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  • Brain · 65 ✖

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  • Segmentation · 65 ✖
Link 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
34547 34547 SRR32092978 SRX27440700 SRS23867512 SRP559408 PRJNA1214750 Reactivation of an Embryonic Cardiac Neural Crest Transcriptional Subcircuit During Zebrafish Heart Regeneration [scRNA seq] GSE287811 Other During vertebrate development the heart primarily arises from mesoderm with crucial contributions from cardiac neural crest cells that migrate to the heart and form a variety of cardiovascular derivatives. Here by integrating bulk and single cell RNAseq with ATAC seq we identify a gene regulatory subcircuit specific to migratory cardiac crest cells composed of key transcription factors egr1 sox9a tfap2a and ets1. Notably we show that cells expressing the canonical neural crest gene sox10 are essential for proper cardiac regeneration in adult zebrafish. Furthermore expression of all transcription factors from the migratory cardiac crest gene subcircuit are xxx post injury at the wound edge. Together our results uncover a developmental gene regulatory network that is important for cardiac neural crest fate determination with key factors re activated during regeneration. Overall design: mcherry+ cells from 16 somite stage zebrafish embryos migratory cardiac neural crest stage were FAC sorted from Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP and analyzed using 10X Chromium Single Cell three prime v3.1 sequencing.       mch+ CdNC cells from 16ss zebrafish embryos GSM8751763   source name:midbrain hindbrain boundary to somite 6|tissue:midbrain hindbrain boundary to somite 6|transgenic line:Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP|cell type:Cardiac Neural Crest|age:16 somite stage|geo loc name:missing|collection date:missing mch+ CdNC cells from 16ss zebrafish embryos Reads were mapped to GRCz11 and initial quality control was performed using Cell Ranger v7.20. Scanpy was used for further quality control filtering clustering and downstream analysis. Assembly: GRCz11 Supplementary files format and content: tab separated barcodes and features files as well as matrix file. midbrain hindbrain boundary to somite 6   mch+ CdNC cells from 16 somite stage Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP embryos were dissected dissociated and FAC sorted. Single cell libraries were prepared using the Chromium Single Cell 3’ v3.1 reagent kit 10X Genomics PN 1000075 according to manufacturer's protocol.   tissue:midbrain hindbrain boundary to somite 6|transgenic line:Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP|cell type:Cardiac Neural Crest|age:16 somite stage GSM8751763 GSM8751763: mch+ CdNC cells from 16ss zebrafish embryos; Danio rerio; RNA Seq GSM8751763 r1 GSM8751763 1 mch+ CdNC cells from 16 somite stage Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP embryos were dissected dissociated and FAC sorted. Single cell libraries were prepared using the Chromium Single Cell three prime v3.1 reagent kit 10X Genomics PN 1000075 according to manufacturer's protocol.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP559408     SE6898_SA80357_S1_L001_R1_001.fastq.gz SE6898_SA80357_S1_L001_R2_001.fastq.gz fastq fastq 71160584348.0 235631074.0 GSM8751763 r1 0:151 1:151 A:17520054424;C:13126677931;G:14006245844;T:26493745251;N:13860898 151 151     17520054424 13126677931 14006245844 26493745251 13860898 SRX27440700 SRS23867512 SRA2058075 Martik Lab, Molecular and Cell Biology, University of California Berkeley Martik Lab, Molecular and Cell Biology, University of California Berkeley                       T B mate1 technical by mapping diff illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2025-01-23 Segmentation Embryo Brain Nervous System
34554 34554 SRR32104359 SRX27449951 SRS23876473 SRP559533 PRJNA1214751 Reactivation of an Embryonic Cardiac Neural Crest Transcriptional Subcircuit During Zebrafish Heart Regeneration [bulk RNA seq] GSE287815 Transcriptome Analysis During vertebrate development the heart primarily arises from mesoderm with crucial contributions from cardiac neural crest cells that migrate to the heart and form a variety of cardiovascular derivatives. Here by integrating bulk and single cell RNAseq with ATAC seq we identify a gene regulatory subcircuit specific to migratory cardiac crest cells composed of key transcription factors egr1 sox9a tfap2a and ets1. Notably we show that cells expressing the canonical neural crest gene sox10 are essential for proper cardiac regeneration in adult zebrafish. Furthermore expression of all transcription factors from the migratory cardiac crest gene subcircuit are xxx post injury at the wound edge. Together our results uncover a developmental gene regulatory network that is important for cardiac neural crest fate determination with key factors re activated during regeneration. Overall design: Migratory cardiac neural crest cells mcherry + and non neural crest cells from the same tissue mcherry were FAC sorted from 16 somite stage Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP embryos. Migratory trunk neural crest cells GFP + were FAC sorted from 24hpf Tg 4.9sox10:eGFP embryos.       17hpf Negative CNC 3 GSM8751784   source name:non neural crest from midbrain hindbrain boundary to somite 6|tissue:non neural crest from midbrain hindbrain boundary to somite 6|cell type:non neural crest|transgenic line:Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP|age:16 somite stage 17hpf|fluorophore:mcherry |geo loc name:missing|collection date:missing 17hpf Negative CNC 3 Reads were mapped zebrafish genome GRCz10 using Bowtie 2. Transcript counts were determined using featureCounts Subread. Differential gene expression was performed using DEseq. Assembly: GRCz10 Supplementary files format and content: tab delimited text file included for cardiac neural crest and non neural crest samples non neural crest from midbrain hindbrain boundary to somite 6   mch+ CdNC cells and mch non neural crest cells from 16 somite stage Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP embryos were dissected dissociated and FAC sorted. GFP+ cells were sorted from 24hpf Tg 4.9sox10:eGFP embryos were dissected dissociated and FAC sorted. Tissues were dissociated in Accumax and then sorted BD FACSAria™ Fusion Flow Cytometer. cDNA was prepared from each sample using the SMART Seq® v4 Ultra® Low Input RNA Kit. Standard Illumina protocols were used to construct each sequencing library and an Illumina HiSeq2500 sequencer at the Millard and Muriel Jacobs Genetics and Genomics Laboratory California Institute of Technology Pasadena CA for 50 million single ended reads.   tissue:non neural crest from midbrain hindbrain boundary to somite 6|cell type:non neural crest|transgenic line:Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP|age:16 somite stage 17hpf|fluorophore:mcherry GSM8751784 GSM8751784: 17hpf Negative CNC 3; Danio rerio; RNA Seq GSM8751784 r1 GSM8751784 1 mch+ CdNC cells and mch non neural crest cells from 16 somite stage Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP embryos were dissected dissociated and FAC sorted. GFP+ cells were sorted from 24hpf Tg 4.9sox10:eGFP embryos were dissected dissociated and FAC sorted. Tissues were dissociated in Accumax and then sorted BD FACSAria™ Fusion Flow Cytometer. cDNA was prepared from each sample using the SMART Seq® v4 Ultra® Low Input RNA Kit. Standard Illumina protocols were used to construct each sequencing library and an Illumina HiSeq2500 sequencer at the Millard and Muriel Jacobs Genetics and Genomics Laboratory California Institute of Technology Pasadena CA for 50 million single ended reads.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP559533     Sox10_neg_17hpf_CNC_3_22029_combined_filtered.fastq.gz fastq 6549316700.0 65493167.0 GSM8751784 r1 0:100 A:1904137226;C:1372226751;G:1395882591;T:1876995541;N:74591 100       1904137226 1372226751 1395882591 1876995541 74591 SRX27449951 SRS23876473 SRA2058978 Martik Lab, Molecular and Cell Biology, University of California Berkeley Martik Lab, Molecular and Cell Biology, University of California Berkeley                       B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   United States 2025-01-23 Segmentation Embryo Brain Nervous System
34555 34555 SRR32104360 SRX27449950 SRS23876471 SRP559533 PRJNA1214751 Reactivation of an Embryonic Cardiac Neural Crest Transcriptional Subcircuit During Zebrafish Heart Regeneration [bulk RNA seq] GSE287815 Transcriptome Analysis During vertebrate development the heart primarily arises from mesoderm with crucial contributions from cardiac neural crest cells that migrate to the heart and form a variety of cardiovascular derivatives. Here by integrating bulk and single cell RNAseq with ATAC seq we identify a gene regulatory subcircuit specific to migratory cardiac crest cells composed of key transcription factors egr1 sox9a tfap2a and ets1. Notably we show that cells expressing the canonical neural crest gene sox10 are essential for proper cardiac regeneration in adult zebrafish. Furthermore expression of all transcription factors from the migratory cardiac crest gene subcircuit are xxx post injury at the wound edge. Together our results uncover a developmental gene regulatory network that is important for cardiac neural crest fate determination with key factors re activated during regeneration. Overall design: Migratory cardiac neural crest cells mcherry + and non neural crest cells from the same tissue mcherry were FAC sorted from 16 somite stage Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP embryos. Migratory trunk neural crest cells GFP + were FAC sorted from 24hpf Tg 4.9sox10:eGFP embryos.       17hpf Negative CNC 2 GSM8751783   source name:non neural crest from midbrain hindbrain boundary to somite 6|tissue:non neural crest from midbrain hindbrain boundary to somite 6|cell type:non neural crest|transgenic line:Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP|age:16 somite stage 17hpf|fluorophore:mcherry |geo loc name:missing|collection date:missing 17hpf Negative CNC 2 Reads were mapped zebrafish genome GRCz10 using Bowtie 2. Transcript counts were determined using featureCounts Subread. Differential gene expression was performed using DEseq. Assembly: GRCz10 Supplementary files format and content: tab delimited text file included for cardiac neural crest and non neural crest samples non neural crest from midbrain hindbrain boundary to somite 6   mch+ CdNC cells and mch non neural crest cells from 16 somite stage Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP embryos were dissected dissociated and FAC sorted. GFP+ cells were sorted from 24hpf Tg 4.9sox10:eGFP embryos were dissected dissociated and FAC sorted. Tissues were dissociated in Accumax and then sorted BD FACSAria™ Fusion Flow Cytometer. cDNA was prepared from each sample using the SMART Seq® v4 Ultra® Low Input RNA Kit. Standard Illumina protocols were used to construct each sequencing library and an Illumina HiSeq2500 sequencer at the Millard and Muriel Jacobs Genetics and Genomics Laboratory California Institute of Technology Pasadena CA for 50 million single ended reads.   tissue:non neural crest from midbrain hindbrain boundary to somite 6|cell type:non neural crest|transgenic line:Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP|age:16 somite stage 17hpf|fluorophore:mcherry GSM8751783 GSM8751783: 17hpf Negative CNC 2; Danio rerio; RNA Seq GSM8751783 r1 GSM8751783 1 mch+ CdNC cells and mch non neural crest cells from 16 somite stage Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP embryos were dissected dissociated and FAC sorted. GFP+ cells were sorted from 24hpf Tg 4.9sox10:eGFP embryos were dissected dissociated and FAC sorted. Tissues were dissociated in Accumax and then sorted BD FACSAria™ Fusion Flow Cytometer. cDNA was prepared from each sample using the SMART Seq® v4 Ultra® Low Input RNA Kit. Standard Illumina protocols were used to construct each sequencing library and an Illumina HiSeq2500 sequencer at the Millard and Muriel Jacobs Genetics and Genomics Laboratory California Institute of Technology Pasadena CA for 50 million single ended reads.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP559533     Sox10_neg_17hpf_CNC_2_21339_combined_filtered.fastq.gz fastq 2595442300.0 51908846.0 GSM8751783 r1 0:50 A:735396784;C:561568693;G:572114011;T:726356371;N:6441 50       735396784 561568693 572114011 726356371 6441 SRX27449950 SRS23876471 SRA2058978 Martik Lab, Molecular and Cell Biology, University of California Berkeley Martik Lab, Molecular and Cell Biology, University of California Berkeley                       B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   United States 2025-01-23 Segmentation Embryo Brain Nervous System
34556 34556 SRR32104361 SRX27449949 SRS23876470 SRP559533 PRJNA1214751 Reactivation of an Embryonic Cardiac Neural Crest Transcriptional Subcircuit During Zebrafish Heart Regeneration [bulk RNA seq] GSE287815 Transcriptome Analysis During vertebrate development the heart primarily arises from mesoderm with crucial contributions from cardiac neural crest cells that migrate to the heart and form a variety of cardiovascular derivatives. Here by integrating bulk and single cell RNAseq with ATAC seq we identify a gene regulatory subcircuit specific to migratory cardiac crest cells composed of key transcription factors egr1 sox9a tfap2a and ets1. Notably we show that cells expressing the canonical neural crest gene sox10 are essential for proper cardiac regeneration in adult zebrafish. Furthermore expression of all transcription factors from the migratory cardiac crest gene subcircuit are xxx post injury at the wound edge. Together our results uncover a developmental gene regulatory network that is important for cardiac neural crest fate determination with key factors re activated during regeneration. Overall design: Migratory cardiac neural crest cells mcherry + and non neural crest cells from the same tissue mcherry were FAC sorted from 16 somite stage Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP embryos. Migratory trunk neural crest cells GFP + were FAC sorted from 24hpf Tg 4.9sox10:eGFP embryos.       17hpf Negative CNC 1 GSM8751782   source name:non neural crest from midbrain hindbrain boundary to somite 6|tissue:non neural crest from midbrain hindbrain boundary to somite 6|cell type:non neural crest|transgenic line:Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP|age:16 somite stage 17hpf|fluorophore:mcherry |geo loc name:missing|collection date:missing 17hpf Negative CNC 1 Reads were mapped zebrafish genome GRCz10 using Bowtie 2. Transcript counts were determined using featureCounts Subread. Differential gene expression was performed using DEseq. Assembly: GRCz10 Supplementary files format and content: tab delimited text file included for cardiac neural crest and non neural crest samples non neural crest from midbrain hindbrain boundary to somite 6   mch+ CdNC cells and mch non neural crest cells from 16 somite stage Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP embryos were dissected dissociated and FAC sorted. GFP+ cells were sorted from 24hpf Tg 4.9sox10:eGFP embryos were dissected dissociated and FAC sorted. Tissues were dissociated in Accumax and then sorted BD FACSAria™ Fusion Flow Cytometer. cDNA was prepared from each sample using the SMART Seq® v4 Ultra® Low Input RNA Kit. Standard Illumina protocols were used to construct each sequencing library and an Illumina HiSeq2500 sequencer at the Millard and Muriel Jacobs Genetics and Genomics Laboratory California Institute of Technology Pasadena CA for 50 million single ended reads.   tissue:non neural crest from midbrain hindbrain boundary to somite 6|cell type:non neural crest|transgenic line:Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP|age:16 somite stage 17hpf|fluorophore:mcherry GSM8751782 GSM8751782: 17hpf Negative CNC 1; Danio rerio; RNA Seq GSM8751782 r1 GSM8751782 1 mch+ CdNC cells and mch non neural crest cells from 16 somite stage Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP embryos were dissected dissociated and FAC sorted. GFP+ cells were sorted from 24hpf Tg 4.9sox10:eGFP embryos were dissected dissociated and FAC sorted. Tissues were dissociated in Accumax and then sorted BD FACSAria™ Fusion Flow Cytometer. cDNA was prepared from each sample using the SMART Seq® v4 Ultra® Low Input RNA Kit. Standard Illumina protocols were used to construct each sequencing library and an Illumina HiSeq2500 sequencer at the Millard and Muriel Jacobs Genetics and Genomics Laboratory California Institute of Technology Pasadena CA for 50 million single ended reads.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP559533     Sox10_neg_17hpf_CNC_1_21310_combined_filtered.fastq.gz fastq 2554400850.0 51088017.0 GSM8751782 r1 0:50 A:739730182;C:537827580;G:551508245;T:725296198;N:38645 50       739730182 537827580 551508245 725296198 38645 SRX27449949 SRS23876470 SRA2058978 Martik Lab, Molecular and Cell Biology, University of California Berkeley Martik Lab, Molecular and Cell Biology, University of California Berkeley                       B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   United States 2025-01-23 Segmentation Embryo Brain Nervous System
