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
35385,SRR32649448,SRX27953870,SRS24319775,SRP569567,PRJNA1234533,Delta family protocadhins contribute to protoglomerular targeting of olfactory sensory neuron axons in the olfactory bulb,GSE291626,Transcriptome Analysis,To understand how neural circuits are assembled  it is essential to identify and characterize the axonal guidance cues and receptors that determine the axonal trajectories and connections between neurons. We performed single cell RNA sequencing of olfactory sensory neurons from zebrafish to identify candidate axonal guidance related genes that are differentially expressed according to sensory axon target location in the olfactory bulb. Among the candidates we identified were several members of the non clustered delta protocadherin family of adhesion molecules. We found that two members of the delta1 protocadherin family  pcdh7b and pcdh11  are most highly expressed in sensory neurons that project to the DZ protoglomerulus. Knocking down either one impairs the ability of sensory axons to terminate within the DZ protoglomerulus  but does not affect the ability of other sensory axons from terminating normally in the CZ protoglomerulus. In contrast  two members of the delta2 protocadherin family  pcdh10b and pcdh17  are most highly expressed in sensory neurons that project to the CZ protoglomerulus. Knocking down pcdh10b induces ectopic terminations of CZ projecting sensory axons. Knocking down pcdh17 induces substantial ectopic axonal trajectories and impairs CZ projecting sensory axons from finding and terminating in the CZ protoglomerulus. Knockdowns of either pcdh10b or pcdh17 do not affect DZ projecting sensory axons. These findings suggest that delta1 protocadherins help DZ projecting sensory axons enter and remain within the DZ protoglomerulus  while delta2 protocadherins help CZ projecting sensory axons navigate to the CZ protoglomerulus. Overall design: Roughly 2000 zebrafish embryos we sacraficed at 36  48 hpf and 72 hpf. Olfactory tissue was dissociated in FACSmax dissosciation medium and then FACsorted to isolate OMP:RFP positive neurons.,,,,OMP positive Olfactory Sensory Neurons from 48pf Zebrafish,GSM8838717,,source name:Olfactory Sensory Tissue|tissue:Olfactory Sensory Tissue|cell line:Olactory Sensory Neurons|cell type:Neurons|sample age:48 hpf|genotype:Tgomp:lyn RFP|geo loc name:missing|collection date:missing,OMP positive Olfactory Sensory Neurons from 48pf Zebrafish,Cell Ranger V3.0.1 Assembly: GRCz11 Supplementary files format and content: Demultiplexed 10x Genomics Files.,Olfactory Sensory Tissue,,10X Genomics V3.3,,tissue:Olfactory Sensory Tissue|cell line:Olactory Sensory Neurons|cell type:Neurons|sample age:48 hpf|genotype:Tgomp:lyn RFP,GSM8838717,GSM8838717: OMP positive Olfactory Sensory Neurons from 48pf Zebrafish; Danio rerio; RNA Seq,GSM8838717 r1,GSM8838717,1,10X Genomics V3.3,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP569567,,loader:fastq load.py,97364_S5_L001_I1_001.fastq.gz 97364_S5_L001_R1_001.fastq.gz 97364_S5_L001_R2_001.fastq.gz,fastq fastq fastq,7455743360.0,57351872.0,GSM8838717 r1,0:8 1:28 2:94,A:1588619193;C:1118423731;G:1232237797;T:1451670240;N:125007,8,28,94,,1588619193,1118423731,1232237797,1451670240,125007,SRX27953870,SRS24319775,SRA2091725,"Department of Neuroscience, University of Pennsylvania","Department of Neuroscience, University of Pennsylvania",,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2025-03-11,Hatching,Embryo,Brain,Nervous System
35386,SRR32649449,SRX27953870,SRS24319775,SRP569567,PRJNA1234533,Delta family protocadhins contribute to protoglomerular targeting of olfactory sensory neuron axons in the olfactory bulb,GSE291626,Transcriptome Analysis,To understand how neural circuits are assembled  it is essential to identify and characterize the axonal guidance cues and receptors that determine the axonal trajectories and connections between neurons. We performed single cell RNA sequencing of olfactory sensory neurons from zebrafish to identify candidate axonal guidance related genes that are differentially expressed according to sensory axon target location in the olfactory bulb. Among the candidates we identified were several members of the non clustered delta protocadherin family of adhesion molecules. We found that two members of the delta1 protocadherin family  pcdh7b and pcdh11  are most highly expressed in sensory neurons that project to the DZ protoglomerulus. Knocking down either one impairs the ability of sensory axons to terminate within the DZ protoglomerulus  but does not affect the ability of other sensory axons from terminating normally in the CZ protoglomerulus. In contrast  two members of the delta2 protocadherin family  pcdh10b and pcdh17  are most highly expressed in sensory neurons that project to the CZ protoglomerulus. Knocking down pcdh10b induces ectopic terminations of CZ projecting sensory axons. Knocking down pcdh17 induces substantial ectopic axonal trajectories and impairs CZ projecting sensory axons from finding and terminating in the CZ protoglomerulus. Knockdowns of either pcdh10b or pcdh17 do not affect DZ projecting sensory axons. These findings suggest that delta1 protocadherins help DZ projecting sensory axons enter and remain within the DZ protoglomerulus  while delta2 protocadherins help CZ projecting sensory axons navigate to the CZ protoglomerulus. Overall design: Roughly 2000 zebrafish embryos we sacraficed at 36  48 hpf and 72 hpf. Olfactory tissue was dissociated in FACSmax dissosciation medium and then FACsorted to isolate OMP:RFP positive neurons.,,,,OMP positive Olfactory Sensory Neurons from 48pf Zebrafish,GSM8838717,,source name:Olfactory Sensory Tissue|tissue:Olfactory Sensory Tissue|cell line:Olactory Sensory Neurons|cell type:Neurons|sample age:48 hpf|genotype:Tgomp:lyn RFP|geo loc name:missing|collection date:missing,OMP positive Olfactory Sensory Neurons from 48pf Zebrafish,Cell Ranger V3.0.1 Assembly: GRCz11 Supplementary files format and content: Demultiplexed 10x Genomics Files.,Olfactory Sensory Tissue,,10X Genomics V3.3,,tissue:Olfactory Sensory Tissue|cell line:Olactory Sensory Neurons|cell type:Neurons|sample age:48 hpf|genotype:Tgomp:lyn RFP,GSM8838717,GSM8838717: OMP positive Olfactory Sensory Neurons from 48pf Zebrafish; Danio rerio; RNA Seq,GSM8838717 r1,GSM8838717,1,10X Genomics V3.3,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP569567,,loader:fastq load.py,97364_S5_L002_I1_001.fastq.gz 97364_S5_L002_R1_001.fastq.gz 97364_S5_L002_R2_001.fastq.gz,fastq fastq fastq,7445521460.0,57273242.0,GSM8838717 r2,0:8 1:28 2:94,A:1586585615;C:1115323543;G:1231863598;T:1449738354;N:173638,8,28,94,,1586585615,1115323543,1231863598,1449738354,173638,SRX27953870,SRS24319775,SRA2091725,"Department of Neuroscience, University of Pennsylvania","Department of Neuroscience, University of Pennsylvania",,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2025-03-11,Hatching,Embryo,Brain,Nervous System
39828,SRR2437828,SRX1321832,SRS1109643,SRP062493,PRJNA293106,Danio rerio Raw sequence reads,PRJNA293106,Metagenomics,Zebrafish Hypoxia RNAseq,,,RNAseq at 48hpf following normoxia,,48hpf normoxia,,strain:TU|age:48hpf|sex:not determined|tissue:brain|treatment:normoxia|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Embryonic Development Hypoxia Versus Normoxia RNAseq: Sample       48hpf normoxia,48hpf.normoxia.3.10329X16,48hpf.normoxia.3.10329X16,We collected whole RNA from zebrafish at five different embryonic developmental stages with experimental triplicates for each stage time point and experimental condition.  For hypoxia  we placed developing embryos in pre conditioned media in a sealed plexiglass chamber set to a reduced oxygen concentration for 12 hour periods. Immediately following hypoxia or normoxia embryos were sacrificed and RNA collected.  We used 1% pO2 for ages up to 48 hpf and 4% pO2 for older ages.  At the time point for collection embryos were dissected and only head tissue was used for subsequent RNA preparation.  RNA was prepared with a miRNeasy kit Qiagen. Quality of total RNAs was checked using a NanoDrop 2000 Spectrometer and an Agilent 2100 Bioanalyzer.  The sequencing libraries were created using the Illumina TruSeq Stranded Total RNA Sample Preparation Kit with Ribo Zero. These libraries were sequenced on an Illumina HiSeq2000 sequencer for 50 cycles ie. 50 nucleotides  single end  stranded using Illumina’s version 3 chemistry. 6 samples were multiplexed together in each lane of the sequencer  providing an average yield of 25.1 million reads per sample. The base calling was performed using Illumina’s CASAVA version 1.8.2 software.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP062493,,,10329X16_130822_SN141_0719_AD2CK5ACXX_6.txt.gz,fastq,985942500.0,19718850.0,48hpf.normoxia.3.10329X16,0:50,A:251856100;C:223081125;G:216430606;T:294554748;N:19921,50,,,,251856100,223081125,216430606,294554748,19921,SRX1321832,SRS1109643,SRA289450,University of Utah|Bonkowsky,University of Utah,1,0.94791,,0.26704,,0.68708,,0.54445,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,United States,2015-10-10,Hatching,Embryo,Brain,Nervous System
39830,SRR2433795,SRX1321830,SRS1109644,SRP062493,PRJNA293106,Danio rerio Raw sequence reads,PRJNA293106,Metagenomics,Zebrafish Hypoxia RNAseq,,,RNAseq at 60hpf following normoxia,,60hpf Normoxia,,strain:TU|age:60hpf|sex:not determined|tissue:brain|treatment:normoxia|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Embryonic Development Hypoxia Versus Normoxia RNAseq: Sample       60hpf Normoxia,60hpf.normoxia.3.,60hpf.normoxia.3.,We collected whole RNA from zebrafish at five different embryonic developmental stages with experimental triplicates for each stage time point and experimental condition.  For hypoxia  we placed developing embryos in pre conditioned media in a sealed plexiglass chamber set to a reduced oxygen concentration for 12 hour periods. Immediately following hypoxia or normoxia embryos were sacrificed and RNA collected.  We used 1% pO2 for ages up to 48 hpf and 4% pO2 for older ages.  At the time point for collection embryos were dissected and only head tissue was used for subsequent RNA preparation.  RNA was prepared with a miRNeasy kit Qiagen. Quality of total RNAs was checked using a NanoDrop 2000 Spectrometer and an Agilent 2100 Bioanalyzer.  The sequencing libraries were created using the Illumina TruSeq Stranded Total RNA Sample Preparation Kit with Ribo Zero. These libraries were sequenced on an Illumina HiSeq2000 sequencer for 50 cycles ie. 50 nucleotides  single end  stranded using Illumina’s version 3 chemistry. 6 samples were multiplexed together in each lane of the sequencer  providing an average yield of 25.1 million reads per sample. The base calling was performed using Illumina’s CASAVA version 1.8.2 software.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP062493,,,10329X8_130822_SN141_0719_AD2CK5ACXX_5.txt.gz,fastq,1112799950.0,22255999.0,60hpf.normoxia.3.,0:50,A:294304558;C:248234752;G:238088577;T:332109252;N:62811,50,,,,294304558,248234752,238088577,332109252,62811,SRX1321830,SRS1109644,SRA289450,University of Utah|Bonkowsky,University of Utah,1,0.94922,,0.34314,,0.67838,,0.51455,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,United States,2015-10-10,Hatching,Embryo,Brain,Nervous System
39832,SRR2417497,SRX1321828,SRS1109646,SRP062493,PRJNA293106,Danio rerio Raw sequence reads,PRJNA293106,Metagenomics,Zebrafish Hypoxia RNAseq,,,RNAseq at 48hpf following hypoxia,,48hpf hypoxia,,strain:TU|age:48hpf|sex:not determined|tissue:brain|treatment:hypoxia|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Embryonic Development Hypoxia Versus Normoxia RNAseq: Sample       48hpf hypoxia,48hpf.hypoxia.3.10329X25,48hpf.hypoxia.3.10329X25,We collected whole RNA from zebrafish at five different embryonic developmental stages with experimental triplicates for each stage time point and experimental condition.  For hypoxia  we placed developing embryos in pre conditioned media in a sealed plexiglass chamber set to a reduced oxygen concentration for 12 hour periods. Immediately following hypoxia or normoxia embryos were sacrificed and RNA collected.  We used 1% pO2 for ages up to 48 hpf and 4% pO2 for older ages.  At the time point for collection embryos were dissected and only head tissue was used for subsequent RNA preparation.  RNA was prepared with a miRNeasy kit Qiagen. Quality of total RNAs was checked using a NanoDrop 2000 Spectrometer and an Agilent 2100 Bioanalyzer.  The sequencing libraries were created using the Illumina TruSeq Stranded Total RNA Sample Preparation Kit with Ribo Zero. These libraries were sequenced on an Illumina HiSeq2000 sequencer for 50 cycles ie. 50 nucleotides  single end  stranded using Illumina’s version 3 chemistry. 6 samples were multiplexed together in each lane of the sequencer  providing an average yield of 25.1 million reads per sample. The base calling was performed using Illumina’s CASAVA version 1.8.2 software.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP062493,,,10329X25_130822_SN141_0719_AD2CK5ACXX_8.txt.gz,fastq,1234710500.0,24694210.0,48hpf.hypoxia.3.10329X25,0:50,A:309392529;C:284311489;G:275471070;T:365515358;N:20054,50,,,,309392529,284311489,275471070,365515358,20054,SRX1321828,SRS1109646,SRA289450,University of Utah|Bonkowsky,University of Utah,1,0.94675,,0.25877,,0.71453,,0.5239,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,United States,2015-09-16,Hatching,Embryo,Brain,Nervous System
39833,SRR2417496,SRX1321827,SRS1109644,SRP062493,PRJNA293106,Danio rerio Raw sequence reads,PRJNA293106,Metagenomics,Zebrafish Hypoxia RNAseq,,,RNAseq at 60hpf following normoxia,,60hpf Normoxia,,strain:TU|age:60hpf|sex:not determined|tissue:brain|treatment:normoxia|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Embryonic Development Hypoxia Versus Normoxia RNAseq: Sample       60hpf Normoxia,60hpf.normoxia.2.10329X28,60hpf.normoxia.2.10329X28,We collected whole RNA from zebrafish at five different embryonic developmental stages with experimental triplicates for each stage time point and experimental condition.  For hypoxia  we placed developing embryos in pre conditioned media in a sealed plexiglass chamber set to a reduced oxygen concentration for 12 hour periods. Immediately following hypoxia or normoxia embryos were sacrificed and RNA collected.  We used 1% pO2 for ages up to 48 hpf and 4% pO2 for older ages.  At the time point for collection embryos were dissected and only head tissue was used for subsequent RNA preparation.  RNA was prepared with a miRNeasy kit Qiagen. Quality of total RNAs was checked using a NanoDrop 2000 Spectrometer and an Agilent 2100 Bioanalyzer.  The sequencing libraries were created using the Illumina TruSeq Stranded Total RNA Sample Preparation Kit with Ribo Zero. These libraries were sequenced on an Illumina HiSeq2000 sequencer for 50 cycles ie. 50 nucleotides  single end  stranded using Illumina’s version 3 chemistry. 6 samples were multiplexed together in each lane of the sequencer  providing an average yield of 25.1 million reads per sample. The base calling was performed using Illumina’s CASAVA version 1.8.2 software.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP062493,,,10329X28_130822_SN141_0719_AD2CK5ACXX_8.txt.gz,fastq,1015786750.0,20315735.0,60hpf.normoxia.2.10329X28,0:50,A:259102784;C:230364456;G:226008843;T:300294199;N:16468,50,,,,259102784,230364456,226008843,300294199,16468,SRX1321827,SRS1109644,SRA289450,University of Utah|Bonkowsky,University of Utah,1,0.95197,,0.30503,,0.68333,,0.52243,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,United States,2015-09-16,Hatching,Embryo,Brain,Nervous System
39837,SRR2342161,SRX1321823,SRS1109648,SRP062493,PRJNA293106,Danio rerio Raw sequence reads,PRJNA293106,Metagenomics,Zebrafish Hypoxia RNAseq,,,RNAseq at 60hpf following hypoxia,,60hpf hypoxia,,strain:TU|age:60hpf|sex:not determined|tissue:brain|treatment:hypoxia|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Embryonic Development Hypoxia Versus Normoxia RNAseq: Sample       60hpf hypoxia,60hpf.hypoxia.3.10329X27,60hpf.hypoxia.3.10329X27,We collected whole RNA from zebrafish at five different embryonic developmental stages with experimental triplicates for each stage time point and experimental condition.  For hypoxia  we placed developing embryos in pre conditioned media in a sealed plexiglass chamber set to a reduced oxygen concentration for 12 hour periods. Immediately following hypoxia or normoxia embryos were sacrificed and RNA collected.  We used 1% pO2 for ages up to 48 hpf and 4% pO2 for older ages.  At the time point for collection embryos were dissected and only head tissue was used for subsequent RNA preparation.  RNA was prepared with a miRNeasy kit Qiagen. Quality of total RNAs was checked using a NanoDrop 2000 Spectrometer and an Agilent 2100 Bioanalyzer.  The sequencing libraries were created using the Illumina TruSeq Stranded Total RNA Sample Preparation Kit with Ribo Zero. These libraries were sequenced on an Illumina HiSeq2000 sequencer for 50 cycles ie. 50 nucleotides  single end  stranded using Illumina’s version 3 chemistry. 6 samples were multiplexed together in each lane of the sequencer  providing an average yield of 25.1 million reads per sample. The base calling was performed using Illumina’s CASAVA version 1.8.2 software.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP062493,,,10329X27_130822_SN141_0719_AD2CK5ACXX_8.txt.gz,fastq,1073269500.0,21465390.0,60hpf.hypoxia.3.10329X27,0:50,A:280500644;C:237758835;G:234061287;T:320931292;N:17442,50,,,,280500644,237758835,234061287,320931292,17442,SRX1321823,SRS1109648,SRA289450,University of Utah|Bonkowsky,University of Utah,1,0.94774,,0.36354,,0.70065,,0.51075,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,United States,2015-10-10,Hatching,Embryo,Brain,Nervous System
39838,SRR2341509,SRX1321822,SRS1109643,SRP062493,PRJNA293106,Danio rerio Raw sequence reads,PRJNA293106,Metagenomics,Zebrafish Hypoxia RNAseq,,,RNAseq at 48hpf following normoxia,,48hpf normoxia,,strain:TU|age:48hpf|sex:not determined|tissue:brain|treatment:normoxia|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Embryonic Development Hypoxia Versus Normoxia RNAseq: Sample       48hpf normoxia,48hpf.normoxia.210329X26,48hpf.normoxia.210329X26,We collected whole RNA from zebrafish at five different embryonic developmental stages with experimental triplicates for each stage time point and experimental condition.  For hypoxia  we placed developing embryos in pre conditioned media in a sealed plexiglass chamber set to a reduced oxygen concentration for 12 hour periods. Immediately following hypoxia or normoxia embryos were sacrificed and RNA collected.  We used 1% pO2 for ages up to 48 hpf and 4% pO2 for older ages.  At the time point for collection embryos were dissected and only head tissue was used for subsequent RNA preparation.  RNA was prepared with a miRNeasy kit Qiagen. Quality of total RNAs was checked using a NanoDrop 2000 Spectrometer and an Agilent 2100 Bioanalyzer.  The sequencing libraries were created using the Illumina TruSeq Stranded Total RNA Sample Preparation Kit with Ribo Zero. These libraries were sequenced on an Illumina HiSeq2000 sequencer for 50 cycles ie. 50 nucleotides  single end  stranded using Illumina’s version 3 chemistry. 6 samples were multiplexed together in each lane of the sequencer  providing an average yield of 25.1 million reads per sample. The base calling was performed using Illumina’s CASAVA version 1.8.2 software.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP062493,,,10329X26_130822_SN141_0719_AD2CK5ACXX_8.txt.gz,fastq,1075868850.0,21517377.0,48hpf.normoxia.210329X26,0:50,A:271795722;C:246789566;G:240496674;T:316769688;N:17200,50,,,,271795722,246789566,240496674,316769688,17200,SRX1321822,SRS1109643,SRA289450,University of Utah|Bonkowsky,University of Utah,1,0.94644,,0.26805,,0.68745,,0.53833,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,United States,2015-10-10,Hatching,Embryo,Brain,Nervous System
39844,SRR2241311,SRX1321816,SRS1109644,SRP062493,PRJNA293106,Danio rerio Raw sequence reads,PRJNA293106,Metagenomics,Zebrafish Hypoxia RNAseq,,,RNAseq at 60hpf following normoxia,,60hpf Normoxia,,strain:TU|age:60hpf|sex:not determined|tissue:brain|treatment:normoxia|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Embryonic Development Hypoxia Versus Normoxia RNAseq: Sample       60hpf Normoxia,60hpf.normoxia.1.10329X18,60hpf.normoxia.1.10329X18,We collected whole RNA from zebrafish at five different embryonic developmental stages with experimental triplicates for each stage time point and experimental condition.  For hypoxia  we placed developing embryos in pre conditioned media in a sealed plexiglass chamber set to a reduced oxygen concentration for 12 hour periods. Immediately following hypoxia or normoxia embryos were sacrificed and RNA collected.  We used 1% pO2 for ages up to 48 hpf and 4% pO2 for older ages.  At the time point for collection embryos were dissected and only head tissue was used for subsequent RNA preparation.  RNA was prepared with a miRNeasy kit Qiagen. Quality of total RNAs was checked using a NanoDrop 2000 Spectrometer and an Agilent 2100 Bioanalyzer.  The sequencing libraries were created using the Illumina TruSeq Stranded Total RNA Sample Preparation Kit with Ribo Zero. These libraries were sequenced on an Illumina HiSeq2000 sequencer for 50 cycles ie. 50 nucleotides  single end  stranded using Illumina’s version 3 chemistry. 6 samples were multiplexed together in each lane of the sequencer  providing an average yield of 25.1 million reads per sample. The base calling was performed using Illumina’s CASAVA version 1.8.2 software.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP062493,,,10329X18_130822_SN141_0719_AD2CK5ACXX_6.txt.gz,fastq,1118115050.0,22362301.0,60hpf.normoxia.1.10329X18,0:50,A:287072563;C:255244675;G:248573701;T:327203388;N:20723,50,,,,287072563,255244675,248573701,327203388,20723,SRX1321816,SRS1109644,SRA289450,University of Utah|Bonkowsky,University of Utah,1,0.93238,,0.30064,,0.68574,,0.51934,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,United States,2015-10-10,Hatching,Embryo,Brain,Nervous System
39845,SRR2240748,SRX1321815,SRS1109648,SRP062493,PRJNA293106,Danio rerio Raw sequence reads,PRJNA293106,Metagenomics,Zebrafish Hypoxia RNAseq,,,RNAseq at 60hpf following hypoxia,,60hpf hypoxia,,strain:TU|age:60hpf|sex:not determined|tissue:brain|treatment:hypoxia|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Embryonic Development Hypoxia Versus Normoxia RNAseq: Sample       60hpf hypoxia,60hpf.hypoxia.2.10329X17,60hpf.hypoxia.2.10329X17,We collected whole RNA from zebrafish at five different embryonic developmental stages with experimental triplicates for each stage time point and experimental condition.  For hypoxia  we placed developing embryos in pre conditioned media in a sealed plexiglass chamber set to a reduced oxygen concentration for 12 hour periods. Immediately following hypoxia or normoxia embryos were sacrificed and RNA collected.  We used 1% pO2 for ages up to 48 hpf and 4% pO2 for older ages.  At the time point for collection embryos were dissected and only head tissue was used for subsequent RNA preparation.  RNA was prepared with a miRNeasy kit Qiagen. Quality of total RNAs was checked using a NanoDrop 2000 Spectrometer and an Agilent 2100 Bioanalyzer.  The sequencing libraries were created using the Illumina TruSeq Stranded Total RNA Sample Preparation Kit with Ribo Zero. These libraries were sequenced on an Illumina HiSeq2000 sequencer for 50 cycles ie. 50 nucleotides  single end  stranded using Illumina’s version 3 chemistry. 6 samples were multiplexed together in each lane of the sequencer  providing an average yield of 25.1 million reads per sample. The base calling was performed using Illumina’s CASAVA version 1.8.2 software.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP062493,,,10329X17_130822_SN141_0719_AD2CK5ACXX_6.txt.gz,fastq,1074686900.0,21493738.0,60hpf.hypoxia.2.10329X17,0:50,A:276432361;C:244039609;G:234638386;T:319556004;N:20540,50,,,,276432361,244039609,234638386,319556004,20540,SRX1321815,SRS1109648,SRA289450,University of Utah|Bonkowsky,University of Utah,1,0.9502,,0.3077,,0.6899,,0.50645,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,United States,2015-09-03,Hatching,Embryo,Brain,Nervous System
39846,SRR2239869,SRX1321814,SRS1109646,SRP062493,PRJNA293106,Danio rerio Raw sequence reads,PRJNA293106,Metagenomics,Zebrafish Hypoxia RNAseq,,,RNAseq at 48hpf following hypoxia,,48hpf hypoxia,,strain:TU|age:48hpf|sex:not determined|tissue:brain|treatment:hypoxia|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Embryonic Development Hypoxia Versus Normoxia RNAseq: Sample       48hpf hypoxia,48hpf.hypoxia.2.10329X15,48hpf.hypoxia.2.10329X15,We collected whole RNA from zebrafish at five different embryonic developmental stages with experimental triplicates for each stage time point and experimental condition.  For hypoxia  we placed developing embryos in pre conditioned media in a sealed plexiglass chamber set to a reduced oxygen concentration for 12 hour periods. Immediately following hypoxia or normoxia embryos were sacrificed and RNA collected.  We used 1% pO2 for ages up to 48 hpf and 4% pO2 for older ages.  At the time point for collection embryos were dissected and only head tissue was used for subsequent RNA preparation.  RNA was prepared with a miRNeasy kit Qiagen. Quality of total RNAs was checked using a NanoDrop 2000 Spectrometer and an Agilent 2100 Bioanalyzer.  The sequencing libraries were created using the Illumina TruSeq Stranded Total RNA Sample Preparation Kit with Ribo Zero. These libraries were sequenced on an Illumina HiSeq2000 sequencer for 50 cycles ie. 50 nucleotides  single end  stranded using Illumina’s version 3 chemistry. 6 samples were multiplexed together in each lane of the sequencer  providing an average yield of 25.1 million reads per sample. The base calling was performed using Illumina’s CASAVA version 1.8.2 software.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP062493,,,10329X15_130822_SN141_0719_AD2CK5ACXX_6.txt.gz,fastq,1111913550.0,22238271.0,48hpf.hypoxia.2.10329X15,0:50,A:288023952;C:248947169;G:243195362;T:331723738;N:23329,50,,,,288023952,248947169,243195362,331723738,23329,SRX1321814,SRS1109646,SRA289450,University of Utah|Bonkowsky,University of Utah,1,0.93753,,0.34521,,0.70246,,0.51535,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,United States,2015-10-10,Hatching,Embryo,Brain,Nervous System
39852,SRR2225888,SRX1321808,SRS1109648,SRP062493,PRJNA293106,Danio rerio Raw sequence reads,PRJNA293106,Metagenomics,Zebrafish Hypoxia RNAseq,,,RNAseq at 60hpf following hypoxia,,60hpf hypoxia,,strain:TU|age:60hpf|sex:not determined|tissue:brain|treatment:hypoxia|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Embryonic Development Hypoxia Versus Normoxia RNAseq: Sample       60hpf hypoxia,60hpf.hypoxia.1.10329X7,60hpf.hypoxia.1.10329X7,We collected whole RNA from zebrafish at five different embryonic developmental stages with experimental triplicates for each stage time point and experimental condition.  For hypoxia  we placed developing embryos in pre conditioned media in a sealed plexiglass chamber set to a reduced oxygen concentration for 12 hour periods. Immediately following hypoxia or normoxia embryos were sacrificed and RNA collected.  We used 1% pO2 for ages up to 48 hpf and 4% pO2 for older ages.  At the time point for collection embryos were dissected and only head tissue was used for subsequent RNA preparation.  RNA was prepared with a miRNeasy kit Qiagen. Quality of total RNAs was checked using a NanoDrop 2000 Spectrometer and an Agilent 2100 Bioanalyzer.  The sequencing libraries were created using the Illumina TruSeq Stranded Total RNA Sample Preparation Kit with Ribo Zero. These libraries were sequenced on an Illumina HiSeq2000 sequencer for 50 cycles ie. 50 nucleotides  single end  stranded using Illumina’s version 3 chemistry. 6 samples were multiplexed together in each lane of the sequencer  providing an average yield of 25.1 million reads per sample. The base calling was performed using Illumina’s CASAVA version 1.8.2 software.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP062493,,,10329X7_130822_SN141_0719_AD2CK5ACXX_5.txt.gz,fastq,1102232350.0,22044647.0,60hpf.hypoxia.1.10329X7,0:50,A:288570352;C:247978180;G:238128703;T:327492563;N:62552,50,,,,288570352,247978180,238128703,327492563,62552,SRX1321808,SRS1109648,SRA289450,University of Utah|Bonkowsky,University of Utah,1,0.94824,,0.31808,,0.69244,,0.51505,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,United States,2015-10-10,Hatching,Embryo,Brain,Nervous System
39853,SRR2225789,SRX1321807,SRS1109646,SRP062493,PRJNA293106,Danio rerio Raw sequence reads,PRJNA293106,Metagenomics,Zebrafish Hypoxia RNAseq,,,RNAseq at 48hpf following hypoxia,,48hpf hypoxia,,strain:TU|age:48hpf|sex:not determined|tissue:brain|treatment:hypoxia|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Embryonic Development Hypoxia Versus Normoxia RNAseq: Sample       48hpf hypoxia,48hpf.hypoxia.1.10329X6,48hpf.hypoxia.1.10329X6,We collected whole RNA from zebrafish at five different embryonic developmental stages with experimental triplicates for each stage time point and experimental condition.  For hypoxia  we placed developing embryos in pre conditioned media in a sealed plexiglass chamber set to a reduced oxygen concentration for 12 hour periods. Immediately following hypoxia or normoxia embryos were sacrificed and RNA collected.  We used 1% pO2 for ages up to 48 hpf and 4% pO2 for older ages.  At the time point for collection embryos were dissected and only head tissue was used for subsequent RNA preparation.  RNA was prepared with a miRNeasy kit Qiagen. Quality of total RNAs was checked using a NanoDrop 2000 Spectrometer and an Agilent 2100 Bioanalyzer.  The sequencing libraries were created using the Illumina TruSeq Stranded Total RNA Sample Preparation Kit with Ribo Zero. These libraries were sequenced on an Illumina HiSeq2000 sequencer for 50 cycles ie. 50 nucleotides  single end  stranded using Illumina’s version 3 chemistry. 6 samples were multiplexed together in each lane of the sequencer  providing an average yield of 25.1 million reads per sample. The base calling was performed using Illumina’s CASAVA version 1.8.2 software.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP062493,,,10329X6_130822_SN141_0719_AD2CK5ACXX_4.txt.gz,fastq,1250042950.0,25000859.0,48hpf.hypoxia.1.10329X6,0:50,A:312511165;C:283310381;G:277279378;T:376891744;N:50282,50,,,,312511165,283310381,277279378,376891744,50282,SRX1321807,SRS1109646,SRA289450,University of Utah|Bonkowsky,University of Utah,1,0.94959,,0.28331,,0.68757,,0.53976,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,United States,2015-09-01,Hatching,Embryo,Brain,Nervous System
39856,SRR2222835,SRX1321804,SRS1109643,SRP062493,PRJNA293106,Danio rerio Raw sequence reads,PRJNA293106,Metagenomics,Zebrafish Hypoxia RNAseq,,,RNAseq at 48hpf following normoxia,,48hpf normoxia,,strain:TU|age:48hpf|sex:not determined|tissue:brain|treatment:normoxia|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Embryonic Development Hypoxia Versus Normoxia RNAseq: Sample       48hpf normoxia,48hpf.1.10329X1,48hpf.1.10329X1,We collected whole RNA from zebrafish at five different embryonic developmental stages with experimental triplicates for each stage time point and experimental condition.  For hypoxia  we placed developing embryos in pre conditioned media in a sealed plexiglass chamber set to a reduced oxygen concentration for 12 hour periods. Immediately following hypoxia or normoxia embryos were sacrificed and RNA collected.  We used 1% pO2 for ages up to 48 hpf and 4% pO2 for older ages.  At the time point for collection embryos were dissected and only head tissue was used for subsequent RNA preparation.  RNA was prepared with a miRNeasy kit Qiagen. Quality of total RNAs was checked using a NanoDrop 2000 Spectrometer and an Agilent 2100 Bioanalyzer.  The sequencing libraries were created using the Illumina TruSeq Stranded Total RNA Sample Preparation Kit with Ribo Zero. These libraries were sequenced on an Illumina HiSeq2000 sequencer for 50 cycles ie. 50 nucleotides  single end  stranded using Illumina’s version 3 chemistry. 6 samples were multiplexed together in each lane of the sequencer  providing an average yield of 25.1 million reads per sample. The base calling was performed using Illumina’s CASAVA version 1.8.2 software.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP062493,,,10329X1_130822_SN141_0719_AD2CK5ACXX_4.txt.gz,fastq,1215136450.0,24302729.0,48hpf.1.10329X1,0:50,A:291802893;C:276442849;G:277217342;T:369624915;N:48451,50,,,,291802893,276442849,277217342,369624915,48451,SRX1321804,SRS1109643,SRA289450,University of Utah|Bonkowsky,University of Utah,1,0.95575,,0.23021,,0.72679,,0.60296,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,United States,2015-09-01,Hatching,Embryo,Brain,Nervous System
41297,SRR8173226,SRX4993779,SRS4029191,SRP168138,PRJNA340009,RNASeq of OMP and TRPC2 neuronal population of zebrafish olfactory sensory neurons,GSE86023,Transcriptome Analysis,RNASeq was performed on mRNA obtained from OMP expressing and TRPC2 expressing olfactory sensory neurons from 48hpf zebrafish embryos. Single cell suspensions of 48hpf olfactory epithelia were FAC sorted to obtain RFP expressing or venus expressing cells RFP sample1: 3500 cells  RFP sample2: 5500 cells. Venus sample1: 676 cells  venus sample2:201 cells. RNA was extracted using QIAGEN RNEasy kit and cDNA was synthesized using a custom oligo dT primer containing T7 promoter sequence courtesy of Jim Eberwine  University of Pennsylvanina. In vitro RNA amplification was carried out through one round for OMP:RFP neurons and through two rounds for TRPC2:venus neurons as per the protocol in Morris et al  2011. Adapter tagged libraries were synthesized using Illumina TruSeq v2.0 and deep sequenced on HiSeq2500 to obtain 100million reads per sample. Overall design: Examination of mRNA expression profiles from 2 types of olfactory sensory neurons,,pubmed:29020985,,TRPC2 2,GSM2290761,,tissue:TRPC2 expressing olfactory sensory neurons|strain:Tubingen/TLF|embryo stage:48hpf|cell type:olfactory sensory neurons|neuron subtype:TRPC2,TRPC2 2,Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence  then mapped tozebrafish GRCz10 whole genome. Reads per millionrpm values were calculated by dividing the number of read counts for a gene by the total number of uniquely mapped reads in million for that sample. Alignment – STAR algorithm Gene counts – VERSE Genome build: Ensemble zebrafish assembly GRCz10 Supplementary files format and content: Comma separated text files include raw gene counts or gene counts in reads per million for each sample,TRPC2 expressing olfactory sensory neurons,Olfactory epithelia were dissected and single cell suspensions were prepared using trypsin to dissociate the cells. Fluorescence assisted cell sorting FACS was used to obtain RFP only and venus only cell populations. Cells were collected in RNA lysis buffer.,Total cellular RNA was extracted using Qiagen Rneasy micro kit. T7 oligodT primers were used for reverse transcription of mRNA during cDNA synthesis. RNA amplification was performed using T7 Megascript kit through one for OMP neurons two rounds for TRPC2 neurons. Illumina TruSeq v2.0 kit was used as per manufacturer's protocol.,Zebrafish embryos expressing OMP:RFP or TRPC2:venus were harvested and incubated at 28.5oC till 48hpf.,strain:Tubingen/TLF|embryo stage:48hpf|cell type:olfactory sensory neurons|neuron subtype:TRPC2,GSM2290761,GSM2290761: TRPC2 2; Danio rerio; RNA Seq,GSM2290761,,1,Total cellular RNA was extracted using Qiagen Rneasy micro kit. T7 oligodT primers were used for reverse transcription of mRNA during cDNA synthesis. RNA amplification was performed using T7 Megascript kit through one for OMP neurons two rounds for TRPC2 neurons. Illumina TruSeq v2.0 kit was used as per manufacturer's protocol.,GEO Accession:GSM2290761,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP168138,,,FGC0977_s_3_1_CTTGTA.fastq.gz FGC0977_s_3_2_CTTGTA.fastq.gz,fastq fastq,19333122000.0,96665610.0,GSM2290761 r1,0:100 1:100,A:5708354504;C:3932203444;G:3891575387;T:5798440967;N:2547698,100,100,,,5708354504,3932203444,3891575387,5798440967,2547698,SRX4993779,SRS4029191,SRA807287,GEO,"Jonathan Raper, Neuroscience, University of Pennsylvania",2,0.89122,0.8929,0.18042,0.18083,0.7903,0.79182,0.61137,0.61123,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2016-08-24,Hatching,Embryo,Brain,Nervous System
41298,SRR8173225,SRX4993778,SRS4029190,SRP168138,PRJNA340009,RNASeq of OMP and TRPC2 neuronal population of zebrafish olfactory sensory neurons,GSE86023,Transcriptome Analysis,RNASeq was performed on mRNA obtained from OMP expressing and TRPC2 expressing olfactory sensory neurons from 48hpf zebrafish embryos. Single cell suspensions of 48hpf olfactory epithelia were FAC sorted to obtain RFP expressing or venus expressing cells RFP sample1: 3500 cells  RFP sample2: 5500 cells. Venus sample1: 676 cells  venus sample2:201 cells. RNA was extracted using QIAGEN RNEasy kit and cDNA was synthesized using a custom oligo dT primer containing T7 promoter sequence courtesy of Jim Eberwine  University of Pennsylvanina. In vitro RNA amplification was carried out through one round for OMP:RFP neurons and through two rounds for TRPC2:venus neurons as per the protocol in Morris et al  2011. Adapter tagged libraries were synthesized using Illumina TruSeq v2.0 and deep sequenced on HiSeq2500 to obtain 100million reads per sample. Overall design: Examination of mRNA expression profiles from 2 types of olfactory sensory neurons,,pubmed:29020985,,TRPC2 1,GSM2290760,,tissue:TRPC2 expressing olfactory sensory neurons|strain:Tubingen/TLF|embryo stage:48hpf|cell type:olfactory sensory neurons|neuron subtype:TRPC2,TRPC2 1,Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence  then mapped tozebrafish GRCz10 whole genome. Reads per millionrpm values were calculated by dividing the number of read counts for a gene by the total number of uniquely mapped reads in million for that sample. Alignment – STAR algorithm Gene counts – VERSE Genome build: Ensemble zebrafish assembly GRCz10 Supplementary files format and content: Comma separated text files include raw gene counts or gene counts in reads per million for each sample,TRPC2 expressing olfactory sensory neurons,Olfactory epithelia were dissected and single cell suspensions were prepared using trypsin to dissociate the cells. Fluorescence assisted cell sorting FACS was used to obtain RFP only and venus only cell populations. Cells were collected in RNA lysis buffer.,Total cellular RNA was extracted using Qiagen Rneasy micro kit. T7 oligodT primers were used for reverse transcription of mRNA during cDNA synthesis. RNA amplification was performed using T7 Megascript kit through one for OMP neurons two rounds for TRPC2 neurons. Illumina TruSeq v2.0 kit was used as per manufacturer's protocol.,Zebrafish embryos expressing OMP:RFP or TRPC2:venus were harvested and incubated at 28.5oC till 48hpf.,strain:Tubingen/TLF|embryo stage:48hpf|cell type:olfactory sensory neurons|neuron subtype:TRPC2,GSM2290760,GSM2290760: TRPC2 1; Danio rerio; RNA Seq,GSM2290760,,1,Total cellular RNA was extracted using Qiagen Rneasy micro kit. T7 oligodT primers were used for reverse transcription of mRNA during cDNA synthesis. RNA amplification was performed using T7 Megascript kit through one for OMP neurons two rounds for TRPC2 neurons. Illumina TruSeq v2.0 kit was used as per manufacturer's protocol.,GEO Accession:GSM2290760,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP168138,,,FGC0977_s_3_1_GCCAAT.fastq.gz FGC0977_s_3_2_GCCAAT.fastq.gz,fastq fastq,19933298800.0,99666494.0,GSM2290760 r1,0:100 1:100,A:5663223656;C:4194804658;G:4197360143;T:5875323942;N:2586401,100,100,,,5663223656,4194804658,4197360143,5875323942,2586401,SRX4993778,SRS4029190,SRA807287,GEO,"Jonathan Raper, Neuroscience, University of Pennsylvania",2,0.84844,0.84265,0.10791,0.1071,0.80886,0.81026,0.57202,0.57988,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2016-08-24,Hatching,Embryo,Brain,Nervous System
