.8 mm SL 2 wpf and 7 mm SL 3wpf. To enrich for skeletal tissues  brain and eyes were removed before dissociation. To aid in dissection and transcript analysis  fish carried two transgenes   117BMPER: egfp and sp7: mcherry. Cells were analyzed by scRNAseq.,,,,WT 7.0 mm,GSM7871948,,source name:craniofacial skeletal tissues|tissue:craniofacial skeletal tissues|genotype:WT|geo loc name:missing|collection date:missing,WT 7.0 mm,Demultiplexing  barcoded processing  gene counting  and aggregation were performed using Cell Ranger software version 3.1.0 10X Genomics Assembly: danRer11 Supplementary files format and content: Tab separated values files and matrix files,craniofacial skeletal tissues,,Fish were euthanized and transferred to ice cold PBS. In <2 min  we cut off the head just above the pectoral fins  and removed the eyes and brain to enrich for musculoskeletal tissue.The remaining skull was rinsed 2X in PBS  and transferred to a dissociation buffer containing 0.25% trypsin EDTA and 10mg/mL collagenase at 30°. Alternating between pipetting and incubation at 30°  the tissue was fully dissociated  again in <2 min. Digestion was stopped by addition of DMEM w/ 10% BSA. post centrifugation at 700g for 5min  cells were resuspended in PBS  centrifuged again to wash  and the final pellet resuspended in 100μL of FACS buffer 1x PBS  2% BSA and 1mM EDTA. Single cells were isolated by filtration through a 40μm nylon mesh. Cells were loaded onto 10X Genomics microfluidic chips and processed for scRNAseq according to manufacturer's instructions.,,tissue:craniofacial skeletal tissues|genotype:WT,GSM7871948,GSM7871948: WT 7.0 mm; Danio rerio; RNA Seq,GSM7871948 r1,GSM7871948,1,Fish were euthanized and transferred to ice cold PBS. In <2 min  we cut off the head just above the pectoral fins  and removed the eyes and brain to enrich for musculoskeletal tissue.The remaining skull was rinsed 2X in PBS  and transferred to a dissociation buffer containing 0.25% trypsin EDTA and 10mg/mL collagenase at 30°. Alternating between pipetting and incubation at 30°  the tissue was fully dissociated  again in <2 min. Digestion was stopped by addition of DMEM w/ 10% BSA. post centrifugation at 700g for 5min  cells were resuspended in PBS  centrifuged again to wash  and the final pellet resuspended in 100μL of FACS buffer 1x PBS  2% BSA and 1mM EDTA. Single cells were isolated by filtration through a 40μm nylon mesh. Cells were loaded onto 10X Genomics microfluidic chips and processed for scRNAseq according to manufacturer's instructions.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP469198,,loader:fastq load.py,FS_WT0621_S1_L004_R2_001.fastq.gz FS_WT0621_S1_L004_R1_001.fastq.gz FS_WT0621_S1_L004_I1_001.fastq.gz,fastq fastq fastq,4270514446.0,33626098.0,GSM7871948 r4,0:8 1:28 2:91,A:868634109;C:669284353;G:773305808;T:748175261;N:575387,8,28,91,,868634109,669284353,773305808,748175261,575387,SRX22289208,SRS19340290,SRA1742079,Boston University,Boston University,1,0.8822,,0.23032,,0.80695,,0.58745,,91,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-10-30,Undetermined,Undetermined,Multi-tissue,Multi-system
28715,SRR26588127,SRX22289207,SRS19340289,SRP469198,PRJNA1033661,scRNAseq of skeletal tissue during zebrafish craniofacial development,GSE246579,Transcriptome Analysis,We used scRNAseq to characterize differentiation of cell populations during zebrafish craniofacial development. We focused critical stages during suture formation  and compared wildtype fish to mutants lacking the transcription factor sp7  that display striking abnormalities in skull and suture formation. Overall design: Dissociated cells were isolated from heads of wildtype and sp7 mutant zebrafish at  5.8 mm SL 2 wpf and 7 mm SL 3wpf. To enrich for skeletal tissues  brain and eyes were removed before dissociation. To aid in dissection and transcript analysis  fish carried two transgenes   117BMPER: egfp and sp7: mcherry. Cells were analyzed by scRNAseq.,,,,sp7 mutant 5.8 mm,GSM7871947,,source name:craniofacial skeletal tissues|tissue:craniofacial skeletal tissues|genotype:sp7 / |geo loc name:missing|collection date:missing,sp7 mutant 5.8 mm,Demultiplexing  barcoded processing  gene counting  and aggregation were performed using Cell Ranger software version 3.1.0 10X Genomics Assembly: danRer11 Supplementary files format and content: Tab separated values files and matrix files,craniofacial skeletal tissues,,Fish were euthanized and transferred to ice cold PBS. In <2 min  we cut off the head just above the pectoral fins  and removed the eyes and brain to enrich for musculoskeletal tissue.The remaining skull was rinsed 2X in PBS  and transferred to a dissociation buffer containing 0.25% trypsin EDTA and 10mg/mL collagenase at 30°. Alternating between pipetting and incubation at 30°  the tissue was fully dissociated  again in <2 min. Digestion was stopped by addition of DMEM w/ 10% BSA. post centrifugation at 700g for 5min  cells were resuspended in PBS  centrifuged again to wash  and the final pellet resuspended in 100μL of FACS buffer 1x PBS  2% BSA and 1mM EDTA. Single cells were isolated by filtration through a 40μm nylon mesh. Cells were loaded onto 10X Genomics microfluidic chips and processed for scRNAseq according to manufacturer's instructions.,,tissue:craniofacial skeletal tissues|genotype:sp7 / ,GSM7871947,GSM7871947: sp7 mutant 5.8 mm; Danio rerio; RNA Seq,GSM7871947 r1,GSM7871947,1,Fish were euthanized and transferred to ice cold PBS. In <2 min  we cut off the head just above the pectoral fins  and removed the eyes and brain to enrich for musculoskeletal tissue.The remaining skull was rinsed 2X in PBS  and transferred to a dissociation buffer containing 0.25% trypsin EDTA and 10mg/mL collagenase at 30°. Alternating between pipetting and incubation at 30°  the tissue was fully dissociated  again in <2 min. Digestion was stopped by addition of DMEM w/ 10% BSA. post centrifugation at 700g for 5min  cells were resuspended in PBS  centrifuged again to wash  and the final pellet resuspended in 100μL of FACS buffer 1x PBS  2% BSA and 1mM EDTA. Single cells were isolated by filtration through a 40μm nylon mesh. Cells were loaded onto 10X Genomics microfluidic chips and processed for scRNAseq according to manufacturer's instructions.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP469198,,loader:fastq load.py,FS_Mutant0628_S4_L001_R2_001.fastq.gz FS_Mutant0628_S4_L001_R1_001.fastq.gz FS_Mutant0628_S4_L001_I1_001.fastq.gz,fastq fastq fastq,3870633229.0,30477427.0,GSM7871947 r1,0:8 1:28 2:91,A:784323459;C:609892390;G:730737771;T:648119651;N:372586,8,28,91,,784323459,609892390,730737771,648119651,372586,SRX22289207,SRS19340289,SRA1742079,Boston University,Boston University,1,0.83967,,0.19678,,0.84027,,0.62798,,91,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-10-30,Undetermined,Undetermined,Multi-tissue,Multi-system
28716,SRR26588128,SRX22289207,SRS19340289,SRP469198,PRJNA1033661,scRNAseq of skeletal tissue during zebrafish craniofacial development,GSE246579,Transcriptome Analysis,We used scRNAseq to characterize differentiation of cell populations during zebrafish craniofacial development. We focused critical stages during suture formation  and compared wildtype fish to mutants lacking the transcription factor sp7  that display striking abnormalities in skull and suture formation. Overall design: Dissociated cells were isolated from heads of wildtype and sp7 mutant zebrafish at  5.8 mm SL 2 wpf and 7 mm SL 3wpf. To enrich for skeletal tissues  brain and eyes were removed before dissociation. To aid in dissection and transcript analysis  fish carried two transgenes   117BMPER: egfp and sp7: mcherry. Cells were analyzed by scRNAseq.,,,,sp7 mutant 5.8 mm,GSM7871947,,source name:craniofacial skeletal tissues|tissue:craniofacial skeletal tissues|genotype:sp7 / |geo loc name:missing|collection date:missing,sp7 mutant 5.8 mm,Demultiplexing  barcoded processing  gene counting  and aggregation were performed using Cell Ranger software version 3.1.0 10X Genomics Assembly: danRer11 Supplementary files format and content: Tab separated values files and matrix files,craniofacial skeletal tissues,,Fish were euthanized and transferred to ice cold PBS. In <2 min  we cut off the head just above the pectoral fins  and removed the eyes and brain to enrich for musculoskeletal tissue.The remaining skull was rinsed 2X in PBS  and transferred to a dissociation buffer containing 0.25% trypsin EDTA and 10mg/mL collagenase at 30°. Alternating between pipetting and incubation at 30°  the tissue was fully dissociated  again in <2 min. Digestion was stopped by addition of DMEM w/ 10% BSA. post centrifugation at 700g for 5min  cells were resuspended in PBS  centrifuged again to wash  and the final pellet resuspended in 100μL of FACS buffer 1x PBS  2% BSA and 1mM EDTA. Single cells were isolated by filtration through a 40μm nylon mesh. Cells were loaded onto 10X Genomics microfluidic chips and processed for scRNAseq according to manufacturer's instructions.,,tissue:craniofacial skeletal tissues|genotype:sp7 / ,GSM7871947,GSM7871947: sp7 mutant 5.8 mm; Danio rerio; RNA Seq,GSM7871947 r1,GSM7871947,1,Fish were euthanized and transferred to ice cold PBS. In <2 min  we cut off the head just above the pectoral fins  and removed the eyes and brain to enrich for musculoskeletal tissue.The remaining skull was rinsed 2X in PBS  and transferred to a dissociation buffer containing 0.25% trypsin EDTA and 10mg/mL collagenase at 30°. Alternating between pipetting and incubation at 30°  the tissue was fully dissociated  again in <2 min. Digestion was stopped by addition of DMEM w/ 10% BSA. post centrifugation at 700g for 5min  cells were resuspended in PBS  centrifuged again to wash  and the final pellet resuspended in 100μL of FACS buffer 1x PBS  2% BSA and 1mM EDTA. Single cells were isolated by filtration through a 40μm nylon mesh. Cells were loaded onto 10X Genomics microfluidic chips and processed for scRNAseq according to manufacturer's instructions.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP469198,,loader:fastq load.py,FS_Mutant0628_S4_L002_R2_001.fastq.gz FS_Mutant0628_S4_L002_R1_001.fastq.gz FS_Mutant0628_S4_L002_I1_001.fastq.gz,fastq fastq fastq,3795705896.0,29887448.0,GSM7871947 r2,0:8 1:28 2:91,A:769584134;C:598310890;G:715720368;T:635803045;N:339331,8,28,91,,769584134,598310890,715720368,635803045,339331,SRX22289207,SRS19340289,SRA1742079,Boston University,Boston University,1,0.83992,,0.199,,0.84094,,0.63528,,91,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-10-30,Undetermined,Undetermined,Multi-tissue,Multi-system
28717,SRR26588129,SRX22289207,SRS19340289,SRP469198,PRJNA1033661,scRNAseq of skeletal tissue during zebrafish craniofacial development,GSE246579,Transcriptome Analysis,We used scRNAseq to characterize differentiation of cell populations during zebrafish craniofacial development. We focused critical stages during suture formation  and compared wildtype fish to mutants lacking the transcription factor sp7  that display striking abnormalities in skull and suture formation. Overall design: Dissociated cells were isolated from heads of wildtype and sp7 mutant zebrafish at  5.8 mm SL 2 wpf and 7 mm SL 3wpf. To enrich for skeletal tissues  brain and eyes were removed before dissociation. To aid in dissection and transcript analysis  fish carried two transgenes   117BMPER: egfp and sp7: mcherry. Cells were analyzed by scRNAseq.,,,,sp7 mutant 5.8 mm,GSM7871947,,source name:craniofacial skeletal tissues|tissue:craniofacial skeletal tissues|genotype:sp7 / |geo loc name:missing|collection date:missing,sp7 mutant 5.8 mm,Demultiplexing  barcoded processing  gene counting  and aggregation were performed using Cell Ranger software version 3.1.0 10X Genomics Assembly: danRer11 Supplementary files format and content: Tab separated values files and matrix files,craniofacial skeletal tissues,,Fish were euthanized and transferred to ice cold PBS. In <2 min  we cut off the head just above the pectoral fins  and removed the eyes and brain to enrich for musculoskeletal tissue.The remaining skull was rinsed 2X in PBS  and transferred to a dissociation buffer containing 0.25% trypsin EDTA and 10mg/mL collagenase at 30°. Alternating between pipetting and incubation at 30°  the tissue was fully dissociated  again in <2 min. Digestion was stopped by addition of DMEM w/ 10% BSA. post centrifugation at 700g for 5min  cells were resuspended in PBS  centrifuged again to wash  and the final pellet resuspended in 100μL of FACS buffer 1x PBS  2% BSA and 1mM EDTA. Single cells were isolated by filtration through a 40μm nylon mesh. Cells were loaded onto 10X Genomics microfluidic chips and processed for scRNAseq according to manufacturer's instructions.,,tissue:craniofacial skeletal tissues|genotype:sp7 / ,GSM7871947,GSM7871947: sp7 mutant 5.8 mm; Danio rerio; RNA Seq,GSM7871947 r1,GSM7871947,1,Fish were euthanized and transferred to ice cold PBS. In <2 min  we cut off the head just above the pectoral fins  and removed the eyes and brain to enrich for musculoskeletal tissue.The remaining skull was rinsed 2X in PBS  and transferred to a dissociation buffer containing 0.25% trypsin EDTA and 10mg/mL collagenase at 30°. Alternating between pipetting and incubation at 30°  the tissue was fully dissociated  again in <2 min. Digestion was stopped by addition of DMEM w/ 10% BSA. post centrifugation at 700g for 5min  cells were resuspended in PBS  centrifuged again to wash  and the final pellet resuspended in 100μL of FACS buffer 1x PBS  2% BSA and 1mM EDTA. Single cells were isolated by filtration through a 40μm nylon mesh. Cells were loaded onto 10X Genomics microfluidic chips and processed for scRNAseq according to manufacturer's instructions.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP469198,,loader:fastq load.py,FS_Mutant0628_S4_L003_I1_001.fastq.gz FS_Mutant0628_S4_L003_R1_001.fastq.gz FS_Mutant0628_S4_L003_R2_001.fastq.gz,fastq fastq fastq,3882075802.0,30567526.0,GSM7871947 r3,0:8 1:28 2:91,A:786373431;C:613286785;G:731993747;T:649408434;N:582469,8,28,91,,786373431,613286785,731993747,649408434,582469,SRX22289207,SRS19340289,SRA1742079,Boston University,Boston University,1,0.83867,,0.19884,,0.83826,,0.63213,,91,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-10-30,Undetermined,Undetermined,Multi-tissue,Multi-system
28718,SRR26588130,SRX22289207,SRS19340289,SRP469198,PRJNA1033661,scRNAseq of skeletal tissue during zebrafish craniofacial development,GSE246579,Transcriptome Analysis,We used scRNAseq to characterize differentiation of cell populations during zebrafish craniofacial development. We focused critical stages during suture formation  and compared wildtype fish to mutants lacking the transcription factor sp7  that display striking abnormalities in skull and suture formation. Overall design: Dissociated cells were isolated from heads of wildtype and sp7 mutant zebrafish at  5.8 mm SL 2 wpf and 7 mm SL 3wpf. To enrich for skeletal tissues  brain and eyes were removed before dissociation. To aid in dissection and transcript analysis  fish carried two transgenes   117BMPER: egfp and sp7: mcherry. Cells were analyzed by scRNAseq.,,,,sp7 mutant 5.8 mm,GSM7871947,,source name:craniofacial skeletal tissues|tissue:craniofacial skeletal tissues|genotype:sp7 / |geo loc name:missing|collection date:missing,sp7 mutant 5.8 mm,Demultiplexing  barcoded processing  gene counting  and aggregation were performed using Cell Ranger software version 3.1.0 10X Genomics Assembly: danRer11 Supplementary files format and content: Tab separated values files and matrix files,craniofacial skeletal tissues,,Fish were euthanized and transferred to ice cold PBS. In <2 min  we cut off the head just above the pectoral fins  and removed the eyes and brain to enrich for musculoskeletal tissue.The remaining skull was rinsed 2X in PBS  and transferred to a dissociation buffer containing 0.25% trypsin EDTA and 10mg/mL collagenase at 30°. Alternating between pipetting and incubation at 30°  the tissue was fully dissociated  again in <2 min. Digestion was stopped by addition of DMEM w/ 10% BSA. post centrifugation at 700g for 5min  cells were resuspended in PBS  centrifuged again to wash  and the final pellet resuspended in 100μL of FACS buffer 1x PBS  2% BSA and 1mM EDTA. Single cells were isolated by filtration through a 40μm nylon mesh. Cells were loaded onto 10X Genomics microfluidic chips and processed for scRNAseq according to manufacturer's instructions.,,tissue:craniofacial skeletal tissues|genotype:sp7 / ,GSM7871947,GSM7871947: sp7 mutant 5.8 mm; Danio rerio; RNA Seq,GSM7871947 r1,GSM7871947,1,Fish were euthanized and transferred to ice cold PBS. In <2 min  we cut off the head just above the pectoral fins  and removed the eyes and brain to enrich for musculoskeletal tissue.The remaining skull was rinsed 2X in PBS  and transferred to a dissociation buffer containing 0.25% trypsin EDTA and 10mg/mL collagenase at 30°. Alternating between pipetting and incubation at 30°  the tissue was fully dissociated  again in <2 min. Digestion was stopped by addition of DMEM w/ 10% BSA. post centrifugation at 700g for 5min  cells were resuspended in PBS  centrifuged again to wash  and the final pellet resuspended in 100μL of FACS buffer 1x PBS  2% BSA and 1mM EDTA. Single cells were isolated by filtration through a 40μm nylon mesh. Cells were loaded onto 10X Genomics microfluidic chips and processed for scRNAseq according to manufacturer's instructions.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP469198,,loader:fastq load.py,FS_Mutant0628_S4_L004_R2_001.fastq.gz FS_Mutant0628_S4_L004_R1_001.fastq.gz FS_Mutant0628_S4_L004_I1_001.fastq.gz,fastq fastq fastq,3821331575.0,30089225.0,GSM7871947 r4,0:8 1:28 2:91,A:774445827;C:603171063;G:720511073;T:639476444;N:515068,8,28,91,,774445827,603171063,720511073,639476444,515068,SRX22289207,SRS19340289,SRA1742079,Boston University,Boston University,1,0.84008,,0.19754,,0.84076,,0.63418,,91,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-10-30,Undetermined,Undetermined,Multi-tissue,Multi-system
28719,SRR26588131,SRX22289206,SRS19340291,SRP469198,PRJNA1033661,scRNAseq of skeletal tissue during zebrafish craniofacial development,GSE246579,Transcriptome Analysis,We used scRNAseq to characterize differentiation of cell populations during zebrafish craniofacial development. We focused critical stages during suture formation  and compared wildtype fish to mutants lacking the transcription factor sp7  that display striking abnormalities in skull and suture formation. Overall design: Dissociated cells were isolated from heads of wildtype and sp7 mutant zebrafish at  5.8 mm SL 2 wpf and 7 mm SL 3wpf. To enrich for skeletal tissues  brain and eyes were removed before dissociation. To aid in dissection and transcript analysis  fish carried two transgenes   117BMPER: egfp and sp7: mcherry. Cells were analyzed by scRNAseq.,,,,sp7 mutant 7.0 mm,GSM7871946,,source name:craniofacial skeletal tissues|tissue:craniofacial skeletal tissues|genotype:sp7 / |geo loc name:missing|collection date:missing,sp7 mutant  7.0 mm,Demultiplexing  barcoded processing  gene counting  and aggregation were performed using Cell Ranger software version 3.1.0 10X Genomics Assembly: danRer11 Supplementary files format and content: Tab separated values files and matrix files,craniofacial skeletal tissues,,Fish were euthanized and transferred to ice cold PBS. In <2 min  we cut off the head just above the pectoral fins  and removed the eyes and brain to enrich for musculoskeletal tissue.The remaining skull was rinsed 2X in PBS  and transferred to a dissociation buffer containing 0.25% trypsin EDTA and 10mg/mL collagenase at 30°. Alternating between pipetting and incubation at 30°  the tissue was fully dissociated  again in <2 min. Digestion was stopped by addition of DMEM w/ 10% BSA. post centrifugation at 700g for 5min  cells were resuspended in PBS  centrifuged again to wash  and the final pellet resuspended in 100μL of FACS buffer 1x PBS  2% BSA and 1mM EDTA. Single cells were isolated by filtration through a 40μm nylon mesh. Cells were loaded onto 10X Genomics microfluidic chips and processed for scRNAseq according to manufacturer's instructions.,,tissue:craniofacial skeletal tissues|genotype:sp7 / ,GSM7871946,GSM7871946: sp7 mutant  7.0 mm; Danio rerio; RNA Seq,GSM7871946 r1,GSM7871946,1,Fish were euthanized and transferred to ice cold PBS. In <2 min  we cut off the head just above the pectoral fins  and removed the eyes and brain to enrich for musculoskeletal tissue.The remaining skull was rinsed 2X in PBS  and transferred to a dissociation buffer containing 0.25% trypsin EDTA and 10mg/mL collagenase at 30°. Alternating between pipetting and incubation at 30°  the tissue was fully dissociated  again in <2 min. Digestion was stopped by addition of DMEM w/ 10% BSA. post centrifugation at 700g for 5min  cells were resuspended in PBS  centrifuged again to wash  and the final pellet resuspended in 100μL of FACS buffer 1x PBS  2% BSA and 1mM EDTA. Single cells were isolated by filtration through a 40μm nylon mesh. Cells were loaded onto 10X Genomics microfluidic chips and processed for scRNAseq according to manufacturer's instructions.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP469198,,loader:fastq load.py,FS_Mutant0621_S2_L001_I1_001.fastq.gz FS_Mutant0621_S2_L001_R1_001.fastq.gz FS_Mutant0621_S2_L001_R2_001.fastq.gz,fastq fastq fastq,4256651761.0,33516943.0,GSM7871946 r1,0:8 1:28 2:91,A:862245132;C:673711733;G:766388204;T:747287820;N:408924,8,28,91,,862245132,673711733,766388204,747287820,408924,SRX22289206,SRS19340291,SRA1742079,Boston University,Boston University,1,0.89937,,0.20157,,0.80691,,0.60147,,91,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-10-30,Undetermined,Undetermined,Multi-tissue,Multi-system
28720,SRR26588132,SRX22289206,SRS19340291,SRP469198,PRJNA1033661,scRNAseq of skeletal tissue during zebrafish craniofacial development,GSE246579,Transcriptome Analysis,We used scRNAseq to characterize differentiation of cell populations during zebrafish craniofacial development. We focused critical stages during suture formation  and compared wildtype fish to mutants lacking the transcription factor sp7  that display striking abnormalities in skull and suture formation. Overall design: Dissociated cells were isolated from heads of wildtype and sp7 mutant zebrafish at  5.8 mm SL 2 wpf and 7 mm SL 3wpf. To enrich for skeletal tissues  brain and eyes were removed before dissociation. To aid in dissection and transcript analysis  fish carried two transgenes   117BMPER: egfp and sp7: mcherry. Cells were analyzed by scRNAseq.,,,,sp7 mutant 7.0 mm,GSM7871946,,source name:craniofacial skeletal tissues|tissue:craniofacial skeletal tissues|genotype:sp7 / |geo loc name:missing|collection date:missing,sp7 mutant  7.0 mm,Demultiplexing  barcoded processing  gene counting  and aggregation were performed using Cell Ranger software version 3.1.0 10X Genomics Assembly: danRer11 Supplementary files format and content: Tab separated values files and matrix files,craniofacial skeletal tissues,,Fish were euthanized and transferred to ice cold PBS. In <2 min  we cut off the head just above the pectoral fins  and removed the eyes and brain to enrich for musculoskeletal tissue.The remaining skull was rinsed 2X in PBS  and transferred to a dissociation buffer containing 0.25% trypsin EDTA and 10mg/mL collagenase at 30°. Alternating between pipetting and incubation at 30°  the tissue was fully dissociated  again in <2 min. Digestion was stopped by addition of DMEM w/ 10% BSA. post centrifugation at 700g for 5min  cells were resuspended in PBS  centrifuged again to wash  and the final pellet resuspended in 100μL of FACS buffer 1x PBS  2% BSA and 1mM EDTA. Single cells were isolated by filtration through a 40μm nylon mesh. Cells were loaded onto 10X Genomics microfluidic chips and processed for scRNAseq according to manufacturer's instructions.,,tissue:craniofacial skeletal tissues|genotype:sp7 / ,GSM7871946,GSM7871946: sp7 mutant  7.0 mm; Danio rerio; RNA Seq,GSM7871946 r1,GSM7871946,1,Fish were euthanized and transferred to ice cold PBS. In <2 min  we cut off the head just above the pectoral fins  and removed the eyes and brain to enrich for musculoskeletal tissue.The remaining skull was rinsed 2X in PBS  and transferred to a dissociation buffer containing 0.25% trypsin EDTA and 10mg/mL collagenase at 30°. Alternating between pipetting and incubation at 30°  the tissue was fully dissociated  again in <2 min. Digestion was stopped by addition of DMEM w/ 10% BSA. post centrifugation at 700g for 5min  cells were resuspended in PBS  centrifuged again to wash  and the final pellet resuspended in 100μL of FACS buffer 1x PBS  2% BSA and 1mM EDTA. Single cells were isolated by filtration through a 40μm nylon mesh. Cells were loaded onto 10X Genomics microfluidic chips and processed for scRNAseq according to manufacturer's instructions.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP469198,,loader:fastq load.py,FS_Mutant0621_S2_L002_I1_001.fastq.gz FS_Mutant0621_S2_L002_R1_001.fastq.gz FS_Mutant0621_S2_L002_R2_001.fastq.gz,fastq fastq fastq,4173795437.0,32864531.0,GSM7871946 r2,0:8 1:28 2:91,A:846056609;C:660910650;G:750849639;T:732486246;N:369177,8,28,91,,846056609,660910650,750849639,732486246,369177,SRX22289206,SRS19340291,SRA1742079,Boston University,Boston University,1,0.89896,,0.20107,,0.80415,,0.60881,,91,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-10-30,Undetermined,Undetermined,Multi-tissue,Multi-system
28721,SRR26588133,SRX22289206,SRS19340291,SRP469198,PRJNA1033661,scRNAseq of skeletal tissue during zebrafish craniofacial development,GSE246579,Transcriptome Analysis,We used scRNAseq to characterize differentiation of cell populations during zebrafish craniofacial development. We focused critical stages during suture formation  and compared wildtype fish to mutants lacking the transcription factor sp7  that display striking abnormalities in skull and suture formation. Overall design: Dissociated cells were isolated from heads of wildtype and sp7 mutant zebrafish at  5.8 mm SL 2 wpf and 7 mm SL 3wpf. To enrich for skeletal tissues  brain and eyes were removed before dissociation. To aid in dissection and transcript analysis  fish carried two transgenes   117BMPER: egfp and sp7: mcherry. Cells were analyzed by scRNAseq.,,,,sp7 mutant 7.0 mm,GSM7871946,,source name:craniofacial skeletal tissues|tissue:craniofacial skeletal tissues|genotype:sp7 / |geo loc name:missing|collection date:missing,sp7 mutant  7.0 mm,Demultiplexing  barcoded processing  gene counting  and aggregation were performed using Cell Ranger software version 3.1.0 10X Genomics Assembly: danRer11 Supplementary files format and content: Tab separated values files and matrix files,craniofacial skeletal tissues,,Fish were euthanized and transferred to ice cold PBS. In <2 min  we cut off the head just above the pectoral fins  and removed the eyes and brain to enrich for musculoskeletal tissue.The remaining skull was rinsed 2X in PBS  and transferred to a dissociation buffer containing 0.25% trypsin EDTA and 10mg/mL collagenase at 30°. Alternating between pipetting and incubation at 30°  the tissue was fully dissociated  again in <2 min. Digestion was stopped by addition of DMEM w/ 10% BSA. post centrifugation at 700g for 5min  cells were resuspended in PBS  centrifuged again to wash  and the final pellet resuspended in 100μL of FACS buffer 1x PBS  2% BSA and 1mM EDTA. Single cells were isolated by filtration through a 40μm nylon mesh. Cells were loaded onto 10X Genomics microfluidic chips and processed for scRNAseq according to manufacturer's instructions.,,tissue:craniofacial skeletal tissues|genotype:sp7 / ,GSM7871946,GSM7871946: sp7 mutant  7.0 mm; Danio rerio; RNA Seq,GSM7871946 r1,GSM7871946,1,Fish were euthanized and transferred to ice cold PBS. In <2 min  we cut off the head just above the pectoral fins  and removed the eyes and brain to enrich for musculoskeletal tissue.The remaining skull was rinsed 2X in PBS  and transferred to a dissociation buffer containing 0.25% trypsin EDTA and 10mg/mL collagenase at 30°. Alternating between pipetting and incubation at 30°  the tissue was fully dissociated  again in <2 min. Digestion was stopped by addition of DMEM w/ 10% BSA. post centrifugation at 700g for 5min  cells were resuspended in PBS  centrifuged again to wash  and the final pellet resuspended in 100μL of FACS buffer 1x PBS  2% BSA and 1mM EDTA. Single cells were isolated by filtration through a 40μm nylon mesh. Cells were loaded onto 10X Genomics microfluidic chips and processed for scRNAseq according to manufacturer's instructions.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP469198,,loader:fastq load.py,FS_Mutant0621_S2_L003_I1_001.fastq.gz FS_Mutant0621_S2_L003_R1_001.fastq.gz FS_Mutant0621_S2_L003_R2_001.fastq.gz,fastq fastq fastq,4291089081.0,33788103.0,GSM7871946 r3,0:8 1:28 2:91,A:869084749;C:681276277;G:772278057;T:751443489;N:634801,8,28,91,,869084749,681276277,772278057,751443489,634801,SRX22289206,SRS19340291,SRA1742079,Boston University,Boston University,1,0.89995,,0.20079,,0.80505,,0.60752,,91,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-10-30,Undetermined,Undetermined,Multi-tissue,Multi-system
28722,SRR26588134,SRX22289206,SRS19340291,SRP469198,PRJNA1033661,scRNAseq of skeletal tissue during zebrafish craniofacial development,GSE246579,Transcriptome Analysis,We used scRNAseq to characterize differentiation of cell populations during zebrafish craniofacial development. We focused critical stages during suture formation  and compared wildtype fish to mutants lacking the transcription factor sp7  that display striking abnormalities in skull and suture formation. Overall design: Dissociated cells were isolated from heads of wildtype and sp7 mutant zebrafish at  5.8 mm SL 2 wpf and 7 mm SL 3wpf. To enrich for skeletal tissues  brain and eyes were removed before dissociation. To aid in dissection and transcript analysis  fish carried two transgenes   117BMPER: egfp and sp7: mcherry. Cells were analyzed by scRNAseq.,,,,sp7 mutant 7.0 mm,GSM7871946,,source name:craniofacial skeletal tissues|tissue:craniofacial skeletal tissues|genotype:sp7 / |geo loc name:missing|collection date:missing,sp7 mutant  7.0 mm,Demultiplexing  barcoded processing  gene counting  and aggregation were performed using Cell Ranger software version 3.1.0 10X Genomics Assembly: danRer11 Supplementary files format and content: Tab separated values files and matrix files,craniofacial skeletal tissues,,Fish were euthanized and transferred to ice cold PBS. In <2 min  we cut off the head just above the pectoral fins  and removed the eyes and brain to enrich for musculoskeletal tissue.The remaining skull was rinsed 2X in PBS  and transferred to a dissociation buffer containing 0.25% trypsin EDTA and 10mg/mL collagenase at 30°. Alternating between pipetting and incubation at 30°  the tissue was fully dissociated  again in <2 min. Digestion was stopped by addition of DMEM w/ 10% BSA. post centrifugation at 700g for 5min  cells were resuspended in PBS  centrifuged again to wash  and the final pellet resuspended in 100μL of FACS buffer 1x PBS  2% BSA and 1mM EDTA. Single cells were isolated by filtration through a 40μm nylon mesh. Cells were loaded onto 10X Genomics microfluidic chips and processed for scRNAseq according to manufacturer's instructions.,,tissue:craniofacial skeletal tissues|genotype:sp7 / ,GSM7871946,GSM7871946: sp7 mutant  7.0 mm; Danio rerio; RNA Seq,GSM7871946 r1,GSM7871946,1,Fish were euthanized and transferred to ice cold PBS. In <2 min  we cut off the head just above the pectoral fins  and removed the eyes and brain to enrich for musculoskeletal tissue.The remaining skull was rinsed 2X in PBS  and transferred to a dissociation buffer containing 0.25% trypsin EDTA and 10mg/mL collagenase at 30°. Alternating between pipetting and incubation at 30°  the tissue was fully dissociated  again in <2 min. Digestion was stopped by addition of DMEM w/ 10% BSA. post centrifugation at 700g for 5min  cells were resuspended in PBS  centrifuged again to wash  and the final pellet resuspended in 100μL of FACS buffer 1x PBS  2% BSA and 1mM EDTA. Single cells were isolated by filtration through a 40μm nylon mesh. Cells were loaded onto 10X Genomics microfluidic chips and processed for scRNAseq according to manufacturer's instructions.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP469198,,loader:fastq load.py,FS_Mutant0621_S2_L004_I1_001.fastq.gz FS_Mutant0621_S2_L004_R1_001.fastq.gz FS_Mutant0621_S2_L004_R2_001.fastq.gz,fastq fastq fastq,4221057598.0,33236674.0,GSM7871946 r4,0:8 1:28 2:91,A:855377679;C:669535108;G:759458317;T:739600774;N:565456,8,28,91,,855377679,669535108,759458317,739600774,565456,SRX22289206,SRS19340291,SRA1742079,Boston University,Boston University,1,0.90012,,0.20095,,0.80562,,0.60729,,91,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-10-30,Undetermined,Undetermined,Multi-tissue,Multi-system
29812,SRR27466771,SRX23138319,SRS20089385,SRP482605,PRJNA1062705,Comparative transcriptomics coupled to developmental grading via transgenic Zebrafish reporter strains identifies conserved features in neutrophil maturation,GSE252788,Transcriptome Analysis,Neutrophils are evolutionarily conserved innate immune cells playing pivotal roles in host defence. Zebrafish models have contributed substantially to our understanding of neutrophil functions but similarities to human neutrophil maturation have not been systematically characterized  which limits their applicability to studying human disease. Here we show  by generating and analysing transgenic zebrafish strains representing distinct neutrophil differentiation stages  a high resolution transcriptional profile of neutrophil maturation. We link gene expression at each stage to characteristic transcription factors  including C/ebp ß  which is important for late neutrophil maturation. Cross species comparison of zebrafish  mouse  and human samples confirms high molecular similarity of immature stages and discriminates zebrafish specific from pan species gene signatures. Applying the pan species neutrophil maturation signature to RNA sequencing data from human neuroblastoma patients reveals association between metastatic tumor cell infiltration in the bone marrow and an overall increase in mature neutrophils. Our detailed neutrophil maturation atlas thus provides a valuable resource for studying neutrophil function at different stages across species in health and disease. Overall design: Kidney marrow from 2 adult  six mpf  male zebrafish was isolated  labelled using lipid tagged following MULTI seq protocol  for scRNA seq using 10x Genomics.,,pubmed:38413586,,MF317 A2 GEX zebrafish multiseq,GSM8007850,,source name:Kidney marrow|tissue:Kidney marrow|cell type:Whole kidney marrow PBMCs|geo loc name:missing|collection date:missing,MF317 A2 GEX zebrafish multiseq,We used the CellRanger v3.1.0 software 10x Genomics for cell demultiplexing and alignment and loaded the counts into Seurat v4.0.2. Assembly: GRCz11 3.1.0 zebrafish reference transcriptome that had been expanded to include the sequences of reporter genes Citrine and CFPNTR  sequences from snapgene.com. Supplementary files format and content: compressed matrix files of CellRanger outputs Supplementary files format and content: rds file containting Seurat object Supplementary files format and content: hd5a file containting Seurat object,Kidney marrow,,Each kidney marrow was split into four portions  labelled with lipid anchor plus individual barcode solution 2 μM for 5’ on ice and then incubated with lipid co anchor 2 μM for 5’ on ice. Each cell portion was individually FACS sorted to obtain one population mmp9 NO  INT  HI or WKM. All cells were gated on live gate  for WKM debris was excluded in a FSC/SSC gate  and mmp9 NO  INT  HI were gated on LysC:CFP positivity and different levels of Mmp9:Citrine CAAX expression. Single cell suspensions were immediately subjected to scRNA seq using the Chromium Single Cell Controller and Single Cell 3’ Library & Gel Bead Kit v3.1 10x Genomics  Pleasanton  CA  according to the manufacturer’s protocols 10x Genomics and sequenced by protocol.,,tissue:Kidney marrow|cell type:Whole kidney marrow PBMCs,GSM8007850,GSM8007850: MF317 A2 GEX zebrafish multiseq; Danio rerio; RNA Seq,GSM8007850 r1,GSM8007850,1,Each kidney marrow was split into four portions  labelled with lipid anchor plus individual barcode solution 2 μM for five prime on ice and then incubated with lipid co anchor 2 μM for five prime on ice. Each cell portion was individually FACS sorted to obtain one population mmp9 NO  INT  HI or WKM. All cells were gated on live gate  for WKM debris was excluded in a FSC/SSC gate  and mmp9 NO  INT  HI were gated on LysC:CFP positivity and different levels of Mmp9:Citrine CAAX expression. Single cell suspensions were immediately subjected to scRNA seq using the Chromium Single Cell Controller and Single Cell three prime Library & Gel Bead Kit v3.1 10x Genomics  Pleasanton  CA  according to the manufacturer's protocols 10x Genomics and sequenced by protocol.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP482605,,loader:fastq load.py,MF317_A2_GEX_zebrafish_multiseq_S3_L004_I1_001.fastq.gz MF317_A2_GEX_zebrafish_multiseq_S3_L004_R1_001.fastq.gz MF317_A2_GEX_zebrafish_multiseq_S3_L004_R2_001.fastq.gz,fastq fastq fastq,20397464955.0,151092333.0,GSM8007850 r1,0:8 1:29 2:98,A:4317555978;C:3264550330;G:3319063129;T:3903632022;N:2247175,8,29,98,,4317555978,3264550330,3319063129,3903632022,2247175,SRX23138319,SRS20089385,,,"Developmental Cancer Genomics, St. Anna Children's Cancer Research Institute (CCRI)",,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Austria,2024-01-09,Undetermined,Adult,Multi-tissue,Multi-system
29813,SRR27466772,SRX23138319,SRS20089385,SRP482605,PRJNA1062705,Comparative transcriptomics coupled to developmental grading via transgenic Zebrafish reporter strains identifies conserved features in neutrophil maturation,GSE252788,Transcriptome Analysis,Neutrophils are evolutionarily conserved innate immune cells playing pivotal roles in host defence. Zebrafish models have contributed substantially to our understanding of neutrophil functions but similarities to human neutrophil maturation have not been systematically characterized  which limits their applicability to studying human disease. Here we show  by generating and analysing transgenic zebrafish strains representing distinct neutrophil differentiation stages  a high resolution transcriptional profile of neutrophil maturation. We link gene expression at each stage to characteristic transcription factors  including C/ebp ß  which is important for late neutrophil maturation. Cross species comparison of zebrafish  mouse  and human samples confirms high molecular similarity of immature stages and discriminates zebrafish specific from pan species gene signatures. Applying the pan species neutrophil maturation signature to RNA sequencing data from human neuroblastoma patients reveals association between metastatic tumor cell infiltration in the bone marrow and an overall increase in mature neutrophils. Our detailed neutrophil maturation atlas thus provides a valuable resource for studying neutrophil function at different stages across species in health and disease. Overall design: Kidney marrow from 2 adult  six mpf  male zebrafish was isolated  labelled using lipid tagged following MULTI seq protocol  for scRNA seq using 10x Genomics.,,pubmed:38413586,,MF317 A2 GEX zebrafish multiseq,GSM8007850,,source name:Kidney marrow|tissue:Kidney marrow|cell type:Whole kidney marrow PBMCs|geo loc name:missing|collection date:missing,MF317 A2 GEX zebrafish multiseq,We used the CellRanger v3.1.0 software 10x Genomics for cell demultiplexing and alignment and loaded the counts into Seurat v4.0.2. Assembly: GRCz11 3.1.0 zebrafish reference transcriptome that had been expanded to include the sequences of reporter genes Citrine and CFPNTR  sequences from snapgene.com. Supplementary files format and content: compressed matrix files of CellRanger outputs Supplementary files format and content: rds file containting Seurat object Supplementary files format and content: hd5a file containting Seurat object,Kidney marrow,,Each kidney marrow was split into four portions  labelled with lipid anchor plus individual barcode solution 2 μM for 5’ on ice and then incubated with lipid co anchor 2 μM for 5’ on ice. Each cell portion was individually FACS sorted to obtain one population mmp9 NO  INT  HI or WKM. All cells were gated on live gate  for WKM debris was excluded in a FSC/SSC gate  and mmp9 NO  INT  HI were gated on LysC:CFP positivity and different levels of Mmp9:Citrine CAAX expression. Single cell suspensions were immediately subjected to scRNA seq using the Chromium Single Cell Controller and Single Cell 3’ Library & Gel Bead Kit v3.1 10x Genomics  Pleasanton  CA  according to the manufacturer’s protocols 10x Genomics and sequenced by protocol.,,tissue:Kidney marrow|cell type:Whole kidney marrow PBMCs,GSM8007850,GSM8007850: MF317 A2 GEX zebrafish multiseq; Danio rerio; RNA Seq,GSM8007850 r1,GSM8007850,1,Each kidney marrow was split into four portions  labelled with lipid anchor plus individual barcode solution 2 μM for five prime on ice and then incubated with lipid co anchor 2 μM for five prime on ice. Each cell portion was individually FACS sorted to obtain one population mmp9 NO  INT  HI or WKM. All cells were gated on live gate  for WKM debris was excluded in a FSC/SSC gate  and mmp9 NO  INT  HI were gated on LysC:CFP positivity and different levels of Mmp9:Citrine CAAX expression. Single cell suspensions were immediately subjected to scRNA seq using the Chromium Single Cell Controller and Single Cell three prime Library & Gel Bead Kit v3.1 10x Genomics  Pleasanton  CA  according to the manufacturer's protocols 10x Genomics and sequenced by protocol.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP482605,,loader:fastq load.py,MF317_A2_barcode_zebrafish_multiseq_S68024_S10_L004_I1_001.fastq.gz MF317_A2_barcode_zebrafish_multiseq_S68024_S10_L004_R1_001.fastq.gz MF317_A2_barcode_zebrafish_multiseq_S68024_S10_L004_R2_001.fastq.gz,fastq fastq fastq,609557670.0,4515242.0,GSM8007850 r2,0:8 1:29 2:98,A:288037892;C:47138905;G:85961330;T:21289087;N:66502,8,29,98,,288037892,47138905,85961330,21289087,66502,SRX23138319,SRS20089385,,,"Developmental Cancer Genomics, St. Anna Children's Cancer Research Institute (CCRI)",,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Austria,2024-01-09,Undetermined,Adult,Multi-tissue,Multi-system