38287 38287 SRR1616929 SRX736533 SRS724633 SRP049069 PRJNA264333 A spinal opsin controls early neural activity and drives a behavioral light response GSE62527 Transcriptome Analysis Purpose: using RNA seq as a screening tool to determine candidate genes of interest within a genetically defined neural subpopulation in the zebrafish embryonic spinal cord. Results: The early embryonic spinal cord displays patterns of spontaneous activity that generate the earliest motor behavior in the zebrafish. We show the behavior and the neural activity to be inhibited by environmental levels of light. Since at these young ages the fish is blind and since restricted illumination patterns on the trunk of the fish can elicit a photo response we hypothesized that the photo inhibition is an intrinsic property of the active central pattern generator network within the spinal cord. We FACS isolated cells from this network as well as those from a panneuronal population and sequenced mRNAs. Through differential expression analysis we identified vertebrate ancient long opsin a as a candidate and then further validated its function in the circuit through knockdown and rescue experiments. Overall design: RNA sequencing of 2 FACS purified neural populations from zebrafish spinal cord.   pubmed:25484291   HuC FP+ GSM1528408   tissue:spinal neurons|gal4 driver:HuC|population:panneuronal HuC FP+ Illumina Casava1.8 software used for basecalling. Sequenced reads were mapped to Zv9 using Tophat v1.4.0 FPKMs were generated using Cufflinks v2.1.1 and compared using Cuffdiff Genome build: Zv9 Supplementary files format and content: tab delimited text file with FPKM for each sample spinal neurons Tails dissected free at the level of the 3rd somite and dissociated with trypsin/collagenase before FACS Fluorescent neural cell bodies were FACS sorted into Trizol and flash frozen before total RNA extraction and polyA selection. RNA libraries were prepared for sequencing using standard Illumina protocols 20 hpf embryos were used gal4 driver:HuC|population:panneuronal GSM1528408 GSM1528408: HuC FP+; Danio rerio; RNA Seq GSM1528408   1 Fluorescent neural cell bodies were FACS sorted into Trizol and flash frozen before total RNA extraction and polyA selection. RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM1528408 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP049069     HuCFP_R2.fastq HuCFP_R1.fastq fastq fastq 5590606800.0 27953034.0 GSM1528408 r1 0:100 1:100 A:1550775239;C:1214652319;G:1269909429;T:1544634947;N:10634866 100 100     1550775239 1214652319 1269909429 1544634947 10634866 SRX736533 SRS724633 SRA192701 GEO Isacoff, MCB, UC Berkeley 2 0.90003 0.87337 0.19389 0.18827 0.74594 0.75041 0.50589 0.50314 100 100 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2014-10-20 Segmentation Embryo Brain Nervous System
38288 38288 SRR1616928 SRX736532 SRS724632 SRP049069 PRJNA264333 A spinal opsin controls early neural activity and drives a behavioral light response GSE62527 Transcriptome Analysis Purpose: using RNA seq as a screening tool to determine candidate genes of interest within a genetically defined neural subpopulation in the zebrafish embryonic spinal cord. Results: The early embryonic spinal cord displays patterns of spontaneous activity that generate the earliest motor behavior in the zebrafish. We show the behavior and the neural activity to be inhibited by environmental levels of light. Since at these young ages the fish is blind and since restricted illumination patterns on the trunk of the fish can elicit a photo response we hypothesized that the photo inhibition is an intrinsic property of the active central pattern generator network within the spinal cord. We FACS isolated cells from this network as well as those from a panneuronal population and sequenced mRNAs. Through differential expression analysis we identified vertebrate ancient long opsin a as a candidate and then further validated its function in the circuit through knockdown and rescue experiments. Overall design: RNA sequencing of 2 FACS purified neural populations from zebrafish spinal cord.   pubmed:25484291   1020 FP+ GSM1528407   tissue:spinal neurons|gal4 driver:1020st|population:olig2+ subpopulation 1020 FP+ Illumina Casava1.8 software used for basecalling. Sequenced reads were mapped to Zv9 using Tophat v1.4.0 FPKMs were generated using Cufflinks v2.1.1 and compared using Cuffdiff Genome build: Zv9 Supplementary files format and content: tab delimited text file with FPKM for each sample spinal neurons Tails dissected free at the level of the 3rd somite and dissociated with trypsin/collagenase before FACS Fluorescent neural cell bodies were FACS sorted into Trizol and flash frozen before total RNA extraction and polyA selection. RNA libraries were prepared for sequencing using standard Illumina protocols 20 hpf embryos were used gal4 driver:1020st|population:olig2+ subpopulation GSM1528407 GSM1528407: 1020 FP+; Danio rerio; RNA Seq GSM1528407   1 Fluorescent neural cell bodies were FACS sorted into Trizol and flash frozen before total RNA extraction and polyA selection. RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM1528407 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP049069     1020FP_R2.fastq 1020FP_R1.fastq fastq fastq 9750838400.0 48754192.0 GSM1528407 r1 0:100 1:100 A:2741372249;C:2106643378;G:2204482450;T:2679721349;N:18618974 100 100     2741372249 2106643378 2204482450 2679721349 18618974 SRX736532 SRS724632 SRA192701 GEO Isacoff, MCB, UC Berkeley 2 0.9073 0.88227 0.16046 0.15465 0.74385 0.7469 0.50468 0.50034 100 100 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2014-10-20 Segmentation Embryo Brain Nervous System
55642 55642 SRR10586524 SRX7266915 SRS5761459 SRP234691 PRJNA593445 A single cell transcriptome atlas of the developing zebrafish hindbrain [scRNA Seq] GSE141427 Transcriptome Analysis Purpose: The goal of this study is to understand the progressive patterning of neurogenesis of the developing zebrafish hindbrain. 16hpf 24hpf and 44hpf zebrafish hindbrains were used for single cell RNA sequencing with the aim to uncover hindbrain development. Methods: 40 microdissected hindbrains per each stage were dissociated at loaded into the 10x Genomics Chromium Platform and sequenced using Illumina HiSeq 4000. Conclusions: Our study constitute a resource of hindbrain gene expression during development. We have identified transcriptional programs involved in: rhombomere segmental identity dorso ventral patterning boundary and centre progenitor cells and temporal regulation of neurogenesis. Overall design: 16hpf 24hpf 44hpf hindbrains were used for single cell RNA sequencing 10xGenomics Chromium Platform and sequenced using Illumina HiSeq 4000. parent bioproject:PRJNA593433 pubmed:32094115   16hpf Hindbrain scRNA seq GSM4202680   source name:Dissected hindbrain and surrounding tissues|tissue:Dissected hindbrain and surrounding tissues|Stage:16hpf|strain:LondonAB|genotype:wt|growth:25°C 16hpf Hindbrain scRNA seq 10X’s Cell Ranger software was used to de multiplex Illumina BCL output create fastq files and generate single cell feature counts for each library Three 10X libraries representing the 16hpf 24hpf and 44hpf stages of embryonic development were aggregated using the 10X software “cellranger aggr” function which sub samples reads such that all libraries have the same effective sequencing depth. Genome build: GRCz10 Supplementary files format and content: Tab delimited text file containing aggregated Cell Ranger counts Dissected hindbrain and surrounding tissues   Embryos were decorionated and deyolked in DMEM with high Glucose no Glutamine no Calcium 11530556 Gibco; hindbrains were micro dissected using 0.33mm micro fine sterile needles; 40 tissues per stage were polled together and immediately processed for cell dissociation; samples were incubated with FACS max cell dissociation solution T200100 Amsbio supplemented with 1mg/ml Papain 10108014001 Sigma for 25min at 37°C and resuspended one time during incubation; cells were then transferred to HBSS no calcium no magnesium no phenol red; 11140035 ThermoFisher Scientific supplemented with 5%FBS rock inhibitor Y 27632 Stem Cell Technologies and 1X non essential amino acids 11140035 ThermoFisher Scientific; cells were further disaggregated by pipetting and filtered several times using 20µm strainers 130 101 812 Miltenyi Biotech GmbH RNA libraries were prepared for sequencing using Chromium Single Cell three prime v2 protocol PN 120233 10X Genomics; cDNA amplification involved 12 PCR cycles   tissue:Dissected hindbrain and surrounding tissues|Stage:16hpf|strain:LondonAB|genotype:wt|growth:25°C GSM4202680 GSM4202680: 16hpf Hindbrain scRNA seq; Danio rerio; RNA Seq GSM4202680   1 Embryos were decorionated and deyolked in DMEM with high Glucose no Glutamine no Calcium 11530556 Gibco; hindbrains were micro dissected using 0.33mm micro fine sterile needles; 40 tissues per stage were polled together and immediately processed for cell dissociation; samples were incubated with FACS max cell dissociation solution T200100 Amsbio supplemented with 1mg/ml Papain 10108014001 Sigma for 25min at 37°C and resuspended one time during incubation; cells were then transferred to HBSS no calcium no magnesium no phenol red; 11140035 ThermoFisher Scientific supplemented with 5%FBS rock inhibitor Y 27632 Stem Cell Technologies and 1X non essential amino acids 11140035 ThermoFisher Scientific; cells were further disaggregated by pipetting and filtered several times using 20µm strainers 130 101 812 Miltenyi Biotech GmbH RNA libraries were prepared for sequencing using Chromium Single Cell three prime v2 protocol PN 120233 10X Genomics; cDNA amplification involved 12 PCR cycles GEO Accession:GSM4202680 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP234691   loader:fastq load.py|options: readTypes=TTB read1PairFiles=TAM677A1 S2 L008 I1 001.fastq.gz read2PairFiles=TAM677A1 S2 L008 R1 001.fastq.gz read3PairFiles=TAM677A1 S2 L008 R2 001.fastq.gz TAM677A1_S2_L008_R2_001.fastq.gz TAM677A1_S2_L008_R1_001.fastq.gz TAM677A1_S2_L008_I1_001.fastq.gz fastq fastq fastq 72155333460.0 343596826.0 GSM4202680 r1 0:8 1:101 2:101 A:16535121466;C:12722320120;G:13646437290;T:29245478028;N:5976556 8 101 101   16535121466 12722320120 13646437290 29245478028 5976556 SRX7266915 SRS5761459 SRA1006557 GEO The Francis Crick Institute 1 0.91053   0.09489   0.848   0.50461   101   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United Kingdom 2019-12-04 Segmentation Embryo Brain Nervous System
61293 61293 SRR12661692 SRX9142578 SRS7383882 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   zBr20hpf3 S1 GSM4793195   source name:zebrafish brain|tissue:brain|developmental stage:20hpf zBr20hpf3 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 cont… 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:20hpf GSM4793195 GSM4793195: zBr20hpf3 S1; Danio rerio; RNA Seq GSM4793195   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:GSM4793195 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP282920   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=zBr20hpf3 S1 L001 I1 001.fastq.gz read2PairFiles=zBr20hpf3 S1 L001 R1 001.fastq.gz read3PairFiles=zBr20hpf3 S1 L001 R2 001.fastq.gz zBr20hpf3_S1_L001_I1_001.fastq.gz zBr20hpf3_S1_L001_R1_001.fastq.gz zBr20hpf3_S1_L001_R2_001.fastq.gz fastq fastq fastq 11498972820.0 124988835.0 GSM4793195 r1 0:8 1:26 2:58 A:3133794084;C:2522668218;G:2829499377;T:3008689496;N:4321645 8 26 58   3133794084 2522668218 2829499377 3008689496 4321645 SRX9142578 SRS7383882 SRA1127180 GEO Harvard University 1 0.93284   0.13615   0.79044   0.48806   58   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2020-09-17 Segmentation Embryo Brain Nervous System
61294 61294 SRR12661693 SRX9142578 SRS7383882 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   zBr20hpf3 S1 GSM4793195   source name:zebrafish brain|tissue:brain|developmental stage:20hpf zBr20hpf3 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 cont… 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:20hpf GSM4793195 GSM4793195: zBr20hpf3 S1; Danio rerio; RNA Seq GSM4793195   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:GSM4793195 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP282920   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=zBr20hpf3 S1 L002 I1 001.fastq.gz read2PairFiles=zBr20hpf3 S1 L002 R1 001.fastq.gz read3PairFiles=zBr20hpf3 S1 L002 R2 001.fastq.gz zBr20hpf3_S1_L002_I1_001.fastq.gz zBr20hpf3_S1_L002_R1_001.fastq.gz zBr20hpf3_S1_L002_R2_001.fastq.gz fastq fastq fastq 10641572288.0 115669264.0 GSM4793195 r2 0:8 1:26 2:58 A:2966322006;C:2338158431;G:2537148329;T:2796104125;N:3839397 8 26 58   2966322006 2338158431 2537148329 2796104125 3839397 SRX9142578 SRS7383882 SRA1127180 GEO Harvard University 1 0.93106   0.14611   0.8144   0.50908   58   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2020-09-17 Segmentation Embryo Brain Nervous System
