{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where experiment.library_selection = \"cDNA\", technology = \"generic-scrnaseq-only\" and tissue_curation = \"Whole Organism\"", "rows": [[25324, "SRR25820349", "SRX21542119", "SRS18751470", "SRP457651", "PRJNA1010830", "Identifying hand2 downstream targets in cardiomyocyte during early cardiogenesis", "GSE241971", "Other", "hand2 reporter expressing cardiac cells fail to migrate to the midline. To investigate the underlying molecular changes we sequenced mRNA from 3900 and 3836 hand2 reporter expressing single cells from 24 hpf hand2 FLD / and hand2 FLD+/? sibling embryos respectively. Furthermore hand2 is broadly expressed within the LPM which gives rise to various cell lineages and tissues including the cardiovascular system blood kidneys mesothelium and limb connective tissue. To further investigate the requirement of Hand2 in the early events of cardiac lineage specification in zebrafish we aim to characterize the early hand2 expressing cardiac precursors by using embryonic CM H3K27ac ChIP seq and ATAC seq data. Overall design: scRNA seq: WT: hand2 reporter expressing single cells from 24 hpf hand2 FLD+/? Embryos; mutants: hand2 reporter expressing single cells from 24 hpf hand2 FLD / sibling embryos. ATAC seq and CGIP seq: Comparing myl7:GFP+ CMs with myl7:GFP cells", null, "pubmed:39658721", null, "MUT replicate1 scRNA", "GSM7746945", null, "source name:whole embryo|tissue:whole embryo|cell type:hand2 reporter expressing single cells|genotype:hand2 mutants|geo loc name:missing|collection date:missing", "MUT replicate1 scRNA", "demultiplexing star solo mapping: ' soloType CB UMI Simple soloBarcodeReadLength 0 soloCellFilter EmptyDrops CR 5000 0.99 10 45000 90000 500 0.01 20000 0.01 10000' Assembly: danio rerio/101 Supplementary files format and content: 10x based mtx raw count matrix barcodes and genes", "whole embryo", null, "10xGenomics", null, "tissue:whole embryo|cell type:hand2 reporter expressing single cells|genotype:hand2 mutants", "GSM7746945", "GSM7746945: MUT replicate1 scRNA; Danio rerio; RNA Seq", "GSM7746945 r1", "GSM7746945", "1", "10xGenomics", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP457651", null, null, "Yanli_10x_Mut_24hpf_R2.fastq.gz Yanli_10x_Mut_24hpf_R1.fastq.gz", "fastq fastq", 12703207777.0, 159786155.0, "GSM7746945 r1", "0:28 1:51.50", "A:3417159154;C:2758515982;G:2823785724;T:3638099229;N:65647688", 28, 51, null, null, 3417159154, 2758515982, 2823785724, 3638099229, 65647688, "SRX21542119", "SRS18751470", "SRA1702565", "Max Planck Institute for Heart and Lung Research", "Max Planck Institute for Heart and Lung Research", 2, 0.00189, 0.93843, 0.0006, 0.12822, 0.99571, 0.781, 0.38429, 0.49855, 28, 52, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_generic", "generic-scrnaseq-only", null, "Germany", "2023-08-30", "Undetermined", "Embryo", "Whole Organism", "All anatomical structures"], [25325, "SRR25820350", "SRX21542118", "SRS18751469", "SRP457651", "PRJNA1010830", "Identifying hand2 downstream targets in cardiomyocyte during early cardiogenesis", "GSE241971", "Other", "hand2 reporter expressing cardiac cells fail to migrate to the midline. To investigate the underlying molecular changes we sequenced mRNA from 3900 and 3836 hand2 reporter expressing single cells from 24 hpf hand2 FLD / and hand2 FLD+/? sibling embryos respectively. Furthermore hand2 is broadly expressed within the LPM which gives rise to various cell lineages and tissues including the cardiovascular system blood kidneys mesothelium and limb connective tissue. To further investigate the requirement of Hand2 in the early events of cardiac lineage specification in zebrafish we aim to characterize the early hand2 expressing cardiac precursors by using embryonic CM H3K27ac ChIP seq and ATAC seq data. Overall design: scRNA seq: WT: hand2 reporter expressing single cells from 24 hpf hand2 FLD+/? Embryos; mutants: hand2 reporter expressing single cells from 24 hpf hand2 FLD / sibling embryos. ATAC seq and CGIP seq: Comparing myl7:GFP+ CMs with myl7:GFP cells", null, "pubmed:39658721", null, "WT replicate 1 scRNA", "GSM7746944", null, "source name:whole embryo|tissue:whole embryo|cell type:hand2 reporter expressing single cells|genotype:WT|geo