29814,SRR27466773,SRX23138318,SRS20089387,SRP482605,PRJNA1062705,Comparative transcriptomics coupled to developmental grading via transgenic Zebrafish reporter strains identifies conserved features in neutrophil maturation,GSE252788,Transcriptome Analysis,Neutrophils are evolutionarily conserved innate immune cells playing pivotal roles in host defence. Zebrafish models have contributed substantially to our understanding of neutrophil functions but similarities to human neutrophil maturation have not been systematically characterized  which limits their applicability to studying human disease. Here we show  by generating and analysing transgenic zebrafish strains representing distinct neutrophil differentiation stages  a high resolution transcriptional profile of neutrophil maturation. We link gene expression at each stage to characteristic transcription factors  including C/ebp ß  which is important for late neutrophil maturation. Cross species comparison of zebrafish  mouse  and human samples confirms high molecular similarity of immature stages and discriminates zebrafish specific from pan species gene signatures. Applying the pan species neutrophil maturation signature to RNA sequencing data from human neuroblastoma patients reveals association between metastatic tumor cell infiltration in the bone marrow and an overall increase in mature neutrophils. Our detailed neutrophil maturation atlas thus provides a valuable resource for studying neutrophil function at different stages across species in health and disease. Overall design: Kidney marrow from 2 adult  six mpf  male zebrafish was isolated  labelled using lipid tagged following MULTI seq protocol  for scRNA seq using 10x Genomics.,,pubmed:38413586,,MF317 A1 GEX zebrafish multiseq,GSM8007849,,source name:Kidney marrow|tissue:Kidney marrow|cell type:Neutrophils|geo loc name:missing|collection date:missing,MF317 A1 GEX zebrafish multiseq,We used the CellRanger v3.1.0 software 10x Genomics for cell demultiplexing and alignment and loaded the counts into Seurat v4.0.2. Assembly: GRCz11 3.1.0 zebrafish reference transcriptome that had been expanded to include the sequences of reporter genes Citrine and CFPNTR  sequences from snapgene.com. Supplementary files format and content: compressed matrix files of CellRanger outputs Supplementary files format and content: rds file containting Seurat object Supplementary files format and content: hd5a file containting Seurat object,Kidney marrow,,Each kidney marrow was split into four portions  labelled with lipid anchor plus individual barcode solution 2 μM for 5’ on ice and then incubated with lipid co anchor 2 μM for 5’ on ice. Each cell portion was individually FACS sorted to obtain one population mmp9 NO  INT  HI or WKM. All cells were gated on live gate  for WKM debris was excluded in a FSC/SSC gate  and mmp9 NO  INT  HI were gated on LysC:CFP positivity and different levels of Mmp9:Citrine CAAX expression. Single cell suspensions were immediately subjected to scRNA seq using the Chromium Single Cell Controller and Single Cell 3’ Library & Gel Bead Kit v3.1 10x Genomics  Pleasanton  CA  according to the manufacturer’s protocols 10x Genomics and sequenced by protocol.,,tissue:Kidney marrow|cell type:Neutrophils,GSM8007849,GSM8007849: MF317 A1 GEX zebrafish multiseq; Danio rerio; RNA Seq,GSM8007849 r1,GSM8007849,1,Each kidney marrow was split into four portions  labelled with lipid anchor plus individual barcode solution 2 μM for five prime on ice and then incubated with lipid co anchor 2 μM for five prime on ice. Each cell portion was individually FACS sorted to obtain one population mmp9 NO  INT  HI or WKM. All cells were gated on live gate  for WKM debris was excluded in a FSC/SSC gate  and mmp9 NO  INT  HI were gated on LysC:CFP positivity and different levels of Mmp9:Citrine CAAX expression. Single cell suspensions were immediately subjected to scRNA seq using the Chromium Single Cell Controller and Single Cell three prime Library & Gel Bead Kit v3.1 10x Genomics  Pleasanton  CA  according to the manufacturer's protocols 10x Genomics and sequenced by protocol.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP482605,,loader:fastq load.py,MF317_A1_GEX_zebrafish_multiseq_S1_L004_I1_001.fastq.gz MF317_A1_GEX_zebrafish_multiseq_S1_L004_R1_001.fastq.gz MF317_A1_GEX_zebrafish_multiseq_S1_L004_R2_001.fastq.gz,fastq fastq fastq,20471343840.0,151639584.0,GSM8007849 r1,0:8 1:29 2:98,A:4574898668;C:2902052527;G:3115258212;T:4266202403;N:2267422,8,29,98,,4574898668,2902052527,3115258212,4266202403,2267422,SRX23138318,SRS20089387,,,"Developmental Cancer Genomics, St. Anna Children's Cancer Research Institute (CCRI)",,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Austria,2024-01-09,Undetermined,Adult,Multi-tissue,Multi-system
29815,SRR27466774,SRX23138318,SRS20089387,SRP482605,PRJNA1062705,Comparative transcriptomics coupled to developmental grading via transgenic Zebrafish reporter strains identifies conserved features in neutrophil maturation,GSE252788,Transcriptome Analysis,Neutrophils are evolutionarily conserved innate immune cells playing pivotal roles in host defence. Zebrafish models have contributed substantially to our understanding of neutrophil functions but similarities to human neutrophil maturation have not been systematically characterized  which limits their applicability to studying human disease. Here we show  by generating and analysing transgenic zebrafish strains representing distinct neutrophil differentiation stages  a high resolution transcriptional profile of neutrophil maturation. We link gene expression at each stage to characteristic transcription factors  including C/ebp ß  which is important for late neutrophil maturation. Cross species comparison of zebrafish  mouse  and human samples confirms high molecular similarity of immature stages and discriminates zebrafish specific from pan species gene signatures. Applying the pan species neutrophil maturation signature to RNA sequencing data from human neuroblastoma patients reveals association between metastatic tumor cell infiltration in the bone marrow and an overall increase in mature neutrophils. Our detailed neutrophil maturation atlas thus provides a valuable resource for studying neutrophil function at different stages across species in health and disease. Overall design: Kidney marrow from 2 adult  six mpf  male zebrafish was isolated  labelled using lipid tagged following MULTI seq protocol  for scRNA seq using 10x Genomics.,,pubmed:38413586,,MF317 A1 GEX zebrafish multiseq,GSM8007849,,source name:Kidney marrow|tissue:Kidney marrow|cell type:Neutrophils|geo loc name:missing|collection date:missing,MF317 A1 GEX zebrafish multiseq,We used the CellRanger v3.1.0 software 10x Genomics for cell demultiplexing and alignment and loaded the counts into Seurat v4.0.2. Assembly: GRCz11 3.1.0 zebrafish reference transcriptome that had been expanded to include the sequences of reporter genes Citrine and CFPNTR  sequences from snapgene.com. Supplementary files format and content: compressed matrix files of CellRanger outputs Supplementary files format and content: rds file containting Seurat object Supplementary files format and content: hd5a file containting Seurat object,Kidney marrow,,Each kidney marrow was split into four portions  labelled with lipid anchor plus individual barcode solution 2 μM for 5’ on ice and then incubated with lipid co anchor 2 μM for 5’ on ice. Each cell portion was individually FACS sorted to obtain one population mmp9 NO  INT  HI or WKM. All cells were gated on live gate  for WKM debris was excluded in a FSC/SSC gate  and mmp9 NO  INT  HI were gated on LysC:CFP positivity and different levels of Mmp9:Citrine CAAX expression. Single cell suspensions were immediately subjected to scRNA seq using the Chromium Single Cell Controller and Single Cell 3’ Library & Gel Bead Kit v3.1 10x Genomics  Pleasanton  CA  according to the manufacturer’s protocols 10x Genomics and sequenced by protocol.,,tissue:Kidney marrow|cell type:Neutrophils,GSM8007849,GSM8007849: MF317 A1 GEX zebrafish multiseq; Danio rerio; RNA Seq,GSM8007849 r1,GSM8007849,1,Each kidney marrow was split into four portions  labelled with lipid anchor plus individual barcode solution 2 μM for five prime on ice and then incubated with lipid co anchor 2 μM for five prime on ice. Each cell portion was individually FACS sorted to obtain one population mmp9 NO  INT  HI or WKM. All cells were gated on live gate  for WKM debris was excluded in a FSC/SSC gate  and mmp9 NO  INT  HI were gated on LysC:CFP positivity and different levels of Mmp9:Citrine CAAX expression. Single cell suspensions were immediately subjected to scRNA seq using the Chromium Single Cell Controller and Single Cell three prime Library & Gel Bead Kit v3.1 10x Genomics  Pleasanton  CA  according to the manufacturer's protocols 10x Genomics and sequenced by protocol.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP482605,,loader:fastq load.py,MF317_A1_barcode_zebrafish_multiseq_S68025_S5_L004_I1_001.fastq.gz MF317_A1_barcode_zebrafish_multiseq_S68025_S5_L004_R1_001.fastq.gz MF317_A1_barcode_zebrafish_multiseq_S68025_S5_L004_R2_001.fastq.gz,fastq fastq fastq,205092135.0,1519201.0,GSM8007849 r2,0:8 1:29 2:98,A:96315447;C:12651302;G:31425404;T:8467378;N:22167,8,29,98,,96315447,12651302,31425404,8467378,22167,SRX23138318,SRS20089387,,,"Developmental Cancer Genomics, St. Anna Children's Cancer Research Institute (CCRI)",,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Austria,2024-01-09,Undetermined,Adult,Multi-tissue,Multi-system
33900,SRR30879294,SRX26276609,SRS22814231,SRP536515,PRJNA1168532,scRNAseq analysis of WT and tfeb tfe3s triple knock out zebrafish embryos at 4 dpf,GSE278733,Transcriptome Analysis,The transcription factors tfeb and tfe3 belong to the MiT/TFE gene family and are known as master regulators of lysosomal function and autophagy. In normal conditions  they are sequestered in the cytosol of the cells and their nuclear translocation is finely regulated in response to a huge array of cell signals; however  the role of these transcription factors during vertebrate development remains unclear. We used zebrafish to investigate tfeb and tfe3 role during embryo development and in adult organs. We generated knock out KO alleles for all the zebrafish tfeb and tfe3s isoforms. Our data show that triple KO tfeb tfe3a tfe3b animals are lethal  and these transcription factors are involved in pancreas and liver development. Overall design: Wild type WT and tfeb tfe3a tfe3b triple knock out TKO embryos were collected at 4 dpf dpf  and GFP+ neurons and pancreatic acinar cells or dsRED+ hepatocytes and pancreatic endocrine beta cells cells from dissociated embryos were isolated by Fluorescence activated cell sorting FACS and analyzed by scRNA seq.,,,,dsRED+ TKO 4 dpf,GSM8553899,,tissue:4 dpf dpf type:hepatocytes and pancreatic endocrine beta cells|genotype:tfeb tfe3a tfe3a triple KO TKO|geo loc name:missing|collection date:missing,dsRED+ TKO 4 dpf,Following sequencing  an average 25 000 reads per cell were generated. The bcl files were demultiplexed into a FASTQ  aligned to Danio.rerio genome and single cell 3′ gene counting were performed by the standard 10X Genomics’s CellRanger mkfastq software V7.0.1. The single cell QC was generated by 10X Genomics’s CellRanger and visualized using 10X Genomics’s LoupeTM Cell Browser. Valid barcode reads in all samples were >95%. Reads aligned to zebrafish genome were >70% in all samples  while anti sense reads were <2% in all samples. All key metrics were within the expected range and did not trigger any errors or warnings in the Cell Ranger web summaries. Assembly: Zebrafish genome reference GRCz10 Supplementary files format and content: Tab separated values files matrix files,4 dpf,,WT and TKO embryos were collected at 4 dpf  and GFP+ or dsRED+ cells from dissociated embryos were were isolated by FACS. For GFP+ cells  a manual resection of the tail and the head of each embryo was performed to enrich the pancreatic population of GFP+ cells. Single cell suspensions were generated using a previously published protocol DOI: 10.1016/j.mex.2018.10.009. 10 000 cells were targeted from each sample cell suspension. The cells were washed twice with PBS+0.04% BSA and resuspended in about 500 cells per microliter. Single cells were captured using 10x Genomics Chromium. 10X Genomics’s Chromium instrument and Dual index Single Cell 3′ Reagent kit V3.1 were used to prepare the individually barcoded single cell RNA Seq libraries following the manufacturer’s protocol. Libraries quality was assessed by the TapeStation 4200 traces Agilent BioAnalyzer High Sensitivity Kit and quantitated by the Qubit system.,,tissue:4 dpf type:hepatocytes and pancreatic endocrine beta cells|genotype:tfeb tfe3a tfe3a triple KO TKO,GSM8553899,GSM8553899: dsRED+ TKO 4 dpf; Danio rerio; RNA Seq,GSM8553899 r1,GSM8553899,1,WT and TKO embryos were collected at 4 dpf  and GFP+ or dsRED+ cells from dissociated embryos were were isolated by FACS. For GFP+ cells  a manual resection of the tail and the head of each embryo was performed to enrich the pancreatic population of GFP+ cells. Single cell suspensions were generated using a previously published protocol DOI: 10.1016/j.mex.2018.10.009. 10 000 cells were targeted from each sample cell suspension. The cells were washed twice with PBS+0.04% BSA and resuspended in about 500 cells per microliter. Single cells were captured using 10x Genomics Chromium. 10X Genomics's Chromium instrument and Dual index Single Cell 3′ Reagent kit V3.1 were used to prepare the individually barcoded single cell RNA Seq libraries following the manufacturer's protocol. Libraries quality was assessed by the TapeStation 4200 traces Agilent BioAnalyzer High Sensitivity Kit and quantitated by the Qubit system.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP536515,,loader:fastq load.py,TKO_dsRED_S2_L001_I1_001.fastq.gz TKO_dsRED_S2_L001_I2_001.fastq.gz TKO_dsRED_S2_L001_R1_001.fastq.gz TKO_dsRED_S2_L001_R2_001.fastq.gz,fastq fastq fastq fastq,3764848932.0,27281514.0,GSM8553899 r1,0:10 1:10 2:28 3:90,A:692470222;C:567540605;G:576111845;T:618305574;N:908014,10,10,28,90,692470222,567540605,576111845,618305574,908014,SRX26276609,SRS22814231,SRA1985700,nih,nih,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-10-03,Larval,Larval,Multi-tissue,Multi-system
33901,SRR30879295,SRX26276609,SRS22814231,SRP536515,PRJNA1168532,scRNAseq analysis of WT and tfeb tfe3s triple knock out zebrafish embryos at 4 dpf,GSE278733,Transcriptome Analysis,The transcription factors tfeb and tfe3 belong to the MiT/TFE gene family and are known as master regulators of lysosomal function and autophagy. In normal conditions  they are sequestered in the cytosol of the cells and their nuclear translocation is finely regulated in response to a huge array of cell signals; however  the role of these transcription factors during vertebrate development remains unclear. We used zebrafish to investigate tfeb and tfe3 role during embryo development and in adult organs. We generated knock out KO alleles for all the zebrafish tfeb and tfe3s isoforms. Our data show that triple KO tfeb tfe3a tfe3b animals are lethal  and these transcription factors are involved in pancreas and liver development. Overall design: Wild type WT and tfeb tfe3a tfe3b triple knock out TKO embryos were collected at 4 dpf dpf  and GFP+ neurons and pancreatic acinar cells or dsRED+ hepatocytes and pancreatic endocrine beta cells cells from dissociated embryos were isolated by Fluorescence activated cell sorting FACS and analyzed by scRNA seq.,,,,dsRED+ TKO 4 dpf,GSM8553899,,tissue:4 dpf dpf type:hepatocytes and pancreatic endocrine beta cells|genotype:tfeb tfe3a tfe3a triple KO TKO|geo loc name:missing|collection date:missing,dsRED+ TKO 4 dpf,Following sequencing  an average 25 000 reads per cell were generated. The bcl files were demultiplexed into a FASTQ  aligned to Danio.rerio genome and single cell 3′ gene counting were performed by the standard 10X Genomics’s CellRanger mkfastq software V7.0.1. The single cell QC was generated by 10X Genomics’s CellRanger and visualized using 10X Genomics’s LoupeTM Cell Browser. Valid barcode reads in all samples were >95%. Reads aligned to zebrafish genome were >70% in all samples  while anti sense reads were <2% in all samples. All key metrics were within the expected range and did not trigger any errors or warnings in the Cell Ranger web summaries. Assembly: Zebrafish genome reference GRCz10 Supplementary files format and content: Tab separated values files matrix files,4 dpf,,WT and TKO embryos were collected at 4 dpf  and GFP+ or dsRED+ cells from dissociated embryos were were isolated by FACS. For GFP+ cells  a manual resection of the tail and the head of each embryo was performed to enrich the pancreatic population of GFP+ cells. Single cell suspensions were generated using a previously published protocol DOI: 10.1016/j.mex.2018.10.009. 10 000 cells were targeted from each sample cell suspension. The cells were washed twice with PBS+0.04% BSA and resuspended in about 500 cells per microliter. Single cells were captured using 10x Genomics Chromium. 10X Genomics’s Chromium instrument and Dual index Single Cell 3′ Reagent kit V3.1 were used to prepare the individually barcoded single cell RNA Seq libraries following the manufacturer’s protocol. Libraries quality was assessed by the TapeStation 4200 traces Agilent BioAnalyzer High Sensitivity Kit and quantitated by the Qubit system.,,tissue:4 dpf type:hepatocytes and pancreatic endocrine beta cells|genotype:tfeb tfe3a tfe3a triple KO TKO,GSM8553899,GSM8553899: dsRED+ TKO 4 dpf; Danio rerio; RNA Seq,GSM8553899 r1,GSM8553899,1,WT and TKO embryos were collected at 4 dpf  and GFP+ or dsRED+ cells from dissociated embryos were were isolated by FACS. For GFP+ cells  a manual resection of the tail and the head of each embryo was performed to enrich the pancreatic population of GFP+ cells. Single cell suspensions were generated using a previously published protocol DOI: 10.1016/j.mex.2018.10.009. 10 000 cells were targeted from each sample cell suspension. The cells were washed twice with PBS+0.04% BSA and resuspended in about 500 cells per microliter. Single cells were captured using 10x Genomics Chromium. 10X Genomics's Chromium instrument and Dual index Single Cell 3′ Reagent kit V3.1 were used to prepare the individually barcoded single cell RNA Seq libraries following the manufacturer's protocol. Libraries quality was assessed by the TapeStation 4200 traces Agilent BioAnalyzer High Sensitivity Kit and quantitated by the Qubit system.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP536515,,loader:fastq load.py,TKO_dsRED_S2_L002_I1_001.fastq.gz TKO_dsRED_S2_L002_I2_001.fastq.gz TKO_dsRED_S2_L002_R1_001.fastq.gz TKO_dsRED_S2_L002_R2_001.fastq.gz,fastq fastq fastq fastq,3726674544.0,27004888.0,GSM8553899 r2,0:10 1:10 2:28 3:90,A:685914766;C:561837246;G:569990126;T:611748773;N:949009,10,10,28,90,685914766,561837246,569990126,611748773,949009,SRX26276609,SRS22814231,SRA1985700,nih,nih,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-10-03,Larval,Larval,Multi-tissue,Multi-system
33902,SRR30879296,SRX26276609,SRS22814231,SRP536515,PRJNA1168532,scRNAseq analysis of WT and tfeb tfe3s triple knock out zebrafish embryos at 4 dpf,GSE278733,Transcriptome Analysis,The transcription factors tfeb and tfe3 belong to the MiT/TFE gene family and are known as master regulators of lysosomal function and autophagy. In normal conditions  they are sequestered in the cytosol of the cells and their nuclear translocation is finely regulated in response to a huge array of cell signals; however  the role of these transcription factors during vertebrate development remains unclear. We used zebrafish to investigate tfeb and tfe3 role during embryo development and in adult organs. We generated knock out KO alleles for all the zebrafish tfeb and tfe3s isoforms. Our data show that triple KO tfeb tfe3a tfe3b animals are lethal  and these transcription factors are involved in pancreas and liver development. Overall design: Wild type WT and tfeb tfe3a tfe3b triple knock out TKO embryos were collected at 4 dpf dpf  and GFP+ neurons and pancreatic acinar cells or dsRED+ hepatocytes and pancreatic endocrine beta cells cells from dissociated embryos were isolated by Fluorescence activated cell sorting FACS and analyzed by scRNA seq.,,,,dsRED+ TKO 4 dpf,GSM8553899,,tissue:4 dpf dpf type:hepatocytes and pancreatic endocrine beta cells|genotype:tfeb tfe3a tfe3a triple KO TKO|geo loc name:missing|collection date:missing,dsRED+ TKO 4 dpf,Following sequencing  an average 25 000 reads per cell were generated. The bcl files were demultiplexed into a FASTQ  aligned to Danio.rerio genome and single cell 3′ gene counting were performed by the standard 10X Genomics’s CellRanger mkfastq software V7.0.1. The single cell QC was generated by 10X Genomics’s CellRanger and visualized using 10X Genomics’s LoupeTM Cell Browser. Valid barcode reads in all samples were >95%. Reads aligned to zebrafish genome were >70% in all samples  while anti sense reads were <2% in all samples. All key metrics were within the expected range and did not trigger any errors or warnings in the Cell Ranger web summaries. Assembly: Zebrafish genome reference GRCz10 Supplementary files format and content: Tab separated values files matrix files,4 dpf,,WT and TKO embryos were collected at 4 dpf  and GFP+ or dsRED+ cells from dissociated embryos were were isolated by FACS. For GFP+ cells  a manual resection of the tail and the head of each embryo was performed to enrich the pancreatic population of GFP+ cells. Single cell suspensions were generated using a previously published protocol DOI: 10.1016/j.mex.2018.10.009. 10 000 cells were targeted from each sample cell suspension. The cells were washed twice with PBS+0.04% BSA and resuspended in about 500 cells per microliter. Single cells were captured using 10x Genomics Chromium. 10X Genomics’s Chromium instrument and Dual index Single Cell 3′ Reagent kit V3.1 were used to prepare the individually barcoded single cell RNA Seq libraries following the manufacturer’s protocol. Libraries quality was assessed by the TapeStation 4200 traces Agilent BioAnalyzer High Sensitivity Kit and quantitated by the Qubit system.,,tissue:4 dpf type:hepatocytes and pancreatic endocrine beta cells|genotype:tfeb tfe3a tfe3a triple KO TKO,GSM8553899,GSM8553899: dsRED+ TKO 4 dpf; Danio rerio; RNA Seq,GSM8553899 r1,GSM8553899,1,WT and TKO embryos were collected at 4 dpf  and GFP+ or dsRED+ cells from dissociated embryos were were isolated by FACS. For GFP+ cells  a manual resection of the tail and the head of each embryo was performed to enrich the pancreatic population of GFP+ cells. Single cell suspensions were generated using a previously published protocol DOI: 10.1016/j.mex.2018.10.009. 10 000 cells were targeted from each sample cell suspension. The cells were washed twice with PBS+0.04% BSA and resuspended in about 500 cells per microliter. Single cells were captured using 10x Genomics Chromium. 10X Genomics's Chromium instrument and Dual index Single Cell 3′ Reagent kit V3.1 were used to prepare the individually barcoded single cell RNA Seq libraries following the manufacturer's protocol. Libraries quality was assessed by the TapeStation 4200 traces Agilent BioAnalyzer High Sensitivity Kit and quantitated by the Qubit system.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP536515,,loader:fastq load.py,TKO_dsRED_S2_L003_I1_001.fastq.gz TKO_dsRED_S2_L003_I2_001.fastq.gz TKO_dsRED_S2_L003_R1_001.fastq.gz TKO_dsRED_S2_L003_R2_001.fastq.gz,fastq fastq fastq fastq,3722937918.0,26977811.0,GSM8553899 r3,0:10 1:10 2:28 3:90,A:676537253;C:555568581;G:563937331;T:604713745;N:27246080,10,10,28,90,676537253,555568581,563937331,604713745,27246080,SRX26276609,SRS22814231,SRA1985700,nih,nih,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-10-03,Larval,Larval,Multi-tissue,Multi-system
33903,SRR30879297,SRX26276609,SRS22814231,SRP536515,PRJNA1168532,scRNAseq analysis of WT and tfeb tfe3s triple knock out zebrafish embryos at 4 dpf,GSE278733,Transcriptome Analysis,The transcription factors tfeb and tfe3 belong to the MiT/TFE gene family and are known as master regulators of lysosomal function and autophagy. In normal conditions  they are sequestered in the cytosol of the cells and their nuclear translocation is finely regulated in response to a huge array of cell signals; however  the role of these transcription factors during vertebrate development remains unclear. We used zebrafish to investigate tfeb and tfe3 role during embryo development and in adult organs. We generated knock out KO alleles for all the zebrafish tfeb and tfe3s isoforms. Our data show that triple KO tfeb tfe3a tfe3b animals are lethal  and these transcription factors are involved in pancreas and liver development. Overall design: Wild type WT and tfeb tfe3a tfe3b triple knock out TKO embryos were collected at 4 dpf dpf  and GFP+ neurons and pancreatic acinar cells or dsRED+ hepatocytes and pancreatic endocrine beta cells cells from dissociated embryos were isolated by Fluorescence activated cell sorting FACS and analyzed by scRNA seq.,,,,dsRED+ TKO 4 dpf,GSM8553899,,tissue:4 dpf dpf type:hepatocytes and pancreatic endocrine beta cells|genotype:tfeb tfe3a tfe3a triple KO TKO|geo loc name:missing|collection date:missing,dsRED+ TKO 4 dpf,Following sequencing  an average 25 000 reads per cell were generated. The bcl files were demultiplexed into a FASTQ  aligned to Danio.rerio genome and single cell 3′ gene counting were performed by the standard 10X Genomics’s CellRanger mkfastq software V7.0.1. The single cell QC was generated by 10X Genomics’s CellRanger and visualized using 10X Genomics’s LoupeTM Cell Browser. Valid barcode reads in all samples were >95%. Reads aligned to zebrafish genome were >70% in all samples  while anti sense reads were <2% in all samples. All key metrics were within the expected range and did not trigger any errors or warnings in the Cell Ranger web summaries. Assembly: Zebrafish genome reference GRCz10 Supplementary files format and content: Tab separated values files matrix files,4 dpf,,WT and TKO embryos were collected at 4 dpf  and GFP+ or dsRED+ cells from dissociated embryos were were isolated by FACS. For GFP+ cells  a manual resection of the tail and the head of each embryo was performed to enrich the pancreatic population of GFP+ cells. Single cell suspensions were generated using a previously published protocol DOI: 10.1016/j.mex.2018.10.009. 10 000 cells were targeted from each sample cell suspension. The cells were washed twice with PBS+0.04% BSA and resuspended in about 500 cells per microliter. Single cells were captured using 10x Genomics Chromium. 10X Genomics’s Chromium instrument and Dual index Single Cell 3′ Reagent kit V3.1 were used to prepare the individually barcoded single cell RNA Seq libraries following the manufacturer’s protocol. Libraries quality was assessed by the TapeStation 4200 traces Agilent BioAnalyzer High Sensitivity Kit and quantitated by the Qubit system.,,tissue:4 dpf type:hepatocytes and pancreatic endocrine beta cells|genotype:tfeb tfe3a tfe3a triple KO TKO,GSM8553899,GSM8553899: dsRED+ TKO 4 dpf; Danio rerio; RNA Seq,GSM8553899 r1,GSM8553899,1,WT and TKO embryos were collected at 4 dpf  and GFP+ or dsRED+ cells from dissociated embryos were were isolated by FACS. For GFP+ cells  a manual resection of the tail and the head of each embryo was performed to enrich the pancreatic population of GFP+ cells. Single cell suspensions were generated using a previously published protocol DOI: 10.1016/j.mex.2018.10.009. 10 000 cells were targeted from each sample cell suspension. The cells were washed twice with PBS+0.04% BSA and resuspended in about 500 cells per microliter. Single cells were captured using 10x Genomics Chromium. 10X Genomics's Chromium instrument and Dual index Single Cell 3′ Reagent kit V3.1 were used to prepare the individually barcoded single cell RNA Seq libraries following the manufacturer's protocol. Libraries quality was assessed by the TapeStation 4200 traces Agilent BioAnalyzer High Sensitivity Kit and quantitated by the Qubit system.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP536515,,loader:fastq load.py,TKO_dsRED_S2_L004_I1_001.fastq.gz TKO_dsRED_S2_L004_I2_001.fastq.gz TKO_dsRED_S2_L004_R1_001.fastq.gz TKO_dsRED_S2_L004_R2_001.fastq.gz,fastq fastq fastq fastq,3758183394.0,27233213.0,GSM8553899 r4,0:10 1:10 2:28 3:90,A:692108990;C:566665777;G:574900426;T:617012755;N:301222,10,10,28,90,692108990,566665777,574900426,617012755,301222,SRX26276609,SRS22814231,SRA1985700,nih,nih,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-10-03,Larval,Larval,Multi-tissue,Multi-system
33904,SRR30879298,SRX26276608,SRS22814230,SRP536515,PRJNA1168532,scRNAseq analysis of WT and tfeb tfe3s triple knock out zebrafish embryos at 4 dpf,GSE278733,Transcriptome Analysis,The transcription factors tfeb and tfe3 belong to the MiT/TFE gene family and are known as master regulators of lysosomal function and autophagy. In normal conditions  they are sequestered in the cytosol of the cells and their nuclear translocation is finely regulated in response to a huge array of cell signals; however  the role of these transcription factors during vertebrate development remains unclear. We used zebrafish to investigate tfeb and tfe3 role during embryo development and in adult organs. We generated knock out KO alleles for all the zebrafish tfeb and tfe3s isoforms. Our data show that triple KO tfeb tfe3a tfe3b animals are lethal  and these transcription factors are involved in pancreas and liver development. Overall design: Wild type WT and tfeb tfe3a tfe3b triple knock out TKO embryos were collected at 4 dpf dpf  and GFP+ neurons and pancreatic acinar cells or dsRED+ hepatocytes and pancreatic endocrine beta cells cells from dissociated embryos were isolated by Fluorescence activated cell sorting FACS and analyzed by scRNA seq.,,,,dsRED+ WT 4 dpf,GSM8553898,,tissue:4 dpf dpf type:hepatocytes and pancreatic endocrine beta cells|genotype:WT  EK strain|geo loc name:missing|collection date:missing,dsRED+ WT 4 dpf,Following sequencing  an average 25 000 reads per cell were generated. The bcl files were demultiplexed into a FASTQ  aligned to Danio.rerio genome and single cell 3′ gene counting were performed by the standard 10X Genomics’s CellRanger mkfastq software V7.0.1. The single cell QC was generated by 10X Genomics’s CellRanger and visualized using 10X Genomics’s LoupeTM Cell Browser. Valid barcode reads in all samples were >95%. Reads aligned to zebrafish genome were >70% in all samples  while anti sense reads were <2% in all samples. All key metrics were within the expected range and did not trigger any errors or warnings in the Cell Ranger web summaries. Assembly: Zebrafish genome reference GRCz10 Supplementary files format and content: Tab separated values files matrix files,4 dpf,,WT and TKO embryos were collected at 4 dpf  and GFP+ or dsRED+ cells from dissociated embryos were were isolated by FACS. For GFP+ cells  a manual resection of the tail and the head of each embryo was performed to enrich the pancreatic population of GFP+ cells. Single cell suspensions were generated using a previously published protocol DOI: 10.1016/j.mex.2018.10.009. 10 000 cells were targeted from each sample cell suspension. The cells were washed twice with PBS+0.04% BSA and resuspended in about 500 cells per microliter. Single cells were captured using 10x Genomics Chromium. 10X Genomics’s Chromium instrument and Dual index Single Cell 3′ Reagent kit V3.1 were used to prepare the individually barcoded single cell RNA Seq libraries following the manufacturer’s protocol. Libraries quality was assessed by the TapeStation 4200 traces Agilent BioAnalyzer High Sensitivity Kit and quantitated by the Qubit system.,,tissue:4 dpf type:hepatocytes and pancreatic endocrine beta cells|genotype:WT  EK strain,GSM8553898,GSM8553898: dsRED+ WT 4 dpf; Danio rerio; RNA Seq,GSM8553898 r1,GSM8553898,1,WT and TKO embryos were collected at 4 dpf  and GFP+ or dsRED+ cells from dissociated embryos were were isolated by FACS. For GFP+ cells  a manual resection of the tail and the head of each embryo was performed to enrich the pancreatic population of GFP+ cells. Single cell suspensions were generated using a previously published protocol DOI: 10.1016/j.mex.2018.10.009. 10 000 cells were targeted from each sample cell suspension. The cells were washed twice with PBS+0.04% BSA and resuspended in about 500 cells per microliter. Single cells were captured using 10x Genomics Chromium. 10X Genomics's Chromium instrument and Dual index Single Cell 3′ Reagent kit V3.1 were used to prepare the individually barcoded single cell RNA Seq libraries following the manufacturer's protocol. Libraries quality was assessed by the TapeStation 4200 traces Agilent BioAnalyzer High Sensitivity Kit and quantitated by the Qubit system.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP536515,,loader:fastq load.py,WT_dsRED_S1_L001_I1_001.fastq.gz WT_dsRED_S1_L001_I2_001.fastq.gz WT_dsRED_S1_L001_R1_001.fastq.gz WT_dsRED_S1_L001_R2_001.fastq.gz,fastq fastq fastq fastq,4039025952.0,29268304.0,GSM8553898 r1,0:10 1:10 2:28 3:90,A:743074639;C:613897517;G:610150022;T:666064959;N:960223,10,10,28,90,743074639,613897517,610150022,666064959,960223,SRX26276608,SRS22814230,SRA1985700,nih,nih,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-10-03,Larval,Larval,Multi-tissue,Multi-system
33905,SRR30879299,SRX26276608,SRS22814230,SRP536515,PRJNA1168532,scRNAseq analysis of WT and tfeb tfe3s triple knock out zebrafish embryos at 4 dpf,GSE278733,Transcriptome Analysis,The transcription factors tfeb and tfe3 belong to the MiT/TFE gene family and are known as master regulators of lysosomal function and autophagy. In normal conditions  they are sequestered in the cytosol of the cells and their nuclear translocation is finely regulated in response to a huge array of cell signals; however  the role of these transcription factors during vertebrate development remains unclear. We used zebrafish to investigate tfeb and tfe3 role during embryo development and in adult organs. We generated knock out KO alleles for all the zebrafish tfeb and tfe3s isoforms. Our data show that triple KO tfeb tfe3a tfe3b animals are lethal  and these transcription factors are involved in pancreas and liver development. Overall design: Wild type WT and tfeb tfe3a tfe3b triple knock out TKO embryos were collected at 4 dpf dpf  and GFP+ neurons and pancreatic acinar cells or dsRED+ hepatocytes and pancreatic endocrine beta cells cells from dissociated embryos were isolated by Fluorescence activated cell sorting FACS and analyzed by scRNA seq.,,,,dsRED+ WT 4 dpf,GSM8553898,,tissue:4 dpf dpf type:hepatocytes and pancreatic endocrine beta cells|genotype:WT  EK strain|geo loc name:missing|collection date:missing,dsRED+ WT 4 dpf,Following sequencing  an average 25 000 reads per cell were generated. The bcl files were demultiplexed into a FASTQ  aligned to Danio.rerio genome and single cell 3′ gene counting were performed by the standard 10X Genomics’s CellRanger mkfastq software V7.0.1. The single cell QC was generated by 10X Genomics’s CellRanger and visualized using 10X Genomics’s LoupeTM Cell Browser. Valid barcode reads in all samples were >95%. Reads aligned to zebrafish genome were >70% in all samples  while anti sense reads were <2% in all samples. All key metrics were within the expected range and did not trigger any errors or warnings in the Cell Ranger web summaries. Assembly: Zebrafish genome reference GRCz10 Supplementary files format and content: Tab separated values files matrix files,4 dpf,,WT and TKO embryos were collected at 4 dpf  and GFP+ or dsRED+ cells from dissociated embryos were were isolated by FACS. For GFP+ cells  a manual resection of the tail and the head of each embryo was performed to enrich the pancreatic population of GFP+ cells. Single cell suspensions were generated using a previously published protocol DOI: 10.1016/j.mex.2018.10.009. 10 000 cells were targeted from each sample cell suspension. The cells were washed twice with PBS+0.04% BSA and resuspended in about 500 cells per microliter. Single cells were captured using 10x Genomics Chromium. 10X Genomics’s Chromium instrument and Dual index Single Cell 3′ Reagent kit V3.1 were used to prepare the individually barcoded single cell RNA Seq libraries following the manufacturer’s protocol. Libraries quality was assessed by the TapeStation 4200 traces Agilent BioAnalyzer High Sensitivity Kit and quantitated by the Qubit system.,,tissue:4 dpf type:hepatocytes and pancreatic endocrine beta cells|genotype:WT  EK strain,GSM8553898,GSM8553898: dsRED+ WT 4 dpf; Danio rerio; RNA Seq,GSM8553898 r1,GSM8553898,1,WT and TKO embryos were collected at 4 dpf  and GFP+ or dsRED+ cells from dissociated embryos were were isolated by FACS. For GFP+ cells  a manual resection of the tail and the head of each embryo was performed to enrich the pancreatic population of GFP+ cells. Single cell suspensions were generated using a previously published protocol DOI: 10.1016/j.mex.2018.10.009. 10 000 cells were targeted from each sample cell suspension. The cells were washed twice with PBS+0.04% BSA and resuspended in about 500 cells per microliter. Single cells were captured using 10x Genomics Chromium. 10X Genomics's Chromium instrument and Dual index Single Cell 3′ Reagent kit V3.1 were used to prepare the individually barcoded single cell RNA Seq libraries following the manufacturer's protocol. Libraries quality was assessed by the TapeStation 4200 traces Agilent BioAnalyzer High Sensitivity Kit and quantitated by the Qubit system.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP536515,,loader:fastq load.py,WT_dsRED_S1_L002_I1_001.fastq.gz WT_dsRED_S1_L002_I2_001.fastq.gz WT_dsRED_S1_L002_R1_001.fastq.gz WT_dsRED_S1_L002_R2_001.fastq.gz,fastq fastq fastq fastq,3995500476.0,28952902.0,GSM8553898 r2,0:10 1:10 2:28 3:90,A:735710467;C:607339644;G:603122849;T:658578339;N:1009881,10,10,28,90,735710467,607339644,603122849,658578339,1009881,SRX26276608,SRS22814230,SRA1985700,nih,nih,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-10-03,Larval,Larval,Multi-tissue,Multi-system