61295 61295 SRR12661694 SRX9142578 SRS7383882 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   zBr20hpf3 S1 GSM4793195   source name:zebrafish brain|tissue:brain|developmental stage:20hpf zBr20hpf3 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 cont… 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:20hpf GSM4793195 GSM4793195: zBr20hpf3 S1; Danio rerio; RNA Seq GSM4793195   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:GSM4793195 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP282920   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=zBr20hpf3 S1 L003 I1 001.fastq.gz read2PairFiles=zBr20hpf3 S1 L003 R1 001.fastq.gz read3PairFiles=zBr20hpf3 S1 L003 R2 001.fastq.gz zBr20hpf3_S1_L003_I1_001.fastq.gz zBr20hpf3_S1_L003_R1_001.fastq.gz zBr20hpf3_S1_L003_R2_001.fastq.gz fastq fastq fastq 10765850120.0 117020110.0 GSM4793195 r3 0:8 1:26 2:58 A:2982609518;C:2360548322;G:2590598329;T:2829989645;N:2104306 8 26 58   2982609518 2360548322 2590598329 2829989645 2104306 SRX9142578 SRS7383882 SRA1127180 GEO Harvard University 1 0.93165   0.14318   0.80379   0.50107   58   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2020-09-17 Segmentation Embryo Brain Nervous System
61296 61296 SRR12661695 SRX9142578 SRS7383882 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   zBr20hpf3 S1 GSM4793195   source name:zebrafish brain|tissue:brain|developmental stage:20hpf zBr20hpf3 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 cont… 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:20hpf GSM4793195 GSM4793195: zBr20hpf3 S1; Danio rerio; RNA Seq GSM4793195   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:GSM4793195 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP282920   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=zBr20hpf3 S1 L004 I1 001.fastq.gz read2PairFiles=zBr20hpf3 S1 L004 R1 001.fastq.gz read3PairFiles=zBr20hpf3 S1 L004 R2 001.fastq.gz zBr20hpf3_S1_L004_I1_001.fastq.gz zBr20hpf3_S1_L004_R1_001.fastq.gz zBr20hpf3_S1_L004_R2_001.fastq.gz fastq fastq fastq 10730257436.0 116633233.0 GSM4793195 r4 0:8 1:26 2:58 A:2987923739;C:2354670735;G:2563401857;T:2822306276;N:1954829 8 26 58   2987923739 2354670735 2563401857 2822306276 1954829 SRX9142578 SRS7383882 SRA1127180 GEO Harvard University 1 0.9314   0.14668   0.81598   0.5019   58   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2020-09-17 Segmentation Embryo Brain Nervous System
61297 61297 SRR12661688 SRX9142577 SRS7383881 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   zBr20hpf2 S2 GSM4793194   source name:zebrafish brain|tissue:brain|developmental stage:20hpf zBr20hpf2 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 cont… 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:20hpf GSM4793194 GSM4793194: zBr20hpf2 S2; Danio rerio; RNA Seq GSM4793194   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:GSM4793194 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP282920   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=zBr20hpf2 S2 L001 I1 001.fastq.gz read2PairFiles=zBr20hpf2 S2 L001 R1 001.fastq.gz read3PairFiles=zBr20hpf2 S2 L001 R2 001.fastq.gz zBr20hpf2_S2_L001_I1_001.fastq.gz zBr20hpf2_S2_L001_R1_001.fastq.gz zBr20hpf2_S2_L001_R2_001.fastq.gz fastq fastq fastq 1498814688.0 16291464.0 GSM4793194 r1 0:8 1:26 2:58 A:411909554;C:335143931;G:367761096;T:383644519;N:355588 8 26 58   411909554 335143931 367761096 383644519 355588 SRX9142577 SRS7383881 SRA1127180 GEO Harvard University 1 0.94387   0.09723   0.84124   0.48253   58   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2020-09-17 Segmentation Embryo Brain Nervous System
61298 61298 SRR12661689 SRX9142577 SRS7383881 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   zBr20hpf2 S2 GSM4793194   source name:zebrafish brain|tissue:brain|developmental stage:20hpf zBr20hpf2 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 cont… 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:20hpf GSM4793194 GSM4793194: zBr20hpf2 S2; Danio rerio; RNA Seq GSM4793194   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:GSM4793194 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP282920   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=zBr20hpf2 S2 L002 I1 001.fastq.gz read2PairFiles=zBr20hpf2 S2 L002 R1 001.fastq.gz read3PairFiles=zBr20hpf2 S2 L002 R2 001.fastq.gz zBr20hpf2_S2_L002_I1_001.fastq.gz zBr20hpf2_S2_L002_R1_001.fastq.gz zBr20hpf2_S2_L002_R2_001.fastq.gz fastq fastq fastq 1474290800.0 16024900.0 GSM4793194 r2 0:8 1:26 2:58 A:407737074;C:329798024;G:359432561;T:377022278;N:300863 8 26 58   407737074 329798024 359432561 377022278 300863 SRX9142577 SRS7383881 SRA1127180 GEO Harvard University 1 0.94327   0.09995   0.84283   0.4851   58   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2020-09-17 Segmentation Embryo Brain Nervous System
61299 61299 SRR12661690 SRX9142577 SRS7383881 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   zBr20hpf2 S2 GSM4793194   source name:zebrafish brain|tissue:brain|developmental stage:20hpf zBr20hpf2 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 cont… 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:20hpf GSM4793194 GSM4793194: zBr20hpf2 S2; Danio rerio; RNA Seq GSM4793194   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:GSM4793194 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP282920   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=zBr20hpf2 S2 L003 I1 001.fastq.gz read2PairFiles=zBr20hpf2 S2 L003 R1 001.fastq.gz read3PairFiles=zBr20hpf2 S2 L003 R2 001.fastq.gz zBr20hpf2_S2_L003_I1_001.fastq.gz zBr20hpf2_S2_L003_R1_001.fastq.gz zBr20hpf2_S2_L003_R2_001.fastq.gz fastq fastq fastq 1447109492.0 15729451.0 GSM4793194 r3 0:8 1:26 2:58 A:398119555;C:322813636;G:354802892;T:371154114;N:219295 8 26 58   398119555 322813636 354802892 371154114 219295 SRX9142577 SRS7383881 SRA1127180 GEO Harvard University 1 0.94367   0.09812   0.84189   0.48431   58   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2020-09-17 Segmentation Embryo Brain Nervous System
61300 61300 SRR12661691 SRX9142577 SRS7383881 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   zBr20hpf2 S2 GSM4793194   source name:zebrafish brain|tissue:brain|developmental stage:20hpf zBr20hpf2 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 cont… 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:20hpf GSM4793194 GSM4793194: zBr20hpf2 S2; Danio rerio; RNA Seq GSM4793194   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:GSM4793194 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP282920   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=zBr20hpf2 S2 L004 I1 001.fastq.gz read2PairFiles=zBr20hpf2 S2 L004 R1 001.fastq.gz read3PairFiles=zBr20hpf2 S2 L004 R2 001.fastq.gz zBr20hpf2_S2_L004_I1_001.fastq.gz zBr20hpf2_S2_L004_R1_001.fastq.gz zBr20hpf2_S2_L004_R2_001.fastq.gz fastq fastq fastq 1504028144.0 16348132.0 GSM4793194 r4 0:8 1:26 2:58 A:412410843;C:336192539;G:370588866;T:384647822;N:188074 8 26 58   412410843 336192539 370588866 384647822 188074 SRX9142577 SRS7383881 SRA1127180 GEO Harvard University 1 0.94439   0.0968   0.83761   0.48662   58   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2020-09-17 Segmentation Embryo Brain Nervous System
61301 61301 SRR12661684 SRX9142576 SRS7383880 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   zBr20hpf1 S1 GSM4793193   source name:zebrafish brain|tissue:brain|developmental stage:20hpf zBr20hpf1 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 cont… 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:20hpf GSM4793193 GSM4793193: zBr20hpf1 S1; Danio rerio; RNA Seq GSM4793193   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:GSM4793193 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP282920   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=zBr20hpf1 S1 L001 I1 001.fastq.gz read2PairFiles=zBr20hpf1 S1 L001 R1 001.fastq.gz read3PairFiles=zBr20hpf1 S1 L001 R2 001.fastq.gz zBr20hpf1_S1_L001_I1_001.fastq.gz zBr20hpf1_S1_L001_R1_001.fastq.gz zBr20hpf1_S1_L001_R2_001.fastq.gz fastq fastq fastq 1686610056.0 18332718.0 GSM4793193 r1 0:8 1:26 2:58 A:462763372;C:374399298;G:409698682;T:439340454;N:408250 8 26 58   462763372 374399298 409698682 439340454 408250 SRX9142576 SRS7383880 SRA1127180 GEO Harvard University 1 0.94536   0.10202   0.83851   0.47937   58   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2020-09-17 Segmentation Embryo Brain Nervous System
61302 61302 SRR12661685 SRX9142576 SRS7383880 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   zBr20hpf1 S1 GSM4793193   source name:zebrafish brain|tissue:brain|developmental stage:20hpf zBr20hpf1 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 cont… 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:20hpf GSM4793193 GSM4793193: zBr20hpf1 S1; Danio rerio; RNA Seq GSM4793193   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:GSM4793193 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP282920   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=zBr20hpf1 S1 L002 I1 001.fastq.gz read2PairFiles=zBr20hpf1 S1 L002 R1 001.fastq.gz read3PairFiles=zBr20hpf1 S1 L002 R2 001.fastq.gz zBr20hpf1_S1_L002_I1_001.fastq.gz zBr20hpf1_S1_L002_R1_001.fastq.gz zBr20hpf1_S1_L002_R2_001.fastq.gz fastq fastq fastq 1657273464.0 18013842.0 GSM4793193 r2 0:8 1:26 2:58 A:456965746;C:368071443;G:400521589;T:431378528;N:336158 8 26 58   456965746 368071443 400521589 431378528 336158 SRX9142576 SRS7383880 SRA1127180 GEO Harvard University 1 0.94556   0.1012   0.83638   0.48393   58   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2020-09-17 Segmentation Embryo Brain Nervous System
61303 61303 SRR12661686 SRX9142576 SRS7383880 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   zBr20hpf1 S1 GSM4793193   source name:zebrafish brain|tissue:brain|developmental stage:20hpf zBr20hpf1 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 cont… 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:20hpf GSM4793193 GSM4793193: zBr20hpf1 S1; Danio rerio; RNA Seq GSM4793193   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:GSM4793193 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP282920   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=zBr20hpf1 S1 L003 I1 001.fastq.gz read2PairFiles=zBr20hpf1 S1 L003 R1 001.fastq.gz read3PairFiles=zBr20hpf1 S1 L003 R2 001.fastq.gz zBr20hpf1_S1_L003_I1_001.fastq.gz zBr20hpf1_S1_L003_R1_001.fastq.gz zBr20hpf1_S1_L003_R2_001.fastq.gz fastq fastq fastq 1637570100.0 17799675.0 GSM4793193 r3 0:8 1:26 2:58 A:449755610;C:362812678;G:397503125;T:427235434;N:263253 8 26 58   449755610 362812678 397503125 427235434 263253 SRX9142576 SRS7383880 SRA1127180 GEO Harvard University 1 0.94465   0.10236   0.83532   0.48247   58   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2020-09-17 Segmentation Embryo Brain Nervous System
61304 61304 SRR12661687 SRX9142576 SRS7383880 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   zBr20hpf1 S1 GSM4793193   source name:zebrafish brain|tissue:brain|developmental stage:20hpf zBr20hpf1 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 cont… 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:20hpf GSM4793193 GSM4793193: zBr20hpf1 S1; Danio rerio; RNA Seq GSM4793193   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:GSM4793193 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP282920   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=zBr20hpf1 S1 L004 I1 001.fastq.gz read2PairFiles=zBr20hpf1 S1 L004 R1 001.fastq.gz read3PairFiles=zBr20hpf1 S1 L004 R2 001.fastq.gz zBr20hpf1_S1_L004_I1_001.fastq.gz zBr20hpf1_S1_L004_R1_001.fastq.gz zBr20hpf1_S1_L004_R2_001.fastq.gz fastq fastq fastq 1691787724.0 18388997.0 GSM4793193 r4 0:8 1:26 2:58 A:463427943;C:375377365;G:412594467;T:440177154;N:210795 8 26 58   463427943 375377365 412594467 440177154 210795 SRX9142576 SRS7383880 SRA1127180 GEO Harvard University 1 0.94532   0.09928   0.83305   0.4692   58   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2020-09-17 Segmentation Embryo Brain Nervous System
61305 61305 SRR12661552 SRX9142575 SRS7383879 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   zBr18hpf2 18S S4 GSM4793192   source name:zebrafish brain|tissue:brain|developmental stage:18hpf 18somites zBr18hpf2 18S 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 cont… 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:18hpf 18somites GSM4793192 GSM4793192: zBr18hpf2 18S S4; Danio rerio; RNA Seq GSM4793192   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:GSM4793192 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP282920   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=zBr18hpf2 18S S4 L001 I1 001.fastq.gz read2PairFiles=zBr18hpf2 18S S4 L001 R1 001.fastq.gz read3PairFiles=zBr18hpf2 18S S4 L001 R2 001.fastq.gz zBr18hpf2_18S_S4_L001_I1_001.fastq.gz zBr18hpf2_18S_S4_L001_R1_001.fastq.gz zBr18hpf2_18S_S4_L001_R2_001.fastq.gz fastq fastq fastq 2245095320.0 24403210.0 GSM4793192 r1 0:8 1:26 2:58 A:613524159;C:501131702;G:550080994;T:580162092;N:196373 8 26 58   613524159 501131702 550080994 580162092 196373 SRX9142575 SRS7383879 SRA1127180 GEO Harvard University 1 0.94061   0.12174   0.81639   0.47871   58   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2020-09-17 Segmentation Embryo Brain Nervous System
61306 61306 SRR12661553 SRX9142575 SRS7383879 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   zBr18hpf2 18S S4 GSM4793192   source name:zebrafish brain|tissue:brain|developmental stage:18hpf 18somites zBr18hpf2 18S 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 cont… 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:18hpf 18somites GSM4793192 GSM4793192: zBr18hpf2 18S S4; Danio rerio; RNA Seq GSM4793192   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:GSM4793192 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP282920   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=zBr18hpf2 18S S4 L002 I1 001.fastq.gz read2PairFiles=zBr18hpf2 18S S4 L002 R1 001.fastq.gz read3PairFiles=zBr18hpf2 18S S4 L002 R2 001.fastq.gz zBr18hpf2_18S_S4_L002_I1_001.fastq.gz zBr18hpf2_18S_S4_L002_R1_001.fastq.gz zBr18hpf2_18S_S4_L002_R2_001.fastq.gz fastq fastq fastq 2159426116.0 23472023.0 GSM4793192 r2 0:8 1:26 2:58 A:591755308;C:482099749;G:527517530;T:557879947;N:173582 8 26 58   591755308 482099749 527517530 557879947 173582 SRX9142575 SRS7383879 SRA1127180 GEO Harvard University 1 0.9424   0.1235   0.81799   0.50256   58   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2020-09-17 Segmentation Embryo Brain Nervous System
61307 61307 SRR12661554 SRX9142575 SRS7383879 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   zBr18hpf2 18S S4 GSM4793192   source name:zebrafish brain|tissue:brain|developmental stage:18hpf 18somites zBr18hpf2 18S 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 cont… 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:18hpf 18somites GSM4793192 GSM4793192: zBr18hpf2 18S S4; Danio rerio; RNA Seq GSM4793192   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:GSM4793192 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP282920   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=zBr18hpf2 18S S4 L003 I1 001.fastq.gz read2PairFiles=zBr18hpf2 18S S4 L003 R1 001.fastq.gz read3PairFiles=zBr18hpf2 18S S4 L003 R2 001.fastq.gz zBr18hpf2_18S_S4_L003_I1_001.fastq.gz zBr18hpf2_18S_S4_L003_R1_001.fastq.gz zBr18hpf2_18S_S4_L003_R2_001.fastq.gz fastq fastq fastq 2207837896.0 23998238.0 GSM4793192 r3 0:8 1:26 2:58 A:603401720;C:492449088;G:541664815;T:570168873;N:153400 8 26 58   603401720 492449088 541664815 570168873 153400 SRX9142575 SRS7383879 SRA1127180 GEO Harvard University 1 0.9405   0.12318   0.81363   0.504   58   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2020-09-17 Segmentation Embryo Brain Nervous System