loc name:missing|collection date:missing", "WT replicate 1 scRNA", "demultiplexing star solo mapping: ' soloType CB UMI Simple soloBarcodeReadLength 0 soloCellFilter EmptyDrops CR 5000 0.99 10 45000 90000 500 0.01 20000 0.01 10000' Assembly: danio rerio/101 Supplementary files format and content: 10x based mtx raw count matrix barcodes and genes", "whole embryo", null, "10xGenomics", null, "tissue:whole embryo|cell type:hand2 reporter expressing single cells|genotype:WT", "GSM7746944", "GSM7746944: WT replicate 1 scRNA; Danio rerio; RNA Seq", "GSM7746944 r1", "GSM7746944", "1", "10xGenomics", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP457651", null, null, "Yanli_10x_WT_24hpf_R2.fastq.gz Yanli_10x_WT_24hpf_R1.fastq.gz", "fastq fastq", 9691697994.0, 121912639.0, "GSM7746944 r1", "0:28 1:51.50", "A:2617434834;C:2102210357;G:2159290265;T:2762773221;N:49989317", 28, 51, null, null, 2617434834, 2102210357, 2159290265, 2762773221, 49989317, "SRX21542118", "SRS18751469", "SRA1702565", "Max Planck Institute for Heart and Lung Research", "Max Planck Institute for Heart and Lung Research", 2, 0.00175, 0.93872, 0.00057, 0.12715, 0.99584, 0.78713, 0.40888, 0.504, 28, 52, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_generic", "generic-scrnaseq-only", null, "Germany", "2023-08-30", "Undetermined", "Embryo", "Whole Organism", "All anatomical structures"], [28611, "SRR26471890", "SRX22175831", "SRS19233331", "SRP467949", "PRJNA1031141", "Cebp1 and Cebp\u00df transcriptional axis controls eosinophilopoiesis in zebrafish [bulkRNA Seq]", "GSE246037", "Transcriptome Analysis", "Eosinophils are well known to regulate host protection from parasites and have been reported to paticipate many other physiologic and pathologic processes. Understanding the role of eosinophils in these processes requires a better understanding of eosinophilopoiesis. Using a zebrafish model we have identified an eosinophil lineage specific marker eslec. Using this marker we have established a Tgeslec:eGFP reporter line which specifically labels zebrafish eosinophil lineage cells from early life through maturity. Spatial temporal analysis of eslec+ cells demonstrated organ distribution at the larval stage. By single cell RNA Seq of eslec+ cells tissue distributed eosinophils were found to have similar differentiation paths but different tissue specific expression profiles. Genetic analysis demonstrated a Cebp1 and Cebp\u00df transcriptional axis that regulated eosinophilopoiesis in which Cebp1 directly targeted cebpb to inhibit eosinophil differentiationthe commitment differentiation and maturation of the eosinophil lineage. In summary this study characterized eosinophil development in multiple dimensions including spatial temporal patterns expression profiles and genetic regulators. The results provide for a better understanding of eosinophilopoiesis. Overall design: For the RNA Seq analysis of eosinophils from different genotypes eslec:eGFP+ eosinophils were sorted from whole larvae 7 dpf and lysed. The lysates were directly applied to reverse transcription and amplification. Enriched cDNA were then fragmented adpator tagged and purified for further sequencing.", "parent bioproject:PRJNA814534", "pubmed:38280871", null, "cebpb mut eos 2", "GSM7854238", null, "source name:eosinophils|strain:AB strain|tissue:whole larvae|genotype:cebpb / |transgene:Tgeslec:eGFP|geo loc name:missing|collection date:missing", "cebpb mut eos 2", "Post quality control the fastq files were mapped to the zebrafish genome with the \"STAR\" package. Mapped reads were annotated with the \"FeatureCounts\" package. Annotated reads were applied to the \"DESeq2\" package for differential expressed genes analysis. The sample to sample distance heatmaps were generated by \"pheatmap\" with the output of \"DESeq2\". The gene expression heatmaps were generated by \"pheatmap\" with the Z score of the TPM matrix. Assembly: GRCz11 Supplementary files format and content: Normalized matrix table with Transcripts Per Kilobase TPM for every gene and every sample", "eosinophils", null, "Whole larvae were ground and digested into cell suspensions. The cell suspensions were then analyzed with FACS and the eGFP+ cells 500 cells for each sample were sorted into lysis buffer. The