33906,SRR30879300,SRX26276608,SRS22814230,SRP536515,PRJNA1168532,scRNAseq analysis of WT and tfeb tfe3s triple knock out zebrafish embryos at 4 dpf,GSE278733,Transcriptome Analysis,The transcription factors tfeb and tfe3 belong to the MiT/TFE gene family and are known as master regulators of lysosomal function and autophagy. In normal conditions  they are sequestered in the cytosol of the cells and their nuclear translocation is finely regulated in response to a huge array of cell signals; however  the role of these transcription factors during vertebrate development remains unclear. We used zebrafish to investigate tfeb and tfe3 role during embryo development and in adult organs. We generated knock out KO alleles for all the zebrafish tfeb and tfe3s isoforms. Our data show that triple KO tfeb tfe3a tfe3b animals are lethal  and these transcription factors are involved in pancreas and liver development. Overall design: Wild type WT and tfeb tfe3a tfe3b triple knock out TKO embryos were collected at 4 dpf dpf  and GFP+ neurons and pancreatic acinar cells or dsRED+ hepatocytes and pancreatic endocrine beta cells cells from dissociated embryos were isolated by Fluorescence activated cell sorting FACS and analyzed by scRNA seq.,,,,dsRED+ WT 4 dpf,GSM8553898,,tissue:4 dpf dpf type:hepatocytes and pancreatic endocrine beta cells|genotype:WT  EK strain|geo loc name:missing|collection date:missing,dsRED+ WT 4 dpf,Following sequencing  an average 25 000 reads per cell were generated. The bcl files were demultiplexed into a FASTQ  aligned to Danio.rerio genome and single cell 3′ gene counting were performed by the standard 10X Genomics’s CellRanger mkfastq software V7.0.1. The single cell QC was generated by 10X Genomics’s CellRanger and visualized using 10X Genomics’s LoupeTM Cell Browser. Valid barcode reads in all samples were >95%. Reads aligned to zebrafish genome were >70% in all samples  while anti sense reads were <2% in all samples. All key metrics were within the expected range and did not trigger any errors or warnings in the Cell Ranger web summaries. Assembly: Zebrafish genome reference GRCz10 Supplementary files format and content: Tab separated values files matrix files,4 dpf,,WT and TKO embryos were collected at 4 dpf  and GFP+ or dsRED+ cells from dissociated embryos were were isolated by FACS. For GFP+ cells  a manual resection of the tail and the head of each embryo was performed to enrich the pancreatic population of GFP+ cells. Single cell suspensions were generated using a previously published protocol DOI: 10.1016/j.mex.2018.10.009. 10 000 cells were targeted from each sample cell suspension. The cells were washed twice with PBS+0.04% BSA and resuspended in about 500 cells per microliter. Single cells were captured using 10x Genomics Chromium. 10X Genomics’s Chromium instrument and Dual index Single Cell 3′ Reagent kit V3.1 were used to prepare the individually barcoded single cell RNA Seq libraries following the manufacturer’s protocol. Libraries quality was assessed by the TapeStation 4200 traces Agilent BioAnalyzer High Sensitivity Kit and quantitated by the Qubit system.,,tissue:4 dpf type:hepatocytes and pancreatic endocrine beta cells|genotype:WT  EK strain,GSM8553898,GSM8553898: dsRED+ WT 4 dpf; Danio rerio; RNA Seq,GSM8553898 r1,GSM8553898,1,WT and TKO embryos were collected at 4 dpf  and GFP+ or dsRED+ cells from dissociated embryos were were isolated by FACS. For GFP+ cells  a manual resection of the tail and the head of each embryo was performed to enrich the pancreatic population of GFP+ cells. Single cell suspensions were generated using a previously published protocol DOI: 10.1016/j.mex.2018.10.009. 10 000 cells were targeted from each sample cell suspension. The cells were washed twice with PBS+0.04% BSA and resuspended in about 500 cells per microliter. Single cells were captured using 10x Genomics Chromium. 10X Genomics's Chromium instrument and Dual index Single Cell 3′ Reagent kit V3.1 were used to prepare the individually barcoded single cell RNA Seq libraries following the manufacturer's protocol. Libraries quality was assessed by the TapeStation 4200 traces Agilent BioAnalyzer High Sensitivity Kit and quantitated by the Qubit system.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP536515,,loader:fastq load.py,WT_dsRED_S1_L003_I1_001.fastq.gz WT_dsRED_S1_L003_I2_001.fastq.gz WT_dsRED_S1_L003_R1_001.fastq.gz WT_dsRED_S1_L003_R2_001.fastq.gz,fastq fastq fastq fastq,3989006196.0,28905842.0,GSM8553898 r3,0:10 1:10 2:28 3:90,A:725297656;C:600094089;G:596392169;T:650543321;N:29198545,10,10,28,90,725297656,600094089,596392169,650543321,29198545,SRX26276608,SRS22814230,SRA1985700,nih,nih,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-10-03,Larval,Larval,Multi-tissue,Multi-system
33907,SRR30879301,SRX26276608,SRS22814230,SRP536515,PRJNA1168532,scRNAseq analysis of WT and tfeb tfe3s triple knock out zebrafish embryos at 4 dpf,GSE278733,Transcriptome Analysis,The transcription factors tfeb and tfe3 belong to the MiT/TFE gene family and are known as master regulators of lysosomal function and autophagy. In normal conditions  they are sequestered in the cytosol of the cells and their nuclear translocation is finely regulated in response to a huge array of cell signals; however  the role of these transcription factors during vertebrate development remains unclear. We used zebrafish to investigate tfeb and tfe3 role during embryo development and in adult organs. We generated knock out KO alleles for all the zebrafish tfeb and tfe3s isoforms. Our data show that triple KO tfeb tfe3a tfe3b animals are lethal  and these transcription factors are involved in pancreas and liver development. Overall design: Wild type WT and tfeb tfe3a tfe3b triple knock out TKO embryos were collected at 4 dpf dpf  and GFP+ neurons and pancreatic acinar cells or dsRED+ hepatocytes and pancreatic endocrine beta cells cells from dissociated embryos were isolated by Fluorescence activated cell sorting FACS and analyzed by scRNA seq.,,,,dsRED+ WT 4 dpf,GSM8553898,,tissue:4 dpf dpf type:hepatocytes and pancreatic endocrine beta cells|genotype:WT  EK strain|geo loc name:missing|collection date:missing,dsRED+ WT 4 dpf,Following sequencing  an average 25 000 reads per cell were generated. The bcl files were demultiplexed into a FASTQ  aligned to Danio.rerio genome and single cell 3′ gene counting were performed by the standard 10X Genomics’s CellRanger mkfastq software V7.0.1. The single cell QC was generated by 10X Genomics’s CellRanger and visualized using 10X Genomics’s LoupeTM Cell Browser. Valid barcode reads in all samples were >95%. Reads aligned to zebrafish genome were >70% in all samples  while anti sense reads were <2% in all samples. All key metrics were within the expected range and did not trigger any errors or warnings in the Cell Ranger web summaries. Assembly: Zebrafish genome reference GRCz10 Supplementary files format and content: Tab separated values files matrix files,4 dpf,,WT and TKO embryos were collected at 4 dpf  and GFP+ or dsRED+ cells from dissociated embryos were were isolated by FACS. For GFP+ cells  a manual resection of the tail and the head of each embryo was performed to enrich the pancreatic population of GFP+ cells. Single cell suspensions were generated using a previously published protocol DOI: 10.1016/j.mex.2018.10.009. 10 000 cells were targeted from each sample cell suspension. The cells were washed twice with PBS+0.04% BSA and resuspended in about 500 cells per microliter. Single cells were captured using 10x Genomics Chromium. 10X Genomics’s Chromium instrument and Dual index Single Cell 3′ Reagent kit V3.1 were used to prepare the individually barcoded single cell RNA Seq libraries following the manufacturer’s protocol. Libraries quality was assessed by the TapeStation 4200 traces Agilent BioAnalyzer High Sensitivity Kit and quantitated by the Qubit system.,,tissue:4 dpf type:hepatocytes and pancreatic endocrine beta cells|genotype:WT  EK strain,GSM8553898,GSM8553898: dsRED+ WT 4 dpf; Danio rerio; RNA Seq,GSM8553898 r1,GSM8553898,1,WT and TKO embryos were collected at 4 dpf  and GFP+ or dsRED+ cells from dissociated embryos were were isolated by FACS. For GFP+ cells  a manual resection of the tail and the head of each embryo was performed to enrich the pancreatic population of GFP+ cells. Single cell suspensions were generated using a previously published protocol DOI: 10.1016/j.mex.2018.10.009. 10 000 cells were targeted from each sample cell suspension. The cells were washed twice with PBS+0.04% BSA and resuspended in about 500 cells per microliter. Single cells were captured using 10x Genomics Chromium. 10X Genomics's Chromium instrument and Dual index Single Cell 3′ Reagent kit V3.1 were used to prepare the individually barcoded single cell RNA Seq libraries following the manufacturer's protocol. Libraries quality was assessed by the TapeStation 4200 traces Agilent BioAnalyzer High Sensitivity Kit and quantitated by the Qubit system.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP536515,,loader:fastq load.py,WT_dsRED_S1_L004_I1_001.fastq.gz WT_dsRED_S1_L004_I2_001.fastq.gz WT_dsRED_S1_L004_R1_001.fastq.gz WT_dsRED_S1_L004_R2_001.fastq.gz,fastq fastq fastq fastq,4028525946.0,29192217.0,GSM8553898 r4,0:10 1:10 2:28 3:90,A:742291215;C:612398679;G:608091658;T:664191759;N:326219,10,10,28,90,742291215,612398679,608091658,664191759,326219,SRX26276608,SRS22814230,SRA1985700,nih,nih,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-10-03,Larval,Larval,Multi-tissue,Multi-system
66749,SRR23717086,SRX19578256,SRS16961238,SRP342742,PRJNA773777,Activation of lineage competence in hemogenic endothelium precedes the formation of hematopoietic stem cell heterogeneity [Zebrafish.scRNA seq],GSE186423,Transcriptome Analysis,Using a combination of single cell multi omics  lineage tracing and functional assays  we show that embryonic HSPCs are originated from heterogeneous hemogenic endothelial cells HECs during zebrafish embryogenesis. Overall design: Hematopoietic stem and progenitor cells HSPCs are considered as a heterogeneous population  but where and how HSPC heterogeneity occurs remain unclear. Here  we performed scRNA seq and scATAC seq with zebrafish 36 hpf VDA derived kdrl+runx1   kdrl+runx1+  and kdrl runx1+ cells. To determine the transcriptional signatures of spi2+ lineages in zebrafish  we performed STRT seq with spi2: Gal4;UAS:GFP+ kdrl:mCherry+ HECs and spi2: Gal4;UAS:GFP+ kdrl:mCherry  hematopoietic cells at 36 hpf. To investigate the underlying molecular mechanism upon spi2 deficiency  we performed scRNA seq with the sorted ECs kdrl+runx1   HECs kdrl+runx1+ and hematopoietic cells kdrl runx1+ from spi2 morphants at 36 hpf. To determine whether spi2 can directly modulate transcriptional programs in EC/HEC  we examined genome wide spi2 binding by cut tag assay in fli1a flag spi2 EGFP+ cells sorted from trunk region of Tg fli1a flag spi2 GFP embryos at 36 hpf.,parent bioproject:PRJNA773771,pubmed:37016019,,36 hpf Zebrafish VDA scRNA seq spi2 morphant,GSM7083029,,source name:Zebrafish VDA|tissue:Zebrafish VDA 36hpf|cells:VDA derived kdrl+runx1   kdrl+runx1+  and kdrl runx1+ cells|Stage:36 hpf,36 hpf Zebrafish VDA scRNA seq spi2 morphant,For scRNA seq  and scATAC seq based on 10x Genomics，raw data files were processed by Cell Ranger software suite with default mapping parameters  using the GRCz11 reference genome. For STRT seq  raw reads were first de multiplexed by barcode sequences in reads 2 to yield separate read files for individual cells  then the transcripts sequences of each cell in reads 1 were separated based on corresponding reads 2. Simultaneously  UMI sequences in reads 2 were integrated into reads 1. The template switching oligo TSO sequence  polyA sequence and the low quality reads N > 10% in reads 1 were subsequently removed by Python scripts and Trimmomatic version 0.36. Next  the clean reads were aligned to the zebrafish genome GRCz11 from Ensembl using HISAT2 version 2.1.0 with known gene annotation. Only protein coding genes were retained and the abundance of each gene were estimated by counting the reads that duplicated UMIs have been excluded. For cut&tag  reads were aligned to GRCz11 by Bowtie2. Only uniquely mapped reads with mapping quality score ≥ 30 were kept using Samtools software. post merging replicates  MACS2 was used for the peak calling. Assembly: GRCz11,Zebrafish VDA,,For 10x Genomics based scRNA seq and scATAC seq in zebrafish  40 000 mCherry+ GFP  cells  40 000 mCherry+ GFP+ cells and 30 000 mCherry  GFP+ cells were sorted from Tg kdrl:mCherry/runx1:enGFP at 36 hpf. For STRT seq in zebrafish  single spi2: Gal4;UAS:GFP+ kdrl:mCherry+ HECs and spi2: Gal4;UAS:GFP+ kdrl:mCherry  hematopoietic cells were sorted from the trunk region of Tg spi2: Gal4;UAS:GFP/ kdrl:mCherry at 36 hpf. For scRNA seq of spi2 morphants at 36 hpf in zebrafish  ECs kdrl+runx1   HECs kdrl+runx1+ and hematopoietic cells kdrl runx1+ were sorted. For bulk CUT&TAG in zebrafish  fli1a flag spi2 EGFP+ cells were sorted from the trunk region of Tg fli1a flag spi2 GFP embryos at 36 hpf. For 10x Genomics based scRNA seq and scATAC seq in zebrafish  we loaded 20 000 cells for further 10x Genomics based scRNA seq and 90 000 cells for further 10x Genomics based scATAC seq. For scRNA seq  libraries were prepared using Single Cell 3’ Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For ATAC seq  nuclei were isolated and washed according to the methods supplied by 10x Genomics. Libraries were prepared using the Chromium Chip E Single Cell Kit and Chromium Single Cell ATAC Library & Gel Bead Kit  and further sequenced on an Illumina Novaseq6000 platform to generate 50 bp paired end reads. For 10x Genomics based scRNA seq in mice  libraries were prepared using Single Cell 3’ Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For STRT seq in zebrafish  the end repair and dA tailing of the DNA fragments and ligation of the adaptors to the DNA fragments were performed according to the KAPA Hyper Prep Kits with PCR Library Amplification/Illumina series. post the adaptor ligation step  the final PCR was performed. The libraries were sequenced on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For bulk CUT&TAG  libraries were prepared according to Hyperactive In Situ ChIP Library Prep Kit for Illumina and sequenced on an Illumina NovaSeq6000 platform to generate 150 bp paired end reads.,,tissue:Zebrafish VDA 36hpf|cells:VDA derived kdrl+runx1   kdrl+runx1+  and kdrl runx1+ cells|Stage:36 hpf,GSM7083029,GSM7083029: 36 hpf Zebrafish VDA scRNA seq spi2 morphant; Danio rerio; RNA Seq,GSM7083029 r1,GSM7083029,1,For 10x Genomics based scRNA seq and scATAC seq in zebrafish  40 000 mCherry+ GFP  cells  40 000 mCherry+ GFP+ cells and 30 000 mCherry  GFP+ cells were sorted from Tg kdrl:mCherry/runx1:enGFP at 36 hpf. For STRT seq in zebrafish  single spi2: Gal4;UAS:GFP+ kdrl:mCherry+ HECs and spi2: Gal4;UAS:GFP+ kdrl:mCherry  hematopoietic cells were sorted from the trunk region of Tg spi2: Gal4;UAS:GFP/ kdrl:mCherry at 36 hpf. For scRNA seq of spi2 morphants at 36 hpf in zebrafish  ECs kdrl+runx1   HECs kdrl+runx1+ and hematopoietic cells kdrl runx1+ were sorted. For bulk CUT&TAG in zebrafish  fli1a flag spi2 EGFP+ cells were sorted from the trunk region of Tg fli1a flag spi2 GFP embryos at 36 hpf. For 10x Genomics based scRNA seq and scATAC seq in zebrafish  we loaded 20 000 cells for further 10x Genomics based scRNA seq and 90 000 cells for further 10x Genomics based scATAC seq. For scRNA seq  libraries were prepared using Single Cell three prime Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For ATAC seq  nuclei were isolated and washed according to the methods supplied by 10x Genomics. Libraries were prepared using the Chromium Chip E Single Cell Kit and Chromium Single Cell ATAC Library & Gel Bead Kit  and further sequenced on an Illumina Novaseq6000 platform to generate 50 bp paired end reads. For 10x Genomics based scRNA seq in mice  libraries were prepared using Single Cell three prime Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For STRT seq in zebrafish  the end repair and dA tailing of the DNA fragments and ligation of the adaptors to the DNA fragments were performed according to the KAPA Hyper Prep Kits with PCR Library Amplification/Illumina series. post the adaptor ligation step  the final PCR was performed. The libraries were sequenced on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For bulk CUT&TAG  libraries were prepared according to Hyperactive In Situ ChIP Library Prep Kit for Illumina and sequenced on an Illumina NovaSeq6000 platform to generate 150 bp paired end reads.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP342742,,,210954C_spi2_MO_S1_L001_R1_001.fastq.gz 210954C_spi2_MO_S1_L001_R2_001.fastq.gz,fastq fastq,38657555700.0,128858519.0,GSM7083029 r1,0:150 1:150,A:16254027461;C:6972577611;G:6733828903;T:8696771854;N:349871,150,150,,,16254027461,6972577611,6733828903,8696771854,349871,SRX19578256,SRS16961238,SRA1601408,"Group of Hematopoiesis and Cardiovascular Development, INSTITUTE OF ZOOLOGY, CHINESE ACADEMY OF SCIENCES","Group of Hematopoiesis and Cardiovascular Development, INSTITUTE OF ZOOLOGY, CHINESE ACADEMY OF SCIENCES",2,0.0,0.92157,0.0,0.12849,1.0,0.7811,,0.5613,150,150,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,China,2023-03-06,Pharyngula,Embryo,Multi-tissue,Multi-system
66750,SRR23717087,SRX19578256,SRS16961238,SRP342742,PRJNA773777,Activation of lineage competence in hemogenic endothelium precedes the formation of hematopoietic stem cell heterogeneity [Zebrafish.scRNA seq],GSE186423,Transcriptome Analysis,Using a combination of single cell multi omics  lineage tracing and functional assays  we show that embryonic HSPCs are originated from heterogeneous hemogenic endothelial cells HECs during zebrafish embryogenesis. Overall design: Hematopoietic stem and progenitor cells HSPCs are considered as a heterogeneous population  but where and how HSPC heterogeneity occurs remain unclear. Here  we performed scRNA seq and scATAC seq with zebrafish 36 hpf VDA derived kdrl+runx1   kdrl+runx1+  and kdrl runx1+ cells. To determine the transcriptional signatures of spi2+ lineages in zebrafish  we performed STRT seq with spi2: Gal4;UAS:GFP+ kdrl:mCherry+ HECs and spi2: Gal4;UAS:GFP+ kdrl:mCherry  hematopoietic cells at 36 hpf. To investigate the underlying molecular mechanism upon spi2 deficiency  we performed scRNA seq with the sorted ECs kdrl+runx1   HECs kdrl+runx1+ and hematopoietic cells kdrl runx1+ from spi2 morphants at 36 hpf. To determine whether spi2 can directly modulate transcriptional programs in EC/HEC  we examined genome wide spi2 binding by cut tag assay in fli1a flag spi2 EGFP+ cells sorted from trunk region of Tg fli1a flag spi2 GFP embryos at 36 hpf.,parent bioproject:PRJNA773771,pubmed:37016019,,36 hpf Zebrafish VDA scRNA seq spi2 morphant,GSM7083029,,source name:Zebrafish VDA|tissue:Zebrafish VDA 36hpf|cells:VDA derived kdrl+runx1   kdrl+runx1+  and kdrl runx1+ cells|Stage:36 hpf,36 hpf Zebrafish VDA scRNA seq spi2 morphant,For scRNA seq  and scATAC seq based on 10x Genomics，raw data files were processed by Cell Ranger software suite with default mapping parameters  using the GRCz11 reference genome. For STRT seq  raw reads were first de multiplexed by barcode sequences in reads 2 to yield separate read files for individual cells  then the transcripts sequences of each cell in reads 1 were separated based on corresponding reads 2. Simultaneously  UMI sequences in reads 2 were integrated into reads 1. The template switching oligo TSO sequence  polyA sequence and the low quality reads N > 10% in reads 1 were subsequently removed by Python scripts and Trimmomatic version 0.36. Next  the clean reads were aligned to the zebrafish genome GRCz11 from Ensembl using HISAT2 version 2.1.0 with known gene annotation. Only protein coding genes were retained and the abundance of each gene were estimated by counting the reads that duplicated UMIs have been excluded. For cut&tag  reads were aligned to GRCz11 by Bowtie2. Only uniquely mapped reads with mapping quality score ≥ 30 were kept using Samtools software. post merging replicates  MACS2 was used for the peak calling. Assembly: GRCz11,Zebrafish VDA,,For 10x Genomics based scRNA seq and scATAC seq in zebrafish  40 000 mCherry+ GFP  cells  40 000 mCherry+ GFP+ cells and 30 000 mCherry  GFP+ cells were sorted from Tg kdrl:mCherry/runx1:enGFP at 36 hpf. For STRT seq in zebrafish  single spi2: Gal4;UAS:GFP+ kdrl:mCherry+ HECs and spi2: Gal4;UAS:GFP+ kdrl:mCherry  hematopoietic cells were sorted from the trunk region of Tg spi2: Gal4;UAS:GFP/ kdrl:mCherry at 36 hpf. For scRNA seq of spi2 morphants at 36 hpf in zebrafish  ECs kdrl+runx1   HECs kdrl+runx1+ and hematopoietic cells kdrl runx1+ were sorted. For bulk CUT&TAG in zebrafish  fli1a flag spi2 EGFP+ cells were sorted from the trunk region of Tg fli1a flag spi2 GFP embryos at 36 hpf. For 10x Genomics based scRNA seq and scATAC seq in zebrafish  we loaded 20 000 cells for further 10x Genomics based scRNA seq and 90 000 cells for further 10x Genomics based scATAC seq. For scRNA seq  libraries were prepared using Single Cell 3’ Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For ATAC seq  nuclei were isolated and washed according to the methods supplied by 10x Genomics. Libraries were prepared using the Chromium Chip E Single Cell Kit and Chromium Single Cell ATAC Library & Gel Bead Kit  and further sequenced on an Illumina Novaseq6000 platform to generate 50 bp paired end reads. For 10x Genomics based scRNA seq in mice  libraries were prepared using Single Cell 3’ Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For STRT seq in zebrafish  the end repair and dA tailing of the DNA fragments and ligation of the adaptors to the DNA fragments were performed according to the KAPA Hyper Prep Kits with PCR Library Amplification/Illumina series. post the adaptor ligation step  the final PCR was performed. The libraries were sequenced on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For bulk CUT&TAG  libraries were prepared according to Hyperactive In Situ ChIP Library Prep Kit for Illumina and sequenced on an Illumina NovaSeq6000 platform to generate 150 bp paired end reads.,,tissue:Zebrafish VDA 36hpf|cells:VDA derived kdrl+runx1   kdrl+runx1+  and kdrl runx1+ cells|Stage:36 hpf,GSM7083029,GSM7083029: 36 hpf Zebrafish VDA scRNA seq spi2 morphant; Danio rerio; RNA Seq,GSM7083029 r1,GSM7083029,1,For 10x Genomics based scRNA seq and scATAC seq in zebrafish  40 000 mCherry+ GFP  cells  40 000 mCherry+ GFP+ cells and 30 000 mCherry  GFP+ cells were sorted from Tg kdrl:mCherry/runx1:enGFP at 36 hpf. For STRT seq in zebrafish  single spi2: Gal4;UAS:GFP+ kdrl:mCherry+ HECs and spi2: Gal4;UAS:GFP+ kdrl:mCherry  hematopoietic cells were sorted from the trunk region of Tg spi2: Gal4;UAS:GFP/ kdrl:mCherry at 36 hpf. For scRNA seq of spi2 morphants at 36 hpf in zebrafish  ECs kdrl+runx1   HECs kdrl+runx1+ and hematopoietic cells kdrl runx1+ were sorted. For bulk CUT&TAG in zebrafish  fli1a flag spi2 EGFP+ cells were sorted from the trunk region of Tg fli1a flag spi2 GFP embryos at 36 hpf. For 10x Genomics based scRNA seq and scATAC seq in zebrafish  we loaded 20 000 cells for further 10x Genomics based scRNA seq and 90 000 cells for further 10x Genomics based scATAC seq. For scRNA seq  libraries were prepared using Single Cell three prime Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For ATAC seq  nuclei were isolated and washed according to the methods supplied by 10x Genomics. Libraries were prepared using the Chromium Chip E Single Cell Kit and Chromium Single Cell ATAC Library & Gel Bead Kit  and further sequenced on an Illumina Novaseq6000 platform to generate 50 bp paired end reads. For 10x Genomics based scRNA seq in mice  libraries were prepared using Single Cell three prime Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For STRT seq in zebrafish  the end repair and dA tailing of the DNA fragments and ligation of the adaptors to the DNA fragments were performed according to the KAPA Hyper Prep Kits with PCR Library Amplification/Illumina series. post the adaptor ligation step  the final PCR was performed. The libraries were sequenced on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For bulk CUT&TAG  libraries were prepared according to Hyperactive In Situ ChIP Library Prep Kit for Illumina and sequenced on an Illumina NovaSeq6000 platform to generate 150 bp paired end reads.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP342742,,,210954C_spi2_MO_S1_L002_R1_001.fastq.gz 210954C_spi2_MO_S1_L002_R2_001.fastq.gz,fastq fastq,39767723700.0,132559079.0,GSM7083029 r2,0:150 1:150,A:16740739613;C:7166687108;G:6926997738;T:8932937589;N:361652,150,150,,,16740739613,7166687108,6926997738,8932937589,361652,SRX19578256,SRS16961238,SRA1601408,"Group of Hematopoiesis and Cardiovascular Development, INSTITUTE OF ZOOLOGY, CHINESE ACADEMY OF SCIENCES","Group of Hematopoiesis and Cardiovascular Development, INSTITUTE OF ZOOLOGY, CHINESE ACADEMY OF SCIENCES",2,0.0,0.92006,0.0,0.12624,1.0,0.7808,,0.56645,150,150,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,China,2023-03-06,Pharyngula,Embryo,Multi-tissue,Multi-system
66751,SRR23717088,SRX19578256,SRS16961238,SRP342742,PRJNA773777,Activation of lineage competence in hemogenic endothelium precedes the formation of hematopoietic stem cell heterogeneity [Zebrafish.scRNA seq],GSE186423,Transcriptome Analysis,Using a combination of single cell multi omics  lineage tracing and functional assays  we show that embryonic HSPCs are originated from heterogeneous hemogenic endothelial cells HECs during zebrafish embryogenesis. Overall design: Hematopoietic stem and progenitor cells HSPCs are considered as a heterogeneous population  but where and how HSPC heterogeneity occurs remain unclear. Here  we performed scRNA seq and scATAC seq with zebrafish 36 hpf VDA derived kdrl+runx1   kdrl+runx1+  and kdrl runx1+ cells. To determine the transcriptional signatures of spi2+ lineages in zebrafish  we performed STRT seq with spi2: Gal4;UAS:GFP+ kdrl:mCherry+ HECs and spi2: Gal4;UAS:GFP+ kdrl:mCherry  hematopoietic cells at 36 hpf. To investigate the underlying molecular mechanism upon spi2 deficiency  we performed scRNA seq with the sorted ECs kdrl+runx1   HECs kdrl+runx1+ and hematopoietic cells kdrl runx1+ from spi2 morphants at 36 hpf. To determine whether spi2 can directly modulate transcriptional programs in EC/HEC  we examined genome wide spi2 binding by cut tag assay in fli1a flag spi2 EGFP+ cells sorted from trunk region of Tg fli1a flag spi2 GFP embryos at 36 hpf.,parent bioproject:PRJNA773771,pubmed:37016019,,36 hpf Zebrafish VDA scRNA seq spi2 morphant,GSM7083029,,source name:Zebrafish VDA|tissue:Zebrafish VDA 36hpf|cells:VDA derived kdrl+runx1   kdrl+runx1+  and kdrl runx1+ cells|Stage:36 hpf,36 hpf Zebrafish VDA scRNA seq spi2 morphant,For scRNA seq  and scATAC seq based on 10x Genomics，raw data files were processed by Cell Ranger software suite with default mapping parameters  using the GRCz11 reference genome. For STRT seq  raw reads were first de multiplexed by barcode sequences in reads 2 to yield separate read files for individual cells  then the transcripts sequences of each cell in reads 1 were separated based on corresponding reads 2. Simultaneously  UMI sequences in reads 2 were integrated into reads 1. The template switching oligo TSO sequence  polyA sequence and the low quality reads N > 10% in reads 1 were subsequently removed by Python scripts and Trimmomatic version 0.36. Next  the clean reads were aligned to the zebrafish genome GRCz11 from Ensembl using HISAT2 version 2.1.0 with known gene annotation. Only protein coding genes were retained and the abundance of each gene were estimated by counting the reads that duplicated UMIs have been excluded. For cut&tag  reads were aligned to GRCz11 by Bowtie2. Only uniquely mapped reads with mapping quality score ≥ 30 were kept using Samtools software. post merging replicates  MACS2 was used for the peak calling. Assembly: GRCz11,Zebrafish VDA,,For 10x Genomics based scRNA seq and scATAC seq in zebrafish  40 000 mCherry+ GFP  cells  40 000 mCherry+ GFP+ cells and 30 000 mCherry  GFP+ cells were sorted from Tg kdrl:mCherry/runx1:enGFP at 36 hpf. For STRT seq in zebrafish  single spi2: Gal4;UAS:GFP+ kdrl:mCherry+ HECs and spi2: Gal4;UAS:GFP+ kdrl:mCherry  hematopoietic cells were sorted from the trunk region of Tg spi2: Gal4;UAS:GFP/ kdrl:mCherry at 36 hpf. For scRNA seq of spi2 morphants at 36 hpf in zebrafish  ECs kdrl+runx1   HECs kdrl+runx1+ and hematopoietic cells kdrl runx1+ were sorted. For bulk CUT&TAG in zebrafish  fli1a flag spi2 EGFP+ cells were sorted from the trunk region of Tg fli1a flag spi2 GFP embryos at 36 hpf. For 10x Genomics based scRNA seq and scATAC seq in zebrafish  we loaded 20 000 cells for further 10x Genomics based scRNA seq and 90 000 cells for further 10x Genomics based scATAC seq. For scRNA seq  libraries were prepared using Single Cell 3’ Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For ATAC seq  nuclei were isolated and washed according to the methods supplied by 10x Genomics. Libraries were prepared using the Chromium Chip E Single Cell Kit and Chromium Single Cell ATAC Library & Gel Bead Kit  and further sequenced on an Illumina Novaseq6000 platform to generate 50 bp paired end reads. For 10x Genomics based scRNA seq in mice  libraries were prepared using Single Cell 3’ Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For STRT seq in zebrafish  the end repair and dA tailing of the DNA fragments and ligation of the adaptors to the DNA fragments were performed according to the KAPA Hyper Prep Kits with PCR Library Amplification/Illumina series. post the adaptor ligation step  the final PCR was performed. The libraries were sequenced on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For bulk CUT&TAG  libraries were prepared according to Hyperactive In Situ ChIP Library Prep Kit for Illumina and sequenced on an Illumina NovaSeq6000 platform to generate 150 bp paired end reads.,,tissue:Zebrafish VDA 36hpf|cells:VDA derived kdrl+runx1   kdrl+runx1+  and kdrl runx1+ cells|Stage:36 hpf,GSM7083029,GSM7083029: 36 hpf Zebrafish VDA scRNA seq spi2 morphant; Danio rerio; RNA Seq,GSM7083029 r1,GSM7083029,1,For 10x Genomics based scRNA seq and scATAC seq in zebrafish  40 000 mCherry+ GFP  cells  40 000 mCherry+ GFP+ cells and 30 000 mCherry  GFP+ cells were sorted from Tg kdrl:mCherry/runx1:enGFP at 36 hpf. For STRT seq in zebrafish  single spi2: Gal4;UAS:GFP+ kdrl:mCherry+ HECs and spi2: Gal4;UAS:GFP+ kdrl:mCherry  hematopoietic cells were sorted from the trunk region of Tg spi2: Gal4;UAS:GFP/ kdrl:mCherry at 36 hpf. For scRNA seq of spi2 morphants at 36 hpf in zebrafish  ECs kdrl+runx1   HECs kdrl+runx1+ and hematopoietic cells kdrl runx1+ were sorted. For bulk CUT&TAG in zebrafish  fli1a flag spi2 EGFP+ cells were sorted from the trunk region of Tg fli1a flag spi2 GFP embryos at 36 hpf. For 10x Genomics based scRNA seq and scATAC seq in zebrafish  we loaded 20 000 cells for further 10x Genomics based scRNA seq and 90 000 cells for further 10x Genomics based scATAC seq. For scRNA seq  libraries were prepared using Single Cell three prime Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For ATAC seq  nuclei were isolated and washed according to the methods supplied by 10x Genomics. Libraries were prepared using the Chromium Chip E Single Cell Kit and Chromium Single Cell ATAC Library & Gel Bead Kit  and further sequenced on an Illumina Novaseq6000 platform to generate 50 bp paired end reads. For 10x Genomics based scRNA seq in mice  libraries were prepared using Single Cell three prime Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For STRT seq in zebrafish  the end repair and dA tailing of the DNA fragments and ligation of the adaptors to the DNA fragments were performed according to the KAPA Hyper Prep Kits with PCR Library Amplification/Illumina series. post the adaptor ligation step  the final PCR was performed. The libraries were sequenced on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For bulk CUT&TAG  libraries were prepared according to Hyperactive In Situ ChIP Library Prep Kit for Illumina and sequenced on an Illumina NovaSeq6000 platform to generate 150 bp paired end reads.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP342742,,,210954C_spi2_MO_S1_L003_R1_001.fastq.gz 210954C_spi2_MO_S1_L003_R2_001.fastq.gz,fastq fastq,33826342500.0,112754475.0,GSM7083029 r3,0:150 1:150,A:14247560719;C:6101219095;G:5882384356;T:7594866748;N:311582,150,150,,,14247560719,6101219095,5882384356,7594866748,311582,SRX19578256,SRS16961238,SRA1601408,"Group of Hematopoiesis and Cardiovascular Development, INSTITUTE OF ZOOLOGY, CHINESE ACADEMY OF SCIENCES","Group of Hematopoiesis and Cardiovascular Development, INSTITUTE OF ZOOLOGY, CHINESE ACADEMY OF SCIENCES",2,0.0,0.91535,0.0,0.12519,1.0,0.7833,,0.56425,150,150,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,China,2023-03-06,Pharyngula,Embryo,Multi-tissue,Multi-system
66752,SRR23717089,SRX19578256,SRS16961238,SRP342742,PRJNA773777,Activation of lineage competence in hemogenic endothelium precedes the formation of hematopoietic stem cell heterogeneity [Zebrafish.scRNA seq],GSE186423,Transcriptome Analysis,Using a combination of single cell multi omics  lineage tracing and functional assays  we show that embryonic HSPCs are originated from heterogeneous hemogenic endothelial cells HECs during zebrafish embryogenesis. Overall design: Hematopoietic stem and progenitor cells HSPCs are considered as a heterogeneous population  but where and how HSPC heterogeneity occurs remain unclear. Here  we performed scRNA seq and scATAC seq with zebrafish 36 hpf VDA derived kdrl+runx1   kdrl+runx1+  and kdrl runx1+ cells. To determine the transcriptional signatures of spi2+ lineages in zebrafish  we performed STRT seq with spi2: Gal4;UAS:GFP+ kdrl:mCherry+ HECs and spi2: Gal4;UAS:GFP+ kdrl:mCherry  hematopoietic cells at 36 hpf. To investigate the underlying molecular mechanism upon spi2 deficiency  we performed scRNA seq with the sorted ECs kdrl+runx1   HECs kdrl+runx1+ and hematopoietic cells kdrl runx1+ from spi2 morphants at 36 hpf. To determine whether spi2 can directly modulate transcriptional programs in EC/HEC  we examined genome wide spi2 binding by cut tag assay in fli1a flag spi2 EGFP+ cells sorted from trunk region of Tg fli1a flag spi2 GFP embryos at 36 hpf.,parent bioproject:PRJNA773771,pubmed:37016019,,36 hpf Zebrafish VDA scRNA seq spi2 morphant,GSM7083029,,source name:Zebrafish VDA|tissue:Zebrafish VDA 36hpf|cells:VDA derived kdrl+runx1   kdrl+runx1+  and kdrl runx1+ cells|Stage:36 hpf,36 hpf Zebrafish VDA scRNA seq spi2 morphant,For scRNA seq  and scATAC seq based on 10x Genomics，raw data files were processed by Cell Ranger software suite with default mapping parameters  using the GRCz11 reference genome. For STRT seq  raw reads were first de multiplexed by barcode sequences in reads 2 to yield separate read files for individual cells  then the transcripts sequences of each cell in reads 1 were separated based on corresponding reads 2. Simultaneously  UMI sequences in reads 2 were integrated into reads 1. The template switching oligo TSO sequence  polyA sequence and the low quality reads N > 10% in reads 1 were subsequently removed by Python scripts and Trimmomatic version 0.36. Next  the clean reads were aligned to the zebrafish genome GRCz11 from Ensembl using HISAT2 version 2.1.0 with known gene annotation. Only protein coding genes were retained and the abundance of each gene were estimated by counting the reads that duplicated UMIs have been excluded. For cut&tag  reads were aligned to GRCz11 by Bowtie2. Only uniquely mapped reads with mapping quality score ≥ 30 were kept using Samtools software. post merging replicates  MACS2 was used for the peak calling. Assembly: GRCz11,Zebrafish VDA,,For 10x Genomics based scRNA seq and scATAC seq in zebrafish  40 000 mCherry+ GFP  cells  40 000 mCherry+ GFP+ cells and 30 000 mCherry  GFP+ cells were sorted from Tg kdrl:mCherry/runx1:enGFP at 36 hpf. For STRT seq in zebrafish  single spi2: Gal4;UAS:GFP+ kdrl:mCherry+ HECs and spi2: Gal4;UAS:GFP+ kdrl:mCherry  hematopoietic cells were sorted from the trunk region of Tg spi2: Gal4;UAS:GFP/ kdrl:mCherry at 36 hpf. For scRNA seq of spi2 morphants at 36 hpf in zebrafish  ECs kdrl+runx1   HECs kdrl+runx1+ and hematopoietic cells kdrl runx1+ were sorted. For bulk CUT&TAG in zebrafish  fli1a flag spi2 EGFP+ cells were sorted from the trunk region of Tg fli1a flag spi2 GFP embryos at 36 hpf. For 10x Genomics based scRNA seq and scATAC seq in zebrafish  we loaded 20 000 cells for further 10x Genomics based scRNA seq and 90 000 cells for further 10x Genomics based scATAC seq. For scRNA seq  libraries were prepared using Single Cell 3’ Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For ATAC seq  nuclei were isolated and washed according to the methods supplied by 10x Genomics. Libraries were prepared using the Chromium Chip E Single Cell Kit and Chromium Single Cell ATAC Library & Gel Bead Kit  and further sequenced on an Illumina Novaseq6000 platform to generate 50 bp paired end reads. For 10x Genomics based scRNA seq in mice  libraries were prepared using Single Cell 3’ Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For STRT seq in zebrafish  the end repair and dA tailing of the DNA fragments and ligation of the adaptors to the DNA fragments were performed according to the KAPA Hyper Prep Kits with PCR Library Amplification/Illumina series. post the adaptor ligation step  the final PCR was performed. The libraries were sequenced on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For bulk CUT&TAG  libraries were prepared according to Hyperactive In Situ ChIP Library Prep Kit for Illumina and sequenced on an Illumina NovaSeq6000 platform to generate 150 bp paired end reads.,,tissue:Zebrafish VDA 36hpf|cells:VDA derived kdrl+runx1   kdrl+runx1+  and kdrl runx1+ cells|Stage:36 hpf,GSM7083029,GSM7083029: 36 hpf Zebrafish VDA scRNA seq spi2 morphant; Danio rerio; RNA Seq,GSM7083029 r1,GSM7083029,1,For 10x Genomics based scRNA seq and scATAC seq in zebrafish  40 000 mCherry+ GFP  cells  40 000 mCherry+ GFP+ cells and 30 000 mCherry  GFP+ cells were sorted from Tg kdrl:mCherry/runx1:enGFP at 36 hpf. For STRT seq in zebrafish  single spi2: Gal4;UAS:GFP+ kdrl:mCherry+ HECs and spi2: Gal4;UAS:GFP+ kdrl:mCherry  hematopoietic cells were sorted from the trunk region of Tg spi2: Gal4;UAS:GFP/ kdrl:mCherry at 36 hpf. For scRNA seq of spi2 morphants at 36 hpf in zebrafish  ECs kdrl+runx1   HECs kdrl+runx1+ and hematopoietic cells kdrl runx1+ were sorted. For bulk CUT&TAG in zebrafish  fli1a flag spi2 EGFP+ cells were sorted from the trunk region of Tg fli1a flag spi2 GFP embryos at 36 hpf. For 10x Genomics based scRNA seq and scATAC seq in zebrafish  we loaded 20 000 cells for further 10x Genomics based scRNA seq and 90 000 cells for further 10x Genomics based scATAC seq. For scRNA seq  libraries were prepared using Single Cell three prime Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For ATAC seq  nuclei were isolated and washed according to the methods supplied by 10x Genomics. Libraries were prepared using the Chromium Chip E Single Cell Kit and Chromium Single Cell ATAC Library & Gel Bead Kit  and further sequenced on an Illumina Novaseq6000 platform to generate 50 bp paired end reads. For 10x Genomics based scRNA seq in mice  libraries were prepared using Single Cell three prime Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For STRT seq in zebrafish  the end repair and dA tailing of the DNA fragments and ligation of the adaptors to the DNA fragments were performed according to the KAPA Hyper Prep Kits with PCR Library Amplification/Illumina series. post the adaptor ligation step  the final PCR was performed. The libraries were sequenced on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For bulk CUT&TAG  libraries were prepared according to Hyperactive In Situ ChIP Library Prep Kit for Illumina and sequenced on an Illumina NovaSeq6000 platform to generate 150 bp paired end reads.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP342742,,,210954C_spi2_MO_S1_L004_R1_001.fastq.gz 210954C_spi2_MO_S1_L004_R2_001.fastq.gz,fastq fastq,42436674900.0,141455583.0,GSM7083029 r4,0:150 1:150,A:17850346993;C:7641162936;G:7380219938;T:9564565232;N:379801,150,150,,,17850346993,7641162936,7380219938,9564565232,379801,SRX19578256,SRS16961238,SRA1601408,"Group of Hematopoiesis and Cardiovascular Development, INSTITUTE OF ZOOLOGY, CHINESE ACADEMY OF SCIENCES","Group of Hematopoiesis and Cardiovascular Development, INSTITUTE OF ZOOLOGY, CHINESE ACADEMY OF SCIENCES",2,0.0,0.91972,0.0,0.12638,1.0,0.78131,,0.56385,150,150,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,China,2023-03-06,Pharyngula,Embryo,Multi-tissue,Multi-system