41299,SRR8173224,SRX4993777,SRS4029189,SRP168138,PRJNA340009,RNASeq of OMP and TRPC2 neuronal population of zebrafish olfactory sensory neurons,GSE86023,Transcriptome Analysis,RNASeq was performed on mRNA obtained from OMP expressing and TRPC2 expressing olfactory sensory neurons from 48hpf zebrafish embryos. Single cell suspensions of 48hpf olfactory epithelia were FAC sorted to obtain RFP expressing or venus expressing cells RFP sample1: 3500 cells  RFP sample2: 5500 cells. Venus sample1: 676 cells  venus sample2:201 cells. RNA was extracted using QIAGEN RNEasy kit and cDNA was synthesized using a custom oligo dT primer containing T7 promoter sequence courtesy of Jim Eberwine  University of Pennsylvanina. In vitro RNA amplification was carried out through one round for OMP:RFP neurons and through two rounds for TRPC2:venus neurons as per the protocol in Morris et al  2011. Adapter tagged libraries were synthesized using Illumina TruSeq v2.0 and deep sequenced on HiSeq2500 to obtain 100million reads per sample. Overall design: Examination of mRNA expression profiles from 2 types of olfactory sensory neurons,,pubmed:29020985,,OMP 2,GSM2290759,,tissue:OMP expressing olfactory sensory neurons|strain:Tubingen/TLF|embryo stage:48hpf|cell type:olfactory sensory neurons|neuron subtype:OMP,OMP 2,Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence  then mapped tozebrafish GRCz10 whole genome. Reads per millionrpm values were calculated by dividing the number of read counts for a gene by the total number of uniquely mapped reads in million for that sample. Alignment – STAR algorithm Gene counts – VERSE Genome build: Ensemble zebrafish assembly GRCz10 Supplementary files format and content: Comma separated text files include raw gene counts or gene counts in reads per million for each sample,OMP expressing olfactory sensory neurons,Olfactory epithelia were dissected and single cell suspensions were prepared using trypsin to dissociate the cells. Fluorescence assisted cell sorting FACS was used to obtain RFP only and venus only cell populations. Cells were collected in RNA lysis buffer.,Total cellular RNA was extracted using Qiagen Rneasy micro kit. T7 oligodT primers were used for reverse transcription of mRNA during cDNA synthesis. RNA amplification was performed using T7 Megascript kit through one for OMP neurons two rounds for TRPC2 neurons. Illumina TruSeq v2.0 kit was used as per manufacturer's protocol.,Zebrafish embryos expressing OMP:RFP or TRPC2:venus were harvested and incubated at 28.5oC till 48hpf.,strain:Tubingen/TLF|embryo stage:48hpf|cell type:olfactory sensory neurons|neuron subtype:OMP,GSM2290759,GSM2290759: OMP 2; Danio rerio; RNA Seq,GSM2290759,,1,Total cellular RNA was extracted using Qiagen Rneasy micro kit. T7 oligodT primers were used for reverse transcription of mRNA during cDNA synthesis. RNA amplification was performed using T7 Megascript kit through one for OMP neurons two rounds for TRPC2 neurons. Illumina TruSeq v2.0 kit was used as per manufacturer's protocol.,GEO Accession:GSM2290759,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP168138,,,FGC0805_s_6_1_CTTGTA.fastq.gz FGC0805_s_6_2_CTTGTA.fastq.gz,fastq fastq,25768751000.0,128843755.0,GSM2290759 r1,0:100 1:100,A:6815152641;C:6065596177;G:5514207833;T:7360566579;N:13227770,100,100,,,6815152641,6065596177,5514207833,7360566579,13227770,SRX4993777,SRS4029189,SRA807287,GEO,"Jonathan Raper, Neuroscience, University of Pennsylvania",2,0.94122,0.87325,0.12592,0.11103,0.7235,0.73563,0.4808,0.5167,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2016-08-24,Hatching,Embryo,Brain,Nervous System
41300,SRR8173223,SRX4993776,SRS4029188,SRP168138,PRJNA340009,RNASeq of OMP and TRPC2 neuronal population of zebrafish olfactory sensory neurons,GSE86023,Transcriptome Analysis,RNASeq was performed on mRNA obtained from OMP expressing and TRPC2 expressing olfactory sensory neurons from 48hpf zebrafish embryos. Single cell suspensions of 48hpf olfactory epithelia were FAC sorted to obtain RFP expressing or venus expressing cells RFP sample1: 3500 cells  RFP sample2: 5500 cells. Venus sample1: 676 cells  venus sample2:201 cells. RNA was extracted using QIAGEN RNEasy kit and cDNA was synthesized using a custom oligo dT primer containing T7 promoter sequence courtesy of Jim Eberwine  University of Pennsylvanina. In vitro RNA amplification was carried out through one round for OMP:RFP neurons and through two rounds for TRPC2:venus neurons as per the protocol in Morris et al  2011. Adapter tagged libraries were synthesized using Illumina TruSeq v2.0 and deep sequenced on HiSeq2500 to obtain 100million reads per sample. Overall design: Examination of mRNA expression profiles from 2 types of olfactory sensory neurons,,pubmed:29020985,,OMP 1,GSM2290758,,tissue:OMP expressing olfactory sensory neurons|strain:Tubingen/TLF|embryo stage:48hpf|cell type:olfactory sensory neurons|neuron subtype:OMP,OMP 1,Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence  then mapped tozebrafish GRCz10 whole genome. Reads per millionrpm values were calculated by dividing the number of read counts for a gene by the total number of uniquely mapped reads in million for that sample. Alignment – STAR algorithm Gene counts – VERSE Genome build: Ensemble zebrafish assembly GRCz10 Supplementary files format and content: Comma separated text files include raw gene counts or gene counts in reads per million for each sample,OMP expressing olfactory sensory neurons,Olfactory epithelia were dissected and single cell suspensions were prepared using trypsin to dissociate the cells. Fluorescence assisted cell sorting FACS was used to obtain RFP only and venus only cell populations. Cells were collected in RNA lysis buffer.,Total cellular RNA was extracted using Qiagen Rneasy micro kit. T7 oligodT primers were used for reverse transcription of mRNA during cDNA synthesis. RNA amplification was performed using T7 Megascript kit through one for OMP neurons two rounds for TRPC2 neurons. Illumina TruSeq v2.0 kit was used as per manufacturer's protocol.,Zebrafish embryos expressing OMP:RFP or TRPC2:venus were harvested and incubated at 28.5oC till 48hpf.,strain:Tubingen/TLF|embryo stage:48hpf|cell type:olfactory sensory neurons|neuron subtype:OMP,GSM2290758,GSM2290758: OMP 1; Danio rerio; RNA Seq,GSM2290758,,1,Total cellular RNA was extracted using Qiagen Rneasy micro kit. T7 oligodT primers were used for reverse transcription of mRNA during cDNA synthesis. RNA amplification was performed using T7 Megascript kit through one for OMP neurons two rounds for TRPC2 neurons. Illumina TruSeq v2.0 kit was used as per manufacturer's protocol.,GEO Accession:GSM2290758,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP168138,,,FGC0805_s_6_2_GCCAAT.fastq.gz FGC0805_s_6_1_GCCAAT.fastq.gz,fastq fastq,24051320600.0,120256603.0,GSM2290758 r1,0:100 1:100,A:6601023193;C:5427909703;G:4902326306;T:7107644194;N:12417204,100,100,,,6601023193,5427909703,4902326306,7107644194,12417204,SRX4993776,SRS4029188,SRA807287,GEO,"Jonathan Raper, Neuroscience, University of Pennsylvania",2,0.92859,0.84572,0.19924,0.173,0.71713,0.73154,0.54902,0.55157,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2016-08-24,Hatching,Embryo,Brain,Nervous System
48097,SRR7041789,SRX3973827,SRS3199286,SRP141198,PRJNA451019,Potential role of gas6 in zebrafish hindbrain development,GSE113396,Transcriptome Analysis,identification of differentially expressed genes in gas6 homozygous mutant hindbrain when compared to wildtype hindbrain in zebrafish Overall design: Total RNA was extracted from dissected hindbrain of gas6 homzygous mutants and wildtype embryos at 48hpf using the RNeasy Mini Kit Qiagen. Three libraries from wildtype embryos and three libraries from gas6 mutants were then generated from 3mg RNA using the TruSeq Stranded mRNA Library Prep Kit Illumina. All libraries were analyzed for quality on a bioanalyzer prior to sequencing Agilent 2100 BioAnalyzer.,parent bioproject:PRJNA451178,pubmed:29945667,,gas6 /  mutant replicate 3 gas6mut,GSM3105075,,source name:dissected hindbrain|developmental stage:48 hpf /  mutant|tissue:hindbrain,gas6 /  mutant replicate 3 gas6mut,reads quality check with FastQC alignment and read counts with RSEM v1.2.28 Normalized abundance measurements and identification of differentially expressed genes with DESeq2 Genome build: GRCz10/DanRer7 Supplementary files format and content: .tsv containing read count tmp values from each replicate  adjusted p values  and fold change compared to wildtype samples for all genes detected,dissected hindbrain,,Total RNA was extracted from dissected hindbrain of gas6 homzygous mutants and wildtype embryos at 48hpf using the RNeasy Mini Kit Qiagen. Three libraries from wildtype embryos and three libraries from gas6 mutants were then generated from 3mg RNA using the TruSeq Stranded mRNA Library Prep Kit Illumina. All libraries were analyzed for quality on a bioanalyzer prior to sequencing Agilent 2100 BioAnalyzer.,zebrafish egg water maintained at 28°C,developmental stage:48 hpf /  mutant|tissue:hindbrain,GSM3105075,GSM3105075: gas6 /  mutant replicate 3 gas6mut; Danio rerio; RNA Seq,GSM3105075,,1,Total RNA was extracted from dissected hindbrain of gas6 homzygous mutants and wildtype embryos at 48hpf using the RNeasy Mini Kit Qiagen. Three libraries from wildtype embryos and three libraries from gas6 mutants were then generated from 3mg RNA using the TruSeq Stranded mRNA Library Prep Kit Illumina. All libraries were analyzed for quality on a bioanalyzer prior to sequencing Agilent 2100 BioAnalyzer.,GEO Accession:GSM3105075,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP141198,,,Mut3.fastq.gz,fastq,3795018900.0,37950189.0,GSM3105075 r1,0:100,A:918996199;C:928143353;G:923182529;T:1021402181;N:3294638,100,,,,918996199,928143353,923182529,1021402181,3294638,SRX3973827,SRS3199286,SRA693051,GEO,"Biochemistry and Molecular Pharmacology, UMass Medical School",1,0.95946,,0.06073,,0.68235,,0.46562,,100,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United States,2018-04-19,Hatching,Embryo,Brain,Nervous System
48098,SRR7041788,SRX3973826,SRS3199287,SRP141198,PRJNA451019,Potential role of gas6 in zebrafish hindbrain development,GSE113396,Transcriptome Analysis,identification of differentially expressed genes in gas6 homozygous mutant hindbrain when compared to wildtype hindbrain in zebrafish Overall design: Total RNA was extracted from dissected hindbrain of gas6 homzygous mutants and wildtype embryos at 48hpf using the RNeasy Mini Kit Qiagen. Three libraries from wildtype embryos and three libraries from gas6 mutants were then generated from 3mg RNA using the TruSeq Stranded mRNA Library Prep Kit Illumina. All libraries were analyzed for quality on a bioanalyzer prior to sequencing Agilent 2100 BioAnalyzer.,parent bioproject:PRJNA451178,pubmed:29945667,,gas6 /  mutant replicate 2 gas6mut,GSM3105074,,source name:dissected hindbrain|developmental stage:48 hpf /  mutant|tissue:hindbrain,gas6 /  mutant replicate 2 gas6mut,reads quality check with FastQC alignment and read counts with RSEM v1.2.28 Normalized abundance measurements and identification of differentially expressed genes with DESeq2 Genome build: GRCz10/DanRer7 Supplementary files format and content: .tsv containing read count tmp values from each replicate  adjusted p values  and fold change compared to wildtype samples for all genes detected,dissected hindbrain,,Total RNA was extracted from dissected hindbrain of gas6 homzygous mutants and wildtype embryos at 48hpf using the RNeasy Mini Kit Qiagen. Three libraries from wildtype embryos and three libraries from gas6 mutants were then generated from 3mg RNA using the TruSeq Stranded mRNA Library Prep Kit Illumina. All libraries were analyzed for quality on a bioanalyzer prior to sequencing Agilent 2100 BioAnalyzer.,zebrafish egg water maintained at 28°C,developmental stage:48 hpf /  mutant|tissue:hindbrain,GSM3105074,GSM3105074: gas6 /  mutant replicate 2 gas6mut; Danio rerio; RNA Seq,GSM3105074,,1,Total RNA was extracted from dissected hindbrain of gas6 homzygous mutants and wildtype embryos at 48hpf using the RNeasy Mini Kit Qiagen. Three libraries from wildtype embryos and three libraries from gas6 mutants were then generated from 3mg RNA using the TruSeq Stranded mRNA Library Prep Kit Illumina. All libraries were analyzed for quality on a bioanalyzer prior to sequencing Agilent 2100 BioAnalyzer.,GEO Accession:GSM3105074,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP141198,,,Mut2.fastq.gz,fastq,3729663500.0,37296635.0,GSM3105074 r1,0:100,A:909818849;C:902636895;G:904978335;T:1008966488;N:3262933,100,,,,909818849,902636895,904978335,1008966488,3262933,SRX3973826,SRS3199287,SRA693051,GEO,"Biochemistry and Molecular Pharmacology, UMass Medical School",1,0.95717,,0.06681,,0.68217,,0.46864,,100,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United States,2018-04-19,Hatching,Embryo,Brain,Nervous System
48099,SRR7041787,SRX3973825,SRS3199285,SRP141198,PRJNA451019,Potential role of gas6 in zebrafish hindbrain development,GSE113396,Transcriptome Analysis,identification of differentially expressed genes in gas6 homozygous mutant hindbrain when compared to wildtype hindbrain in zebrafish Overall design: Total RNA was extracted from dissected hindbrain of gas6 homzygous mutants and wildtype embryos at 48hpf using the RNeasy Mini Kit Qiagen. Three libraries from wildtype embryos and three libraries from gas6 mutants were then generated from 3mg RNA using the TruSeq Stranded mRNA Library Prep Kit Illumina. All libraries were analyzed for quality on a bioanalyzer prior to sequencing Agilent 2100 BioAnalyzer.,parent bioproject:PRJNA451178,pubmed:29945667,,gas6 /  mutant replicate 1 gas6mut,GSM3105073,,source name:dissected hindbrain|developmental stage:48 hpf /  mutant|tissue:hindbrain,gas6 /  mutant replicate 1 gas6mut,reads quality check with FastQC alignment and read counts with RSEM v1.2.28 Normalized abundance measurements and identification of differentially expressed genes with DESeq2 Genome build: GRCz10/DanRer7 Supplementary files format and content: .tsv containing read count tmp values from each replicate  adjusted p values  and fold change compared to wildtype samples for all genes detected,dissected hindbrain,,Total RNA was extracted from dissected hindbrain of gas6 homzygous mutants and wildtype embryos at 48hpf using the RNeasy Mini Kit Qiagen. Three libraries from wildtype embryos and three libraries from gas6 mutants were then generated from 3mg RNA using the TruSeq Stranded mRNA Library Prep Kit Illumina. All libraries were analyzed for quality on a bioanalyzer prior to sequencing Agilent 2100 BioAnalyzer.,zebrafish egg water maintained at 28°C,developmental stage:48 hpf /  mutant|tissue:hindbrain,GSM3105073,GSM3105073: gas6 /  mutant replicate 1 gas6mut; Danio rerio; RNA Seq,GSM3105073,,1,Total RNA was extracted from dissected hindbrain of gas6 homzygous mutants and wildtype embryos at 48hpf using the RNeasy Mini Kit Qiagen. Three libraries from wildtype embryos and three libraries from gas6 mutants were then generated from 3mg RNA using the TruSeq Stranded mRNA Library Prep Kit Illumina. All libraries were analyzed for quality on a bioanalyzer prior to sequencing Agilent 2100 BioAnalyzer.,GEO Accession:GSM3105073,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP141198,,,Mut1.fastq.gz,fastq,2554222700.0,25542227.0,GSM3105073 r1,0:100,A:629483819;C:619623433;G:604226674;T:698705739;N:2183035,100,,,,629483819,619623433,604226674,698705739,2183035,SRX3973825,SRS3199285,SRA693051,GEO,"Biochemistry and Molecular Pharmacology, UMass Medical School",1,0.9561,,0.07094,,0.67838,,0.46772,,100,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United States,2018-04-19,Hatching,Embryo,Brain,Nervous System
48100,SRR7041786,SRX3973824,SRS3199283,SRP141198,PRJNA451019,Potential role of gas6 in zebrafish hindbrain development,GSE113396,Transcriptome Analysis,identification of differentially expressed genes in gas6 homozygous mutant hindbrain when compared to wildtype hindbrain in zebrafish Overall design: Total RNA was extracted from dissected hindbrain of gas6 homzygous mutants and wildtype embryos at 48hpf using the RNeasy Mini Kit Qiagen. Three libraries from wildtype embryos and three libraries from gas6 mutants were then generated from 3mg RNA using the TruSeq Stranded mRNA Library Prep Kit Illumina. All libraries were analyzed for quality on a bioanalyzer prior to sequencing Agilent 2100 BioAnalyzer.,parent bioproject:PRJNA451178,pubmed:29945667,,wildtype control replicate 3 gas6mut,GSM3105072,,source name:dissected hindbrain|developmental stage:48 hpf control|tissue:hindbrain,wildtype control replicate 3 gas6mut,reads quality check with FastQC alignment and read counts with RSEM v1.2.28 Normalized abundance measurements and identification of differentially expressed genes with DESeq2 Genome build: GRCz10/DanRer7 Supplementary files format and content: .tsv containing read count tmp values from each replicate  adjusted p values  and fold change compared to wildtype samples for all genes detected,dissected hindbrain,,Total RNA was extracted from dissected hindbrain of gas6 homzygous mutants and wildtype embryos at 48hpf using the RNeasy Mini Kit Qiagen. Three libraries from wildtype embryos and three libraries from gas6 mutants were then generated from 3mg RNA using the TruSeq Stranded mRNA Library Prep Kit Illumina. All libraries were analyzed for quality on a bioanalyzer prior to sequencing Agilent 2100 BioAnalyzer.,zebrafish egg water maintained at 28°C,developmental stage:48 hpf control|tissue:hindbrain,GSM3105072,GSM3105072: wildtype control replicate 3 gas6mut; Danio rerio; RNA Seq,GSM3105072,,1,Total RNA was extracted from dissected hindbrain of gas6 homzygous mutants and wildtype embryos at 48hpf using the RNeasy Mini Kit Qiagen. Three libraries from wildtype embryos and three libraries from gas6 mutants were then generated from 3mg RNA using the TruSeq Stranded mRNA Library Prep Kit Illumina. All libraries were analyzed for quality on a bioanalyzer prior to sequencing Agilent 2100 BioAnalyzer.,GEO Accession:GSM3105072,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP141198,,,WT3.fastq.gz,fastq,3024416800.0,30244168.0,GSM3105072 r1,0:100,A:748173237;C:725813083;G:722763689;T:825021244;N:2645547,100,,,,748173237,725813083,722763689,825021244,2645547,SRX3973824,SRS3199283,SRA693051,GEO,"Biochemistry and Molecular Pharmacology, UMass Medical School",1,0.95777,,0.0748,,0.69059,,0.46902,,100,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United States,2018-04-19,Hatching,Embryo,Brain,Nervous System
48101,SRR7041785,SRX3973823,SRS3199284,SRP141198,PRJNA451019,Potential role of gas6 in zebrafish hindbrain development,GSE113396,Transcriptome Analysis,identification of differentially expressed genes in gas6 homozygous mutant hindbrain when compared to wildtype hindbrain in zebrafish Overall design: Total RNA was extracted from dissected hindbrain of gas6 homzygous mutants and wildtype embryos at 48hpf using the RNeasy Mini Kit Qiagen. Three libraries from wildtype embryos and three libraries from gas6 mutants were then generated from 3mg RNA using the TruSeq Stranded mRNA Library Prep Kit Illumina. All libraries were analyzed for quality on a bioanalyzer prior to sequencing Agilent 2100 BioAnalyzer.,parent bioproject:PRJNA451178,pubmed:29945667,,wildtype control replicate 2 gas6mut,GSM3105071,,source name:dissected hindbrain|developmental stage:48 hpf control|tissue:hindbrain,wildtype control replicate 2 gas6mut,reads quality check with FastQC alignment and read counts with RSEM v1.2.28 Normalized abundance measurements and identification of differentially expressed genes with DESeq2 Genome build: GRCz10/DanRer7 Supplementary files format and content: .tsv containing read count tmp values from each replicate  adjusted p values  and fold change compared to wildtype samples for all genes detected,dissected hindbrain,,Total RNA was extracted from dissected hindbrain of gas6 homzygous mutants and wildtype embryos at 48hpf using the RNeasy Mini Kit Qiagen. Three libraries from wildtype embryos and three libraries from gas6 mutants were then generated from 3mg RNA using the TruSeq Stranded mRNA Library Prep Kit Illumina. All libraries were analyzed for quality on a bioanalyzer prior to sequencing Agilent 2100 BioAnalyzer.,zebrafish egg water maintained at 28°C,developmental stage:48 hpf control|tissue:hindbrain,GSM3105071,GSM3105071: wildtype control replicate 2 gas6mut; Danio rerio; RNA Seq,GSM3105071,,1,Total RNA was extracted from dissected hindbrain of gas6 homzygous mutants and wildtype embryos at 48hpf using the RNeasy Mini Kit Qiagen. Three libraries from wildtype embryos and three libraries from gas6 mutants were then generated from 3mg RNA using the TruSeq Stranded mRNA Library Prep Kit Illumina. All libraries were analyzed for quality on a bioanalyzer prior to sequencing Agilent 2100 BioAnalyzer.,GEO Accession:GSM3105071,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP141198,,,WT2.fastq.gz,fastq,3358506900.0,33585069.0,GSM3105071 r1,0:100,A:816072735;C:817548352;G:813692655;T:908273519;N:2919639,100,,,,816072735,817548352,813692655,908273519,2919639,SRX3973823,SRS3199284,SRA693051,GEO,"Biochemistry and Molecular Pharmacology, UMass Medical School",1,0.9596,,0.06574,,0.69197,,0.46749,,100,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United States,2018-04-19,Hatching,Embryo,Brain,Nervous System
48102,SRR7041784,SRX3973822,SRS3199282,SRP141198,PRJNA451019,Potential role of gas6 in zebrafish hindbrain development,GSE113396,Transcriptome Analysis,identification of differentially expressed genes in gas6 homozygous mutant hindbrain when compared to wildtype hindbrain in zebrafish Overall design: Total RNA was extracted from dissected hindbrain of gas6 homzygous mutants and wildtype embryos at 48hpf using the RNeasy Mini Kit Qiagen. Three libraries from wildtype embryos and three libraries from gas6 mutants were then generated from 3mg RNA using the TruSeq Stranded mRNA Library Prep Kit Illumina. All libraries were analyzed for quality on a bioanalyzer prior to sequencing Agilent 2100 BioAnalyzer.,parent bioproject:PRJNA451178,pubmed:29945667,,wildtype control replicate 1 gas6mut,GSM3105070,,source name:dissected hindbrain|developmental stage:48 hpf control|tissue:hindbrain,wildtype control replicate 1 gas6mut,reads quality check with FastQC alignment and read counts with RSEM v1.2.28 Normalized abundance measurements and identification of differentially expressed genes with DESeq2 Genome build: GRCz10/DanRer7 Supplementary files format and content: .tsv containing read count tmp values from each replicate  adjusted p values  and fold change compared to wildtype samples for all genes detected,dissected hindbrain,,Total RNA was extracted from dissected hindbrain of gas6 homzygous mutants and wildtype embryos at 48hpf using the RNeasy Mini Kit Qiagen. Three libraries from wildtype embryos and three libraries from gas6 mutants were then generated from 3mg RNA using the TruSeq Stranded mRNA Library Prep Kit Illumina. All libraries were analyzed for quality on a bioanalyzer prior to sequencing Agilent 2100 BioAnalyzer.,zebrafish egg water maintained at 28°C,developmental stage:48 hpf control|tissue:hindbrain,GSM3105070,GSM3105070: wildtype control replicate 1 gas6mut; Danio rerio; RNA Seq,GSM3105070,,1,Total RNA was extracted from dissected hindbrain of gas6 homzygous mutants and wildtype embryos at 48hpf using the RNeasy Mini Kit Qiagen. Three libraries from wildtype embryos and three libraries from gas6 mutants were then generated from 3mg RNA using the TruSeq Stranded mRNA Library Prep Kit Illumina. All libraries were analyzed for quality on a bioanalyzer prior to sequencing Agilent 2100 BioAnalyzer.,GEO Accession:GSM3105070,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP141198,,,WT1.fastq.gz,fastq,3390648900.0,33906489.0,GSM3105070 r1,0:100,A:815584808;C:833592815;G:824903141;T:913622836;N:2945300,100,,,,815584808,833592815,824903141,913622836,2945300,SRX3973822,SRS3199282,SRA693051,GEO,"Biochemistry and Molecular Pharmacology, UMass Medical School",1,0.96267,,0.05448,,0.69798,,0.46774,,100,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United States,2018-04-19,Hatching,Embryo,Brain,Nervous System
59879,SRR12060553,SRX8588729,SRS6880197,SRP268145,PRJNA640816,An atlas of neural crest lineages along the posterior developing zebrafish at single cell resolution,GSE152906,Transcriptome Analysis,Neural crest cells NCCs are vertebrate stem cells that give rise to various cell types throughout the developing body in early life. Here  we utilized single cell transcriptomic analyses to delineate NCC derivatives along the posterior developing vertebrate  zebrafish  during the late embryonic to early larval stage  a period when NCCs are actively differentiating into distinct cellular lineages. We identified several major NCC/NCC derived cell types including mesenchyme  neural crest  neural  neuronal  glial  and pigment  from which we resolved over three dozen cellular subtypes. We dissected gene expression signatures of pigment progenitors delineating into chromatophore lineages  mesenchyme subtypes  and enteric NCCs transforming into enteric neurons. Global analysis of NCC derivatives revealed they were demarcated by combinatorial hox gene codes  with distinct profiles within neuronal cells. From these analyses  we present a comprehensive cell type atlas that can be utilized as a valuable resource for further mechanistic and evolutionary investigations of NCC differentiation. Overall design: To characterize the neural crest cell lineages present in the posterior zebrafish during the embryonic to larval transition 48 hpf 72 hpf we utilized single cell RNA sequencing scRNA Seq on the 10x Genomics Chromium platform to build a dataset from GFP+ cells collected from sox10:GFP embryos.,,pubmed:33591267;pubmed:38234831;pubmed:38809858,,Sox10+ 68 70hpf,GSM4629199,,tissue:Derivative Sox10+ Neural Crest|genotype/variation: 4.9sox10:EGFP ba2Tg|developmental stage:68 hpf 70 hpf|cell type:FACS isolated  4.9sox10:EGFP+ cells,Sox10+ 68 70hpf,Illumina NextSeq 500 used for basecalling CellRanger v2.1.0 software facilitated genomic alignment  filtering  barcode reading  and exportation for further analysis Genome build: DanioGRCz10 Supplementary files format and content: 10X Genomics Chromim Filtered Gene BC Cellular Barcodes barcodes.tsv and genes genes.tsv; 10X Genomics Chromium Raw Gene BC Cellular Matrix matrix.mtx,Derivative Sox10+ Neural Crest,none,Posterior tissue Vagal and trunk domains were harvested; Single cell suspension was prepared via digestion in 37°C 1X Accumax buffer Sigma Aldrich  A7089 for 30 45 minutes. Suspension was washed in Hank's Buffer 1x HBSS; 2.5 mg/mL BSA; 10μM pH8 HEPES  concentrated via centrifugation 200 rcf for 10 minutes at 4°C in a small volume of Hank's buffer  and sorted for GFP+ cells via FACS. GFP+ cells were used as input for the 10X Genomics Chromium platform using the 10X Single Cell 3’ V2 chemistry kit for 10 000 cells. RNA libraries were prepared for sequencing using standard Illumina protocols following the 10x Genomics pipeline,Embryos were collected synchronously  batched by stage. All embryos were raised according to standard practices in E3 embryonic media for the first 24 hours and then transfered to 1X 1 phenyl 2 thiourea PTU/E3 solution. At 24 hpf  embryos were sorted manually for GFP expression. Developmentally delayed or malformed embryos were removed. All work was conducted under protocols approved by and in accordance with  Rice University Institutional Animal Care and Use Committee IACUC.,genotype/variation: 4.9sox10:EGFP ba2Tg|developmental stage:68 hpf 70 hpf|cell type:FACS isolated  4.9sox10:EGFP+ cells,GSM4629199,GSM4629199: Sox10+ 68 70hpf; Danio rerio; RNA Seq,GSM4629199,,1,Posterior tissue Vagal and trunk domains were harvested; Single cell suspension was prepared via digestion in 37°C 1X Accumax buffer Sigma Aldrich  A7089 for 30 45 minutes. Suspension was washed in Hank's Buffer 1x HBSS; 2.5 mg/mL BSA; 10μM pH8 HEPES  concentrated via centrifugation 200 rcf for 10 minutes at 4°C in a small volume of Hank's buffer  and sorted for GFP+ cells via FACS. GFP+ cells were used as input for the 10X Genomics Chromium platform using the 10X Single Cell three prime V2 chemistry kit for 10 000 cells. RNA libraries were prepared for sequencing using standard Illumina protocols following the 10x Genomics pipeline,GEO Accession:GSM4629199,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP268145,,loader:fastq load.py|options:  platform=Illumina   readTypes=BBT   read1PairFiles=GFPplus S1 L001 R1 001.fastq   read2PairFiles=GFPplus S1 L001 R2 001.fastq   read3PairFiles=GFPplus S1 L001 I1 001.fastq,GFPplus_S1_L001_I1_001.fastq GFPplus_S1_L001_R1_001.fastq GFPplus_S1_L001_R2_001.fastq,fastq fastq fastq,6274319830.0,39710885.0,GSM4629199 r1,0:26 1:124 2:8,A:1841798453;C:1283501945;G:1425301974;T:1723079104;N:638354,26,124,8,,1841798453,1283501945,1425301974,1723079104,638354,SRX8588729,SRS6880197,SRA1089349,GEO,"The Uribe Laboratory, BioSciences, Rice University",2,0.00247,0.91739,0.00057,0.08148,0.99486,0.8098,0.40168,0.49704,26,124,T,B,sc-like readlen,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2020-06-20,Hatching,Embryo,Brain,Nervous System
59880,SRR12060554,SRX8588729,SRS6880197,SRP268145,PRJNA640816,An atlas of neural crest lineages along the posterior developing zebrafish at single cell resolution,GSE152906,Transcriptome Analysis,Neural crest cells NCCs are vertebrate stem cells that give rise to various cell types throughout the developing body in early life. Here  we utilized single cell transcriptomic analyses to delineate NCC derivatives along the posterior developing vertebrate  zebrafish  during the late embryonic to early larval stage  a period when NCCs are actively differentiating into distinct cellular lineages. We identified several major NCC/NCC derived cell types including mesenchyme  neural crest  neural  neuronal  glial  and pigment  from which we resolved over three dozen cellular subtypes. We dissected gene expression signatures of pigment progenitors delineating into chromatophore lineages  mesenchyme subtypes  and enteric NCCs transforming into enteric neurons. Global analysis of NCC derivatives revealed they were demarcated by combinatorial hox gene codes  with distinct profiles within neuronal cells. From these analyses  we present a comprehensive cell type atlas that can be utilized as a valuable resource for further mechanistic and evolutionary investigations of NCC differentiation. Overall design: To characterize the neural crest cell lineages present in the posterior zebrafish during the embryonic to larval transition 48 hpf 72 hpf we utilized single cell RNA sequencing scRNA Seq on the 10x Genomics Chromium platform to build a dataset from GFP+ cells collected from sox10:GFP embryos.,,pubmed:33591267;pubmed:38234831;pubmed:38809858,,Sox10+ 68 70hpf,GSM4629199,,tissue:Derivative Sox10+ Neural Crest|genotype/variation: 4.9sox10:EGFP ba2Tg|developmental stage:68 hpf 70 hpf|cell type:FACS isolated  4.9sox10:EGFP+ cells,Sox10+ 68 70hpf,Illumina NextSeq 500 used for basecalling CellRanger v2.1.0 software facilitated genomic alignment  filtering  barcode reading  and exportation for further analysis Genome build: DanioGRCz10 Supplementary files format and content: 10X Genomics Chromim Filtered Gene BC Cellular Barcodes barcodes.tsv and genes genes.tsv; 10X Genomics Chromium Raw Gene BC Cellular Matrix matrix.mtx,Derivative Sox10+ Neural Crest,none,Posterior tissue Vagal and trunk domains were harvested; Single cell suspension was prepared via digestion in 37°C 1X Accumax buffer Sigma Aldrich  A7089 for 30 45 minutes. Suspension was washed in Hank's Buffer 1x HBSS; 2.5 mg/mL BSA; 10μM pH8 HEPES  concentrated via centrifugation 200 rcf for 10 minutes at 4°C in a small volume of Hank's buffer  and sorted for GFP+ cells via FACS. GFP+ cells were used as input for the 10X Genomics Chromium platform using the 10X Single Cell 3’ V2 chemistry kit for 10 000 cells. RNA libraries were prepared for sequencing using standard Illumina protocols following the 10x Genomics pipeline,Embryos were collected synchronously  batched by stage. All embryos were raised according to standard practices in E3 embryonic media for the first 24 hours and then transfered to 1X 1 phenyl 2 thiourea PTU/E3 solution. At 24 hpf  embryos were sorted manually for GFP expression. Developmentally delayed or malformed embryos were removed. All work was conducted under protocols approved by and in accordance with  Rice University Institutional Animal Care and Use Committee IACUC.,genotype/variation: 4.9sox10:EGFP ba2Tg|developmental stage:68 hpf 70 hpf|cell type:FACS isolated  4.9sox10:EGFP+ cells,GSM4629199,GSM4629199: Sox10+ 68 70hpf; Danio rerio; RNA Seq,GSM4629199,,1,Posterior tissue Vagal and trunk domains were harvested; Single cell suspension was prepared via digestion in 37°C 1X Accumax buffer Sigma Aldrich  A7089 for 30 45 minutes. Suspension was washed in Hank's Buffer 1x HBSS; 2.5 mg/mL BSA; 10μM pH8 HEPES  concentrated via centrifugation 200 rcf for 10 minutes at 4°C in a small volume of Hank's buffer  and sorted for GFP+ cells via FACS. GFP+ cells were used as input for the 10X Genomics Chromium platform using the 10X Single Cell three prime V2 chemistry kit for 10 000 cells. RNA libraries were prepared for sequencing using standard Illumina protocols following the 10x Genomics pipeline,GEO Accession:GSM4629199,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP268145,,loader:fastq load.py|options:  platform=Illumina   readTypes=BBT   read1PairFiles=GFPplus S1 L002 R1 001.fastq   read2PairFiles=GFPplus S1 L002 R2 001.fastq   read3PairFiles=GFPplus S1 L002 I1 001.fastq,,,3615497884.0,22882898.0,GSM4629199 r2,0:26 1:124 2:8,A:1062722875;C:724671651;G:825496420;T:1002262450;N:344488,26,124,8,,1062722875,724671651,825496420,1002262450,344488,SRX8588729,SRS6880197,SRA1089349,GEO,"The Uribe Laboratory, BioSciences, Rice University",2,0.00228,0.91709,0.00071,0.08087,0.99557,0.80984,0.37288,0.50652,26,124,T,B,sc-like readlen,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2020-06-20,Hatching,Embryo,Brain,Nervous System
59881,SRR12060555,SRX8588729,SRS6880197,SRP268145,PRJNA640816,An atlas of neural crest lineages along the posterior developing zebrafish at single cell resolution,GSE152906,Transcriptome Analysis,Neural crest cells NCCs are vertebrate stem cells that give rise to various cell types throughout the developing body in early life. Here  we utilized single cell transcriptomic analyses to delineate NCC derivatives along the posterior developing vertebrate  zebrafish  during the late embryonic to early larval stage  a period when NCCs are actively differentiating into distinct cellular lineages. We identified several major NCC/NCC derived cell types including mesenchyme  neural crest  neural  neuronal  glial  and pigment  from which we resolved over three dozen cellular subtypes. We dissected gene expression signatures of pigment progenitors delineating into chromatophore lineages  mesenchyme subtypes  and enteric NCCs transforming into enteric neurons. Global analysis of NCC derivatives revealed they were demarcated by combinatorial hox gene codes  with distinct profiles within neuronal cells. From these analyses  we present a comprehensive cell type atlas that can be utilized as a valuable resource for further mechanistic and evolutionary investigations of NCC differentiation. Overall design: To characterize the neural crest cell lineages present in the posterior zebrafish during the embryonic to larval transition 48 hpf 72 hpf we utilized single cell RNA sequencing scRNA Seq on the 10x Genomics Chromium platform to build a dataset from GFP+ cells collected from sox10:GFP embryos.,,pubmed:33591267;pubmed:38234831;pubmed:38809858,,Sox10+ 68 70hpf,GSM4629199,,tissue:Derivative Sox10+ Neural Crest|genotype/variation: 4.9sox10:EGFP ba2Tg|developmental stage:68 hpf 70 hpf|cell type:FACS isolated  4.9sox10:EGFP+ cells,Sox10+ 68 70hpf,Illumina NextSeq 500 used for basecalling CellRanger v2.1.0 software facilitated genomic alignment  filtering  barcode reading  and exportation for further analysis Genome build: DanioGRCz10 Supplementary files format and content: 10X Genomics Chromim Filtered Gene BC Cellular Barcodes barcodes.tsv and genes genes.tsv; 10X Genomics Chromium Raw Gene BC Cellular Matrix matrix.mtx,Derivative Sox10+ Neural Crest,none,Posterior tissue Vagal and trunk domains were harvested; Single cell suspension was prepared via digestion in 37°C 1X Accumax buffer Sigma Aldrich  A7089 for 30 45 minutes. Suspension was washed in Hank's Buffer 1x HBSS; 2.5 mg/mL BSA; 10μM pH8 HEPES  concentrated via centrifugation 200 rcf for 10 minutes at 4°C in a small volume of Hank's buffer  and sorted for GFP+ cells via FACS. GFP+ cells were used as input for the 10X Genomics Chromium platform using the 10X Single Cell 3’ V2 chemistry kit for 10 000 cells. RNA libraries were prepared for sequencing using standard Illumina protocols following the 10x Genomics pipeline,Embryos were collected synchronously  batched by stage. All embryos were raised according to standard practices in E3 embryonic media for the first 24 hours and then transfered to 1X 1 phenyl 2 thiourea PTU/E3 solution. At 24 hpf  embryos were sorted manually for GFP expression. Developmentally delayed or malformed embryos were removed. All work was conducted under protocols approved by and in accordance with  Rice University Institutional Animal Care and Use Committee IACUC.,genotype/variation: 4.9sox10:EGFP ba2Tg|developmental stage:68 hpf 70 hpf|cell type:FACS isolated  4.9sox10:EGFP+ cells,GSM4629199,GSM4629199: Sox10+ 68 70hpf; Danio rerio; RNA Seq,GSM4629199,,1,Posterior tissue Vagal and trunk domains were harvested; Single cell suspension was prepared via digestion in 37°C 1X Accumax buffer Sigma Aldrich  A7089 for 30 45 minutes. Suspension was washed in Hank's Buffer 1x HBSS; 2.5 mg/mL BSA; 10μM pH8 HEPES  concentrated via centrifugation 200 rcf for 10 minutes at 4°C in a small volume of Hank's buffer  and sorted for GFP+ cells via FACS. GFP+ cells were used as input for the 10X Genomics Chromium platform using the 10X Single Cell three prime V2 chemistry kit for 10 000 cells. RNA libraries were prepared for sequencing using standard Illumina protocols following the 10x Genomics pipeline,GEO Accession:GSM4629199,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP268145,,loader:fastq load.py|options:  platform=Illumina   readTypes=BBT   read1PairFiles=GFPplus S1 L003 R1 001.fastq   read2PairFiles=GFPplus S1 L003 R2 001.fastq   read3PairFiles=GFPplus S1 L003 I1 001.fastq,GFPplus_S1_L003_I1_001.fastq GFPplus_S1_L003_R1_001.fastq GFPplus_S1_L003_R2_001.fastq,fastq fastq fastq,6350185110.0,40191045.0,GSM4629199 r3,0:26 1:124 2:8,A:1852452135;C:1299393173;G:1456328475;T:1740481266;N:1530061,26,124,8,,1852452135,1299393173,1456328475,1740481266,1530061,SRX8588729,SRS6880197,SRA1089349,GEO,"The Uribe Laboratory, BioSciences, Rice University",2,0.00235,0.91442,0.00069,0.08011,0.99535,0.80813,0.37864,0.50714,26,124,T,B,sc-like readlen,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2020-06-20,Hatching,Embryo,Brain,Nervous System