lysates were directly applied to reverse transcription and amplification. Enriched cDNA were then fragmented adpator tagged and purified for further sequencing.", null, "strain:AB strain|tissue:whole larvae|genotype:cebpb / |transgene:Tgeslec:eGFP", "GSM7854238", "GSM7854238: cebpb mut eos 2; Danio rerio; RNA Seq", "GSM7854238 r1", "GSM7854238", "1", "Whole larvae were ground and digested into cell suspensions. The cell suspensions were then analyzed with FACS and the eGFP+ cells 500 cells for each sample were sorted into lysis buffer. The lysates were directly applied to reverse transcription and amplification. Enriched cDNA were then fragmented adpator tagged and purified for further sequencing.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP467949", null, "loader:fastq load.py", "F2_1.fq.gz F2_2.fq.gz", "fastq fastq", 6304806000.0, 21016020.0, "GSM7854238 r1", "0:150 1:150", "A:1797551316;C:1332146220;G:1348919312;T:1826125402;N:63750", 150, 150, null, null, 1797551316, 1332146220, 1348919312, 1826125402, 63750, "SRX22175831", "SRS19233331", "SRA1737851", "South China University of Technology", "South China University of Technology", 2, 0.90391, 0.90473, 0.3135, 0.31222, 0.83753, 0.83613, 0.53444, 0.53443, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "sc_generic", "single_cell_generic", "generic-scrnaseq-only", null, "China", "2023-10-23", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [28612, "SRR26471891", "SRX22175830", "SRS19233328", "SRP467949", "PRJNA1031141", "Cebp1 and Cebp\u00df transcriptional axis controls eosinophilopoiesis in zebrafish [bulkRNA Seq]", "GSE246037", "Transcriptome Analysis", "Eosinophils are well known to regulate host protection from parasites and have been reported to paticipate many other physiologic and pathologic processes. Understanding the role of eosinophils in these processes requires a better understanding of eosinophilopoiesis. Using a zebrafish model we have identified an eosinophil lineage specific marker eslec. Using this marker we have established a Tgeslec:eGFP reporter line which specifically labels zebrafish eosinophil lineage cells from early life through maturity. Spatial temporal analysis of eslec+ cells demonstrated organ distribution at the larval stage. By single cell RNA Seq of eslec+ cells tissue distributed eosinophils were found to have similar differentiation paths but different tissue specific expression profiles. Genetic analysis demonstrated a Cebp1 and Cebp\u00df transcriptional axis that regulated eosinophilopoiesis in which Cebp1 directly targeted cebpb to inhibit eosinophil differentiationthe commitment differentiation and maturation of the eosinophil lineage. In summary this study characterized eosinophil development in multiple dimensions including spatial temporal patterns expression profiles and genetic regulators. The results provide for a better understanding of eosinophilopoiesis. Overall design: For the RNA Seq analysis of eosinophils from different genotypes eslec:eGFP+ eosinophils were sorted from whole larvae 7 dpf and lysed. The lysates were directly applied to reverse transcription and amplification. Enriched cDNA were then fragmented adpator tagged and purified for further sequencing.", "parent bioproject:PRJNA814534", "pubmed:38280871", null, "cebpb wt eos 1", "GSM7854239", null, "source name:eosinophils|strain:AB strain|tissue:whole larvae|genotype:wild type|transgene:Tgeslec:eGFP|geo loc name:missing|collection date:missing", "cebpb wt eos 1", "Post quality control the fastq files were mapped to the zebrafish genome with the \"STAR\" package. Mapped reads were annotated with the \"FeatureCounts\" package. Annotated reads were applied to the \"DESeq2\" package for differential expressed genes analysis. The sample to sample distance heatmaps were generated by \"pheatmap\" with the output of \"DESeq2\". The gene expression heatmaps were generated by \"pheatmap\" with the Z score of the TPM matrix. Assembly: GRCz11 Supplementary files format and content: Normalized matrix table with Transcripts Per Kilobase TPM for every gene and every sample", "eosinophils", null, "Whole larvae were ground and digested into cell suspensions. The cell suspensions were then analyzed with FACS and the eGFP+ cells 500 cells