66753,SRR16539848,SRX12742420,SRS10690646,SRP342742,PRJNA773777,Activation of lineage competence in hemogenic endothelium precedes the formation of hematopoietic stem cell heterogeneity [Zebrafish.scRNA seq],GSE186423,Transcriptome Analysis,Using a combination of single cell multi omics  lineage tracing and functional assays  we show that embryonic HSPCs are originated from heterogeneous hemogenic endothelial cells HECs during zebrafish embryogenesis. Overall design: Hematopoietic stem and progenitor cells HSPCs are considered as a heterogeneous population  but where and how HSPC heterogeneity occurs remain unclear. Here  we performed scRNA seq and scATAC seq with zebrafish 36 hpf VDA derived kdrl+runx1   kdrl+runx1+  and kdrl runx1+ cells. To determine the transcriptional signatures of spi2+ lineages in zebrafish  we performed STRT seq with spi2: Gal4;UAS:GFP+ kdrl:mCherry+ HECs and spi2: Gal4;UAS:GFP+ kdrl:mCherry  hematopoietic cells at 36 hpf. To investigate the underlying molecular mechanism upon spi2 deficiency  we performed scRNA seq with the sorted ECs kdrl+runx1   HECs kdrl+runx1+ and hematopoietic cells kdrl runx1+ from spi2 morphants at 36 hpf. To determine whether spi2 can directly modulate transcriptional programs in EC/HEC  we examined genome wide spi2 binding by cut tag assay in fli1a flag spi2 EGFP+ cells sorted from trunk region of Tg fli1a flag spi2 GFP embryos at 36 hpf.,parent bioproject:PRJNA773771,pubmed:37016019,,36 hpf Zebrafish VDA scRNA seq,GSM5651458,,source name:Zebrafish VDA|tissue:Zebrafish VDA 36hpf|cells:VDA derived kdrl+runx1   kdrl+runx1+  and kdrl runx1+ cells|Stage:36 hpf,36 hpf Zebrafish VDA scRNA seq,For scRNA seq  and scATAC seq based on 10x Genomics，raw data files were processed by Cell Ranger software suite with default mapping parameters  using the GRCz11 reference genome. For STRT seq  raw reads were first de multiplexed by barcode sequences in reads 2 to yield separate read files for individual cells  then the transcripts sequences of each cell in reads 1 were separated based on corresponding reads 2. Simultaneously  UMI sequences in reads 2 were integrated into reads 1. The template switching oligo TSO sequence  polyA sequence and the low quality reads N > 10% in reads 1 were subsequently removed by Python scripts and Trimmomatic version 0.36. Next  the clean reads were aligned to the zebrafish genome GRCz11 from Ensembl using HISAT2 version 2.1.0 with known gene annotation. Only protein coding genes were retained and the abundance of each gene were estimated by counting the reads that duplicated UMIs have been excluded. For cut&tag  reads were aligned to GRCz11 by Bowtie2. Only uniquely mapped reads with mapping quality score ≥ 30 were kept using Samtools software. post merging replicates  MACS2 was used for the peak calling. Assembly: GRCz11,Zebrafish VDA,,For 10x Genomics based scRNA seq and scATAC seq in zebrafish  40 000 mCherry+ GFP  cells  40 000 mCherry+ GFP+ cells and 30 000 mCherry  GFP+ cells were sorted from Tg kdrl:mCherry/runx1:enGFP at 36 hpf. For STRT seq in zebrafish  single spi2: Gal4;UAS:GFP+ kdrl:mCherry+ HECs and spi2: Gal4;UAS:GFP+ kdrl:mCherry  hematopoietic cells were sorted from the trunk region of Tg spi2: Gal4;UAS:GFP/ kdrl:mCherry at 36 hpf. For scRNA seq of spi2 morphants at 36 hpf in zebrafish  ECs kdrl+runx1   HECs kdrl+runx1+ and hematopoietic cells kdrl runx1+ were sorted. For bulk CUT&TAG in zebrafish  fli1a flag spi2 EGFP+ cells were sorted from the trunk region of Tg fli1a flag spi2 GFP embryos at 36 hpf. For 10x Genomics based scRNA seq and scATAC seq in zebrafish  we loaded 20 000 cells for further 10x Genomics based scRNA seq and 90 000 cells for further 10x Genomics based scATAC seq. For scRNA seq  libraries were prepared using Single Cell 3’ Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For ATAC seq  nuclei were isolated and washed according to the methods supplied by 10x Genomics. Libraries were prepared using the Chromium Chip E Single Cell Kit and Chromium Single Cell ATAC Library & Gel Bead Kit  and further sequenced on an Illumina Novaseq6000 platform to generate 50 bp paired end reads. For 10x Genomics based scRNA seq in mice  libraries were prepared using Single Cell 3’ Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For STRT seq in zebrafish  the end repair and dA tailing of the DNA fragments and ligation of the adaptors to the DNA fragments were performed according to the KAPA Hyper Prep Kits with PCR Library Amplification/Illumina series. post the adaptor ligation step  the final PCR was performed. The libraries were sequenced on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For bulk CUT&TAG  libraries were prepared according to Hyperactive In Situ ChIP Library Prep Kit for Illumina and sequenced on an Illumina NovaSeq6000 platform to generate 150 bp paired end reads.,,tissue:Zebrafish VDA 36hpf|cells:VDA derived kdrl+runx1   kdrl+runx1+  and kdrl runx1+ cells|Stage:36 hpf,GSM5651458,GSM5651458: 36 hpf Zebrafish VDA scRNA seq; Danio rerio; RNA Seq,GSM5651458 r1,GSM5651458,1,For 10x Genomics based scRNA seq and scATAC seq in zebrafish  40 000 mCherry+ GFP  cells  40 000 mCherry+ GFP+ cells and 30 000 mCherry  GFP+ cells were sorted from Tg kdrl:mCherry/runx1:enGFP at 36 hpf. For STRT seq in zebrafish  single spi2: Gal4;UAS:GFP+ kdrl:mCherry+ HECs and spi2: Gal4;UAS:GFP+ kdrl:mCherry  hematopoietic cells were sorted from the trunk region of Tg spi2: Gal4;UAS:GFP/ kdrl:mCherry at 36 hpf. For scRNA seq of spi2 morphants at 36 hpf in zebrafish  ECs kdrl+runx1   HECs kdrl+runx1+ and hematopoietic cells kdrl runx1+ were sorted. For bulk CUT&TAG in zebrafish  fli1a flag spi2 EGFP+ cells were sorted from the trunk region of Tg fli1a flag spi2 GFP embryos at 36 hpf. For 10x Genomics based scRNA seq and scATAC seq in zebrafish  we loaded 20 000 cells for further 10x Genomics based scRNA seq and 90 000 cells for further 10x Genomics based scATAC seq. For scRNA seq  libraries were prepared using Single Cell three prime Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For ATAC seq  nuclei were isolated and washed according to the methods supplied by 10x Genomics. Libraries were prepared using the Chromium Chip E Single Cell Kit and Chromium Single Cell ATAC Library & Gel Bead Kit  and further sequenced on an Illumina Novaseq6000 platform to generate 50 bp paired end reads. For 10x Genomics based scRNA seq in mice  libraries were prepared using Single Cell three prime Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For STRT seq in zebrafish  the end repair and dA tailing of the DNA fragments and ligation of the adaptors to the DNA fragments were performed according to the KAPA Hyper Prep Kits with PCR Library Amplification/Illumina series. post the adaptor ligation step  the final PCR was performed. The libraries were sequenced on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For bulk CUT&TAG  libraries were prepared according to Hyperactive In Situ ChIP Library Prep Kit for Illumina and sequenced on an Illumina NovaSeq6000 platform to generate 150 bp paired end reads.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP342742,,,190718O_ECHEHSC_R_1_1_R1.fq.gz 190718O_ECHEHSC_R_1_1_R2.fq.gz,fastq fastq,42862683000.0,142875610.0,GSM5651458 r1,0:150 1:150,A:19056076938;C:7513613524;G:7148399243;T:9144249423;N:343872,150,150,,,19056076938,7513613524,7148399243,9144249423,343872,SRX12742420,SRS10690646,SRA1600571,"Group of Hematopoiesis and Cardiovascular Development, INSTITUTE OF ZOOLOGY, CHINESE ACADEMY OF SCIENCES","Group of Hematopoiesis and Cardiovascular Development, INSTITUTE OF ZOOLOGY, CHINESE ACADEMY OF SCIENCES",2,0.0,0.92848,0.0,0.09872,1.0,0.81797,,0.52595,150,150,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,China,2021-10-22,Pharyngula,Embryo,Multi-tissue,Multi-system
66754,SRR16539849,SRX12742420,SRS10690646,SRP342742,PRJNA773777,Activation of lineage competence in hemogenic endothelium precedes the formation of hematopoietic stem cell heterogeneity [Zebrafish.scRNA seq],GSE186423,Transcriptome Analysis,Using a combination of single cell multi omics  lineage tracing and functional assays  we show that embryonic HSPCs are originated from heterogeneous hemogenic endothelial cells HECs during zebrafish embryogenesis. Overall design: Hematopoietic stem and progenitor cells HSPCs are considered as a heterogeneous population  but where and how HSPC heterogeneity occurs remain unclear. Here  we performed scRNA seq and scATAC seq with zebrafish 36 hpf VDA derived kdrl+runx1   kdrl+runx1+  and kdrl runx1+ cells. To determine the transcriptional signatures of spi2+ lineages in zebrafish  we performed STRT seq with spi2: Gal4;UAS:GFP+ kdrl:mCherry+ HECs and spi2: Gal4;UAS:GFP+ kdrl:mCherry  hematopoietic cells at 36 hpf. To investigate the underlying molecular mechanism upon spi2 deficiency  we performed scRNA seq with the sorted ECs kdrl+runx1   HECs kdrl+runx1+ and hematopoietic cells kdrl runx1+ from spi2 morphants at 36 hpf. To determine whether spi2 can directly modulate transcriptional programs in EC/HEC  we examined genome wide spi2 binding by cut tag assay in fli1a flag spi2 EGFP+ cells sorted from trunk region of Tg fli1a flag spi2 GFP embryos at 36 hpf.,parent bioproject:PRJNA773771,pubmed:37016019,,36 hpf Zebrafish VDA scRNA seq,GSM5651458,,source name:Zebrafish VDA|tissue:Zebrafish VDA 36hpf|cells:VDA derived kdrl+runx1   kdrl+runx1+  and kdrl runx1+ cells|Stage:36 hpf,36 hpf Zebrafish VDA scRNA seq,For scRNA seq  and scATAC seq based on 10x Genomics，raw data files were processed by Cell Ranger software suite with default mapping parameters  using the GRCz11 reference genome. For STRT seq  raw reads were first de multiplexed by barcode sequences in reads 2 to yield separate read files for individual cells  then the transcripts sequences of each cell in reads 1 were separated based on corresponding reads 2. Simultaneously  UMI sequences in reads 2 were integrated into reads 1. The template switching oligo TSO sequence  polyA sequence and the low quality reads N > 10% in reads 1 were subsequently removed by Python scripts and Trimmomatic version 0.36. Next  the clean reads were aligned to the zebrafish genome GRCz11 from Ensembl using HISAT2 version 2.1.0 with known gene annotation. Only protein coding genes were retained and the abundance of each gene were estimated by counting the reads that duplicated UMIs have been excluded. For cut&tag  reads were aligned to GRCz11 by Bowtie2. Only uniquely mapped reads with mapping quality score ≥ 30 were kept using Samtools software. post merging replicates  MACS2 was used for the peak calling. Assembly: GRCz11,Zebrafish VDA,,For 10x Genomics based scRNA seq and scATAC seq in zebrafish  40 000 mCherry+ GFP  cells  40 000 mCherry+ GFP+ cells and 30 000 mCherry  GFP+ cells were sorted from Tg kdrl:mCherry/runx1:enGFP at 36 hpf. For STRT seq in zebrafish  single spi2: Gal4;UAS:GFP+ kdrl:mCherry+ HECs and spi2: Gal4;UAS:GFP+ kdrl:mCherry  hematopoietic cells were sorted from the trunk region of Tg spi2: Gal4;UAS:GFP/ kdrl:mCherry at 36 hpf. For scRNA seq of spi2 morphants at 36 hpf in zebrafish  ECs kdrl+runx1   HECs kdrl+runx1+ and hematopoietic cells kdrl runx1+ were sorted. For bulk CUT&TAG in zebrafish  fli1a flag spi2 EGFP+ cells were sorted from the trunk region of Tg fli1a flag spi2 GFP embryos at 36 hpf. For 10x Genomics based scRNA seq and scATAC seq in zebrafish  we loaded 20 000 cells for further 10x Genomics based scRNA seq and 90 000 cells for further 10x Genomics based scATAC seq. For scRNA seq  libraries were prepared using Single Cell 3’ Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For ATAC seq  nuclei were isolated and washed according to the methods supplied by 10x Genomics. Libraries were prepared using the Chromium Chip E Single Cell Kit and Chromium Single Cell ATAC Library & Gel Bead Kit  and further sequenced on an Illumina Novaseq6000 platform to generate 50 bp paired end reads. For 10x Genomics based scRNA seq in mice  libraries were prepared using Single Cell 3’ Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For STRT seq in zebrafish  the end repair and dA tailing of the DNA fragments and ligation of the adaptors to the DNA fragments were performed according to the KAPA Hyper Prep Kits with PCR Library Amplification/Illumina series. post the adaptor ligation step  the final PCR was performed. The libraries were sequenced on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For bulk CUT&TAG  libraries were prepared according to Hyperactive In Situ ChIP Library Prep Kit for Illumina and sequenced on an Illumina NovaSeq6000 platform to generate 150 bp paired end reads.,,tissue:Zebrafish VDA 36hpf|cells:VDA derived kdrl+runx1   kdrl+runx1+  and kdrl runx1+ cells|Stage:36 hpf,GSM5651458,GSM5651458: 36 hpf Zebrafish VDA scRNA seq; Danio rerio; RNA Seq,GSM5651458 r1,GSM5651458,1,For 10x Genomics based scRNA seq and scATAC seq in zebrafish  40 000 mCherry+ GFP  cells  40 000 mCherry+ GFP+ cells and 30 000 mCherry  GFP+ cells were sorted from Tg kdrl:mCherry/runx1:enGFP at 36 hpf. For STRT seq in zebrafish  single spi2: Gal4;UAS:GFP+ kdrl:mCherry+ HECs and spi2: Gal4;UAS:GFP+ kdrl:mCherry  hematopoietic cells were sorted from the trunk region of Tg spi2: Gal4;UAS:GFP/ kdrl:mCherry at 36 hpf. For scRNA seq of spi2 morphants at 36 hpf in zebrafish  ECs kdrl+runx1   HECs kdrl+runx1+ and hematopoietic cells kdrl runx1+ were sorted. For bulk CUT&TAG in zebrafish  fli1a flag spi2 EGFP+ cells were sorted from the trunk region of Tg fli1a flag spi2 GFP embryos at 36 hpf. For 10x Genomics based scRNA seq and scATAC seq in zebrafish  we loaded 20 000 cells for further 10x Genomics based scRNA seq and 90 000 cells for further 10x Genomics based scATAC seq. For scRNA seq  libraries were prepared using Single Cell three prime Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For ATAC seq  nuclei were isolated and washed according to the methods supplied by 10x Genomics. Libraries were prepared using the Chromium Chip E Single Cell Kit and Chromium Single Cell ATAC Library & Gel Bead Kit  and further sequenced on an Illumina Novaseq6000 platform to generate 50 bp paired end reads. For 10x Genomics based scRNA seq in mice  libraries were prepared using Single Cell three prime Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For STRT seq in zebrafish  the end repair and dA tailing of the DNA fragments and ligation of the adaptors to the DNA fragments were performed according to the KAPA Hyper Prep Kits with PCR Library Amplification/Illumina series. post the adaptor ligation step  the final PCR was performed. The libraries were sequenced on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For bulk CUT&TAG  libraries were prepared according to Hyperactive In Situ ChIP Library Prep Kit for Illumina and sequenced on an Illumina NovaSeq6000 platform to generate 150 bp paired end reads.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP342742,,,190718O_ECHEHSC_R_2_1_R1.fq.gz 190718O_ECHEHSC_R_2_1_R2.fq.gz,fastq fastq,45613780500.0,152045935.0,GSM5651458 r2,0:150 1:150,A:20279847027;C:7989810705;G:7602659881;T:9741099780;N:363107,150,150,,,20279847027,7989810705,7602659881,9741099780,363107,SRX12742420,SRS10690646,SRA1600571,"Group of Hematopoiesis and Cardiovascular Development, INSTITUTE OF ZOOLOGY, CHINESE ACADEMY OF SCIENCES","Group of Hematopoiesis and Cardiovascular Development, INSTITUTE OF ZOOLOGY, CHINESE ACADEMY OF SCIENCES",2,0.0,0.92821,0.0,0.09747,1.0,0.81706,,0.52451,150,150,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,China,2021-10-22,Pharyngula,Embryo,Multi-tissue,Multi-system
66755,SRR16539850,SRX12742420,SRS10690646,SRP342742,PRJNA773777,Activation of lineage competence in hemogenic endothelium precedes the formation of hematopoietic stem cell heterogeneity [Zebrafish.scRNA seq],GSE186423,Transcriptome Analysis,Using a combination of single cell multi omics  lineage tracing and functional assays  we show that embryonic HSPCs are originated from heterogeneous hemogenic endothelial cells HECs during zebrafish embryogenesis. Overall design: Hematopoietic stem and progenitor cells HSPCs are considered as a heterogeneous population  but where and how HSPC heterogeneity occurs remain unclear. Here  we performed scRNA seq and scATAC seq with zebrafish 36 hpf VDA derived kdrl+runx1   kdrl+runx1+  and kdrl runx1+ cells. To determine the transcriptional signatures of spi2+ lineages in zebrafish  we performed STRT seq with spi2: Gal4;UAS:GFP+ kdrl:mCherry+ HECs and spi2: Gal4;UAS:GFP+ kdrl:mCherry  hematopoietic cells at 36 hpf. To investigate the underlying molecular mechanism upon spi2 deficiency  we performed scRNA seq with the sorted ECs kdrl+runx1   HECs kdrl+runx1+ and hematopoietic cells kdrl runx1+ from spi2 morphants at 36 hpf. To determine whether spi2 can directly modulate transcriptional programs in EC/HEC  we examined genome wide spi2 binding by cut tag assay in fli1a flag spi2 EGFP+ cells sorted from trunk region of Tg fli1a flag spi2 GFP embryos at 36 hpf.,parent bioproject:PRJNA773771,pubmed:37016019,,36 hpf Zebrafish VDA scRNA seq,GSM5651458,,source name:Zebrafish VDA|tissue:Zebrafish VDA 36hpf|cells:VDA derived kdrl+runx1   kdrl+runx1+  and kdrl runx1+ cells|Stage:36 hpf,36 hpf Zebrafish VDA scRNA seq,For scRNA seq  and scATAC seq based on 10x Genomics，raw data files were processed by Cell Ranger software suite with default mapping parameters  using the GRCz11 reference genome. For STRT seq  raw reads were first de multiplexed by barcode sequences in reads 2 to yield separate read files for individual cells  then the transcripts sequences of each cell in reads 1 were separated based on corresponding reads 2. Simultaneously  UMI sequences in reads 2 were integrated into reads 1. The template switching oligo TSO sequence  polyA sequence and the low quality reads N > 10% in reads 1 were subsequently removed by Python scripts and Trimmomatic version 0.36. Next  the clean reads were aligned to the zebrafish genome GRCz11 from Ensembl using HISAT2 version 2.1.0 with known gene annotation. Only protein coding genes were retained and the abundance of each gene were estimated by counting the reads that duplicated UMIs have been excluded. For cut&tag  reads were aligned to GRCz11 by Bowtie2. Only uniquely mapped reads with mapping quality score ≥ 30 were kept using Samtools software. post merging replicates  MACS2 was used for the peak calling. Assembly: GRCz11,Zebrafish VDA,,For 10x Genomics based scRNA seq and scATAC seq in zebrafish  40 000 mCherry+ GFP  cells  40 000 mCherry+ GFP+ cells and 30 000 mCherry  GFP+ cells were sorted from Tg kdrl:mCherry/runx1:enGFP at 36 hpf. For STRT seq in zebrafish  single spi2: Gal4;UAS:GFP+ kdrl:mCherry+ HECs and spi2: Gal4;UAS:GFP+ kdrl:mCherry  hematopoietic cells were sorted from the trunk region of Tg spi2: Gal4;UAS:GFP/ kdrl:mCherry at 36 hpf. For scRNA seq of spi2 morphants at 36 hpf in zebrafish  ECs kdrl+runx1   HECs kdrl+runx1+ and hematopoietic cells kdrl runx1+ were sorted. For bulk CUT&TAG in zebrafish  fli1a flag spi2 EGFP+ cells were sorted from the trunk region of Tg fli1a flag spi2 GFP embryos at 36 hpf. For 10x Genomics based scRNA seq and scATAC seq in zebrafish  we loaded 20 000 cells for further 10x Genomics based scRNA seq and 90 000 cells for further 10x Genomics based scATAC seq. For scRNA seq  libraries were prepared using Single Cell 3’ Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For ATAC seq  nuclei were isolated and washed according to the methods supplied by 10x Genomics. Libraries were prepared using the Chromium Chip E Single Cell Kit and Chromium Single Cell ATAC Library & Gel Bead Kit  and further sequenced on an Illumina Novaseq6000 platform to generate 50 bp paired end reads. For 10x Genomics based scRNA seq in mice  libraries were prepared using Single Cell 3’ Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For STRT seq in zebrafish  the end repair and dA tailing of the DNA fragments and ligation of the adaptors to the DNA fragments were performed according to the KAPA Hyper Prep Kits with PCR Library Amplification/Illumina series. post the adaptor ligation step  the final PCR was performed. The libraries were sequenced on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For bulk CUT&TAG  libraries were prepared according to Hyperactive In Situ ChIP Library Prep Kit for Illumina and sequenced on an Illumina NovaSeq6000 platform to generate 150 bp paired end reads.,,tissue:Zebrafish VDA 36hpf|cells:VDA derived kdrl+runx1   kdrl+runx1+  and kdrl runx1+ cells|Stage:36 hpf,GSM5651458,GSM5651458: 36 hpf Zebrafish VDA scRNA seq; Danio rerio; RNA Seq,GSM5651458 r1,GSM5651458,1,For 10x Genomics based scRNA seq and scATAC seq in zebrafish  40 000 mCherry+ GFP  cells  40 000 mCherry+ GFP+ cells and 30 000 mCherry  GFP+ cells were sorted from Tg kdrl:mCherry/runx1:enGFP at 36 hpf. For STRT seq in zebrafish  single spi2: Gal4;UAS:GFP+ kdrl:mCherry+ HECs and spi2: Gal4;UAS:GFP+ kdrl:mCherry  hematopoietic cells were sorted from the trunk region of Tg spi2: Gal4;UAS:GFP/ kdrl:mCherry at 36 hpf. For scRNA seq of spi2 morphants at 36 hpf in zebrafish  ECs kdrl+runx1   HECs kdrl+runx1+ and hematopoietic cells kdrl runx1+ were sorted. For bulk CUT&TAG in zebrafish  fli1a flag spi2 EGFP+ cells were sorted from the trunk region of Tg fli1a flag spi2 GFP embryos at 36 hpf. For 10x Genomics based scRNA seq and scATAC seq in zebrafish  we loaded 20 000 cells for further 10x Genomics based scRNA seq and 90 000 cells for further 10x Genomics based scATAC seq. For scRNA seq  libraries were prepared using Single Cell three prime Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For ATAC seq  nuclei were isolated and washed according to the methods supplied by 10x Genomics. Libraries were prepared using the Chromium Chip E Single Cell Kit and Chromium Single Cell ATAC Library & Gel Bead Kit  and further sequenced on an Illumina Novaseq6000 platform to generate 50 bp paired end reads. For 10x Genomics based scRNA seq in mice  libraries were prepared using Single Cell three prime Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For STRT seq in zebrafish  the end repair and dA tailing of the DNA fragments and ligation of the adaptors to the DNA fragments were performed according to the KAPA Hyper Prep Kits with PCR Library Amplification/Illumina series. post the adaptor ligation step  the final PCR was performed. The libraries were sequenced on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For bulk CUT&TAG  libraries were prepared according to Hyperactive In Situ ChIP Library Prep Kit for Illumina and sequenced on an Illumina NovaSeq6000 platform to generate 150 bp paired end reads.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP342742,,,190718O_ECHEHSC_R_3_1_R1.fq.gz 190718O_ECHEHSC_R_3_1_R2.fq.gz,fastq fastq,57137293500.0,190457645.0,GSM5651458 r3,0:150 1:150,A:25401821096;C:10031650741;G:9533037288;T:12170324099;N:460276,150,150,,,25401821096,10031650741,9533037288,12170324099,460276,SRX12742420,SRS10690646,SRA1600571,"Group of Hematopoiesis and Cardiovascular Development, INSTITUTE OF ZOOLOGY, CHINESE ACADEMY OF SCIENCES","Group of Hematopoiesis and Cardiovascular Development, INSTITUTE OF ZOOLOGY, CHINESE ACADEMY OF SCIENCES",2,0.0,0.92958,0.0,0.09774,1.0,0.81773,,0.52455,150,150,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,China,2021-10-22,Pharyngula,Embryo,Multi-tissue,Multi-system
66756,SRR16539851,SRX12742420,SRS10690646,SRP342742,PRJNA773777,Activation of lineage competence in hemogenic endothelium precedes the formation of hematopoietic stem cell heterogeneity [Zebrafish.scRNA seq],GSE186423,Transcriptome Analysis,Using a combination of single cell multi omics  lineage tracing and functional assays  we show that embryonic HSPCs are originated from heterogeneous hemogenic endothelial cells HECs during zebrafish embryogenesis. Overall design: Hematopoietic stem and progenitor cells HSPCs are considered as a heterogeneous population  but where and how HSPC heterogeneity occurs remain unclear. Here  we performed scRNA seq and scATAC seq with zebrafish 36 hpf VDA derived kdrl+runx1   kdrl+runx1+  and kdrl runx1+ cells. To determine the transcriptional signatures of spi2+ lineages in zebrafish  we performed STRT seq with spi2: Gal4;UAS:GFP+ kdrl:mCherry+ HECs and spi2: Gal4;UAS:GFP+ kdrl:mCherry  hematopoietic cells at 36 hpf. To investigate the underlying molecular mechanism upon spi2 deficiency  we performed scRNA seq with the sorted ECs kdrl+runx1   HECs kdrl+runx1+ and hematopoietic cells kdrl runx1+ from spi2 morphants at 36 hpf. To determine whether spi2 can directly modulate transcriptional programs in EC/HEC  we examined genome wide spi2 binding by cut tag assay in fli1a flag spi2 EGFP+ cells sorted from trunk region of Tg fli1a flag spi2 GFP embryos at 36 hpf.,parent bioproject:PRJNA773771,pubmed:37016019,,36 hpf Zebrafish VDA scRNA seq,GSM5651458,,source name:Zebrafish VDA|tissue:Zebrafish VDA 36hpf|cells:VDA derived kdrl+runx1   kdrl+runx1+  and kdrl runx1+ cells|Stage:36 hpf,36 hpf Zebrafish VDA scRNA seq,For scRNA seq  and scATAC seq based on 10x Genomics，raw data files were processed by Cell Ranger software suite with default mapping parameters  using the GRCz11 reference genome. For STRT seq  raw reads were first de multiplexed by barcode sequences in reads 2 to yield separate read files for individual cells  then the transcripts sequences of each cell in reads 1 were separated based on corresponding reads 2. Simultaneously  UMI sequences in reads 2 were integrated into reads 1. The template switching oligo TSO sequence  polyA sequence and the low quality reads N > 10% in reads 1 were subsequently removed by Python scripts and Trimmomatic version 0.36. Next  the clean reads were aligned to the zebrafish genome GRCz11 from Ensembl using HISAT2 version 2.1.0 with known gene annotation. Only protein coding genes were retained and the abundance of each gene were estimated by counting the reads that duplicated UMIs have been excluded. For cut&tag  reads were aligned to GRCz11 by Bowtie2. Only uniquely mapped reads with mapping quality score ≥ 30 were kept using Samtools software. post merging replicates  MACS2 was used for the peak calling. Assembly: GRCz11,Zebrafish VDA,,For 10x Genomics based scRNA seq and scATAC seq in zebrafish  40 000 mCherry+ GFP  cells  40 000 mCherry+ GFP+ cells and 30 000 mCherry  GFP+ cells were sorted from Tg kdrl:mCherry/runx1:enGFP at 36 hpf. For STRT seq in zebrafish  single spi2: Gal4;UAS:GFP+ kdrl:mCherry+ HECs and spi2: Gal4;UAS:GFP+ kdrl:mCherry  hematopoietic cells were sorted from the trunk region of Tg spi2: Gal4;UAS:GFP/ kdrl:mCherry at 36 hpf. For scRNA seq of spi2 morphants at 36 hpf in zebrafish  ECs kdrl+runx1   HECs kdrl+runx1+ and hematopoietic cells kdrl runx1+ were sorted. For bulk CUT&TAG in zebrafish  fli1a flag spi2 EGFP+ cells were sorted from the trunk region of Tg fli1a flag spi2 GFP embryos at 36 hpf. For 10x Genomics based scRNA seq and scATAC seq in zebrafish  we loaded 20 000 cells for further 10x Genomics based scRNA seq and 90 000 cells for further 10x Genomics based scATAC seq. For scRNA seq  libraries were prepared using Single Cell 3’ Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For ATAC seq  nuclei were isolated and washed according to the methods supplied by 10x Genomics. Libraries were prepared using the Chromium Chip E Single Cell Kit and Chromium Single Cell ATAC Library & Gel Bead Kit  and further sequenced on an Illumina Novaseq6000 platform to generate 50 bp paired end reads. For 10x Genomics based scRNA seq in mice  libraries were prepared using Single Cell 3’ Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For STRT seq in zebrafish  the end repair and dA tailing of the DNA fragments and ligation of the adaptors to the DNA fragments were performed according to the KAPA Hyper Prep Kits with PCR Library Amplification/Illumina series. post the adaptor ligation step  the final PCR was performed. The libraries were sequenced on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For bulk CUT&TAG  libraries were prepared according to Hyperactive In Situ ChIP Library Prep Kit for Illumina and sequenced on an Illumina NovaSeq6000 platform to generate 150 bp paired end reads.,,tissue:Zebrafish VDA 36hpf|cells:VDA derived kdrl+runx1   kdrl+runx1+  and kdrl runx1+ cells|Stage:36 hpf,GSM5651458,GSM5651458: 36 hpf Zebrafish VDA scRNA seq; Danio rerio; RNA Seq,GSM5651458 r1,GSM5651458,1,For 10x Genomics based scRNA seq and scATAC seq in zebrafish  40 000 mCherry+ GFP  cells  40 000 mCherry+ GFP+ cells and 30 000 mCherry  GFP+ cells were sorted from Tg kdrl:mCherry/runx1:enGFP at 36 hpf. For STRT seq in zebrafish  single spi2: Gal4;UAS:GFP+ kdrl:mCherry+ HECs and spi2: Gal4;UAS:GFP+ kdrl:mCherry  hematopoietic cells were sorted from the trunk region of Tg spi2: Gal4;UAS:GFP/ kdrl:mCherry at 36 hpf. For scRNA seq of spi2 morphants at 36 hpf in zebrafish  ECs kdrl+runx1   HECs kdrl+runx1+ and hematopoietic cells kdrl runx1+ were sorted. For bulk CUT&TAG in zebrafish  fli1a flag spi2 EGFP+ cells were sorted from the trunk region of Tg fli1a flag spi2 GFP embryos at 36 hpf. For 10x Genomics based scRNA seq and scATAC seq in zebrafish  we loaded 20 000 cells for further 10x Genomics based scRNA seq and 90 000 cells for further 10x Genomics based scATAC seq. For scRNA seq  libraries were prepared using Single Cell three prime Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For ATAC seq  nuclei were isolated and washed according to the methods supplied by 10x Genomics. Libraries were prepared using the Chromium Chip E Single Cell Kit and Chromium Single Cell ATAC Library & Gel Bead Kit  and further sequenced on an Illumina Novaseq6000 platform to generate 50 bp paired end reads. For 10x Genomics based scRNA seq in mice  libraries were prepared using Single Cell three prime Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For STRT seq in zebrafish  the end repair and dA tailing of the DNA fragments and ligation of the adaptors to the DNA fragments were performed according to the KAPA Hyper Prep Kits with PCR Library Amplification/Illumina series. post the adaptor ligation step  the final PCR was performed. The libraries were sequenced on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For bulk CUT&TAG  libraries were prepared according to Hyperactive In Situ ChIP Library Prep Kit for Illumina and sequenced on an Illumina NovaSeq6000 platform to generate 150 bp paired end reads.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP342742,,,190718O_ECHEHSC_R_4_1_R1.fq.gz 190718O_ECHEHSC_R_4_1_R2.fq.gz,fastq fastq,29835023100.0,99450077.0,GSM5651458 r4,0:150 1:150,A:13290644326;C:5233486555;G:4966979633;T:6343677510;N:235076,150,150,,,13290644326,5233486555,4966979633,6343677510,235076,SRX12742420,SRS10690646,SRA1600571,"Group of Hematopoiesis and Cardiovascular Development, INSTITUTE OF ZOOLOGY, CHINESE ACADEMY OF SCIENCES","Group of Hematopoiesis and Cardiovascular Development, INSTITUTE OF ZOOLOGY, CHINESE ACADEMY OF SCIENCES",2,0.0,0.92872,0.0,0.098,1.0,0.8185,,0.52198,150,150,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,China,2021-10-22,Pharyngula,Embryo,Multi-tissue,Multi-system
71058,SRR21152616,SRX17164237,SRS14735586,SRP393251,PRJNA871903,Single cell transcriptomic profiling of the zebrafish inner ear reveals molecularly distinct hair cell and supporting cell subtypes,GSE211728,Transcriptome Analysis,A major cause of human deafness and vestibular dysfunction is permanent loss of the mechanosensory hair cells of the inner ear. In non mammalian vertebrates such as zebrafish  regeneration of missing hair cells can occur throughout life. While a comparative approach has the potential to reveal the basis of such differential regenerative ability  the degree to which the inner ears of fish and mammals share common hair and supporting cell types remains unresolved. Here we perform single cell RNA sequencing of the zebrafish inner ear at embryonic through adult stages to catalog the diversity of hair and non sensory supporting cells. We identify a putative progenitor population for hair and supporting cells  as well as distinct hair and supporting cell types in the maculae versus cristae. The hair and supporting cell types differ from those described for the lateral line  a distributed mechanosensory organ in zebrafish in which most studies of hair cell regeneration have been conducted. In the maculae  we identify two subtypes of hair cells that share gene expression with mammalian striolar or extrastriolar hair cells. In situ hybridization reveals that these hair cell subtypes occupy distinct spatial domains within the two major macular organs  the utricle and saccule  consistent with the reported distinct electrophysiological properties of hair cells within these domains. These findings suggest that primitive specialization of spatially distinct striolar and extrastriolar hair cells likely arose in the last common ancestor of fish and mammals. The similarities of inner ear cell type composition between fish and mammals also support using zebrafish as a relevant model for understanding inner ear specific hair cell function and regeneration. Overall design: Inner ears were dissected from the Sox10Cre;UbiSwitch zebrafish at 14dpf n=35 and 12mpf n=6. Converted cells were isolated by Fluorescence activated cell sorting FACS according to the presence or absence of mCherry signal and analyzed using 10x genomics based scRNAseq. Reads were aligned to danRer11 using the Cellranger pipeline,,pubmed:36598134,,12mpf Sox10CreUbiswitch ear,GSM6500164,,source name:inner ear|tissue:inner ear|sample type:nuclear RNA|cell type:mixed|genotype:Sox10:Cre; ubb:LOXP EGFP LOXP mCherry|age:12 mpf,12mpf Sox10CreUbiswitch ear,Base calling and sample were demultiplexed by bcl2fastq performed by the single cell sequencing and CyTOF core at Chilren's Hospital Los Angeles Sequences were alinged to danRer11 and UMI counts were created using cellranger count v6.0.0 14dpf or cellranger arc count v2.0.0 12mpf Downstream analysis was performed in R and Python Assembly: danRer11 Supplementary files format and content: .csv files filtered barcode feature count matrix for each individual library Supplementary files format and content: .rds file of Seurat Object containing raw count matrix of integrated libraries  including the two libraries here and other published data,inner ear,,For 14 dpf animals  heads from converted Sox10:Cre; ubb:LOXP EGFP LOXP mCherry fish were decapitated at the level of the pectoral fin with eyes and brains removed. For 12 mpf animals  utricle  saccule  and lagena were extracted from converted Sox10:Cre; ubb:LOXP EGFP LOXP mCherry fish post brains and otolith crystals were removed. Dissected heads and otic sensory patches were then incubated in fresh Ringer’s solution for 5–10 min  followed by mechanical and enzymatic dissociation by pipetting every 5 min in protease solution 0.25% trypsin Life Technologies  15090 046  1 mM EDTA  and 400 mg/mL Collagenase D Sigma  11088882001 in PBS and incubated at 28.5 °C for 20–30 min or until full dissociation. Reaction was stopped by adding 6× stop solution 6 mM CaCl2 and 30% fetal bovine serum FBS in PBS. Cells were pelleted 376 × g  5 min  4 °C and resuspended in suspension media 1% FBS  0.8 mM CaCl2  50 U/mL penicillin  and 0.05 mg/mL streptomycin Sigma Aldrich  St. Louis  MO in phenol red free Leibovitz’s L15 medium Life Technologies twice. Final volumes of 500 μL resuspended cells were placed on ice and fluorescence activated cell sorted FACS to isolate live cells that excluded the nuclear stain DAPI 10X Genomics Chromium Single Cell 3′ Library and Gel Bead Kit v.3.1 dpf 14 dpf or Single Cell Multiome ATAC + Gene Expression kit 12 mpf,,tissue:inner ear|sample type:nuclear RNA|cell type:mixed|genotype:Sox10:Cre; ubb:LOXP EGFP LOXP mCherry|age:12 mpf,GSM6500164,GSM6500164: 12mpf Sox10CreUbiswitch ear; Danio rerio; RNA Seq,GSM6500164 r1,GSM6500164,1,For 14 dpf animals  heads from converted Sox10:Cre; ubb:LOXP EGFP LOXP mCherry fish were decapitated at the level of the pectoral fin with eyes and brains removed. For 12 mpf animals  utricle  saccule  and lagena were extracted from converted Sox10:Cre; ubb:LOXP EGFP LOXP mCherry fish post brains and otolith crystals were removed. Dissected heads and otic sensory patches were then incubated in fresh Ringer's solution for 5–10 min  followed by mechanical and enzymatic dissociation by pipetting every 5 min in protease solution 0.25% trypsin Life Technologies  15090 046  1 mM EDTA  and 400 mg/mL Collagenase D Sigma  11088882001 in PBS and incubated at 28.5 °C for 20–30 min or until full dissociation. Reaction was stopped by adding 6× stop solution 6 mM CaCl2 and 30% fetal bovine serum FBS in PBS. Cells were pelleted 376 × g  5 min  4 °C and resuspended in suspension media 1% FBS  0.8 mM CaCl2  50 U/mL penicillin  and 0.05 mg/mL streptomycin Sigma Aldrich  St. Louis  MO in phenol red free Leibovitz's L15 medium Life Technologies twice. Final volumes of 500 μL resuspended cells were placed on ice and fluorescence activated cell sorted FACS to isolate live cells that excluded the nuclear stain DAPI 10X Genomics Chromium Single Cell 3′ Library and Gel Bead Kit v.3.1 dpf 14 dpf or Single Cell Multiome ATAC + Gene Expression kit 12 mpf,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP393251,,loader:fastq load.py,sox10Cre_UbiSwitch_12mpf_ear_snRNA1_S6_L001_R1_001.fastq.gz sox10Cre_UbiSwitch_12mpf_ear_snRNA1_S6_L001_R2_001.fastq.gz,fastq fastq,16297154772.0,123961990.0,GSM6500164 r1,0:29 1:102.47,A:4776377223;C:3475545962;G:3470510289;T:4559999591;N:14721707,29,102,,,4776377223,3475545962,3470510289,4559999591,14721707,SRX17164237,SRS14735586,SRA1480233,University of Southern California,University of Southern California,2,0.0107,0.86542,0.00542,0.28105,0.99208,0.83329,0.49663,0.78501,29,102,T,B,sc-like readlen,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-08-21,Adult,Adult,Multi-tissue,Multi-system