59882,SRR12060556,SRX8588729,SRS6880197,SRP268145,PRJNA640816,An atlas of neural crest lineages along the posterior developing zebrafish at single cell resolution,GSE152906,Transcriptome Analysis,Neural crest cells NCCs are vertebrate stem cells that give rise to various cell types throughout the developing body in early life. Here  we utilized single cell transcriptomic analyses to delineate NCC derivatives along the posterior developing vertebrate  zebrafish  during the late embryonic to early larval stage  a period when NCCs are actively differentiating into distinct cellular lineages. We identified several major NCC/NCC derived cell types including mesenchyme  neural crest  neural  neuronal  glial  and pigment  from which we resolved over three dozen cellular subtypes. We dissected gene expression signatures of pigment progenitors delineating into chromatophore lineages  mesenchyme subtypes  and enteric NCCs transforming into enteric neurons. Global analysis of NCC derivatives revealed they were demarcated by combinatorial hox gene codes  with distinct profiles within neuronal cells. From these analyses  we present a comprehensive cell type atlas that can be utilized as a valuable resource for further mechanistic and evolutionary investigations of NCC differentiation. Overall design: To characterize the neural crest cell lineages present in the posterior zebrafish during the embryonic to larval transition 48 hpf 72 hpf we utilized single cell RNA sequencing scRNA Seq on the 10x Genomics Chromium platform to build a dataset from GFP+ cells collected from sox10:GFP embryos.,,pubmed:33591267;pubmed:38234831;pubmed:38809858,,Sox10+ 68 70hpf,GSM4629199,,tissue:Derivative Sox10+ Neural Crest|genotype/variation: 4.9sox10:EGFP ba2Tg|developmental stage:68 hpf 70 hpf|cell type:FACS isolated  4.9sox10:EGFP+ cells,Sox10+ 68 70hpf,Illumina NextSeq 500 used for basecalling CellRanger v2.1.0 software facilitated genomic alignment  filtering  barcode reading  and exportation for further analysis Genome build: DanioGRCz10 Supplementary files format and content: 10X Genomics Chromim Filtered Gene BC Cellular Barcodes barcodes.tsv and genes genes.tsv; 10X Genomics Chromium Raw Gene BC Cellular Matrix matrix.mtx,Derivative Sox10+ Neural Crest,none,Posterior tissue Vagal and trunk domains were harvested; Single cell suspension was prepared via digestion in 37°C 1X Accumax buffer Sigma Aldrich  A7089 for 30 45 minutes. Suspension was washed in Hank's Buffer 1x HBSS; 2.5 mg/mL BSA; 10μM pH8 HEPES  concentrated via centrifugation 200 rcf for 10 minutes at 4°C in a small volume of Hank's buffer  and sorted for GFP+ cells via FACS. GFP+ cells were used as input for the 10X Genomics Chromium platform using the 10X Single Cell 3’ V2 chemistry kit for 10 000 cells. RNA libraries were prepared for sequencing using standard Illumina protocols following the 10x Genomics pipeline,Embryos were collected synchronously  batched by stage. All embryos were raised according to standard practices in E3 embryonic media for the first 24 hours and then transfered to 1X 1 phenyl 2 thiourea PTU/E3 solution. At 24 hpf  embryos were sorted manually for GFP expression. Developmentally delayed or malformed embryos were removed. All work was conducted under protocols approved by and in accordance with  Rice University Institutional Animal Care and Use Committee IACUC.,genotype/variation: 4.9sox10:EGFP ba2Tg|developmental stage:68 hpf 70 hpf|cell type:FACS isolated  4.9sox10:EGFP+ cells,GSM4629199,GSM4629199: Sox10+ 68 70hpf; Danio rerio; RNA Seq,GSM4629199,,1,Posterior tissue Vagal and trunk domains were harvested; Single cell suspension was prepared via digestion in 37°C 1X Accumax buffer Sigma Aldrich  A7089 for 30 45 minutes. Suspension was washed in Hank's Buffer 1x HBSS; 2.5 mg/mL BSA; 10μM pH8 HEPES  concentrated via centrifugation 200 rcf for 10 minutes at 4°C in a small volume of Hank's buffer  and sorted for GFP+ cells via FACS. GFP+ cells were used as input for the 10X Genomics Chromium platform using the 10X Single Cell three prime V2 chemistry kit for 10 000 cells. RNA libraries were prepared for sequencing using standard Illumina protocols following the 10x Genomics pipeline,GEO Accession:GSM4629199,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP268145,,loader:fastq load.py|options:  allowEarlyFileEnd   platform=Illumina   readTypes=BBT   read1PairFiles=GFPplus S1 L004 R1 001.fastq   read2PairFiles=GFPplus S1 L004 R2 001.fastq   read3PairFiles=GFPplus S1 L004 I1 001.fastq,,,5812557404.0,36788338.0,GSM4629199 r4,0:26 1:124 2:8,A:1702052926;C:1187088636;G:1324270973;T:1598146532;N:998337,26,124,8,,1702052926,1187088636,1324270973,1598146532,998337,SRX8588729,SRS6880197,SRA1089349,GEO,"The Uribe Laboratory, BioSciences, Rice University",2,0.00277,0.91719,0.00069,0.08091,0.9945,0.80783,0.39641,0.51387,26,124,T,B,sc-like readlen,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2020-06-20,Hatching,Embryo,Brain,Nervous System
59883,SRR12060549,SRX8588728,SRS6880196,SRP268145,PRJNA640816,An atlas of neural crest lineages along the posterior developing zebrafish at single cell resolution,GSE152906,Transcriptome Analysis,Neural crest cells NCCs are vertebrate stem cells that give rise to various cell types throughout the developing body in early life. Here  we utilized single cell transcriptomic analyses to delineate NCC derivatives along the posterior developing vertebrate  zebrafish  during the late embryonic to early larval stage  a period when NCCs are actively differentiating into distinct cellular lineages. We identified several major NCC/NCC derived cell types including mesenchyme  neural crest  neural  neuronal  glial  and pigment  from which we resolved over three dozen cellular subtypes. We dissected gene expression signatures of pigment progenitors delineating into chromatophore lineages  mesenchyme subtypes  and enteric NCCs transforming into enteric neurons. Global analysis of NCC derivatives revealed they were demarcated by combinatorial hox gene codes  with distinct profiles within neuronal cells. From these analyses  we present a comprehensive cell type atlas that can be utilized as a valuable resource for further mechanistic and evolutionary investigations of NCC differentiation. Overall design: To characterize the neural crest cell lineages present in the posterior zebrafish during the embryonic to larval transition 48 hpf 72 hpf we utilized single cell RNA sequencing scRNA Seq on the 10x Genomics Chromium platform to build a dataset from GFP+ cells collected from sox10:GFP embryos.,,pubmed:33591267;pubmed:38234831;pubmed:38809858,,Sox10+ 48 50hpf,GSM4629198,,tissue:Derivative Sox10+ Neural Crest|genotype/variation: 4.9sox10:EGFP ba2Tg|developmental stage:48 hpf 50 hpf|cell type:FACS isolated  4.9sox10:EGFP+ cells,Sox10+ 48 50hpf,Illumina NextSeq 500 used for basecalling CellRanger v2.1.0 software facilitated genomic alignment  filtering  barcode reading  and exportation for further analysis Genome build: DanioGRCz10 Supplementary files format and content: 10X Genomics Chromim Filtered Gene BC Cellular Barcodes barcodes.tsv and genes genes.tsv; 10X Genomics Chromium Raw Gene BC Cellular Matrix matrix.mtx,Derivative Sox10+ Neural Crest,none,Posterior tissue Vagal and trunk domains were harvested; Single cell suspension was prepared via digestion in 37°C 1X Accumax buffer Sigma Aldrich  A7089 for 30 45 minutes. Suspension was washed in Hank's Buffer 1x HBSS; 2.5 mg/mL BSA; 10μM pH8 HEPES  concentrated via centrifugation 200 rcf for 10 minutes at 4°C in a small volume of Hank's buffer  and sorted for GFP+ cells via FACS. GFP+ cells were used as input for the 10X Genomics Chromium platform using the 10X Single Cell 3’ V2 chemistry kit for 10 000 cells. RNA libraries were prepared for sequencing using standard Illumina protocols following the 10x Genomics pipeline,Embryos were collected synchronously  batched by stage. All embryos were raised according to standard practices in E3 embryonic media for the first 24 hours and then transfered to 1X 1 phenyl 2 thiourea PTU/E3 solution. At 24 hpf  embryos were sorted manually for GFP expression. Developmentally delayed or malformed embryos were removed. All work was conducted under protocols approved by and in accordance with  Rice University Institutional Animal Care and Use Committee IACUC.,genotype/variation: 4.9sox10:EGFP ba2Tg|developmental stage:48 hpf 50 hpf|cell type:FACS isolated  4.9sox10:EGFP+ cells,GSM4629198,GSM4629198: Sox10+ 48 50hpf; Danio rerio; RNA Seq,GSM4629198,,1,Posterior tissue Vagal and trunk domains were harvested; Single cell suspension was prepared via digestion in 37°C 1X Accumax buffer Sigma Aldrich  A7089 for 30 45 minutes. Suspension was washed in Hank's Buffer 1x HBSS; 2.5 mg/mL BSA; 10μM pH8 HEPES  concentrated via centrifugation 200 rcf for 10 minutes at 4°C in a small volume of Hank's buffer  and sorted for GFP+ cells via FACS. GFP+ cells were used as input for the 10X Genomics Chromium platform using the 10X Single Cell three prime V2 chemistry kit for 10 000 cells. RNA libraries were prepared for sequencing using standard Illumina protocols following the 10x Genomics pipeline,GEO Accession:GSM4629198,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP268145,,loader:fastq load.py|options:  platform=Illumina   readTypes=BBT   read1PairFiles=Sox10Enriched 48h S1 L001 R1 001 mod.fastq   read2PairFiles=Sox10Enriched 48h S1 L001 R2 001.fastq   read3PairFiles=Sox10Enriched 48h S1 L001 I1 001 mod.fastq,,,1616949090.0,10233855.0,GSM4629198 r1,0:26 1:124 2:8,A:456678394;C:358389976;G:376486936;T:425174329;N:219455,26,124,8,,456678394,358389976,376486936,425174329,219455,SRX8588728,SRS6880196,SRA1089349,GEO,"The Uribe Laboratory, BioSciences, Rice University",2,0.01006,0.95005,0.00118,0.07248,0.98175,0.8351,0.41141,0.49367,26,124,T,B,sc-like readlen,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2020-06-20,Hatching,Embryo,Brain,Nervous System
59884,SRR12060550,SRX8588728,SRS6880196,SRP268145,PRJNA640816,An atlas of neural crest lineages along the posterior developing zebrafish at single cell resolution,GSE152906,Transcriptome Analysis,Neural crest cells NCCs are vertebrate stem cells that give rise to various cell types throughout the developing body in early life. Here  we utilized single cell transcriptomic analyses to delineate NCC derivatives along the posterior developing vertebrate  zebrafish  during the late embryonic to early larval stage  a period when NCCs are actively differentiating into distinct cellular lineages. We identified several major NCC/NCC derived cell types including mesenchyme  neural crest  neural  neuronal  glial  and pigment  from which we resolved over three dozen cellular subtypes. We dissected gene expression signatures of pigment progenitors delineating into chromatophore lineages  mesenchyme subtypes  and enteric NCCs transforming into enteric neurons. Global analysis of NCC derivatives revealed they were demarcated by combinatorial hox gene codes  with distinct profiles within neuronal cells. From these analyses  we present a comprehensive cell type atlas that can be utilized as a valuable resource for further mechanistic and evolutionary investigations of NCC differentiation. Overall design: To characterize the neural crest cell lineages present in the posterior zebrafish during the embryonic to larval transition 48 hpf 72 hpf we utilized single cell RNA sequencing scRNA Seq on the 10x Genomics Chromium platform to build a dataset from GFP+ cells collected from sox10:GFP embryos.,,pubmed:33591267;pubmed:38234831;pubmed:38809858,,Sox10+ 48 50hpf,GSM4629198,,tissue:Derivative Sox10+ Neural Crest|genotype/variation: 4.9sox10:EGFP ba2Tg|developmental stage:48 hpf 50 hpf|cell type:FACS isolated  4.9sox10:EGFP+ cells,Sox10+ 48 50hpf,Illumina NextSeq 500 used for basecalling CellRanger v2.1.0 software facilitated genomic alignment  filtering  barcode reading  and exportation for further analysis Genome build: DanioGRCz10 Supplementary files format and content: 10X Genomics Chromim Filtered Gene BC Cellular Barcodes barcodes.tsv and genes genes.tsv; 10X Genomics Chromium Raw Gene BC Cellular Matrix matrix.mtx,Derivative Sox10+ Neural Crest,none,Posterior tissue Vagal and trunk domains were harvested; Single cell suspension was prepared via digestion in 37°C 1X Accumax buffer Sigma Aldrich  A7089 for 30 45 minutes. Suspension was washed in Hank's Buffer 1x HBSS; 2.5 mg/mL BSA; 10μM pH8 HEPES  concentrated via centrifugation 200 rcf for 10 minutes at 4°C in a small volume of Hank's buffer  and sorted for GFP+ cells via FACS. GFP+ cells were used as input for the 10X Genomics Chromium platform using the 10X Single Cell 3’ V2 chemistry kit for 10 000 cells. RNA libraries were prepared for sequencing using standard Illumina protocols following the 10x Genomics pipeline,Embryos were collected synchronously  batched by stage. All embryos were raised according to standard practices in E3 embryonic media for the first 24 hours and then transfered to 1X 1 phenyl 2 thiourea PTU/E3 solution. At 24 hpf  embryos were sorted manually for GFP expression. Developmentally delayed or malformed embryos were removed. All work was conducted under protocols approved by and in accordance with  Rice University Institutional Animal Care and Use Committee IACUC.,genotype/variation: 4.9sox10:EGFP ba2Tg|developmental stage:48 hpf 50 hpf|cell type:FACS isolated  4.9sox10:EGFP+ cells,GSM4629198,GSM4629198: Sox10+ 48 50hpf; Danio rerio; RNA Seq,GSM4629198,,1,Posterior tissue Vagal and trunk domains were harvested; Single cell suspension was prepared via digestion in 37°C 1X Accumax buffer Sigma Aldrich  A7089 for 30 45 minutes. Suspension was washed in Hank's Buffer 1x HBSS; 2.5 mg/mL BSA; 10μM pH8 HEPES  concentrated via centrifugation 200 rcf for 10 minutes at 4°C in a small volume of Hank's buffer  and sorted for GFP+ cells via FACS. GFP+ cells were used as input for the 10X Genomics Chromium platform using the 10X Single Cell three prime V2 chemistry kit for 10 000 cells. RNA libraries were prepared for sequencing using standard Illumina protocols following the 10x Genomics pipeline,GEO Accession:GSM4629198,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP268145,,loader:fastq load.py|options:  platform=Illumina   readTypes=BBT   read1PairFiles=Sox10Enriched 48h S1 L002 R1 001 mod.fastq   read2PairFiles=Sox10Enriched 48h S1 L002 R2 001.fastq   read3PairFiles=Sox10Enriched 48h S1 L002 I1 001 mod.fastq,,,1382737000.0,8751500.0,GSM4629198 r2,0:26 1:124 2:8,A:393565729;C:306444540;G:319283385;T:363276484;N:166862,26,124,8,,393565729,306444540,319283385,363276484,166862,SRX8588728,SRS6880196,SRA1089349,GEO,"The Uribe Laboratory, BioSciences, Rice University",2,0.01049,0.94963,0.00135,0.07338,0.98192,0.83952,0.3958,0.49146,26,124,T,B,sc-like readlen,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2020-06-20,Hatching,Embryo,Brain,Nervous System
59885,SRR12060551,SRX8588728,SRS6880196,SRP268145,PRJNA640816,An atlas of neural crest lineages along the posterior developing zebrafish at single cell resolution,GSE152906,Transcriptome Analysis,Neural crest cells NCCs are vertebrate stem cells that give rise to various cell types throughout the developing body in early life. Here  we utilized single cell transcriptomic analyses to delineate NCC derivatives along the posterior developing vertebrate  zebrafish  during the late embryonic to early larval stage  a period when NCCs are actively differentiating into distinct cellular lineages. We identified several major NCC/NCC derived cell types including mesenchyme  neural crest  neural  neuronal  glial  and pigment  from which we resolved over three dozen cellular subtypes. We dissected gene expression signatures of pigment progenitors delineating into chromatophore lineages  mesenchyme subtypes  and enteric NCCs transforming into enteric neurons. Global analysis of NCC derivatives revealed they were demarcated by combinatorial hox gene codes  with distinct profiles within neuronal cells. From these analyses  we present a comprehensive cell type atlas that can be utilized as a valuable resource for further mechanistic and evolutionary investigations of NCC differentiation. Overall design: To characterize the neural crest cell lineages present in the posterior zebrafish during the embryonic to larval transition 48 hpf 72 hpf we utilized single cell RNA sequencing scRNA Seq on the 10x Genomics Chromium platform to build a dataset from GFP+ cells collected from sox10:GFP embryos.,,pubmed:33591267;pubmed:38234831;pubmed:38809858,,Sox10+ 48 50hpf,GSM4629198,,tissue:Derivative Sox10+ Neural Crest|genotype/variation: 4.9sox10:EGFP ba2Tg|developmental stage:48 hpf 50 hpf|cell type:FACS isolated  4.9sox10:EGFP+ cells,Sox10+ 48 50hpf,Illumina NextSeq 500 used for basecalling CellRanger v2.1.0 software facilitated genomic alignment  filtering  barcode reading  and exportation for further analysis Genome build: DanioGRCz10 Supplementary files format and content: 10X Genomics Chromim Filtered Gene BC Cellular Barcodes barcodes.tsv and genes genes.tsv; 10X Genomics Chromium Raw Gene BC Cellular Matrix matrix.mtx,Derivative Sox10+ Neural Crest,none,Posterior tissue Vagal and trunk domains were harvested; Single cell suspension was prepared via digestion in 37°C 1X Accumax buffer Sigma Aldrich  A7089 for 30 45 minutes. Suspension was washed in Hank's Buffer 1x HBSS; 2.5 mg/mL BSA; 10μM pH8 HEPES  concentrated via centrifugation 200 rcf for 10 minutes at 4°C in a small volume of Hank's buffer  and sorted for GFP+ cells via FACS. GFP+ cells were used as input for the 10X Genomics Chromium platform using the 10X Single Cell 3’ V2 chemistry kit for 10 000 cells. RNA libraries were prepared for sequencing using standard Illumina protocols following the 10x Genomics pipeline,Embryos were collected synchronously  batched by stage. All embryos were raised according to standard practices in E3 embryonic media for the first 24 hours and then transfered to 1X 1 phenyl 2 thiourea PTU/E3 solution. At 24 hpf  embryos were sorted manually for GFP expression. Developmentally delayed or malformed embryos were removed. All work was conducted under protocols approved by and in accordance with  Rice University Institutional Animal Care and Use Committee IACUC.,genotype/variation: 4.9sox10:EGFP ba2Tg|developmental stage:48 hpf 50 hpf|cell type:FACS isolated  4.9sox10:EGFP+ cells,GSM4629198,GSM4629198: Sox10+ 48 50hpf; Danio rerio; RNA Seq,GSM4629198,,1,Posterior tissue Vagal and trunk domains were harvested; Single cell suspension was prepared via digestion in 37°C 1X Accumax buffer Sigma Aldrich  A7089 for 30 45 minutes. Suspension was washed in Hank's Buffer 1x HBSS; 2.5 mg/mL BSA; 10μM pH8 HEPES  concentrated via centrifugation 200 rcf for 10 minutes at 4°C in a small volume of Hank's buffer  and sorted for GFP+ cells via FACS. GFP+ cells were used as input for the 10X Genomics Chromium platform using the 10X Single Cell three prime V2 chemistry kit for 10 000 cells. RNA libraries were prepared for sequencing using standard Illumina protocols following the 10x Genomics pipeline,GEO Accession:GSM4629198,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP268145,,loader:fastq load.py|options:  platform=Illumina   readTypes=BBT   read1PairFiles=Sox10Enriched 48h S1 L003 R1 001.fastq   read2PairFiles=Sox10Enriched 48h S1 L003 R2 001.fastq   read3PairFiles=Sox10Enriched 48h S1 L003 I1 001.fastq,Sox10Enriched_48h_S1_L003_I1_001.fastq Sox10Enriched_48h_S1_L003_R1_001.fastq Sox10Enriched_48h_S1_L003_R2_001.fastq,fastq fastq fastq,7027816932.0,44479854.0,GSM4629198 r3,0:26 1:124 2:8,A:1977891064;C:1517642706;G:1691754065;T:1838521085;N:2008012,26,124,8,,1977891064,1517642706,1691754065,1838521085,2008012,SRX8588728,SRS6880196,SRA1089349,GEO,"The Uribe Laboratory, BioSciences, Rice University",2,0.01071,0.94964,0.00138,0.06976,0.98123,0.83116,0.39988,0.4831,26,124,T,B,sc-like readlen,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2020-06-20,Hatching,Embryo,Brain,Nervous System
59886,SRR12060552,SRX8588728,SRS6880196,SRP268145,PRJNA640816,An atlas of neural crest lineages along the posterior developing zebrafish at single cell resolution,GSE152906,Transcriptome Analysis,Neural crest cells NCCs are vertebrate stem cells that give rise to various cell types throughout the developing body in early life. Here  we utilized single cell transcriptomic analyses to delineate NCC derivatives along the posterior developing vertebrate  zebrafish  during the late embryonic to early larval stage  a period when NCCs are actively differentiating into distinct cellular lineages. We identified several major NCC/NCC derived cell types including mesenchyme  neural crest  neural  neuronal  glial  and pigment  from which we resolved over three dozen cellular subtypes. We dissected gene expression signatures of pigment progenitors delineating into chromatophore lineages  mesenchyme subtypes  and enteric NCCs transforming into enteric neurons. Global analysis of NCC derivatives revealed they were demarcated by combinatorial hox gene codes  with distinct profiles within neuronal cells. From these analyses  we present a comprehensive cell type atlas that can be utilized as a valuable resource for further mechanistic and evolutionary investigations of NCC differentiation. Overall design: To characterize the neural crest cell lineages present in the posterior zebrafish during the embryonic to larval transition 48 hpf 72 hpf we utilized single cell RNA sequencing scRNA Seq on the 10x Genomics Chromium platform to build a dataset from GFP+ cells collected from sox10:GFP embryos.,,pubmed:33591267;pubmed:38234831;pubmed:38809858,,Sox10+ 48 50hpf,GSM4629198,,tissue:Derivative Sox10+ Neural Crest|genotype/variation: 4.9sox10:EGFP ba2Tg|developmental stage:48 hpf 50 hpf|cell type:FACS isolated  4.9sox10:EGFP+ cells,Sox10+ 48 50hpf,Illumina NextSeq 500 used for basecalling CellRanger v2.1.0 software facilitated genomic alignment  filtering  barcode reading  and exportation for further analysis Genome build: DanioGRCz10 Supplementary files format and content: 10X Genomics Chromim Filtered Gene BC Cellular Barcodes barcodes.tsv and genes genes.tsv; 10X Genomics Chromium Raw Gene BC Cellular Matrix matrix.mtx,Derivative Sox10+ Neural Crest,none,Posterior tissue Vagal and trunk domains were harvested; Single cell suspension was prepared via digestion in 37°C 1X Accumax buffer Sigma Aldrich  A7089 for 30 45 minutes. Suspension was washed in Hank's Buffer 1x HBSS; 2.5 mg/mL BSA; 10μM pH8 HEPES  concentrated via centrifugation 200 rcf for 10 minutes at 4°C in a small volume of Hank's buffer  and sorted for GFP+ cells via FACS. GFP+ cells were used as input for the 10X Genomics Chromium platform using the 10X Single Cell 3’ V2 chemistry kit for 10 000 cells. RNA libraries were prepared for sequencing using standard Illumina protocols following the 10x Genomics pipeline,Embryos were collected synchronously  batched by stage. All embryos were raised according to standard practices in E3 embryonic media for the first 24 hours and then transfered to 1X 1 phenyl 2 thiourea PTU/E3 solution. At 24 hpf  embryos were sorted manually for GFP expression. Developmentally delayed or malformed embryos were removed. All work was conducted under protocols approved by and in accordance with  Rice University Institutional Animal Care and Use Committee IACUC.,genotype/variation: 4.9sox10:EGFP ba2Tg|developmental stage:48 hpf 50 hpf|cell type:FACS isolated  4.9sox10:EGFP+ cells,GSM4629198,GSM4629198: Sox10+ 48 50hpf; Danio rerio; RNA Seq,GSM4629198,,1,Posterior tissue Vagal and trunk domains were harvested; Single cell suspension was prepared via digestion in 37°C 1X Accumax buffer Sigma Aldrich  A7089 for 30 45 minutes. Suspension was washed in Hank's Buffer 1x HBSS; 2.5 mg/mL BSA; 10μM pH8 HEPES  concentrated via centrifugation 200 rcf for 10 minutes at 4°C in a small volume of Hank's buffer  and sorted for GFP+ cells via FACS. GFP+ cells were used as input for the 10X Genomics Chromium platform using the 10X Single Cell three prime V2 chemistry kit for 10 000 cells. RNA libraries were prepared for sequencing using standard Illumina protocols following the 10x Genomics pipeline,GEO Accession:GSM4629198,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP268145,,loader:fastq load.py|options:  platform=Illumina   readTypes=BBT   read1PairFiles=Sox10Enriched 48h S1 L004 R1 001.fastq   read2PairFiles=Sox10Enriched 48h S1 L004 R2 001.fastq   read3PairFiles=Sox10Enriched 48h S1 L004 I1 001.fastq,,,6734234423.0,42621737.0,GSM4629198 r4,0:26 1:124.00 2:8,A:1913564054;C:1452205902;G:1601358930;T:1764533329;N:2572208,26,124,8,,1913564054,1452205902,1601358930,1764533329,2572208,SRX8588728,SRS6880196,SRA1089349,GEO,"The Uribe Laboratory, BioSciences, Rice University",2,0.01026,0.95184,0.00128,0.07207,0.98244,0.835,0.40661,0.49631,26,124,T,B,sc-like readlen,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2020-06-20,Hatching,Embryo,Brain,Nervous System
61241,SRR12661744,SRX9142589,SRS7383893,SRP282920,PRJNA664124,Emergence of neuronal diversity during vertebrate brain development,GSE158142,Transcriptome Analysis,Neurogenesis comprises many steps from progenitor proliferation to neuronal differentiation and maturation. These processes are highly regulated  but the landscape of transcriptional changes underlying brain development are poorly characterized. Here  we describe a developmental single cell RNA seq catalog of 220 000 zebrafish brain cells encompassing 12 stages from 12 hpf to 15 dpf We characterize known and novel gene markers for 800 clusters and provide an overview of the diversification of neurons and progenitors across these timepoints. We also introduce an optimized version of the GESTALT lineage recorder that enables higher expression and recovery of Cas9 edited barcodes to query lineage segregation. Cell type characterization indicates that most embryonic neural progenitor states are transitory and transcriptionally distinct from neural progenitors of post embryonic stages. Reconstruction of cell specification trajectories reveals that late stage retinal neural progenitors transcriptionally overlap cell states observed in the embryo. The zebrafish brain development atlas provides a resource to define and manipulate specific subsets of neurons and to uncover the molecular mechanisms underlying vertebrate neurogenesis. Overall design: 10X Genomics v2 scRNA seq libraries and scGESTALT,,pubmed:33068532,,zBr2dpf6 S4,GSM4793206,,source name:zebrafish brain|tissue:brain|developmental stage:2dpf,zBr2dpf6 S4,Single cell RNA Sequencing data FASTQ files were processed using Cell Ranger v2.0.2 to generate count matrices Transcriptome libraries were mapped to a zebrafish reference built from a custom GTF file and the zebrafish GRCz10 release 86 genome assembly. File uploaded as Danio rerio.GRCz10.86.modified.gtf.gz. Some libraries were sequenced twice as technical replicates marked as *b in raw files and the processing was done using the combination of all data processed data files have comb* prefix scGESTALT libraries were processed using a custom pipeline available at https://github.com/shendurelab/Cas9FateMapping Genome build: GRCz10 Supplementary files format and content: *barcodes.tsv files contain 10X Genomics cell barcodes  *genes.tsv files contain gene names  *matrix.mtx contain transcriptome count data  *web summary.html contain summary statistics for transcript mapping  .rds files are the processed R objects  .txt files contain marker genes identified for each cluster in the dataset  URD*.rds files are the processed R objects for performing URD cell trajectory analysis. tree*.rds files are the final URD objects with cell trajectory trees for the retina and hypothalamus. Supplementary files format and content: scGESTALT data:  Gest zBr15dpf8 and Gest zBr15dpf9 correspond to two samples from the same zebrafish ZF1. Gest zBr15dpf10 and Gest zBr15dpf11 correspond to two samples from the same zebrafish ZF2. Gest zBr15dpf12 and Gest zBr15dpf13 correspond to two samples from the same zebrafish ZF3. Gest zBr15dpf14 and Gest zBr15dpf15 correspond to two samples from the same zebrafish ZF4. Supplementary files format and content: scGESTALT data: *GestMaster.txt contains the 10X Genmoics cell identifiers CellBarcode and CellUMI that were used to matchlineage barcodes to transcriptomes. They also contain lineage barcode sequences HMID column   the t SNE cluster membership number ClusterIdent column  and unique identifier Readname. zfAllMerge FILTEREDUSEME.xlsx contains the merged statistics of all samples  filtered to contain high confidence barcodes  the barcode sequence aligned to a reference unedited sequence mergedRead column  mutations at each target site target[X] columns and the edited sequences at each target site sequence[X] columns were used for downstream analysis. Further details of columns can be found at https://github.com/shendurelab/Cas9FateMapping,zebrafish brain,,Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol  to generate single cell cDNA libraries and prepared for sequencing,,tissue:brain|developmental stage:2dpf,GSM4793206,GSM4793206: zBr2dpf6 S4; Danio rerio; RNA Seq,GSM4793206,,1,Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol  to generate single cell cDNA libraries and prepared for sequencing,GEO Accession:GSM4793206,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP282920,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=zBr2dpf6 S4 L001 I1 001.fastq.gz   read2PairFiles=zBr2dpf6 S4 L001 R1 001.fastq.gz   read3PairFiles=zBr2dpf6 S4 L001 R2 001.fastq.gz,zBr2dpf6_S4_L001_I1_001.fastq.gz zBr2dpf6_S4_L001_R1_001.fastq.gz zBr2dpf6_S4_L001_R2_001.fastq.gz,fastq fastq fastq,1641453328.0,17841884.0,GSM4793206 r1,0:8 1:26 2:58,A:432584064;C:365889139;G:409749859;T:432982043;N:248223,8,26,58,,432584064,365889139,409749859,432982043,248223,SRX9142589,SRS7383893,SRA1127180,GEO,Harvard University,1,0.93894,,0.10335,,0.8141,,0.49836,,58,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2020-09-17,Hatching,Embryo,Brain,Nervous System
61242,SRR12661745,SRX9142589,SRS7383893,SRP282920,PRJNA664124,Emergence of neuronal diversity during vertebrate brain development,GSE158142,Transcriptome Analysis,Neurogenesis comprises many steps from progenitor proliferation to neuronal differentiation and maturation. These processes are highly regulated  but the landscape of transcriptional changes underlying brain development are poorly characterized. Here  we describe a developmental single cell RNA seq catalog of 220 000 zebrafish brain cells encompassing 12 stages from 12 hpf to 15 dpf We characterize known and novel gene markers for 800 clusters and provide an overview of the diversification of neurons and progenitors across these timepoints. We also introduce an optimized version of the GESTALT lineage recorder that enables higher expression and recovery of Cas9 edited barcodes to query lineage segregation. Cell type characterization indicates that most embryonic neural progenitor states are transitory and transcriptionally distinct from neural progenitors of post embryonic stages. Reconstruction of cell specification trajectories reveals that late stage retinal neural progenitors transcriptionally overlap cell states observed in the embryo. The zebrafish brain development atlas provides a resource to define and manipulate specific subsets of neurons and to uncover the molecular mechanisms underlying vertebrate neurogenesis. Overall design: 10X Genomics v2 scRNA seq libraries and scGESTALT,,pubmed:33068532,,zBr2dpf6 S4,GSM4793206,,source name:zebrafish brain|tissue:brain|developmental stage:2dpf,zBr2dpf6 S4,Single cell RNA Sequencing data FASTQ files were processed using Cell Ranger v2.0.2 to generate count matrices Transcriptome libraries were mapped to a zebrafish reference built from a custom GTF file and the zebrafish GRCz10 release 86 genome assembly. File uploaded as Danio rerio.GRCz10.86.modified.gtf.gz. Some libraries were sequenced twice as technical replicates marked as *b in raw files and the processing was done using the combination of all data processed data files have comb* prefix scGESTALT libraries were processed using a custom pipeline available at https://github.com/shendurelab/Cas9FateMapping Genome build: GRCz10 Supplementary files format and content: *barcodes.tsv files contain 10X Genomics cell barcodes  *genes.tsv files contain gene names  *matrix.mtx contain transcriptome count data  *web summary.html contain summary statistics for transcript mapping  .rds files are the processed R objects  .txt files contain marker genes identified for each cluster in the dataset  URD*.rds files are the processed R objects for performing URD cell trajectory analysis. tree*.rds files are the final URD objects with cell trajectory trees for the retina and hypothalamus. Supplementary files format and content: scGESTALT data:  Gest zBr15dpf8 and Gest zBr15dpf9 correspond to two samples from the same zebrafish ZF1. Gest zBr15dpf10 and Gest zBr15dpf11 correspond to two samples from the same zebrafish ZF2. Gest zBr15dpf12 and Gest zBr15dpf13 correspond to two samples from the same zebrafish ZF3. Gest zBr15dpf14 and Gest zBr15dpf15 correspond to two samples from the same zebrafish ZF4. Supplementary files format and content: scGESTALT data: *GestMaster.txt contains the 10X Genmoics cell identifiers CellBarcode and CellUMI that were used to matchlineage barcodes to transcriptomes. They also contain lineage barcode sequences HMID column   the t SNE cluster membership number ClusterIdent column  and unique identifier Readname. zfAllMerge FILTEREDUSEME.xlsx contains the merged statistics of all samples  filtered to contain high confidence barcodes  the barcode sequence aligned to a reference unedited sequence mergedRead column  mutations at each target site target[X] columns and the edited sequences at each target site sequence[X] columns were used for downstream analysis. Further details of columns can be found at https://github.com/shendurelab/Cas9FateMapping,zebrafish brain,,Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol  to generate single cell cDNA libraries and prepared for sequencing,,tissue:brain|developmental stage:2dpf,GSM4793206,GSM4793206: zBr2dpf6 S4; Danio rerio; RNA Seq,GSM4793206,,1,Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol  to generate single cell cDNA libraries and prepared for sequencing,GEO Accession:GSM4793206,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP282920,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=zBr2dpf6 S4 L002 I1 001.fastq.gz   read2PairFiles=zBr2dpf6 S4 L002 R1 001.fastq.gz   read3PairFiles=zBr2dpf6 S4 L002 R2 001.fastq.gz,zBr2dpf6_S4_L002_I1_001.fastq.gz zBr2dpf6_S4_L002_R1_001.fastq.gz zBr2dpf6_S4_L002_R2_001.fastq.gz,fastq fastq fastq,1621686024.0,17627022.0,GSM4793206 r2,0:8 1:26 2:58,A:429417081;C:361894200;G:402117760;T:428002033;N:254950,8,26,58,,429417081,361894200,402117760,428002033,254950,SRX9142589,SRS7383893,SRA1127180,GEO,Harvard University,1,0.94217,,0.10443,,0.81397,,0.50325,,58,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2020-09-17,Hatching,Embryo,Brain,Nervous System
61243,SRR12661746,SRX9142589,SRS7383893,SRP282920,PRJNA664124,Emergence of neuronal diversity during vertebrate brain development,GSE158142,Transcriptome Analysis,Neurogenesis comprises many steps from progenitor proliferation to neuronal differentiation and maturation. These processes are highly regulated  but the landscape of transcriptional changes underlying brain development are poorly characterized. Here  we describe a developmental single cell RNA seq catalog of 220 000 zebrafish brain cells encompassing 12 stages from 12 hpf to 15 dpf We characterize known and novel gene markers for 800 clusters and provide an overview of the diversification of neurons and progenitors across these timepoints. We also introduce an optimized version of the GESTALT lineage recorder that enables higher expression and recovery of Cas9 edited barcodes to query lineage segregation. Cell type characterization indicates that most embryonic neural progenitor states are transitory and transcriptionally distinct from neural progenitors of post embryonic stages. Reconstruction of cell specification trajectories reveals that late stage retinal neural progenitors transcriptionally overlap cell states observed in the embryo. The zebrafish brain development atlas provides a resource to define and manipulate specific subsets of neurons and to uncover the molecular mechanisms underlying vertebrate neurogenesis. Overall design: 10X Genomics v2 scRNA seq libraries and scGESTALT,,pubmed:33068532,,zBr2dpf6 S4,GSM4793206,,source name:zebrafish brain|tissue:brain|developmental stage:2dpf,zBr2dpf6 S4,Single cell RNA Sequencing data FASTQ files were processed using Cell Ranger v2.0.2 to generate count matrices Transcriptome libraries were mapped to a zebrafish reference built from a custom GTF file and the zebrafish GRCz10 release 86 genome assembly. File uploaded as Danio rerio.GRCz10.86.modified.gtf.gz. Some libraries were sequenced twice as technical replicates marked as *b in raw files and the processing was done using the combination of all data processed data files have comb* prefix scGESTALT libraries were processed using a custom pipeline available at https://github.com/shendurelab/Cas9FateMapping Genome build: GRCz10 Supplementary files format and content: *barcodes.tsv files contain 10X Genomics cell barcodes  *genes.tsv files contain gene names  *matrix.mtx contain transcriptome count data  *web summary.html contain summary statistics for transcript mapping  .rds files are the processed R objects  .txt files contain marker genes identified for each cluster in the dataset  URD*.rds files are the processed R objects for performing URD cell trajectory analysis. tree*.rds files are the final URD objects with cell trajectory trees for the retina and hypothalamus. Supplementary files format and content: scGESTALT data:  Gest zBr15dpf8 and Gest zBr15dpf9 correspond to two samples from the same zebrafish ZF1. Gest zBr15dpf10 and Gest zBr15dpf11 correspond to two samples from the same zebrafish ZF2. Gest zBr15dpf12 and Gest zBr15dpf13 correspond to two samples from the same zebrafish ZF3. Gest zBr15dpf14 and Gest zBr15dpf15 correspond to two samples from the same zebrafish ZF4. Supplementary files format and content: scGESTALT data: *GestMaster.txt contains the 10X Genmoics cell identifiers CellBarcode and CellUMI that were used to matchlineage barcodes to transcriptomes. They also contain lineage barcode sequences HMID column   the t SNE cluster membership number ClusterIdent column  and unique identifier Readname. zfAllMerge FILTEREDUSEME.xlsx contains the merged statistics of all samples  filtered to contain high confidence barcodes  the barcode sequence aligned to a reference unedited sequence mergedRead column  mutations at each target site target[X] columns and the edited sequences at each target site sequence[X] columns were used for downstream analysis. Further details of columns can be found at https://github.com/shendurelab/Cas9FateMapping,zebrafish brain,,Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol  to generate single cell cDNA libraries and prepared for sequencing,,tissue:brain|developmental stage:2dpf,GSM4793206,GSM4793206: zBr2dpf6 S4; Danio rerio; RNA Seq,GSM4793206,,1,Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol  to generate single cell cDNA libraries and prepared for sequencing,GEO Accession:GSM4793206,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP282920,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=zBr2dpf6 S4 L003 I1 001.fastq.gz   read2PairFiles=zBr2dpf6 S4 L003 R1 001.fastq.gz   read3PairFiles=zBr2dpf6 S4 L003 R2 001.fastq.gz,zBr2dpf6_S4_L003_I1_001.fastq.gz zBr2dpf6_S4_L003_R1_001.fastq.gz zBr2dpf6_S4_L003_R2_001.fastq.gz,fastq fastq fastq,1609851604.0,17498387.0,GSM4793206 r3,0:8 1:26 2:58,A:426272754;C:358330950;G:399431249;T:425557524;N:259127,8,26,58,,426272754,358330950,399431249,425557524,259127,SRX9142589,SRS7383893,SRA1127180,GEO,Harvard University,1,0.94019,,0.10522,,0.81712,,0.51174,,58,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2020-09-17,Hatching,Embryo,Brain,Nervous System