61308 61308 SRR12661555 SRX9142575 SRS7383879 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   zBr18hpf2 18S S4 GSM4793192   source name:zebrafish brain|tissue:brain|developmental stage:18hpf 18somites zBr18hpf2 18S 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 cont… 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:18hpf 18somites GSM4793192 GSM4793192: zBr18hpf2 18S S4; Danio rerio; RNA Seq GSM4793192   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:GSM4793192 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP282920   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=zBr18hpf2 18S S4 L004 I1 001.fastq.gz read2PairFiles=zBr18hpf2 18S S4 L004 R1 001.fastq.gz read3PairFiles=zBr18hpf2 18S S4 L004 R2 001.fastq.gz zBr18hpf2_18S_S4_L004_I1_001.fastq.gz zBr18hpf2_18S_S4_L004_R1_001.fastq.gz zBr18hpf2_18S_S4_L004_R2_001.fastq.gz fastq fastq fastq 2185438104.0 23754762.0 GSM4793192 r4 0:8 1:26 2:58 A:597870424;C:487183564;G:535849987;T:564386371;N:147758 8 26 58   597870424 487183564 535849987 564386371 147758 SRX9142575 SRS7383879 SRA1127180 GEO Harvard University 1 0.94156   0.12132   0.81637   0.49546   58   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2020-09-17 Segmentation Embryo Brain Nervous System
61309 61309 SRR12661548 SRX9142574 SRS7383878 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   zBr18hpf1 18S S3 GSM4793191   source name:zebrafish brain|tissue:brain|developmental stage:18hpf 18somites zBr18hpf1 18S 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 cont… 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:18hpf 18somites GSM4793191 GSM4793191: zBr18hpf1 18S S3; Danio rerio; RNA Seq GSM4793191   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:GSM4793191 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP282920   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=zBr18hpf1 18S S3 L001 I1 001.fastq.gz read2PairFiles=zBr18hpf1 18S S3 L001 R1 001.fastq.gz read3PairFiles=zBr18hpf1 18S S3 L001 R2 001.fastq.gz zBr18hpf1_18S_S3_L001_I1_001.fastq.gz zBr18hpf1_18S_S3_L001_R1_001.fastq.gz zBr18hpf1_18S_S3_L001_R2_001.fastq.gz fastq fastq fastq 2214588488.0 24071614.0 GSM4793191 r1 0:8 1:26 2:58 A:602278908;C:489477732;G:542009992;T:580626962;N:194894 8 26 58   602278908 489477732 542009992 580626962 194894 SRX9142574 SRS7383878 SRA1127180 GEO Harvard University 1 0.94194   0.11869   0.81805   0.49559   58   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2020-09-17 Segmentation Embryo Brain Nervous System
61310 61310 SRR12661549 SRX9142574 SRS7383878 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   zBr18hpf1 18S S3 GSM4793191   source name:zebrafish brain|tissue:brain|developmental stage:18hpf 18somites zBr18hpf1 18S 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 cont… 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:18hpf 18somites GSM4793191 GSM4793191: zBr18hpf1 18S S3; Danio rerio; RNA Seq GSM4793191   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:GSM4793191 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP282920   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=zBr18hpf1 18S S3 L002 I1 001.fastq.gz read2PairFiles=zBr18hpf1 18S S3 L002 R1 001.fastq.gz read3PairFiles=zBr18hpf1 18S S3 L002 R2 001.fastq.gz zBr18hpf1_18S_S3_L002_I1_001.fastq.gz zBr18hpf1_18S_S3_L002_R1_001.fastq.gz zBr18hpf1_18S_S3_L002_R2_001.fastq.gz fastq fastq fastq 2129138704.0 23142812.0 GSM4793191 r2 0:8 1:26 2:58 A:580775137;C:470741441;G:519375169;T:558073432;N:173525 8 26 58   580775137 470741441 519375169 558073432 173525 SRX9142574 SRS7383878 SRA1127180 GEO Harvard University 1 0.94091   0.11843   0.8214   0.49562   58   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2020-09-17 Segmentation Embryo Brain Nervous System
61311 61311 SRR12661550 SRX9142574 SRS7383878 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   zBr18hpf1 18S S3 GSM4793191   source name:zebrafish brain|tissue:brain|developmental stage:18hpf 18somites zBr18hpf1 18S 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 cont… 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:18hpf 18somites GSM4793191 GSM4793191: zBr18hpf1 18S S3; Danio rerio; RNA Seq GSM4793191   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:GSM4793191 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP282920   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=zBr18hpf1 18S S3 L003 I1 001.fastq.gz read2PairFiles=zBr18hpf1 18S S3 L003 R1 001.fastq.gz read3PairFiles=zBr18hpf1 18S S3 L003 R2 001.fastq.gz zBr18hpf1_18S_S3_L003_I1_001.fastq.gz zBr18hpf1_18S_S3_L003_R1_001.fastq.gz zBr18hpf1_18S_S3_L003_R2_001.fastq.gz fastq fastq fastq 2178649056.0 23680968.0 GSM4793191 r3 0:8 1:26 2:58 A:592436446;C:481175426;G:534076582;T:570810730;N:149872 8 26 58   592436446 481175426 534076582 570810730 149872 SRX9142574 SRS7383878 SRA1127180 GEO Harvard University 1 0.94301   0.11942   0.81836   0.50631   58   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2020-09-17 Segmentation Embryo Brain Nervous System
61312 61312 SRR12661551 SRX9142574 SRS7383878 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   zBr18hpf1 18S S3 GSM4793191   source name:zebrafish brain|tissue:brain|developmental stage:18hpf 18somites zBr18hpf1 18S 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 cont… 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:18hpf 18somites GSM4793191 GSM4793191: zBr18hpf1 18S S3; Danio rerio; RNA Seq GSM4793191   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:GSM4793191 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP282920   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=zBr18hpf1 18S S3 L004 I1 001.fastq.gz read2PairFiles=zBr18hpf1 18S S3 L004 R1 001.fastq.gz read3PairFiles=zBr18hpf1 18S S3 L004 R2 001.fastq.gz zBr18hpf1_18S_S3_L004_I1_001.fastq.gz zBr18hpf1_18S_S3_L004_R1_001.fastq.gz zBr18hpf1_18S_S3_L004_R2_001.fastq.gz fastq fastq fastq 2155279216.0 23426948.0 GSM4793191 r4 0:8 1:26 2:58 A:586891679;C:475865156;G:527755230;T:564621403;N:145748 8 26 58   586891679 475865156 527755230 564621403 145748 SRX9142574 SRS7383878 SRA1127180 GEO Harvard University 1 0.94308   0.11824   0.81891   0.50058   58   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2020-09-17 Segmentation Embryo Brain Nervous System
61313 61313 SRR12661544 SRX9142573 SRS7383877 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   zBr16hpf2 14S S2 GSM4793190   source name:zebrafish brain|tissue:brain|developmental stage:16hpf 14somites zBr16hpf2 14S 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 cont… 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:16hpf 14somites GSM4793190 GSM4793190: zBr16hpf2 14S S2; Danio rerio; RNA Seq GSM4793190   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:GSM4793190 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP282920   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=zBr16hpf2 14S S2 L001 I1 001.fastq.gz read2PairFiles=zBr16hpf2 14S S2 L001 R1 001.fastq.gz read3PairFiles=zBr16hpf2 14S S2 L001 R2 001.fastq.gz zBr16hpf2_14S_S2_L001_I1_001.fastq.gz zBr16hpf2_14S_S2_L001_R1_001.fastq.gz zBr16hpf2_14S_S2_L001_R2_001.fastq.gz fastq fastq fastq 2073007572.0 22532691.0 GSM4793190 r1 0:8 1:26 2:58 A:572862969;C:454174472;G:503190354;T:542601337;N:178440 8 26 58   572862969 454174472 503190354 542601337 178440 SRX9142573 SRS7383877 SRA1127180 GEO Harvard University 1 0.94007   0.1204   0.82629   0.49735   58   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2020-09-17 Segmentation Embryo Brain Nervous System
61314 61314 SRR12661545 SRX9142573 SRS7383877 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   zBr16hpf2 14S S2 GSM4793190   source name:zebrafish brain|tissue:brain|developmental stage:16hpf 14somites zBr16hpf2 14S 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 cont… 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:16hpf 14somites GSM4793190 GSM4793190: zBr16hpf2 14S S2; Danio rerio; RNA Seq GSM4793190   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:GSM4793190 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP282920   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=zBr16hpf2 14S S2 L002 I1 001.fastq.gz read2PairFiles=zBr16hpf2 14S S2 L002 R1 001.fastq.gz read3PairFiles=zBr16hpf2 14S S2 L002 R2 001.fastq.gz zBr16hpf2_14S_S2_L002_I1_001.fastq.gz zBr16hpf2_14S_S2_L002_R1_001.fastq.gz zBr16hpf2_14S_S2_L002_R2_001.fastq.gz fastq fastq fastq 1991134748.0 21642769.0 GSM4793190 r2 0:8 1:26 2:58 A:552124530;C:436378536;G:481647901;T:520828998;N:154783 8 26 58   552124530 436378536 481647901 520828998 154783 SRX9142573 SRS7383877 SRA1127180 GEO Harvard University 1 0.94071   0.12012   0.82741   0.48929   58   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2020-09-17 Segmentation Embryo Brain Nervous System
61315 61315 SRR12661546 SRX9142573 SRS7383877 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   zBr16hpf2 14S S2 GSM4793190   source name:zebrafish brain|tissue:brain|developmental stage:16hpf 14somites zBr16hpf2 14S 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 cont… 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:16hpf 14somites GSM4793190 GSM4793190: zBr16hpf2 14S S2; Danio rerio; RNA Seq GSM4793190   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:GSM4793190 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP282920   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=zBr16hpf2 14S S2 L003 I1 001.fastq.gz read2PairFiles=zBr16hpf2 14S S2 L003 R1 001.fastq.gz read3PairFiles=zBr16hpf2 14S S2 L003 R2 001.fastq.gz zBr16hpf2_14S_S2_L003_I1_001.fastq.gz zBr16hpf2_14S_S2_L003_R1_001.fastq.gz zBr16hpf2_14S_S2_L003_R2_001.fastq.gz fastq fastq fastq 2019616752.0 21952356.0 GSM4793190 r3 0:8 1:26 2:58 A:558279607;C:442003592;G:490855535;T:528340468;N:137550 8 26 58   558279607 442003592 490855535 528340468 137550 SRX9142573 SRS7383877 SRA1127180 GEO Harvard University 1 0.94077   0.1202   0.82449   0.4893   58   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2020-09-17 Segmentation Embryo Brain Nervous System
61316 61316 SRR12661547 SRX9142573 SRS7383877 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   zBr16hpf2 14S S2 GSM4793190   source name:zebrafish brain|tissue:brain|developmental stage:16hpf 14somites zBr16hpf2 14S 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 cont… 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:16hpf 14somites GSM4793190 GSM4793190: zBr16hpf2 14S S2; Danio rerio; RNA Seq GSM4793190   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:GSM4793190 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP282920   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=zBr16hpf2 14S S2 L004 I1 001.fastq.gz read2PairFiles=zBr16hpf2 14S S2 L004 R1 001.fastq.gz read3PairFiles=zBr16hpf2 14S S2 L004 R2 001.fastq.gz zBr16hpf2_14S_S2_L004_I1_001.fastq.gz zBr16hpf2_14S_S2_L004_R1_001.fastq.gz zBr16hpf2_14S_S2_L004_R2_001.fastq.gz fastq fastq fastq 2002314680.0 21764290.0 GSM4793190 r4 0:8 1:26 2:58 A:554197446;C:438127593;G:486247652;T:523609318;N:132671 8 26 58   554197446 438127593 486247652 523609318 132671 SRX9142573 SRS7383877 SRA1127180 GEO Harvard University 1 0.94124   0.11893   0.82556   0.49886   58   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2020-09-17 Segmentation Embryo Brain Nervous System
61317 61317 SRR12661540 SRX9142572 SRS7383876 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   zBr16hpf1 14S S1 GSM4793189   source name:zebrafish brain|tissue:brain|developmental stage:16hpf 14somites zBr16hpf1 14S 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 cont… 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:16hpf 14somites GSM4793189 GSM4793189: zBr16hpf1 14S S1; Danio rerio; RNA Seq GSM4793189   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:GSM4793189 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP282920   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=zBr16hpf1 14S S1 L001 I1 001.fastq.gz read2PairFiles=zBr16hpf1 14S S1 L001 R1 001.fastq.gz read3PairFiles=zBr16hpf1 14S S1 L001 R2 001.fastq.gz zBr16hpf1_14S_S1_L001_I1_001.fastq.gz zBr16hpf1_14S_S1_L001_R1_001.fastq.gz zBr16hpf1_14S_S1_L001_R2_001.fastq.gz fastq fastq fastq 2466217780.0 26806715.0 GSM4793189 r1 0:8 1:26 2:58 A:674841173;C:544628387;G:596838231;T:649690435;N:219554 8 26 58   674841173 544628387 596838231 649690435 219554 SRX9142572 SRS7383876 SRA1127180 GEO Harvard University 1 0.94159   0.11655   0.82347   0.48113   58   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2020-09-17 Segmentation Embryo Brain Nervous System
61318 61318 SRR12661541 SRX9142572 SRS7383876 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   zBr16hpf1 14S S1 GSM4793189   source name:zebrafish brain|tissue:brain|developmental stage:16hpf 14somites zBr16hpf1 14S 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 cont… 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:16hpf 14somites GSM4793189 GSM4793189: zBr16hpf1 14S S1; Danio rerio; RNA Seq GSM4793189   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:GSM4793189 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP282920   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=zBr16hpf1 14S S1 L002 I1 001.fastq.gz read2PairFiles=zBr16hpf1 14S S1 L002 R1 001.fastq.gz read3PairFiles=zBr16hpf1 14S S1 L002 R2 001.fastq.gz zBr16hpf1_14S_S1_L002_I1_001.fastq.gz zBr16hpf1_14S_S1_L002_R1_001.fastq.gz zBr16hpf1_14S_S1_L002_R2_001.fastq.gz fastq fastq fastq 2372103896.0 25783738.0 GSM4793189 r2 0:8 1:26 2:58 A:651005451;C:524063378;G:572137084;T:624705675;N:192308 8 26 58   651005451 524063378 572137084 624705675 192308 SRX9142572 SRS7383876 SRA1127180 GEO Harvard University 1 0.9403   0.11673   0.82556   0.49807   58   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2020-09-17 Segmentation Embryo Brain Nervous System
61319 61319 SRR12661542 SRX9142572 SRS7383876 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   zBr16hpf1 14S S1 GSM4793189   source name:zebrafish brain|tissue:brain|developmental stage:16hpf 14somites zBr16hpf1 14S 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 cont… 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:16hpf 14somites GSM4793189 GSM4793189: zBr16hpf1 14S S1; Danio rerio; RNA Seq GSM4793189   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:GSM4793189 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP282920   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=zBr16hpf1 14S S1 L003 I1 001.fastq.gz read2PairFiles=zBr16hpf1 14S S1 L003 R1 001.fastq.gz read3PairFiles=zBr16hpf1 14S S1 L003 R2 001.fastq.gz zBr16hpf1_14S_S1_L003_I1_001.fastq.gz zBr16hpf1_14S_S1_L003_R1_001.fastq.gz zBr16hpf1_14S_S1_L003_R2_001.fastq.gz fastq fastq fastq 2426820620.0 26378485.0 GSM4793189 r3 0:8 1:26 2:58 A:664096049;C:535519834;G:588171519;T:638867831;N:165387 8 26 58   664096049 535519834 588171519 638867831 165387 SRX9142572 SRS7383876 SRA1127180 GEO Harvard University 1 0.94107   0.11777   0.82337   0.48533   58   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2020-09-17 Segmentation Embryo Brain Nervous System