71059,SRR21152617,SRX17164236,SRS14735585,SRP393251,PRJNA871903,Single cell transcriptomic profiling of the zebrafish inner ear reveals molecularly distinct hair cell and supporting cell subtypes,GSE211728,Transcriptome Analysis,A major cause of human deafness and vestibular dysfunction is permanent loss of the mechanosensory hair cells of the inner ear. In non mammalian vertebrates such as zebrafish  regeneration of missing hair cells can occur throughout life. While a comparative approach has the potential to reveal the basis of such differential regenerative ability  the degree to which the inner ears of fish and mammals share common hair and supporting cell types remains unresolved. Here we perform single cell RNA sequencing of the zebrafish inner ear at embryonic through adult stages to catalog the diversity of hair and non sensory supporting cells. We identify a putative progenitor population for hair and supporting cells  as well as distinct hair and supporting cell types in the maculae versus cristae. The hair and supporting cell types differ from those described for the lateral line  a distributed mechanosensory organ in zebrafish in which most studies of hair cell regeneration have been conducted. In the maculae  we identify two subtypes of hair cells that share gene expression with mammalian striolar or extrastriolar hair cells. In situ hybridization reveals that these hair cell subtypes occupy distinct spatial domains within the two major macular organs  the utricle and saccule  consistent with the reported distinct electrophysiological properties of hair cells within these domains. These findings suggest that primitive specialization of spatially distinct striolar and extrastriolar hair cells likely arose in the last common ancestor of fish and mammals. The similarities of inner ear cell type composition between fish and mammals also support using zebrafish as a relevant model for understanding inner ear specific hair cell function and regeneration. Overall design: Inner ears were dissected from the Sox10Cre;UbiSwitch zebrafish at 14dpf n=35 and 12mpf n=6. Converted cells were isolated by Fluorescence activated cell sorting FACS according to the presence or absence of mCherry signal and analyzed using 10x genomics based scRNAseq. Reads were aligned to danRer11 using the Cellranger pipeline,,pubmed:36598134,,14dpf Sox10CreUbiswitch ear,GSM6500163,,source name:inner ear|tissue:inner ear|cell type:mixed|genotype:Sox10:Cre; ubb:LOXP EGFP LOXP mCherry|age:14 dpf,14dpf Sox10CreUbiswitch ear,Base calling and sample were demultiplexed by bcl2fastq performed by the single cell sequencing and CyTOF core at Chilren's Hospital Los Angeles Sequences were alinged to danRer11 and UMI counts were created using cellranger count v6.0.0 14dpf or cellranger arc count v2.0.0 12mpf Downstream analysis was performed in R and Python Assembly: danRer11 Supplementary files format and content: .csv files filtered barcode feature count matrix for each individual library Supplementary files format and content: .rds file of Seurat Object containing raw count matrix of integrated libraries  including the two libraries here and other published data,inner ear,,For 14 dpf animals  heads from converted Sox10:Cre; ubb:LOXP EGFP LOXP mCherry fish were decapitated at the level of the pectoral fin with eyes and brains removed. For 12 mpf animals  utricle  saccule  and lagena were extracted from converted Sox10:Cre; ubb:LOXP EGFP LOXP mCherry fish post brains and otolith crystals were removed. Dissected heads and otic sensory patches were then incubated in fresh Ringer’s solution for 5–10 min  followed by mechanical and enzymatic dissociation by pipetting every 5 min in protease solution 0.25% trypsin Life Technologies  15090 046  1 mM EDTA  and 400 mg/mL Collagenase D Sigma  11088882001 in PBS and incubated at 28.5 °C for 20–30 min or until full dissociation. Reaction was stopped by adding 6× stop solution 6 mM CaCl2 and 30% fetal bovine serum FBS in PBS. Cells were pelleted 376 × g  5 min  4 °C and resuspended in suspension media 1% FBS  0.8 mM CaCl2  50 U/mL penicillin  and 0.05 mg/mL streptomycin Sigma Aldrich  St. Louis  MO in phenol red free Leibovitz’s L15 medium Life Technologies twice. Final volumes of 500 μL resuspended cells were placed on ice and fluorescence activated cell sorted FACS to isolate live cells that excluded the nuclear stain DAPI 10X Genomics Chromium Single Cell 3′ Library and Gel Bead Kit v.3.1 dpf 14 dpf or Single Cell Multiome ATAC + Gene Expression kit 12 mpf,,tissue:inner ear|cell type:mixed|genotype:Sox10:Cre; ubb:LOXP EGFP LOXP mCherry|age:14 dpf,GSM6500163,GSM6500163: 14dpf Sox10CreUbiswitch ear; Danio rerio; RNA Seq,GSM6500163 r1,GSM6500163,1,For 14 dpf animals  heads from converted Sox10:Cre; ubb:LOXP EGFP LOXP mCherry fish were decapitated at the level of the pectoral fin with eyes and brains removed. For 12 mpf animals  utricle  saccule  and lagena were extracted from converted Sox10:Cre; ubb:LOXP EGFP LOXP mCherry fish post brains and otolith crystals were removed. Dissected heads and otic sensory patches were then incubated in fresh Ringer's solution for 5–10 min  followed by mechanical and enzymatic dissociation by pipetting every 5 min in protease solution 0.25% trypsin Life Technologies  15090 046  1 mM EDTA  and 400 mg/mL Collagenase D Sigma  11088882001 in PBS and incubated at 28.5 °C for 20–30 min or until full dissociation. Reaction was stopped by adding 6× stop solution 6 mM CaCl2 and 30% fetal bovine serum FBS in PBS. Cells were pelleted 376 × g  5 min  4 °C and resuspended in suspension media 1% FBS  0.8 mM CaCl2  50 U/mL penicillin  and 0.05 mg/mL streptomycin Sigma Aldrich  St. Louis  MO in phenol red free Leibovitz's L15 medium Life Technologies twice. Final volumes of 500 μL resuspended cells were placed on ice and fluorescence activated cell sorted FACS to isolate live cells that excluded the nuclear stain DAPI 10X Genomics Chromium Single Cell 3′ Library and Gel Bead Kit v.3.1 dpf 14 dpf or Single Cell Multiome ATAC + Gene Expression kit 12 mpf,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP393251,,loader:fastq load.py,sox10CreUbiSwitch_14dpf_ear_S1_L001_R1_001.fastq.gz sox10CreUbiSwitch_14dpf_ear_S1_L001_R2_001.fastq.gz,fastq fastq,66312808744.0,512252644.0,GSM6500163 r1,0:29 1:100.45,A:19003048692;C:14320898403;G:14949837823;T:17995908285;N:43115541,29,100,,,19003048692,14320898403,14949837823,17995908285,43115541,SRX17164236,SRS14735585,SRA1480233,University of Southern California,University of Southern California,2,0.0023,0.91017,0.00102,0.17968,0.99642,0.78338,0.36213,0.5439,29,101,T,B,sc-like readlen,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-08-21,Larval,Larval,Multi-tissue,Multi-system
72189,SRR22306352,SRX18279949,SRS15772345,SRP408138,PRJNA902019,Temporal single cell transcriptome atlas of zebrafish anterior segment development reveals high degree of conservation between the trabecular meshwork and the annular ligament,GSE218068,Transcriptome Analysis,Anterior segment dysgenesis ASD  resulting in vision impairment  stems from maldevelopment of anterior segment AS tissues. Incidence of ASD has been linked to malfunction of periocular mesenchyme cells POM.  POM cells specify into anterior segment mesenchyme ASM cells which colonize and produce AS tissues. In this study we uncover ASM developmental trajectories associated with formation of the AS Overall design: Using a transgenic line of zebrafish that fluorescently labels the ASM throughout development  Tg[foxc1b:GFP]  we isolated GFP+ ASM cells at several developmental timepoints 48 144hpf and performed single cell RNA sequencing,,pubmed:37024546,,Foxc1b 144hpf,GSM6734161,,source name:Anterior Segment Mesenchyme|tissue:Anterior Segment Mesenchyme|cell line:Tg[foxc1b:GFP]|genotype:AB|developmental stage:144hpf,Foxc1b 144hpf,The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v6.0 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: GRCz11 assembly NCBI Genome accession number: GCA 000002035.4 Supplementary files format and content: Tab separated values files and matrix files,Anterior Segment Mesenchyme,,Zebrrafish embryos from the transgenic line Tg[foxc1b:GFP] were collected every 24 hours between 48hpf and 144hpf. The embryos were anesthetized with 3 amino benzoic acid ethyl ester Tricaine. Then  their eyes were dissected and subsequently collected on ice  before being incubated for 8 minutes in 0.25% Trypsin with EDTA at 37°C. post filtering  the dissociated single cells were sorted for GFP+ at the University of Kentucky Flow Cytometry and Immune Monitoring Core at the Markey Cancer Center. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics.,,tissue:Anterior Segment Mesenchyme|cell line:Tg[foxc1b:GFP]|genotype:AB|developmental stage:144hpf,GSM6734161,GSM6734161: Foxc1b 144hpf; Danio rerio; RNA Seq,GSM6734161 r1,GSM6734161,1,Zebrrafish embryos from the transgenic line Tg[foxc1b:GFP] were collected every 24 hours between 48hpf and 144hpf. The embryos were anesthetized with 3 amino benzoic acid ethyl ester Tricaine. Then  their eyes were dissected and subsequently collected on ice  before being incubated for 8 minutes in 0.25% Trypsin with EDTA at 37°C. post filtering  the dissociated single cells were sorted for GFP+ at the University of Kentucky Flow Cytometry and Immune Monitoring Core at the Markey Cancer Center. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP408138,,loader:fastq load.py,144hpf_A_S2_L001_I1_001.fastq.gz 144hpf_A_S2_L001_R1_001.fastq.gz 144hpf_A_S2_L001_R2_001.fastq.gz,fastq fastq fastq,10071479082.0,54147737.0,GSM6734161 r1,0:8 1:28 2:150,A:2929773310;C:1499798320;G:1653059165;T:2039362600;N:167155,8,28,150,,2929773310,1499798320,1653059165,2039362600,167155,SRX18279949,SRS15772345,SRA1541630,"Famulski, Biology, University of Kentucky","Famulski, Biology, University of Kentucky",1,0.74663,,0.09604,,0.81475,,0.47201,,150,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-11-15,Larval,Larval,Multi-tissue,Multi-system
72190,SRR22306353,SRX18279949,SRS15772345,SRP408138,PRJNA902019,Temporal single cell transcriptome atlas of zebrafish anterior segment development reveals high degree of conservation between the trabecular meshwork and the annular ligament,GSE218068,Transcriptome Analysis,Anterior segment dysgenesis ASD  resulting in vision impairment  stems from maldevelopment of anterior segment AS tissues. Incidence of ASD has been linked to malfunction of periocular mesenchyme cells POM.  POM cells specify into anterior segment mesenchyme ASM cells which colonize and produce AS tissues. In this study we uncover ASM developmental trajectories associated with formation of the AS Overall design: Using a transgenic line of zebrafish that fluorescently labels the ASM throughout development  Tg[foxc1b:GFP]  we isolated GFP+ ASM cells at several developmental timepoints 48 144hpf and performed single cell RNA sequencing,,pubmed:37024546,,Foxc1b 144hpf,GSM6734161,,source name:Anterior Segment Mesenchyme|tissue:Anterior Segment Mesenchyme|cell line:Tg[foxc1b:GFP]|genotype:AB|developmental stage:144hpf,Foxc1b 144hpf,The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v6.0 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: GRCz11 assembly NCBI Genome accession number: GCA 000002035.4 Supplementary files format and content: Tab separated values files and matrix files,Anterior Segment Mesenchyme,,Zebrrafish embryos from the transgenic line Tg[foxc1b:GFP] were collected every 24 hours between 48hpf and 144hpf. The embryos were anesthetized with 3 amino benzoic acid ethyl ester Tricaine. Then  their eyes were dissected and subsequently collected on ice  before being incubated for 8 minutes in 0.25% Trypsin with EDTA at 37°C. post filtering  the dissociated single cells were sorted for GFP+ at the University of Kentucky Flow Cytometry and Immune Monitoring Core at the Markey Cancer Center. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics.,,tissue:Anterior Segment Mesenchyme|cell line:Tg[foxc1b:GFP]|genotype:AB|developmental stage:144hpf,GSM6734161,GSM6734161: Foxc1b 144hpf; Danio rerio; RNA Seq,GSM6734161 r1,GSM6734161,1,Zebrrafish embryos from the transgenic line Tg[foxc1b:GFP] were collected every 24 hours between 48hpf and 144hpf. The embryos were anesthetized with 3 amino benzoic acid ethyl ester Tricaine. Then  their eyes were dissected and subsequently collected on ice  before being incubated for 8 minutes in 0.25% Trypsin with EDTA at 37°C. post filtering  the dissociated single cells were sorted for GFP+ at the University of Kentucky Flow Cytometry and Immune Monitoring Core at the Markey Cancer Center. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP408138,,loader:fastq load.py,144hpf_A_S2_L002_I1_001.fastq.gz 144hpf_A_S2_L002_R1_001.fastq.gz 144hpf_A_S2_L002_R2_001.fastq.gz,fastq fastq fastq,10051484826.0,54040241.0,GSM6734161 r2,0:8 1:28 2:150,A:2923933238;C:1496361942;G:1650442691;T:2035100583;N:197696,8,28,150,,2923933238,1496361942,1650442691,2035100583,197696,SRX18279949,SRS15772345,SRA1541630,"Famulski, Biology, University of Kentucky","Famulski, Biology, University of Kentucky",1,0.7469,,0.09438,,0.81168,,0.47634,,150,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-11-15,Larval,Larval,Multi-tissue,Multi-system
72191,SRR22306354,SRX18279949,SRS15772345,SRP408138,PRJNA902019,Temporal single cell transcriptome atlas of zebrafish anterior segment development reveals high degree of conservation between the trabecular meshwork and the annular ligament,GSE218068,Transcriptome Analysis,Anterior segment dysgenesis ASD  resulting in vision impairment  stems from maldevelopment of anterior segment AS tissues. Incidence of ASD has been linked to malfunction of periocular mesenchyme cells POM.  POM cells specify into anterior segment mesenchyme ASM cells which colonize and produce AS tissues. In this study we uncover ASM developmental trajectories associated with formation of the AS Overall design: Using a transgenic line of zebrafish that fluorescently labels the ASM throughout development  Tg[foxc1b:GFP]  we isolated GFP+ ASM cells at several developmental timepoints 48 144hpf and performed single cell RNA sequencing,,pubmed:37024546,,Foxc1b 144hpf,GSM6734161,,source name:Anterior Segment Mesenchyme|tissue:Anterior Segment Mesenchyme|cell line:Tg[foxc1b:GFP]|genotype:AB|developmental stage:144hpf,Foxc1b 144hpf,The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v6.0 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: GRCz11 assembly NCBI Genome accession number: GCA 000002035.4 Supplementary files format and content: Tab separated values files and matrix files,Anterior Segment Mesenchyme,,Zebrrafish embryos from the transgenic line Tg[foxc1b:GFP] were collected every 24 hours between 48hpf and 144hpf. The embryos were anesthetized with 3 amino benzoic acid ethyl ester Tricaine. Then  their eyes were dissected and subsequently collected on ice  before being incubated for 8 minutes in 0.25% Trypsin with EDTA at 37°C. post filtering  the dissociated single cells were sorted for GFP+ at the University of Kentucky Flow Cytometry and Immune Monitoring Core at the Markey Cancer Center. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics.,,tissue:Anterior Segment Mesenchyme|cell line:Tg[foxc1b:GFP]|genotype:AB|developmental stage:144hpf,GSM6734161,GSM6734161: Foxc1b 144hpf; Danio rerio; RNA Seq,GSM6734161 r1,GSM6734161,1,Zebrrafish embryos from the transgenic line Tg[foxc1b:GFP] were collected every 24 hours between 48hpf and 144hpf. The embryos were anesthetized with 3 amino benzoic acid ethyl ester Tricaine. Then  their eyes were dissected and subsequently collected on ice  before being incubated for 8 minutes in 0.25% Trypsin with EDTA at 37°C. post filtering  the dissociated single cells were sorted for GFP+ at the University of Kentucky Flow Cytometry and Immune Monitoring Core at the Markey Cancer Center. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP408138,,loader:fastq load.py,144hpf_B_S4_L001_I1_001.fastq.gz 144hpf_B_S4_L001_R1_001.fastq.gz 144hpf_B_S4_L001_R2_001.fastq.gz,fastq fastq fastq,11611117518.0,62425363.0,GSM6734161 r3,0:8 1:28 2:150,A:2750439378;C:2074542937;G:2235087515;T:2303545516;N:189104,8,28,150,,2750439378,2074542937,2235087515,2303545516,189104,SRX18279949,SRS15772345,SRA1541630,"Famulski, Biology, University of Kentucky","Famulski, Biology, University of Kentucky",1,0.92993,,0.07791,,0.83057,,0.56478,,150,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-11-15,Larval,Larval,Multi-tissue,Multi-system
72192,SRR22306355,SRX18279949,SRS15772345,SRP408138,PRJNA902019,Temporal single cell transcriptome atlas of zebrafish anterior segment development reveals high degree of conservation between the trabecular meshwork and the annular ligament,GSE218068,Transcriptome Analysis,Anterior segment dysgenesis ASD  resulting in vision impairment  stems from maldevelopment of anterior segment AS tissues. Incidence of ASD has been linked to malfunction of periocular mesenchyme cells POM.  POM cells specify into anterior segment mesenchyme ASM cells which colonize and produce AS tissues. In this study we uncover ASM developmental trajectories associated with formation of the AS Overall design: Using a transgenic line of zebrafish that fluorescently labels the ASM throughout development  Tg[foxc1b:GFP]  we isolated GFP+ ASM cells at several developmental timepoints 48 144hpf and performed single cell RNA sequencing,,pubmed:37024546,,Foxc1b 144hpf,GSM6734161,,source name:Anterior Segment Mesenchyme|tissue:Anterior Segment Mesenchyme|cell line:Tg[foxc1b:GFP]|genotype:AB|developmental stage:144hpf,Foxc1b 144hpf,The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v6.0 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: GRCz11 assembly NCBI Genome accession number: GCA 000002035.4 Supplementary files format and content: Tab separated values files and matrix files,Anterior Segment Mesenchyme,,Zebrrafish embryos from the transgenic line Tg[foxc1b:GFP] were collected every 24 hours between 48hpf and 144hpf. The embryos were anesthetized with 3 amino benzoic acid ethyl ester Tricaine. Then  their eyes were dissected and subsequently collected on ice  before being incubated for 8 minutes in 0.25% Trypsin with EDTA at 37°C. post filtering  the dissociated single cells were sorted for GFP+ at the University of Kentucky Flow Cytometry and Immune Monitoring Core at the Markey Cancer Center. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics.,,tissue:Anterior Segment Mesenchyme|cell line:Tg[foxc1b:GFP]|genotype:AB|developmental stage:144hpf,GSM6734161,GSM6734161: Foxc1b 144hpf; Danio rerio; RNA Seq,GSM6734161 r1,GSM6734161,1,Zebrrafish embryos from the transgenic line Tg[foxc1b:GFP] were collected every 24 hours between 48hpf and 144hpf. The embryos were anesthetized with 3 amino benzoic acid ethyl ester Tricaine. Then  their eyes were dissected and subsequently collected on ice  before being incubated for 8 minutes in 0.25% Trypsin with EDTA at 37°C. post filtering  the dissociated single cells were sorted for GFP+ at the University of Kentucky Flow Cytometry and Immune Monitoring Core at the Markey Cancer Center. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP408138,,loader:fastq load.py,144hpf_B_S4_L002_I1_001.fastq.gz 144hpf_B_S4_L002_R1_001.fastq.gz 144hpf_B_S4_L002_R2_001.fastq.gz,fastq fastq fastq,11608408986.0,62410801.0,GSM6734161 r4,0:8 1:28 2:150,A:2749171529;C:2074699135;G:2234953447;T:2302569589;N:226450,8,28,150,,2749171529,2074699135,2234953447,2302569589,226450,SRX18279949,SRS15772345,SRA1541630,"Famulski, Biology, University of Kentucky","Famulski, Biology, University of Kentucky",1,0.93005,,0.07789,,0.83067,,0.56996,,150,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-11-15,Larval,Larval,Multi-tissue,Multi-system
72193,SRR22306356,SRX18279948,SRS15772344,SRP408138,PRJNA902019,Temporal single cell transcriptome atlas of zebrafish anterior segment development reveals high degree of conservation between the trabecular meshwork and the annular ligament,GSE218068,Transcriptome Analysis,Anterior segment dysgenesis ASD  resulting in vision impairment  stems from maldevelopment of anterior segment AS tissues. Incidence of ASD has been linked to malfunction of periocular mesenchyme cells POM.  POM cells specify into anterior segment mesenchyme ASM cells which colonize and produce AS tissues. In this study we uncover ASM developmental trajectories associated with formation of the AS Overall design: Using a transgenic line of zebrafish that fluorescently labels the ASM throughout development  Tg[foxc1b:GFP]  we isolated GFP+ ASM cells at several developmental timepoints 48 144hpf and performed single cell RNA sequencing,,pubmed:37024546,,Foxc1b 120hpf,GSM6734160,,source name:Anterior Segment Mesenchyme|tissue:Anterior Segment Mesenchyme|cell line:Tg[foxc1b:GFP]|genotype:AB|developmental stage:120hpf,Foxc1b 120hpf,The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v6.0 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: GRCz11 assembly NCBI Genome accession number: GCA 000002035.4 Supplementary files format and content: Tab separated values files and matrix files,Anterior Segment Mesenchyme,,Zebrrafish embryos from the transgenic line Tg[foxc1b:GFP] were collected every 24 hours between 48hpf and 144hpf. The embryos were anesthetized with 3 amino benzoic acid ethyl ester Tricaine. Then  their eyes were dissected and subsequently collected on ice  before being incubated for 8 minutes in 0.25% Trypsin with EDTA at 37°C. post filtering  the dissociated single cells were sorted for GFP+ at the University of Kentucky Flow Cytometry and Immune Monitoring Core at the Markey Cancer Center. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics.,,tissue:Anterior Segment Mesenchyme|cell line:Tg[foxc1b:GFP]|genotype:AB|developmental stage:120hpf,GSM6734160,GSM6734160: Foxc1b 120hpf; Danio rerio; RNA Seq,GSM6734160 r1,GSM6734160,1,Zebrrafish embryos from the transgenic line Tg[foxc1b:GFP] were collected every 24 hours between 48hpf and 144hpf. The embryos were anesthetized with 3 amino benzoic acid ethyl ester Tricaine. Then  their eyes were dissected and subsequently collected on ice  before being incubated for 8 minutes in 0.25% Trypsin with EDTA at 37°C. post filtering  the dissociated single cells were sorted for GFP+ at the University of Kentucky Flow Cytometry and Immune Monitoring Core at the Markey Cancer Center. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP408138,,loader:fastq load.py,120hpf_A_S4_L001_I1_001.fastq.gz 120hpf_A_S4_L001_R1_001.fastq.gz 120hpf_A_S4_L001_R2_001.fastq.gz,fastq fastq fastq,17661611028.0,94954898.0,GSM6734160 r1,0:8 1:28 2:150,A:3911517668;C:3269703971;G:3622776955;T:3438794975;N:441131,8,28,150,,3911517668,3269703971,3622776955,3438794975,441131,SRX18279948,SRS15772344,SRA1541630,"Famulski, Biology, University of Kentucky","Famulski, Biology, University of Kentucky",1,0.92039,,0.2409,,0.82227,,0.62515,,150,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-11-15,Larval,Larval,Multi-tissue,Multi-system
72194,SRR22306357,SRX18279948,SRS15772344,SRP408138,PRJNA902019,Temporal single cell transcriptome atlas of zebrafish anterior segment development reveals high degree of conservation between the trabecular meshwork and the annular ligament,GSE218068,Transcriptome Analysis,Anterior segment dysgenesis ASD  resulting in vision impairment  stems from maldevelopment of anterior segment AS tissues. Incidence of ASD has been linked to malfunction of periocular mesenchyme cells POM.  POM cells specify into anterior segment mesenchyme ASM cells which colonize and produce AS tissues. In this study we uncover ASM developmental trajectories associated with formation of the AS Overall design: Using a transgenic line of zebrafish that fluorescently labels the ASM throughout development  Tg[foxc1b:GFP]  we isolated GFP+ ASM cells at several developmental timepoints 48 144hpf and performed single cell RNA sequencing,,pubmed:37024546,,Foxc1b 120hpf,GSM6734160,,source name:Anterior Segment Mesenchyme|tissue:Anterior Segment Mesenchyme|cell line:Tg[foxc1b:GFP]|genotype:AB|developmental stage:120hpf,Foxc1b 120hpf,The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v6.0 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: GRCz11 assembly NCBI Genome accession number: GCA 000002035.4 Supplementary files format and content: Tab separated values files and matrix files,Anterior Segment Mesenchyme,,Zebrrafish embryos from the transgenic line Tg[foxc1b:GFP] were collected every 24 hours between 48hpf and 144hpf. The embryos were anesthetized with 3 amino benzoic acid ethyl ester Tricaine. Then  their eyes were dissected and subsequently collected on ice  before being incubated for 8 minutes in 0.25% Trypsin with EDTA at 37°C. post filtering  the dissociated single cells were sorted for GFP+ at the University of Kentucky Flow Cytometry and Immune Monitoring Core at the Markey Cancer Center. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics.,,tissue:Anterior Segment Mesenchyme|cell line:Tg[foxc1b:GFP]|genotype:AB|developmental stage:120hpf,GSM6734160,GSM6734160: Foxc1b 120hpf; Danio rerio; RNA Seq,GSM6734160 r1,GSM6734160,1,Zebrrafish embryos from the transgenic line Tg[foxc1b:GFP] were collected every 24 hours between 48hpf and 144hpf. The embryos were anesthetized with 3 amino benzoic acid ethyl ester Tricaine. Then  their eyes were dissected and subsequently collected on ice  before being incubated for 8 minutes in 0.25% Trypsin with EDTA at 37°C. post filtering  the dissociated single cells were sorted for GFP+ at the University of Kentucky Flow Cytometry and Immune Monitoring Core at the Markey Cancer Center. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP408138,,loader:fastq load.py,120hpf_A_S4_L002_I1_001.fastq.gz 120hpf_A_S4_L002_R1_001.fastq.gz 120hpf_A_S4_L002_R2_001.fastq.gz,fastq fastq fastq,18210223794.0,97904429.0,GSM6734160 r2,0:8 1:28 2:150,A:4026424182;C:3375187630;G:3741403732;T:3542247007;N:401799,8,28,150,,4026424182,3375187630,3741403732,3542247007,401799,SRX18279948,SRS15772344,SRA1541630,"Famulski, Biology, University of Kentucky","Famulski, Biology, University of Kentucky",1,0.92102,,0.24243,,0.82026,,0.62741,,150,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-11-15,Larval,Larval,Multi-tissue,Multi-system
72195,SRR22306358,SRX18279948,SRS15772344,SRP408138,PRJNA902019,Temporal single cell transcriptome atlas of zebrafish anterior segment development reveals high degree of conservation between the trabecular meshwork and the annular ligament,GSE218068,Transcriptome Analysis,Anterior segment dysgenesis ASD  resulting in vision impairment  stems from maldevelopment of anterior segment AS tissues. Incidence of ASD has been linked to malfunction of periocular mesenchyme cells POM.  POM cells specify into anterior segment mesenchyme ASM cells which colonize and produce AS tissues. In this study we uncover ASM developmental trajectories associated with formation of the AS Overall design: Using a transgenic line of zebrafish that fluorescently labels the ASM throughout development  Tg[foxc1b:GFP]  we isolated GFP+ ASM cells at several developmental timepoints 48 144hpf and performed single cell RNA sequencing,,pubmed:37024546,,Foxc1b 120hpf,GSM6734160,,source name:Anterior Segment Mesenchyme|tissue:Anterior Segment Mesenchyme|cell line:Tg[foxc1b:GFP]|genotype:AB|developmental stage:120hpf,Foxc1b 120hpf,The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v6.0 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: GRCz11 assembly NCBI Genome accession number: GCA 000002035.4 Supplementary files format and content: Tab separated values files and matrix files,Anterior Segment Mesenchyme,,Zebrrafish embryos from the transgenic line Tg[foxc1b:GFP] were collected every 24 hours between 48hpf and 144hpf. The embryos were anesthetized with 3 amino benzoic acid ethyl ester Tricaine. Then  their eyes were dissected and subsequently collected on ice  before being incubated for 8 minutes in 0.25% Trypsin with EDTA at 37°C. post filtering  the dissociated single cells were sorted for GFP+ at the University of Kentucky Flow Cytometry and Immune Monitoring Core at the Markey Cancer Center. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics.,,tissue:Anterior Segment Mesenchyme|cell line:Tg[foxc1b:GFP]|genotype:AB|developmental stage:120hpf,GSM6734160,GSM6734160: Foxc1b 120hpf; Danio rerio; RNA Seq,GSM6734160 r1,GSM6734160,1,Zebrrafish embryos from the transgenic line Tg[foxc1b:GFP] were collected every 24 hours between 48hpf and 144hpf. The embryos were anesthetized with 3 amino benzoic acid ethyl ester Tricaine. Then  their eyes were dissected and subsequently collected on ice  before being incubated for 8 minutes in 0.25% Trypsin with EDTA at 37°C. post filtering  the dissociated single cells were sorted for GFP+ at the University of Kentucky Flow Cytometry and Immune Monitoring Core at the Markey Cancer Center. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP408138,,loader:fastq load.py,120hpf_B_S1_L001_I1_001.fastq.gz 120hpf_B_S1_L001_R1_001.fastq.gz 120hpf_B_S1_L001_R2_001.fastq.gz,fastq fastq fastq,11209538124.0,60266334.0,GSM6734160 r3,0:8 1:28 2:150,A:2632527168;C:1943667010;G:2109734084;T:2353841888;N:179950,8,28,150,,2632527168,1943667010,2109734084,2353841888,179950,SRX18279948,SRS15772344,SRA1541630,"Famulski, Biology, University of Kentucky","Famulski, Biology, University of Kentucky",1,0.93483,,0.10541,,0.77632,,0.50937,,150,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-11-15,Larval,Larval,Multi-tissue,Multi-system
72196,SRR22306359,SRX18279948,SRS15772344,SRP408138,PRJNA902019,Temporal single cell transcriptome atlas of zebrafish anterior segment development reveals high degree of conservation between the trabecular meshwork and the annular ligament,GSE218068,Transcriptome Analysis,Anterior segment dysgenesis ASD  resulting in vision impairment  stems from maldevelopment of anterior segment AS tissues. Incidence of ASD has been linked to malfunction of periocular mesenchyme cells POM.  POM cells specify into anterior segment mesenchyme ASM cells which colonize and produce AS tissues. In this study we uncover ASM developmental trajectories associated with formation of the AS Overall design: Using a transgenic line of zebrafish that fluorescently labels the ASM throughout development  Tg[foxc1b:GFP]  we isolated GFP+ ASM cells at several developmental timepoints 48 144hpf and performed single cell RNA sequencing,,pubmed:37024546,,Foxc1b 120hpf,GSM6734160,,source name:Anterior Segment Mesenchyme|tissue:Anterior Segment Mesenchyme|cell line:Tg[foxc1b:GFP]|genotype:AB|developmental stage:120hpf,Foxc1b 120hpf,The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v6.0 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: GRCz11 assembly NCBI Genome accession number: GCA 000002035.4 Supplementary files format and content: Tab separated values files and matrix files,Anterior Segment Mesenchyme,,Zebrrafish embryos from the transgenic line Tg[foxc1b:GFP] were collected every 24 hours between 48hpf and 144hpf. The embryos were anesthetized with 3 amino benzoic acid ethyl ester Tricaine. Then  their eyes were dissected and subsequently collected on ice  before being incubated for 8 minutes in 0.25% Trypsin with EDTA at 37°C. post filtering  the dissociated single cells were sorted for GFP+ at the University of Kentucky Flow Cytometry and Immune Monitoring Core at the Markey Cancer Center. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics.,,tissue:Anterior Segment Mesenchyme|cell line:Tg[foxc1b:GFP]|genotype:AB|developmental stage:120hpf,GSM6734160,GSM6734160: Foxc1b 120hpf; Danio rerio; RNA Seq,GSM6734160 r1,GSM6734160,1,Zebrrafish embryos from the transgenic line Tg[foxc1b:GFP] were collected every 24 hours between 48hpf and 144hpf. The embryos were anesthetized with 3 amino benzoic acid ethyl ester Tricaine. Then  their eyes were dissected and subsequently collected on ice  before being incubated for 8 minutes in 0.25% Trypsin with EDTA at 37°C. post filtering  the dissociated single cells were sorted for GFP+ at the University of Kentucky Flow Cytometry and Immune Monitoring Core at the Markey Cancer Center. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP408138,,loader:fastq load.py,120hpf_B_S1_L002_I1_001.fastq.gz 120hpf_B_S1_L002_R1_001.fastq.gz 120hpf_B_S1_L002_R2_001.fastq.gz,fastq fastq fastq,11215815810.0,60300085.0,GSM6734160 r4,0:8 1:28 2:150,A:2633236795;C:1945196823;G:2111252224;T:2355107347;N:219561,8,28,150,,2633236795,1945196823,2111252224,2355107347,219561,SRX18279948,SRS15772344,SRA1541630,"Famulski, Biology, University of Kentucky","Famulski, Biology, University of Kentucky",1,0.9355,,0.10564,,0.77798,,0.51829,,150,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-11-15,Larval,Larval,Multi-tissue,Multi-system
72197,SRR22306360,SRX18279947,SRS15772343,SRP408138,PRJNA902019,Temporal single cell transcriptome atlas of zebrafish anterior segment development reveals high degree of conservation between the trabecular meshwork and the annular ligament,GSE218068,Transcriptome Analysis,Anterior segment dysgenesis ASD  resulting in vision impairment  stems from maldevelopment of anterior segment AS tissues. Incidence of ASD has been linked to malfunction of periocular mesenchyme cells POM.  POM cells specify into anterior segment mesenchyme ASM cells which colonize and produce AS tissues. In this study we uncover ASM developmental trajectories associated with formation of the AS Overall design: Using a transgenic line of zebrafish that fluorescently labels the ASM throughout development  Tg[foxc1b:GFP]  we isolated GFP+ ASM cells at several developmental timepoints 48 144hpf and performed single cell RNA sequencing,,pubmed:37024546,,Foxc1b 96hpf,GSM6734159,,source name:Anterior Segment Mesenchyme|tissue:Anterior Segment Mesenchyme|cell line:Tg[foxc1b:GFP]|genotype:AB|developmental stage:96hpf,Foxc1b 96hpf,The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v6.0 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: GRCz11 assembly NCBI Genome accession number: GCA 000002035.4 Supplementary files format and content: Tab separated values files and matrix files,Anterior Segment Mesenchyme,,Zebrrafish embryos from the transgenic line Tg[foxc1b:GFP] were collected every 24 hours between 48hpf and 144hpf. The embryos were anesthetized with 3 amino benzoic acid ethyl ester Tricaine. Then  their eyes were dissected and subsequently collected on ice  before being incubated for 8 minutes in 0.25% Trypsin with EDTA at 37°C. post filtering  the dissociated single cells were sorted for GFP+ at the University of Kentucky Flow Cytometry and Immune Monitoring Core at the Markey Cancer Center. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics.,,tissue:Anterior Segment Mesenchyme|cell line:Tg[foxc1b:GFP]|genotype:AB|developmental stage:96hpf,GSM6734159,GSM6734159: Foxc1b 96hpf; Danio rerio; RNA Seq,GSM6734159 r1,GSM6734159,1,Zebrrafish embryos from the transgenic line Tg[foxc1b:GFP] were collected every 24 hours between 48hpf and 144hpf. The embryos were anesthetized with 3 amino benzoic acid ethyl ester Tricaine. Then  their eyes were dissected and subsequently collected on ice  before being incubated for 8 minutes in 0.25% Trypsin with EDTA at 37°C. post filtering  the dissociated single cells were sorted for GFP+ at the University of Kentucky Flow Cytometry and Immune Monitoring Core at the Markey Cancer Center. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP408138,,loader:fastq load.py,96hpf_A_S2_L001_I1_001.fastq.gz 96hpf_A_S2_L001_R1_001.fastq.gz 96hpf_A_S2_L001_R2_001.fastq.gz,fastq fastq fastq,21803548308.0,117223378.0,GSM6734159 r1,0:8 1:28 2:150,A:5482362998;C:3549501923;G:3687762678;T:4863332303;N:546798,8,28,150,,5482362998,3549501923,3687762678,4863332303,546798,SRX18279947,SRS15772343,SRA1541630,"Famulski, Biology, University of Kentucky","Famulski, Biology, University of Kentucky",1,0.89515,,0.20559,,0.77676,,0.58787,,150,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-11-15,Larval,Larval,Multi-tissue,Multi-system
72198,SRR22306361,SRX18279947,SRS15772343,SRP408138,PRJNA902019,Temporal single cell transcriptome atlas of zebrafish anterior segment development reveals high degree of conservation between the trabecular meshwork and the annular ligament,GSE218068,Transcriptome Analysis,Anterior segment dysgenesis ASD  resulting in vision impairment  stems from maldevelopment of anterior segment AS tissues. Incidence of ASD has been linked to malfunction of periocular mesenchyme cells POM.  POM cells specify into anterior segment mesenchyme ASM cells which colonize and produce AS tissues. In this study we uncover ASM developmental trajectories associated with formation of the AS Overall design: Using a transgenic line of zebrafish that fluorescently labels the ASM throughout development  Tg[foxc1b:GFP]  we isolated GFP+ ASM cells at several developmental timepoints 48 144hpf and performed single cell RNA sequencing,,pubmed:37024546,,Foxc1b 96hpf,GSM6734159,,source name:Anterior Segment Mesenchyme|tissue:Anterior Segment Mesenchyme|cell line:Tg[foxc1b:GFP]|genotype:AB|developmental stage:96hpf,Foxc1b 96hpf,The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v6.0 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: GRCz11 assembly NCBI Genome accession number: GCA 000002035.4 Supplementary files format and content: Tab separated values files and matrix files,Anterior Segment Mesenchyme,,Zebrrafish embryos from the transgenic line Tg[foxc1b:GFP] were collected every 24 hours between 48hpf and 144hpf. The embryos were anesthetized with 3 amino benzoic acid ethyl ester Tricaine. Then  their eyes were dissected and subsequently collected on ice  before being incubated for 8 minutes in 0.25% Trypsin with EDTA at 37°C. post filtering  the dissociated single cells were sorted for GFP+ at the University of Kentucky Flow Cytometry and Immune Monitoring Core at the Markey Cancer Center. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics.,,tissue:Anterior Segment Mesenchyme|cell line:Tg[foxc1b:GFP]|genotype:AB|developmental stage:96hpf,GSM6734159,GSM6734159: Foxc1b 96hpf; Danio rerio; RNA Seq,GSM6734159 r1,GSM6734159,1,Zebrrafish embryos from the transgenic line Tg[foxc1b:GFP] were collected every 24 hours between 48hpf and 144hpf. The embryos were anesthetized with 3 amino benzoic acid ethyl ester Tricaine. Then  their eyes were dissected and subsequently collected on ice  before being incubated for 8 minutes in 0.25% Trypsin with EDTA at 37°C. post filtering  the dissociated single cells were sorted for GFP+ at the University of Kentucky Flow Cytometry and Immune Monitoring Core at the Markey Cancer Center. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP408138,,loader:fastq load.py,96hpf_A_S2_L002_I1_001.fastq.gz 96hpf_A_S2_L002_R1_001.fastq.gz 96hpf_A_S2_L002_R2_001.fastq.gz,fastq fastq fastq,22445964780.0,120677230.0,GSM6734159 r2,0:8 1:28 2:150,A:5637460026;C:3657615123;G:3802504010;T:5003513398;N:491943,8,28,150,,5637460026,3657615123,3802504010,5003513398,491943,SRX18279947,SRS15772343,SRA1541630,"Famulski, Biology, University of Kentucky","Famulski, Biology, University of Kentucky",1,0.89574,,0.20506,,0.77668,,0.57624,,150,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-11-15,Larval,Larval,Multi-tissue,Multi-system
72199,SRR22306362,SRX18279947,SRS15772343,SRP408138,PRJNA902019,Temporal single cell transcriptome atlas of zebrafish anterior segment development reveals high degree of conservation between the trabecular meshwork and the annular ligament,GSE218068,Transcriptome Analysis,Anterior segment dysgenesis ASD  resulting in vision impairment  stems from maldevelopment of anterior segment AS tissues. Incidence of ASD has been linked to malfunction of periocular mesenchyme cells POM.  POM cells specify into anterior segment mesenchyme ASM cells which colonize and produce AS tissues. In this study we uncover ASM developmental trajectories associated with formation of the AS Overall design: Using a transgenic line of zebrafish that fluorescently labels the ASM throughout development  Tg[foxc1b:GFP]  we isolated GFP+ ASM cells at several developmental timepoints 48 144hpf and performed single cell RNA sequencing,,pubmed:37024546,,Foxc1b 96hpf,GSM6734159,,source name:Anterior Segment Mesenchyme|tissue:Anterior Segment Mesenchyme|cell line:Tg[foxc1b:GFP]|genotype:AB|developmental stage:96hpf,Foxc1b 96hpf,The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v6.0 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: GRCz11 assembly NCBI Genome accession number: GCA 000002035.4 Supplementary files format and content: Tab separated values files and matrix files,Anterior Segment Mesenchyme,,Zebrrafish embryos from the transgenic line Tg[foxc1b:GFP] were collected every 24 hours between 48hpf and 144hpf. The embryos were anesthetized with 3 amino benzoic acid ethyl ester Tricaine. Then  their eyes were dissected and subsequently collected on ice  before being incubated for 8 minutes in 0.25% Trypsin with EDTA at 37°C. post filtering  the dissociated single cells were sorted for GFP+ at the University of Kentucky Flow Cytometry and Immune Monitoring Core at the Markey Cancer Center. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics.,,tissue:Anterior Segment Mesenchyme|cell line:Tg[foxc1b:GFP]|genotype:AB|developmental stage:96hpf,GSM6734159,GSM6734159: Foxc1b 96hpf; Danio rerio; RNA Seq,GSM6734159 r1,GSM6734159,1,Zebrrafish embryos from the transgenic line Tg[foxc1b:GFP] were collected every 24 hours between 48hpf and 144hpf. The embryos were anesthetized with 3 amino benzoic acid ethyl ester Tricaine. Then  their eyes were dissected and subsequently collected on ice  before being incubated for 8 minutes in 0.25% Trypsin with EDTA at 37°C. post filtering  the dissociated single cells were sorted for GFP+ at the University of Kentucky Flow Cytometry and Immune Monitoring Core at the Markey Cancer Center. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP408138,,loader:fastq load.py,96hpf_B_S3_L001_I1_001.fastq.gz 96hpf_B_S3_L001_R1_001.fastq.gz 96hpf_B_S3_L001_R2_001.fastq.gz,fastq fastq fastq,19064211546.0,102495761.0,GSM6734159 r3,0:8 1:28 2:150,A:4336439967;C:3483771778;G:3805326765;T:3748351811;N:473829,8,28,150,,4336439967,3483771778,3805326765,3748351811,473829,SRX18279947,SRS15772343,SRA1541630,"Famulski, Biology, University of Kentucky","Famulski, Biology, University of Kentucky",1,0.91875,,0.20874,,0.80298,,0.59387,,150,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-11-15,Larval,Larval,Multi-tissue,Multi-system