61244,SRR12661747,SRX9142589,SRS7383893,SRP282920,PRJNA664124,Emergence of neuronal diversity during vertebrate brain development,GSE158142,Transcriptome Analysis,Neurogenesis comprises many steps from progenitor proliferation to neuronal differentiation and maturation. These processes are highly regulated  but the landscape of transcriptional changes underlying brain development are poorly characterized. Here  we describe a developmental single cell RNA seq catalog of 220 000 zebrafish brain cells encompassing 12 stages from 12 hpf to 15 dpf We characterize known and novel gene markers for 800 clusters and provide an overview of the diversification of neurons and progenitors across these timepoints. We also introduce an optimized version of the GESTALT lineage recorder that enables higher expression and recovery of Cas9 edited barcodes to query lineage segregation. Cell type characterization indicates that most embryonic neural progenitor states are transitory and transcriptionally distinct from neural progenitors of post embryonic stages. Reconstruction of cell specification trajectories reveals that late stage retinal neural progenitors transcriptionally overlap cell states observed in the embryo. The zebrafish brain development atlas provides a resource to define and manipulate specific subsets of neurons and to uncover the molecular mechanisms underlying vertebrate neurogenesis. Overall design: 10X Genomics v2 scRNA seq libraries and scGESTALT,,pubmed:33068532,,zBr2dpf6 S4,GSM4793206,,source name:zebrafish brain|tissue:brain|developmental stage:2dpf,zBr2dpf6 S4,Single cell RNA Sequencing data FASTQ files were processed using Cell Ranger v2.0.2 to generate count matrices Transcriptome libraries were mapped to a zebrafish reference built from a custom GTF file and the zebrafish GRCz10 release 86 genome assembly. File uploaded as Danio rerio.GRCz10.86.modified.gtf.gz. Some libraries were sequenced twice as technical replicates marked as *b in raw files and the processing was done using the combination of all data processed data files have comb* prefix scGESTALT libraries were processed using a custom pipeline available at https://github.com/shendurelab/Cas9FateMapping Genome build: GRCz10 Supplementary files format and content: *barcodes.tsv files contain 10X Genomics cell barcodes  *genes.tsv files contain gene names  *matrix.mtx contain transcriptome count data  *web summary.html contain summary statistics for transcript mapping  .rds files are the processed R objects  .txt files contain marker genes identified for each cluster in the dataset  URD*.rds files are the processed R objects for performing URD cell trajectory analysis. tree*.rds files are the final URD objects with cell trajectory trees for the retina and hypothalamus. Supplementary files format and content: scGESTALT data:  Gest zBr15dpf8 and Gest zBr15dpf9 correspond to two samples from the same zebrafish ZF1. Gest zBr15dpf10 and Gest zBr15dpf11 correspond to two samples from the same zebrafish ZF2. Gest zBr15dpf12 and Gest zBr15dpf13 correspond to two samples from the same zebrafish ZF3. Gest zBr15dpf14 and Gest zBr15dpf15 correspond to two samples from the same zebrafish ZF4. Supplementary files format and content: scGESTALT data: *GestMaster.txt contains the 10X Genmoics cell identifiers CellBarcode and CellUMI that were used to matchlineage barcodes to transcriptomes. They also contain lineage barcode sequences HMID column   the t SNE cluster membership number ClusterIdent column  and unique identifier Readname. zfAllMerge FILTEREDUSEME.xlsx contains the merged statistics of all samples  filtered to contain high confidence barcodes  the barcode sequence aligned to a reference unedited sequence mergedRead column  mutations at each target site target[X] columns and the edited sequences at each target site sequence[X] columns were used for downstream analysis. Further details of columns can be found at https://github.com/shendurelab/Cas9FateMapping,zebrafish brain,,Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol  to generate single cell cDNA libraries and prepared for sequencing,,tissue:brain|developmental stage:2dpf,GSM4793206,GSM4793206: zBr2dpf6 S4; Danio rerio; RNA Seq,GSM4793206,,1,Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol  to generate single cell cDNA libraries and prepared for sequencing,GEO Accession:GSM4793206,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP282920,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=zBr2dpf6 S4 L004 I1 001.fastq.gz   read2PairFiles=zBr2dpf6 S4 L004 R1 001.fastq.gz   read3PairFiles=zBr2dpf6 S4 L004 R2 001.fastq.gz,zBr2dpf6_S4_L004_I1_001.fastq.gz zBr2dpf6_S4_L004_R1_001.fastq.gz zBr2dpf6_S4_L004_R2_001.fastq.gz,fastq fastq fastq,1585670784.0,17235552.0,GSM4793206 r4,0:8 1:26 2:58,A:420707168;C:353519513;G:392246891;T:418960239;N:236973,8,26,58,,420707168,353519513,392246891,418960239,236973,SRX9142589,SRS7383893,SRA1127180,GEO,Harvard University,1,0.94124,,0.10456,,0.81424,,0.49886,,58,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2020-09-17,Hatching,Embryo,Brain,Nervous System
61245,SRR12661740,SRX9142588,SRS7383892,SRP282920,PRJNA664124,Emergence of neuronal diversity during vertebrate brain development,GSE158142,Transcriptome Analysis,Neurogenesis comprises many steps from progenitor proliferation to neuronal differentiation and maturation. These processes are highly regulated  but the landscape of transcriptional changes underlying brain development are poorly characterized. Here  we describe a developmental single cell RNA seq catalog of 220 000 zebrafish brain cells encompassing 12 stages from 12 hpf to 15 dpf We characterize known and novel gene markers for 800 clusters and provide an overview of the diversification of neurons and progenitors across these timepoints. We also introduce an optimized version of the GESTALT lineage recorder that enables higher expression and recovery of Cas9 edited barcodes to query lineage segregation. Cell type characterization indicates that most embryonic neural progenitor states are transitory and transcriptionally distinct from neural progenitors of post embryonic stages. Reconstruction of cell specification trajectories reveals that late stage retinal neural progenitors transcriptionally overlap cell states observed in the embryo. The zebrafish brain development atlas provides a resource to define and manipulate specific subsets of neurons and to uncover the molecular mechanisms underlying vertebrate neurogenesis. Overall design: 10X Genomics v2 scRNA seq libraries and scGESTALT,,pubmed:33068532,,zBr2dpf5 S3,GSM4793205,,source name:zebrafish brain|tissue:brain|developmental stage:2dpf,zBr2dpf5 S3,Single cell RNA Sequencing data FASTQ files were processed using Cell Ranger v2.0.2 to generate count matrices Transcriptome libraries were mapped to a zebrafish reference built from a custom GTF file and the zebrafish GRCz10 release 86 genome assembly. File uploaded as Danio rerio.GRCz10.86.modified.gtf.gz. Some libraries were sequenced twice as technical replicates marked as *b in raw files and the processing was done using the combination of all data processed data files have comb* prefix scGESTALT libraries were processed using a custom pipeline available at https://github.com/shendurelab/Cas9FateMapping Genome build: GRCz10 Supplementary files format and content: *barcodes.tsv files contain 10X Genomics cell barcodes  *genes.tsv files contain gene names  *matrix.mtx contain transcriptome count data  *web summary.html contain summary statistics for transcript mapping  .rds files are the processed R objects  .txt files contain marker genes identified for each cluster in the dataset  URD*.rds files are the processed R objects for performing URD cell trajectory analysis. tree*.rds files are the final URD objects with cell trajectory trees for the retina and hypothalamus. Supplementary files format and content: scGESTALT data:  Gest zBr15dpf8 and Gest zBr15dpf9 correspond to two samples from the same zebrafish ZF1. Gest zBr15dpf10 and Gest zBr15dpf11 correspond to two samples from the same zebrafish ZF2. Gest zBr15dpf12 and Gest zBr15dpf13 correspond to two samples from the same zebrafish ZF3. Gest zBr15dpf14 and Gest zBr15dpf15 correspond to two samples from the same zebrafish ZF4. Supplementary files format and content: scGESTALT data: *GestMaster.txt contains the 10X Genmoics cell identifiers CellBarcode and CellUMI that were used to matchlineage barcodes to transcriptomes. They also contain lineage barcode sequences HMID column   the t SNE cluster membership number ClusterIdent column  and unique identifier Readname. zfAllMerge FILTEREDUSEME.xlsx contains the merged statistics of all samples  filtered to contain high confidence barcodes  the barcode sequence aligned to a reference unedited sequence mergedRead column  mutations at each target site target[X] columns and the edited sequences at each target site sequence[X] columns were used for downstream analysis. Further details of columns can be found at https://github.com/shendurelab/Cas9FateMapping,zebrafish brain,,Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol  to generate single cell cDNA libraries and prepared for sequencing,,tissue:brain|developmental stage:2dpf,GSM4793205,GSM4793205: zBr2dpf5 S3; Danio rerio; RNA Seq,GSM4793205,,1,Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol  to generate single cell cDNA libraries and prepared for sequencing,GEO Accession:GSM4793205,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP282920,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=zBr2dpf5 S3 L001 I1 001.fastq.gz   read2PairFiles=zBr2dpf5 S3 L001 R1 001.fastq.gz   read3PairFiles=zBr2dpf5 S3 L001 R2 001.fastq.gz,zBr2dpf5_S3_L001_I1_001.fastq.gz zBr2dpf5_S3_L001_R1_001.fastq.gz zBr2dpf5_S3_L001_R2_001.fastq.gz,fastq fastq fastq,1420148340.0,15436395.0,GSM4793205 r1,0:8 1:26 2:58,A:375964274;C:313803783;G:358392750;T:371775975;N:211558,8,26,58,,375964274,313803783,358392750,371775975,211558,SRX9142588,SRS7383892,SRA1127180,GEO,Harvard University,1,0.93862,,0.10359,,0.81308,,0.49243,,58,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2020-09-17,Hatching,Embryo,Brain,Nervous System
61246,SRR12661741,SRX9142588,SRS7383892,SRP282920,PRJNA664124,Emergence of neuronal diversity during vertebrate brain development,GSE158142,Transcriptome Analysis,Neurogenesis comprises many steps from progenitor proliferation to neuronal differentiation and maturation. These processes are highly regulated  but the landscape of transcriptional changes underlying brain development are poorly characterized. Here  we describe a developmental single cell RNA seq catalog of 220 000 zebrafish brain cells encompassing 12 stages from 12 hpf to 15 dpf We characterize known and novel gene markers for 800 clusters and provide an overview of the diversification of neurons and progenitors across these timepoints. We also introduce an optimized version of the GESTALT lineage recorder that enables higher expression and recovery of Cas9 edited barcodes to query lineage segregation. Cell type characterization indicates that most embryonic neural progenitor states are transitory and transcriptionally distinct from neural progenitors of post embryonic stages. Reconstruction of cell specification trajectories reveals that late stage retinal neural progenitors transcriptionally overlap cell states observed in the embryo. The zebrafish brain development atlas provides a resource to define and manipulate specific subsets of neurons and to uncover the molecular mechanisms underlying vertebrate neurogenesis. Overall design: 10X Genomics v2 scRNA seq libraries and scGESTALT,,pubmed:33068532,,zBr2dpf5 S3,GSM4793205,,source name:zebrafish brain|tissue:brain|developmental stage:2dpf,zBr2dpf5 S3,Single cell RNA Sequencing data FASTQ files were processed using Cell Ranger v2.0.2 to generate count matrices Transcriptome libraries were mapped to a zebrafish reference built from a custom GTF file and the zebrafish GRCz10 release 86 genome assembly. File uploaded as Danio rerio.GRCz10.86.modified.gtf.gz. Some libraries were sequenced twice as technical replicates marked as *b in raw files and the processing was done using the combination of all data processed data files have comb* prefix scGESTALT libraries were processed using a custom pipeline available at https://github.com/shendurelab/Cas9FateMapping Genome build: GRCz10 Supplementary files format and content: *barcodes.tsv files contain 10X Genomics cell barcodes  *genes.tsv files contain gene names  *matrix.mtx contain transcriptome count data  *web summary.html contain summary statistics for transcript mapping  .rds files are the processed R objects  .txt files contain marker genes identified for each cluster in the dataset  URD*.rds files are the processed R objects for performing URD cell trajectory analysis. tree*.rds files are the final URD objects with cell trajectory trees for the retina and hypothalamus. Supplementary files format and content: scGESTALT data:  Gest zBr15dpf8 and Gest zBr15dpf9 correspond to two samples from the same zebrafish ZF1. Gest zBr15dpf10 and Gest zBr15dpf11 correspond to two samples from the same zebrafish ZF2. Gest zBr15dpf12 and Gest zBr15dpf13 correspond to two samples from the same zebrafish ZF3. Gest zBr15dpf14 and Gest zBr15dpf15 correspond to two samples from the same zebrafish ZF4. Supplementary files format and content: scGESTALT data: *GestMaster.txt contains the 10X Genmoics cell identifiers CellBarcode and CellUMI that were used to matchlineage barcodes to transcriptomes. They also contain lineage barcode sequences HMID column   the t SNE cluster membership number ClusterIdent column  and unique identifier Readname. zfAllMerge FILTEREDUSEME.xlsx contains the merged statistics of all samples  filtered to contain high confidence barcodes  the barcode sequence aligned to a reference unedited sequence mergedRead column  mutations at each target site target[X] columns and the edited sequences at each target site sequence[X] columns were used for downstream analysis. Further details of columns can be found at https://github.com/shendurelab/Cas9FateMapping,zebrafish brain,,Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol  to generate single cell cDNA libraries and prepared for sequencing,,tissue:brain|developmental stage:2dpf,GSM4793205,GSM4793205: zBr2dpf5 S3; Danio rerio; RNA Seq,GSM4793205,,1,Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol  to generate single cell cDNA libraries and prepared for sequencing,GEO Accession:GSM4793205,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP282920,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=zBr2dpf5 S3 L002 I1 001.fastq.gz   read2PairFiles=zBr2dpf5 S3 L002 R1 001.fastq.gz   read3PairFiles=zBr2dpf5 S3 L002 R2 001.fastq.gz,zBr2dpf5_S3_L002_I1_001.fastq.gz zBr2dpf5_S3_L002_R1_001.fastq.gz zBr2dpf5_S3_L002_R2_001.fastq.gz,fastq fastq fastq,1402315152.0,15242556.0,GSM4793205 r2,0:8 1:26 2:58,A:373114373;C:310158948;G:351441489;T:367374392;N:225950,8,26,58,,373114373,310158948,351441489,367374392,225950,SRX9142588,SRS7383892,SRA1127180,GEO,Harvard University,1,0.9401,,0.10484,,0.81635,,0.51232,,58,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2020-09-17,Hatching,Embryo,Brain,Nervous System
61247,SRR12661742,SRX9142588,SRS7383892,SRP282920,PRJNA664124,Emergence of neuronal diversity during vertebrate brain development,GSE158142,Transcriptome Analysis,Neurogenesis comprises many steps from progenitor proliferation to neuronal differentiation and maturation. These processes are highly regulated  but the landscape of transcriptional changes underlying brain development are poorly characterized. Here  we describe a developmental single cell RNA seq catalog of 220 000 zebrafish brain cells encompassing 12 stages from 12 hpf to 15 dpf We characterize known and novel gene markers for 800 clusters and provide an overview of the diversification of neurons and progenitors across these timepoints. We also introduce an optimized version of the GESTALT lineage recorder that enables higher expression and recovery of Cas9 edited barcodes to query lineage segregation. Cell type characterization indicates that most embryonic neural progenitor states are transitory and transcriptionally distinct from neural progenitors of post embryonic stages. Reconstruction of cell specification trajectories reveals that late stage retinal neural progenitors transcriptionally overlap cell states observed in the embryo. The zebrafish brain development atlas provides a resource to define and manipulate specific subsets of neurons and to uncover the molecular mechanisms underlying vertebrate neurogenesis. Overall design: 10X Genomics v2 scRNA seq libraries and scGESTALT,,pubmed:33068532,,zBr2dpf5 S3,GSM4793205,,source name:zebrafish brain|tissue:brain|developmental stage:2dpf,zBr2dpf5 S3,Single cell RNA Sequencing data FASTQ files were processed using Cell Ranger v2.0.2 to generate count matrices Transcriptome libraries were mapped to a zebrafish reference built from a custom GTF file and the zebrafish GRCz10 release 86 genome assembly. File uploaded as Danio rerio.GRCz10.86.modified.gtf.gz. Some libraries were sequenced twice as technical replicates marked as *b in raw files and the processing was done using the combination of all data processed data files have comb* prefix scGESTALT libraries were processed using a custom pipeline available at https://github.com/shendurelab/Cas9FateMapping Genome build: GRCz10 Supplementary files format and content: *barcodes.tsv files contain 10X Genomics cell barcodes  *genes.tsv files contain gene names  *matrix.mtx contain transcriptome count data  *web summary.html contain summary statistics for transcript mapping  .rds files are the processed R objects  .txt files contain marker genes identified for each cluster in the dataset  URD*.rds files are the processed R objects for performing URD cell trajectory analysis. tree*.rds files are the final URD objects with cell trajectory trees for the retina and hypothalamus. Supplementary files format and content: scGESTALT data:  Gest zBr15dpf8 and Gest zBr15dpf9 correspond to two samples from the same zebrafish ZF1. Gest zBr15dpf10 and Gest zBr15dpf11 correspond to two samples from the same zebrafish ZF2. Gest zBr15dpf12 and Gest zBr15dpf13 correspond to two samples from the same zebrafish ZF3. Gest zBr15dpf14 and Gest zBr15dpf15 correspond to two samples from the same zebrafish ZF4. Supplementary files format and content: scGESTALT data: *GestMaster.txt contains the 10X Genmoics cell identifiers CellBarcode and CellUMI that were used to matchlineage barcodes to transcriptomes. They also contain lineage barcode sequences HMID column   the t SNE cluster membership number ClusterIdent column  and unique identifier Readname. zfAllMerge FILTEREDUSEME.xlsx contains the merged statistics of all samples  filtered to contain high confidence barcodes  the barcode sequence aligned to a reference unedited sequence mergedRead column  mutations at each target site target[X] columns and the edited sequences at each target site sequence[X] columns were used for downstream analysis. Further details of columns can be found at https://github.com/shendurelab/Cas9FateMapping,zebrafish brain,,Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol  to generate single cell cDNA libraries and prepared for sequencing,,tissue:brain|developmental stage:2dpf,GSM4793205,GSM4793205: zBr2dpf5 S3; Danio rerio; RNA Seq,GSM4793205,,1,Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol  to generate single cell cDNA libraries and prepared for sequencing,GEO Accession:GSM4793205,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP282920,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=zBr2dpf5 S3 L003 I1 001.fastq.gz   read2PairFiles=zBr2dpf5 S3 L003 R1 001.fastq.gz   read3PairFiles=zBr2dpf5 S3 L003 R2 001.fastq.gz,zBr2dpf5_S3_L003_I1_001.fastq.gz zBr2dpf5_S3_L003_R1_001.fastq.gz zBr2dpf5_S3_L003_R2_001.fastq.gz,fastq fastq fastq,1390355152.0,15112556.0,GSM4793205 r3,0:8 1:26 2:58,A:369922218;C:306670829;G:348674068;T:364863677;N:224360,8,26,58,,369922218,306670829,348674068,364863677,224360,SRX9142588,SRS7383892,SRA1127180,GEO,Harvard University,1,0.93976,,0.10547,,0.81665,,0.49079,,58,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2020-09-17,Hatching,Embryo,Brain,Nervous System
61248,SRR12661743,SRX9142588,SRS7383892,SRP282920,PRJNA664124,Emergence of neuronal diversity during vertebrate brain development,GSE158142,Transcriptome Analysis,Neurogenesis comprises many steps from progenitor proliferation to neuronal differentiation and maturation. These processes are highly regulated  but the landscape of transcriptional changes underlying brain development are poorly characterized. Here  we describe a developmental single cell RNA seq catalog of 220 000 zebrafish brain cells encompassing 12 stages from 12 hpf to 15 dpf We characterize known and novel gene markers for 800 clusters and provide an overview of the diversification of neurons and progenitors across these timepoints. We also introduce an optimized version of the GESTALT lineage recorder that enables higher expression and recovery of Cas9 edited barcodes to query lineage segregation. Cell type characterization indicates that most embryonic neural progenitor states are transitory and transcriptionally distinct from neural progenitors of post embryonic stages. Reconstruction of cell specification trajectories reveals that late stage retinal neural progenitors transcriptionally overlap cell states observed in the embryo. The zebrafish brain development atlas provides a resource to define and manipulate specific subsets of neurons and to uncover the molecular mechanisms underlying vertebrate neurogenesis. Overall design: 10X Genomics v2 scRNA seq libraries and scGESTALT,,pubmed:33068532,,zBr2dpf5 S3,GSM4793205,,source name:zebrafish brain|tissue:brain|developmental stage:2dpf,zBr2dpf5 S3,Single cell RNA Sequencing data FASTQ files were processed using Cell Ranger v2.0.2 to generate count matrices Transcriptome libraries were mapped to a zebrafish reference built from a custom GTF file and the zebrafish GRCz10 release 86 genome assembly. File uploaded as Danio rerio.GRCz10.86.modified.gtf.gz. Some libraries were sequenced twice as technical replicates marked as *b in raw files and the processing was done using the combination of all data processed data files have comb* prefix scGESTALT libraries were processed using a custom pipeline available at https://github.com/shendurelab/Cas9FateMapping Genome build: GRCz10 Supplementary files format and content: *barcodes.tsv files contain 10X Genomics cell barcodes  *genes.tsv files contain gene names  *matrix.mtx contain transcriptome count data  *web summary.html contain summary statistics for transcript mapping  .rds files are the processed R objects  .txt files contain marker genes identified for each cluster in the dataset  URD*.rds files are the processed R objects for performing URD cell trajectory analysis. tree*.rds files are the final URD objects with cell trajectory trees for the retina and hypothalamus. Supplementary files format and content: scGESTALT data:  Gest zBr15dpf8 and Gest zBr15dpf9 correspond to two samples from the same zebrafish ZF1. Gest zBr15dpf10 and Gest zBr15dpf11 correspond to two samples from the same zebrafish ZF2. Gest zBr15dpf12 and Gest zBr15dpf13 correspond to two samples from the same zebrafish ZF3. Gest zBr15dpf14 and Gest zBr15dpf15 correspond to two samples from the same zebrafish ZF4. Supplementary files format and content: scGESTALT data: *GestMaster.txt contains the 10X Genmoics cell identifiers CellBarcode and CellUMI that were used to matchlineage barcodes to transcriptomes. They also contain lineage barcode sequences HMID column   the t SNE cluster membership number ClusterIdent column  and unique identifier Readname. zfAllMerge FILTEREDUSEME.xlsx contains the merged statistics of all samples  filtered to contain high confidence barcodes  the barcode sequence aligned to a reference unedited sequence mergedRead column  mutations at each target site target[X] columns and the edited sequences at each target site sequence[X] columns were used for downstream analysis. Further details of columns can be found at https://github.com/shendurelab/Cas9FateMapping,zebrafish brain,,Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol  to generate single cell cDNA libraries and prepared for sequencing,,tissue:brain|developmental stage:2dpf,GSM4793205,GSM4793205: zBr2dpf5 S3; Danio rerio; RNA Seq,GSM4793205,,1,Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol  to generate single cell cDNA libraries and prepared for sequencing,GEO Accession:GSM4793205,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP282920,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=zBr2dpf5 S3 L004 I1 001.fastq.gz   read2PairFiles=zBr2dpf5 S3 L004 R1 001.fastq.gz   read3PairFiles=zBr2dpf5 S3 L004 R2 001.fastq.gz,zBr2dpf5_S3_L004_I1_001.fastq.gz zBr2dpf5_S3_L004_R1_001.fastq.gz zBr2dpf5_S3_L004_R2_001.fastq.gz,fastq fastq fastq,1369540980.0,14886315.0,GSM4793205 r4,0:8 1:26 2:58,A:365092529;C:302585103;G:342423761;T:359236028;N:203559,8,26,58,,365092529,302585103,342423761,359236028,203559,SRX9142588,SRS7383892,SRA1127180,GEO,Harvard University,1,0.94114,,0.1047,,0.81874,,0.4829,,58,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2020-09-17,Hatching,Embryo,Brain,Nervous System
61249,SRR12661736,SRX9142587,SRS7383891,SRP282920,PRJNA664124,Emergence of neuronal diversity during vertebrate brain development,GSE158142,Transcriptome Analysis,Neurogenesis comprises many steps from progenitor proliferation to neuronal differentiation and maturation. These processes are highly regulated  but the landscape of transcriptional changes underlying brain development are poorly characterized. Here  we describe a developmental single cell RNA seq catalog of 220 000 zebrafish brain cells encompassing 12 stages from 12 hpf to 15 dpf We characterize known and novel gene markers for 800 clusters and provide an overview of the diversification of neurons and progenitors across these timepoints. We also introduce an optimized version of the GESTALT lineage recorder that enables higher expression and recovery of Cas9 edited barcodes to query lineage segregation. Cell type characterization indicates that most embryonic neural progenitor states are transitory and transcriptionally distinct from neural progenitors of post embryonic stages. Reconstruction of cell specification trajectories reveals that late stage retinal neural progenitors transcriptionally overlap cell states observed in the embryo. The zebrafish brain development atlas provides a resource to define and manipulate specific subsets of neurons and to uncover the molecular mechanisms underlying vertebrate neurogenesis. Overall design: 10X Genomics v2 scRNA seq libraries and scGESTALT,,pubmed:33068532,,zBr2dpf4 S2,GSM4793204,,source name:zebrafish brain|tissue:brain|developmental stage:2dpf,zBr2dpf4 S2,Single cell RNA Sequencing data FASTQ files were processed using Cell Ranger v2.0.2 to generate count matrices Transcriptome libraries were mapped to a zebrafish reference built from a custom GTF file and the zebrafish GRCz10 release 86 genome assembly. File uploaded as Danio rerio.GRCz10.86.modified.gtf.gz. Some libraries were sequenced twice as technical replicates marked as *b in raw files and the processing was done using the combination of all data processed data files have comb* prefix scGESTALT libraries were processed using a custom pipeline available at https://github.com/shendurelab/Cas9FateMapping Genome build: GRCz10 Supplementary files format and content: *barcodes.tsv files contain 10X Genomics cell barcodes  *genes.tsv files contain gene names  *matrix.mtx contain transcriptome count data  *web summary.html contain summary statistics for transcript mapping  .rds files are the processed R objects  .txt files contain marker genes identified for each cluster in the dataset  URD*.rds files are the processed R objects for performing URD cell trajectory analysis. tree*.rds files are the final URD objects with cell trajectory trees for the retina and hypothalamus. Supplementary files format and content: scGESTALT data:  Gest zBr15dpf8 and Gest zBr15dpf9 correspond to two samples from the same zebrafish ZF1. Gest zBr15dpf10 and Gest zBr15dpf11 correspond to two samples from the same zebrafish ZF2. Gest zBr15dpf12 and Gest zBr15dpf13 correspond to two samples from the same zebrafish ZF3. Gest zBr15dpf14 and Gest zBr15dpf15 correspond to two samples from the same zebrafish ZF4. Supplementary files format and content: scGESTALT data: *GestMaster.txt contains the 10X Genmoics cell identifiers CellBarcode and CellUMI that were used to matchlineage barcodes to transcriptomes. They also contain lineage barcode sequences HMID column   the t SNE cluster membership number ClusterIdent column  and unique identifier Readname. zfAllMerge FILTEREDUSEME.xlsx contains the merged statistics of all samples  filtered to contain high confidence barcodes  the barcode sequence aligned to a reference unedited sequence mergedRead column  mutations at each target site target[X] columns and the edited sequences at each target site sequence[X] columns were used for downstream analysis. Further details of columns can be found at https://github.com/shendurelab/Cas9FateMapping,zebrafish brain,,Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol  to generate single cell cDNA libraries and prepared for sequencing,,tissue:brain|developmental stage:2dpf,GSM4793204,GSM4793204: zBr2dpf4 S2; Danio rerio; RNA Seq,GSM4793204,,1,Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol  to generate single cell cDNA libraries and prepared for sequencing,GEO Accession:GSM4793204,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP282920,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=zBr2dpf4 S2 L001 I1 001.fastq.gz   read2PairFiles=zBr2dpf4 S2 L001 R1 001.fastq.gz   read3PairFiles=zBr2dpf4 S2 L001 R2 001.fastq.gz,zBr2dpf4_S2_L001_I1_001.fastq.gz zBr2dpf4_S2_L001_R1_001.fastq.gz zBr2dpf4_S2_L001_R2_001.fastq.gz,fastq fastq fastq,1239134292.0,13468851.0,GSM4793204 r1,0:8 1:26 2:58,A:328796587;C:274709455;G:312200824;T:323245450;N:181976,8,26,58,,328796587,274709455,312200824,323245450,181976,SRX9142587,SRS7383891,SRA1127180,GEO,Harvard University,1,0.93935,,0.10222,,0.81314,,0.49726,,58,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2020-09-17,Hatching,Embryo,Brain,Nervous System
61250,SRR12661737,SRX9142587,SRS7383891,SRP282920,PRJNA664124,Emergence of neuronal diversity during vertebrate brain development,GSE158142,Transcriptome Analysis,Neurogenesis comprises many steps from progenitor proliferation to neuronal differentiation and maturation. These processes are highly regulated  but the landscape of transcriptional changes underlying brain development are poorly characterized. Here  we describe a developmental single cell RNA seq catalog of 220 000 zebrafish brain cells encompassing 12 stages from 12 hpf to 15 dpf We characterize known and novel gene markers for 800 clusters and provide an overview of the diversification of neurons and progenitors across these timepoints. We also introduce an optimized version of the GESTALT lineage recorder that enables higher expression and recovery of Cas9 edited barcodes to query lineage segregation. Cell type characterization indicates that most embryonic neural progenitor states are transitory and transcriptionally distinct from neural progenitors of post embryonic stages. Reconstruction of cell specification trajectories reveals that late stage retinal neural progenitors transcriptionally overlap cell states observed in the embryo. The zebrafish brain development atlas provides a resource to define and manipulate specific subsets of neurons and to uncover the molecular mechanisms underlying vertebrate neurogenesis. Overall design: 10X Genomics v2 scRNA seq libraries and scGESTALT,,pubmed:33068532,,zBr2dpf4 S2,GSM4793204,,source name:zebrafish brain|tissue:brain|developmental stage:2dpf,zBr2dpf4 S2,Single cell RNA Sequencing data FASTQ files were processed using Cell Ranger v2.0.2 to generate count matrices Transcriptome libraries were mapped to a zebrafish reference built from a custom GTF file and the zebrafish GRCz10 release 86 genome assembly. File uploaded as Danio rerio.GRCz10.86.modified.gtf.gz. Some libraries were sequenced twice as technical replicates marked as *b in raw files and the processing was done using the combination of all data processed data files have comb* prefix scGESTALT libraries were processed using a custom pipeline available at https://github.com/shendurelab/Cas9FateMapping Genome build: GRCz10 Supplementary files format and content: *barcodes.tsv files contain 10X Genomics cell barcodes  *genes.tsv files contain gene names  *matrix.mtx contain transcriptome count data  *web summary.html contain summary statistics for transcript mapping  .rds files are the processed R objects  .txt files contain marker genes identified for each cluster in the dataset  URD*.rds files are the processed R objects for performing URD cell trajectory analysis. tree*.rds files are the final URD objects with cell trajectory trees for the retina and hypothalamus. Supplementary files format and content: scGESTALT data:  Gest zBr15dpf8 and Gest zBr15dpf9 correspond to two samples from the same zebrafish ZF1. Gest zBr15dpf10 and Gest zBr15dpf11 correspond to two samples from the same zebrafish ZF2. Gest zBr15dpf12 and Gest zBr15dpf13 correspond to two samples from the same zebrafish ZF3. Gest zBr15dpf14 and Gest zBr15dpf15 correspond to two samples from the same zebrafish ZF4. Supplementary files format and content: scGESTALT data: *GestMaster.txt contains the 10X Genmoics cell identifiers CellBarcode and CellUMI that were used to matchlineage barcodes to transcriptomes. They also contain lineage barcode sequences HMID column   the t SNE cluster membership number ClusterIdent column  and unique identifier Readname. zfAllMerge FILTEREDUSEME.xlsx contains the merged statistics of all samples  filtered to contain high confidence barcodes  the barcode sequence aligned to a reference unedited sequence mergedRead column  mutations at each target site target[X] columns and the edited sequences at each target site sequence[X] columns were used for downstream analysis. Further details of columns can be found at https://github.com/shendurelab/Cas9FateMapping,zebrafish brain,,Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol  to generate single cell cDNA libraries and prepared for sequencing,,tissue:brain|developmental stage:2dpf,GSM4793204,GSM4793204: zBr2dpf4 S2; Danio rerio; RNA Seq,GSM4793204,,1,Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol  to generate single cell cDNA libraries and prepared for sequencing,GEO Accession:GSM4793204,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP282920,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=zBr2dpf4 S2 L002 I1 001.fastq.gz   read2PairFiles=zBr2dpf4 S2 L002 R1 001.fastq.gz   read3PairFiles=zBr2dpf4 S2 L002 R2 001.fastq.gz,zBr2dpf4_S2_L002_I1_001.fastq.gz zBr2dpf4_S2_L002_R1_001.fastq.gz zBr2dpf4_S2_L002_R2_001.fastq.gz,fastq fastq fastq,1223186368.0,13295504.0,GSM4793204 r2,0:8 1:26 2:58,A:326139052;C:271416638;G:306130792;T:319309928;N:189958,8,26,58,,326139052,271416638,306130792,319309928,189958,SRX9142587,SRS7383891,SRA1127180,GEO,Harvard University,1,0.94151,,0.10408,,0.8155,,0.49165,,58,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2020-09-17,Hatching,Embryo,Brain,Nervous System
61251,SRR12661738,SRX9142587,SRS7383891,SRP282920,PRJNA664124,Emergence of neuronal diversity during vertebrate brain development,GSE158142,Transcriptome Analysis,Neurogenesis comprises many steps from progenitor proliferation to neuronal differentiation and maturation. These processes are highly regulated  but the landscape of transcriptional changes underlying brain development are poorly characterized. Here  we describe a developmental single cell RNA seq catalog of 220 000 zebrafish brain cells encompassing 12 stages from 12 hpf to 15 dpf We characterize known and novel gene markers for 800 clusters and provide an overview of the diversification of neurons and progenitors across these timepoints. We also introduce an optimized version of the GESTALT lineage recorder that enables higher expression and recovery of Cas9 edited barcodes to query lineage segregation. Cell type characterization indicates that most embryonic neural progenitor states are transitory and transcriptionally distinct from neural progenitors of post embryonic stages. Reconstruction of cell specification trajectories reveals that late stage retinal neural progenitors transcriptionally overlap cell states observed in the embryo. The zebrafish brain development atlas provides a resource to define and manipulate specific subsets of neurons and to uncover the molecular mechanisms underlying vertebrate neurogenesis. Overall design: 10X Genomics v2 scRNA seq libraries and scGESTALT,,pubmed:33068532,,zBr2dpf4 S2,GSM4793204,,source name:zebrafish brain|tissue:brain|developmental stage:2dpf,zBr2dpf4 S2,Single cell RNA Sequencing data FASTQ files were processed using Cell Ranger v2.0.2 to generate count matrices Transcriptome libraries were mapped to a zebrafish reference built from a custom GTF file and the zebrafish GRCz10 release 86 genome assembly. File uploaded as Danio rerio.GRCz10.86.modified.gtf.gz. Some libraries were sequenced twice as technical replicates marked as *b in raw files and the processing was done using the combination of all data processed data files have comb* prefix scGESTALT libraries were processed using a custom pipeline available at https://github.com/shendurelab/Cas9FateMapping Genome build: GRCz10 Supplementary files format and content: *barcodes.tsv files contain 10X Genomics cell barcodes  *genes.tsv files contain gene names  *matrix.mtx contain transcriptome count data  *web summary.html contain summary statistics for transcript mapping  .rds files are the processed R objects  .txt files contain marker genes identified for each cluster in the dataset  URD*.rds files are the processed R objects for performing URD cell trajectory analysis. tree*.rds files are the final URD objects with cell trajectory trees for the retina and hypothalamus. Supplementary files format and content: scGESTALT data:  Gest zBr15dpf8 and Gest zBr15dpf9 correspond to two samples from the same zebrafish ZF1. Gest zBr15dpf10 and Gest zBr15dpf11 correspond to two samples from the same zebrafish ZF2. Gest zBr15dpf12 and Gest zBr15dpf13 correspond to two samples from the same zebrafish ZF3. Gest zBr15dpf14 and Gest zBr15dpf15 correspond to two samples from the same zebrafish ZF4. Supplementary files format and content: scGESTALT data: *GestMaster.txt contains the 10X Genmoics cell identifiers CellBarcode and CellUMI that were used to matchlineage barcodes to transcriptomes. They also contain lineage barcode sequences HMID column   the t SNE cluster membership number ClusterIdent column  and unique identifier Readname. zfAllMerge FILTEREDUSEME.xlsx contains the merged statistics of all samples  filtered to contain high confidence barcodes  the barcode sequence aligned to a reference unedited sequence mergedRead column  mutations at each target site target[X] columns and the edited sequences at each target site sequence[X] columns were used for downstream analysis. Further details of columns can be found at https://github.com/shendurelab/Cas9FateMapping,zebrafish brain,,Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol  to generate single cell cDNA libraries and prepared for sequencing,,tissue:brain|developmental stage:2dpf,GSM4793204,GSM4793204: zBr2dpf4 S2; Danio rerio; RNA Seq,GSM4793204,,1,Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol  to generate single cell cDNA libraries and prepared for sequencing,GEO Accession:GSM4793204,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP282920,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=zBr2dpf4 S2 L003 I1 001.fastq.gz   read2PairFiles=zBr2dpf4 S2 L003 R1 001.fastq.gz   read3PairFiles=zBr2dpf4 S2 L003 R2 001.fastq.gz,zBr2dpf4_S2_L003_I1_001.fastq.gz zBr2dpf4_S2_L003_R1_001.fastq.gz zBr2dpf4_S2_L003_R2_001.fastq.gz,fastq fastq fastq,1202575884.0,13071477.0,GSM4793204 r3,0:8 1:26 2:58,A:320734552;C:265990332;G:301153552;T:314497332;N:200116,8,26,58,,320734552,265990332,301153552,314497332,200116,SRX9142587,SRS7383891,SRA1127180,GEO,Harvard University,1,0.9402,,0.10292,,0.82063,,0.47643,,58,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2020-09-17,Hatching,Embryo,Brain,Nervous System