61320 61320 SRR12661543 SRX9142572 SRS7383876 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   zBr16hpf1 14S S1 GSM4793189   source name:zebrafish brain|tissue:brain|developmental stage:16hpf 14somites zBr16hpf1 14S 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 cont… 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:16hpf 14somites GSM4793189 GSM4793189: zBr16hpf1 14S S1; Danio rerio; RNA Seq GSM4793189   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:GSM4793189 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP282920   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=zBr16hpf1 14S S1 L004 I1 001.fastq.gz read2PairFiles=zBr16hpf1 14S S1 L004 R1 001.fastq.gz read3PairFiles=zBr16hpf1 14S S1 L004 R2 001.fastq.gz zBr16hpf1_14S_S1_L004_I1_001.fastq.gz zBr16hpf1_14S_S1_L004_R1_001.fastq.gz zBr16hpf1_14S_S1_L004_R2_001.fastq.gz fastq fastq fastq 2401932228.0 26107959.0 GSM4793189 r4 0:8 1:26 2:58 A:657947813;C:529891104;G:581693767;T:632237159;N:162385 8 26 58   657947813 529891104 581693767 632237159 162385 SRX9142572 SRS7383876 SRA1127180 GEO Harvard University 1 0.94082   0.1175   0.82449   0.46907   58   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2020-09-17 Segmentation Embryo Brain Nervous System
61321 61321 SRR12661536 SRX9142571 SRS7383875 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   zBr14hpf2 10S S6 GSM4793188   source name:zebrafish brain|tissue:brain|developmental stage:14hpf 10somites zBr14hpf2 10S S6 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 cont… 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:14hpf 10somites GSM4793188 GSM4793188: zBr14hpf2 10S S6; Danio rerio; RNA Seq GSM4793188   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:GSM4793188 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP282920   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=zBr14hpf2 10S S6 L001 I1 001.fastq.gz read2PairFiles=zBr14hpf2 10S S6 L001 R1 001.fastq.gz read3PairFiles=zBr14hpf2 10S S6 L001 R2 001.fastq.gz zBr14hpf2_10S_S6_L001_I1_001.fastq.gz zBr14hpf2_10S_S6_L001_R1_001.fastq.gz zBr14hpf2_10S_S6_L001_R2_001.fastq.gz fastq fastq fastq 1531779668.0 16649779.0 GSM4793188 r1 0:8 1:26 2:58 A:420873884;C:337607213;G:372541766;T:400392197;N:364608 8 26 58   420873884 337607213 372541766 400392197 364608 SRX9142571 SRS7383875 SRA1127180 GEO Harvard University 1 0.93822   0.11829   0.82639   0.49362   58   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2020-09-17 Segmentation Embryo Brain Nervous System
61322 61322 SRR12661537 SRX9142571 SRS7383875 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   zBr14hpf2 10S S6 GSM4793188   source name:zebrafish brain|tissue:brain|developmental stage:14hpf 10somites zBr14hpf2 10S S6 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 cont… 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:14hpf 10somites GSM4793188 GSM4793188: zBr14hpf2 10S S6; Danio rerio; RNA Seq GSM4793188   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:GSM4793188 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP282920   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=zBr14hpf2 10S S6 L002 I1 001.fastq.gz read2PairFiles=zBr14hpf2 10S S6 L002 R1 001.fastq.gz read3PairFiles=zBr14hpf2 10S S6 L002 R2 001.fastq.gz zBr14hpf2_10S_S6_L002_I1_001.fastq.gz zBr14hpf2_10S_S6_L002_R1_001.fastq.gz zBr14hpf2_10S_S6_L002_R2_001.fastq.gz fastq fastq fastq 1506595864.0 16376042.0 GSM4793188 r2 0:8 1:26 2:58 A:416561484;C:332264478;G:364073758;T:393390330;N:305814 8 26 58   416561484 332264478 364073758 393390330 305814 SRX9142571 SRS7383875 SRA1127180 GEO Harvard University 1 0.93732   0.11656   0.82968   0.4953   58   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2020-09-17 Segmentation Embryo Brain Nervous System
61323 61323 SRR12661538 SRX9142571 SRS7383875 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   zBr14hpf2 10S S6 GSM4793188   source name:zebrafish brain|tissue:brain|developmental stage:14hpf 10somites zBr14hpf2 10S S6 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 cont… 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:14hpf 10somites GSM4793188 GSM4793188: zBr14hpf2 10S S6; Danio rerio; RNA Seq GSM4793188   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:GSM4793188 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP282920   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=zBr14hpf2 10S S6 L003 I1 001.fastq.gz read2PairFiles=zBr14hpf2 10S S6 L003 R1 001.fastq.gz read3PairFiles=zBr14hpf2 10S S6 L003 R2 001.fastq.gz zBr14hpf2_10S_S6_L003_I1_001.fastq.gz zBr14hpf2_10S_S6_L003_R1_001.fastq.gz zBr14hpf2_10S_S6_L003_R2_001.fastq.gz fastq fastq fastq 1483349948.0 16123369.0 GSM4793188 r3 0:8 1:26 2:58 A:408070288;C:326152706;G:360535156;T:388358299;N:233499 8 26 58   408070288 326152706 360535156 388358299 233499 SRX9142571 SRS7383875 SRA1127180 GEO Harvard University 1 0.93652   0.11744   0.82923   0.48391   58   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2020-09-17 Segmentation Embryo Brain Nervous System
61324 61324 SRR12661539 SRX9142571 SRS7383875 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   zBr14hpf2 10S S6 GSM4793188   source name:zebrafish brain|tissue:brain|developmental stage:14hpf 10somites zBr14hpf2 10S S6 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 cont… 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:14hpf 10somites GSM4793188 GSM4793188: zBr14hpf2 10S S6; Danio rerio; RNA Seq GSM4793188   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:GSM4793188 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP282920   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=zBr14hpf2 10S S6 L004 I1 001.fastq.gz read2PairFiles=zBr14hpf2 10S S6 L004 R1 001.fastq.gz read3PairFiles=zBr14hpf2 10S S6 L004 R2 001.fastq.gz zBr14hpf2_10S_S6_L004_I1_001.fastq.gz zBr14hpf2_10S_S6_L004_R1_001.fastq.gz zBr14hpf2_10S_S6_L004_R2_001.fastq.gz fastq fastq fastq 1537207116.0 16708773.0 GSM4793188 r4 0:8 1:26 2:58 A:421463774;C:338684177;G:375486390;T:401383480;N:189295 8 26 58   421463774 338684177 375486390 401383480 189295 SRX9142571 SRS7383875 SRA1127180 GEO Harvard University 1 0.93834   0.11768   0.82586   0.5033   58   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2020-09-17 Segmentation Embryo Brain Nervous System
61325 61325 SRR12661532 SRX9142570 SRS7383874 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   zBr14hpf1 10S S5 GSM4793187   source name:zebrafish brain|tissue:brain|developmental stage:14hpf 10somites zBr14hpf1 10S S5 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 cont… 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:14hpf 10somites GSM4793187 GSM4793187: zBr14hpf1 10S S5; Danio rerio; RNA Seq GSM4793187   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:GSM4793187 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP282920   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=zBr14hpf1 10S S5 L001 I1 001.fastq.gz read2PairFiles=zBr14hpf1 10S S5 L001 R1 001.fastq.gz read3PairFiles=zBr14hpf1 10S S5 L001 R2 001.fastq.gz zBr14hpf1_10S_S5_L001_I1_001.fastq.gz zBr14hpf1_10S_S5_L001_R1_001.fastq.gz zBr14hpf1_10S_S5_L001_R2_001.fastq.gz fastq fastq fastq 1537667852.0 16713781.0 GSM4793187 r1 0:8 1:26 2:58 A:422127039;C:336294662;G:376066351;T:402814314;N:365486 8 26 58   422127039 336294662 376066351 402814314 365486 SRX9142570 SRS7383874 SRA1127180 GEO Harvard University 1 0.93669   0.12272   0.82828   0.50633   58   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2020-09-17 Segmentation Embryo Brain Nervous System
61326 61326 SRR12661533 SRX9142570 SRS7383874 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   zBr14hpf1 10S S5 GSM4793187   source name:zebrafish brain|tissue:brain|developmental stage:14hpf 10somites zBr14hpf1 10S S5 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 cont… 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:14hpf 10somites GSM4793187 GSM4793187: zBr14hpf1 10S S5; Danio rerio; RNA Seq GSM4793187   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:GSM4793187 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP282920   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=zBr14hpf1 10S S5 L002 I1 001.fastq.gz read2PairFiles=zBr14hpf1 10S S5 L002 R1 001.fastq.gz read3PairFiles=zBr14hpf1 10S S5 L002 R2 001.fastq.gz zBr14hpf1_10S_S5_L002_I1_001.fastq.gz zBr14hpf1_10S_S5_L002_R1_001.fastq.gz zBr14hpf1_10S_S5_L002_R2_001.fastq.gz fastq fastq fastq 1513261356.0 16448493.0 GSM4793187 r2 0:8 1:26 2:58 A:418207211;C:331095306;G:367578524;T:396076158;N:304157 8 26 58   418207211 331095306 367578524 396076158 304157 SRX9142570 SRS7383874 SRA1127180 GEO Harvard University 1 0.93515   0.12494   0.82944   0.48855   58   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2020-09-17 Segmentation Embryo Brain Nervous System
61327 61327 SRR12661534 SRX9142570 SRS7383874 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   zBr14hpf1 10S S5 GSM4793187   source name:zebrafish brain|tissue:brain|developmental stage:14hpf 10somites zBr14hpf1 10S S5 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 cont… 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:14hpf 10somites GSM4793187 GSM4793187: zBr14hpf1 10S S5; Danio rerio; RNA Seq GSM4793187   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:GSM4793187 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP282920   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=zBr14hpf1 10S S5 L003 I1 001.fastq.gz read2PairFiles=zBr14hpf1 10S S5 L003 R1 001.fastq.gz read3PairFiles=zBr14hpf1 10S S5 L003 R2 001.fastq.gz zBr14hpf1_10S_S5_L003_I1_001.fastq.gz zBr14hpf1_10S_S5_L003_R1_001.fastq.gz zBr14hpf1_10S_S5_L003_R2_001.fastq.gz fastq fastq fastq 1485111380.0 16142515.0 GSM4793187 r3 0:8 1:26 2:58 A:408170917;C:324002543;G:362920588;T:389784796;N:232536 8 26 58   408170917 324002543 362920588 389784796 232536 SRX9142570 SRS7383874 SRA1127180 GEO Harvard University 1 0.93423   0.12179   0.82798   0.49418   58   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2020-09-17 Segmentation Embryo Brain Nervous System
61328 61328 SRR12661535 SRX9142570 SRS7383874 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   zBr14hpf1 10S S5 GSM4793187   source name:zebrafish brain|tissue:brain|developmental stage:14hpf 10somites zBr14hpf1 10S S5 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 cont… 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:14hpf 10somites GSM4793187 GSM4793187: zBr14hpf1 10S S5; Danio rerio; RNA Seq GSM4793187   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:GSM4793187 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP282920   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=zBr14hpf1 10S S5 L004 I1 001.fastq.gz read2PairFiles=zBr14hpf1 10S S5 L004 R1 001.fastq.gz read3PairFiles=zBr14hpf1 10S S5 L004 R2 001.fastq.gz zBr14hpf1_10S_S5_L004_I1_001.fastq.gz zBr14hpf1_10S_S5_L004_R1_001.fastq.gz zBr14hpf1_10S_S5_L004_R2_001.fastq.gz fastq fastq fastq 1543771960.0 16780130.0 GSM4793187 r4 0:8 1:26 2:58 A:422828628;C:337476631;G:379227920;T:404048890;N:189891 8 26 58   422828628 337476631 379227920 404048890 189891 SRX9142570 SRS7383874 SRA1127180 GEO Harvard University 1 0.93639   0.12103   0.82651   0.49721   58   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2020-09-17 Segmentation Embryo Brain Nervous System
61329 61329 SRR12661524 SRX9142569 SRS7383873 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   zBr12hpf2 S2 GSM4793186   source name:zebrafish brain|tissue:brain|developmental stage:12hpf 6somites zBr12hpf2 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 cont… 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:12hpf 6somites GSM4793186 GSM4793186: zBr12hpf2 S2; Danio rerio; RNA Seq GSM4793186   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:GSM4793186 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP282920   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=zBr12hpf2 S2 L001 I1 001.fastq.gz read2PairFiles=zBr12hpf2 S2 L001 R1 001.fastq.gz read3PairFiles=zBr12hpf2 S2 L001 R2 001.fastq.gz zBr12hpf2_S2_L001_I1_001.fastq.gz zBr12hpf2_S2_L001_R1_001.fastq.gz zBr12hpf2_S2_L001_R2_001.fastq.gz fastq fastq fastq 1319889132.0 14346621.0 GSM4793186 r1 0:8 1:26 2:58 A:365364068;C:292924723;G:306435261;T:354952807;N:212273 8 26 58   365364068 292924723 306435261 354952807 212273 SRX9142569 SRS7383873 SRA1127180 GEO Harvard University 1 0.94017   0.10576   0.87503   0.47805   58   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2020-09-17 Segmentation Embryo Brain Nervous System
61330 61330 SRR12661525 SRX9142569 SRS7383873 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   zBr12hpf2 S2 GSM4793186   source name:zebrafish brain|tissue:brain|developmental stage:12hpf 6somites zBr12hpf2 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 cont… 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:12hpf 6somites GSM4793186 GSM4793186: zBr12hpf2 S2; Danio rerio; RNA Seq GSM4793186   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:GSM4793186 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP282920   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=zBr12hpf2 S2 L002 I1 001.fastq.gz read2PairFiles=zBr12hpf2 S2 L002 R1 001.fastq.gz read3PairFiles=zBr12hpf2 S2 L002 R2 001.fastq.gz zBr12hpf2_S2_L002_I1_001.fastq.gz zBr12hpf2_S2_L002_R1_001.fastq.gz zBr12hpf2_S2_L002_R2_001.fastq.gz fastq fastq fastq 1401826632.0 15237246.0 GSM4793186 r2 0:8 1:26 2:58 A:387181923;C:311646429;G:328763997;T:373919705;N:314578 8 26 58   387181923 311646429 328763997 373919705 314578 SRX9142569 SRS7383873 SRA1127180 GEO Harvard University 1 0.94196   0.10428   0.86764   0.48501   58   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2020-09-17 Segmentation Embryo Brain Nervous System
61331 61331 SRR12661526 SRX9142569 SRS7383873 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   zBr12hpf2 S2 GSM4793186   source name:zebrafish brain|tissue:brain|developmental stage:12hpf 6somites zBr12hpf2 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 cont… 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:12hpf 6somites GSM4793186 GSM4793186: zBr12hpf2 S2; Danio rerio; RNA Seq GSM4793186   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:GSM4793186 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP282920   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=zBr12hpf2 S2 L003 I1 001.fastq.gz read2PairFiles=zBr12hpf2 S2 L003 R1 001.fastq.gz read3PairFiles=zBr12hpf2 S2 L003 R2 001.fastq.gz zBr12hpf2_S2_L003_I1_001.fastq.gz zBr12hpf2_S2_L003_R1_001.fastq.gz zBr12hpf2_S2_L003_R2_001.fastq.gz fastq fastq fastq 1382196500.0 15023875.0 GSM4793186 r3 0:8 1:26 2:58 A:378920637;C:307241578;G:324142763;T:371767541;N:123981 8 26 58   378920637 307241578 324142763 371767541 123981 SRX9142569 SRS7383873 SRA1127180 GEO Harvard University 1 0.94181   0.10374   0.87142   0.48802   58   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2020-09-17 Segmentation Embryo Brain Nervous System