72200,SRR22306363,SRX18279947,SRS15772343,SRP408138,PRJNA902019,Temporal single cell transcriptome atlas of zebrafish anterior segment development reveals high degree of conservation between the trabecular meshwork and the annular ligament,GSE218068,Transcriptome Analysis,Anterior segment dysgenesis ASD  resulting in vision impairment  stems from maldevelopment of anterior segment AS tissues. Incidence of ASD has been linked to malfunction of periocular mesenchyme cells POM.  POM cells specify into anterior segment mesenchyme ASM cells which colonize and produce AS tissues. In this study we uncover ASM developmental trajectories associated with formation of the AS Overall design: Using a transgenic line of zebrafish that fluorescently labels the ASM throughout development  Tg[foxc1b:GFP]  we isolated GFP+ ASM cells at several developmental timepoints 48 144hpf and performed single cell RNA sequencing,,pubmed:37024546,,Foxc1b 96hpf,GSM6734159,,source name:Anterior Segment Mesenchyme|tissue:Anterior Segment Mesenchyme|cell line:Tg[foxc1b:GFP]|genotype:AB|developmental stage:96hpf,Foxc1b 96hpf,The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v6.0 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: GRCz11 assembly NCBI Genome accession number: GCA 000002035.4 Supplementary files format and content: Tab separated values files and matrix files,Anterior Segment Mesenchyme,,Zebrrafish embryos from the transgenic line Tg[foxc1b:GFP] were collected every 24 hours between 48hpf and 144hpf. The embryos were anesthetized with 3 amino benzoic acid ethyl ester Tricaine. Then  their eyes were dissected and subsequently collected on ice  before being incubated for 8 minutes in 0.25% Trypsin with EDTA at 37°C. post filtering  the dissociated single cells were sorted for GFP+ at the University of Kentucky Flow Cytometry and Immune Monitoring Core at the Markey Cancer Center. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics.,,tissue:Anterior Segment Mesenchyme|cell line:Tg[foxc1b:GFP]|genotype:AB|developmental stage:96hpf,GSM6734159,GSM6734159: Foxc1b 96hpf; Danio rerio; RNA Seq,GSM6734159 r1,GSM6734159,1,Zebrrafish embryos from the transgenic line Tg[foxc1b:GFP] were collected every 24 hours between 48hpf and 144hpf. The embryos were anesthetized with 3 amino benzoic acid ethyl ester Tricaine. Then  their eyes were dissected and subsequently collected on ice  before being incubated for 8 minutes in 0.25% Trypsin with EDTA at 37°C. post filtering  the dissociated single cells were sorted for GFP+ at the University of Kentucky Flow Cytometry and Immune Monitoring Core at the Markey Cancer Center. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP408138,,loader:fastq load.py,96hpf_B_S3_L002_I1_001.fastq.gz 96hpf_B_S3_L002_R1_001.fastq.gz 96hpf_B_S3_L002_R2_001.fastq.gz,fastq fastq fastq,19616344548.0,105464218.0,GSM6734159 r4,0:8 1:28 2:150,A:4455009353;C:3588592225;G:3922172348;T:3853423493;N:435281,8,28,150,,4455009353,3588592225,3922172348,3853423493,435281,SRX18279947,SRS15772343,SRA1541630,"Famulski, Biology, University of Kentucky","Famulski, Biology, University of Kentucky",1,0.92045,,0.21078,,0.80322,,0.59961,,150,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-11-15,Larval,Larval,Multi-tissue,Multi-system
72201,SRR22306364,SRX18279946,SRS15772342,SRP408138,PRJNA902019,Temporal single cell transcriptome atlas of zebrafish anterior segment development reveals high degree of conservation between the trabecular meshwork and the annular ligament,GSE218068,Transcriptome Analysis,Anterior segment dysgenesis ASD  resulting in vision impairment  stems from maldevelopment of anterior segment AS tissues. Incidence of ASD has been linked to malfunction of periocular mesenchyme cells POM.  POM cells specify into anterior segment mesenchyme ASM cells which colonize and produce AS tissues. In this study we uncover ASM developmental trajectories associated with formation of the AS Overall design: Using a transgenic line of zebrafish that fluorescently labels the ASM throughout development  Tg[foxc1b:GFP]  we isolated GFP+ ASM cells at several developmental timepoints 48 144hpf and performed single cell RNA sequencing,,pubmed:37024546,,Foxc1b 72hpf,GSM6734158,,source name:Anterior Segment Mesenchyme|tissue:Anterior Segment Mesenchyme|cell line:Tg[foxc1b:GFP]|genotype:AB|developmental stage:72hpf,Foxc1b 72hpf,The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v6.0 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: GRCz11 assembly NCBI Genome accession number: GCA 000002035.4 Supplementary files format and content: Tab separated values files and matrix files,Anterior Segment Mesenchyme,,Zebrrafish embryos from the transgenic line Tg[foxc1b:GFP] were collected every 24 hours between 48hpf and 144hpf. The embryos were anesthetized with 3 amino benzoic acid ethyl ester Tricaine. Then  their eyes were dissected and subsequently collected on ice  before being incubated for 8 minutes in 0.25% Trypsin with EDTA at 37°C. post filtering  the dissociated single cells were sorted for GFP+ at the University of Kentucky Flow Cytometry and Immune Monitoring Core at the Markey Cancer Center. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics.,,tissue:Anterior Segment Mesenchyme|cell line:Tg[foxc1b:GFP]|genotype:AB|developmental stage:72hpf,GSM6734158,GSM6734158: Foxc1b 72hpf; Danio rerio; RNA Seq,GSM6734158 r1,GSM6734158,1,Zebrrafish embryos from the transgenic line Tg[foxc1b:GFP] were collected every 24 hours between 48hpf and 144hpf. The embryos were anesthetized with 3 amino benzoic acid ethyl ester Tricaine. Then  their eyes were dissected and subsequently collected on ice  before being incubated for 8 minutes in 0.25% Trypsin with EDTA at 37°C. post filtering  the dissociated single cells were sorted for GFP+ at the University of Kentucky Flow Cytometry and Immune Monitoring Core at the Markey Cancer Center. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP408138,,loader:fastq load.py,72hpf_A_S3_L003_I1_001.fastq.gz 72hpf_A_S3_L003_R1_001.fastq.gz 72hpf_A_S3_L003_R2_001.fastq.gz,fastq fastq fastq,40892227528.0,222240367.0,GSM6734158 r1,0:8 1:26 2:150,A:11396668180;C:6212386813;G:6930219468;T:8795624716;N:1155873,8,26,150,,11396668180,6212386813,6930219468,8795624716,1155873,SRX18279946,SRS15772342,SRA1541630,"Famulski, Biology, University of Kentucky","Famulski, Biology, University of Kentucky",1,0.85155,,0.07413,,0.82416,,0.54356,,150,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-11-15,Larval,Larval,Multi-tissue,Multi-system
72202,SRR22306365,SRX18279946,SRS15772342,SRP408138,PRJNA902019,Temporal single cell transcriptome atlas of zebrafish anterior segment development reveals high degree of conservation between the trabecular meshwork and the annular ligament,GSE218068,Transcriptome Analysis,Anterior segment dysgenesis ASD  resulting in vision impairment  stems from maldevelopment of anterior segment AS tissues. Incidence of ASD has been linked to malfunction of periocular mesenchyme cells POM.  POM cells specify into anterior segment mesenchyme ASM cells which colonize and produce AS tissues. In this study we uncover ASM developmental trajectories associated with formation of the AS Overall design: Using a transgenic line of zebrafish that fluorescently labels the ASM throughout development  Tg[foxc1b:GFP]  we isolated GFP+ ASM cells at several developmental timepoints 48 144hpf and performed single cell RNA sequencing,,pubmed:37024546,,Foxc1b 72hpf,GSM6734158,,source name:Anterior Segment Mesenchyme|tissue:Anterior Segment Mesenchyme|cell line:Tg[foxc1b:GFP]|genotype:AB|developmental stage:72hpf,Foxc1b 72hpf,The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v6.0 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: GRCz11 assembly NCBI Genome accession number: GCA 000002035.4 Supplementary files format and content: Tab separated values files and matrix files,Anterior Segment Mesenchyme,,Zebrrafish embryos from the transgenic line Tg[foxc1b:GFP] were collected every 24 hours between 48hpf and 144hpf. The embryos were anesthetized with 3 amino benzoic acid ethyl ester Tricaine. Then  their eyes were dissected and subsequently collected on ice  before being incubated for 8 minutes in 0.25% Trypsin with EDTA at 37°C. post filtering  the dissociated single cells were sorted for GFP+ at the University of Kentucky Flow Cytometry and Immune Monitoring Core at the Markey Cancer Center. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics.,,tissue:Anterior Segment Mesenchyme|cell line:Tg[foxc1b:GFP]|genotype:AB|developmental stage:72hpf,GSM6734158,GSM6734158: Foxc1b 72hpf; Danio rerio; RNA Seq,GSM6734158 r1,GSM6734158,1,Zebrrafish embryos from the transgenic line Tg[foxc1b:GFP] were collected every 24 hours between 48hpf and 144hpf. The embryos were anesthetized with 3 amino benzoic acid ethyl ester Tricaine. Then  their eyes were dissected and subsequently collected on ice  before being incubated for 8 minutes in 0.25% Trypsin with EDTA at 37°C. post filtering  the dissociated single cells were sorted for GFP+ at the University of Kentucky Flow Cytometry and Immune Monitoring Core at the Markey Cancer Center. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP408138,,loader:fastq load.py,72hpf_B_S1_L001_I1_001.fastq.gz 72hpf_B_S1_L001_R1_001.fastq.gz 72hpf_B_S1_L001_R2_001.fastq.gz,fastq fastq fastq,22062511830.0,118615655.0,GSM6734158 r2,0:8 1:28 2:150,A:5458179709;C:3697017239;G:3917347244;T:4719255263;N:548795,8,28,150,,5458179709,3697017239,3917347244,4719255263,548795,SRX18279946,SRS15772342,SRA1541630,"Famulski, Biology, University of Kentucky","Famulski, Biology, University of Kentucky",1,0.90794,,0.20159,,0.77638,,0.60922,,150,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-11-15,Larval,Larval,Multi-tissue,Multi-system
72203,SRR22306366,SRX18279946,SRS15772342,SRP408138,PRJNA902019,Temporal single cell transcriptome atlas of zebrafish anterior segment development reveals high degree of conservation between the trabecular meshwork and the annular ligament,GSE218068,Transcriptome Analysis,Anterior segment dysgenesis ASD  resulting in vision impairment  stems from maldevelopment of anterior segment AS tissues. Incidence of ASD has been linked to malfunction of periocular mesenchyme cells POM.  POM cells specify into anterior segment mesenchyme ASM cells which colonize and produce AS tissues. In this study we uncover ASM developmental trajectories associated with formation of the AS Overall design: Using a transgenic line of zebrafish that fluorescently labels the ASM throughout development  Tg[foxc1b:GFP]  we isolated GFP+ ASM cells at several developmental timepoints 48 144hpf and performed single cell RNA sequencing,,pubmed:37024546,,Foxc1b 72hpf,GSM6734158,,source name:Anterior Segment Mesenchyme|tissue:Anterior Segment Mesenchyme|cell line:Tg[foxc1b:GFP]|genotype:AB|developmental stage:72hpf,Foxc1b 72hpf,The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v6.0 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: GRCz11 assembly NCBI Genome accession number: GCA 000002035.4 Supplementary files format and content: Tab separated values files and matrix files,Anterior Segment Mesenchyme,,Zebrrafish embryos from the transgenic line Tg[foxc1b:GFP] were collected every 24 hours between 48hpf and 144hpf. The embryos were anesthetized with 3 amino benzoic acid ethyl ester Tricaine. Then  their eyes were dissected and subsequently collected on ice  before being incubated for 8 minutes in 0.25% Trypsin with EDTA at 37°C. post filtering  the dissociated single cells were sorted for GFP+ at the University of Kentucky Flow Cytometry and Immune Monitoring Core at the Markey Cancer Center. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics.,,tissue:Anterior Segment Mesenchyme|cell line:Tg[foxc1b:GFP]|genotype:AB|developmental stage:72hpf,GSM6734158,GSM6734158: Foxc1b 72hpf; Danio rerio; RNA Seq,GSM6734158 r1,GSM6734158,1,Zebrrafish embryos from the transgenic line Tg[foxc1b:GFP] were collected every 24 hours between 48hpf and 144hpf. The embryos were anesthetized with 3 amino benzoic acid ethyl ester Tricaine. Then  their eyes were dissected and subsequently collected on ice  before being incubated for 8 minutes in 0.25% Trypsin with EDTA at 37°C. post filtering  the dissociated single cells were sorted for GFP+ at the University of Kentucky Flow Cytometry and Immune Monitoring Core at the Markey Cancer Center. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP408138,,loader:fastq load.py,72hpf_B_S1_L002_I1_001.fastq.gz 72hpf_B_S1_L002_R1_001.fastq.gz 72hpf_B_S1_L002_R2_001.fastq.gz,fastq fastq fastq,22834981176.0,122768716.0,GSM6734158 r3,0:8 1:28 2:150,A:5640789338;C:3831330746;G:4062820506;T:4879868419;N:498391,8,28,150,,5640789338,3831330746,4062820506,4879868419,498391,SRX18279946,SRS15772342,SRA1541630,"Famulski, Biology, University of Kentucky","Famulski, Biology, University of Kentucky",1,0.90576,,0.20258,,0.77273,,0.60715,,150,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-11-15,Larval,Larval,Multi-tissue,Multi-system
72204,SRR22306367,SRX18279945,SRS15772341,SRP408138,PRJNA902019,Temporal single cell transcriptome atlas of zebrafish anterior segment development reveals high degree of conservation between the trabecular meshwork and the annular ligament,GSE218068,Transcriptome Analysis,Anterior segment dysgenesis ASD  resulting in vision impairment  stems from maldevelopment of anterior segment AS tissues. Incidence of ASD has been linked to malfunction of periocular mesenchyme cells POM.  POM cells specify into anterior segment mesenchyme ASM cells which colonize and produce AS tissues. In this study we uncover ASM developmental trajectories associated with formation of the AS Overall design: Using a transgenic line of zebrafish that fluorescently labels the ASM throughout development  Tg[foxc1b:GFP]  we isolated GFP+ ASM cells at several developmental timepoints 48 144hpf and performed single cell RNA sequencing,,pubmed:37024546,,Foxc1b 48hpf,GSM6734157,,source name:Anterior Segment Mesenchyme|tissue:Anterior Segment Mesenchyme|cell line:Tg[foxc1b:GFP]|genotype:AB|developmental stage:48hpf,Foxc1b 48hpf,The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v6.0 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: GRCz11 assembly NCBI Genome accession number: GCA 000002035.4 Supplementary files format and content: Tab separated values files and matrix files,Anterior Segment Mesenchyme,,Zebrrafish embryos from the transgenic line Tg[foxc1b:GFP] were collected every 24 hours between 48hpf and 144hpf. The embryos were anesthetized with 3 amino benzoic acid ethyl ester Tricaine. Then  their eyes were dissected and subsequently collected on ice  before being incubated for 8 minutes in 0.25% Trypsin with EDTA at 37°C. post filtering  the dissociated single cells were sorted for GFP+ at the University of Kentucky Flow Cytometry and Immune Monitoring Core at the Markey Cancer Center. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics.,,tissue:Anterior Segment Mesenchyme|cell line:Tg[foxc1b:GFP]|genotype:AB|developmental stage:48hpf,GSM6734157,GSM6734157: Foxc1b 48hpf; Danio rerio; RNA Seq,GSM6734157 r1,GSM6734157,1,Zebrrafish embryos from the transgenic line Tg[foxc1b:GFP] were collected every 24 hours between 48hpf and 144hpf. The embryos were anesthetized with 3 amino benzoic acid ethyl ester Tricaine. Then  their eyes were dissected and subsequently collected on ice  before being incubated for 8 minutes in 0.25% Trypsin with EDTA at 37°C. post filtering  the dissociated single cells were sorted for GFP+ at the University of Kentucky Flow Cytometry and Immune Monitoring Core at the Markey Cancer Center. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP408138,,loader:fastq load.py,48hpf_A_S1_L004_I1_001.fastq.gz 48hpf_A_S1_L004_R1_001.fastq.gz 48hpf_A_S1_L004_R2_001.fastq.gz,fastq fastq fastq,20362974376.0,110668339.0,GSM6734157 r1,0:8 1:26 2:150,A:5123945131;C:3326458224;G:3713701708;T:4435572452;N:573335,8,26,150,,5123945131,3326458224,3713701708,4435572452,573335,SRX18279945,SRS15772341,SRA1541630,"Famulski, Biology, University of Kentucky","Famulski, Biology, University of Kentucky",1,0.9134,,0.07314,,0.81379,,0.49083,,150,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-11-15,Hatching,Embryo,Multi-tissue,Multi-system
72205,SRR22306368,SRX18279945,SRS15772341,SRP408138,PRJNA902019,Temporal single cell transcriptome atlas of zebrafish anterior segment development reveals high degree of conservation between the trabecular meshwork and the annular ligament,GSE218068,Transcriptome Analysis,Anterior segment dysgenesis ASD  resulting in vision impairment  stems from maldevelopment of anterior segment AS tissues. Incidence of ASD has been linked to malfunction of periocular mesenchyme cells POM.  POM cells specify into anterior segment mesenchyme ASM cells which colonize and produce AS tissues. In this study we uncover ASM developmental trajectories associated with formation of the AS Overall design: Using a transgenic line of zebrafish that fluorescently labels the ASM throughout development  Tg[foxc1b:GFP]  we isolated GFP+ ASM cells at several developmental timepoints 48 144hpf and performed single cell RNA sequencing,,pubmed:37024546,,Foxc1b 48hpf,GSM6734157,,source name:Anterior Segment Mesenchyme|tissue:Anterior Segment Mesenchyme|cell line:Tg[foxc1b:GFP]|genotype:AB|developmental stage:48hpf,Foxc1b 48hpf,The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v6.0 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: GRCz11 assembly NCBI Genome accession number: GCA 000002035.4 Supplementary files format and content: Tab separated values files and matrix files,Anterior Segment Mesenchyme,,Zebrrafish embryos from the transgenic line Tg[foxc1b:GFP] were collected every 24 hours between 48hpf and 144hpf. The embryos were anesthetized with 3 amino benzoic acid ethyl ester Tricaine. Then  their eyes were dissected and subsequently collected on ice  before being incubated for 8 minutes in 0.25% Trypsin with EDTA at 37°C. post filtering  the dissociated single cells were sorted for GFP+ at the University of Kentucky Flow Cytometry and Immune Monitoring Core at the Markey Cancer Center. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics.,,tissue:Anterior Segment Mesenchyme|cell line:Tg[foxc1b:GFP]|genotype:AB|developmental stage:48hpf,GSM6734157,GSM6734157: Foxc1b 48hpf; Danio rerio; RNA Seq,GSM6734157 r1,GSM6734157,1,Zebrrafish embryos from the transgenic line Tg[foxc1b:GFP] were collected every 24 hours between 48hpf and 144hpf. The embryos were anesthetized with 3 amino benzoic acid ethyl ester Tricaine. Then  their eyes were dissected and subsequently collected on ice  before being incubated for 8 minutes in 0.25% Trypsin with EDTA at 37°C. post filtering  the dissociated single cells were sorted for GFP+ at the University of Kentucky Flow Cytometry and Immune Monitoring Core at the Markey Cancer Center. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP408138,,loader:fastq load.py,48hpf_B_S3_L001_I1_001.fastq.gz 48hpf_B_S3_L001_R1_001.fastq.gz 48hpf_B_S3_L001_R2_001.fastq.gz,fastq fastq fastq,12341386626.0,66351541.0,GSM6734157 r2,0:8 1:28 2:150,A:2795275569;C:2297425042;G:2482925319;T:2376906238;N:198982,8,28,150,,2795275569,2297425042,2482925319,2376906238,198982,SRX18279945,SRS15772341,SRA1541630,"Famulski, Biology, University of Kentucky","Famulski, Biology, University of Kentucky",1,0.95768,,0.08708,,0.81903,,0.51103,,150,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-11-15,Hatching,Embryo,Multi-tissue,Multi-system
72206,SRR22306369,SRX18279945,SRS15772341,SRP408138,PRJNA902019,Temporal single cell transcriptome atlas of zebrafish anterior segment development reveals high degree of conservation between the trabecular meshwork and the annular ligament,GSE218068,Transcriptome Analysis,Anterior segment dysgenesis ASD  resulting in vision impairment  stems from maldevelopment of anterior segment AS tissues. Incidence of ASD has been linked to malfunction of periocular mesenchyme cells POM.  POM cells specify into anterior segment mesenchyme ASM cells which colonize and produce AS tissues. In this study we uncover ASM developmental trajectories associated with formation of the AS Overall design: Using a transgenic line of zebrafish that fluorescently labels the ASM throughout development  Tg[foxc1b:GFP]  we isolated GFP+ ASM cells at several developmental timepoints 48 144hpf and performed single cell RNA sequencing,,pubmed:37024546,,Foxc1b 48hpf,GSM6734157,,source name:Anterior Segment Mesenchyme|tissue:Anterior Segment Mesenchyme|cell line:Tg[foxc1b:GFP]|genotype:AB|developmental stage:48hpf,Foxc1b 48hpf,The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v6.0 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: GRCz11 assembly NCBI Genome accession number: GCA 000002035.4 Supplementary files format and content: Tab separated values files and matrix files,Anterior Segment Mesenchyme,,Zebrrafish embryos from the transgenic line Tg[foxc1b:GFP] were collected every 24 hours between 48hpf and 144hpf. The embryos were anesthetized with 3 amino benzoic acid ethyl ester Tricaine. Then  their eyes were dissected and subsequently collected on ice  before being incubated for 8 minutes in 0.25% Trypsin with EDTA at 37°C. post filtering  the dissociated single cells were sorted for GFP+ at the University of Kentucky Flow Cytometry and Immune Monitoring Core at the Markey Cancer Center. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics.,,tissue:Anterior Segment Mesenchyme|cell line:Tg[foxc1b:GFP]|genotype:AB|developmental stage:48hpf,GSM6734157,GSM6734157: Foxc1b 48hpf; Danio rerio; RNA Seq,GSM6734157 r1,GSM6734157,1,Zebrrafish embryos from the transgenic line Tg[foxc1b:GFP] were collected every 24 hours between 48hpf and 144hpf. The embryos were anesthetized with 3 amino benzoic acid ethyl ester Tricaine. Then  their eyes were dissected and subsequently collected on ice  before being incubated for 8 minutes in 0.25% Trypsin with EDTA at 37°C. post filtering  the dissociated single cells were sorted for GFP+ at the University of Kentucky Flow Cytometry and Immune Monitoring Core at the Markey Cancer Center. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP408138,,loader:fastq load.py,48hpf_B_S3_L002_I1_001.fastq.gz 48hpf_B_S3_L002_R1_001.fastq.gz 48hpf_B_S3_L002_R2_001.fastq.gz,fastq fastq fastq,12292760832.0,66090112.0,GSM6734157 r3,0:8 1:28 2:150,A:2783844388;C:2288795302;G:2473127346;T:2367511149;N:238615,8,28,150,,2783844388,2288795302,2473127346,2367511149,238615,SRX18279945,SRS15772341,SRA1541630,"Famulski, Biology, University of Kentucky","Famulski, Biology, University of Kentucky",1,0.95903,,0.08687,,0.82085,,0.53794,,150,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-11-15,Hatching,Embryo,Multi-tissue,Multi-system
74464,SRR23824308,SRX19646195,SRS17014005,SRP426909,PRJNA943553,Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish],GSE227190,Transcriptome Analysis,Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast  zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury  single cell transcriptomic analyses were performed on the heart  blood  liver  kidney  and pancreatic islets. Overall design: Upon heart cryoinjury  cells from multiple organs heart  liver  pancreas  and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls.,parent bioproject:PRJNA943547,pubmed:39627536,,WKM Ctrl replicate 2,GSM7092959,,source name:Whole Kidney Marrow|tissue:Whole Kidney Marrow|cell type:Whole Kidney Marrow|genotype:wild type|treatment:Heart cryoinjury,WKM Ctrl replicate 2,Demultiplexing  alignment  filtering  and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction  expression value normalization  clustering  cell type annotation and so on were done scater and scran. For more details and the cell type annotation information  see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format.,Whole Kidney Marrow,Heart cryoinjury or untreated,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells  ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C  the pellet was resuspended in 500 l and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell 3’ GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.,Standard zebrafish husbandry protocol.,tissue:Whole Kidney Marrow|cell type:Whole Kidney Marrow|genotype:wild type|treatment:Heart cryoinjury,GSM7092959,GSM7092959: WKM Ctrl replicate 2; Danio rerio; RNA Seq,GSM7092959 r1,GSM7092959,1,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells  ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C  the pellet was resuspended in 500 l and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell three prime GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP426909,,loader:fastq load.py,Ctrl-WKM-2_S6_L001_R1_001.fastq.gz Ctrl-WKM-2_S6_L001_R2_001.fastq.gz,fastq fastq,5194270202.0,44019239.0,GSM7092959 r1,0:28 1:90,A:1398515411;C:1233312154;G:1232180674;T:1330142923;N:119040,28,90,,,1398515411,1233312154,1232180674,1330142923,119040,SRX19646195,SRS17014005,SRA1603354,"Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine","Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine",2,0.00309,0.88688,0.0009,0.07597,0.99419,0.8434,0.37081,0.54861,28,90,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-03-12,Undetermined,Undetermined,Multi-tissue,Multi-system
74465,SRR23824309,SRX19646195,SRS17014005,SRP426909,PRJNA943553,Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish],GSE227190,Transcriptome Analysis,Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast  zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury  single cell transcriptomic analyses were performed on the heart  blood  liver  kidney  and pancreatic islets. Overall design: Upon heart cryoinjury  cells from multiple organs heart  liver  pancreas  and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls.,parent bioproject:PRJNA943547,pubmed:39627536,,WKM Ctrl replicate 2,GSM7092959,,source name:Whole Kidney Marrow|tissue:Whole Kidney Marrow|cell type:Whole Kidney Marrow|genotype:wild type|treatment:Heart cryoinjury,WKM Ctrl replicate 2,Demultiplexing  alignment  filtering  and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction  expression value normalization  clustering  cell type annotation and so on were done scater and scran. For more details and the cell type annotation information  see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format.,Whole Kidney Marrow,Heart cryoinjury or untreated,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells  ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C  the pellet was resuspended in 500 l and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell 3’ GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.,Standard zebrafish husbandry protocol.,tissue:Whole Kidney Marrow|cell type:Whole Kidney Marrow|genotype:wild type|treatment:Heart cryoinjury,GSM7092959,GSM7092959: WKM Ctrl replicate 2; Danio rerio; RNA Seq,GSM7092959 r1,GSM7092959,1,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells  ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C  the pellet was resuspended in 500 l and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell three prime GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP426909,,loader:fastq load.py,Ctrl-WKM-2_S6_L002_R1_001.fastq.gz Ctrl-WKM-2_S6_L002_R2_001.fastq.gz,fastq fastq,5194814064.0,44023848.0,GSM7092959 r2,0:28 1:90,A:1398346625;C:1233448625;G:1232179725;T:1330726706;N:112383,28,90,,,1398346625,1233448625,1232179725,1330726706,112383,SRX19646195,SRS17014005,SRA1603354,"Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine","Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine",2,0.0031,0.8897,0.00099,0.07765,0.99478,0.84094,0.39012,0.55206,28,90,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-03-12,Undetermined,Undetermined,Multi-tissue,Multi-system
74466,SRR23824310,SRX19646195,SRS17014005,SRP426909,PRJNA943553,Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish],GSE227190,Transcriptome Analysis,Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast  zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury  single cell transcriptomic analyses were performed on the heart  blood  liver  kidney  and pancreatic islets. Overall design: Upon heart cryoinjury  cells from multiple organs heart  liver  pancreas  and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls.,parent bioproject:PRJNA943547,pubmed:39627536,,WKM Ctrl replicate 2,GSM7092959,,source name:Whole Kidney Marrow|tissue:Whole Kidney Marrow|cell type:Whole Kidney Marrow|genotype:wild type|treatment:Heart cryoinjury,WKM Ctrl replicate 2,Demultiplexing  alignment  filtering  and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction  expression value normalization  clustering  cell type annotation and so on were done scater and scran. For more details and the cell type annotation information  see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format.,Whole Kidney Marrow,Heart cryoinjury or untreated,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells  ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C  the pellet was resuspended in 500 l and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell 3’ GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.,Standard zebrafish husbandry protocol.,tissue:Whole Kidney Marrow|cell type:Whole Kidney Marrow|genotype:wild type|treatment:Heart cryoinjury,GSM7092959,GSM7092959: WKM Ctrl replicate 2; Danio rerio; RNA Seq,GSM7092959 r1,GSM7092959,1,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells  ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C  the pellet was resuspended in 500 l and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell three prime GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP426909,,loader:fastq load.py,Ctrl-WKM-2_S6_L003_R2_001.fastq.gz Ctrl-WKM-2_S6_L003_R1_001.fastq.gz,fastq fastq,5266248786.0,44629227.0,GSM7092959 r3,0:28 1:90,A:1416990042;C:1250859074;G:1249886002;T:1348408111;N:105557,28,90,,,1416990042,1250859074,1249886002,1348408111,105557,SRX19646195,SRS17014005,SRA1603354,"Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine","Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine",2,0.00326,0.8894,0.00114,0.07686,0.99427,0.84214,0.42716,0.54905,28,90,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-03-12,Undetermined,Undetermined,Multi-tissue,Multi-system
74467,SRR23824311,SRX19646195,SRS17014005,SRP426909,PRJNA943553,Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish],GSE227190,Transcriptome Analysis,Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast  zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury  single cell transcriptomic analyses were performed on the heart  blood  liver  kidney  and pancreatic islets. Overall design: Upon heart cryoinjury  cells from multiple organs heart  liver  pancreas  and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls.,parent bioproject:PRJNA943547,pubmed:39627536,,WKM Ctrl replicate 2,GSM7092959,,source name:Whole Kidney Marrow|tissue:Whole Kidney Marrow|cell type:Whole Kidney Marrow|genotype:wild type|treatment:Heart cryoinjury,WKM Ctrl replicate 2,Demultiplexing  alignment  filtering  and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction  expression value normalization  clustering  cell type annotation and so on were done scater and scran. For more details and the cell type annotation information  see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format.,Whole Kidney Marrow,Heart cryoinjury or untreated,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells  ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C  the pellet was resuspended in 500 l and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell 3’ GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.,Standard zebrafish husbandry protocol.,tissue:Whole Kidney Marrow|cell type:Whole Kidney Marrow|genotype:wild type|treatment:Heart cryoinjury,GSM7092959,GSM7092959: WKM Ctrl replicate 2; Danio rerio; RNA Seq,GSM7092959 r1,GSM7092959,1,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells  ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C  the pellet was resuspended in 500 l and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell three prime GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP426909,,loader:fastq load.py,Ctrl-WKM-2_S6_L004_R1_001.fastq.gz Ctrl-WKM-2_S6_L004_R2_001.fastq.gz,fastq fastq,5179146850.0,43891075.0,GSM7092959 r4,0:28 1:90,A:1394750319;C:1229159365;G:1227969525;T:1327168248;N:99393,28,90,,,1394750319,1229159365,1227969525,1327168248,99393,SRX19646195,SRS17014005,SRA1603354,"Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine","Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine",2,0.00344,0.88836,0.00108,0.07651,0.99385,0.84248,0.39035,0.55457,28,90,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-03-12,Undetermined,Undetermined,Multi-tissue,Multi-system
74468,SRR23824312,SRX19646194,SRS17014004,SRP426909,PRJNA943553,Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish],GSE227190,Transcriptome Analysis,Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast  zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury  single cell transcriptomic analyses were performed on the heart  blood  liver  kidney  and pancreatic islets. Overall design: Upon heart cryoinjury  cells from multiple organs heart  liver  pancreas  and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls.,parent bioproject:PRJNA943547,pubmed:39627536,,WKM Ctrl replicate 1,GSM7092958,,source name:Whole Kidney Marrow|tissue:Whole Kidney Marrow|cell type:Whole Kidney Marrow|genotype:wild type|treatment:Heart cryoinjury,WKM Ctrl replicate 1,Demultiplexing  alignment  filtering  and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction  expression value normalization  clustering  cell type annotation and so on were done scater and scran. For more details and the cell type annotation information  see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format.,Whole Kidney Marrow,Heart cryoinjury or untreated,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells  ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C  the pellet was resuspended in 500 l and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell 3’ GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.,Standard zebrafish husbandry protocol.,tissue:Whole Kidney Marrow|cell type:Whole Kidney Marrow|genotype:wild type|treatment:Heart cryoinjury,GSM7092958,GSM7092958: WKM Ctrl replicate 1; Danio rerio; RNA Seq,GSM7092958 r1,GSM7092958,1,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells  ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C  the pellet was resuspended in 500 l and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell three prime GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP426909,,loader:fastq load.py,Ctrl-WKM-1_S2_L001_R1_001.fastq.gz Ctrl-WKM-1_S2_L001_R2_001.fastq.gz,fastq fastq,5724434408.0,48512156.0,GSM7092958 r1,0:28 1:90,A:1567228637;C:1329088014;G:1338348271;T:1489638044;N:131442,28,90,,,1567228637,1329088014,1338348271,1489638044,131442,SRX19646194,SRS17014004,SRA1603354,"Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine","Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine",2,0.0034,0.89852,0.00097,0.08358,0.99387,0.82836,0.39872,0.48691,28,90,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-03-12,Undetermined,Undetermined,Multi-tissue,Multi-system
74469,SRR23824313,SRX19646194,SRS17014004,SRP426909,PRJNA943553,Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish],GSE227190,Transcriptome Analysis,Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast  zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury  single cell transcriptomic analyses were performed on the heart  blood  liver  kidney  and pancreatic islets. Overall design: Upon heart cryoinjury  cells from multiple organs heart  liver  pancreas  and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls.,parent bioproject:PRJNA943547,pubmed:39627536,,WKM Ctrl replicate 1,GSM7092958,,source name:Whole Kidney Marrow|tissue:Whole Kidney Marrow|cell type:Whole Kidney Marrow|genotype:wild type|treatment:Heart cryoinjury,WKM Ctrl replicate 1,Demultiplexing  alignment  filtering  and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction  expression value normalization  clustering  cell type annotation and so on were done scater and scran. For more details and the cell type annotation information  see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format.,Whole Kidney Marrow,Heart cryoinjury or untreated,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells  ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C  the pellet was resuspended in 500 l and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell 3’ GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.,Standard zebrafish husbandry protocol.,tissue:Whole Kidney Marrow|cell type:Whole Kidney Marrow|genotype:wild type|treatment:Heart cryoinjury,GSM7092958,GSM7092958: WKM Ctrl replicate 1; Danio rerio; RNA Seq,GSM7092958 r1,GSM7092958,1,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells  ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C  the pellet was resuspended in 500 l and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell three prime GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP426909,,loader:fastq load.py,Ctrl-WKM-1_S2_L002_R1_001.fastq.gz Ctrl-WKM-1_S2_L002_R2_001.fastq.gz,fastq fastq,5722747716.0,48497862.0,GSM7092958 r2,0:28 1:90,A:1566186287;C:1328568122;G:1337682111;T:1490187432;N:123764,28,90,,,1566186287,1328568122,1337682111,1490187432,123764,SRX19646194,SRS17014004,SRA1603354,"Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine","Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine",2,0.00351,0.89791,0.00115,0.08308,0.99322,0.82822,0.38209,0.55877,28,90,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-03-12,Undetermined,Undetermined,Multi-tissue,Multi-system
74470,SRR23824314,SRX19646194,SRS17014004,SRP426909,PRJNA943553,Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish],GSE227190,Transcriptome Analysis,Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast  zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury  single cell transcriptomic analyses were performed on the heart  blood  liver  kidney  and pancreatic islets. Overall design: Upon heart cryoinjury  cells from multiple organs heart  liver  pancreas  and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls.,parent bioproject:PRJNA943547,pubmed:39627536,,WKM Ctrl replicate 1,GSM7092958,,source name:Whole Kidney Marrow|tissue:Whole Kidney Marrow|cell type:Whole Kidney Marrow|genotype:wild type|treatment:Heart cryoinjury,WKM Ctrl replicate 1,Demultiplexing  alignment  filtering  and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction  expression value normalization  clustering  cell type annotation and so on were done scater and scran. For more details and the cell type annotation information  see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format.,Whole Kidney Marrow,Heart cryoinjury or untreated,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells  ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C  the pellet was resuspended in 500 l and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell 3’ GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.,Standard zebrafish husbandry protocol.,tissue:Whole Kidney Marrow|cell type:Whole Kidney Marrow|genotype:wild type|treatment:Heart cryoinjury,GSM7092958,GSM7092958: WKM Ctrl replicate 1; Danio rerio; RNA Seq,GSM7092958 r1,GSM7092958,1,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells  ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C  the pellet was resuspended in 500 l and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell three prime GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP426909,,loader:fastq load.py,Ctrl-WKM-1_S2_L003_R1_001.fastq.gz Ctrl-WKM-1_S2_L003_R2_001.fastq.gz,fastq fastq,5805211662.0,49196709.0,GSM7092958 r3,0:28 1:90,A:1588459908;C:1348306329;G:1357849856;T:1510477621;N:117948,28,90,,,1588459908,1348306329,1357849856,1510477621,117948,SRX19646194,SRS17014004,SRA1603354,"Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine","Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine",2,0.00339,0.89829,0.00109,0.08199,0.99373,0.82836,0.36629,0.48567,28,90,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-03-12,Undetermined,Undetermined,Multi-tissue,Multi-system