61252,SRR12661739,SRX9142587,SRS7383891,SRP282920,PRJNA664124,Emergence of neuronal diversity during vertebrate brain development,GSE158142,Transcriptome Analysis,Neurogenesis comprises many steps from progenitor proliferation to neuronal differentiation and maturation. These processes are highly regulated  but the landscape of transcriptional changes underlying brain development are poorly characterized. Here  we describe a developmental single cell RNA seq catalog of 220 000 zebrafish brain cells encompassing 12 stages from 12 hpf to 15 dpf We characterize known and novel gene markers for 800 clusters and provide an overview of the diversification of neurons and progenitors across these timepoints. We also introduce an optimized version of the GESTALT lineage recorder that enables higher expression and recovery of Cas9 edited barcodes to query lineage segregation. Cell type characterization indicates that most embryonic neural progenitor states are transitory and transcriptionally distinct from neural progenitors of post embryonic stages. Reconstruction of cell specification trajectories reveals that late stage retinal neural progenitors transcriptionally overlap cell states observed in the embryo. The zebrafish brain development atlas provides a resource to define and manipulate specific subsets of neurons and to uncover the molecular mechanisms underlying vertebrate neurogenesis. Overall design: 10X Genomics v2 scRNA seq libraries and scGESTALT,,pubmed:33068532,,zBr2dpf4 S2,GSM4793204,,source name:zebrafish brain|tissue:brain|developmental stage:2dpf,zBr2dpf4 S2,Single cell RNA Sequencing data FASTQ files were processed using Cell Ranger v2.0.2 to generate count matrices Transcriptome libraries were mapped to a zebrafish reference built from a custom GTF file and the zebrafish GRCz10 release 86 genome assembly. File uploaded as Danio rerio.GRCz10.86.modified.gtf.gz. Some libraries were sequenced twice as technical replicates marked as *b in raw files and the processing was done using the combination of all data processed data files have comb* prefix scGESTALT libraries were processed using a custom pipeline available at https://github.com/shendurelab/Cas9FateMapping Genome build: GRCz10 Supplementary files format and content: *barcodes.tsv files contain 10X Genomics cell barcodes  *genes.tsv files contain gene names  *matrix.mtx contain transcriptome count data  *web summary.html contain summary statistics for transcript mapping  .rds files are the processed R objects  .txt files contain marker genes identified for each cluster in the dataset  URD*.rds files are the processed R objects for performing URD cell trajectory analysis. tree*.rds files are the final URD objects with cell trajectory trees for the retina and hypothalamus. Supplementary files format and content: scGESTALT data:  Gest zBr15dpf8 and Gest zBr15dpf9 correspond to two samples from the same zebrafish ZF1. Gest zBr15dpf10 and Gest zBr15dpf11 correspond to two samples from the same zebrafish ZF2. Gest zBr15dpf12 and Gest zBr15dpf13 correspond to two samples from the same zebrafish ZF3. Gest zBr15dpf14 and Gest zBr15dpf15 correspond to two samples from the same zebrafish ZF4. Supplementary files format and content: scGESTALT data: *GestMaster.txt contains the 10X Genmoics cell identifiers CellBarcode and CellUMI that were used to matchlineage barcodes to transcriptomes. They also contain lineage barcode sequences HMID column   the t SNE cluster membership number ClusterIdent column  and unique identifier Readname. zfAllMerge FILTEREDUSEME.xlsx contains the merged statistics of all samples  filtered to contain high confidence barcodes  the barcode sequence aligned to a reference unedited sequence mergedRead column  mutations at each target site target[X] columns and the edited sequences at each target site sequence[X] columns were used for downstream analysis. Further details of columns can be found at https://github.com/shendurelab/Cas9FateMapping,zebrafish brain,,Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol  to generate single cell cDNA libraries and prepared for sequencing,,tissue:brain|developmental stage:2dpf,GSM4793204,GSM4793204: zBr2dpf4 S2; Danio rerio; RNA Seq,GSM4793204,,1,Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol  to generate single cell cDNA libraries and prepared for sequencing,GEO Accession:GSM4793204,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP282920,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=zBr2dpf4 S2 L004 I1 001.fastq.gz   read2PairFiles=zBr2dpf4 S2 L004 R1 001.fastq.gz   read3PairFiles=zBr2dpf4 S2 L004 R2 001.fastq.gz,zBr2dpf4_S2_L004_I1_001.fastq.gz zBr2dpf4_S2_L004_R1_001.fastq.gz zBr2dpf4_S2_L004_R2_001.fastq.gz,fastq fastq fastq,1188718016.0,12920848.0,GSM4793204 r4,0:8 1:26 2:58,A:317586867;C:263420618;G:296857671;T:310674373;N:178487,8,26,58,,317586867,263420618,296857671,310674373,178487,SRX9142587,SRS7383891,SRA1127180,GEO,Harvard University,1,0.94167,,0.10483,,0.81602,,0.49655,,58,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2020-09-17,Hatching,Embryo,Brain,Nervous System
61253,SRR12661732,SRX9142586,SRS7383890,SRP282920,PRJNA664124,Emergence of neuronal diversity during vertebrate brain development,GSE158142,Transcriptome Analysis,Neurogenesis comprises many steps from progenitor proliferation to neuronal differentiation and maturation. These processes are highly regulated  but the landscape of transcriptional changes underlying brain development are poorly characterized. Here  we describe a developmental single cell RNA seq catalog of 220 000 zebrafish brain cells encompassing 12 stages from 12 hpf to 15 dpf We characterize known and novel gene markers for 800 clusters and provide an overview of the diversification of neurons and progenitors across these timepoints. We also introduce an optimized version of the GESTALT lineage recorder that enables higher expression and recovery of Cas9 edited barcodes to query lineage segregation. Cell type characterization indicates that most embryonic neural progenitor states are transitory and transcriptionally distinct from neural progenitors of post embryonic stages. Reconstruction of cell specification trajectories reveals that late stage retinal neural progenitors transcriptionally overlap cell states observed in the embryo. The zebrafish brain development atlas provides a resource to define and manipulate specific subsets of neurons and to uncover the molecular mechanisms underlying vertebrate neurogenesis. Overall design: 10X Genomics v2 scRNA seq libraries and scGESTALT,,pubmed:33068532,,zBr2dpf3 S1,GSM4793203,,source name:zebrafish brain|tissue:brain|developmental stage:2dpf,zBr2dpf3 S1,Single cell RNA Sequencing data FASTQ files were processed using Cell Ranger v2.0.2 to generate count matrices Transcriptome libraries were mapped to a zebrafish reference built from a custom GTF file and the zebrafish GRCz10 release 86 genome assembly. File uploaded as Danio rerio.GRCz10.86.modified.gtf.gz. Some libraries were sequenced twice as technical replicates marked as *b in raw files and the processing was done using the combination of all data processed data files have comb* prefix scGESTALT libraries were processed using a custom pipeline available at https://github.com/shendurelab/Cas9FateMapping Genome build: GRCz10 Supplementary files format and content: *barcodes.tsv files contain 10X Genomics cell barcodes  *genes.tsv files contain gene names  *matrix.mtx contain transcriptome count data  *web summary.html contain summary statistics for transcript mapping  .rds files are the processed R objects  .txt files contain marker genes identified for each cluster in the dataset  URD*.rds files are the processed R objects for performing URD cell trajectory analysis. tree*.rds files are the final URD objects with cell trajectory trees for the retina and hypothalamus. Supplementary files format and content: scGESTALT data:  Gest zBr15dpf8 and Gest zBr15dpf9 correspond to two samples from the same zebrafish ZF1. Gest zBr15dpf10 and Gest zBr15dpf11 correspond to two samples from the same zebrafish ZF2. Gest zBr15dpf12 and Gest zBr15dpf13 correspond to two samples from the same zebrafish ZF3. Gest zBr15dpf14 and Gest zBr15dpf15 correspond to two samples from the same zebrafish ZF4. Supplementary files format and content: scGESTALT data: *GestMaster.txt contains the 10X Genmoics cell identifiers CellBarcode and CellUMI that were used to matchlineage barcodes to transcriptomes. They also contain lineage barcode sequences HMID column   the t SNE cluster membership number ClusterIdent column  and unique identifier Readname. zfAllMerge FILTEREDUSEME.xlsx contains the merged statistics of all samples  filtered to contain high confidence barcodes  the barcode sequence aligned to a reference unedited sequence mergedRead column  mutations at each target site target[X] columns and the edited sequences at each target site sequence[X] columns were used for downstream analysis. Further details of columns can be found at https://github.com/shendurelab/Cas9FateMapping,zebrafish brain,,Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol  to generate single cell cDNA libraries and prepared for sequencing,,tissue:brain|developmental stage:2dpf,GSM4793203,GSM4793203: zBr2dpf3 S1; Danio rerio; RNA Seq,GSM4793203,,1,Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol  to generate single cell cDNA libraries and prepared for sequencing,GEO Accession:GSM4793203,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP282920,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=zBr2dpf3 S1 L001 I1 001.fastq.gz   read2PairFiles=zBr2dpf3 S1 L001 R1 001.fastq.gz   read3PairFiles=zBr2dpf3 S1 L001 R2 001.fastq.gz,zBr2dpf3_S1_L001_I1_001.fastq.gz zBr2dpf3_S1_L001_R1_001.fastq.gz zBr2dpf3_S1_L001_R2_001.fastq.gz,fastq fastq fastq,1226402964.0,13330467.0,GSM4793203 r1,0:8 1:26 2:58,A:326661734;C:276069009;G:303031527;T:320457713;N:182981,8,26,58,,326661734,276069009,303031527,320457713,182981,SRX9142586,SRS7383890,SRA1127180,GEO,Harvard University,1,0.93957,,0.09895,,0.81337,,0.4938,,58,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2020-09-17,Hatching,Embryo,Brain,Nervous System
61254,SRR12661733,SRX9142586,SRS7383890,SRP282920,PRJNA664124,Emergence of neuronal diversity during vertebrate brain development,GSE158142,Transcriptome Analysis,Neurogenesis comprises many steps from progenitor proliferation to neuronal differentiation and maturation. These processes are highly regulated  but the landscape of transcriptional changes underlying brain development are poorly characterized. Here  we describe a developmental single cell RNA seq catalog of 220 000 zebrafish brain cells encompassing 12 stages from 12 hpf to 15 dpf We characterize known and novel gene markers for 800 clusters and provide an overview of the diversification of neurons and progenitors across these timepoints. We also introduce an optimized version of the GESTALT lineage recorder that enables higher expression and recovery of Cas9 edited barcodes to query lineage segregation. Cell type characterization indicates that most embryonic neural progenitor states are transitory and transcriptionally distinct from neural progenitors of post embryonic stages. Reconstruction of cell specification trajectories reveals that late stage retinal neural progenitors transcriptionally overlap cell states observed in the embryo. The zebrafish brain development atlas provides a resource to define and manipulate specific subsets of neurons and to uncover the molecular mechanisms underlying vertebrate neurogenesis. Overall design: 10X Genomics v2 scRNA seq libraries and scGESTALT,,pubmed:33068532,,zBr2dpf3 S1,GSM4793203,,source name:zebrafish brain|tissue:brain|developmental stage:2dpf,zBr2dpf3 S1,Single cell RNA Sequencing data FASTQ files were processed using Cell Ranger v2.0.2 to generate count matrices Transcriptome libraries were mapped to a zebrafish reference built from a custom GTF file and the zebrafish GRCz10 release 86 genome assembly. File uploaded as Danio rerio.GRCz10.86.modified.gtf.gz. Some libraries were sequenced twice as technical replicates marked as *b in raw files and the processing was done using the combination of all data processed data files have comb* prefix scGESTALT libraries were processed using a custom pipeline available at https://github.com/shendurelab/Cas9FateMapping Genome build: GRCz10 Supplementary files format and content: *barcodes.tsv files contain 10X Genomics cell barcodes  *genes.tsv files contain gene names  *matrix.mtx contain transcriptome count data  *web summary.html contain summary statistics for transcript mapping  .rds files are the processed R objects  .txt files contain marker genes identified for each cluster in the dataset  URD*.rds files are the processed R objects for performing URD cell trajectory analysis. tree*.rds files are the final URD objects with cell trajectory trees for the retina and hypothalamus. Supplementary files format and content: scGESTALT data:  Gest zBr15dpf8 and Gest zBr15dpf9 correspond to two samples from the same zebrafish ZF1. Gest zBr15dpf10 and Gest zBr15dpf11 correspond to two samples from the same zebrafish ZF2. Gest zBr15dpf12 and Gest zBr15dpf13 correspond to two samples from the same zebrafish ZF3. Gest zBr15dpf14 and Gest zBr15dpf15 correspond to two samples from the same zebrafish ZF4. Supplementary files format and content: scGESTALT data: *GestMaster.txt contains the 10X Genmoics cell identifiers CellBarcode and CellUMI that were used to matchlineage barcodes to transcriptomes. They also contain lineage barcode sequences HMID column   the t SNE cluster membership number ClusterIdent column  and unique identifier Readname. zfAllMerge FILTEREDUSEME.xlsx contains the merged statistics of all samples  filtered to contain high confidence barcodes  the barcode sequence aligned to a reference unedited sequence mergedRead column  mutations at each target site target[X] columns and the edited sequences at each target site sequence[X] columns were used for downstream analysis. Further details of columns can be found at https://github.com/shendurelab/Cas9FateMapping,zebrafish brain,,Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol  to generate single cell cDNA libraries and prepared for sequencing,,tissue:brain|developmental stage:2dpf,GSM4793203,GSM4793203: zBr2dpf3 S1; Danio rerio; RNA Seq,GSM4793203,,1,Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol  to generate single cell cDNA libraries and prepared for sequencing,GEO Accession:GSM4793203,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP282920,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=zBr2dpf3 S1 L002 I1 001.fastq.gz   read2PairFiles=zBr2dpf3 S1 L002 R1 001.fastq.gz   read3PairFiles=zBr2dpf3 S1 L002 R2 001.fastq.gz,zBr2dpf3_S1_L002_I1_001.fastq.gz zBr2dpf3_S1_L002_R1_001.fastq.gz zBr2dpf3_S1_L002_R2_001.fastq.gz,fastq fastq fastq,1210496624.0,13157572.0,GSM4793203 r2,0:8 1:26 2:58,A:323943138;C:272771349;G:297045042;T:316544450;N:192645,8,26,58,,323943138,272771349,297045042,316544450,192645,SRX9142586,SRS7383890,SRA1127180,GEO,Harvard University,1,0.94096,,0.09908,,0.81416,,0.50044,,58,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2020-09-17,Hatching,Embryo,Brain,Nervous System
61255,SRR12661734,SRX9142586,SRS7383890,SRP282920,PRJNA664124,Emergence of neuronal diversity during vertebrate brain development,GSE158142,Transcriptome Analysis,Neurogenesis comprises many steps from progenitor proliferation to neuronal differentiation and maturation. These processes are highly regulated  but the landscape of transcriptional changes underlying brain development are poorly characterized. Here  we describe a developmental single cell RNA seq catalog of 220 000 zebrafish brain cells encompassing 12 stages from 12 hpf to 15 dpf We characterize known and novel gene markers for 800 clusters and provide an overview of the diversification of neurons and progenitors across these timepoints. We also introduce an optimized version of the GESTALT lineage recorder that enables higher expression and recovery of Cas9 edited barcodes to query lineage segregation. Cell type characterization indicates that most embryonic neural progenitor states are transitory and transcriptionally distinct from neural progenitors of post embryonic stages. Reconstruction of cell specification trajectories reveals that late stage retinal neural progenitors transcriptionally overlap cell states observed in the embryo. The zebrafish brain development atlas provides a resource to define and manipulate specific subsets of neurons and to uncover the molecular mechanisms underlying vertebrate neurogenesis. Overall design: 10X Genomics v2 scRNA seq libraries and scGESTALT,,pubmed:33068532,,zBr2dpf3 S1,GSM4793203,,source name:zebrafish brain|tissue:brain|developmental stage:2dpf,zBr2dpf3 S1,Single cell RNA Sequencing data FASTQ files were processed using Cell Ranger v2.0.2 to generate count matrices Transcriptome libraries were mapped to a zebrafish reference built from a custom GTF file and the zebrafish GRCz10 release 86 genome assembly. File uploaded as Danio rerio.GRCz10.86.modified.gtf.gz. Some libraries were sequenced twice as technical replicates marked as *b in raw files and the processing was done using the combination of all data processed data files have comb* prefix scGESTALT libraries were processed using a custom pipeline available at https://github.com/shendurelab/Cas9FateMapping Genome build: GRCz10 Supplementary files format and content: *barcodes.tsv files contain 10X Genomics cell barcodes  *genes.tsv files contain gene names  *matrix.mtx contain transcriptome count data  *web summary.html contain summary statistics for transcript mapping  .rds files are the processed R objects  .txt files contain marker genes identified for each cluster in the dataset  URD*.rds files are the processed R objects for performing URD cell trajectory analysis. tree*.rds files are the final URD objects with cell trajectory trees for the retina and hypothalamus. Supplementary files format and content: scGESTALT data:  Gest zBr15dpf8 and Gest zBr15dpf9 correspond to two samples from the same zebrafish ZF1. Gest zBr15dpf10 and Gest zBr15dpf11 correspond to two samples from the same zebrafish ZF2. Gest zBr15dpf12 and Gest zBr15dpf13 correspond to two samples from the same zebrafish ZF3. Gest zBr15dpf14 and Gest zBr15dpf15 correspond to two samples from the same zebrafish ZF4. Supplementary files format and content: scGESTALT data: *GestMaster.txt contains the 10X Genmoics cell identifiers CellBarcode and CellUMI that were used to matchlineage barcodes to transcriptomes. They also contain lineage barcode sequences HMID column   the t SNE cluster membership number ClusterIdent column  and unique identifier Readname. zfAllMerge FILTEREDUSEME.xlsx contains the merged statistics of all samples  filtered to contain high confidence barcodes  the barcode sequence aligned to a reference unedited sequence mergedRead column  mutations at each target site target[X] columns and the edited sequences at each target site sequence[X] columns were used for downstream analysis. Further details of columns can be found at https://github.com/shendurelab/Cas9FateMapping,zebrafish brain,,Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol  to generate single cell cDNA libraries and prepared for sequencing,,tissue:brain|developmental stage:2dpf,GSM4793203,GSM4793203: zBr2dpf3 S1; Danio rerio; RNA Seq,GSM4793203,,1,Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol  to generate single cell cDNA libraries and prepared for sequencing,GEO Accession:GSM4793203,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP282920,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=zBr2dpf3 S1 L003 I1 001.fastq.gz   read2PairFiles=zBr2dpf3 S1 L003 R1 001.fastq.gz   read3PairFiles=zBr2dpf3 S1 L003 R2 001.fastq.gz,zBr2dpf3_S1_L003_I1_001.fastq.gz zBr2dpf3_S1_L003_R1_001.fastq.gz zBr2dpf3_S1_L003_R2_001.fastq.gz,fastq fastq fastq,1199729404.0,13040537.0,GSM4793203 r3,0:8 1:26 2:58,A:321141508;C:269565671;G:294529755;T:314294746;N:197724,8,26,58,,321141508,269565671,294529755,314294746,197724,SRX9142586,SRS7383890,SRA1127180,GEO,Harvard University,1,0.94108,,0.102,,0.81606,,0.49463,,58,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2020-09-17,Hatching,Embryo,Brain,Nervous System
61256,SRR12661735,SRX9142586,SRS7383890,SRP282920,PRJNA664124,Emergence of neuronal diversity during vertebrate brain development,GSE158142,Transcriptome Analysis,Neurogenesis comprises many steps from progenitor proliferation to neuronal differentiation and maturation. These processes are highly regulated  but the landscape of transcriptional changes underlying brain development are poorly characterized. Here  we describe a developmental single cell RNA seq catalog of 220 000 zebrafish brain cells encompassing 12 stages from 12 hpf to 15 dpf We characterize known and novel gene markers for 800 clusters and provide an overview of the diversification of neurons and progenitors across these timepoints. We also introduce an optimized version of the GESTALT lineage recorder that enables higher expression and recovery of Cas9 edited barcodes to query lineage segregation. Cell type characterization indicates that most embryonic neural progenitor states are transitory and transcriptionally distinct from neural progenitors of post embryonic stages. Reconstruction of cell specification trajectories reveals that late stage retinal neural progenitors transcriptionally overlap cell states observed in the embryo. The zebrafish brain development atlas provides a resource to define and manipulate specific subsets of neurons and to uncover the molecular mechanisms underlying vertebrate neurogenesis. Overall design: 10X Genomics v2 scRNA seq libraries and scGESTALT,,pubmed:33068532,,zBr2dpf3 S1,GSM4793203,,source name:zebrafish brain|tissue:brain|developmental stage:2dpf,zBr2dpf3 S1,Single cell RNA Sequencing data FASTQ files were processed using Cell Ranger v2.0.2 to generate count matrices Transcriptome libraries were mapped to a zebrafish reference built from a custom GTF file and the zebrafish GRCz10 release 86 genome assembly. File uploaded as Danio rerio.GRCz10.86.modified.gtf.gz. Some libraries were sequenced twice as technical replicates marked as *b in raw files and the processing was done using the combination of all data processed data files have comb* prefix scGESTALT libraries were processed using a custom pipeline available at https://github.com/shendurelab/Cas9FateMapping Genome build: GRCz10 Supplementary files format and content: *barcodes.tsv files contain 10X Genomics cell barcodes  *genes.tsv files contain gene names  *matrix.mtx contain transcriptome count data  *web summary.html contain summary statistics for transcript mapping  .rds files are the processed R objects  .txt files contain marker genes identified for each cluster in the dataset  URD*.rds files are the processed R objects for performing URD cell trajectory analysis. tree*.rds files are the final URD objects with cell trajectory trees for the retina and hypothalamus. Supplementary files format and content: scGESTALT data:  Gest zBr15dpf8 and Gest zBr15dpf9 correspond to two samples from the same zebrafish ZF1. Gest zBr15dpf10 and Gest zBr15dpf11 correspond to two samples from the same zebrafish ZF2. Gest zBr15dpf12 and Gest zBr15dpf13 correspond to two samples from the same zebrafish ZF3. Gest zBr15dpf14 and Gest zBr15dpf15 correspond to two samples from the same zebrafish ZF4. Supplementary files format and content: scGESTALT data: *GestMaster.txt contains the 10X Genmoics cell identifiers CellBarcode and CellUMI that were used to matchlineage barcodes to transcriptomes. They also contain lineage barcode sequences HMID column   the t SNE cluster membership number ClusterIdent column  and unique identifier Readname. zfAllMerge FILTEREDUSEME.xlsx contains the merged statistics of all samples  filtered to contain high confidence barcodes  the barcode sequence aligned to a reference unedited sequence mergedRead column  mutations at each target site target[X] columns and the edited sequences at each target site sequence[X] columns were used for downstream analysis. Further details of columns can be found at https://github.com/shendurelab/Cas9FateMapping,zebrafish brain,,Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol  to generate single cell cDNA libraries and prepared for sequencing,,tissue:brain|developmental stage:2dpf,GSM4793203,GSM4793203: zBr2dpf3 S1; Danio rerio; RNA Seq,GSM4793203,,1,Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol  to generate single cell cDNA libraries and prepared for sequencing,GEO Accession:GSM4793203,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP282920,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=zBr2dpf3 S1 L004 I1 001.fastq.gz   read2PairFiles=zBr2dpf3 S1 L004 R1 001.fastq.gz   read3PairFiles=zBr2dpf3 S1 L004 R2 001.fastq.gz,zBr2dpf3_S1_L004_I1_001.fastq.gz zBr2dpf3_S1_L004_R1_001.fastq.gz zBr2dpf3_S1_L004_R2_001.fastq.gz,fastq fastq fastq,1182541780.0,12853715.0,GSM4793203 r4,0:8 1:26 2:58,A:317147535;C:266216608;G:289343448;T:309653687;N:180502,8,26,58,,317147535,266216608,289343448,309653687,180502,SRX9142586,SRS7383890,SRA1127180,GEO,Harvard University,1,0.94152,,0.10077,,0.81639,,0.48378,,58,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2020-09-17,Hatching,Embryo,Brain,Nervous System
61257,SRR12661728,SRX9142585,SRS7383889,SRP282920,PRJNA664124,Emergence of neuronal diversity during vertebrate brain development,GSE158142,Transcriptome Analysis,Neurogenesis comprises many steps from progenitor proliferation to neuronal differentiation and maturation. These processes are highly regulated  but the landscape of transcriptional changes underlying brain development are poorly characterized. Here  we describe a developmental single cell RNA seq catalog of 220 000 zebrafish brain cells encompassing 12 stages from 12 hpf to 15 dpf We characterize known and novel gene markers for 800 clusters and provide an overview of the diversification of neurons and progenitors across these timepoints. We also introduce an optimized version of the GESTALT lineage recorder that enables higher expression and recovery of Cas9 edited barcodes to query lineage segregation. Cell type characterization indicates that most embryonic neural progenitor states are transitory and transcriptionally distinct from neural progenitors of post embryonic stages. Reconstruction of cell specification trajectories reveals that late stage retinal neural progenitors transcriptionally overlap cell states observed in the embryo. The zebrafish brain development atlas provides a resource to define and manipulate specific subsets of neurons and to uncover the molecular mechanisms underlying vertebrate neurogenesis. Overall design: 10X Genomics v2 scRNA seq libraries and scGESTALT,,pubmed:33068532,,zBr2dpf2 S4,GSM4793202,,source name:zebrafish brain|tissue:brain|developmental stage:2dpf,zBr2dpf2 S4,Single cell RNA Sequencing data FASTQ files were processed using Cell Ranger v2.0.2 to generate count matrices Transcriptome libraries were mapped to a zebrafish reference built from a custom GTF file and the zebrafish GRCz10 release 86 genome assembly. File uploaded as Danio rerio.GRCz10.86.modified.gtf.gz. Some libraries were sequenced twice as technical replicates marked as *b in raw files and the processing was done using the combination of all data processed data files have comb* prefix scGESTALT libraries were processed using a custom pipeline available at https://github.com/shendurelab/Cas9FateMapping Genome build: GRCz10 Supplementary files format and content: *barcodes.tsv files contain 10X Genomics cell barcodes  *genes.tsv files contain gene names  *matrix.mtx contain transcriptome count data  *web summary.html contain summary statistics for transcript mapping  .rds files are the processed R objects  .txt files contain marker genes identified for each cluster in the dataset  URD*.rds files are the processed R objects for performing URD cell trajectory analysis. tree*.rds files are the final URD objects with cell trajectory trees for the retina and hypothalamus. Supplementary files format and content: scGESTALT data:  Gest zBr15dpf8 and Gest zBr15dpf9 correspond to two samples from the same zebrafish ZF1. Gest zBr15dpf10 and Gest zBr15dpf11 correspond to two samples from the same zebrafish ZF2. Gest zBr15dpf12 and Gest zBr15dpf13 correspond to two samples from the same zebrafish ZF3. Gest zBr15dpf14 and Gest zBr15dpf15 correspond to two samples from the same zebrafish ZF4. Supplementary files format and content: scGESTALT data: *GestMaster.txt contains the 10X Genmoics cell identifiers CellBarcode and CellUMI that were used to matchlineage barcodes to transcriptomes. They also contain lineage barcode sequences HMID column   the t SNE cluster membership number ClusterIdent column  and unique identifier Readname. zfAllMerge FILTEREDUSEME.xlsx contains the merged statistics of all samples  filtered to contain high confidence barcodes  the barcode sequence aligned to a reference unedited sequence mergedRead column  mutations at each target site target[X] columns and the edited sequences at each target site sequence[X] columns were used for downstream analysis. Further details of columns can be found at https://github.com/shendurelab/Cas9FateMapping,zebrafish brain,,Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol  to generate single cell cDNA libraries and prepared for sequencing,,tissue:brain|developmental stage:2dpf,GSM4793202,GSM4793202: zBr2dpf2 S4; Danio rerio; RNA Seq,GSM4793202,,1,Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol  to generate single cell cDNA libraries and prepared for sequencing,GEO Accession:GSM4793202,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP282920,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=zBr2dpf2 S4 L001 I1 001.fastq.gz   read2PairFiles=zBr2dpf2 S4 L001 R1 001.fastq.gz   read3PairFiles=zBr2dpf2 S4 L001 R2 001.fastq.gz,zBr2dpf2_S4_L001_I1_001.fastq.gz zBr2dpf2_S4_L001_R1_001.fastq.gz zBr2dpf2_S4_L001_R2_001.fastq.gz,fastq fastq fastq,2354711480.0,25594690.0,GSM4793202 r1,0:8 1:26 2:58,A:638596344;C:520071032;G:581522367;T:613545955;N:975782,8,26,58,,638596344,520071032,581522367,613545955,975782,SRX9142585,SRS7383889,SRA1127180,GEO,Harvard University,1,0.93747,,0.12301,,0.81274,,0.50067,,58,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2020-09-17,Hatching,Embryo,Brain,Nervous System
61258,SRR12661729,SRX9142585,SRS7383889,SRP282920,PRJNA664124,Emergence of neuronal diversity during vertebrate brain development,GSE158142,Transcriptome Analysis,Neurogenesis comprises many steps from progenitor proliferation to neuronal differentiation and maturation. These processes are highly regulated  but the landscape of transcriptional changes underlying brain development are poorly characterized. Here  we describe a developmental single cell RNA seq catalog of 220 000 zebrafish brain cells encompassing 12 stages from 12 hpf to 15 dpf We characterize known and novel gene markers for 800 clusters and provide an overview of the diversification of neurons and progenitors across these timepoints. We also introduce an optimized version of the GESTALT lineage recorder that enables higher expression and recovery of Cas9 edited barcodes to query lineage segregation. Cell type characterization indicates that most embryonic neural progenitor states are transitory and transcriptionally distinct from neural progenitors of post embryonic stages. Reconstruction of cell specification trajectories reveals that late stage retinal neural progenitors transcriptionally overlap cell states observed in the embryo. The zebrafish brain development atlas provides a resource to define and manipulate specific subsets of neurons and to uncover the molecular mechanisms underlying vertebrate neurogenesis. Overall design: 10X Genomics v2 scRNA seq libraries and scGESTALT,,pubmed:33068532,,zBr2dpf2 S4,GSM4793202,,source name:zebrafish brain|tissue:brain|developmental stage:2dpf,zBr2dpf2 S4,Single cell RNA Sequencing data FASTQ files were processed using Cell Ranger v2.0.2 to generate count matrices Transcriptome libraries were mapped to a zebrafish reference built from a custom GTF file and the zebrafish GRCz10 release 86 genome assembly. File uploaded as Danio rerio.GRCz10.86.modified.gtf.gz. Some libraries were sequenced twice as technical replicates marked as *b in raw files and the processing was done using the combination of all data processed data files have comb* prefix scGESTALT libraries were processed using a custom pipeline available at https://github.com/shendurelab/Cas9FateMapping Genome build: GRCz10 Supplementary files format and content: *barcodes.tsv files contain 10X Genomics cell barcodes  *genes.tsv files contain gene names  *matrix.mtx contain transcriptome count data  *web summary.html contain summary statistics for transcript mapping  .rds files are the processed R objects  .txt files contain marker genes identified for each cluster in the dataset  URD*.rds files are the processed R objects for performing URD cell trajectory analysis. tree*.rds files are the final URD objects with cell trajectory trees for the retina and hypothalamus. Supplementary files format and content: scGESTALT data:  Gest zBr15dpf8 and Gest zBr15dpf9 correspond to two samples from the same zebrafish ZF1. Gest zBr15dpf10 and Gest zBr15dpf11 correspond to two samples from the same zebrafish ZF2. Gest zBr15dpf12 and Gest zBr15dpf13 correspond to two samples from the same zebrafish ZF3. Gest zBr15dpf14 and Gest zBr15dpf15 correspond to two samples from the same zebrafish ZF4. Supplementary files format and content: scGESTALT data: *GestMaster.txt contains the 10X Genmoics cell identifiers CellBarcode and CellUMI that were used to matchlineage barcodes to transcriptomes. They also contain lineage barcode sequences HMID column   the t SNE cluster membership number ClusterIdent column  and unique identifier Readname. zfAllMerge FILTEREDUSEME.xlsx contains the merged statistics of all samples  filtered to contain high confidence barcodes  the barcode sequence aligned to a reference unedited sequence mergedRead column  mutations at each target site target[X] columns and the edited sequences at each target site sequence[X] columns were used for downstream analysis. Further details of columns can be found at https://github.com/shendurelab/Cas9FateMapping,zebrafish brain,,Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol  to generate single cell cDNA libraries and prepared for sequencing,,tissue:brain|developmental stage:2dpf,GSM4793202,GSM4793202: zBr2dpf2 S4; Danio rerio; RNA Seq,GSM4793202,,1,Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol  to generate single cell cDNA libraries and prepared for sequencing,GEO Accession:GSM4793202,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP282920,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=zBr2dpf2 S4 L002 I1 001.fastq.gz   read2PairFiles=zBr2dpf2 S4 L002 R1 001.fastq.gz   read3PairFiles=zBr2dpf2 S4 L002 R2 001.fastq.gz,zBr2dpf2_S4_L002_I1_001.fastq.gz zBr2dpf2_S4_L002_R1_001.fastq.gz zBr2dpf2_S4_L002_R2_001.fastq.gz,fastq fastq fastq,2408983200.0,26184600.0,GSM4793202 r2,0:8 1:26 2:58,A:651954485;C:532609422;G:598183054;T:625305824;N:930415,8,26,58,,651954485,532609422,598183054,625305824,930415,SRX9142585,SRS7383889,SRA1127180,GEO,Harvard University,1,0.93328,,0.11839,,0.80687,,0.5125,,58,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2020-09-17,Hatching,Embryo,Brain,Nervous System