for each sample were sorted into lysis buffer. The lysates were directly applied to reverse transcription and amplification. Enriched cDNA were then fragmented adpator tagged and purified for further sequencing.", null, "strain:AB strain|tissue:whole larvae|genotype:wild type|transgene:Tgeslec:eGFP", "GSM7854239", "GSM7854239: cebpb wt eos 1; Danio rerio; RNA Seq", "GSM7854239 r1", "GSM7854239", "1", "Whole larvae were ground and digested into cell suspensions. The cell suspensions were then analyzed with FACS and the eGFP+ cells 500 cells for each sample were sorted into lysis buffer. The lysates were directly applied to reverse transcription and amplification. Enriched cDNA were then fragmented adpator tagged and purified for further sequencing.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP467949", null, "loader:fastq load.py", "Z1_1.fq.gz Z1_2.fq.gz", "fastq fastq", 6180805800.0, 20602686.0, "GSM7854239 r1", "0:150 1:150", "A:1699796929;C:1374020384;G:1377922189;T:1729003691;N:62607", 150, 150, null, null, 1699796929, 1374020384, 1377922189, 1729003691, 62607, "SRX22175830", "SRS19233328", "SRA1737851", "South China University of Technology", "South China University of Technology", 2, 0.91982, 0.9224, 0.18189, 0.18148, 0.82814, 0.82672, 0.51271, 0.5152, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "sc_generic", "single_cell_generic", "generic-scrnaseq-only", null, "China", "2023-10-23", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [28613, "SRR26471892", "SRX22175829", "SRS19233330", "SRP467949", "PRJNA1031141", "Cebp1 and Cebp\u00df transcriptional axis controls eosinophilopoiesis in zebrafish [bulkRNA Seq]", "GSE246037", "Transcriptome Analysis", "Eosinophils are well known to regulate host protection from parasites and have been reported to paticipate many other physiologic and pathologic processes. Understanding the role of eosinophils in these processes requires a better understanding of eosinophilopoiesis. Using a zebrafish model we have identified an eosinophil lineage specific marker eslec. Using this marker we have established a Tgeslec:eGFP reporter line which specifically labels zebrafish eosinophil lineage cells from early life through maturity. Spatial temporal analysis of eslec+ cells demonstrated organ distribution at the larval stage. By single cell RNA Seq of eslec+ cells tissue distributed eosinophils were found to have similar differentiation paths but different tissue specific expression profiles. Genetic analysis demonstrated a Cebp1 and Cebp\u00df transcriptional axis that regulated eosinophilopoiesis in which Cebp1 directly targeted cebpb to inhibit eosinophil differentiationthe commitment differentiation and maturation of the eosinophil lineage. In summary this study characterized eosinophil development in multiple dimensions including spatial temporal patterns expression profiles and genetic regulators. The results provide for a better understanding of eosinophilopoiesis. Overall design: For the RNA Seq analysis of eosinophils from different genotypes eslec:eGFP+ eosinophils were sorted from whole larvae 7 dpf and lysed. The lysates were directly applied to reverse transcription and amplification. Enriched cDNA were then fragmented adpator tagged and purified for further sequencing.", "parent bioproject:PRJNA814534", "pubmed:38280871", null, "cebpb wt eos 2", "GSM7854240", null, "source name:eosinophils|strain:AB strain|tissue:whole larvae|genotype:wild type|transgene:Tgeslec:eGFP|geo loc name:missing|collection date:missing", "cebpb wt eos 2", "Post quality control the fastq files were mapped to the zebrafish genome with the \"STAR\" package. Mapped reads were annotated with the \"FeatureCounts\" package. Annotated reads were applied to the \"DESeq2\" package for differential expressed genes analysis. The sample to sample distance heatmaps were generated by \"pheatmap\" with the output of \"DESeq2\". The gene expression heatmaps were generated by \"pheatmap\" with the Z score of the TPM matrix. Assembly: GRCz11 Supplementary files format and content: Normalized matrix table with Transcripts Per Kilobase TPM for every gene and every sample", "eosinophils", null, "Whole larvae were ground and digested into cell suspensions. The cell suspensions were then