74471,SRR23824315,SRX19646194,SRS17014004,SRP426909,PRJNA943553,Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish],GSE227190,Transcriptome Analysis,Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast  zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury  single cell transcriptomic analyses were performed on the heart  blood  liver  kidney  and pancreatic islets. Overall design: Upon heart cryoinjury  cells from multiple organs heart  liver  pancreas  and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls.,parent bioproject:PRJNA943547,pubmed:39627536,,WKM Ctrl replicate 1,GSM7092958,,source name:Whole Kidney Marrow|tissue:Whole Kidney Marrow|cell type:Whole Kidney Marrow|genotype:wild type|treatment:Heart cryoinjury,WKM Ctrl replicate 1,Demultiplexing  alignment  filtering  and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction  expression value normalization  clustering  cell type annotation and so on were done scater and scran. For more details and the cell type annotation information  see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format.,Whole Kidney Marrow,Heart cryoinjury or untreated,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells  ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C  the pellet was resuspended in 500 l and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell 3’ GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.,Standard zebrafish husbandry protocol.,tissue:Whole Kidney Marrow|cell type:Whole Kidney Marrow|genotype:wild type|treatment:Heart cryoinjury,GSM7092958,GSM7092958: WKM Ctrl replicate 1; Danio rerio; RNA Seq,GSM7092958 r1,GSM7092958,1,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells  ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C  the pellet was resuspended in 500 l and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell three prime GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP426909,,loader:fastq load.py,Ctrl-WKM-1_S2_L004_R1_001.fastq.gz Ctrl-WKM-1_S2_L004_R2_001.fastq.gz,fastq fastq,5706596938.0,48360991.0,GSM7092958 r4,0:28 1:90,A:1562421245;C:1324310664;G:1333276899;T:1486479848;N:108282,28,90,,,1562421245,1324310664,1333276899,1486479848,108282,SRX19646194,SRS17014004,SRA1603354,"Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine","Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine",2,0.00325,0.89893,0.001,0.08305,0.99409,0.82771,0.38551,0.48469,28,90,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-03-12,Undetermined,Undetermined,Multi-tissue,Multi-system
74496,SRR23824340,SRX19646187,SRS17013997,SRP426909,PRJNA943553,Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish],GSE227190,Transcriptome Analysis,Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast  zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury  single cell transcriptomic analyses were performed on the heart  blood  liver  kidney  and pancreatic islets. Overall design: Upon heart cryoinjury  cells from multiple organs heart  liver  pancreas  and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls.,parent bioproject:PRJNA943547,pubmed:39627536,,WKM 7 dpi replicate 2,GSM7092951,,source name:Whole Kidney Marrow|tissue:Whole Kidney Marrow|cell type:Whole Kidney Marrow|genotype:wild type|treatment:Heart cryoinjury,WKM 7 dpi replicate 2,Demultiplexing  alignment  filtering  and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction  expression value normalization  clustering  cell type annotation and so on were done scater and scran. For more details and the cell type annotation information  see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format.,Whole Kidney Marrow,Heart cryoinjury or untreated,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells  ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C  the pellet was resuspended in 500 l and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell 3’ GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.,Standard zebrafish husbandry protocol.,tissue:Whole Kidney Marrow|cell type:Whole Kidney Marrow|genotype:wild type|treatment:Heart cryoinjury,GSM7092951,GSM7092951: WKM 7 dpi replicate 2; Danio rerio; RNA Seq,GSM7092951 r1,GSM7092951,1,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells  ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C  the pellet was resuspended in 500 l and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell three prime GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP426909,,loader:fastq load.py,7dpi-WKM-2_S22_L001_R1_001.fastq.gz 7dpi-WKM-2_S22_L001_R2_001.fastq.gz,fastq fastq,5304844816.0,44956312.0,GSM7092951 r1,0:28 1:90,A:1425725106;C:1263648972;G:1258220580;T:1357129924;N:120234,28,90,,,1425725106,1263648972,1258220580,1357129924,120234,SRX19646187,SRS17013997,SRA1603354,"Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine","Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine",2,0.00449,0.86714,0.00129,0.06514,0.99377,0.84303,0.43042,0.57254,28,90,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-03-12,Undetermined,Undetermined,Multi-tissue,Multi-system
74497,SRR23824341,SRX19646187,SRS17013997,SRP426909,PRJNA943553,Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish],GSE227190,Transcriptome Analysis,Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast  zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury  single cell transcriptomic analyses were performed on the heart  blood  liver  kidney  and pancreatic islets. Overall design: Upon heart cryoinjury  cells from multiple organs heart  liver  pancreas  and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls.,parent bioproject:PRJNA943547,pubmed:39627536,,WKM 7 dpi replicate 2,GSM7092951,,source name:Whole Kidney Marrow|tissue:Whole Kidney Marrow|cell type:Whole Kidney Marrow|genotype:wild type|treatment:Heart cryoinjury,WKM 7 dpi replicate 2,Demultiplexing  alignment  filtering  and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction  expression value normalization  clustering  cell type annotation and so on were done scater and scran. For more details and the cell type annotation information  see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format.,Whole Kidney Marrow,Heart cryoinjury or untreated,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells  ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C  the pellet was resuspended in 500 l and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell 3’ GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.,Standard zebrafish husbandry protocol.,tissue:Whole Kidney Marrow|cell type:Whole Kidney Marrow|genotype:wild type|treatment:Heart cryoinjury,GSM7092951,GSM7092951: WKM 7 dpi replicate 2; Danio rerio; RNA Seq,GSM7092951 r1,GSM7092951,1,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells  ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C  the pellet was resuspended in 500 l and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell three prime GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP426909,,loader:fastq load.py,7dpi-WKM-2_S22_L002_R1_001.fastq.gz 7dpi-WKM-2_S22_L002_R2_001.fastq.gz,fastq fastq,5239083180.0,44399010.0,GSM7092951 r2,0:28 1:90,A:1407415782;C:1248027048;G:1242616066;T:1340911648;N:112636,28,90,,,1407415782,1248027048,1242616066,1340911648,112636,SRX19646187,SRS17013997,SRA1603354,"Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine","Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine",2,0.00481,0.86765,0.00132,0.06608,0.99273,0.84187,0.43387,0.56786,28,90,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-03-12,Undetermined,Undetermined,Multi-tissue,Multi-system
74498,SRR23824354,SRX19646187,SRS17013997,SRP426909,PRJNA943553,Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish],GSE227190,Transcriptome Analysis,Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast  zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury  single cell transcriptomic analyses were performed on the heart  blood  liver  kidney  and pancreatic islets. Overall design: Upon heart cryoinjury  cells from multiple organs heart  liver  pancreas  and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls.,parent bioproject:PRJNA943547,pubmed:39627536,,WKM 7 dpi replicate 2,GSM7092951,,source name:Whole Kidney Marrow|tissue:Whole Kidney Marrow|cell type:Whole Kidney Marrow|genotype:wild type|treatment:Heart cryoinjury,WKM 7 dpi replicate 2,Demultiplexing  alignment  filtering  and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction  expression value normalization  clustering  cell type annotation and so on were done scater and scran. For more details and the cell type annotation information  see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format.,Whole Kidney Marrow,Heart cryoinjury or untreated,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells  ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C  the pellet was resuspended in 500 l and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell 3’ GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.,Standard zebrafish husbandry protocol.,tissue:Whole Kidney Marrow|cell type:Whole Kidney Marrow|genotype:wild type|treatment:Heart cryoinjury,GSM7092951,GSM7092951: WKM 7 dpi replicate 2; Danio rerio; RNA Seq,GSM7092951 r1,GSM7092951,1,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells  ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C  the pellet was resuspended in 500 l and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell three prime GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP426909,,loader:fastq load.py,7dpi-WKM-2_S22_L003_R1_001.fastq.gz 7dpi-WKM-2_S22_L003_R2_001.fastq.gz,fastq fastq,5391479826.0,45690507.0,GSM7092951 r3,0:28 1:90,A:1448063662;C:1284822701;G:1279372271;T:1379111804;N:109388,28,90,,,1448063662,1284822701,1279372271,1379111804,109388,SRX19646187,SRS17013997,SRA1603354,"Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine","Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine",2,0.00459,0.86895,0.00137,0.06695,0.99356,0.84488,0.42512,0.57663,28,90,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-03-12,Undetermined,Undetermined,Multi-tissue,Multi-system
74499,SRR23824355,SRX19646187,SRS17013997,SRP426909,PRJNA943553,Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish],GSE227190,Transcriptome Analysis,Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast  zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury  single cell transcriptomic analyses were performed on the heart  blood  liver  kidney  and pancreatic islets. Overall design: Upon heart cryoinjury  cells from multiple organs heart  liver  pancreas  and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls.,parent bioproject:PRJNA943547,pubmed:39627536,,WKM 7 dpi replicate 2,GSM7092951,,source name:Whole Kidney Marrow|tissue:Whole Kidney Marrow|cell type:Whole Kidney Marrow|genotype:wild type|treatment:Heart cryoinjury,WKM 7 dpi replicate 2,Demultiplexing  alignment  filtering  and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction  expression value normalization  clustering  cell type annotation and so on were done scater and scran. For more details and the cell type annotation information  see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format.,Whole Kidney Marrow,Heart cryoinjury or untreated,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells  ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C  the pellet was resuspended in 500 l and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell 3’ GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.,Standard zebrafish husbandry protocol.,tissue:Whole Kidney Marrow|cell type:Whole Kidney Marrow|genotype:wild type|treatment:Heart cryoinjury,GSM7092951,GSM7092951: WKM 7 dpi replicate 2; Danio rerio; RNA Seq,GSM7092951 r1,GSM7092951,1,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells  ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C  the pellet was resuspended in 500 l and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell three prime GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP426909,,loader:fastq load.py,7dpi-WKM-2_S22_L004_R1_001.fastq.gz 7dpi-WKM-2_S22_L004_R2_001.fastq.gz,fastq fastq,5248727674.0,44480743.0,GSM7092951 r4,0:28 1:90,A:1410656147;C:1249808557;G:1244236491;T:1343925912;N:100567,28,90,,,1410656147,1249808557,1244236491,1343925912,100567,SRX19646187,SRS17013997,SRA1603354,"Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine","Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine",2,0.00445,0.86738,0.0013,0.06588,0.99297,0.8423,0.42409,0.57081,28,90,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-03-12,Undetermined,Undetermined,Multi-tissue,Multi-system
74500,SRR23824342,SRX19646186,SRS17013996,SRP426909,PRJNA943553,Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish],GSE227190,Transcriptome Analysis,Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast  zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury  single cell transcriptomic analyses were performed on the heart  blood  liver  kidney  and pancreatic islets. Overall design: Upon heart cryoinjury  cells from multiple organs heart  liver  pancreas  and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls.,parent bioproject:PRJNA943547,pubmed:39627536,,WKM 7 dpi replicate 1,GSM7092950,,source name:Whole Kidney Marrow|tissue:Whole Kidney Marrow|cell type:Whole Kidney Marrow|genotype:wild type|treatment:Heart cryoinjury,WKM 7 dpi replicate 1,Demultiplexing  alignment  filtering  and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction  expression value normalization  clustering  cell type annotation and so on were done scater and scran. For more details and the cell type annotation information  see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format.,Whole Kidney Marrow,Heart cryoinjury or untreated,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells  ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C  the pellet was resuspended in 500 l and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell 3’ GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.,Standard zebrafish husbandry protocol.,tissue:Whole Kidney Marrow|cell type:Whole Kidney Marrow|genotype:wild type|treatment:Heart cryoinjury,GSM7092950,GSM7092950: WKM 7 dpi replicate 1; Danio rerio; RNA Seq,GSM7092950 r1,GSM7092950,1,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells  ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C  the pellet was resuspended in 500 l and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell three prime GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP426909,,loader:fastq load.py,7dpi-WKM-1_S18_L001_R2_001.fastq.gz 7dpi-WKM-1_S18_L001_R1_001.fastq.gz,fastq fastq,4614142082.0,39102899.0,GSM7092950 r1,0:28 1:90,A:1221539435;C:1116323438;G:1093348138;T:1182827232;N:103839,28,90,,,1221539435,1116323438,1093348138,1182827232,103839,SRX19646186,SRS17013996,SRA1603354,"Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine","Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine",2,0.00406,0.85345,0.00122,0.05709,0.99395,0.84804,0.43589,0.58021,28,90,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-03-12,Undetermined,Undetermined,Multi-tissue,Multi-system
74501,SRR23824343,SRX19646186,SRS17013996,SRP426909,PRJNA943553,Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish],GSE227190,Transcriptome Analysis,Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast  zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury  single cell transcriptomic analyses were performed on the heart  blood  liver  kidney  and pancreatic islets. Overall design: Upon heart cryoinjury  cells from multiple organs heart  liver  pancreas  and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls.,parent bioproject:PRJNA943547,pubmed:39627536,,WKM 7 dpi replicate 1,GSM7092950,,source name:Whole Kidney Marrow|tissue:Whole Kidney Marrow|cell type:Whole Kidney Marrow|genotype:wild type|treatment:Heart cryoinjury,WKM 7 dpi replicate 1,Demultiplexing  alignment  filtering  and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction  expression value normalization  clustering  cell type annotation and so on were done scater and scran. For more details and the cell type annotation information  see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format.,Whole Kidney Marrow,Heart cryoinjury or untreated,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells  ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C  the pellet was resuspended in 500 l and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell 3’ GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.,Standard zebrafish husbandry protocol.,tissue:Whole Kidney Marrow|cell type:Whole Kidney Marrow|genotype:wild type|treatment:Heart cryoinjury,GSM7092950,GSM7092950: WKM 7 dpi replicate 1; Danio rerio; RNA Seq,GSM7092950 r1,GSM7092950,1,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells  ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C  the pellet was resuspended in 500 l and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell three prime GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP426909,,loader:fastq load.py,7dpi-WKM-1_S18_L002_R1_001.fastq.gz 7dpi-WKM-1_S18_L002_R2_001.fastq.gz,fastq fastq,4593976590.0,38932005.0,GSM7092950 r2,0:28 1:90,A:1215610872;C:1111440315;G:1088719031;T:1178107008;N:99364,28,90,,,1215610872,1111440315,1088719031,1178107008,99364,SRX19646186,SRS17013996,SRA1603354,"Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine","Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine",2,0.00457,0.85489,0.00152,0.0572,0.99348,0.84893,0.35025,0.57809,28,90,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-03-12,Undetermined,Undetermined,Multi-tissue,Multi-system
74502,SRR23824352,SRX19646186,SRS17013996,SRP426909,PRJNA943553,Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish],GSE227190,Transcriptome Analysis,Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast  zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury  single cell transcriptomic analyses were performed on the heart  blood  liver  kidney  and pancreatic islets. Overall design: Upon heart cryoinjury  cells from multiple organs heart  liver  pancreas  and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls.,parent bioproject:PRJNA943547,pubmed:39627536,,WKM 7 dpi replicate 1,GSM7092950,,source name:Whole Kidney Marrow|tissue:Whole Kidney Marrow|cell type:Whole Kidney Marrow|genotype:wild type|treatment:Heart cryoinjury,WKM 7 dpi replicate 1,Demultiplexing  alignment  filtering  and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction  expression value normalization  clustering  cell type annotation and so on were done scater and scran. For more details and the cell type annotation information  see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format.,Whole Kidney Marrow,Heart cryoinjury or untreated,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells  ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C  the pellet was resuspended in 500 l and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell 3’ GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.,Standard zebrafish husbandry protocol.,tissue:Whole Kidney Marrow|cell type:Whole Kidney Marrow|genotype:wild type|treatment:Heart cryoinjury,GSM7092950,GSM7092950: WKM 7 dpi replicate 1; Danio rerio; RNA Seq,GSM7092950 r1,GSM7092950,1,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells  ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C  the pellet was resuspended in 500 l and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell three prime GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP426909,,loader:fastq load.py,7dpi-WKM-1_S18_L003_R1_001.fastq.gz 7dpi-WKM-1_S18_L003_R2_001.fastq.gz,fastq fastq,4683123702.0,39687489.0,GSM7092950 r3,0:28 1:90,A:1239167418;C:1133378913;G:1110025813;T:1200456657;N:94901,28,90,,,1239167418,1133378913,1110025813,1200456657,94901,SRX19646186,SRS17013996,SRA1603354,"Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine","Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine",2,0.00461,0.85316,0.00136,0.05779,0.99342,0.84879,0.45151,0.57995,28,90,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-03-12,Undetermined,Undetermined,Multi-tissue,Multi-system
74503,SRR23824353,SRX19646186,SRS17013996,SRP426909,PRJNA943553,Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish],GSE227190,Transcriptome Analysis,Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast  zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury  single cell transcriptomic analyses were performed on the heart  blood  liver  kidney  and pancreatic islets. Overall design: Upon heart cryoinjury  cells from multiple organs heart  liver  pancreas  and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls.,parent bioproject:PRJNA943547,pubmed:39627536,,WKM 7 dpi replicate 1,GSM7092950,,source name:Whole Kidney Marrow|tissue:Whole Kidney Marrow|cell type:Whole Kidney Marrow|genotype:wild type|treatment:Heart cryoinjury,WKM 7 dpi replicate 1,Demultiplexing  alignment  filtering  and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction  expression value normalization  clustering  cell type annotation and so on were done scater and scran. For more details and the cell type annotation information  see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format.,Whole Kidney Marrow,Heart cryoinjury or untreated,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells  ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C  the pellet was resuspended in 500 l and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell 3’ GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.,Standard zebrafish husbandry protocol.,tissue:Whole Kidney Marrow|cell type:Whole Kidney Marrow|genotype:wild type|treatment:Heart cryoinjury,GSM7092950,GSM7092950: WKM 7 dpi replicate 1; Danio rerio; RNA Seq,GSM7092950 r1,GSM7092950,1,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells  ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C  the pellet was resuspended in 500 l and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell three prime GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP426909,,loader:fastq load.py,7dpi-WKM-1_S18_L004_R2_001.fastq.gz 7dpi-WKM-1_S18_L004_R1_001.fastq.gz,fastq fastq,4592030652.0,38915514.0,GSM7092950 r4,0:28 1:90,A:1215524167;C:1110582945;G:1087749475;T:1178087315;N:86750,28,90,,,1215524167,1110582945,1087749475,1178087315,86750,SRX19646186,SRS17013996,SRA1603354,"Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine","Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine",2,0.00436,0.85419,0.00129,0.05769,0.99373,0.84774,0.37268,0.58314,28,90,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-03-12,Undetermined,Undetermined,Multi-tissue,Multi-system
74528,SRR23824372,SRX19646179,SRS17013989,SRP426909,PRJNA943553,Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish],GSE227190,Transcriptome Analysis,Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast  zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury  single cell transcriptomic analyses were performed on the heart  blood  liver  kidney  and pancreatic islets. Overall design: Upon heart cryoinjury  cells from multiple organs heart  liver  pancreas  and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls.,parent bioproject:PRJNA943547,pubmed:39627536,,WKM 1 dpi replicate 2,GSM7092943,,source name:Whole Kidney Marrow|tissue:Whole Kidney Marrow|cell type:Whole Kidney Marrow|genotype:wild type|treatment:Heart cryoinjury,WKM 1 dpi replicate 2,Demultiplexing  alignment  filtering  and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction  expression value normalization  clustering  cell type annotation and so on were done scater and scran. For more details and the cell type annotation information  see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format.,Whole Kidney Marrow,Heart cryoinjury or untreated,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells  ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C  the pellet was resuspended in 500 l and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell 3’ GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.,Standard zebrafish husbandry protocol.,tissue:Whole Kidney Marrow|cell type:Whole Kidney Marrow|genotype:wild type|treatment:Heart cryoinjury,GSM7092943,GSM7092943: WKM 1 dpi replicate 2; Danio rerio; RNA Seq,GSM7092943 r1,GSM7092943,1,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells  ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C  the pellet was resuspended in 500 l and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell three prime GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP426909,,loader:fastq load.py,1dpi-WKM-2_S14_L001_R1_001.fastq.gz 1dpi-WKM-2_S14_L001_R2_001.fastq.gz,fastq fastq,4503800990.0,38167805.0,GSM7092943 r1,0:28 1:90,A:1248352720;C:1030070974;G:1053667995;T:1171606946;N:102355,28,90,,,1248352720,1030070974,1053667995,1171606946,102355,SRX19646179,SRS17013989,SRA1603354,"Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine","Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine",2,0.00404,0.88157,0.00136,0.10856,0.99316,0.81615,0.4,0.55334,28,90,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-03-12,Undetermined,Undetermined,Multi-tissue,Multi-system
74529,SRR23824373,SRX19646179,SRS17013989,SRP426909,PRJNA943553,Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish],GSE227190,Transcriptome Analysis,Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast  zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury  single cell transcriptomic analyses were performed on the heart  blood  liver  kidney  and pancreatic islets. Overall design: Upon heart cryoinjury  cells from multiple organs heart  liver  pancreas  and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls.,parent bioproject:PRJNA943547,pubmed:39627536,,WKM 1 dpi replicate 2,GSM7092943,,source name:Whole Kidney Marrow|tissue:Whole Kidney Marrow|cell type:Whole Kidney Marrow|genotype:wild type|treatment:Heart cryoinjury,WKM 1 dpi replicate 2,Demultiplexing  alignment  filtering  and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction  expression value normalization  clustering  cell type annotation and so on were done scater and scran. For more details and the cell type annotation information  see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format.,Whole Kidney Marrow,Heart cryoinjury or untreated,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells  ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C  the pellet was resuspended in 500 l and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell 3’ GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.,Standard zebrafish husbandry protocol.,tissue:Whole Kidney Marrow|cell type:Whole Kidney Marrow|genotype:wild type|treatment:Heart cryoinjury,GSM7092943,GSM7092943: WKM 1 dpi replicate 2; Danio rerio; RNA Seq,GSM7092943 r1,GSM7092943,1,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells  ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C  the pellet was resuspended in 500 l and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell three prime GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP426909,,loader:fastq load.py,1dpi-WKM-2_S14_L002_R1_001.fastq.gz 1dpi-WKM-2_S14_L002_R2_001.fastq.gz,fastq fastq,4531566744.0,38403108.0,GSM7092943 r2,0:28 1:90,A:1255485872;C:1036592881;G:1060058376;T:1179332155;N:97460,28,90,,,1255485872,1036592881,1060058376,1179332155,97460,SRX19646179,SRS17013989,SRA1603354,"Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine","Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine",2,0.00412,0.88028,0.00143,0.10789,0.99269,0.81779,0.43243,0.55729,28,90,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-03-12,Undetermined,Undetermined,Multi-tissue,Multi-system
74530,SRR23824386,SRX19646179,SRS17013989,SRP426909,PRJNA943553,Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish],GSE227190,Transcriptome Analysis,Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast  zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury  single cell transcriptomic analyses were performed on the heart  blood  liver  kidney  and pancreatic islets. Overall design: Upon heart cryoinjury  cells from multiple organs heart  liver  pancreas  and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls.,parent bioproject:PRJNA943547,pubmed:39627536,,WKM 1 dpi replicate 2,GSM7092943,,source name:Whole Kidney Marrow|tissue:Whole Kidney Marrow|cell type:Whole Kidney Marrow|genotype:wild type|treatment:Heart cryoinjury,WKM 1 dpi replicate 2,Demultiplexing  alignment  filtering  and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction  expression value normalization  clustering  cell type annotation and so on were done scater and scran. For more details and the cell type annotation information  see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format.,Whole Kidney Marrow,Heart cryoinjury or untreated,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells  ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C  the pellet was resuspended in 500 l and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell 3’ GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.,Standard zebrafish husbandry protocol.,tissue:Whole Kidney Marrow|cell type:Whole Kidney Marrow|genotype:wild type|treatment:Heart cryoinjury,GSM7092943,GSM7092943: WKM 1 dpi replicate 2; Danio rerio; RNA Seq,GSM7092943 r1,GSM7092943,1,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells  ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C  the pellet was resuspended in 500 l and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell three prime GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP426909,,loader:fastq load.py,1dpi-WKM-2_S14_L003_R1_001.fastq.gz 1dpi-WKM-2_S14_L003_R2_001.fastq.gz,fastq fastq,4578982212.0,38804934.0,GSM7092943 r3,0:28 1:90,A:1268278355;C:1047870699;G:1071633982;T:1191106598;N:92578,28,90,,,1268278355,1047870699,1071633982,1191106598,92578,SRX19646179,SRS17013989,SRA1603354,"Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine","Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine",2,0.00402,0.88112,0.00132,0.10858,0.99273,0.81744,0.37667,0.55459,28,90,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-03-12,Undetermined,Undetermined,Multi-tissue,Multi-system
74531,SRR23824387,SRX19646179,SRS17013989,SRP426909,PRJNA943553,Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish],GSE227190,Transcriptome Analysis,Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast  zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury  single cell transcriptomic analyses were performed on the heart  blood  liver  kidney  and pancreatic islets. Overall design: Upon heart cryoinjury  cells from multiple organs heart  liver  pancreas  and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls.,parent bioproject:PRJNA943547,pubmed:39627536,,WKM 1 dpi replicate 2,GSM7092943,,source name:Whole Kidney Marrow|tissue:Whole Kidney Marrow|cell type:Whole Kidney Marrow|genotype:wild type|treatment:Heart cryoinjury,WKM 1 dpi replicate 2,Demultiplexing  alignment  filtering  and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction  expression value normalization  clustering  cell type annotation and so on were done scater and scran. For more details and the cell type annotation information  see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format.,Whole Kidney Marrow,Heart cryoinjury or untreated,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells  ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C  the pellet was resuspended in 500 l and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell 3’ GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.,Standard zebrafish husbandry protocol.,tissue:Whole Kidney Marrow|cell type:Whole Kidney Marrow|genotype:wild type|treatment:Heart cryoinjury,GSM7092943,GSM7092943: WKM 1 dpi replicate 2; Danio rerio; RNA Seq,GSM7092943 r1,GSM7092943,1,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells  ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C  the pellet was resuspended in 500 l and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell three prime GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP426909,,loader:fastq load.py,1dpi-WKM-2_S14_L004_R1_001.fastq.gz 1dpi-WKM-2_S14_L004_R2_001.fastq.gz,fastq fastq,4501130650.0,38145175.0,GSM7092943 r4,0:28 1:90,A:1247734516;C:1029108415;G:1052304350;T:1171897826;N:85543,28,90,,,1247734516,1029108415,1052304350,1171897826,85543,SRX19646179,SRS17013989,SRA1603354,"Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine","Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine",2,0.00387,0.88277,0.00131,0.10996,0.99306,0.81665,0.38742,0.55963,28,90,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-03-12,Undetermined,Undetermined,Multi-tissue,Multi-system
74536,SRR23824376,SRX19646177,SRS17013987,SRP426909,PRJNA943553,Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish],GSE227190,Transcriptome Analysis,Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast  zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury  single cell transcriptomic analyses were performed on the heart  blood  liver  kidney  and pancreatic islets. Overall design: Upon heart cryoinjury  cells from multiple organs heart  liver  pancreas  and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls.,parent bioproject:PRJNA943547,pubmed:39627536,,WKM 1 dpi replicate 1,GSM7092942,,source name:Whole Kidney Marrow|tissue:Whole Kidney Marrow|cell type:Whole Kidney Marrow|genotype:wild type|treatment:Heart cryoinjury,WKM 1 dpi replicate 1,Demultiplexing  alignment  filtering  and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction  expression value normalization  clustering  cell type annotation and so on were done scater and scran. For more details and the cell type annotation information  see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format.,Whole Kidney Marrow,Heart cryoinjury or untreated,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells  ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C  the pellet was resuspended in 500 l and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell 3’ GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.,Standard zebrafish husbandry protocol.,tissue:Whole Kidney Marrow|cell type:Whole Kidney Marrow|genotype:wild type|treatment:Heart cryoinjury,GSM7092942,GSM7092942: WKM 1 dpi replicate 1; Danio rerio; RNA Seq,GSM7092942 r1,GSM7092942,1,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells  ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C  the pellet was resuspended in 500 l and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell three prime GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP426909,,loader:fastq load.py,1dpi-WKM-1_S10_L001_R1_001.fastq.gz 1dpi-WKM-1_S10_L001_R2_001.fastq.gz,fastq fastq,4817345870.0,40824965.0,GSM7092942 r1,0:28 1:90,A:1315196669;C:1111105805;G:1137917005;T:1253015765;N:110626,28,90,,,1315196669,1111105805,1137917005,1253015765,110626,SRX19646177,SRS17013987,SRA1603354,"Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine","Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine",2,0.0051,0.90847,0.00156,0.08428,0.99115,0.82629,0.35389,0.55535,28,90,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-03-12,Undetermined,Undetermined,Multi-tissue,Multi-system
74537,SRR23824377,SRX19646177,SRS17013987,SRP426909,PRJNA943553,Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish],GSE227190,Transcriptome Analysis,Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast  zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury  single cell transcriptomic analyses were performed on the heart  blood  liver  kidney  and pancreatic islets. Overall design: Upon heart cryoinjury  cells from multiple organs heart  liver  pancreas  and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls.,parent bioproject:PRJNA943547,pubmed:39627536,,WKM 1 dpi replicate 1,GSM7092942,,source name:Whole Kidney Marrow|tissue:Whole Kidney Marrow|cell type:Whole Kidney Marrow|genotype:wild type|treatment:Heart cryoinjury,WKM 1 dpi replicate 1,Demultiplexing  alignment  filtering  and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction  expression value normalization  clustering  cell type annotation and so on were done scater and scran. For more details and the cell type annotation information  see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format.,Whole Kidney Marrow,Heart cryoinjury or untreated,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells  ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C  the pellet was resuspended in 500 l and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell 3’ GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.,Standard zebrafish husbandry protocol.,tissue:Whole Kidney Marrow|cell type:Whole Kidney Marrow|genotype:wild type|treatment:Heart cryoinjury,GSM7092942,GSM7092942: WKM 1 dpi replicate 1; Danio rerio; RNA Seq,GSM7092942 r1,GSM7092942,1,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells  ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C  the pellet was resuspended in 500 l and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell three prime GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP426909,,loader:fastq load.py,1dpi-WKM-1_S10_L002_R1_001.fastq.gz 1dpi-WKM-1_S10_L002_R2_001.fastq.gz,fastq fastq,4812199182.0,40781349.0,GSM7092942 r2,0:28 1:90,A:1313522999;C:1109854806;G:1136485050;T:1252230444;N:105883,28,90,,,1313522999,1109854806,1136485050,1252230444,105883,SRX19646177,SRS17013987,SRA1603354,"Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine","Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine",2,0.00496,0.90951,0.0016,0.08555,0.99153,0.82444,0.36209,0.54165,28,90,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-03-12,Undetermined,Undetermined,Multi-tissue,Multi-system
74538,SRR23824384,SRX19646177,SRS17013987,SRP426909,PRJNA943553,Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish],GSE227190,Transcriptome Analysis,Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast  zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury  single cell transcriptomic analyses were performed on the heart  blood  liver  kidney  and pancreatic islets. Overall design: Upon heart cryoinjury  cells from multiple organs heart  liver  pancreas  and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls.,parent bioproject:PRJNA943547,pubmed:39627536,,WKM 1 dpi replicate 1,GSM7092942,,source name:Whole Kidney Marrow|tissue:Whole Kidney Marrow|cell type:Whole Kidney Marrow|genotype:wild type|treatment:Heart cryoinjury,WKM 1 dpi replicate 1,Demultiplexing  alignment  filtering  and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction  expression value normalization  clustering  cell type annotation and so on were done scater and scran. For more details and the cell type annotation information  see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format.,Whole Kidney Marrow,Heart cryoinjury or untreated,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells  ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C  the pellet was resuspended in 500 l and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell 3’ GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.,Standard zebrafish husbandry protocol.,tissue:Whole Kidney Marrow|cell type:Whole Kidney Marrow|genotype:wild type|treatment:Heart cryoinjury,GSM7092942,GSM7092942: WKM 1 dpi replicate 1; Danio rerio; RNA Seq,GSM7092942 r1,GSM7092942,1,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells  ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C  the pellet was resuspended in 500 l and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell three prime GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP426909,,loader:fastq load.py,1dpi-WKM-1_S10_L003_R1_001.fastq.gz 1dpi-WKM-1_S10_L003_R2_001.fastq.gz,fastq fastq,4891238178.0,41451171.0,GSM7092942 r3,0:28 1:90,A:1334595456;C:1128535220;G:1155791236;T:1272216383;N:99883,28,90,,,1334595456,1128535220,1155791236,1272216383,99883,SRX19646177,SRS17013987,SRA1603354,"Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine","Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine",2,0.00508,0.90903,0.00176,0.08466,0.9917,0.82692,0.34112,0.48297,28,90,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-03-12,Undetermined,Undetermined,Multi-tissue,Multi-system
74539,SRR23824385,SRX19646177,SRS17013987,SRP426909,PRJNA943553,Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish],GSE227190,Transcriptome Analysis,Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast  zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury  single cell transcriptomic analyses were performed on the heart  blood  liver  kidney  and pancreatic islets. Overall design: Upon heart cryoinjury  cells from multiple organs heart  liver  pancreas  and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls.,parent bioproject:PRJNA943547,pubmed:39627536,,WKM 1 dpi replicate 1,GSM7092942,,source name:Whole Kidney Marrow|tissue:Whole Kidney Marrow|cell type:Whole Kidney Marrow|genotype:wild type|treatment:Heart cryoinjury,WKM 1 dpi replicate 1,Demultiplexing  alignment  filtering  and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction  expression value normalization  clustering  cell type annotation and so on were done scater and scran. For more details and the cell type annotation information  see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format.,Whole Kidney Marrow,Heart cryoinjury or untreated,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells  ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C  the pellet was resuspended in 500 l and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell 3’ GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.,Standard zebrafish husbandry protocol.,tissue:Whole Kidney Marrow|cell type:Whole Kidney Marrow|genotype:wild type|treatment:Heart cryoinjury,GSM7092942,GSM7092942: WKM 1 dpi replicate 1; Danio rerio; RNA Seq,GSM7092942 r1,GSM7092942,1,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells  ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C  the pellet was resuspended in 500 l and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell three prime GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP426909,,loader:fastq load.py,1dpi-WKM-1_S10_L004_R1_001.fastq.gz 1dpi-WKM-1_S10_L004_R2_001.fastq.gz,fastq fastq,4800326966.0,40680737.0,GSM7092942 r4,0:28 1:90,A:1310904356;C:1106594205;G:1133104241;T:1249633119;N:91045,28,90,,,1310904356,1106594205,1133104241,1249633119,91045,SRX19646177,SRS17013987,SRA1603354,"Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine","Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine",2,0.00507,0.91017,0.00176,0.08423,0.99172,0.82475,0.32547,0.54695,28,90,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-03-12,Undetermined,Undetermined,Multi-tissue,Multi-system