61259,SRR12661730,SRX9142585,SRS7383889,SRP282920,PRJNA664124,Emergence of neuronal diversity during vertebrate brain development,GSE158142,Transcriptome Analysis,Neurogenesis comprises many steps from progenitor proliferation to neuronal differentiation and maturation. These processes are highly regulated  but the landscape of transcriptional changes underlying brain development are poorly characterized. Here  we describe a developmental single cell RNA seq catalog of 220 000 zebrafish brain cells encompassing 12 stages from 12 hpf to 15 dpf We characterize known and novel gene markers for 800 clusters and provide an overview of the diversification of neurons and progenitors across these timepoints. We also introduce an optimized version of the GESTALT lineage recorder that enables higher expression and recovery of Cas9 edited barcodes to query lineage segregation. Cell type characterization indicates that most embryonic neural progenitor states are transitory and transcriptionally distinct from neural progenitors of post embryonic stages. Reconstruction of cell specification trajectories reveals that late stage retinal neural progenitors transcriptionally overlap cell states observed in the embryo. The zebrafish brain development atlas provides a resource to define and manipulate specific subsets of neurons and to uncover the molecular mechanisms underlying vertebrate neurogenesis. Overall design: 10X Genomics v2 scRNA seq libraries and scGESTALT,,pubmed:33068532,,zBr2dpf2 S4,GSM4793202,,source name:zebrafish brain|tissue:brain|developmental stage:2dpf,zBr2dpf2 S4,Single cell RNA Sequencing data FASTQ files were processed using Cell Ranger v2.0.2 to generate count matrices Transcriptome libraries were mapped to a zebrafish reference built from a custom GTF file and the zebrafish GRCz10 release 86 genome assembly. File uploaded as Danio rerio.GRCz10.86.modified.gtf.gz. Some libraries were sequenced twice as technical replicates marked as *b in raw files and the processing was done using the combination of all data processed data files have comb* prefix scGESTALT libraries were processed using a custom pipeline available at https://github.com/shendurelab/Cas9FateMapping Genome build: GRCz10 Supplementary files format and content: *barcodes.tsv files contain 10X Genomics cell barcodes  *genes.tsv files contain gene names  *matrix.mtx contain transcriptome count data  *web summary.html contain summary statistics for transcript mapping  .rds files are the processed R objects  .txt files contain marker genes identified for each cluster in the dataset  URD*.rds files are the processed R objects for performing URD cell trajectory analysis. tree*.rds files are the final URD objects with cell trajectory trees for the retina and hypothalamus. Supplementary files format and content: scGESTALT data:  Gest zBr15dpf8 and Gest zBr15dpf9 correspond to two samples from the same zebrafish ZF1. Gest zBr15dpf10 and Gest zBr15dpf11 correspond to two samples from the same zebrafish ZF2. Gest zBr15dpf12 and Gest zBr15dpf13 correspond to two samples from the same zebrafish ZF3. Gest zBr15dpf14 and Gest zBr15dpf15 correspond to two samples from the same zebrafish ZF4. Supplementary files format and content: scGESTALT data: *GestMaster.txt contains the 10X Genmoics cell identifiers CellBarcode and CellUMI that were used to matchlineage barcodes to transcriptomes. They also contain lineage barcode sequences HMID column   the t SNE cluster membership number ClusterIdent column  and unique identifier Readname. zfAllMerge FILTEREDUSEME.xlsx contains the merged statistics of all samples  filtered to contain high confidence barcodes  the barcode sequence aligned to a reference unedited sequence mergedRead column  mutations at each target site target[X] columns and the edited sequences at each target site sequence[X] columns were used for downstream analysis. Further details of columns can be found at https://github.com/shendurelab/Cas9FateMapping,zebrafish brain,,Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol  to generate single cell cDNA libraries and prepared for sequencing,,tissue:brain|developmental stage:2dpf,GSM4793202,GSM4793202: zBr2dpf2 S4; Danio rerio; RNA Seq,GSM4793202,,1,Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol  to generate single cell cDNA libraries and prepared for sequencing,GEO Accession:GSM4793202,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP282920,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=zBr2dpf2 S4 L003 I1 001.fastq.gz   read2PairFiles=zBr2dpf2 S4 L003 R1 001.fastq.gz   read3PairFiles=zBr2dpf2 S4 L003 R2 001.fastq.gz,zBr2dpf2_S4_L003_I1_001.fastq.gz zBr2dpf2_S4_L003_R1_001.fastq.gz zBr2dpf2_S4_L003_R2_001.fastq.gz,fastq fastq fastq,2341118940.0,25446945.0,GSM4793202 r3,0:8 1:26 2:58,A:633434861;C:516351967;G:580375245;T:609706687;N:1250180,8,26,58,,633434861,516351967,580375245,609706687,1250180,SRX9142585,SRS7383889,SRA1127180,GEO,Harvard University,1,0.93685,,0.12022,,0.80876,,0.49292,,58,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2020-09-17,Hatching,Embryo,Brain,Nervous System
61260,SRR12661731,SRX9142585,SRS7383889,SRP282920,PRJNA664124,Emergence of neuronal diversity during vertebrate brain development,GSE158142,Transcriptome Analysis,Neurogenesis comprises many steps from progenitor proliferation to neuronal differentiation and maturation. These processes are highly regulated  but the landscape of transcriptional changes underlying brain development are poorly characterized. Here  we describe a developmental single cell RNA seq catalog of 220 000 zebrafish brain cells encompassing 12 stages from 12 hpf to 15 dpf We characterize known and novel gene markers for 800 clusters and provide an overview of the diversification of neurons and progenitors across these timepoints. We also introduce an optimized version of the GESTALT lineage recorder that enables higher expression and recovery of Cas9 edited barcodes to query lineage segregation. Cell type characterization indicates that most embryonic neural progenitor states are transitory and transcriptionally distinct from neural progenitors of post embryonic stages. Reconstruction of cell specification trajectories reveals that late stage retinal neural progenitors transcriptionally overlap cell states observed in the embryo. The zebrafish brain development atlas provides a resource to define and manipulate specific subsets of neurons and to uncover the molecular mechanisms underlying vertebrate neurogenesis. Overall design: 10X Genomics v2 scRNA seq libraries and scGESTALT,,pubmed:33068532,,zBr2dpf2 S4,GSM4793202,,source name:zebrafish brain|tissue:brain|developmental stage:2dpf,zBr2dpf2 S4,Single cell RNA Sequencing data FASTQ files were processed using Cell Ranger v2.0.2 to generate count matrices Transcriptome libraries were mapped to a zebrafish reference built from a custom GTF file and the zebrafish GRCz10 release 86 genome assembly. File uploaded as Danio rerio.GRCz10.86.modified.gtf.gz. Some libraries were sequenced twice as technical replicates marked as *b in raw files and the processing was done using the combination of all data processed data files have comb* prefix scGESTALT libraries were processed using a custom pipeline available at https://github.com/shendurelab/Cas9FateMapping Genome build: GRCz10 Supplementary files format and content: *barcodes.tsv files contain 10X Genomics cell barcodes  *genes.tsv files contain gene names  *matrix.mtx contain transcriptome count data  *web summary.html contain summary statistics for transcript mapping  .rds files are the processed R objects  .txt files contain marker genes identified for each cluster in the dataset  URD*.rds files are the processed R objects for performing URD cell trajectory analysis. tree*.rds files are the final URD objects with cell trajectory trees for the retina and hypothalamus. Supplementary files format and content: scGESTALT data:  Gest zBr15dpf8 and Gest zBr15dpf9 correspond to two samples from the same zebrafish ZF1. Gest zBr15dpf10 and Gest zBr15dpf11 correspond to two samples from the same zebrafish ZF2. Gest zBr15dpf12 and Gest zBr15dpf13 correspond to two samples from the same zebrafish ZF3. Gest zBr15dpf14 and Gest zBr15dpf15 correspond to two samples from the same zebrafish ZF4. Supplementary files format and content: scGESTALT data: *GestMaster.txt contains the 10X Genmoics cell identifiers CellBarcode and CellUMI that were used to matchlineage barcodes to transcriptomes. They also contain lineage barcode sequences HMID column   the t SNE cluster membership number ClusterIdent column  and unique identifier Readname. zfAllMerge FILTEREDUSEME.xlsx contains the merged statistics of all samples  filtered to contain high confidence barcodes  the barcode sequence aligned to a reference unedited sequence mergedRead column  mutations at each target site target[X] columns and the edited sequences at each target site sequence[X] columns were used for downstream analysis. Further details of columns can be found at https://github.com/shendurelab/Cas9FateMapping,zebrafish brain,,Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol  to generate single cell cDNA libraries and prepared for sequencing,,tissue:brain|developmental stage:2dpf,GSM4793202,GSM4793202: zBr2dpf2 S4; Danio rerio; RNA Seq,GSM4793202,,1,Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol  to generate single cell cDNA libraries and prepared for sequencing,GEO Accession:GSM4793202,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP282920,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=zBr2dpf2 S4 L004 I1 001.fastq.gz   read2PairFiles=zBr2dpf2 S4 L004 R1 001.fastq.gz   read3PairFiles=zBr2dpf2 S4 L004 R2 001.fastq.gz,zBr2dpf2_S4_L004_I1_001.fastq.gz zBr2dpf2_S4_L004_R1_001.fastq.gz zBr2dpf2_S4_L004_R2_001.fastq.gz,fastq fastq fastq,2349677792.0,25539976.0,GSM4793202 r4,0:8 1:26 2:58,A:636175613;C:518571269;G:582465073;T:611220740;N:1245097,8,26,58,,636175613,518571269,582465073,611220740,1245097,SRX9142585,SRS7383889,SRA1127180,GEO,Harvard University,1,0.9331,,0.11925,,0.81126,,0.51211,,58,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2020-09-17,Hatching,Embryo,Brain,Nervous System
61261,SRR12661724,SRX9142584,SRS7383888,SRP282920,PRJNA664124,Emergence of neuronal diversity during vertebrate brain development,GSE158142,Transcriptome Analysis,Neurogenesis comprises many steps from progenitor proliferation to neuronal differentiation and maturation. These processes are highly regulated  but the landscape of transcriptional changes underlying brain development are poorly characterized. Here  we describe a developmental single cell RNA seq catalog of 220 000 zebrafish brain cells encompassing 12 stages from 12 hpf to 15 dpf We characterize known and novel gene markers for 800 clusters and provide an overview of the diversification of neurons and progenitors across these timepoints. We also introduce an optimized version of the GESTALT lineage recorder that enables higher expression and recovery of Cas9 edited barcodes to query lineage segregation. Cell type characterization indicates that most embryonic neural progenitor states are transitory and transcriptionally distinct from neural progenitors of post embryonic stages. Reconstruction of cell specification trajectories reveals that late stage retinal neural progenitors transcriptionally overlap cell states observed in the embryo. The zebrafish brain development atlas provides a resource to define and manipulate specific subsets of neurons and to uncover the molecular mechanisms underlying vertebrate neurogenesis. Overall design: 10X Genomics v2 scRNA seq libraries and scGESTALT,,pubmed:33068532,,zBr2dpf1 S3,GSM4793201,,source name:zebrafish brain|tissue:brain|developmental stage:2dpf,zBr2dpf1 S3,Single cell RNA Sequencing data FASTQ files were processed using Cell Ranger v2.0.2 to generate count matrices Transcriptome libraries were mapped to a zebrafish reference built from a custom GTF file and the zebrafish GRCz10 release 86 genome assembly. File uploaded as Danio rerio.GRCz10.86.modified.gtf.gz. Some libraries were sequenced twice as technical replicates marked as *b in raw files and the processing was done using the combination of all data processed data files have comb* prefix scGESTALT libraries were processed using a custom pipeline available at https://github.com/shendurelab/Cas9FateMapping Genome build: GRCz10 Supplementary files format and content: *barcodes.tsv files contain 10X Genomics cell barcodes  *genes.tsv files contain gene names  *matrix.mtx contain transcriptome count data  *web summary.html contain summary statistics for transcript mapping  .rds files are the processed R objects  .txt files contain marker genes identified for each cluster in the dataset  URD*.rds files are the processed R objects for performing URD cell trajectory analysis. tree*.rds files are the final URD objects with cell trajectory trees for the retina and hypothalamus. Supplementary files format and content: scGESTALT data:  Gest zBr15dpf8 and Gest zBr15dpf9 correspond to two samples from the same zebrafish ZF1. Gest zBr15dpf10 and Gest zBr15dpf11 correspond to two samples from the same zebrafish ZF2. Gest zBr15dpf12 and Gest zBr15dpf13 correspond to two samples from the same zebrafish ZF3. Gest zBr15dpf14 and Gest zBr15dpf15 correspond to two samples from the same zebrafish ZF4. Supplementary files format and content: scGESTALT data: *GestMaster.txt contains the 10X Genmoics cell identifiers CellBarcode and CellUMI that were used to matchlineage barcodes to transcriptomes. They also contain lineage barcode sequences HMID column   the t SNE cluster membership number ClusterIdent column  and unique identifier Readname. zfAllMerge FILTEREDUSEME.xlsx contains the merged statistics of all samples  filtered to contain high confidence barcodes  the barcode sequence aligned to a reference unedited sequence mergedRead column  mutations at each target site target[X] columns and the edited sequences at each target site sequence[X] columns were used for downstream analysis. Further details of columns can be found at https://github.com/shendurelab/Cas9FateMapping,zebrafish brain,,Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol  to generate single cell cDNA libraries and prepared for sequencing,,tissue:brain|developmental stage:2dpf,GSM4793201,GSM4793201: zBr2dpf1 S3; Danio rerio; RNA Seq,GSM4793201,,1,Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol  to generate single cell cDNA libraries and prepared for sequencing,GEO Accession:GSM4793201,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP282920,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=zBr2dpf1 S3 L001 I1 001.fastq.gz   read2PairFiles=zBr2dpf1 S3 L001 R1 001.fastq.gz   read3PairFiles=zBr2dpf1 S3 L001 R2 001.fastq.gz,zBr2dpf1_S3_L001_I1_001.fastq.gz zBr2dpf1_S3_L001_R1_001.fastq.gz zBr2dpf1_S3_L001_R2_001.fastq.gz,fastq fastq fastq,1987661932.0,21605021.0,GSM4793201 r1,0:8 1:26 2:58,A:547658132;C:438461740;G:482039584;T:518683029;N:819447,8,26,58,,547658132,438461740,482039584,518683029,819447,SRX9142584,SRS7383888,SRA1127180,GEO,Harvard University,1,0.9374,,0.12231,,0.81034,,0.50204,,58,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2020-09-17,Hatching,Embryo,Brain,Nervous System
61262,SRR12661725,SRX9142584,SRS7383888,SRP282920,PRJNA664124,Emergence of neuronal diversity during vertebrate brain development,GSE158142,Transcriptome Analysis,Neurogenesis comprises many steps from progenitor proliferation to neuronal differentiation and maturation. These processes are highly regulated  but the landscape of transcriptional changes underlying brain development are poorly characterized. Here  we describe a developmental single cell RNA seq catalog of 220 000 zebrafish brain cells encompassing 12 stages from 12 hpf to 15 dpf We characterize known and novel gene markers for 800 clusters and provide an overview of the diversification of neurons and progenitors across these timepoints. We also introduce an optimized version of the GESTALT lineage recorder that enables higher expression and recovery of Cas9 edited barcodes to query lineage segregation. Cell type characterization indicates that most embryonic neural progenitor states are transitory and transcriptionally distinct from neural progenitors of post embryonic stages. Reconstruction of cell specification trajectories reveals that late stage retinal neural progenitors transcriptionally overlap cell states observed in the embryo. The zebrafish brain development atlas provides a resource to define and manipulate specific subsets of neurons and to uncover the molecular mechanisms underlying vertebrate neurogenesis. Overall design: 10X Genomics v2 scRNA seq libraries and scGESTALT,,pubmed:33068532,,zBr2dpf1 S3,GSM4793201,,source name:zebrafish brain|tissue:brain|developmental stage:2dpf,zBr2dpf1 S3,Single cell RNA Sequencing data FASTQ files were processed using Cell Ranger v2.0.2 to generate count matrices Transcriptome libraries were mapped to a zebrafish reference built from a custom GTF file and the zebrafish GRCz10 release 86 genome assembly. File uploaded as Danio rerio.GRCz10.86.modified.gtf.gz. Some libraries were sequenced twice as technical replicates marked as *b in raw files and the processing was done using the combination of all data processed data files have comb* prefix scGESTALT libraries were processed using a custom pipeline available at https://github.com/shendurelab/Cas9FateMapping Genome build: GRCz10 Supplementary files format and content: *barcodes.tsv files contain 10X Genomics cell barcodes  *genes.tsv files contain gene names  *matrix.mtx contain transcriptome count data  *web summary.html contain summary statistics for transcript mapping  .rds files are the processed R objects  .txt files contain marker genes identified for each cluster in the dataset  URD*.rds files are the processed R objects for performing URD cell trajectory analysis. tree*.rds files are the final URD objects with cell trajectory trees for the retina and hypothalamus. Supplementary files format and content: scGESTALT data:  Gest zBr15dpf8 and Gest zBr15dpf9 correspond to two samples from the same zebrafish ZF1. Gest zBr15dpf10 and Gest zBr15dpf11 correspond to two samples from the same zebrafish ZF2. Gest zBr15dpf12 and Gest zBr15dpf13 correspond to two samples from the same zebrafish ZF3. Gest zBr15dpf14 and Gest zBr15dpf15 correspond to two samples from the same zebrafish ZF4. Supplementary files format and content: scGESTALT data: *GestMaster.txt contains the 10X Genmoics cell identifiers CellBarcode and CellUMI that were used to matchlineage barcodes to transcriptomes. They also contain lineage barcode sequences HMID column   the t SNE cluster membership number ClusterIdent column  and unique identifier Readname. zfAllMerge FILTEREDUSEME.xlsx contains the merged statistics of all samples  filtered to contain high confidence barcodes  the barcode sequence aligned to a reference unedited sequence mergedRead column  mutations at each target site target[X] columns and the edited sequences at each target site sequence[X] columns were used for downstream analysis. Further details of columns can be found at https://github.com/shendurelab/Cas9FateMapping,zebrafish brain,,Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol  to generate single cell cDNA libraries and prepared for sequencing,,tissue:brain|developmental stage:2dpf,GSM4793201,GSM4793201: zBr2dpf1 S3; Danio rerio; RNA Seq,GSM4793201,,1,Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol  to generate single cell cDNA libraries and prepared for sequencing,GEO Accession:GSM4793201,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP282920,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=zBr2dpf1 S3 L002 I1 001.fastq.gz   read2PairFiles=zBr2dpf1 S3 L002 R1 001.fastq.gz   read3PairFiles=zBr2dpf1 S3 L002 R2 001.fastq.gz,zBr2dpf1_S3_L002_I1_001.fastq.gz zBr2dpf1_S3_L002_R1_001.fastq.gz zBr2dpf1_S3_L002_R2_001.fastq.gz,fastq fastq fastq,2033328248.0,22101394.0,GSM4793201 r2,0:8 1:26 2:58,A:559220760;C:448909094;G:495806062;T:528599097;N:793235,8,26,58,,559220760,448909094,495806062,528599097,793235,SRX9142584,SRS7383888,SRA1127180,GEO,Harvard University,1,0.93264,,0.11766,,0.80941,,0.48857,,58,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2020-09-17,Hatching,Embryo,Brain,Nervous System
61263,SRR12661726,SRX9142584,SRS7383888,SRP282920,PRJNA664124,Emergence of neuronal diversity during vertebrate brain development,GSE158142,Transcriptome Analysis,Neurogenesis comprises many steps from progenitor proliferation to neuronal differentiation and maturation. These processes are highly regulated  but the landscape of transcriptional changes underlying brain development are poorly characterized. Here  we describe a developmental single cell RNA seq catalog of 220 000 zebrafish brain cells encompassing 12 stages from 12 hpf to 15 dpf We characterize known and novel gene markers for 800 clusters and provide an overview of the diversification of neurons and progenitors across these timepoints. We also introduce an optimized version of the GESTALT lineage recorder that enables higher expression and recovery of Cas9 edited barcodes to query lineage segregation. Cell type characterization indicates that most embryonic neural progenitor states are transitory and transcriptionally distinct from neural progenitors of post embryonic stages. Reconstruction of cell specification trajectories reveals that late stage retinal neural progenitors transcriptionally overlap cell states observed in the embryo. The zebrafish brain development atlas provides a resource to define and manipulate specific subsets of neurons and to uncover the molecular mechanisms underlying vertebrate neurogenesis. Overall design: 10X Genomics v2 scRNA seq libraries and scGESTALT,,pubmed:33068532,,zBr2dpf1 S3,GSM4793201,,source name:zebrafish brain|tissue:brain|developmental stage:2dpf,zBr2dpf1 S3,Single cell RNA Sequencing data FASTQ files were processed using Cell Ranger v2.0.2 to generate count matrices Transcriptome libraries were mapped to a zebrafish reference built from a custom GTF file and the zebrafish GRCz10 release 86 genome assembly. File uploaded as Danio rerio.GRCz10.86.modified.gtf.gz. Some libraries were sequenced twice as technical replicates marked as *b in raw files and the processing was done using the combination of all data processed data files have comb* prefix scGESTALT libraries were processed using a custom pipeline available at https://github.com/shendurelab/Cas9FateMapping Genome build: GRCz10 Supplementary files format and content: *barcodes.tsv files contain 10X Genomics cell barcodes  *genes.tsv files contain gene names  *matrix.mtx contain transcriptome count data  *web summary.html contain summary statistics for transcript mapping  .rds files are the processed R objects  .txt files contain marker genes identified for each cluster in the dataset  URD*.rds files are the processed R objects for performing URD cell trajectory analysis. tree*.rds files are the final URD objects with cell trajectory trees for the retina and hypothalamus. Supplementary files format and content: scGESTALT data:  Gest zBr15dpf8 and Gest zBr15dpf9 correspond to two samples from the same zebrafish ZF1. Gest zBr15dpf10 and Gest zBr15dpf11 correspond to two samples from the same zebrafish ZF2. Gest zBr15dpf12 and Gest zBr15dpf13 correspond to two samples from the same zebrafish ZF3. Gest zBr15dpf14 and Gest zBr15dpf15 correspond to two samples from the same zebrafish ZF4. Supplementary files format and content: scGESTALT data: *GestMaster.txt contains the 10X Genmoics cell identifiers CellBarcode and CellUMI that were used to matchlineage barcodes to transcriptomes. They also contain lineage barcode sequences HMID column   the t SNE cluster membership number ClusterIdent column  and unique identifier Readname. zfAllMerge FILTEREDUSEME.xlsx contains the merged statistics of all samples  filtered to contain high confidence barcodes  the barcode sequence aligned to a reference unedited sequence mergedRead column  mutations at each target site target[X] columns and the edited sequences at each target site sequence[X] columns were used for downstream analysis. Further details of columns can be found at https://github.com/shendurelab/Cas9FateMapping,zebrafish brain,,Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol  to generate single cell cDNA libraries and prepared for sequencing,,tissue:brain|developmental stage:2dpf,GSM4793201,GSM4793201: zBr2dpf1 S3; Danio rerio; RNA Seq,GSM4793201,,1,Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol  to generate single cell cDNA libraries and prepared for sequencing,GEO Accession:GSM4793201,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP282920,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=zBr2dpf1 S3 L003 I1 001.fastq.gz   read2PairFiles=zBr2dpf1 S3 L003 R1 001.fastq.gz   read3PairFiles=zBr2dpf1 S3 L003 R2 001.fastq.gz,zBr2dpf1_S3_L003_I1_001.fastq.gz zBr2dpf1_S3_L003_R1_001.fastq.gz zBr2dpf1_S3_L003_R2_001.fastq.gz,fastq fastq fastq,1979332620.0,21514485.0,GSM4793201 r3,0:8 1:26 2:58,A:544014432;C:436050802;G:481964973;T:516249939;N:1052474,8,26,58,,544014432,436050802,481964973,516249939,1052474,SRX9142584,SRS7383888,SRA1127180,GEO,Harvard University,1,0.93728,,0.12144,,0.80977,,0.4891,,58,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2020-09-17,Hatching,Embryo,Brain,Nervous System
61264,SRR12661727,SRX9142584,SRS7383888,SRP282920,PRJNA664124,Emergence of neuronal diversity during vertebrate brain development,GSE158142,Transcriptome Analysis,Neurogenesis comprises many steps from progenitor proliferation to neuronal differentiation and maturation. These processes are highly regulated  but the landscape of transcriptional changes underlying brain development are poorly characterized. Here  we describe a developmental single cell RNA seq catalog of 220 000 zebrafish brain cells encompassing 12 stages from 12 hpf to 15 dpf We characterize known and novel gene markers for 800 clusters and provide an overview of the diversification of neurons and progenitors across these timepoints. We also introduce an optimized version of the GESTALT lineage recorder that enables higher expression and recovery of Cas9 edited barcodes to query lineage segregation. Cell type characterization indicates that most embryonic neural progenitor states are transitory and transcriptionally distinct from neural progenitors of post embryonic stages. Reconstruction of cell specification trajectories reveals that late stage retinal neural progenitors transcriptionally overlap cell states observed in the embryo. The zebrafish brain development atlas provides a resource to define and manipulate specific subsets of neurons and to uncover the molecular mechanisms underlying vertebrate neurogenesis. Overall design: 10X Genomics v2 scRNA seq libraries and scGESTALT,,pubmed:33068532,,zBr2dpf1 S3,GSM4793201,,source name:zebrafish brain|tissue:brain|developmental stage:2dpf,zBr2dpf1 S3,Single cell RNA Sequencing data FASTQ files were processed using Cell Ranger v2.0.2 to generate count matrices Transcriptome libraries were mapped to a zebrafish reference built from a custom GTF file and the zebrafish GRCz10 release 86 genome assembly. File uploaded as Danio rerio.GRCz10.86.modified.gtf.gz. Some libraries were sequenced twice as technical replicates marked as *b in raw files and the processing was done using the combination of all data processed data files have comb* prefix scGESTALT libraries were processed using a custom pipeline available at https://github.com/shendurelab/Cas9FateMapping Genome build: GRCz10 Supplementary files format and content: *barcodes.tsv files contain 10X Genomics cell barcodes  *genes.tsv files contain gene names  *matrix.mtx contain transcriptome count data  *web summary.html contain summary statistics for transcript mapping  .rds files are the processed R objects  .txt files contain marker genes identified for each cluster in the dataset  URD*.rds files are the processed R objects for performing URD cell trajectory analysis. tree*.rds files are the final URD objects with cell trajectory trees for the retina and hypothalamus. Supplementary files format and content: scGESTALT data:  Gest zBr15dpf8 and Gest zBr15dpf9 correspond to two samples from the same zebrafish ZF1. Gest zBr15dpf10 and Gest zBr15dpf11 correspond to two samples from the same zebrafish ZF2. Gest zBr15dpf12 and Gest zBr15dpf13 correspond to two samples from the same zebrafish ZF3. Gest zBr15dpf14 and Gest zBr15dpf15 correspond to two samples from the same zebrafish ZF4. Supplementary files format and content: scGESTALT data: *GestMaster.txt contains the 10X Genmoics cell identifiers CellBarcode and CellUMI that were used to matchlineage barcodes to transcriptomes. They also contain lineage barcode sequences HMID column   the t SNE cluster membership number ClusterIdent column  and unique identifier Readname. zfAllMerge FILTEREDUSEME.xlsx contains the merged statistics of all samples  filtered to contain high confidence barcodes  the barcode sequence aligned to a reference unedited sequence mergedRead column  mutations at each target site target[X] columns and the edited sequences at each target site sequence[X] columns were used for downstream analysis. Further details of columns can be found at https://github.com/shendurelab/Cas9FateMapping,zebrafish brain,,Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol  to generate single cell cDNA libraries and prepared for sequencing,,tissue:brain|developmental stage:2dpf,GSM4793201,GSM4793201: zBr2dpf1 S3; Danio rerio; RNA Seq,GSM4793201,,1,Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol  to generate single cell cDNA libraries and prepared for sequencing,GEO Accession:GSM4793201,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP282920,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=zBr2dpf1 S3 L004 I1 001.fastq.gz   read2PairFiles=zBr2dpf1 S3 L004 R1 001.fastq.gz   read3PairFiles=zBr2dpf1 S3 L004 R2 001.fastq.gz,zBr2dpf1_S3_L004_I1_001.fastq.gz zBr2dpf1_S3_L004_R1_001.fastq.gz zBr2dpf1_S3_L004_R2_001.fastq.gz,fastq fastq fastq,1985591380.0,21582515.0,GSM4793201 r4,0:8 1:26 2:58,A:546156700;C:437670969;G:483468285;T:517254669;N:1040757,8,26,58,,546156700,437670969,483468285,517254669,1040757,SRX9142584,SRS7383888,SRA1127180,GEO,Harvard University,1,0.93535,,0.12099,,0.8102,,0.48932,,58,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2020-09-17,Hatching,Embryo,Brain,Nervous System
64255,SRR14376450,SRX10728755,SRS8816986,SRP318111,PRJNA726733,SMARTseq data of zebrafish sox10+ cells,GSE173696,Transcriptome Analysis,The goals of this study are to compare  transcriptome profiling mRNA level and singnaling pathways between slc30a1 mutant zebrafish and their siblings. We found pathways in cell differentiation and migration were different between these two groups  and the stem markers of nueral crest progenitors were upregulated in mutants. Overall design: sox10+ cells from slc30a1 mutant zebrafish and their siblings at 2 dpf and 2.5 dpf were sorting out by FACS machine  whole RNA were extraced and performed SMARTseq analysis.,,pubmed:34977877,,sox10+ cells  mut2.5 2,GSM5277056,,source name:sox10+ cells|genotype:slc30a1 mutant|age:2.5 dpf|tissue:neural crest|cell type:sox10+ cells,sox10+ cells  mut2.5 2,Illumina Novaseq 6000 were used for basecalling Reads of samples were aligned to Ensembl Danio rerio zebrafish genome GRCz11 http://www.ensembl.org/ using HISAT package. The mapped reads of each sample were assembled using StringTie and all transcriptomes were merged to reconstruct a comprehensive transcriptome using perl scripts StringTie and edgeR were used to estimate the expression levels of all transcripts StringTie was used to calculate FPKM for quantification of mRNAs Genome build: GRCz11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample,sox10+ cells,,Cell populations were directly homogenized into Trizol LS reagent Invitrogen. Total RNA was immediately extracted using a Direct zol RNA kit R2050  Zymo Research. Library construction started from fragmented cDNA  and then the paired end sequencing was performed by Illumina Novaseq 6000. SMARTseq,,genotype:slc30a1 mutant|age:2.5 dpf|tissue:neural crest|cell type:sox10+ cells,GSM5277056,GSM5277056: mut2.5 2; Danio rerio; RNA Seq,GSM5277056,,1,Cell populations were directly homogenized into Trizol LS reagent Invitrogen. Total RNA was immediately extracted using a Direct zol RNA kit R2050  Zymo Research. Library construction started from fragmented cDNA  and then the paired end sequencing was performed by Illumina Novaseq 6000. SMARTseq,GEO Accession:GSM5277056,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP318111,,loader:fastq load.py,mut2.5_2_Clean_Data1.fq.gz mut2.5_2_Clean_Data2.fq.gz,fastq fastq,7494559311.0,25435082.0,GSM5277056 r1,0:147.32 1:147.33,A:2012711910;C:1737952486;G:1750832324;T:1992995509;N:67082,147,147,,,2012711910,1737952486,1750832324,1992995509,67082,SRX10728755,SRS8816986,SRA1226391,GEO,Zhejiang University School of Medicine,2,0.94683,0.93749,0.06937,0.06842,0.71017,0.71338,0.55169,0.54499,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2021-05-01,Hatching,Embryo,Brain,Nervous System
64256,SRR14376449,SRX10728754,SRS8816985,SRP318111,PRJNA726733,SMARTseq data of zebrafish sox10+ cells,GSE173696,Transcriptome Analysis,The goals of this study are to compare  transcriptome profiling mRNA level and singnaling pathways between slc30a1 mutant zebrafish and their siblings. We found pathways in cell differentiation and migration were different between these two groups  and the stem markers of nueral crest progenitors were upregulated in mutants. Overall design: sox10+ cells from slc30a1 mutant zebrafish and their siblings at 2 dpf and 2.5 dpf were sorting out by FACS machine  whole RNA were extraced and performed SMARTseq analysis.,,pubmed:34977877,,sox10+ cells  mut2.5 1,GSM5277055,,source name:sox10+ cells|genotype:slc30a1 mutant|age:2.5 dpf|tissue:neural crest|cell type:sox10+ cells,sox10+ cells  mut2.5 1,Illumina Novaseq 6000 were used for basecalling Reads of samples were aligned to Ensembl Danio rerio zebrafish genome GRCz11 http://www.ensembl.org/ using HISAT package. The mapped reads of each sample were assembled using StringTie and all transcriptomes were merged to reconstruct a comprehensive transcriptome using perl scripts StringTie and edgeR were used to estimate the expression levels of all transcripts StringTie was used to calculate FPKM for quantification of mRNAs Genome build: GRCz11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample,sox10+ cells,,Cell populations were directly homogenized into Trizol LS reagent Invitrogen. Total RNA was immediately extracted using a Direct zol RNA kit R2050  Zymo Research. Library construction started from fragmented cDNA  and then the paired end sequencing was performed by Illumina Novaseq 6000. SMARTseq,,genotype:slc30a1 mutant|age:2.5 dpf|tissue:neural crest|cell type:sox10+ cells,GSM5277055,GSM5277055: mut2.5 1; Danio rerio; RNA Seq,GSM5277055,,1,Cell populations were directly homogenized into Trizol LS reagent Invitrogen. Total RNA was immediately extracted using a Direct zol RNA kit R2050  Zymo Research. Library construction started from fragmented cDNA  and then the paired end sequencing was performed by Illumina Novaseq 6000. SMARTseq,GEO Accession:GSM5277055,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP318111,,loader:fastq load.py,mut2.5_1_Clean_Data1.fq.gz mut2.5_1_Clean_Data2.fq.gz,fastq fastq,6770834157.0,22988965.0,GSM5277055 r1,0:147.26 1:147.27,A:1812068028;C:1575549455;G:1587510974;T:1795645065;N:60635,147,147,,,1812068028,1575549455,1587510974,1795645065,60635,SRX10728754,SRS8816985,SRA1226391,GEO,Zhejiang University School of Medicine,2,0.94538,0.93895,0.07576,0.07445,0.71334,0.71518,0.54004,0.53664,145,145,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2021-05-01,Hatching,Embryo,Brain,Nervous System
64257,SRR14376448,SRX10728753,SRS8816984,SRP318111,PRJNA726733,SMARTseq data of zebrafish sox10+ cells,GSE173696,Transcriptome Analysis,The goals of this study are to compare  transcriptome profiling mRNA level and singnaling pathways between slc30a1 mutant zebrafish and their siblings. We found pathways in cell differentiation and migration were different between these two groups  and the stem markers of nueral crest progenitors were upregulated in mutants. Overall design: sox10+ cells from slc30a1 mutant zebrafish and their siblings at 2 dpf and 2.5 dpf were sorting out by FACS machine  whole RNA were extraced and performed SMARTseq analysis.,,pubmed:34977877,,sox10+ cells  Con2.5 2,GSM5277054,,source name:sox10+ cells|genotype:control|age:2.5 dpf|tissue:neural crest|cell type:sox10+ cells,sox10+ cells  Con2.5 2,Illumina Novaseq 6000 were used for basecalling Reads of samples were aligned to Ensembl Danio rerio zebrafish genome GRCz11 http://www.ensembl.org/ using HISAT package. The mapped reads of each sample were assembled using StringTie and all transcriptomes were merged to reconstruct a comprehensive transcriptome using perl scripts StringTie and edgeR were used to estimate the expression levels of all transcripts StringTie was used to calculate FPKM for quantification of mRNAs Genome build: GRCz11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample,sox10+ cells,,Cell populations were directly homogenized into Trizol LS reagent Invitrogen. Total RNA was immediately extracted using a Direct zol RNA kit R2050  Zymo Research. Library construction started from fragmented cDNA  and then the paired end sequencing was performed by Illumina Novaseq 6000. SMARTseq,,genotype:control|age:2.5 dpf|tissue:neural crest|cell type:sox10+ cells,GSM5277054,GSM5277054: Con2.5 2; Danio rerio; RNA Seq,GSM5277054,,1,Cell populations were directly homogenized into Trizol LS reagent Invitrogen. Total RNA was immediately extracted using a Direct zol RNA kit R2050  Zymo Research. Library construction started from fragmented cDNA  and then the paired end sequencing was performed by Illumina Novaseq 6000. SMARTseq,GEO Accession:GSM5277054,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP318111,,loader:fastq load.py,con2.5_2_Clean_Data1.fq.gz con2.5_2_Clean_Data2.fq.gz,fastq fastq,6575961047.0,22426463.0,GSM5277054 r1,0:146.60 1:146.62,A:1769853076;C:1523906075;G:1532087686;T:1750054929;N:59281,146,146,,,1769853076,1523906075,1532087686,1750054929,59281,SRX10728753,SRS8816984,SRA1226391,GEO,Zhejiang University School of Medicine,2,0.94173,0.93962,0.07618,0.07558,0.71478,0.71666,0.53585,0.54278,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2021-05-01,Hatching,Embryo,Brain,Nervous System
64258,SRR14376447,SRX10728752,SRS8816983,SRP318111,PRJNA726733,SMARTseq data of zebrafish sox10+ cells,GSE173696,Transcriptome Analysis,The goals of this study are to compare  transcriptome profiling mRNA level and singnaling pathways between slc30a1 mutant zebrafish and their siblings. We found pathways in cell differentiation and migration were different between these two groups  and the stem markers of nueral crest progenitors were upregulated in mutants. Overall design: sox10+ cells from slc30a1 mutant zebrafish and their siblings at 2 dpf and 2.5 dpf were sorting out by FACS machine  whole RNA were extraced and performed SMARTseq analysis.,,pubmed:34977877,,sox10+ cells  Con2.5 1,GSM5277053,,source name:sox10+ cells|genotype:control|age:2.5 dpf|tissue:neural crest|cell type:sox10+ cells,sox10+ cells  Con2.5 1,Illumina Novaseq 6000 were used for basecalling Reads of samples were aligned to Ensembl Danio rerio zebrafish genome GRCz11 http://www.ensembl.org/ using HISAT package. The mapped reads of each sample were assembled using StringTie and all transcriptomes were merged to reconstruct a comprehensive transcriptome using perl scripts StringTie and edgeR were used to estimate the expression levels of all transcripts StringTie was used to calculate FPKM for quantification of mRNAs Genome build: GRCz11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample,sox10+ cells,,Cell populations were directly homogenized into Trizol LS reagent Invitrogen. Total RNA was immediately extracted using a Direct zol RNA kit R2050  Zymo Research. Library construction started from fragmented cDNA  and then the paired end sequencing was performed by Illumina Novaseq 6000. SMARTseq,,genotype:control|age:2.5 dpf|tissue:neural crest|cell type:sox10+ cells,GSM5277053,GSM5277053: Con2.5 1; Danio rerio; RNA Seq,GSM5277053,,1,Cell populations were directly homogenized into Trizol LS reagent Invitrogen. Total RNA was immediately extracted using a Direct zol RNA kit R2050  Zymo Research. Library construction started from fragmented cDNA  and then the paired end sequencing was performed by Illumina Novaseq 6000. SMARTseq,GEO Accession:GSM5277053,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP318111,,loader:fastq load.py,con2.5_1_Clean_Data1.fq.gz con2.5_1_Clean_Data2.fq.gz,fastq fastq,7993324015.0,27211075.0,GSM5277053 r1,0:146.87 1:146.88,A:2138458217;C:1863213107;G:1876318724;T:2115262513;N:71454,146,146,,,2138458217,1863213107,1876318724,2115262513,71454,SRX10728752,SRS8816983,SRA1226391,GEO,Zhejiang University School of Medicine,2,0.94651,0.93985,0.06158,0.06123,0.72226,0.72409,0.53968,0.53426,140,140,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2021-05-01,Hatching,Embryo,Brain,Nervous System