analyzed with FACS and the eGFP+ cells 500 cells for each sample were sorted into lysis buffer. The lysates were directly applied to reverse transcription and amplification. Enriched cDNA were then fragmented adpator tagged and purified for further sequencing.", null, "strain:AB strain|tissue:whole larvae|genotype:wild type|transgene:Tgeslec:eGFP", "GSM7854240", "GSM7854240: cebpb wt eos 2; Danio rerio; RNA Seq", "GSM7854240 r1", "GSM7854240", "1", "Whole larvae were ground and digested into cell suspensions. The cell suspensions were then analyzed with FACS and the eGFP+ cells 500 cells for each sample were sorted into lysis buffer. The lysates were directly applied to reverse transcription and amplification. Enriched cDNA were then fragmented adpator tagged and purified for further sequencing.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP467949", null, "loader:fastq load.py", "Z2_1.fq.gz Z2_2.fq.gz", "fastq fastq", 6693470100.0, 22311567.0, "GSM7854240 r1", "0:150 1:150", "A:1840742978;C:1484923084;G:1499378237;T:1868364754;N:61047", 150, 150, null, null, 1840742978, 1484923084, 1499378237, 1868364754, 61047, "SRX22175829", "SRS19233330", "SRA1737851", "South China University of Technology", "South China University of Technology", 2, 0.92056, 0.92353, 0.18668, 0.18721, 0.82771, 0.82696, 0.53034, 0.52277, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "sc_generic", "single_cell_generic", "generic-scrnaseq-only", null, "China", "2023-10-23", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [28614, "SRR26471893", "SRX22175828", "SRS19233332", "SRP467949", "PRJNA1031141", "Cebp1 and Cebp\u00df transcriptional axis controls eosinophilopoiesis in zebrafish [bulkRNA Seq]", "GSE246037", "Transcriptome Analysis", "Eosinophils are well known to regulate host protection from parasites and have been reported to paticipate many other physiologic and pathologic processes. Understanding the role of eosinophils in these processes requires a better understanding of eosinophilopoiesis. Using a zebrafish model we have identified an eosinophil lineage specific marker eslec. Using this marker we have established a Tgeslec:eGFP reporter line which specifically labels zebrafish eosinophil lineage cells from early life through maturity. Spatial temporal analysis of eslec+ cells demonstrated organ distribution at the larval stage. By single cell RNA Seq of eslec+ cells tissue distributed eosinophils were found to have similar differentiation paths but different tissue specific expression profiles. Genetic analysis demonstrated a Cebp1 and Cebp\u00df transcriptional axis that regulated eosinophilopoiesis in which Cebp1 directly targeted cebpb to inhibit eosinophil differentiationthe commitment differentiation and maturation of the eosinophil lineage. In summary this study characterized eosinophil development in multiple dimensions including spatial temporal patterns expression profiles and genetic regulators. The results provide for a better understanding of eosinophilopoiesis. Overall design: For the RNA Seq analysis of eosinophils from different genotypes eslec:eGFP+ eosinophils were sorted from whole larvae 7 dpf and lysed. The lysates were directly applied to reverse transcription and amplification. Enriched cDNA were then fragmented adpator tagged and purified for further sequencing.", "parent bioproject:PRJNA814534", "pubmed:38280871", null, "cebpb mut eos 1", "GSM7854237", null, "source name:eosinophils|strain:AB strain|tissue:whole larvae|genotype:cebpb / |transgene:Tgeslec:eGFP|geo loc name:missing|collection date:missing", "cebpb mut eos 1", "Post quality control the fastq files were mapped to the zebrafish genome with the \"STAR\" package. Mapped reads were annotated with the \"FeatureCounts\" package. Annotated reads were applied to the \"DESeq2\" package for differential expressed genes analysis. The sample to sample distance heatmaps were generated by \"pheatmap\" with the output of \"DESeq2\". The gene expression heatmaps were generated by \"pheatmap\" with the Z score of the TPM matrix. Assembly: GRCz11 Supplementary files format and content: Normalized matrix table with Transcripts Per Kilobase TPM for every gene and every sample", "eosinophils", null, "Whole larvae were ground and digested