61332 61332 SRR12661527 SRX9142569 SRS7383873 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   zBr12hpf2 S2 GSM4793186   source name:zebrafish brain|tissue:brain|developmental stage:12hpf 6somites zBr12hpf2 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 cont… 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:12hpf 6somites GSM4793186 GSM4793186: zBr12hpf2 S2; Danio rerio; RNA Seq GSM4793186   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:GSM4793186 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP282920   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=zBr12hpf2 S2 L004 I1 001.fastq.gz read2PairFiles=zBr12hpf2 S2 L004 R1 001.fastq.gz read3PairFiles=zBr12hpf2 S2 L004 R2 001.fastq.gz zBr12hpf2_S2_L004_I1_001.fastq.gz zBr12hpf2_S2_L004_R1_001.fastq.gz zBr12hpf2_S2_L004_R2_001.fastq.gz fastq fastq fastq 1396349320.0 15177710.0 GSM4793186 r4 0:8 1:26 2:58 A:384801789;C:310616550;G:327699440;T:373103344;N:128197 8 26 58   384801789 310616550 327699440 373103344 128197 SRX9142569 SRS7383873 SRA1127180 GEO Harvard University 1 0.94207   0.10548   0.87178   0.47549   58   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2020-09-17 Segmentation Embryo Brain Nervous System
61333 61333 SRR12661528 SRX9142569 SRS7383873 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   zBr12hpf2 S2 GSM4793186   source name:zebrafish brain|tissue:brain|developmental stage:12hpf 6somites zBr12hpf2 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 cont… 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:12hpf 6somites GSM4793186 GSM4793186: zBr12hpf2 S2; Danio rerio; RNA Seq GSM4793186   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:GSM4793186 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP282920   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=zBr12hpf2b S2 L001 I1 001.fastq.gz read2PairFiles=zBr12hpf2b S2 L001 R1 001.fastq.gz read3PairFiles=zBr12hpf2b S2 L001 R2 001.fastq.gz zBr12hpf2b_S2_L001_I1_001.fastq.gz zBr12hpf2b_S2_L001_R1_001.fastq.gz zBr12hpf2b_S2_L001_R2_001.fastq.gz fastq fastq fastq 1476082592.0 16044376.0 GSM4793186 r5 0:8 1:26 2:58 A:397001997;C:326512420;G:359122618;T:392866651;N:578906 8 26 58   397001997 326512420 359122618 392866651 578906 SRX9142569 SRS7383873 SRA1127180 GEO Harvard University 1 0.94521   0.09379   0.83414   0.48296   58   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2020-09-17 Segmentation Embryo Brain Nervous System
61334 61334 SRR12661529 SRX9142569 SRS7383873 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   zBr12hpf2 S2 GSM4793186   source name:zebrafish brain|tissue:brain|developmental stage:12hpf 6somites zBr12hpf2 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 cont… 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:12hpf 6somites GSM4793186 GSM4793186: zBr12hpf2 S2; Danio rerio; RNA Seq GSM4793186   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:GSM4793186 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP282920   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=zBr12hpf2b S2 L002 I1 001.fastq.gz read2PairFiles=zBr12hpf2b S2 L002 R1 001.fastq.gz read3PairFiles=zBr12hpf2b S2 L002 R2 001.fastq.gz zBr12hpf2b_S2_L002_I1_001.fastq.gz zBr12hpf2b_S2_L002_R1_001.fastq.gz zBr12hpf2b_S2_L002_R2_001.fastq.gz fastq fastq fastq 1439443960.0 15646130.0 GSM4793186 r6 0:8 1:26 2:58 A:391336166;C:319076858;G:346241865;T:382298448;N:490623 8 26 58   391336166 319076858 346241865 382298448 490623 SRX9142569 SRS7383873 SRA1127180 GEO Harvard University 1 0.94757   0.0974   0.83956   0.49093   58   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2020-09-17 Segmentation Embryo Brain Nervous System
61335 61335 SRR12661530 SRX9142569 SRS7383873 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   zBr12hpf2 S2 GSM4793186   source name:zebrafish brain|tissue:brain|developmental stage:12hpf 6somites zBr12hpf2 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 cont… 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:12hpf 6somites GSM4793186 GSM4793186: zBr12hpf2 S2; Danio rerio; RNA Seq GSM4793186   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:GSM4793186 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP282920   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=zBr12hpf2b S2 L003 I1 001.fastq.gz read2PairFiles=zBr12hpf2b S2 L003 R1 001.fastq.gz read3PairFiles=zBr12hpf2b S2 L003 R2 001.fastq.gz zBr12hpf2b_S2_L003_I1_001.fastq.gz zBr12hpf2b_S2_L003_R1_001.fastq.gz zBr12hpf2b_S2_L003_R2_001.fastq.gz fastq fastq fastq 1332285028.0 14481359.0 GSM4793186 r7 0:8 1:26 2:58 A:363675496;C:294660861;G:316244639;T:357411128;N:292904 8 26 58   363675496 294660861 316244639 357411128 292904 SRX9142569 SRS7383873 SRA1127180 GEO Harvard University 1 0.94428   0.09777   0.85506   0.48151   58   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2020-09-17 Segmentation Embryo Brain Nervous System
61336 61336 SRR12661531 SRX9142569 SRS7383873 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   zBr12hpf2 S2 GSM4793186   source name:zebrafish brain|tissue:brain|developmental stage:12hpf 6somites zBr12hpf2 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 cont… 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:12hpf 6somites GSM4793186 GSM4793186: zBr12hpf2 S2; Danio rerio; RNA Seq GSM4793186   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:GSM4793186 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP282920   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=zBr12hpf2b S2 L004 I1 001.fastq.gz read2PairFiles=zBr12hpf2b S2 L004 R1 001.fastq.gz read3PairFiles=zBr12hpf2b S2 L004 R2 001.fastq.gz zBr12hpf2b_S2_L004_I1_001.fastq.gz zBr12hpf2b_S2_L004_R1_001.fastq.gz zBr12hpf2b_S2_L004_R2_001.fastq.gz fastq fastq fastq 1392878620.0 15139985.0 GSM4793186 r8 0:8 1:26 2:58 A:377888258;C:308446409;G:335321694;T:370938385;N:283874 8 26 58   377888258 308446409 335321694 370938385 283874 SRX9142569 SRS7383873 SRA1127180 GEO Harvard University 1 0.94642   0.09759   0.83759   0.45476   58   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2020-09-17 Segmentation Embryo Brain Nervous System
61337 61337 SRR12661516 SRX9142568 SRS7383872 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   zBr12hpf1 S1 GSM4793185   source name:zebrafish brain|tissue:brain|developmental stage:12hpf 6somites zBr12hpf1 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 cont… 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:12hpf 6somites GSM4793185 GSM4793185: zBr12hpf1 S1; Danio rerio; RNA Seq GSM4793185   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:GSM4793185 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP282920   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=zBr12hpf1 S1 L001 I1 001.fastq.gz read2PairFiles=zBr12hpf1 S1 L001 R1 001.fastq.gz read3PairFiles=zBr12hpf1 S1 L001 R2 001.fastq.gz zBr12hpf1_S1_L001_I1_001.fastq.gz zBr12hpf1_S1_L001_R1_001.fastq.gz zBr12hpf1_S1_L001_R2_001.fastq.gz fastq fastq fastq 1770258756.0 19241943.0 GSM4793185 r1 0:8 1:26 2:58 A:487954269;C:394067531;G:414708165;T:473246705;N:282086 8 26 58   487954269 394067531 414708165 473246705 282086 SRX9142568 SRS7383872 SRA1127180 GEO Harvard University 1 0.94055   0.10658   0.87336   0.47563   58   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2020-09-17 Segmentation Embryo Brain Nervous System
61338 61338 SRR12661517 SRX9142568 SRS7383872 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   zBr12hpf1 S1 GSM4793185   source name:zebrafish brain|tissue:brain|developmental stage:12hpf 6somites zBr12hpf1 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 cont… 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:12hpf 6somites GSM4793185 GSM4793185: zBr12hpf1 S1; Danio rerio; RNA Seq GSM4793185   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:GSM4793185 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP282920   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=zBr12hpf1 S1 L002 I1 001.fastq.gz read2PairFiles=zBr12hpf1 S1 L002 R1 001.fastq.gz read3PairFiles=zBr12hpf1 S1 L002 R2 001.fastq.gz zBr12hpf1_S1_L002_I1_001.fastq.gz zBr12hpf1_S1_L002_R1_001.fastq.gz zBr12hpf1_S1_L002_R2_001.fastq.gz fastq fastq fastq 1884577496.0 20484538.0 GSM4793185 r2 0:8 1:26 2:58 A:518516274;C:420150808;G:445696909;T:499796120;N:417385 8 26 58   518516274 420150808 445696909 499796120 417385 SRX9142568 SRS7383872 SRA1127180 GEO Harvard University 1 0.94103   0.10852   0.8692   0.47056   58   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2020-09-17 Segmentation Embryo Brain Nervous System
61339 61339 SRR12661518 SRX9142568 SRS7383872 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   zBr12hpf1 S1 GSM4793185   source name:zebrafish brain|tissue:brain|developmental stage:12hpf 6somites zBr12hpf1 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 cont… 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:12hpf 6somites GSM4793185 GSM4793185: zBr12hpf1 S1; Danio rerio; RNA Seq GSM4793185   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:GSM4793185 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP282920   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=zBr12hpf1 S1 L003 I1 001.fastq.gz read2PairFiles=zBr12hpf1 S1 L003 R1 001.fastq.gz read3PairFiles=zBr12hpf1 S1 L003 R2 001.fastq.gz zBr12hpf1_S1_L003_I1_001.fastq.gz zBr12hpf1_S1_L003_R1_001.fastq.gz zBr12hpf1_S1_L003_R2_001.fastq.gz fastq fastq fastq 1855610376.0 20169678.0 GSM4793185 r3 0:8 1:26 2:58 A:506634432;C:413625169;G:439053060;T:496134272;N:163443 8 26 58   506634432 413625169 439053060 496134272 163443 SRX9142568 SRS7383872 SRA1127180 GEO Harvard University 1 0.94188   0.10631   0.87351   0.47992   58   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2020-09-17 Segmentation Embryo Brain Nervous System
61340 61340 SRR12661519 SRX9142568 SRS7383872 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   zBr12hpf1 S1 GSM4793185   source name:zebrafish brain|tissue:brain|developmental stage:12hpf 6somites zBr12hpf1 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 cont… 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:12hpf 6somites GSM4793185 GSM4793185: zBr12hpf1 S1; Danio rerio; RNA Seq GSM4793185   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:GSM4793185 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP282920   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=zBr12hpf1 S1 L004 I1 001.fastq.gz read2PairFiles=zBr12hpf1 S1 L004 R1 001.fastq.gz read3PairFiles=zBr12hpf1 S1 L004 R2 001.fastq.gz zBr12hpf1_S1_L004_I1_001.fastq.gz zBr12hpf1_S1_L004_R1_001.fastq.gz zBr12hpf1_S1_L004_R2_001.fastq.gz fastq fastq fastq 1877838588.0 20411289.0 GSM4793185 r4 0:8 1:26 2:58 A:515452323;C:418841907;G:444542994;T:498828150;N:173214 8 26 58   515452323 418841907 444542994 498828150 173214 SRX9142568 SRS7383872 SRA1127180 GEO Harvard University 1 0.93999   0.10753   0.87192   0.47745   58   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2020-09-17 Segmentation Embryo Brain Nervous System
61341 61341 SRR12661520 SRX9142568 SRS7383872 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   zBr12hpf1 S1 GSM4793185   source name:zebrafish brain|tissue:brain|developmental stage:12hpf 6somites zBr12hpf1 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 cont… 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:12hpf 6somites GSM4793185 GSM4793185: zBr12hpf1 S1; Danio rerio; RNA Seq GSM4793185   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:GSM4793185 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP282920   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=zBr12hpf1b S1 L001 I1 001.fastq.gz read2PairFiles=zBr12hpf1b S1 L001 R1 001.fastq.gz read3PairFiles=zBr12hpf1b S1 L001 R2 001.fastq.gz zBr12hpf1b_S1_L001_I1_001.fastq.gz zBr12hpf1b_S1_L001_R1_001.fastq.gz zBr12hpf1b_S1_L001_R2_001.fastq.gz fastq fastq fastq 1985080964.0 21576967.0 GSM4793185 r5 0:8 1:26 2:58 A:532808565;C:439927042;G:486211847;T:525368008;N:765502 8 26 58   532808565 439927042 486211847 525368008 765502 SRX9142568 SRS7383872 SRA1127180 GEO Harvard University 1 0.9448   0.0961   0.83575   0.47861   58   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2020-09-17 Segmentation Embryo Brain Nervous System
61342 61342 SRR12661521 SRX9142568 SRS7383872 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   zBr12hpf1 S1 GSM4793185   source name:zebrafish brain|tissue:brain|developmental stage:12hpf 6somites zBr12hpf1 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 cont… 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:12hpf 6somites GSM4793185 GSM4793185: zBr12hpf1 S1; Danio rerio; RNA Seq GSM4793185   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:GSM4793185 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP282920   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=zBr12hpf1b S1 L002 I1 001.fastq.gz read2PairFiles=zBr12hpf1b S1 L002 R1 001.fastq.gz read3PairFiles=zBr12hpf1b S1 L002 R2 001.fastq.gz zBr12hpf1b_S1_L002_I1_001.fastq.gz zBr12hpf1b_S1_L002_R1_001.fastq.gz zBr12hpf1b_S1_L002_R2_001.fastq.gz fastq fastq fastq 1938481308.0 21070449.0 GSM4793185 r6 0:8 1:26 2:58 A:525810043;C:430538781;G:469587494;T:511885220;N:659770 8 26 58   525810043 430538781 469587494 511885220 659770 SRX9142568 SRS7383872 SRA1127180 GEO Harvard University 1 0.94516   0.10027   0.83958   0.48876   58   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2020-09-17 Segmentation Embryo Brain Nervous System
61343 61343 SRR12661522 SRX9142568 SRS7383872 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   zBr12hpf1 S1 GSM4793185   source name:zebrafish brain|tissue:brain|developmental stage:12hpf 6somites zBr12hpf1 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 cont… 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:12hpf 6somites GSM4793185 GSM4793185: zBr12hpf1 S1; Danio rerio; RNA Seq GSM4793185   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:GSM4793185 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP282920   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=zBr12hpf1b S1 L003 I1 001.fastq.gz read2PairFiles=zBr12hpf1b S1 L003 R1 001.fastq.gz read3PairFiles=zBr12hpf1b S1 L003 R2 001.fastq.gz zBr12hpf1b_S1_L003_I1_001.fastq.gz zBr12hpf1b_S1_L003_R1_001.fastq.gz zBr12hpf1b_S1_L003_R2_001.fastq.gz fastq fastq fastq 1785529376.0 19407928.0 GSM4793185 r7 0:8 1:26 2:58 A:486068803;C:395678143;G:427372563;T:476029628;N:380239 8 26 58   486068803 395678143 427372563 476029628 380239 SRX9142568 SRS7383872 SRA1127180 GEO Harvard University 1 0.94413   0.10243   0.85456   0.48333   58   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2020-09-17 Segmentation Embryo Brain Nervous System