64259,SRR14376446,SRX10728751,SRS8816982,SRP318111,PRJNA726733,SMARTseq data of zebrafish sox10+ cells,GSE173696,Transcriptome Analysis,The goals of this study are to compare  transcriptome profiling mRNA level and singnaling pathways between slc30a1 mutant zebrafish and their siblings. We found pathways in cell differentiation and migration were different between these two groups  and the stem markers of nueral crest progenitors were upregulated in mutants. Overall design: sox10+ cells from slc30a1 mutant zebrafish and their siblings at 2 dpf and 2.5 dpf were sorting out by FACS machine  whole RNA were extraced and performed SMARTseq analysis.,,pubmed:34977877,,sox10+ cells  mut2 2,GSM5277052,,source name:sox10+ cells|genotype:slc30a1 mutant|age:2 dpf|tissue:neural crest|cell type:sox10+ cells,sox10+ cells  mut2 2,Illumina Novaseq 6000 were used for basecalling Reads of samples were aligned to Ensembl Danio rerio zebrafish genome GRCz11 http://www.ensembl.org/ using HISAT package. The mapped reads of each sample were assembled using StringTie and all transcriptomes were merged to reconstruct a comprehensive transcriptome using perl scripts StringTie and edgeR were used to estimate the expression levels of all transcripts StringTie was used to calculate FPKM for quantification of mRNAs Genome build: GRCz11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample,sox10+ cells,,Cell populations were directly homogenized into Trizol LS reagent Invitrogen. Total RNA was immediately extracted using a Direct zol RNA kit R2050  Zymo Research. Library construction started from fragmented cDNA  and then the paired end sequencing was performed by Illumina Novaseq 6000. SMARTseq,,genotype:slc30a1 mutant|age:2 dpf|tissue:neural crest|cell type:sox10+ cells,GSM5277052,GSM5277052: mut2 2; Danio rerio; RNA Seq,GSM5277052,,1,Cell populations were directly homogenized into Trizol LS reagent Invitrogen. Total RNA was immediately extracted using a Direct zol RNA kit R2050  Zymo Research. Library construction started from fragmented cDNA  and then the paired end sequencing was performed by Illumina Novaseq 6000. SMARTseq,GEO Accession:GSM5277052,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP318111,,loader:fastq load.py,mut2_Clean_Data1.fq.gz mut2_Clean_Data2.fq.gz,fastq fastq,8685333412.0,29705351.0,GSM5277052 r1,0:146.18 1:146.20,A:2324608385;C:2027961536;G:2033826317;T:2298888032;N:49142,146,146,,,2324608385,2027961536,2033826317,2298888032,49142,SRX10728751,SRS8816982,SRA1226391,GEO,Zhejiang University School of Medicine,2,0.9449,0.94327,0.03739,0.037,0.76187,0.76286,0.51902,0.50644,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2021-05-01,Hatching,Embryo,Brain,Nervous System
64260,SRR14376445,SRX10728750,SRS8816981,SRP318111,PRJNA726733,SMARTseq data of zebrafish sox10+ cells,GSE173696,Transcriptome Analysis,The goals of this study are to compare  transcriptome profiling mRNA level and singnaling pathways between slc30a1 mutant zebrafish and their siblings. We found pathways in cell differentiation and migration were different between these two groups  and the stem markers of nueral crest progenitors were upregulated in mutants. Overall design: sox10+ cells from slc30a1 mutant zebrafish and their siblings at 2 dpf and 2.5 dpf were sorting out by FACS machine  whole RNA were extraced and performed SMARTseq analysis.,,pubmed:34977877,,sox10+ cells  mut2 1,GSM5277051,,source name:sox10+ cells|genotype:slc30a1 mutant|age:2 dpf|tissue:neural crest|cell type:sox10+ cells,sox10+ cells  mut2 1,Illumina Novaseq 6000 were used for basecalling Reads of samples were aligned to Ensembl Danio rerio zebrafish genome GRCz11 http://www.ensembl.org/ using HISAT package. The mapped reads of each sample were assembled using StringTie and all transcriptomes were merged to reconstruct a comprehensive transcriptome using perl scripts StringTie and edgeR were used to estimate the expression levels of all transcripts StringTie was used to calculate FPKM for quantification of mRNAs Genome build: GRCz11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample,sox10+ cells,,Cell populations were directly homogenized into Trizol LS reagent Invitrogen. Total RNA was immediately extracted using a Direct zol RNA kit R2050  Zymo Research. Library construction started from fragmented cDNA  and then the paired end sequencing was performed by Illumina Novaseq 6000. SMARTseq,,genotype:slc30a1 mutant|age:2 dpf|tissue:neural crest|cell type:sox10+ cells,GSM5277051,GSM5277051: mut2 1; Danio rerio; RNA Seq,GSM5277051,,1,Cell populations were directly homogenized into Trizol LS reagent Invitrogen. Total RNA was immediately extracted using a Direct zol RNA kit R2050  Zymo Research. Library construction started from fragmented cDNA  and then the paired end sequencing was performed by Illumina Novaseq 6000. SMARTseq,GEO Accession:GSM5277051,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP318111,,loader:fastq load.py,mut1_Clean_Data1.fq.gz mut1_Clean_Data2.fq.gz,fastq fastq,9812394203.0,33082555.0,GSM5277051 r1,0:148.29 1:148.31,A:2653980250;C:2265916544;G:2271837314;T:2620605605;N:54490,148,148,,,2653980250,2265916544,2271837314,2620605605,54490,SRX10728750,SRS8816981,SRA1226391,GEO,Zhejiang University School of Medicine,2,0.94573,0.93739,0.04453,0.04435,0.73996,0.74257,0.55993,0.55784,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2021-05-01,Hatching,Embryo,Brain,Nervous System
64261,SRR14376444,SRX10728749,SRS8816980,SRP318111,PRJNA726733,SMARTseq data of zebrafish sox10+ cells,GSE173696,Transcriptome Analysis,The goals of this study are to compare  transcriptome profiling mRNA level and singnaling pathways between slc30a1 mutant zebrafish and their siblings. We found pathways in cell differentiation and migration were different between these two groups  and the stem markers of nueral crest progenitors were upregulated in mutants. Overall design: sox10+ cells from slc30a1 mutant zebrafish and their siblings at 2 dpf and 2.5 dpf were sorting out by FACS machine  whole RNA were extraced and performed SMARTseq analysis.,,pubmed:34977877,,sox10+ cells  Con2 2,GSM5277050,,source name:sox10+ cells|genotype:control|age:2 dpf|tissue:neural crest|cell type:sox10+ cells,sox10+ cells  Con2 2,Illumina Novaseq 6000 were used for basecalling Reads of samples were aligned to Ensembl Danio rerio zebrafish genome GRCz11 http://www.ensembl.org/ using HISAT package. The mapped reads of each sample were assembled using StringTie and all transcriptomes were merged to reconstruct a comprehensive transcriptome using perl scripts StringTie and edgeR were used to estimate the expression levels of all transcripts StringTie was used to calculate FPKM for quantification of mRNAs Genome build: GRCz11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample,sox10+ cells,,Cell populations were directly homogenized into Trizol LS reagent Invitrogen. Total RNA was immediately extracted using a Direct zol RNA kit R2050  Zymo Research. Library construction started from fragmented cDNA  and then the paired end sequencing was performed by Illumina Novaseq 6000. SMARTseq,,genotype:control|age:2 dpf|tissue:neural crest|cell type:sox10+ cells,GSM5277050,GSM5277050: Con2 2; Danio rerio; RNA Seq,GSM5277050,,1,Cell populations were directly homogenized into Trizol LS reagent Invitrogen. Total RNA was immediately extracted using a Direct zol RNA kit R2050  Zymo Research. Library construction started from fragmented cDNA  and then the paired end sequencing was performed by Illumina Novaseq 6000. SMARTseq,GEO Accession:GSM5277050,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP318111,,loader:fastq load.py,con2_Clean_Data1.fq.gz con2_Clean_Data2.fq.gz,fastq fastq,6562017327.0,22133886.0,GSM5277050 r1,0:148.23 1:148.24,A:1768000404;C:1519120771;G:1524128982;T:1750730516;N:36654,148,148,,,1768000404,1519120771,1524128982,1750730516,36654,SRX10728749,SRS8816980,SRA1226391,GEO,Zhejiang University School of Medicine,2,0.94243,0.9414,0.03946,0.03954,0.73904,0.74105,0.4702,0.46577,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2021-05-01,Hatching,Embryo,Brain,Nervous System
64262,SRR14376443,SRX10728748,SRS8816979,SRP318111,PRJNA726733,SMARTseq data of zebrafish sox10+ cells,GSE173696,Transcriptome Analysis,The goals of this study are to compare  transcriptome profiling mRNA level and singnaling pathways between slc30a1 mutant zebrafish and their siblings. We found pathways in cell differentiation and migration were different between these two groups  and the stem markers of nueral crest progenitors were upregulated in mutants. Overall design: sox10+ cells from slc30a1 mutant zebrafish and their siblings at 2 dpf and 2.5 dpf were sorting out by FACS machine  whole RNA were extraced and performed SMARTseq analysis.,,pubmed:34977877,,sox10+ cells  Con2 1,GSM5277049,,source name:sox10+ cells|genotype:control|age:2 dpf|tissue:neural crest|cell type:sox10+ cells,sox10+ cells  Con2 1,Illumina Novaseq 6000 were used for basecalling Reads of samples were aligned to Ensembl Danio rerio zebrafish genome GRCz11 http://www.ensembl.org/ using HISAT package. The mapped reads of each sample were assembled using StringTie and all transcriptomes were merged to reconstruct a comprehensive transcriptome using perl scripts StringTie and edgeR were used to estimate the expression levels of all transcripts StringTie was used to calculate FPKM for quantification of mRNAs Genome build: GRCz11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample,sox10+ cells,,Cell populations were directly homogenized into Trizol LS reagent Invitrogen. Total RNA was immediately extracted using a Direct zol RNA kit R2050  Zymo Research. Library construction started from fragmented cDNA  and then the paired end sequencing was performed by Illumina Novaseq 6000. SMARTseq,,genotype:control|age:2 dpf|tissue:neural crest|cell type:sox10+ cells,GSM5277049,GSM5277049: Con2 1; Danio rerio; RNA Seq,GSM5277049,,1,Cell populations were directly homogenized into Trizol LS reagent Invitrogen. Total RNA was immediately extracted using a Direct zol RNA kit R2050  Zymo Research. Library construction started from fragmented cDNA  and then the paired end sequencing was performed by Illumina Novaseq 6000. SMARTseq,GEO Accession:GSM5277049,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP318111,,loader:fastq load.py,con1_Clean_Data1.fq.gz con1_Clean_Data2.fq.gz,fastq fastq,10808740801.0,36657845.0,GSM5277049 r1,0:147.42 1:147.43,A:2906915272;C:2511975697;G:2517545013;T:2872243705;N:61114,147,147,,,2906915272,2511975697,2517545013,2872243705,61114,SRX10728748,SRS8816979,SRA1226391,GEO,Zhejiang University School of Medicine,2,0.94437,0.94025,0.04046,0.0404,0.75866,0.75909,0.52788,0.52798,150,147,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2021-05-01,Hatching,Embryo,Brain,Nervous System
65100,SRR14923958,SRX11237258,SRS9283133,SRP325759,PRJNA741770,Single cell profiling of cranial neural crest diversification across a vertebrate lifetime,GSE178969,Other,The cranial neural crest CNC is a vertebrate specific population that generates a huge diversity of derivatives  including the bulk of the connective and skeletal tissues of the head. How neural crest cells generate the appropriate cell types for distinct head regions over time remains unresolved. Here we profile RNA expression scRNAseq and chromatin accessibility snATACseq of the zebrafish cranial neural crest lineage at single cell resolution from embryos to adults. Overall design: To recover the cell heterogeneity and lineage information in the span of a life time of a fish  we collected the converted cells from embryonic stages 1.5  2 dpf  larval stage 3  5  and 14 dpf  juvenile stage 60 dpf  to adult stage 150 or 210 dpf. We used a cranial neural crest converted zebrafish line   28.5Sox10:Cre;bactin:BFP to DsRed  to permanantly convert and label the CNCC derived cells. The converted cells were collected and subjected to single cell sequencing for both their transcriptome and open chromatin region using Chromium platform of 10X Genomic. For biological and technical control  we include replicates for both scRNAseq and snATACseq at various stages. We include an additional line  fli1a:eGFP/sox10:dsRed  for a biological and positive control of CNCC of 1.5 dpf  sample.,,pubmed:35013168,,scRNAseq Sox10 Cre bact BtR 2dpf rep 1,GSM5402430,,tissue:Cranial neural crest derived cells|cell type:Cranial neural crest derived cells|transgene1:TgMmu.Sox10 Mmu.Fos:Crezf384|transgene2:Tgactab2:loxP BFP STOP loxP dsRed|developmental stage:2 dpf|facs markers:Zombie  / dsRed+,scRNAseq Sox10 Cre bact BtR 2dpf rep 1,For scRNAseq libraries  Cellranger v3.0.0 10X Genomics was used for demultiplexing  alignment  and raw count matrix generation. The alignment was performed against zebrafish genome index built with GRCz11.fa and GRCz11.98.gtf. For snATACseq libraries  Cellranger ATAC v1.2.0 10X Genomics was used for alignment against zebrafish genome index built with GRCz11.fa  JASPAR2020  and GRCz11.98.gtf  peak calling  and peak by cell count matrix generation with default parameters. QC step for the library was performed along with the Cellranger or Cellranger ATAC alignment process. We performed a second round of peak calling for our snATACseq data using package Snaptools and SnapATAC. We first removed cell debris  low quality cells  and cell duplicates  by setting cutoffs based on percentage of reads in peaks > 30 for 60 dpf  > 45 for 210 dpf  and > 50 for the rest and fragment number within peaks 5 000 – 30 000 for 5 dpf  1 000 – 11 000 for 14 dpf  and 1 000 – 20 000 for the rest.  To  recover every aligned fragment  we binned the genome into 5 kb sections and constructed the bin by cell matrices bmats for each library by Snaptools from the positional sorted bam files generated by cellranger atac. The cells were filtered  dimensionally reduced by diffusion map  and clustered with inputs of the first 34 dimensions followed the SnapATAC vignette. The specific peaks were called for each cluster by the wrapped MACS2 function in SnapATAC with parameter gsize = 1.5e9  shift = 100  ext = 200  and qval = 5e 2. The finalized and refined peak profile was derived by collapsing and merging all 175 individual peak files to about 450K peaks. The count matrices of both scRNAseq and snATACseq data were analyzed by R package Seurat and Signac. The count matrices of each sample were aggregated if there is any replicate. For scRNAseq data  the matrices are normalized NormalizeData and scaled for the top 2 000 variable genes FindVariableFeatures and ScaleData. The scaled matrices were dimensional reduced to 50 principal components 60 components for 150 dpf  which then subjected to neighbor finding FindNeighbors  k = 20 and clustering FindClusters  resolution = 0.8. The data were visualized through UMAP with 50 principal components as input. For snATACseq data  the matrices are dimensionally reduced 30 latent semantic indices LSIs through RunTFIDF and RunSVD functions. The neighbor finding  clustering  and visualization are performed with the second to the thirtieth LSIs as input algoritm = 3 for FindClusters. Genome build: GRCz11 Supplementary files format and content: Each sample comes with four processed data files: a tab delimited cell barcode file tsv  a tab delimited feature file with genes for scRNAseq or peaks for snATACseq tsv  a sparse matrix of count table mtx  and a cluster table tsv. The previous three files are suffice for creating a single cell count matrix. The cluster table can be further added to recreat the corresponding cluster information as published.,Cranial neural crest derived cells,,Dissected heads from converted Sox10:cre; bactin:loxP eGFP loxP DsRed fish were incubated in fresh Ringer’s solution 5 10 min  followed by mechanical and enzymatic dissociation by pipetting every 5 minutes 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 minutes or until full dissociation. Reaction was stopped by 6X stop solution 6 mM CaCl2 and 30% fetal bovine serum FBS in PBS. Cells were pelleted 2000 rpm  5 minute  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 sorted by fluorescence activated cell sorting FACS to isolate live cells that excluded the cytoplasmic stain Zombie green BioLegend  423111 or the nuclear stain DAPI. Live cells were sorted into PBS solution containing 0.04% BSA and loaded to 10X Genomics microfluidic chips. The version 2 of Chromium Single Cell three prime Reagent Kits was used for RNA extraction. For snATACseq library construction  we used the same cell dissociation and sorting protocol as for scRNAseq  with isolation of live cells that excluded the cytoplasmic stain Zombie green product information. Nuclei isolation was performed per manufacturer’s instructions 10X Genomic  protocol CG000169. Cells were incubated with lysis buffer on ice for 90 second  followed by integrity check of nuclei under fluorescence microscope with DAPI before library synthesis. For scRNAseq  the cell lysis  polyA pull down  tagging with cell barcode  and RNA:DNA hybrid synthesis were performed in the GEMs per manufacturer's instruction. GEMs containing barcoded single cell cDNA  were lysis for further fragmentation and ligation of illumina P5 and P7 ends. Libraries were sequenced to depths of at least 1 000 000 reads per cell for each library. For snATACseq  the open chromatins of the isolated nuclei were targeted and tagged by transposase  barcoded and ligated with Illumina P5 sequence in the individually encapsulated GEMs per manufacturer's instruction. Barcoded single nucleus genomic DNA were released from GEMs and pulled down for further ligation of library specific index and Illumina P7 sequence. Libraries were sequenced to depths of at least 75 000 read pairs per nucleus for each library.,The Institutional Animal Care and Use Committee of the University of Southern California approved all animal experiments Protocol 20771. Zebrafish embryos Danio rerio were raised in embryo media at 28.5°C. For adults  in the institute vivarium according to Protocol 20771.,cell type:Cranial neural crest derived cells|transgene1:TgMmu.Sox10 Mmu.Fos:Crezf384|transgene2:Tgactab2:loxP BFP STOP loxP dsRed|developmental stage:2 dpf|facs markers:Zombie  / dsRed+,GSM5402430,GSM5402430: scRNAseq Sox10 Cre bact BtR 2dpf rep 1; Danio rerio; RNA Seq,GSM5402430,,1,Dissected heads from converted Sox10:cre; bactin:loxP eGFP loxP DsRed fish were incubated in fresh Ringer's solution 5 10 min  followed by mechanical and enzymatic dissociation by pipetting every 5 minutes 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 minutes or until full dissociation. Reaction was stopped by 6X stop solution 6 mM CaCl2 and 30% fetal bovine serum FBS in PBS. Cells were pelleted 2000 rpm  5 minute  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 sorted by fluorescence activated cell sorting FACS to isolate live cells that excluded the cytoplasmic stain Zombie green BioLegend  423111 or the nuclear stain DAPI. Live cells were sorted into PBS solution containing 0.04% BSA and loaded to 10X Genomics microfluidic chips. The version 2 of Chromium Single Cell three prime Reagent Kits was used for RNA extraction. For snATACseq library construction  we used the same cell dissociation and sorting protocol as for scRNAseq  with isolation of live cells that excluded the cytoplasmic stain Zombie green product information. Nuclei isolation was performed per manufacturer's instructions 10X Genomic  protocol CG000169. Cells were incubated with lysis buffer on ice for 90 second  followed by integrity check of nuclei under fluorescence microscope with DAPI before library synthesis. For scRNAseq  the cell lysis  polyA pull down  tagging with cell barcode  and RNA:DNA hybrid synthesis were performed in the GEMs per manufacturer's instruction. GEMs containing barcoded single cell cDNA  were lysis for further fragmentation and ligation of illumina P5 and P7 ends. Libraries were sequenced to depths of at least 1 000 000 reads per cell for each library. For snATACseq  the open chromatins of the isolated nuclei were targeted and tagged by transposase  barcoded and ligated with Illumina P5 sequence in the individually encapsulated GEMs per manufacturer's instruction. Barcoded single nucleus genomic DNA were released from GEMs and pulled down for further ligation of library specific index and Illumina P7 sequence. Libraries were sequenced to depths of at least 75 000 read pairs per nucleus for each library.,GEO Accession:GSM5402430,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP325759,,,scRNAseq_Sox10_Cre_bact_BtR_2dpf_rep_1_S1_L001_R1_001.fastq.gz scRNAseq_Sox10_Cre_bact_BtR_2dpf_rep_1_S1_L001_R2_001.fastq.gz,fastq fastq,34509011947.0,234007853.0,GSM5402430 r1,0:27 1:120.47,A:9735364598;C:7434652978;G:7783819912;T:9534313520;N:20860939,27,120,,,9735364598,7434652978,7783819912,9534313520,20860939,SRX11237258,SRS9283133,SRA1250944,GEO,"Crump Lab, Stem Cell, USC",2,0.0067,0.90889,0.00161,0.09851,0.98518,0.8173,0.48738,0.49248,27,120,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,United States,2021-06-27,Hatching,Embryo,Brain,Nervous System
65101,SRR14923959,SRX11237258,SRS9283133,SRP325759,PRJNA741770,Single cell profiling of cranial neural crest diversification across a vertebrate lifetime,GSE178969,Other,The cranial neural crest CNC is a vertebrate specific population that generates a huge diversity of derivatives  including the bulk of the connective and skeletal tissues of the head. How neural crest cells generate the appropriate cell types for distinct head regions over time remains unresolved. Here we profile RNA expression scRNAseq and chromatin accessibility snATACseq of the zebrafish cranial neural crest lineage at single cell resolution from embryos to adults. Overall design: To recover the cell heterogeneity and lineage information in the span of a life time of a fish  we collected the converted cells from embryonic stages 1.5  2 dpf  larval stage 3  5  and 14 dpf  juvenile stage 60 dpf  to adult stage 150 or 210 dpf. We used a cranial neural crest converted zebrafish line   28.5Sox10:Cre;bactin:BFP to DsRed  to permanantly convert and label the CNCC derived cells. The converted cells were collected and subjected to single cell sequencing for both their transcriptome and open chromatin region using Chromium platform of 10X Genomic. For biological and technical control  we include replicates for both scRNAseq and snATACseq at various stages. We include an additional line  fli1a:eGFP/sox10:dsRed  for a biological and positive control of CNCC of 1.5 dpf  sample.,,pubmed:35013168,,scRNAseq Sox10 Cre bact BtR 2dpf rep 1,GSM5402430,,tissue:Cranial neural crest derived cells|cell type:Cranial neural crest derived cells|transgene1:TgMmu.Sox10 Mmu.Fos:Crezf384|transgene2:Tgactab2:loxP BFP STOP loxP dsRed|developmental stage:2 dpf|facs markers:Zombie  / dsRed+,scRNAseq Sox10 Cre bact BtR 2dpf rep 1,For scRNAseq libraries  Cellranger v3.0.0 10X Genomics was used for demultiplexing  alignment  and raw count matrix generation. The alignment was performed against zebrafish genome index built with GRCz11.fa and GRCz11.98.gtf. For snATACseq libraries  Cellranger ATAC v1.2.0 10X Genomics was used for alignment against zebrafish genome index built with GRCz11.fa  JASPAR2020  and GRCz11.98.gtf  peak calling  and peak by cell count matrix generation with default parameters. QC step for the library was performed along with the Cellranger or Cellranger ATAC alignment process. We performed a second round of peak calling for our snATACseq data using package Snaptools and SnapATAC. We first removed cell debris  low quality cells  and cell duplicates  by setting cutoffs based on percentage of reads in peaks > 30 for 60 dpf  > 45 for 210 dpf  and > 50 for the rest and fragment number within peaks 5 000 – 30 000 for 5 dpf  1 000 – 11 000 for 14 dpf  and 1 000 – 20 000 for the rest.  To  recover every aligned fragment  we binned the genome into 5 kb sections and constructed the bin by cell matrices bmats for each library by Snaptools from the positional sorted bam files generated by cellranger atac. The cells were filtered  dimensionally reduced by diffusion map  and clustered with inputs of the first 34 dimensions followed the SnapATAC vignette. The specific peaks were called for each cluster by the wrapped MACS2 function in SnapATAC with parameter gsize = 1.5e9  shift = 100  ext = 200  and qval = 5e 2. The finalized and refined peak profile was derived by collapsing and merging all 175 individual peak files to about 450K peaks. The count matrices of both scRNAseq and snATACseq data were analyzed by R package Seurat and Signac. The count matrices of each sample were aggregated if there is any replicate. For scRNAseq data  the matrices are normalized NormalizeData and scaled for the top 2 000 variable genes FindVariableFeatures and ScaleData. The scaled matrices were dimensional reduced to 50 principal components 60 components for 150 dpf  which then subjected to neighbor finding FindNeighbors  k = 20 and clustering FindClusters  resolution = 0.8. The data were visualized through UMAP with 50 principal components as input. For snATACseq data  the matrices are dimensionally reduced 30 latent semantic indices LSIs through RunTFIDF and RunSVD functions. The neighbor finding  clustering  and visualization are performed with the second to the thirtieth LSIs as input algoritm = 3 for FindClusters. Genome build: GRCz11 Supplementary files format and content: Each sample comes with four processed data files: a tab delimited cell barcode file tsv  a tab delimited feature file with genes for scRNAseq or peaks for snATACseq tsv  a sparse matrix of count table mtx  and a cluster table tsv. The previous three files are suffice for creating a single cell count matrix. The cluster table can be further added to recreat the corresponding cluster information as published.,Cranial neural crest derived cells,,Dissected heads from converted Sox10:cre; bactin:loxP eGFP loxP DsRed fish were incubated in fresh Ringer’s solution 5 10 min  followed by mechanical and enzymatic dissociation by pipetting every 5 minutes 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 minutes or until full dissociation. Reaction was stopped by 6X stop solution 6 mM CaCl2 and 30% fetal bovine serum FBS in PBS. Cells were pelleted 2000 rpm  5 minute  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 sorted by fluorescence activated cell sorting FACS to isolate live cells that excluded the cytoplasmic stain Zombie green BioLegend  423111 or the nuclear stain DAPI. Live cells were sorted into PBS solution containing 0.04% BSA and loaded to 10X Genomics microfluidic chips. The version 2 of Chromium Single Cell three prime Reagent Kits was used for RNA extraction. For snATACseq library construction  we used the same cell dissociation and sorting protocol as for scRNAseq  with isolation of live cells that excluded the cytoplasmic stain Zombie green product information. Nuclei isolation was performed per manufacturer’s instructions 10X Genomic  protocol CG000169. Cells were incubated with lysis buffer on ice for 90 second  followed by integrity check of nuclei under fluorescence microscope with DAPI before library synthesis. For scRNAseq  the cell lysis  polyA pull down  tagging with cell barcode  and RNA:DNA hybrid synthesis were performed in the GEMs per manufacturer's instruction. GEMs containing barcoded single cell cDNA  were lysis for further fragmentation and ligation of illumina P5 and P7 ends. Libraries were sequenced to depths of at least 1 000 000 reads per cell for each library. For snATACseq  the open chromatins of the isolated nuclei were targeted and tagged by transposase  barcoded and ligated with Illumina P5 sequence in the individually encapsulated GEMs per manufacturer's instruction. Barcoded single nucleus genomic DNA were released from GEMs and pulled down for further ligation of library specific index and Illumina P7 sequence. Libraries were sequenced to depths of at least 75 000 read pairs per nucleus for each library.,The Institutional Animal Care and Use Committee of the University of Southern California approved all animal experiments Protocol 20771. Zebrafish embryos Danio rerio were raised in embryo media at 28.5°C. For adults  in the institute vivarium according to Protocol 20771.,cell type:Cranial neural crest derived cells|transgene1:TgMmu.Sox10 Mmu.Fos:Crezf384|transgene2:Tgactab2:loxP BFP STOP loxP dsRed|developmental stage:2 dpf|facs markers:Zombie  / dsRed+,GSM5402430,GSM5402430: scRNAseq Sox10 Cre bact BtR 2dpf rep 1; Danio rerio; RNA Seq,GSM5402430,,1,Dissected heads from converted Sox10:cre; bactin:loxP eGFP loxP DsRed fish were incubated in fresh Ringer's solution 5 10 min  followed by mechanical and enzymatic dissociation by pipetting every 5 minutes 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 minutes or until full dissociation. Reaction was stopped by 6X stop solution 6 mM CaCl2 and 30% fetal bovine serum FBS in PBS. Cells were pelleted 2000 rpm  5 minute  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 sorted by fluorescence activated cell sorting FACS to isolate live cells that excluded the cytoplasmic stain Zombie green BioLegend  423111 or the nuclear stain DAPI. Live cells were sorted into PBS solution containing 0.04% BSA and loaded to 10X Genomics microfluidic chips. The version 2 of Chromium Single Cell three prime Reagent Kits was used for RNA extraction. For snATACseq library construction  we used the same cell dissociation and sorting protocol as for scRNAseq  with isolation of live cells that excluded the cytoplasmic stain Zombie green product information. Nuclei isolation was performed per manufacturer's instructions 10X Genomic  protocol CG000169. Cells were incubated with lysis buffer on ice for 90 second  followed by integrity check of nuclei under fluorescence microscope with DAPI before library synthesis. For scRNAseq  the cell lysis  polyA pull down  tagging with cell barcode  and RNA:DNA hybrid synthesis were performed in the GEMs per manufacturer's instruction. GEMs containing barcoded single cell cDNA  were lysis for further fragmentation and ligation of illumina P5 and P7 ends. Libraries were sequenced to depths of at least 1 000 000 reads per cell for each library. For snATACseq  the open chromatins of the isolated nuclei were targeted and tagged by transposase  barcoded and ligated with Illumina P5 sequence in the individually encapsulated GEMs per manufacturer's instruction. Barcoded single nucleus genomic DNA were released from GEMs and pulled down for further ligation of library specific index and Illumina P7 sequence. Libraries were sequenced to depths of at least 75 000 read pairs per nucleus for each library.,GEO Accession:GSM5402430,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP325759,,,scRNAseq_Sox10_Cre_bact_BtR_2dpf_rep_1_S2_L001_R1_001.fastq.gz scRNAseq_Sox10_Cre_bact_BtR_2dpf_rep_1_S2_L001_R2_001.fastq.gz,fastq fastq,26483068005.0,179583089.0,GSM5402430 r2,0:27 1:120.47,A:7463902133;C:5664415217;G:5936015741;T:7402606959;N:16127955,27,120,,,7463902133,5664415217,5936015741,7402606959,16127955,SRX11237258,SRS9283133,SRA1250944,GEO,"Crump Lab, Stem Cell, USC",2,0.00625,0.90722,0.00139,0.09946,0.98579,0.81576,0.47629,0.50931,27,121,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,United States,2021-06-27,Hatching,Embryo,Brain,Nervous System
65102,SRR14923960,SRX11237258,SRS9283133,SRP325759,PRJNA741770,Single cell profiling of cranial neural crest diversification across a vertebrate lifetime,GSE178969,Other,The cranial neural crest CNC is a vertebrate specific population that generates a huge diversity of derivatives  including the bulk of the connective and skeletal tissues of the head. How neural crest cells generate the appropriate cell types for distinct head regions over time remains unresolved. Here we profile RNA expression scRNAseq and chromatin accessibility snATACseq of the zebrafish cranial neural crest lineage at single cell resolution from embryos to adults. Overall design: To recover the cell heterogeneity and lineage information in the span of a life time of a fish  we collected the converted cells from embryonic stages 1.5  2 dpf  larval stage 3  5  and 14 dpf  juvenile stage 60 dpf  to adult stage 150 or 210 dpf. We used a cranial neural crest converted zebrafish line   28.5Sox10:Cre;bactin:BFP to DsRed  to permanantly convert and label the CNCC derived cells. The converted cells were collected and subjected to single cell sequencing for both their transcriptome and open chromatin region using Chromium platform of 10X Genomic. For biological and technical control  we include replicates for both scRNAseq and snATACseq at various stages. We include an additional line  fli1a:eGFP/sox10:dsRed  for a biological and positive control of CNCC of 1.5 dpf  sample.,,pubmed:35013168,,scRNAseq Sox10 Cre bact BtR 2dpf rep 1,GSM5402430,,tissue:Cranial neural crest derived cells|cell type:Cranial neural crest derived cells|transgene1:TgMmu.Sox10 Mmu.Fos:Crezf384|transgene2:Tgactab2:loxP BFP STOP loxP dsRed|developmental stage:2 dpf|facs markers:Zombie  / dsRed+,scRNAseq Sox10 Cre bact BtR 2dpf rep 1,For scRNAseq libraries  Cellranger v3.0.0 10X Genomics was used for demultiplexing  alignment  and raw count matrix generation. The alignment was performed against zebrafish genome index built with GRCz11.fa and GRCz11.98.gtf. For snATACseq libraries  Cellranger ATAC v1.2.0 10X Genomics was used for alignment against zebrafish genome index built with GRCz11.fa  JASPAR2020  and GRCz11.98.gtf  peak calling  and peak by cell count matrix generation with default parameters. QC step for the library was performed along with the Cellranger or Cellranger ATAC alignment process. We performed a second round of peak calling for our snATACseq data using package Snaptools and SnapATAC. We first removed cell debris  low quality cells  and cell duplicates  by setting cutoffs based on percentage of reads in peaks > 30 for 60 dpf  > 45 for 210 dpf  and > 50 for the rest and fragment number within peaks 5 000 – 30 000 for 5 dpf  1 000 – 11 000 for 14 dpf  and 1 000 – 20 000 for the rest.  To  recover every aligned fragment  we binned the genome into 5 kb sections and constructed the bin by cell matrices bmats for each library by Snaptools from the positional sorted bam files generated by cellranger atac. The cells were filtered  dimensionally reduced by diffusion map  and clustered with inputs of the first 34 dimensions followed the SnapATAC vignette. The specific peaks were called for each cluster by the wrapped MACS2 function in SnapATAC with parameter gsize = 1.5e9  shift = 100  ext = 200  and qval = 5e 2. The finalized and refined peak profile was derived by collapsing and merging all 175 individual peak files to about 450K peaks. The count matrices of both scRNAseq and snATACseq data were analyzed by R package Seurat and Signac. The count matrices of each sample were aggregated if there is any replicate. For scRNAseq data  the matrices are normalized NormalizeData and scaled for the top 2 000 variable genes FindVariableFeatures and ScaleData. The scaled matrices were dimensional reduced to 50 principal components 60 components for 150 dpf  which then subjected to neighbor finding FindNeighbors  k = 20 and clustering FindClusters  resolution = 0.8. The data were visualized through UMAP with 50 principal components as input. For snATACseq data  the matrices are dimensionally reduced 30 latent semantic indices LSIs through RunTFIDF and RunSVD functions. The neighbor finding  clustering  and visualization are performed with the second to the thirtieth LSIs as input algoritm = 3 for FindClusters. Genome build: GRCz11 Supplementary files format and content: Each sample comes with four processed data files: a tab delimited cell barcode file tsv  a tab delimited feature file with genes for scRNAseq or peaks for snATACseq tsv  a sparse matrix of count table mtx  and a cluster table tsv. The previous three files are suffice for creating a single cell count matrix. The cluster table can be further added to recreat the corresponding cluster information as published.,Cranial neural crest derived cells,,Dissected heads from converted Sox10:cre; bactin:loxP eGFP loxP DsRed fish were incubated in fresh Ringer’s solution 5 10 min  followed by mechanical and enzymatic dissociation by pipetting every 5 minutes 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 minutes or until full dissociation. Reaction was stopped by 6X stop solution 6 mM CaCl2 and 30% fetal bovine serum FBS in PBS. Cells were pelleted 2000 rpm  5 minute  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 sorted by fluorescence activated cell sorting FACS to isolate live cells that excluded the cytoplasmic stain Zombie green BioLegend  423111 or the nuclear stain DAPI. Live cells were sorted into PBS solution containing 0.04% BSA and loaded to 10X Genomics microfluidic chips. The version 2 of Chromium Single Cell three prime Reagent Kits was used for RNA extraction. For snATACseq library construction  we used the same cell dissociation and sorting protocol as for scRNAseq  with isolation of live cells that excluded the cytoplasmic stain Zombie green product information. Nuclei isolation was performed per manufacturer’s instructions 10X Genomic  protocol CG000169. Cells were incubated with lysis buffer on ice for 90 second  followed by integrity check of nuclei under fluorescence microscope with DAPI before library synthesis. For scRNAseq  the cell lysis  polyA pull down  tagging with cell barcode  and RNA:DNA hybrid synthesis were performed in the GEMs per manufacturer's instruction. GEMs containing barcoded single cell cDNA  were lysis for further fragmentation and ligation of illumina P5 and P7 ends. Libraries were sequenced to depths of at least 1 000 000 reads per cell for each library. For snATACseq  the open chromatins of the isolated nuclei were targeted and tagged by transposase  barcoded and ligated with Illumina P5 sequence in the individually encapsulated GEMs per manufacturer's instruction. Barcoded single nucleus genomic DNA were released from GEMs and pulled down for further ligation of library specific index and Illumina P7 sequence. Libraries were sequenced to depths of at least 75 000 read pairs per nucleus for each library.,The Institutional Animal Care and Use Committee of the University of Southern California approved all animal experiments Protocol 20771. Zebrafish embryos Danio rerio were raised in embryo media at 28.5°C. For adults  in the institute vivarium according to Protocol 20771.,cell type:Cranial neural crest derived cells|transgene1:TgMmu.Sox10 Mmu.Fos:Crezf384|transgene2:Tgactab2:loxP BFP STOP loxP dsRed|developmental stage:2 dpf|facs markers:Zombie  / dsRed+,GSM5402430,GSM5402430: scRNAseq Sox10 Cre bact BtR 2dpf rep 1; Danio rerio; RNA Seq,GSM5402430,,1,Dissected heads from converted Sox10:cre; bactin:loxP eGFP loxP DsRed fish were incubated in fresh Ringer's solution 5 10 min  followed by mechanical and enzymatic dissociation by pipetting every 5 minutes 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 minutes or until full dissociation. Reaction was stopped by 6X stop solution 6 mM CaCl2 and 30% fetal bovine serum FBS in PBS. Cells were pelleted 2000 rpm  5 minute  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 sorted by fluorescence activated cell sorting FACS to isolate live cells that excluded the cytoplasmic stain Zombie green BioLegend  423111 or the nuclear stain DAPI. Live cells were sorted into PBS solution containing 0.04% BSA and loaded to 10X Genomics microfluidic chips. The version 2 of Chromium Single Cell three prime Reagent Kits was used for RNA extraction. For snATACseq library construction  we used the same cell dissociation and sorting protocol as for scRNAseq  with isolation of live cells that excluded the cytoplasmic stain Zombie green product information. Nuclei isolation was performed per manufacturer's instructions 10X Genomic  protocol CG000169. Cells were incubated with lysis buffer on ice for 90 second  followed by integrity check of nuclei under fluorescence microscope with DAPI before library synthesis. For scRNAseq  the cell lysis  polyA pull down  tagging with cell barcode  and RNA:DNA hybrid synthesis were performed in the GEMs per manufacturer's instruction. GEMs containing barcoded single cell cDNA  were lysis for further fragmentation and ligation of illumina P5 and P7 ends. Libraries were sequenced to depths of at least 1 000 000 reads per cell for each library. For snATACseq  the open chromatins of the isolated nuclei were targeted and tagged by transposase  barcoded and ligated with Illumina P5 sequence in the individually encapsulated GEMs per manufacturer's instruction. Barcoded single nucleus genomic DNA were released from GEMs and pulled down for further ligation of library specific index and Illumina P7 sequence. Libraries were sequenced to depths of at least 75 000 read pairs per nucleus for each library.,GEO Accession:GSM5402430,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP325759,,,scRNAseq_Sox10_Cre_bact_BtR_2dpf_rep_1_S3_L001_R1_001.fastq.gz scRNAseq_Sox10_Cre_bact_BtR_2dpf_rep_1_S3_L001_R2_001.fastq.gz,fastq fastq,27440650225.0,186073336.0,GSM5402430 r3,0:27 1:120.47,A:7742385079;C:5902727351;G:6167343580;T:7611521012;N:16673203,27,120,,,7742385079,5902727351,6167343580,7611521012,16673203,SRX11237258,SRS9283133,SRA1250944,GEO,"Crump Lab, Stem Cell, USC",2,0.00649,0.9115,0.00146,0.09874,0.98528,0.81998,0.49796,0.49778,27,120,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,United States,2021-06-27,Hatching,Embryo,Brain,Nervous System