into cell suspensions. The cell suspensions were then analyzed with FACS and the eGFP+ cells 500 cells for each sample were sorted into lysis buffer. The lysates were directly applied to reverse transcription and amplification. Enriched cDNA were then fragmented adpator tagged and purified for further sequencing.", null, "strain:AB strain|tissue:whole larvae|genotype:cebpb / |transgene:Tgeslec:eGFP", "GSM7854237", "GSM7854237: cebpb mut eos 1; Danio rerio; RNA Seq", "GSM7854237 r1", "GSM7854237", "1", "Whole larvae were ground and digested into cell suspensions. The cell suspensions were then analyzed with FACS and the eGFP+ cells 500 cells for each sample were sorted into lysis buffer. The lysates were directly applied to reverse transcription and amplification. Enriched cDNA were then fragmented adpator tagged and purified for further sequencing.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP467949", null, "loader:fastq load.py", "F1_1.fq.gz F1_2.fq.gz", "fastq fastq", 7774783500.0, 25915945.0, "GSM7854237 r1", "0:150 1:150", "A:2205128515;C:1660071767;G:1677499789;T:2232048253;N:35176", 150, 150, null, null, 2205128515, 1660071767, 1677499789, 2232048253, 35176, "SRX22175828", "SRS19233332", "SRA1737851", "South China University of Technology", "South China University of Technology", 2, 0.90668, 0.90886, 0.34302, 0.34395, 0.81943, 0.81937, 0.5348, 0.54523, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "sc_generic", "single_cell_generic", "generic-scrnaseq-only", null, "China", "2023-10-23", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [28615, "SRR26471894", "SRX22175827", "SRS19233329", "SRP467949", "PRJNA1031141", "Cebp1 and Cebp\u00df transcriptional axis controls eosinophilopoiesis in zebrafish [bulkRNA Seq]", "GSE246037", "Transcriptome Analysis", "Eosinophils are well known to regulate host protection from parasites and have been reported to paticipate many other physiologic and pathologic processes. Understanding the role of eosinophils in these processes requires a better understanding of eosinophilopoiesis. Using a zebrafish model we have identified an eosinophil lineage specific marker eslec. Using this marker we have established a Tgeslec:eGFP reporter line which specifically labels zebrafish eosinophil lineage cells from early life through maturity. Spatial temporal analysis of eslec+ cells demonstrated organ distribution at the larval stage. By single cell RNA Seq of eslec+ cells tissue distributed eosinophils were found to have similar differentiation paths but different tissue specific expression profiles. Genetic analysis demonstrated a Cebp1 and Cebp\u00df transcriptional axis that regulated eosinophilopoiesis in which Cebp1 directly targeted cebpb to inhibit eosinophil differentiationthe commitment differentiation and maturation of the eosinophil lineage. In summary this study characterized eosinophil development in multiple dimensions including spatial temporal patterns expression profiles and genetic regulators. The results provide for a better understanding of eosinophilopoiesis. Overall design: For the RNA Seq analysis of eosinophils from different genotypes eslec:eGFP+ eosinophils were sorted from whole larvae 7 dpf and lysed. The lysates were directly applied to reverse transcription and amplification. Enriched cDNA were then fragmented adpator tagged and purified for further sequencing.", "parent bioproject:PRJNA814534", "pubmed:38280871", null, "cebp1 wt eos 2", "GSM7854236", null, "source name:eosinophils|strain:AB strain|tissue:whole larvae|genotype:wild type|transgene:Tgeslec:eGFP|geo loc name:missing|collection date:missing", "cebp1 wt eos 2", "Post quality control the fastq files were mapped to the zebrafish genome with the \"STAR\" package. Mapped reads were annotated with the \"FeatureCounts\" package. Annotated reads were applied to the \"DESeq2\" package for differential expressed genes analysis. The sample to sample distance heatmaps were generated by \"pheatmap\" with the output of \"DESeq2\". The gene expression heatmaps were generated by \"pheatmap\" with the Z score of the TPM matrix. Assembly: GRCz11 Supplementary files format and content: Normalized matrix table with Transcripts Per Kilobase TPM for every gene and every sample", "eosinophils", null, "Whole