61344 61344 SRR12661523 SRX9142568 SRS7383872 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   zBr12hpf1 S1 GSM4793185   source name:zebrafish brain|tissue:brain|developmental stage:12hpf 6somites zBr12hpf1 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 cont… 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:12hpf 6somites GSM4793185 GSM4793185: zBr12hpf1 S1; Danio rerio; RNA Seq GSM4793185   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:GSM4793185 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP282920   loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=zBr12hpf1b S1 L004 I1 001.fastq.gz read2PairFiles=zBr12hpf1b S1 L004 R1 001.fastq.gz read3PairFiles=zBr12hpf1b S1 L004 R2 001.fastq.gz zBr12hpf1b_S1_L004_I1_001.fastq.gz zBr12hpf1b_S1_L004_R1_001.fastq.gz zBr12hpf1b_S1_L004_R2_001.fastq.gz fastq fastq fastq 1870339944.0 20329782.0 GSM4793185 r8 0:8 1:26 2:58 A:506449824;C:414955605;G:453319112;T:495229592;N:385811 8 26 58   506449824 414955605 453319112 495229592 385811 SRX9142568 SRS7383872 SRA1127180 GEO Harvard University 1 0.94608   0.10186   0.83792   0.48186   58   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2020-09-17 Segmentation Embryo Brain Nervous System
65480 65480 SRR15321083 SRX11625561 SRS9659652 SRP330794 PRJNA751418 Epigenetic dynamics shaping melanophore and iridophore cell fate in zebrafish GSE181287 Other We charted the global changes in the epigenetic landscape including DNA methylation and chromatin accessibility during neural crest differentiation into melanophores and iridophores in zebrafish to identify epigenetic determinants shaping cell type specific gene expression. Motif enrichment in the epigenetically dynamic regions revealed putative transcription factors that might be responsible for driving pigment cell identity. Through this effort in the relatively uncharacterized iridophores we validate alx4a as a necessary and sufficient transcription factor for iridophore differentiation and present evidence on alx4a's potential regulatory role in guanine synthesis pathway. Overall design: ATAC seq RNA Seq WGBS were generated for 15 somite NCC 24 hpf NCC 4 dpf 5 dpf Melanophore and 4 dpf 5 dpf Iridophore cells from zebrafish.   pubmed:34607603   RNA seq 15somite NCC rep2 GSM5494233   tissue:Neural crest cells|genotype:TgcrestinA:EGFP|developmental stage:15 somite|cell type:Neural crest cells RNA seq 15somite NCC rep2 All libraries were sequenced on Illumina NextSeq 500 platforms. Reads were adapter trimmed with cutadapt. RNA seq reads were aligned to danRer10 genome using STAR. WGBS reads were aligned to danRer10 using bismark with standard parameters. omniATAC seq reads were aligned to danRer10 using bwa mem. Genome build: danRer10 Supplementary files format and content: bigWig bedGraph and text files. Neural crest cells TgcrestinA:EGFP embryos at designated biological time points were dechorionated with Pronase rinsed with egg water to remove the chorion and collected into 1.5ml Eppendorf tubes on ice. 4 dpf 5 dpf mlphaj120 larvae were anesthetized with Tricane for 15 minutes and collected into 50ml conical tubes on ice. Single cells were dissociated from embryos using Gibco TrypLE Express enzyme solution. Neural crest GFP positive cells were sorted and collected on Beckman Couter MoFlo. Melanophore and iridophore were isolated using published protocol developed by the Johnson lab Higdon et al. 2013. Genomic DNA for WGBS was purified from NCCs and pigment cells via phenol chloroform:isoamyl alcohol PCI extraction and ethanol precipitation method. RNA was collected using Trizol following manufacturer's recommendation. Published omniATAC seq protocol was followed to extract materials for ATAC seq. RNA seq libraries were then constructed with TruSeq RNA Library Prep Kit v2 Illumina RS 122 2001 following manufacturer’s instructions. gDNA was bisulfite treated using EZ DNA Methylation Direct kit Zymo D5020 and processed with TruSeq DNA Methylation Kit Illumina 15066014 to generate Illumina compatible WGBS libraries. Published omniATAC seq was followed to generate ATAC seq data.   genotype:TgcrestinA:EGFP|developmental stage:15 somite|cell type:Neural crest cells GSM5494233 GSM5494233: RNA seq 15somite NCC rep2; Danio rerio; RNA Seq GSM5494233   1 Single cells were dissociated from embryos using Gibco TrypLE Express enzyme solution. Neural crest GFP positive cells were sorted and collected on Beckman Couter MoFlo. Melanophore and iridophore were isolated using published protocol developed by the Johnson lab Higdon et al. 2013. Genomic DNA for WGBS was purified from NCCs and pigment cells via phenol chloroform:isoamyl alcohol PCI extraction and ethanol precipitation method. RNA was collected using Trizol following manufacturer's recommendation. Published omniATAC seq protocol was followed to extract materials for ATAC seq. RNA seq libraries were then constructed with TruSeq RNA Library Prep Kit v2 Illumina RS 122 2001 following manufacturer's instructions. gDNA was bisulfite treated using EZ DNA Methylation Direct kit Zymo D5020 and processed with TruSeq DNA Methylation Kit Illumina 15066014 to generate Illumina compatible WGBS libraries. Published omniATAC seq was followed to generate ATAC seq data. GEO Accession:GSM5494233 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP330794     RNA_15somite_GFPpositive_Rep2_R1.fastq.gz RNA_15somite_GFPpositive_Rep2_R2.fastq.gz fastq fastq 12345817350.0 82305449.0 GSM5494233 r1 0:75 1:75 A:3205348060;C:2986348356;G:2961321721;T:3189065016;N:3734197 75 75     3205348060 2986348356 2961321721 3189065016 3734197 SRX11625561 SRS9659652 SRA1268156 GEO Ting Wang Lab, Genetics, Washington University in St. Louis 2 0.9469 0.94234 0.09688 0.09669 0.72425 0.72697 0.47109 0.47154 75 75 B B biological fallback assumption illumina nextseq unknown cdna_unspecified trueseq bulk unknown unknown   United States 2021-08-01 Segmentation Embryo Brain Nervous System
65481 65481 SRR15321082 SRX11625560 SRS9659651 SRP330794 PRJNA751418 Epigenetic dynamics shaping melanophore and iridophore cell fate in zebrafish GSE181287 Other We charted the global changes in the epigenetic landscape including DNA methylation and chromatin accessibility during neural crest differentiation into melanophores and iridophores in zebrafish to identify epigenetic determinants shaping cell type specific gene expression. Motif enrichment in the epigenetically dynamic regions revealed putative transcription factors that might be responsible for driving pigment cell identity. Through this effort in the relatively uncharacterized iridophores we validate alx4a as a necessary and sufficient transcription factor for iridophore differentiation and present evidence on alx4a's potential regulatory role in guanine synthesis pathway. Overall design: ATAC seq RNA Seq WGBS were generated for 15 somite NCC 24 hpf NCC 4 dpf 5 dpf Melanophore and 4 dpf 5 dpf Iridophore cells from zebrafish.   pubmed:34607603   RNA seq 15somite NCC rep1 GSM5494232   tissue:Neural crest cells|genotype:TgcrestinA:EGFP|developmental stage:15 somite|cell type:Neural crest cells RNA seq 15somite NCC rep1 All libraries were sequenced on Illumina NextSeq 500 platforms. Reads were adapter trimmed with cutadapt. RNA seq reads were aligned to danRer10 genome using STAR. WGBS reads were aligned to danRer10 using bismark with standard parameters. omniATAC seq reads were aligned to danRer10 using bwa mem. Genome build: danRer10 Supplementary files format and content: bigWig bedGraph and text files. Neural crest cells TgcrestinA:EGFP embryos at designated biological time points were dechorionated with Pronase rinsed with egg water to remove the chorion and collected into 1.5ml Eppendorf tubes on ice. 4 dpf 5 dpf mlphaj120 larvae were anesthetized with Tricane for 15 minutes and collected into 50ml conical tubes on ice. Single cells were dissociated from embryos using Gibco TrypLE Express enzyme solution. Neural crest GFP positive cells were sorted and collected on Beckman Couter MoFlo. Melanophore and iridophore were isolated using published protocol developed by the Johnson lab Higdon et al. 2013. Genomic DNA for WGBS was purified from NCCs and pigment cells via phenol chloroform:isoamyl alcohol PCI extraction and ethanol precipitation method. RNA was collected using Trizol following manufacturer's recommendation. Published omniATAC seq protocol was followed to extract materials for ATAC seq. RNA seq libraries were then constructed with TruSeq RNA Library Prep Kit v2 Illumina RS 122 2001 following manufacturer’s instructions. gDNA was bisulfite treated using EZ DNA Methylation Direct kit Zymo D5020 and processed with TruSeq DNA Methylation Kit Illumina 15066014 to generate Illumina compatible WGBS libraries. Published omniATAC seq was followed to generate ATAC seq data.   genotype:TgcrestinA:EGFP|developmental stage:15 somite|cell type:Neural crest cells GSM5494232 GSM5494232: RNA seq 15somite NCC rep1; Danio rerio; RNA Seq GSM5494232   1 Single cells were dissociated from embryos using Gibco TrypLE Express enzyme solution. Neural crest GFP positive cells were sorted and collected on Beckman Couter MoFlo. Melanophore and iridophore were isolated using published protocol developed by the Johnson lab Higdon et al. 2013. Genomic DNA for WGBS was purified from NCCs and pigment cells via phenol chloroform:isoamyl alcohol PCI extraction and ethanol precipitation method. RNA was collected using Trizol following manufacturer's recommendation. Published omniATAC seq protocol was followed to extract materials for ATAC seq. RNA seq libraries were then constructed with TruSeq RNA Library Prep Kit v2 Illumina RS 122 2001 following manufacturer's instructions. gDNA was bisulfite treated using EZ DNA Methylation Direct kit Zymo D5020 and processed with TruSeq DNA Methylation Kit Illumina 15066014 to generate Illumina compatible WGBS libraries. Published omniATAC seq was followed to generate ATAC seq data. GEO Accession:GSM5494232 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP330794     RNA_15somite_GFPpositive_Rep1_R1.fastq.gz RNA_15somite_GFPpositive_Rep1_R2.fastq.gz fastq fastq 4873066350.0 32487109.0 GSM5494232 r1 0:75 1:75 A:1279685777;C:1165675124;G:1163342068;T:1262630342;N:1733039 75 75     1279685777 1165675124 1163342068 1262630342 1733039 SRX11625560 SRS9659651 SRA1268156 GEO Ting Wang Lab, Genetics, Washington University in St. Louis 2 0.94795 0.94582 0.09748 0.09594 0.73091 0.73693 0.47989 0.47785 75 75 B B biological fallback assumption illumina nextseq unknown cdna_unspecified trueseq bulk unknown unknown   United States 2021-08-01 Segmentation Embryo Brain Nervous System
70436 70436 SRR19846950 SRX15890625 SRS13579729 SRP383494 PRJNA852585 Control of cranial ectomesenchyme fate by Nr2f nuclear receptors GSE206903 Transcriptome Analysis Certain cranial neural crest cells are uniquely endowed with the ability to make skeletal cell types otherwise only derived from mesoderm. As these cells migrate into the pharyngeal arches they downregulate neural crest specifier genes and upregulate so called ectomesenchyme genes characteristic of skeletal progenitors. While both external and cell autonomous factors have been proposed as triggers of this transition the details remain obscure. Here we report the Nr2f nuclear receptors as novel intrinsic activators of the ectomesenchyme program: zebrafish nr2f5 and nr2f2; nr2f5 mutants show a marked delay in upregulation of ectomesenchyme genes such as dlx2a prrx1a/b sox9a twist1a and fli1a and in downregulation of the non ectomesenchyme specifier sox10. Depending on genotype mutants partially or fully recover likely via functional redundancy with other Nr2f genes. Loss of sox10 fully rescued skeletal development in nr2f5 single but not nr2f2; nr2f5 double mutants while the ectomesenchyme defect persisted in both. Sox10 perdurance thus antagonizes the recovery rather than causing the initial aberration. Unraveling the mechanics of Nr2f function will help solve the enduring puzzle of how cranial neural crest acquire skeletal potency. Overall design: Bulk RNA seq was performed on FACS purified zebrafish neural crest cells expressing sox10:DsRed from 20 hpf nr2f2[unknown]; nr2f5[mutant] embryos 2 replicates: n = 88 & 35 and wild type control embryos 2 replicates: n = 110 & 120.   pubmed:36367707   sox10:DsRed+ neural crest cells from 20 hpf wild type embryos biol rep 2 GSM6266712   tissue:sox10:DsRed+ neural crest cells|cell type:sox10:DsRed+ neural crest cells|genotype:wild type|developmental stage:20 hpf sox10:DsRed+ neural crest cells from 20 hpf wild type embryos biol rep 2 Illumina control software was used for base calling. Sequences were pseudoaligned and quantified at TPM values using Kallisto. Assembly: GRCz11 Supplementary files format and content: TPM Barske2022.txt: Tab delimited text file includes TPM values for each transcript. sox10:DsRed+ neural crest cells   Total RNA was extracted from sorted cells using the RNeasy Micro kit Qiagen. The purified RNA samples were tested for quality and quantity on a BioAnalyzer and then reverse transcribed into cDNA using the SMARTer kit. cDNA amplification was adjusted based on the RNA input and the size and amount of cDNA was measured by BioAnalyzer. Sonication was performed on an S2 ultrasonicator. DNA libraries were created with the Kapa Hyper Prep kit and NextFlex adapters assessed by Bioanalyzer and quantified using the Kapa Library Quantification kit.   cell type:sox10:DsRed+ neural crest cells|genotype:wild type|developmental stage:20 hpf GSM6266712 GSM6266712: sox10:DsRed+ neural crest cells from 20 hpf wild type embryos biol rep 2; Danio rerio; RNA Seq GSM6266712 r1 GSM6266712 1 Total RNA was extracted from sorted cells using the RNeasy Micro kit Qiagen. The purified RNA samples were tested for quality and quantity on a BioAnalyzer and then reverse transcribed into cDNA using the SMARTer kit. cDNA amplification was adjusted based on the RNA input and the size and amount of cDNA was measured by BioAnalyzer. Sonication was performed on an S2 ultrasonicator. DNA libraries were created with the Kapa Hyper Prep kit and NextFlex adapters assessed by Bioanalyzer and quantified using the Kapa Library Quantification kit.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP383494   loader:fastq load.py sox10DsRed-CON2-S6-R1.fastq.gz sox10DsRed-CON2-S6_R2_001.fastq.gz fastq fastq 4876722704.0 32083702.0 GSM6266712 r1 0:76 1:76 A:1342673931;C:1107276249;G:1150211941;T:1276364234;N:196349 76 76     1342673931 1107276249 1150211941 1276364234 196349 SRX15890625 SRS13579729     Human Genetics, Cincinnati Children's Hospital Medical Center 2 0.8977 0.90038 0.03951 0.04044 0.75777 0.76331 0.46312 0.4722 76 76 B B biological fallback assumption illumina hiseq_era full_length cdna_unspecified smarter bulk bulk bulk   United States 2022-06-24 Segmentation Embryo Brain Nervous System