65103,SRR14923961,SRX11237258,SRS9283133,SRP325759,PRJNA741770,Single cell profiling of cranial neural crest diversification across a vertebrate lifetime,GSE178969,Other,The cranial neural crest CNC is a vertebrate specific population that generates a huge diversity of derivatives  including the bulk of the connective and skeletal tissues of the head. How neural crest cells generate the appropriate cell types for distinct head regions over time remains unresolved. Here we profile RNA expression scRNAseq and chromatin accessibility snATACseq of the zebrafish cranial neural crest lineage at single cell resolution from embryos to adults. Overall design: To recover the cell heterogeneity and lineage information in the span of a life time of a fish  we collected the converted cells from embryonic stages 1.5  2 dpf  larval stage 3  5  and 14 dpf  juvenile stage 60 dpf  to adult stage 150 or 210 dpf. We used a cranial neural crest converted zebrafish line   28.5Sox10:Cre;bactin:BFP to DsRed  to permanantly convert and label the CNCC derived cells. The converted cells were collected and subjected to single cell sequencing for both their transcriptome and open chromatin region using Chromium platform of 10X Genomic. For biological and technical control  we include replicates for both scRNAseq and snATACseq at various stages. We include an additional line  fli1a:eGFP/sox10:dsRed  for a biological and positive control of CNCC of 1.5 dpf  sample.,,pubmed:35013168,,scRNAseq Sox10 Cre bact BtR 2dpf rep 1,GSM5402430,,tissue:Cranial neural crest derived cells|cell type:Cranial neural crest derived cells|transgene1:TgMmu.Sox10 Mmu.Fos:Crezf384|transgene2:Tgactab2:loxP BFP STOP loxP dsRed|developmental stage:2 dpf|facs markers:Zombie  / dsRed+,scRNAseq Sox10 Cre bact BtR 2dpf rep 1,For scRNAseq libraries  Cellranger v3.0.0 10X Genomics was used for demultiplexing  alignment  and raw count matrix generation. The alignment was performed against zebrafish genome index built with GRCz11.fa and GRCz11.98.gtf. For snATACseq libraries  Cellranger ATAC v1.2.0 10X Genomics was used for alignment against zebrafish genome index built with GRCz11.fa  JASPAR2020  and GRCz11.98.gtf  peak calling  and peak by cell count matrix generation with default parameters. QC step for the library was performed along with the Cellranger or Cellranger ATAC alignment process. We performed a second round of peak calling for our snATACseq data using package Snaptools and SnapATAC. We first removed cell debris  low quality cells  and cell duplicates  by setting cutoffs based on percentage of reads in peaks > 30 for 60 dpf  > 45 for 210 dpf  and > 50 for the rest and fragment number within peaks 5 000 – 30 000 for 5 dpf  1 000 – 11 000 for 14 dpf  and 1 000 – 20 000 for the rest.  To  recover every aligned fragment  we binned the genome into 5 kb sections and constructed the bin by cell matrices bmats for each library by Snaptools from the positional sorted bam files generated by cellranger atac. The cells were filtered  dimensionally reduced by diffusion map  and clustered with inputs of the first 34 dimensions followed the SnapATAC vignette. The specific peaks were called for each cluster by the wrapped MACS2 function in SnapATAC with parameter gsize = 1.5e9  shift = 100  ext = 200  and qval = 5e 2. The finalized and refined peak profile was derived by collapsing and merging all 175 individual peak files to about 450K peaks. The count matrices of both scRNAseq and snATACseq data were analyzed by R package Seurat and Signac. The count matrices of each sample were aggregated if there is any replicate. For scRNAseq data  the matrices are normalized NormalizeData and scaled for the top 2 000 variable genes FindVariableFeatures and ScaleData. The scaled matrices were dimensional reduced to 50 principal components 60 components for 150 dpf  which then subjected to neighbor finding FindNeighbors  k = 20 and clustering FindClusters  resolution = 0.8. The data were visualized through UMAP with 50 principal components as input. For snATACseq data  the matrices are dimensionally reduced 30 latent semantic indices LSIs through RunTFIDF and RunSVD functions. The neighbor finding  clustering  and visualization are performed with the second to the thirtieth LSIs as input algoritm = 3 for FindClusters. Genome build: GRCz11 Supplementary files format and content: Each sample comes with four processed data files: a tab delimited cell barcode file tsv  a tab delimited feature file with genes for scRNAseq or peaks for snATACseq tsv  a sparse matrix of count table mtx  and a cluster table tsv. The previous three files are suffice for creating a single cell count matrix. The cluster table can be further added to recreat the corresponding cluster information as published.,Cranial neural crest derived cells,,Dissected heads from converted Sox10:cre; bactin:loxP eGFP loxP DsRed fish were incubated in fresh Ringer’s solution 5 10 min  followed by mechanical and enzymatic dissociation by pipetting every 5 minutes 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 minutes or until full dissociation. Reaction was stopped by 6X stop solution 6 mM CaCl2 and 30% fetal bovine serum FBS in PBS. Cells were pelleted 2000 rpm  5 minute  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 sorted by fluorescence activated cell sorting FACS to isolate live cells that excluded the cytoplasmic stain Zombie green BioLegend  423111 or the nuclear stain DAPI. Live cells were sorted into PBS solution containing 0.04% BSA and loaded to 10X Genomics microfluidic chips. The version 2 of Chromium Single Cell three prime Reagent Kits was used for RNA extraction. For snATACseq library construction  we used the same cell dissociation and sorting protocol as for scRNAseq  with isolation of live cells that excluded the cytoplasmic stain Zombie green product information. Nuclei isolation was performed per manufacturer’s instructions 10X Genomic  protocol CG000169. Cells were incubated with lysis buffer on ice for 90 second  followed by integrity check of nuclei under fluorescence microscope with DAPI before library synthesis. For scRNAseq  the cell lysis  polyA pull down  tagging with cell barcode  and RNA:DNA hybrid synthesis were performed in the GEMs per manufacturer's instruction. GEMs containing barcoded single cell cDNA  were lysis for further fragmentation and ligation of illumina P5 and P7 ends. Libraries were sequenced to depths of at least 1 000 000 reads per cell for each library. For snATACseq  the open chromatins of the isolated nuclei were targeted and tagged by transposase  barcoded and ligated with Illumina P5 sequence in the individually encapsulated GEMs per manufacturer's instruction. Barcoded single nucleus genomic DNA were released from GEMs and pulled down for further ligation of library specific index and Illumina P7 sequence. Libraries were sequenced to depths of at least 75 000 read pairs per nucleus for each library.,The Institutional Animal Care and Use Committee of the University of Southern California approved all animal experiments Protocol 20771. Zebrafish embryos Danio rerio were raised in embryo media at 28.5°C. For adults  in the institute vivarium according to Protocol 20771.,cell type:Cranial neural crest derived cells|transgene1:TgMmu.Sox10 Mmu.Fos:Crezf384|transgene2:Tgactab2:loxP BFP STOP loxP dsRed|developmental stage:2 dpf|facs markers:Zombie  / dsRed+,GSM5402430,GSM5402430: scRNAseq Sox10 Cre bact BtR 2dpf rep 1; Danio rerio; RNA Seq,GSM5402430,,1,Dissected heads from converted Sox10:cre; bactin:loxP eGFP loxP DsRed fish were incubated in fresh Ringer's solution 5 10 min  followed by mechanical and enzymatic dissociation by pipetting every 5 minutes 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 minutes or until full dissociation. Reaction was stopped by 6X stop solution 6 mM CaCl2 and 30% fetal bovine serum FBS in PBS. Cells were pelleted 2000 rpm  5 minute  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 sorted by fluorescence activated cell sorting FACS to isolate live cells that excluded the cytoplasmic stain Zombie green BioLegend  423111 or the nuclear stain DAPI. Live cells were sorted into PBS solution containing 0.04% BSA and loaded to 10X Genomics microfluidic chips. The version 2 of Chromium Single Cell three prime Reagent Kits was used for RNA extraction. For snATACseq library construction  we used the same cell dissociation and sorting protocol as for scRNAseq  with isolation of live cells that excluded the cytoplasmic stain Zombie green product information. Nuclei isolation was performed per manufacturer's instructions 10X Genomic  protocol CG000169. Cells were incubated with lysis buffer on ice for 90 second  followed by integrity check of nuclei under fluorescence microscope with DAPI before library synthesis. For scRNAseq  the cell lysis  polyA pull down  tagging with cell barcode  and RNA:DNA hybrid synthesis were performed in the GEMs per manufacturer's instruction. GEMs containing barcoded single cell cDNA  were lysis for further fragmentation and ligation of illumina P5 and P7 ends. Libraries were sequenced to depths of at least 1 000 000 reads per cell for each library. For snATACseq  the open chromatins of the isolated nuclei were targeted and tagged by transposase  barcoded and ligated with Illumina P5 sequence in the individually encapsulated GEMs per manufacturer's instruction. Barcoded single nucleus genomic DNA were released from GEMs and pulled down for further ligation of library specific index and Illumina P7 sequence. Libraries were sequenced to depths of at least 75 000 read pairs per nucleus for each library.,GEO Accession:GSM5402430,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP325759,,,scRNAseq_Sox10_Cre_bact_BtR_2dpf_rep_1_S4_L001_R1_001.fastq.gz scRNAseq_Sox10_Cre_bact_BtR_2dpf_rep_1_S4_L001_R2_001.fastq.gz,fastq fastq,15200849836.0,103076294.0,GSM5402430 r4,0:27 1:120.47,A:4297470339;C:3254279112;G:3405931007;T:4233976402;N:9192976,27,120,,,4297470339,3254279112,3405931007,4233976402,9192976,SRX11237258,SRS9283133,SRA1250944,GEO,"Crump Lab, Stem Cell, USC",2,0.00626,0.91136,0.00135,0.10084,0.98537,0.81797,0.49528,0.50672,27,120,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,United States,2021-06-27,Hatching,Embryo,Brain,Nervous System
68598,SRR18049402,SRX14201672,SRS12022091,SRP360102,PRJNA807540,Nrf2 dictates the neuronal survival and differentiation of embryonic zebrafish harboring compromised tRNA synthetase,GSE196846,Transcriptome Analysis,tRNA synthetase deficiency leads to unfolded protein responses in neuronal disorders; however  its function in embryonic neurogenesis remains unclear. This study identified an aars1cq71/cq71 mutant zebrafish allele that showed increased neuronal apoptosis and compromised neurogenesis. aars1 transcripts were highly expressed in primary neural progenitor cells  and their aberration resulted in protein overloading and activated Perk. nfe2l2b  a paralog of mammalian Nfe2l2  which encodes Nrf2  is a pivotal executor of Perk signaling that regulates neuronal phenotypes in aars1cq71/cq71 mutants. Interference of nfe2l2b in nfe2l2b?1/?1 mutants did not affect global larval development. However  aars1cq71/cq71;nfe2l2b?1/?1 mutant embryos exhibited increased neuronal cell survival and neurogenesis compared with their aars1cq71/cq71 siblings. nfe2l2b was harnessed by Perk at two levels. Its transcript was regulated by Chop  an implementer of Perk. It was also phosphorylated by Perk. Both pathways synergistically assured the nuclear functions of nfe2l2b to control cell survival by targeting p53. Our study extends the understanding of tRNA synthetase in neurogenesis and implies that Nrf2 is a cue to mitigate neurodegenerative pathogenesis. Overall design: Single cell analyses of zebrafish midbrain by 10X Genomics,,pubmed:35929539,,midbrain aars1ENU / ,GSM5903027,,source name:midbrain|developmental stage:2 dpf|tissue:midbrain|genotype:aars1ENU /  mutant,midbrain aars1ENU / ,The scRNA seq data were aligned to the zebrafish reference genome Danio rerio  GRCz11 by cellranger 5.0.0. The resulting matrix was inputted into Seurat v3 for quality control  filtration  dimensionality reduction  clustering analysis and differential expressed genes analysis Genome build: GRCz11 Supplementary files format and content: Cell Ranger output files barcodes.tsv.gz  features.tsv.gz  matrix.mtx.gz,midbrain,,The 10x RNA seq libraries were constructed using Chromium single cell gene expression platform and Chromium Chromium Single Cell three prime Reagent v3 Kits according to the manufacture's protocol.,,developmental stage:2 dpf|tissue:midbrain|genotype:aars1ENU /  mutant,GSM5903027,GSM5903027: midbrain aars1ENU / ; Danio rerio; RNA Seq,GSM5903027 r1,GSM5903027,1,The 10x RNA seq libraries were constructed using Chromium single cell gene expression platform and Chromium Chromium Single Cell three prime Reagent v3 Kits according to the manufacture's protocol.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP360102,,,R21001156-MUT-MUT-1_combined_R1.fastq.gz R21001156-MUT-MUT-1_combined_R2.fastq.gz,fastq fastq,27575933400.0,91919778.0,GSM5903027 r1,0:150 1:150,A:11721973614;C:4814188024;G:4730547766;T:6308524645;N:699351,150,150,,,11721973614,4814188024,4730547766,6308524645,699351,SRX14201672,SRS12022091,SRA1374754,"Institute of Developmental Biology and Regenerative Medicine, Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, Southwest University","Institute of Developmental Biology and Regenerative Medicine, Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, Southwest University",2,0.0,0.91413,0.0,0.20444,1.0,0.78555,,0.54347,150,150,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,small_rna,unknown,sc,single_cell_droplet,10x,,China,2022-02-16,Hatching,Embryo,Brain,Nervous System
68599,SRR18049403,SRX14201672,SRS12022091,SRP360102,PRJNA807540,Nrf2 dictates the neuronal survival and differentiation of embryonic zebrafish harboring compromised tRNA synthetase,GSE196846,Transcriptome Analysis,tRNA synthetase deficiency leads to unfolded protein responses in neuronal disorders; however  its function in embryonic neurogenesis remains unclear. This study identified an aars1cq71/cq71 mutant zebrafish allele that showed increased neuronal apoptosis and compromised neurogenesis. aars1 transcripts were highly expressed in primary neural progenitor cells  and their aberration resulted in protein overloading and activated Perk. nfe2l2b  a paralog of mammalian Nfe2l2  which encodes Nrf2  is a pivotal executor of Perk signaling that regulates neuronal phenotypes in aars1cq71/cq71 mutants. Interference of nfe2l2b in nfe2l2b?1/?1 mutants did not affect global larval development. However  aars1cq71/cq71;nfe2l2b?1/?1 mutant embryos exhibited increased neuronal cell survival and neurogenesis compared with their aars1cq71/cq71 siblings. nfe2l2b was harnessed by Perk at two levels. Its transcript was regulated by Chop  an implementer of Perk. It was also phosphorylated by Perk. Both pathways synergistically assured the nuclear functions of nfe2l2b to control cell survival by targeting p53. Our study extends the understanding of tRNA synthetase in neurogenesis and implies that Nrf2 is a cue to mitigate neurodegenerative pathogenesis. Overall design: Single cell analyses of zebrafish midbrain by 10X Genomics,,pubmed:35929539,,midbrain aars1ENU / ,GSM5903027,,source name:midbrain|developmental stage:2 dpf|tissue:midbrain|genotype:aars1ENU /  mutant,midbrain aars1ENU / ,The scRNA seq data were aligned to the zebrafish reference genome Danio rerio  GRCz11 by cellranger 5.0.0. The resulting matrix was inputted into Seurat v3 for quality control  filtration  dimensionality reduction  clustering analysis and differential expressed genes analysis Genome build: GRCz11 Supplementary files format and content: Cell Ranger output files barcodes.tsv.gz  features.tsv.gz  matrix.mtx.gz,midbrain,,The 10x RNA seq libraries were constructed using Chromium single cell gene expression platform and Chromium Chromium Single Cell three prime Reagent v3 Kits according to the manufacture's protocol.,,developmental stage:2 dpf|tissue:midbrain|genotype:aars1ENU /  mutant,GSM5903027,GSM5903027: midbrain aars1ENU / ; Danio rerio; RNA Seq,GSM5903027 r1,GSM5903027,1,The 10x RNA seq libraries were constructed using Chromium single cell gene expression platform and Chromium Chromium Single Cell three prime Reagent v3 Kits according to the manufacture's protocol.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP360102,,,R21001156-MUT-MUT-2_combined_R1.fastq.gz R21001156-MUT-MUT-2_combined_R2.fastq.gz,fastq fastq,20079501600.0,66931672.0,GSM5903027 r2,0:150 1:150,A:8561310772;C:3509305835;G:3437688198;T:4570677254;N:519541,150,150,,,8561310772,3509305835,3437688198,4570677254,519541,SRX14201672,SRS12022091,SRA1374754,"Institute of Developmental Biology and Regenerative Medicine, Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, Southwest University","Institute of Developmental Biology and Regenerative Medicine, Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, Southwest University",2,0.0,0.91296,0.0,0.20619,1.0,0.78837,,0.53145,150,150,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,small_rna,unknown,sc,single_cell_droplet,10x,,China,2022-02-16,Hatching,Embryo,Brain,Nervous System
68600,SRR18049404,SRX14201672,SRS12022091,SRP360102,PRJNA807540,Nrf2 dictates the neuronal survival and differentiation of embryonic zebrafish harboring compromised tRNA synthetase,GSE196846,Transcriptome Analysis,tRNA synthetase deficiency leads to unfolded protein responses in neuronal disorders; however  its function in embryonic neurogenesis remains unclear. This study identified an aars1cq71/cq71 mutant zebrafish allele that showed increased neuronal apoptosis and compromised neurogenesis. aars1 transcripts were highly expressed in primary neural progenitor cells  and their aberration resulted in protein overloading and activated Perk. nfe2l2b  a paralog of mammalian Nfe2l2  which encodes Nrf2  is a pivotal executor of Perk signaling that regulates neuronal phenotypes in aars1cq71/cq71 mutants. Interference of nfe2l2b in nfe2l2b?1/?1 mutants did not affect global larval development. However  aars1cq71/cq71;nfe2l2b?1/?1 mutant embryos exhibited increased neuronal cell survival and neurogenesis compared with their aars1cq71/cq71 siblings. nfe2l2b was harnessed by Perk at two levels. Its transcript was regulated by Chop  an implementer of Perk. It was also phosphorylated by Perk. Both pathways synergistically assured the nuclear functions of nfe2l2b to control cell survival by targeting p53. Our study extends the understanding of tRNA synthetase in neurogenesis and implies that Nrf2 is a cue to mitigate neurodegenerative pathogenesis. Overall design: Single cell analyses of zebrafish midbrain by 10X Genomics,,pubmed:35929539,,midbrain aars1ENU / ,GSM5903027,,source name:midbrain|developmental stage:2 dpf|tissue:midbrain|genotype:aars1ENU /  mutant,midbrain aars1ENU / ,The scRNA seq data were aligned to the zebrafish reference genome Danio rerio  GRCz11 by cellranger 5.0.0. The resulting matrix was inputted into Seurat v3 for quality control  filtration  dimensionality reduction  clustering analysis and differential expressed genes analysis Genome build: GRCz11 Supplementary files format and content: Cell Ranger output files barcodes.tsv.gz  features.tsv.gz  matrix.mtx.gz,midbrain,,The 10x RNA seq libraries were constructed using Chromium single cell gene expression platform and Chromium Chromium Single Cell three prime Reagent v3 Kits according to the manufacture's protocol.,,developmental stage:2 dpf|tissue:midbrain|genotype:aars1ENU /  mutant,GSM5903027,GSM5903027: midbrain aars1ENU / ; Danio rerio; RNA Seq,GSM5903027 r1,GSM5903027,1,The 10x RNA seq libraries were constructed using Chromium single cell gene expression platform and Chromium Chromium Single Cell three prime Reagent v3 Kits according to the manufacture's protocol.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP360102,,,R21001156-MUT-MUT-3_combined_R1.fastq.gz R21001156-MUT-MUT-3_combined_R2.fastq.gz,fastq fastq,28233133200.0,94110444.0,GSM5903027 r3,0:150 1:150,A:12021563474;C:4929633967;G:4838726958;T:6442481777;N:727024,150,150,,,12021563474,4929633967,4838726958,6442481777,727024,SRX14201672,SRS12022091,SRA1374754,"Institute of Developmental Biology and Regenerative Medicine, Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, Southwest University","Institute of Developmental Biology and Regenerative Medicine, Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, Southwest University",2,0.0,0.91374,0.0,0.20276,1.0,0.78709,,0.54761,150,150,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,small_rna,unknown,sc,single_cell_droplet,10x,,China,2022-02-16,Hatching,Embryo,Brain,Nervous System
68601,SRR18049405,SRX14201672,SRS12022091,SRP360102,PRJNA807540,Nrf2 dictates the neuronal survival and differentiation of embryonic zebrafish harboring compromised tRNA synthetase,GSE196846,Transcriptome Analysis,tRNA synthetase deficiency leads to unfolded protein responses in neuronal disorders; however  its function in embryonic neurogenesis remains unclear. This study identified an aars1cq71/cq71 mutant zebrafish allele that showed increased neuronal apoptosis and compromised neurogenesis. aars1 transcripts were highly expressed in primary neural progenitor cells  and their aberration resulted in protein overloading and activated Perk. nfe2l2b  a paralog of mammalian Nfe2l2  which encodes Nrf2  is a pivotal executor of Perk signaling that regulates neuronal phenotypes in aars1cq71/cq71 mutants. Interference of nfe2l2b in nfe2l2b?1/?1 mutants did not affect global larval development. However  aars1cq71/cq71;nfe2l2b?1/?1 mutant embryos exhibited increased neuronal cell survival and neurogenesis compared with their aars1cq71/cq71 siblings. nfe2l2b was harnessed by Perk at two levels. Its transcript was regulated by Chop  an implementer of Perk. It was also phosphorylated by Perk. Both pathways synergistically assured the nuclear functions of nfe2l2b to control cell survival by targeting p53. Our study extends the understanding of tRNA synthetase in neurogenesis and implies that Nrf2 is a cue to mitigate neurodegenerative pathogenesis. Overall design: Single cell analyses of zebrafish midbrain by 10X Genomics,,pubmed:35929539,,midbrain aars1ENU / ,GSM5903027,,source name:midbrain|developmental stage:2 dpf|tissue:midbrain|genotype:aars1ENU /  mutant,midbrain aars1ENU / ,The scRNA seq data were aligned to the zebrafish reference genome Danio rerio  GRCz11 by cellranger 5.0.0. The resulting matrix was inputted into Seurat v3 for quality control  filtration  dimensionality reduction  clustering analysis and differential expressed genes analysis Genome build: GRCz11 Supplementary files format and content: Cell Ranger output files barcodes.tsv.gz  features.tsv.gz  matrix.mtx.gz,midbrain,,The 10x RNA seq libraries were constructed using Chromium single cell gene expression platform and Chromium Chromium Single Cell three prime Reagent v3 Kits according to the manufacture's protocol.,,developmental stage:2 dpf|tissue:midbrain|genotype:aars1ENU /  mutant,GSM5903027,GSM5903027: midbrain aars1ENU / ; Danio rerio; RNA Seq,GSM5903027 r1,GSM5903027,1,The 10x RNA seq libraries were constructed using Chromium single cell gene expression platform and Chromium Chromium Single Cell three prime Reagent v3 Kits according to the manufacture's protocol.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP360102,,,R21001156-MUT-MUT-4_combined_R1.fastq.gz R21001156-MUT-MUT-4_combined_R2.fastq.gz,fastq fastq,29338440600.0,97794802.0,GSM5903027 r4,0:150 1:150,A:12492098582;C:5126694946;G:5024273043;T:6694617197;N:756832,150,150,,,12492098582,5126694946,5024273043,6694617197,756832,SRX14201672,SRS12022091,SRA1374754,"Institute of Developmental Biology and Regenerative Medicine, Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, Southwest University","Institute of Developmental Biology and Regenerative Medicine, Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, Southwest University",2,0.0,0.91524,0.0,0.20406,1.0,0.78727,,0.55004,150,150,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,small_rna,unknown,sc,single_cell_droplet,10x,,China,2022-02-16,Hatching,Embryo,Brain,Nervous System
68602,SRR18049406,SRX14201671,SRS12022090,SRP360102,PRJNA807540,Nrf2 dictates the neuronal survival and differentiation of embryonic zebrafish harboring compromised tRNA synthetase,GSE196846,Transcriptome Analysis,tRNA synthetase deficiency leads to unfolded protein responses in neuronal disorders; however  its function in embryonic neurogenesis remains unclear. This study identified an aars1cq71/cq71 mutant zebrafish allele that showed increased neuronal apoptosis and compromised neurogenesis. aars1 transcripts were highly expressed in primary neural progenitor cells  and their aberration resulted in protein overloading and activated Perk. nfe2l2b  a paralog of mammalian Nfe2l2  which encodes Nrf2  is a pivotal executor of Perk signaling that regulates neuronal phenotypes in aars1cq71/cq71 mutants. Interference of nfe2l2b in nfe2l2b?1/?1 mutants did not affect global larval development. However  aars1cq71/cq71;nfe2l2b?1/?1 mutant embryos exhibited increased neuronal cell survival and neurogenesis compared with their aars1cq71/cq71 siblings. nfe2l2b was harnessed by Perk at two levels. Its transcript was regulated by Chop  an implementer of Perk. It was also phosphorylated by Perk. Both pathways synergistically assured the nuclear functions of nfe2l2b to control cell survival by targeting p53. Our study extends the understanding of tRNA synthetase in neurogenesis and implies that Nrf2 is a cue to mitigate neurodegenerative pathogenesis. Overall design: Single cell analyses of zebrafish midbrain by 10X Genomics,,pubmed:35929539,,midbrain sibling,GSM5903026,,source name:midbrain|developmental stage:2 dpf|tissue:midbrain|genotype:sibling,midbrain sibling,The scRNA seq data were aligned to the zebrafish reference genome Danio rerio  GRCz11 by cellranger 5.0.0. The resulting matrix was inputted into Seurat v3 for quality control  filtration  dimensionality reduction  clustering analysis and differential expressed genes analysis Genome build: GRCz11 Supplementary files format and content: Cell Ranger output files barcodes.tsv.gz  features.tsv.gz  matrix.mtx.gz,midbrain,,The 10x RNA seq libraries were constructed using Chromium single cell gene expression platform and Chromium Chromium Single Cell three prime Reagent v3 Kits according to the manufacture's protocol.,,developmental stage:2 dpf|tissue:midbrain|genotype:sibling,GSM5903026,GSM5903026: midbrain sibling; Danio rerio; RNA Seq,GSM5903026 r1,GSM5903026,1,The 10x RNA seq libraries were constructed using Chromium single cell gene expression platform and Chromium Chromium Single Cell three prime Reagent v3 Kits according to the manufacture's protocol.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP360102,,,R21001155-SIB-SIB-1_combined_R1.fastq.gz R21001155-SIB-SIB-1_combined_R2.fastq.gz,fastq fastq,21090589800.0,70301966.0,GSM5903026 r1,0:150 1:150,A:8985120834;C:3633190080;G:3571027373;T:4900711222;N:540291,150,150,,,8985120834,3633190080,3571027373,4900711222,540291,SRX14201671,SRS12022090,SRA1374754,"Institute of Developmental Biology and Regenerative Medicine, Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, Southwest University","Institute of Developmental Biology and Regenerative Medicine, Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, Southwest University",2,0.0,0.91144,0.0,0.2079,1.0,0.79628,,0.51661,150,150,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,small_rna,unknown,sc,single_cell_droplet,10x,,China,2022-02-16,Hatching,Embryo,Brain,Nervous System
68603,SRR18049407,SRX14201671,SRS12022090,SRP360102,PRJNA807540,Nrf2 dictates the neuronal survival and differentiation of embryonic zebrafish harboring compromised tRNA synthetase,GSE196846,Transcriptome Analysis,tRNA synthetase deficiency leads to unfolded protein responses in neuronal disorders; however  its function in embryonic neurogenesis remains unclear. This study identified an aars1cq71/cq71 mutant zebrafish allele that showed increased neuronal apoptosis and compromised neurogenesis. aars1 transcripts were highly expressed in primary neural progenitor cells  and their aberration resulted in protein overloading and activated Perk. nfe2l2b  a paralog of mammalian Nfe2l2  which encodes Nrf2  is a pivotal executor of Perk signaling that regulates neuronal phenotypes in aars1cq71/cq71 mutants. Interference of nfe2l2b in nfe2l2b?1/?1 mutants did not affect global larval development. However  aars1cq71/cq71;nfe2l2b?1/?1 mutant embryos exhibited increased neuronal cell survival and neurogenesis compared with their aars1cq71/cq71 siblings. nfe2l2b was harnessed by Perk at two levels. Its transcript was regulated by Chop  an implementer of Perk. It was also phosphorylated by Perk. Both pathways synergistically assured the nuclear functions of nfe2l2b to control cell survival by targeting p53. Our study extends the understanding of tRNA synthetase in neurogenesis and implies that Nrf2 is a cue to mitigate neurodegenerative pathogenesis. Overall design: Single cell analyses of zebrafish midbrain by 10X Genomics,,pubmed:35929539,,midbrain sibling,GSM5903026,,source name:midbrain|developmental stage:2 dpf|tissue:midbrain|genotype:sibling,midbrain sibling,The scRNA seq data were aligned to the zebrafish reference genome Danio rerio  GRCz11 by cellranger 5.0.0. The resulting matrix was inputted into Seurat v3 for quality control  filtration  dimensionality reduction  clustering analysis and differential expressed genes analysis Genome build: GRCz11 Supplementary files format and content: Cell Ranger output files barcodes.tsv.gz  features.tsv.gz  matrix.mtx.gz,midbrain,,The 10x RNA seq libraries were constructed using Chromium single cell gene expression platform and Chromium Chromium Single Cell three prime Reagent v3 Kits according to the manufacture's protocol.,,developmental stage:2 dpf|tissue:midbrain|genotype:sibling,GSM5903026,GSM5903026: midbrain sibling; Danio rerio; RNA Seq,GSM5903026 r1,GSM5903026,1,The 10x RNA seq libraries were constructed using Chromium single cell gene expression platform and Chromium Chromium Single Cell three prime Reagent v3 Kits according to the manufacture's protocol.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP360102,,,R21001155-SIB-SIB-2_combined_R1.fastq.gz R21001155-SIB-SIB-2_combined_R2.fastq.gz,fastq fastq,24006132600.0,80020442.0,GSM5903026 r2,0:150 1:150,A:10242745683;C:4139089540;G:4060437946;T:5563245415;N:614016,150,150,,,10242745683,4139089540,4060437946,5563245415,614016,SRX14201671,SRS12022090,SRA1374754,"Institute of Developmental Biology and Regenerative Medicine, Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, Southwest University","Institute of Developmental Biology and Regenerative Medicine, Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, Southwest University",2,0.0,0.91328,0.0,0.207,1.0,0.79304,,0.52006,150,150,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,small_rna,unknown,sc,single_cell_droplet,10x,,China,2022-02-16,Hatching,Embryo,Brain,Nervous System
68604,SRR18049408,SRX14201671,SRS12022090,SRP360102,PRJNA807540,Nrf2 dictates the neuronal survival and differentiation of embryonic zebrafish harboring compromised tRNA synthetase,GSE196846,Transcriptome Analysis,tRNA synthetase deficiency leads to unfolded protein responses in neuronal disorders; however  its function in embryonic neurogenesis remains unclear. This study identified an aars1cq71/cq71 mutant zebrafish allele that showed increased neuronal apoptosis and compromised neurogenesis. aars1 transcripts were highly expressed in primary neural progenitor cells  and their aberration resulted in protein overloading and activated Perk. nfe2l2b  a paralog of mammalian Nfe2l2  which encodes Nrf2  is a pivotal executor of Perk signaling that regulates neuronal phenotypes in aars1cq71/cq71 mutants. Interference of nfe2l2b in nfe2l2b?1/?1 mutants did not affect global larval development. However  aars1cq71/cq71;nfe2l2b?1/?1 mutant embryos exhibited increased neuronal cell survival and neurogenesis compared with their aars1cq71/cq71 siblings. nfe2l2b was harnessed by Perk at two levels. Its transcript was regulated by Chop  an implementer of Perk. It was also phosphorylated by Perk. Both pathways synergistically assured the nuclear functions of nfe2l2b to control cell survival by targeting p53. Our study extends the understanding of tRNA synthetase in neurogenesis and implies that Nrf2 is a cue to mitigate neurodegenerative pathogenesis. Overall design: Single cell analyses of zebrafish midbrain by 10X Genomics,,pubmed:35929539,,midbrain sibling,GSM5903026,,source name:midbrain|developmental stage:2 dpf|tissue:midbrain|genotype:sibling,midbrain sibling,The scRNA seq data were aligned to the zebrafish reference genome Danio rerio  GRCz11 by cellranger 5.0.0. The resulting matrix was inputted into Seurat v3 for quality control  filtration  dimensionality reduction  clustering analysis and differential expressed genes analysis Genome build: GRCz11 Supplementary files format and content: Cell Ranger output files barcodes.tsv.gz  features.tsv.gz  matrix.mtx.gz,midbrain,,The 10x RNA seq libraries were constructed using Chromium single cell gene expression platform and Chromium Chromium Single Cell three prime Reagent v3 Kits according to the manufacture's protocol.,,developmental stage:2 dpf|tissue:midbrain|genotype:sibling,GSM5903026,GSM5903026: midbrain sibling; Danio rerio; RNA Seq,GSM5903026 r1,GSM5903026,1,The 10x RNA seq libraries were constructed using Chromium single cell gene expression platform and Chromium Chromium Single Cell three prime Reagent v3 Kits according to the manufacture's protocol.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP360102,,,R21001155-SIB-SIB-3_combined_R1.fastq.gz R21001155-SIB-SIB-3_combined_R2.fastq.gz,fastq fastq,29309592600.0,97698642.0,GSM5903026 r3,0:150 1:150,A:12514997087;C:5052977357;G:4953884313;T:6786981055;N:752788,150,150,,,12514997087,5052977357,4953884313,6786981055,752788,SRX14201671,SRS12022090,SRA1374754,"Institute of Developmental Biology and Regenerative Medicine, Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, Southwest University","Institute of Developmental Biology and Regenerative Medicine, Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, Southwest University",2,0.0,0.91247,0.0,0.20575,1.0,0.79348,,0.5142,150,150,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,small_rna,unknown,sc,single_cell_droplet,10x,,China,2022-02-16,Hatching,Embryo,Brain,Nervous System
68605,SRR18049409,SRX14201671,SRS12022090,SRP360102,PRJNA807540,Nrf2 dictates the neuronal survival and differentiation of embryonic zebrafish harboring compromised tRNA synthetase,GSE196846,Transcriptome Analysis,tRNA synthetase deficiency leads to unfolded protein responses in neuronal disorders; however  its function in embryonic neurogenesis remains unclear. This study identified an aars1cq71/cq71 mutant zebrafish allele that showed increased neuronal apoptosis and compromised neurogenesis. aars1 transcripts were highly expressed in primary neural progenitor cells  and their aberration resulted in protein overloading and activated Perk. nfe2l2b  a paralog of mammalian Nfe2l2  which encodes Nrf2  is a pivotal executor of Perk signaling that regulates neuronal phenotypes in aars1cq71/cq71 mutants. Interference of nfe2l2b in nfe2l2b?1/?1 mutants did not affect global larval development. However  aars1cq71/cq71;nfe2l2b?1/?1 mutant embryos exhibited increased neuronal cell survival and neurogenesis compared with their aars1cq71/cq71 siblings. nfe2l2b was harnessed by Perk at two levels. Its transcript was regulated by Chop  an implementer of Perk. It was also phosphorylated by Perk. Both pathways synergistically assured the nuclear functions of nfe2l2b to control cell survival by targeting p53. Our study extends the understanding of tRNA synthetase in neurogenesis and implies that Nrf2 is a cue to mitigate neurodegenerative pathogenesis. Overall design: Single cell analyses of zebrafish midbrain by 10X Genomics,,pubmed:35929539,,midbrain sibling,GSM5903026,,source name:midbrain|developmental stage:2 dpf|tissue:midbrain|genotype:sibling,midbrain sibling,The scRNA seq data were aligned to the zebrafish reference genome Danio rerio  GRCz11 by cellranger 5.0.0. The resulting matrix was inputted into Seurat v3 for quality control  filtration  dimensionality reduction  clustering analysis and differential expressed genes analysis Genome build: GRCz11 Supplementary files format and content: Cell Ranger output files barcodes.tsv.gz  features.tsv.gz  matrix.mtx.gz,midbrain,,The 10x RNA seq libraries were constructed using Chromium single cell gene expression platform and Chromium Chromium Single Cell three prime Reagent v3 Kits according to the manufacture's protocol.,,developmental stage:2 dpf|tissue:midbrain|genotype:sibling,GSM5903026,GSM5903026: midbrain sibling; Danio rerio; RNA Seq,GSM5903026 r1,GSM5903026,1,The 10x RNA seq libraries were constructed using Chromium single cell gene expression platform and Chromium Chromium Single Cell three prime Reagent v3 Kits according to the manufacture's protocol.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP360102,,,R21001155-SIB-SIB-4_combined_R1.fastq.gz R21001155-SIB-SIB-4_combined_R2.fastq.gz,fastq fastq,23471604900.0,78238683.0,GSM5903026 r4,0:150 1:150,A:10019038734;C:4041693743;G:3964544535;T:5445723595;N:604293,150,150,,,10019038734,4041693743,3964544535,5445723595,604293,SRX14201671,SRS12022090,SRA1374754,"Institute of Developmental Biology and Regenerative Medicine, Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, Southwest University","Institute of Developmental Biology and Regenerative Medicine, Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, Southwest University",2,0.0,0.913,0.0,0.20768,1.0,0.79405,,0.52888,150,150,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,small_rna,unknown,sc,single_cell_droplet,10x,,China,2022-02-16,Hatching,Embryo,Brain,Nervous System