75092,SRR24239717,SRX20035842,SRS17374857,SRP433739,PRJNA958104,The secreted neuronal signal Spock1 regulates the blood brain barrier,GSE230236,Transcriptome Analysis,The blood brain barrier BBB is a unique set of properties of the brain vasculature which severely restricts its permeability to proteins and small molecules. Classic chick quail chimera studies showed that these properties are not intrinsic to the brain vasculature but rather are induced by surrounding neural tissue. Here we identify Spock1 as a candidate neuronal signal for regulating BBB permeability in zebrafish and mice. Mosaic genetic analysis shows that neuronally expressed Spock1 is cell non autonomously required for a functional BBB. Leakage in spock1 mutants is associated with altered extracellular matrix ECM  increased endothelial transcytosis  and altered pericyte endothelial interactions. Furthermore  a single dose of recombinant SPOCK1  into spock1 mutants quenches gelatinase activity  restores vascular expression of BBB genes including mcamb   and partially restores barrier function. These analyses support a model in which neuronally secreted Spock1 induces BBB properties by altering the ECM  thereby regulating pericyte endothelial interactions and downstream vascular gene expression. Overall design: Bulk RNAseq Libraries 66 71 of leaky mutant and wild type siblings to identify the genetic lesion responsible for the leaky phenotype. These analyses revealed linkage to chr14  and more specifically to the spock1 gene. scRNAseq Library scDRBrain of dissected spock1 mutant and wild type brains was then used to identify all cell type specific changes in gene expression in the mutant background.,,pubmed:37437574,,scRNA seq for WT and hm41 larval heads  3 and 5dpf,GSM7208220,,tissue:mixed|cell type:mixed|genotype:mixed|time:3 dpf  5 dpf|geo loc name:missing|collection date:missing,scRNA seq for WT and hm41 larval heads  3 and 5dpf,Sequencing reads were mapped to the Zebrafish GRCz11 R101 genome assembly using a custom python pipeline as previously described see Zilionis et al.  Nature Protocols 2017 and https://github.com/indrops/. Multi seq hashtags were identified using custom code available at: https://github.com/AllonKleinLab/klunctions/tree/master/Ignas/Hashing. We first removed background cell barcodes by only considering transcriptomes with greater than 350 UMIs for downstream analysis. In order to remove dead cells  transcriptomes were further filtered by mitochondrial read percentage >20%. Cell demultiplexing was performed by manual inspection. Specifically  thresholds were drawn to delineate single cells from background and multiplet populations. The resulting counts matrix was normalized to the mean UMIs per cell in the dataset. Assembly: GRCz11 Supplementary files format and content: The gene counts matrix is an output from rsem differential gene expression analysis and is a raw counts estimate   not normalized for each gene. The first column is gene name and then post that each column represents an individual sample WT for the first 3 and then MUT for the last 3. Supplementary files format and content: The h5ad file contains the counts matrix for the demultiplexed single cell data. This file also holds relevant genotype and timepoint annotations as well as Multi seq barcode counts for each cell.,mixed,,Dissected brain tissues were dissociated using a modified protocol adapted from Bresciani et. al. 2018 PMID: 30364607. Briefly  chemical dissociations were performed at 30.5°C using a mixture of 0.25% Trypsin EDTA  Collagenase/Dispase 8 mg/mL and DNaseI 20 µg/mL for 15 20 minutes with gentle pipetting every 2.5 minutes. The dissociations were quenched using DMEM + 10% fetal bovine serum and filtered through a 40 µM cell strainer. The dissociation mixtures were spun down twice at 700g for 5 min and washed with PBS. The mixtures were then resuspended in PBS and barcoded using Multi seq as described in McGinnis et. al. 2019 PMID: 31209384 with slight modifications. For each sample  80 pmoles of Lipid modified oligos LMOs were used to hash every 500k cells. The hashing reaction was quenched using PBS + 1% BSA. The barcoded samples were pooled into a single tube and washed twice with PBS + 1% BSA 700g for 5 min.. The pooled cell mixture was resuspended in PBS + 0.1%BSA + 18% Optiprep at a final concentration of 300k cells/mL prior to single cell capture with inDrops. Single cell transcriptomes were captured by the Single cell Core SCC at the Harvard Medical School as previously described Zilionis et al.  Nature Protocols 2017 using the inDrops V3 chemistry. The Single cell Core at the Harvard Medical School prepared the gene expression inDrops v3 chemistry and Multi seq libraries.,,cell type:mixed|genotype:mixed|time:3 dpf  5 dpf,GSM7208220,GSM7208220: scRNA seq for WT and hm41 larval heads  3 and 5dpf; Danio rerio; RNA Seq,GSM7208220 r1,GSM7208220,1,Dissected brain tissues were dissociated using a modified protocol adapted from Bresciani et. al. 2018 PMID: 30364607. Briefly  chemical dissociations were performed at 30.5°C using a mixture of 0.25% Trypsin EDTA  Collagenase/Dispase 8 mg/mL and DNaseI 20 µg/mL for 15 20 minutes with gentle pipetting every 2.5 minutes. The dissociations were quenched using DMEM + 10% fetal bovine serum and filtered through a 40 µM cell strainer. The dissociation mixtures were spun down twice at 700g for 5 min and washed with PBS. The mixtures were then resuspended in PBS and barcoded using Multi seq as described in McGinnis et. al. 2019 PMID: 31209384 with slight modifications. For each sample  80 pmoles of Lipid modified oligos LMOs were used to hash every 500k cells. The hashing reaction was quenched using PBS + 1% BSA. The barcoded samples were pooled into a single tube and washed twice with PBS + 1% BSA 700g for 5 min.. The pooled cell mixture was resuspended in PBS + 0.1%BSA + 18% Optiprep at a final concentration of 300k cells/mL prior to single cell capture with inDrops. Single cell transcriptomes were captured by the Single cell Core SCC at the Harvard Medical School as previously described Zilionis et al.  Nature Protocols 2017 using the inDrops V3 chemistry. The Single cell Core at the Harvard Medical School prepared the gene expression inDrops v3 chemistry and Multi seq libraries.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP433739,,loader:fastq load.py|options:  readTypes=BTBT   read1PairFiles=Undetermined S0 L001 R1 001.fastq.gz   read2PairFiles=Undetermined S0 L001 R2 001.fastq.gz   read3PairFiles=Undetermined S0 L001 R3 001.fastq.gz   read4PairFiles=Undetermined S0 L001 R4 001.fastq.gz,,,548653863228.0,4729774683.0,GSM7208220 r1,,,,,,,,,,,,SRX20035842,SRS17374857,SRA1728506,"Megason Lab, Systems Biology, Harvard Medical School","Megason Lab, Systems Biology, Harvard Medical School",2,0.83589,0.0,0.23127,0.0,0.7723,1.0,0.46689,,86,8,B,T,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,indrops,,United States,2023-04-21,Larval,Larval,Multi-tissue,Multi-system
75485,SRR24641284,SRX20421319,SRS17735852,SRP438460,PRJNA973994,sc RNAseq of the day 4 zebrafish spinal cord,GSE232801,Transcriptome Analysis,Identification of the neuronal types that form the specialized circuits controlling distinct behaviors has benefited greatly from the simplicity offered by zebrafish.  Electrophysiological studies have shown that additional to connectivity  understanding of circuitry requires identification of functional specializations among individual circuit components  such as those that regulate levels of transmitter release and neuronal excitability. In this study we use single cell RNAseq scRNAseq to identify molecular distinctions causal to the unique physiology of primary motoneuron PMn function  as well as associated specialized interneurons that are tailored specifically for mediation of the powerful escape response. Generating scRNA seq datasets that provide both a wide overview of the cellular populations of the spinal cord and a granular view of the zebrafish motor neurons. Overall design: Cells from the spinal cords of 150 tgSAIG213a;EGFP zebrafish were analyzed via scRNA seq and populations of interneurons were identified based on established markers. For examination of Motor neurons we additionally preformed FACS on cells dissociated from spinal cords of 150 tgmnx1:GFP zebrafish.,,pubmed:37333232;pubmed:37975797,,Spinal cord  saig  rep 2,GSM7383491,,source name:spine|tissue:spine|cell type:mixed spinal cells|genotype:TgSAIG213A;EGFP|developmental stage:4 dpf|geo loc name:missing|collection date:missing,Spinal cord  saig  rep 2,Barcode processing and gene counting were preformed using Cell ranger software v6.1.1 10X Genomics. Reads were aligned to a reference genome made using cellrangers mkref command using the GRCz11.fa and the zebrafish custom ref.GTF provided as a supplimental file. The zebrafish custom ref.GTF is a lightly modified version of the Lawson v 1.4.3 annotation Lawson et al  2020  eLife in which GFP has been added and a number of naming mistakes have been corrected. Normalization  integration  and quality control were preformed using Seurat. Clustering of the data was preformed using the Lieden algorithm implemented in Seurat with varying parameters depending on the sample. Clusters with markers indicating contamination hindbrain and muscle were removed as were clusters where over 90% of cells came from only one experimental run. Neurons and glia were isolated based on the expression of markers within clusters  snap25a and elavl4 for neurons and slc1a2b  gfap  myrf and sox10 for glia. Neurons were then sub clustered into 33 clusters and identities were assigned to 21 of them based on both established markers in the literature and a number of novel markers we were able to validate. Motor neurons were isolated in the dataset based on the expression of motor neuron markers  mnx1  mnx2b  isl1  and cholinergic markers slc18a3a  and chata within clusters. Motor neurons isolated this way were then integrated together using Seurat. Assembly: GRCz11 Supplementary files format and content: Tab seperated value files  and matrix files providing the processed count matrices for each sample Supplementary files format and content: RDS file providing the Seurat data object for the integrated spinal samples Supplementary files format and content: RDS file providing the Seurat data object for the annotated set of clustered neurons from the integrated spinal samples Supplementary files format and content: RDS file providing the Seurat data object for the integrated set of isolated motor neurons from all samples Supplementary files format and content: GTF format record of the reference genome used in the creation of this data set,spine,,About 150 dpf 4 dpf larva were euthanized in 0.02% tricaine  and individually decapitated behind the hindbrain. They were incubated with 20 mg/ml collagenase in bath solution 134 mM NaCl  2.9 mM KCl  1.2 mM MgCl2  2.1 mM CaCl2  and 10 mM Na HEPES  pH 7.8  ∼290 mOsm at 28 °C for 1.5 hr  with intermittent trituration using a p200 pipette aid at 0  0.5 hr and1 hr of the incubation. For the purpose of isolating spinal cords from remaining tissue  the final trituration was done using fire polished Pasteur pipettes with decreased opening sizes 300  200  100 μm respectively.  Intact spinal cords were transferred to L15 media and washed 3 times with fresh media. The spinal cords were incubated with 0.25% trypsin solution in 1xPBS containing 1 mM EDTA at 28 °C for 25 min. The digestion was terminated by adding 500 μl stop solution L15 with 1% fetal bovine serum. The tissue was collected by spinning at 400 g for 3 min at 4°C  washed once with L15 and resuspended in 200 μl of L15 media. Spinal cord cells were dissociated by triturating the digested tissue with fire polished Pasteur pipettes with 80 100 μm opening. The solution was filtered through a 35μm strainer into a siliconized collection tube. The suspension was examined on a microscope for cell count  Trypan blue staining based   viability test and proportion of dispersed single cells. Samples with a viability above 70% were used for sequencing. For FACS sorted samples single cell suspension was prepared as above from Tgmnx1:GFP fish and were FAC sorted for EGFP+ cells using a 100 μm nozzle on a BD inFlux cell sorter Flow Cytometry Shared Resource  OHSU Single cell capture  cDNA synthesis and library preparation were performed by the Massive Parallel Sequencing Shared Resource at OHSU using the 10x Genomics Chromium v3.0 reagent kit. Single cell suspension for the two full spinal cord replicates targeted 10 000 15 000 cells  for the two FACS sorted samples 4 000 5 000 cells were targeted.,,tissue:spine|cell type:mixed spinal cells|genotype:TgSAIG213A;EGFP|developmental stage:4 dpf,GSM7383491,GSM7383491: Spinal cord  saig  rep 2; Danio rerio; RNA Seq,GSM7383491 r1,GSM7383491,1,About 150 dpf 4 dpf larva were euthanized in 0.02% tricaine  and individually decapitated behind the hindbrain. They were incubated with 20 mg/ml collagenase in bath solution 134 mM NaCl  2.9 mM KCl  1.2 mM MgCl2  2.1 mM CaCl2  and 10 mM Na HEPES  pH 7.8  ∼290 mOsm at 28 °C for 1.5 hr  with intermittent trituration using a p200 pipette aid at 0  0.5 hr and1 hr of the incubation. For the purpose of isolating spinal cords from remaining tissue  the final trituration was done using fire polished Pasteur pipettes with decreased opening sizes 300  200  100 μm respectively.  Intact spinal cords were transferred to L15 media and washed 3 times with fresh media. The spinal cords were incubated with 0.25% trypsin solution in 1xPBS containing 1 mM EDTA at 28 °C for 25 min. The digestion was terminated by adding 500 μl stop solution L15 with 1% fetal bovine serum. The tissue was collected by spinning at 400 g for 3 min at 4°C  washed once with L15 and resuspended in 200 μl of L15 media. Spinal cord cells were dissociated by triturating the digested tissue with fire polished Pasteur pipettes with 80 100 μm opening. The solution was filtered through a 35μm strainer into a siliconized collection tube. The suspension was examined on a microscope for cell count  Trypan blue staining based   viability test and proportion of dispersed single cells. Samples with a viability above 70% were used for sequencing. For FACS sorted samples single cell suspension was prepared as above from Tgmnx1:GFP fish and were FAC sorted for EGFP+ cells using a 100 μm nozzle on a BD inFlux cell sorter Flow Cytometry Shared Resource  OHSU Single cell capture  cDNA synthesis and library preparation were performed by the Massive Parallel Sequencing Shared Resource at OHSU using the 10x Genomics Chromium v3.0 reagent kit. Single cell suspension for the two full spinal cord replicates targeted 10 000 15 000 cells  for the two FACS sorted samples 4 000 5 000 cells were targeted.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP438460,,loader:fastq load.py,CEL220215PB_HW220228_SAIG_D4_S7_L002_I1_001.fastq.gz CEL220215PB_HW220228_SAIG_D4_S7_L002_I2_001.fastq.gz CEL220215PB_HW220228_SAIG_D4_S7_L002_R1_001.fastq.gz CEL220215PB_HW220228_SAIG_D4_S7_L002_R2_001.fastq.gz,fastq fastq fastq fastq,87300948384.0,632615568.0,GSM7383491 r1,0:10 1:10 2:28 3:90,A:15979295368;C:12462816135;G:14111684172;T:14380604641;N:1000804,10,10,28,90,15979295368,12462816135,14111684172,14380604641,1000804,SRX20421319,SRS17735852,SRA1640659,"Brehm, Vollum, Oregon Health and Science University","Brehm, Vollum, Oregon Health and Science University",1,0.91442,,0.24198,,0.80691,,0.64235,,90,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-05-18,Larval,Larval,Multi-tissue,Multi-system
75486,SRR24641285,SRX20421318,SRS17735853,SRP438460,PRJNA973994,sc RNAseq of the day 4 zebrafish spinal cord,GSE232801,Transcriptome Analysis,Identification of the neuronal types that form the specialized circuits controlling distinct behaviors has benefited greatly from the simplicity offered by zebrafish.  Electrophysiological studies have shown that additional to connectivity  understanding of circuitry requires identification of functional specializations among individual circuit components  such as those that regulate levels of transmitter release and neuronal excitability. In this study we use single cell RNAseq scRNAseq to identify molecular distinctions causal to the unique physiology of primary motoneuron PMn function  as well as associated specialized interneurons that are tailored specifically for mediation of the powerful escape response. Generating scRNA seq datasets that provide both a wide overview of the cellular populations of the spinal cord and a granular view of the zebrafish motor neurons. Overall design: Cells from the spinal cords of 150 tgSAIG213a;EGFP zebrafish were analyzed via scRNA seq and populations of interneurons were identified based on established markers. For examination of Motor neurons we additionally preformed FACS on cells dissociated from spinal cords of 150 tgmnx1:GFP zebrafish.,,pubmed:37333232;pubmed:37975797,,Spinal cord  saig  rep 1,GSM7383490,,source name:spine|tissue:spine|cell type:mixed spinal cells|genotype:TgSAIG213A;EGFP|developmental stage:4 dpf|geo loc name:missing|collection date:missing,Spinal cord  saig  rep 1,Barcode processing and gene counting were preformed using Cell ranger software v6.1.1 10X Genomics. Reads were aligned to a reference genome made using cellrangers mkref command using the GRCz11.fa and the zebrafish custom ref.GTF provided as a supplimental file. The zebrafish custom ref.GTF is a lightly modified version of the Lawson v 1.4.3 annotation Lawson et al  2020  eLife in which GFP has been added and a number of naming mistakes have been corrected. Normalization  integration  and quality control were preformed using Seurat. Clustering of the data was preformed using the Lieden algorithm implemented in Seurat with varying parameters depending on the sample. Clusters with markers indicating contamination hindbrain and muscle were removed as were clusters where over 90% of cells came from only one experimental run. Neurons and glia were isolated based on the expression of markers within clusters  snap25a and elavl4 for neurons and slc1a2b  gfap  myrf and sox10 for glia. Neurons were then sub clustered into 33 clusters and identities were assigned to 21 of them based on both established markers in the literature and a number of novel markers we were able to validate. Motor neurons were isolated in the dataset based on the expression of motor neuron markers  mnx1  mnx2b  isl1  and cholinergic markers slc18a3a  and chata within clusters. Motor neurons isolated this way were then integrated together using Seurat. Assembly: GRCz11 Supplementary files format and content: Tab seperated value files  and matrix files providing the processed count matrices for each sample Supplementary files format and content: RDS file providing the Seurat data object for the integrated spinal samples Supplementary files format and content: RDS file providing the Seurat data object for the annotated set of clustered neurons from the integrated spinal samples Supplementary files format and content: RDS file providing the Seurat data object for the integrated set of isolated motor neurons from all samples Supplementary files format and content: GTF format record of the reference genome used in the creation of this data set,spine,,About 150 dpf 4 dpf larva were euthanized in 0.02% tricaine  and individually decapitated behind the hindbrain. They were incubated with 20 mg/ml collagenase in bath solution 134 mM NaCl  2.9 mM KCl  1.2 mM MgCl2  2.1 mM CaCl2  and 10 mM Na HEPES  pH 7.8  ∼290 mOsm at 28 °C for 1.5 hr  with intermittent trituration using a p200 pipette aid at 0  0.5 hr and1 hr of the incubation. For the purpose of isolating spinal cords from remaining tissue  the final trituration was done using fire polished Pasteur pipettes with decreased opening sizes 300  200  100 μm respectively.  Intact spinal cords were transferred to L15 media and washed 3 times with fresh media. The spinal cords were incubated with 0.25% trypsin solution in 1xPBS containing 1 mM EDTA at 28 °C for 25 min. The digestion was terminated by adding 500 μl stop solution L15 with 1% fetal bovine serum. The tissue was collected by spinning at 400 g for 3 min at 4°C  washed once with L15 and resuspended in 200 μl of L15 media. Spinal cord cells were dissociated by triturating the digested tissue with fire polished Pasteur pipettes with 80 100 μm opening. The solution was filtered through a 35μm strainer into a siliconized collection tube. The suspension was examined on a microscope for cell count  Trypan blue staining based   viability test and proportion of dispersed single cells. Samples with a viability above 70% were used for sequencing. For FACS sorted samples single cell suspension was prepared as above from Tgmnx1:GFP fish and were FAC sorted for EGFP+ cells using a 100 μm nozzle on a BD inFlux cell sorter Flow Cytometry Shared Resource  OHSU Single cell capture  cDNA synthesis and library preparation were performed by the Massive Parallel Sequencing Shared Resource at OHSU using the 10x Genomics Chromium v3.0 reagent kit. Single cell suspension for the two full spinal cord replicates targeted 10 000 15 000 cells  for the two FACS sorted samples 4 000 5 000 cells were targeted.,,tissue:spine|cell type:mixed spinal cells|genotype:TgSAIG213A;EGFP|developmental stage:4 dpf,GSM7383490,GSM7383490: Spinal cord  saig  rep 1; Danio rerio; RNA Seq,GSM7383490 r1,GSM7383490,1,About 150 dpf 4 dpf larva were euthanized in 0.02% tricaine  and individually decapitated behind the hindbrain. They were incubated with 20 mg/ml collagenase in bath solution 134 mM NaCl  2.9 mM KCl  1.2 mM MgCl2  2.1 mM CaCl2  and 10 mM Na HEPES  pH 7.8  ∼290 mOsm at 28 °C for 1.5 hr  with intermittent trituration using a p200 pipette aid at 0  0.5 hr and1 hr of the incubation. For the purpose of isolating spinal cords from remaining tissue  the final trituration was done using fire polished Pasteur pipettes with decreased opening sizes 300  200  100 μm respectively.  Intact spinal cords were transferred to L15 media and washed 3 times with fresh media. The spinal cords were incubated with 0.25% trypsin solution in 1xPBS containing 1 mM EDTA at 28 °C for 25 min. The digestion was terminated by adding 500 μl stop solution L15 with 1% fetal bovine serum. The tissue was collected by spinning at 400 g for 3 min at 4°C  washed once with L15 and resuspended in 200 μl of L15 media. Spinal cord cells were dissociated by triturating the digested tissue with fire polished Pasteur pipettes with 80 100 μm opening. The solution was filtered through a 35μm strainer into a siliconized collection tube. The suspension was examined on a microscope for cell count  Trypan blue staining based   viability test and proportion of dispersed single cells. Samples with a viability above 70% were used for sequencing. For FACS sorted samples single cell suspension was prepared as above from Tgmnx1:GFP fish and were FAC sorted for EGFP+ cells using a 100 μm nozzle on a BD inFlux cell sorter Flow Cytometry Shared Resource  OHSU Single cell capture  cDNA synthesis and library preparation were performed by the Massive Parallel Sequencing Shared Resource at OHSU using the 10x Genomics Chromium v3.0 reagent kit. Single cell suspension for the two full spinal cord replicates targeted 10 000 15 000 cells  for the two FACS sorted samples 4 000 5 000 cells were targeted.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP438460,,loader:fastq load.py,CEL210928PB_HW1011_SAIG_D4_S2_L001_I1_001.fastq.gz CEL210928PB_HW1011_SAIG_D4_S2_L001_I2_001.fastq.gz CEL210928PB_HW1011_SAIG_D4_S2_L001_R1_001.fastq.gz CEL210928PB_HW1011_SAIG_D4_S2_L001_R2_001.fastq.gz,fastq fastq fastq fastq,75351686080.0,342507664.0,GSM7383490 r1,0:10 1:10 2:100 3:100,A:18301848290;C:13693616371;G:14262218620;T:22242052659;N:1796860,10,10,100,100,18301848290,13693616371,14262218620,22242052659,1796860,SRX20421318,SRS17735853,SRA1640659,"Brehm, Vollum, Oregon Health and Science University","Brehm, Vollum, Oregon Health and Science University",2,0.0,0.87984,0.0,0.23039,1.0,0.81763,,0.6272,100,100,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-05-18,Larval,Larval,Multi-tissue,Multi-system
75487,SRR24641286,SRX20421318,SRS17735853,SRP438460,PRJNA973994,sc RNAseq of the day 4 zebrafish spinal cord,GSE232801,Transcriptome Analysis,Identification of the neuronal types that form the specialized circuits controlling distinct behaviors has benefited greatly from the simplicity offered by zebrafish.  Electrophysiological studies have shown that additional to connectivity  understanding of circuitry requires identification of functional specializations among individual circuit components  such as those that regulate levels of transmitter release and neuronal excitability. In this study we use single cell RNAseq scRNAseq to identify molecular distinctions causal to the unique physiology of primary motoneuron PMn function  as well as associated specialized interneurons that are tailored specifically for mediation of the powerful escape response. Generating scRNA seq datasets that provide both a wide overview of the cellular populations of the spinal cord and a granular view of the zebrafish motor neurons. Overall design: Cells from the spinal cords of 150 tgSAIG213a;EGFP zebrafish were analyzed via scRNA seq and populations of interneurons were identified based on established markers. For examination of Motor neurons we additionally preformed FACS on cells dissociated from spinal cords of 150 tgmnx1:GFP zebrafish.,,pubmed:37333232;pubmed:37975797,,Spinal cord  saig  rep 1,GSM7383490,,source name:spine|tissue:spine|cell type:mixed spinal cells|genotype:TgSAIG213A;EGFP|developmental stage:4 dpf|geo loc name:missing|collection date:missing,Spinal cord  saig  rep 1,Barcode processing and gene counting were preformed using Cell ranger software v6.1.1 10X Genomics. Reads were aligned to a reference genome made using cellrangers mkref command using the GRCz11.fa and the zebrafish custom ref.GTF provided as a supplimental file. The zebrafish custom ref.GTF is a lightly modified version of the Lawson v 1.4.3 annotation Lawson et al  2020  eLife in which GFP has been added and a number of naming mistakes have been corrected. Normalization  integration  and quality control were preformed using Seurat. Clustering of the data was preformed using the Lieden algorithm implemented in Seurat with varying parameters depending on the sample. Clusters with markers indicating contamination hindbrain and muscle were removed as were clusters where over 90% of cells came from only one experimental run. Neurons and glia were isolated based on the expression of markers within clusters  snap25a and elavl4 for neurons and slc1a2b  gfap  myrf and sox10 for glia. Neurons were then sub clustered into 33 clusters and identities were assigned to 21 of them based on both established markers in the literature and a number of novel markers we were able to validate. Motor neurons were isolated in the dataset based on the expression of motor neuron markers  mnx1  mnx2b  isl1  and cholinergic markers slc18a3a  and chata within clusters. Motor neurons isolated this way were then integrated together using Seurat. Assembly: GRCz11 Supplementary files format and content: Tab seperated value files  and matrix files providing the processed count matrices for each sample Supplementary files format and content: RDS file providing the Seurat data object for the integrated spinal samples Supplementary files format and content: RDS file providing the Seurat data object for the annotated set of clustered neurons from the integrated spinal samples Supplementary files format and content: RDS file providing the Seurat data object for the integrated set of isolated motor neurons from all samples Supplementary files format and content: GTF format record of the reference genome used in the creation of this data set,spine,,About 150 dpf 4 dpf larva were euthanized in 0.02% tricaine  and individually decapitated behind the hindbrain. They were incubated with 20 mg/ml collagenase in bath solution 134 mM NaCl  2.9 mM KCl  1.2 mM MgCl2  2.1 mM CaCl2  and 10 mM Na HEPES  pH 7.8  ∼290 mOsm at 28 °C for 1.5 hr  with intermittent trituration using a p200 pipette aid at 0  0.5 hr and1 hr of the incubation. For the purpose of isolating spinal cords from remaining tissue  the final trituration was done using fire polished Pasteur pipettes with decreased opening sizes 300  200  100 μm respectively.  Intact spinal cords were transferred to L15 media and washed 3 times with fresh media. The spinal cords were incubated with 0.25% trypsin solution in 1xPBS containing 1 mM EDTA at 28 °C for 25 min. The digestion was terminated by adding 500 μl stop solution L15 with 1% fetal bovine serum. The tissue was collected by spinning at 400 g for 3 min at 4°C  washed once with L15 and resuspended in 200 μl of L15 media. Spinal cord cells were dissociated by triturating the digested tissue with fire polished Pasteur pipettes with 80 100 μm opening. The solution was filtered through a 35μm strainer into a siliconized collection tube. The suspension was examined on a microscope for cell count  Trypan blue staining based   viability test and proportion of dispersed single cells. Samples with a viability above 70% were used for sequencing. For FACS sorted samples single cell suspension was prepared as above from Tgmnx1:GFP fish and were FAC sorted for EGFP+ cells using a 100 μm nozzle on a BD inFlux cell sorter Flow Cytometry Shared Resource  OHSU Single cell capture  cDNA synthesis and library preparation were performed by the Massive Parallel Sequencing Shared Resource at OHSU using the 10x Genomics Chromium v3.0 reagent kit. Single cell suspension for the two full spinal cord replicates targeted 10 000 15 000 cells  for the two FACS sorted samples 4 000 5 000 cells were targeted.,,tissue:spine|cell type:mixed spinal cells|genotype:TgSAIG213A;EGFP|developmental stage:4 dpf,GSM7383490,GSM7383490: Spinal cord  saig  rep 1; Danio rerio; RNA Seq,GSM7383490 r1,GSM7383490,1,About 150 dpf 4 dpf larva were euthanized in 0.02% tricaine  and individually decapitated behind the hindbrain. They were incubated with 20 mg/ml collagenase in bath solution 134 mM NaCl  2.9 mM KCl  1.2 mM MgCl2  2.1 mM CaCl2  and 10 mM Na HEPES  pH 7.8  ∼290 mOsm at 28 °C for 1.5 hr  with intermittent trituration using a p200 pipette aid at 0  0.5 hr and1 hr of the incubation. For the purpose of isolating spinal cords from remaining tissue  the final trituration was done using fire polished Pasteur pipettes with decreased opening sizes 300  200  100 μm respectively.  Intact spinal cords were transferred to L15 media and washed 3 times with fresh media. The spinal cords were incubated with 0.25% trypsin solution in 1xPBS containing 1 mM EDTA at 28 °C for 25 min. The digestion was terminated by adding 500 μl stop solution L15 with 1% fetal bovine serum. The tissue was collected by spinning at 400 g for 3 min at 4°C  washed once with L15 and resuspended in 200 μl of L15 media. Spinal cord cells were dissociated by triturating the digested tissue with fire polished Pasteur pipettes with 80 100 μm opening. The solution was filtered through a 35μm strainer into a siliconized collection tube. The suspension was examined on a microscope for cell count  Trypan blue staining based   viability test and proportion of dispersed single cells. Samples with a viability above 70% were used for sequencing. For FACS sorted samples single cell suspension was prepared as above from Tgmnx1:GFP fish and were FAC sorted for EGFP+ cells using a 100 μm nozzle on a BD inFlux cell sorter Flow Cytometry Shared Resource  OHSU Single cell capture  cDNA synthesis and library preparation were performed by the Massive Parallel Sequencing Shared Resource at OHSU using the 10x Genomics Chromium v3.0 reagent kit. Single cell suspension for the two full spinal cord replicates targeted 10 000 15 000 cells  for the two FACS sorted samples 4 000 5 000 cells were targeted.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP438460,,loader:fastq load.py,CEL210928PB_HW1011_SAIG_D4_S2_L002_I1_001.fastq.gz CEL210928PB_HW1011_SAIG_D4_S2_L002_I2_001.fastq.gz CEL210928PB_HW1011_SAIG_D4_S2_L002_R1_001.fastq.gz CEL210928PB_HW1011_SAIG_D4_S2_L002_R2_001.fastq.gz,fastq fastq fastq fastq,76811238680.0,349141994.0,GSM7383490 r2,0:10 1:10 2:100 3:100,A:18612770086;C:13983377544;G:14583499379;T:22647109701;N:1642090,10,10,100,100,18612770086,13983377544,14583499379,22647109701,1642090,SRX20421318,SRS17735853,SRA1640659,"Brehm, Vollum, Oregon Health and Science University","Brehm, Vollum, Oregon Health and Science University",2,9e-05,0.87854,0.0,0.2305,0.99997,0.81793,0.0,0.65388,100,100,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-05-18,Larval,Larval,Multi-tissue,Multi-system
76725,SRR25288287,SRX21031898,SRS18304344,SRP449631,PRJNA994919,Diverse Epithelial Lymphocytes in Zebrafish Revealed Using a Novel Scale Biopsy Method,GSE237417,Transcriptome Analysis,Zebrafish Danio rerio are a compelling model to study lymphocytes because zebrafish and humans have similar adaptive immune systems  including their lymphocytes. Antibodies that recognize zebrafish proteins are sparse  so many investigators utilize transgenic  lymphocyte specific fluorophore labeled lines. Human and zebrafish lymphocyte types are conserved  but many aspects of zebrafish lymphocyte biology remain uninvestigated  including lymphocytes in peripheral tissues  like epidermis. Here  we report the first study focused on zebrafish epidermal lymphocytes  using scales. Obtaining zebrafish blood via non lethal methods is difficult; scales represent a source to longitudinally sample live fish. We developed a novel biopsy technique  collecting scales to analyze epithelial lymphocytes from several fluorescently labeled lines. We imaged scales via confocal microscopy and demonstrated multiple lymphocyte types in scales/epidermis  quantifying them flow cytometrically. We profiled gene expression of scale  thymic  and marrow lymphocytes from the same animals  revealing B  and T lineage signatures. Single cell qRT PCR and RNA sequencing scRNA seq show not only canonical B and T cells  but also novel lymphocyte populations not described previously. To validate longitudinal scale biopsies  we serially sampled scales from fish treated with dexamethasone DXM  demonstrating epidermal lymphocyte responses. To analyze cells functionally  we employed a bead ingestion assay  showing thymic  marrow  and epidermal lymphocytes have phagocytic activity. In summary  we establish a novel  non lethal technique to obtain zebrafish lymphocytes  providing the first quantification  expression profiling  and functional data DXM responses and phagocytosis from epidermal lymphocytes in the zebrafish model. Overall design: This experimental study aimed to investigate the gene expression profiles of individual lymphocytes from the zebrafish lck:GFP transgenic line by using single cell RNA sequencing scRNA seq analysis. We performed scRNA seq on GFPhi thymocytes and GFPlo scale/marrow cells from lck:GFP fish which mark different lymphocyte populations. scRNA seq data reveal diverse thymic  scale  and marrow lymphocyte populations for subsequent transcriptomic analysis and isolation of specific cell types.,,pubmed:39503619,,Kidney Marrow S2,GSM7611260,,source name:Kidney Marrow|tissue:Kidney Marrow|cell line:NA|cell type:Lymphocytes|genotype:lck:GFP|geo loc name:missing|collection date:missing,Kidney Marrow S2,post conversion to fastq files  reads for each sample were processed and aggregated using the 10x Genomics Cell Ranger v.6.0.0 pipeline no normalization  default settings and processed in the Seurat R package v.4.3.0. We obtained transcriptomes for 6 359 cells post Cell Ranger processing. SoupX v.1.6.2 was used to model and remove ambient RNA contamination per sample  and scDblFinder v.1.12.0 was used to detect potential multiplets default settings  per individual tissue type. Additional QC filtering was performed to remove potential dead or dying cells along with cells exhibiting abnormal read/gene counts and high levels of mitochondrial transcripts  resulting in 1 890 usable cells for our analysis. Using fastMNN  cells were normalized and integrated  and then clustered within Seurat Leiden algorithm. Clustering resolution was optimized using the clustree package v.0.5.0. Cluster boundaries were manually examined and fine tuned to optimize biological interpretation. Collective diagnostic gene signatures corresponding to published gene lists and our own sc qRT PCR results were explored using Seurat and UCell v.2.2.0. Preferential gene markers were determined for each distinct population using the FindAllMarkers function within Seurat  to aid in cell type assignment p.adj ≤ 0.05  min.pct = 0.25. Assembly: GRCz11 Supplementary files format and content: Tab delimited value files and matrices.,Kidney Marrow,,For procedures  zebrafish subjects were anesthetized with 0.02% tricaine methanesulfonate. Thymus  kidney marrow and scale samples were dissected and placed in 500 ul cell media RPMI + 1% FBS + 1% Pen/Strep. Single cell suspensions were prepped by dissociating tissues using a pestle and passed through 35 um filters. Various fluorescent populations were sorted from the lymphoid and precursor gates using a BD FACSJazz Instrument analysis performed in FlowJo softare. Following creation of single cell emulsions  uniquely identifiable 1st strand template single cell cDNA libraries were generated from each cell by emulsion PCR. 2nd strand cDNA was generated and ligated to compatible Illumina adapters. Libraries were loaded onto single NovaSeq 6000 lanes and sequenced  using read lengths of 28 bp for the first read  120 bp for the second read  and 8 base index reads.,,tissue:Kidney Marrow|cell line:NA|cell type:Lymphocytes|genotype:lck:GFP,GSM7611260,GSM7611260: Kidney Marrow S2; Danio rerio; RNA Seq,GSM7611260 r1,GSM7611260,1,For procedures  zebrafish subjects were anesthetized with 0.02% tricaine methanesulfonate. Thymus  kidney marrow and scale samples were dissected and placed in 500 ul cell media RPMI + 1% FBS + 1% Pen/Strep. Single cell suspensions were prepped by dissociating tissues using a pestle and passed through 35 um filters. Various fluorescent populations were sorted from the lymphoid and precursor gates using a BD FACSJazz Instrument analysis performed in FlowJo softare. Following creation of single cell emulsions  uniquely identifiable 1st strand template single cell cDNA libraries were generated from each cell by emulsion PCR. 2nd strand cDNA was generated and ligated to compatible Illumina adapters. Libraries were loaded onto single NovaSeq 6000 lanes and sequenced  using read lengths of 28 bp for the first read  120 bp for the second read  and 8 base index reads.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP449631,,loader:fastq load.py,3_Mo_1ck_KM_S2_L001_I1_001.fastq.gz 3_Mo_1ck_KM_S2_L001_R1_001.fastq.gz 3_Mo_1ck_KM_S2_L001_R2_001.fastq.gz,fastq fastq fastq,14406058368.0,92346528.0,GSM7611260 r1,0:8 1:28 2:120,A:3212551102;C:2439333260;G:2665663309;T:2763896751;N:138938,8,28,120,,3212551102,2439333260,2665663309,2763896751,138938,SRX21031898,SRS18304344,SRA1673435,"Pediatrics, University of Oklahoma Health Sciences Center","Pediatrics, University of Oklahoma Health Sciences Center",1,0.92665,,0.1896,,0.8268,,0.56354,,120,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-07-14,Undetermined,Undetermined,Multi-tissue,Multi-system