larvae were ground and digested into cell suspensions. The cell suspensions were then analyzed with FACS and the eGFP+ cells 500 cells for each sample were sorted into lysis buffer. The lysates were directly applied to reverse transcription and amplification. Enriched cDNA were then fragmented adpator tagged and purified for further sequencing.", null, "strain:AB strain|tissue:whole larvae|genotype:wild type|transgene:Tgeslec:eGFP", "GSM7854236", "GSM7854236: cebp1 wt eos 2; Danio rerio; RNA Seq", "GSM7854236 r1", "GSM7854236", "1", "Whole larvae were ground and digested into cell suspensions. The cell suspensions were then analyzed with FACS and the eGFP+ cells 500 cells for each sample were sorted into lysis buffer. The lysates were directly applied to reverse transcription and amplification. Enriched cDNA were then fragmented adpator tagged and purified for further sequencing.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP467949", null, "loader:fastq load.py", "W2_1.fq.gz W2_2.fq.gz", "fastq fastq", 6478425300.0, 21594751.0, "GSM7854236 r1", "0:150 1:150", "A:2031706672;C:1135087913;G:1324534931;T:1987064653;N:31131", 150, 150, null, null, 2031706672, 1135087913, 1324534931, 1987064653, 31131, "SRX22175827", "SRS19233329", "SRA1737851", "South China University of Technology", "South China University of Technology", 2, 0.74912, 0.74531, 0.50454, 0.49737, 0.79255, 0.78539, 0.63484, 0.64052, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "sc_generic", "single_cell_generic", "generic-scrnaseq-only", null, "China", "2023-10-23", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [28616, "SRR26471895", "SRX22175826", "SRS19233326", "SRP467949", "PRJNA1031141", "Cebp1 and Cebp\u00df transcriptional axis controls eosinophilopoiesis in zebrafish [bulkRNA Seq]", "GSE246037", "Transcriptome Analysis", "Eosinophils are well known to regulate host protection from parasites and have been reported to paticipate many other physiologic and pathologic processes. Understanding the role of eosinophils in these processes requires a better understanding of eosinophilopoiesis. Using a zebrafish model we have identified an eosinophil lineage specific marker eslec. Using this marker we have established a Tgeslec:eGFP reporter line which specifically labels zebrafish eosinophil lineage cells from early life through maturity. Spatial temporal analysis of eslec+ cells demonstrated organ distribution at the larval stage. By single cell RNA Seq of eslec+ cells tissue distributed eosinophils were found to have similar differentiation paths but different tissue specific expression profiles. Genetic analysis demonstrated a Cebp1 and Cebp\u00df transcriptional axis that regulated eosinophilopoiesis in which Cebp1 directly targeted cebpb to inhibit eosinophil differentiationthe commitment differentiation and maturation of the eosinophil lineage. In summary this study characterized eosinophil development in multiple dimensions including spatial temporal patterns expression profiles and genetic regulators. The results provide for a better understanding of eosinophilopoiesis. Overall design: For the RNA Seq analysis of eosinophils from different genotypes eslec:eGFP+ eosinophils were sorted from whole larvae 7 dpf and lysed. The lysates were directly applied to reverse transcription and amplification. Enriched cDNA were then fragmented adpator tagged and purified for further sequencing.", "parent bioproject:PRJNA814534", "pubmed:38280871", null, "cebp1 wt eos 1", "GSM7854235", null, "source name:eosinophils|strain:AB strain|tissue:whole larvae|genotype:wild type|transgene:Tgeslec:eGFP|geo loc name:missing|collection date:missing", "cebp1 wt eos 1", "Post quality control the fastq files were mapped to the zebrafish genome with the \"STAR\" package. Mapped reads were annotated with the \"FeatureCounts\" package. Annotated reads were applied to the \"DESeq2\" package for differential expressed genes analysis. The sample to sample distance heatmaps were generated by \"pheatmap\" with the output of \"DESeq2\". The gene expression heatmaps were generated by \"pheatmap\" with the Z score of the TPM matrix. Assembly: GRCz11 Supplementary files format and content: Normalized matrix table with Transcripts Per Kilobase