70437 70437 SRR19846951 SRX15890624 SRS13579728 SRP383494 PRJNA852585 Control of cranial ectomesenchyme fate by Nr2f nuclear receptors GSE206903 Transcriptome Analysis Certain cranial neural crest cells are uniquely endowed with the ability to make skeletal cell types otherwise only derived from mesoderm. As these cells migrate into the pharyngeal arches they downregulate neural crest specifier genes and upregulate so called ectomesenchyme genes characteristic of skeletal progenitors. While both external and cell autonomous factors have been proposed as triggers of this transition the details remain obscure. Here we report the Nr2f nuclear receptors as novel intrinsic activators of the ectomesenchyme program: zebrafish nr2f5 and nr2f2; nr2f5 mutants show a marked delay in upregulation of ectomesenchyme genes such as dlx2a prrx1a/b sox9a twist1a and fli1a and in downregulation of the non ectomesenchyme specifier sox10. Depending on genotype mutants partially or fully recover likely via functional redundancy with other Nr2f genes. Loss of sox10 fully rescued skeletal development in nr2f5 single but not nr2f2; nr2f5 double mutants while the ectomesenchyme defect persisted in both. Sox10 perdurance thus antagonizes the recovery rather than causing the initial aberration. Unraveling the mechanics of Nr2f function will help solve the enduring puzzle of how cranial neural crest acquire skeletal potency. Overall design: Bulk RNA seq was performed on FACS purified zebrafish neural crest cells expressing sox10:DsRed from 20 hpf nr2f2[unknown]; nr2f5[mutant] embryos 2 replicates: n = 88 & 35 and wild type control embryos 2 replicates: n = 110 & 120.   pubmed:36367707   sox10:DsRed+ neural crest cells from 20 hpf wild type embryos biol rep 1 GSM6266711   tissue:sox10:DsRed+ neural crest cells|cell type:sox10:DsRed+ neural crest cells|genotype:wild type|developmental stage:20 hpf sox10:DsRed+ neural crest cells from 20 hpf wild type embryos biol rep 1 Illumina control software was used for base calling. Sequences were pseudoaligned and quantified at TPM values using Kallisto. Assembly: GRCz11 Supplementary files format and content: TPM Barske2022.txt: Tab delimited text file includes TPM values for each transcript. sox10:DsRed+ neural crest cells   Total RNA was extracted from sorted cells using the RNeasy Micro kit Qiagen. The purified RNA samples were tested for quality and quantity on a BioAnalyzer and then reverse transcribed into cDNA using the SMARTer kit. cDNA amplification was adjusted based on the RNA input and the size and amount of cDNA was measured by BioAnalyzer. Sonication was performed on an S2 ultrasonicator. DNA libraries were created with the Kapa Hyper Prep kit and NextFlex adapters assessed by Bioanalyzer and quantified using the Kapa Library Quantification kit.   cell type:sox10:DsRed+ neural crest cells|genotype:wild type|developmental stage:20 hpf GSM6266711 GSM6266711: sox10:DsRed+ neural crest cells from 20 hpf wild type embryos biol rep 1; Danio rerio; RNA Seq GSM6266711 r1 GSM6266711 1 Total RNA was extracted from sorted cells using the RNeasy Micro kit Qiagen. The purified RNA samples were tested for quality and quantity on a BioAnalyzer and then reverse transcribed into cDNA using the SMARTer kit. cDNA amplification was adjusted based on the RNA input and the size and amount of cDNA was measured by BioAnalyzer. Sonication was performed on an S2 ultrasonicator. DNA libraries were created with the Kapa Hyper Prep kit and NextFlex adapters assessed by Bioanalyzer and quantified using the Kapa Library Quantification kit.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP383494   loader:fastq load.py sox10DsRed-CON1-S5-R1.fastq.gz sox10DsRed-CON1-S5-R2.fastq.gz fastq fastq 4875797328.0 32077614.0 GSM6266711 r1 0:76 1:76 A:1340486054;C:1109815504;G:1153492417;T:1271807986;N:195367 76 76     1340486054 1109815504 1153492417 1271807986 195367 SRX15890624 SRS13579728     Human Genetics, Cincinnati Children's Hospital Medical Center 2 0.92525 0.92846 0.04508 0.04513 0.75789 0.76217 0.47713 0.47624 76 76 B B biological fallback assumption illumina hiseq_era full_length cdna_unspecified smarter bulk bulk bulk   United States 2022-06-24 Segmentation Embryo Brain Nervous System
70438 70438 SRR19846952 SRX15890623 SRS13579727 SRP383494 PRJNA852585 Control of cranial ectomesenchyme fate by Nr2f nuclear receptors GSE206903 Transcriptome Analysis Certain cranial neural crest cells are uniquely endowed with the ability to make skeletal cell types otherwise only derived from mesoderm. As these cells migrate into the pharyngeal arches they downregulate neural crest specifier genes and upregulate so called ectomesenchyme genes characteristic of skeletal progenitors. While both external and cell autonomous factors have been proposed as triggers of this transition the details remain obscure. Here we report the Nr2f nuclear receptors as novel intrinsic activators of the ectomesenchyme program: zebrafish nr2f5 and nr2f2; nr2f5 mutants show a marked delay in upregulation of ectomesenchyme genes such as dlx2a prrx1a/b sox9a twist1a and fli1a and in downregulation of the non ectomesenchyme specifier sox10. Depending on genotype mutants partially or fully recover likely via functional redundancy with other Nr2f genes. Loss of sox10 fully rescued skeletal development in nr2f5 single but not nr2f2; nr2f5 double mutants while the ectomesenchyme defect persisted in both. Sox10 perdurance thus antagonizes the recovery rather than causing the initial aberration. Unraveling the mechanics of Nr2f function will help solve the enduring puzzle of how cranial neural crest acquire skeletal potency. Overall design: Bulk RNA seq was performed on FACS purified zebrafish neural crest cells expressing sox10:DsRed from 20 hpf nr2f2[unknown]; nr2f5[mutant] embryos 2 replicates: n = 88 & 35 and wild type control embryos 2 replicates: n = 110 & 120.   pubmed:36367707   sox10:DsRed+ neural crest cells from 20 hpf nr2f2;nr2f5 mutant embryos biol rep 2 GSM6266710   tissue:sox10:DsRed+ neural crest cells|cell type:sox10:DsRed+ neural crest cells|genotype:nr2f2[unk]; nr2f5[mut]|developmental stage:20 hpf sox10:DsRed+ neural crest cells from 20 hpf nr2f2;nr2f5 mutant embryos biol rep 2 Illumina control software was used for base calling. Sequences were pseudoaligned and quantified at TPM values using Kallisto. Assembly: GRCz11 Supplementary files format and content: TPM Barske2022.txt: Tab delimited text file includes TPM values for each transcript. sox10:DsRed+ neural crest cells   Total RNA was extracted from sorted cells using the RNeasy Micro kit Qiagen. The purified RNA samples were tested for quality and quantity on a BioAnalyzer and then reverse transcribed into cDNA using the SMARTer kit. cDNA amplification was adjusted based on the RNA input and the size and amount of cDNA was measured by BioAnalyzer. Sonication was performed on an S2 ultrasonicator. DNA libraries were created with the Kapa Hyper Prep kit and NextFlex adapters assessed by Bioanalyzer and quantified using the Kapa Library Quantification kit.   cell type:sox10:DsRed+ neural crest cells|genotype:nr2f2[unk]; nr2f5[mut]|developmental stage:20 hpf GSM6266710 GSM6266710: sox10:DsRed+ neural crest cells from 20 hpf nr2f2;nr2f5 mutant embryos biol rep 2; Danio rerio; RNA Seq GSM6266710 r1 GSM6266710 1 Total RNA was extracted from sorted cells using the RNeasy Micro kit Qiagen. The purified RNA samples were tested for quality and quantity on a BioAnalyzer and then reverse transcribed into cDNA using the SMARTer kit. cDNA amplification was adjusted based on the RNA input and the size and amount of cDNA was measured by BioAnalyzer. Sonication was performed on an S2 ultrasonicator. DNA libraries were created with the Kapa Hyper Prep kit and NextFlex adapters assessed by Bioanalyzer and quantified using the Kapa Library Quantification kit.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP383494   loader:fastq load.py sox10DsRed-MUT2-S2-R1.fastq.gz sox10DsRed-MUT2-S2-R2.fastq.gz fastq fastq 4289333904.0 28219302.0 GSM6266710 r1 0:76 1:76 A:1191429143;C:963361475;G:1000468087;T:1133905434;N:169765 76 76     1191429143 963361475 1000468087 1133905434 169765 SRX15890623 SRS13579727     Human Genetics, Cincinnati Children's Hospital Medical Center 2 0.8017 0.80251 0.0318 0.03187 0.78106 0.78606 0.46375 0.46931 76 76 B B biological fallback assumption illumina hiseq_era full_length cdna_unspecified smarter bulk bulk bulk   United States 2022-06-24 Segmentation Embryo Brain Nervous System
70439 70439 SRR19846953 SRX15890622 SRS13579726 SRP383494 PRJNA852585 Control of cranial ectomesenchyme fate by Nr2f nuclear receptors GSE206903 Transcriptome Analysis Certain cranial neural crest cells are uniquely endowed with the ability to make skeletal cell types otherwise only derived from mesoderm. As these cells migrate into the pharyngeal arches they downregulate neural crest specifier genes and upregulate so called ectomesenchyme genes characteristic of skeletal progenitors. While both external and cell autonomous factors have been proposed as triggers of this transition the details remain obscure. Here we report the Nr2f nuclear receptors as novel intrinsic activators of the ectomesenchyme program: zebrafish nr2f5 and nr2f2; nr2f5 mutants show a marked delay in upregulation of ectomesenchyme genes such as dlx2a prrx1a/b sox9a twist1a and fli1a and in downregulation of the non ectomesenchyme specifier sox10. Depending on genotype mutants partially or fully recover likely via functional redundancy with other Nr2f genes. Loss of sox10 fully rescued skeletal development in nr2f5 single but not nr2f2; nr2f5 double mutants while the ectomesenchyme defect persisted in both. Sox10 perdurance thus antagonizes the recovery rather than causing the initial aberration. Unraveling the mechanics of Nr2f function will help solve the enduring puzzle of how cranial neural crest acquire skeletal potency. Overall design: Bulk RNA seq was performed on FACS purified zebrafish neural crest cells expressing sox10:DsRed from 20 hpf nr2f2[unknown]; nr2f5[mutant] embryos 2 replicates: n = 88 & 35 and wild type control embryos 2 replicates: n = 110 & 120.   pubmed:36367707   sox10:DsRed+ neural crest cells from 20 hpf nr2f2;nr2f5 mutant embryos biol rep 1 GSM6266709   tissue:sox10:DsRed+ neural crest cells|cell type:sox10:DsRed+ neural crest cells|genotype:nr2f2[unk]; nr2f5[mut]|developmental stage:20 hpf sox10:DsRed+ neural crest cells from 20 hpf nr2f2;nr2f5 mutant embryos biol rep 1 Illumina control software was used for base calling. Sequences were pseudoaligned and quantified at TPM values using Kallisto. Assembly: GRCz11 Supplementary files format and content: TPM Barske2022.txt: Tab delimited text file includes TPM values for each transcript. sox10:DsRed+ neural crest cells   Total RNA was extracted from sorted cells using the RNeasy Micro kit Qiagen. The purified RNA samples were tested for quality and quantity on a BioAnalyzer and then reverse transcribed into cDNA using the SMARTer kit. cDNA amplification was adjusted based on the RNA input and the size and amount of cDNA was measured by BioAnalyzer. Sonication was performed on an S2 ultrasonicator. DNA libraries were created with the Kapa Hyper Prep kit and NextFlex adapters assessed by Bioanalyzer and quantified using the Kapa Library Quantification kit.   cell type:sox10:DsRed+ neural crest cells|genotype:nr2f2[unk]; nr2f5[mut]|developmental stage:20 hpf GSM6266709 GSM6266709: sox10:DsRed+ neural crest cells from 20 hpf nr2f2;nr2f5 mutant embryos biol rep 1; Danio rerio; RNA Seq GSM6266709 r1 GSM6266709 1 Total RNA was extracted from sorted cells using the RNeasy Micro kit Qiagen. The purified RNA samples were tested for quality and quantity on a BioAnalyzer and then reverse transcribed into cDNA using the SMARTer kit. cDNA amplification was adjusted based on the RNA input and the size and amount of cDNA was measured by BioAnalyzer. Sonication was performed on an S2 ultrasonicator. DNA libraries were created with the Kapa Hyper Prep kit and NextFlex adapters assessed by Bioanalyzer and quantified using the Kapa Library Quantification kit.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP383494   loader:fastq load.py sox10DsRed-MUT1-S1-R1.fastq.gz sox10DsRed-MUT1-S1_R2_001.fastq.gz fastq fastq 4812271816.0 31659683.0 GSM6266709 r1 0:76 1:76 A:1327161695;C:1091694077;G:1133722041;T:1259497189;N:196814 76 76     1327161695 1091694077 1133722041 1259497189 196814 SRX15890622 SRS13579726     Human Genetics, Cincinnati Children's Hospital Medical Center 2 0.90398 0.90573 0.03493 0.0351 0.76928 0.77429 0.46651 0.46743 76 76 B B biological fallback assumption illumina hiseq_era full_length cdna_unspecified smarter bulk bulk bulk   United States 2022-06-24 Segmentation Embryo Brain Nervous System

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CREATE TABLE run_metadata("run.accession" VARCHAR, "experiment.accession" VARCHAR, "sample.accession" VARCHAR, "study.accession" VARCHAR, bioproject VARCHAR, "study.title" VARCHAR, "study.alias" VARCHAR, "study.type" VARCHAR, "study.abstract" VARCHAR, "study.attributes" VARCHAR, "study.PMIDs" VARCHAR, "sample.description" VARCHAR, "sample.title" VARCHAR, "sample.alias" VARCHAR, "sample.centername" VARCHAR, "sample.attributes" VARCHAR, "GEOsample.title" VARCHAR, "GEOsample.dataprocessing" VARCHAR, "GEOsample.source" VARCHAR, "GEOsample.treatmentprotocol" VARCHAR, "GEOsample.extractprotocol" VARCHAR, "GEOsample.growthprotocol" VARCHAR, "GEOsample.characteristics" VARCHAR, "GEOsample.accession" VARCHAR, "experiment.title" VARCHAR, "experiment.alias" VARCHAR, "experiment.library_name" VARCHAR, "experiment.design_description" VARCHAR, "experiment.library_construction_protocol" VARCHAR, "experiment.attributes" VARCHAR, "experiment.library_strategy" VARCHAR, "experiment.library_source" VARCHAR, "experiment.library_selection" VARCHAR, "experiment.library_layout" VARCHAR, "experiment.platform" VARCHAR, "experiment.instrument_model" VARCHAR, "experiment.spot_descriptor" VARCHAR, "experiment.study_ref" VARCHAR, "run.title" VARCHAR, "run.attributes" VARCHAR, "run.filename" VARCHAR, "run.semantic_name" VARCHAR, "run.total_bases" DOUBLE, "run.total_spots" DOUBLE, "run.alias" VARCHAR, "run.read_lengths" VARCHAR, "run.base_counts" VARCHAR, "run.r1_length" BIGINT, "run.r2_length" BIGINT, "run.r3_length" BIGINT, "run.r4_length" BIGINT, "run.Acount" BIGINT, "run.Ccount" BIGINT, "run.Gcount" BIGINT, "run.Tcount" BIGINT, "run.Ncount" BIGINT, "run.experiment" VARCHAR, "run.pool_member" VARCHAR, "submission.accession" VARCHAR, "submission.srasource" VARCHAR, "submission.bioprojectsource" VARCHAR, "seqdetective.n_mates" BIGINT, "seqdetective.mapping_rate.mate1" DOUBLE, "seqdetective.mapping_rate.mate2" DOUBLE, "seqdetective.nofeature_rate.mate1" DOUBLE, "seqdetective.nofeature_rate.mate2" DOUBLE, "seqdetective.sparsity.mate1" DOUBLE, "seqdetective.sparsity.mate2" DOUBLE, "seqdetective.pos_strand_rate.mate1" DOUBLE, "seqdetective.pos_strand_rate.mate2" DOUBLE, "seqdetective.readlen.mate1" BIGINT, "seqdetective.readlen.mate2" BIGINT, "seqdetective.judgement.mate1" VARCHAR, "seqdetective.judgement.mate2" VARCHAR, "seqdetective.judgement.reason" VARCHAR, platform_family VARCHAR, instrument_generation VARCHAR, read_bias VARCHAR, selection_class VARCHAR, prep_kit VARCHAR, sc_or_bulk VARCHAR, tech_class VARCHAR, technology VARCHAR, tech_variant VARCHAR, "submission.bioprojectsource.country" VARCHAR, earliest_date DATE, devstage_curation VARCHAR, devstage_curation_coarse VARCHAR, tissue_curation VARCHAR, tissue_curation_coarse VARCHAR);;
CREATE INDEX idx_run_bioproject ON run_metadata(bioproject);;
CREATE INDEX idx_run_run_accession ON run_metadata("run.accession");;