TPM for every gene and every sample", "eosinophils", null, "Whole larvae were ground and digested into cell suspensions. The cell suspensions were then analyzed with FACS and the eGFP+ cells 500 cells for each sample were sorted into lysis buffer. The lysates were directly applied to reverse transcription and amplification. Enriched cDNA were then fragmented adpator tagged and purified for further sequencing.", null, "strain:AB strain|tissue:whole larvae|genotype:wild type|transgene:Tgeslec:eGFP", "GSM7854235", "GSM7854235: cebp1 wt eos 1; Danio rerio; RNA Seq", "GSM7854235 r1", "GSM7854235", "1", "Whole larvae were ground and digested into cell suspensions. The cell suspensions were then analyzed with FACS and the eGFP+ cells 500 cells for each sample were sorted into lysis buffer. The lysates were directly applied to reverse transcription and amplification. Enriched cDNA were then fragmented adpator tagged and purified for further sequencing.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP467949", null, "loader:fastq load.py", "W1_2.fq.gz W1_1.fq.gz", "fastq fastq", 6194437200.0, 20648124.0, "GSM7854235 r1", "0:150 1:150", "A:1953684038;C:1067667551;G:1247879965;T:1925172690;N:32956", 150, 150, null, null, 1953684038, 1067667551, 1247879965, 1925172690, 32956, "SRX22175826", "SRS19233326", "SRA1737851", "South China University of Technology", "South China University of Technology", 2, 0.76007, 0.76295, 0.54521, 0.54298, 0.78244, 0.77281, 0.62357, 0.62562, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "sc_generic", "single_cell_generic", "generic-scrnaseq-only", null, "China", "2023-10-23", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [28617, "SRR26471896", "SRX22175825", "SRS19233327", "SRP467949", "PRJNA1031141", "Cebp1 and Cebp\u00df transcriptional axis controls eosinophilopoiesis in zebrafish [bulkRNA Seq]", "GSE246037", "Transcriptome Analysis", "Eosinophils are well known to regulate host protection from parasites and have been reported to paticipate many other physiologic and pathologic processes. Understanding the role of eosinophils in these processes requires a better understanding of eosinophilopoiesis. Using a zebrafish model we have identified an eosinophil lineage specific marker eslec. Using this marker we have established a Tgeslec:eGFP reporter line which specifically labels zebrafish eosinophil lineage cells from early life through maturity. Spatial temporal analysis of eslec+ cells demonstrated organ distribution at the larval stage. By single cell RNA Seq of eslec+ cells tissue distributed eosinophils were found to have similar differentiation paths but different tissue specific expression profiles. Genetic analysis demonstrated a Cebp1 and Cebp\u00df transcriptional axis that regulated eosinophilopoiesis in which Cebp1 directly targeted cebpb to inhibit eosinophil differentiationthe commitment differentiation and maturation of the eosinophil lineage. In summary this study characterized eosinophil development in multiple dimensions including spatial temporal patterns expression profiles and genetic regulators. The results provide for a better understanding of eosinophilopoiesis. Overall design: For the RNA Seq analysis of eosinophils from different genotypes eslec:eGFP+ eosinophils were sorted from whole larvae 7 dpf and lysed. The lysates were directly applied to reverse transcription and amplification. Enriched cDNA were then fragmented adpator tagged and purified for further sequencing.", "parent bioproject:PRJNA814534", "pubmed:38280871", null, "cebp1 mut eos 2", "GSM7854234", null, "source name:eosinophils|strain:AB strain|tissue:whole larvae|genotype:cebp1 / |transgene:Tgeslec:eGFP|geo loc name:missing|collection date:missing", "cebp1 mut eos 2", "Post quality control the fastq files were mapped to the zebrafish genome with the \"STAR\" package. Mapped reads were annotated with the \"FeatureCounts\" package. Annotated reads were applied to the \"DESeq2\" package for differential expressed genes analysis. The sample to sample distance heatmaps were generated by \"pheatmap\" with the output of \"DESeq2\". The gene expression heatmaps were generated by \"pheatmap\" with the Z score of the TPM matrix. Assembly: GRCz11 Supplementary files format and content: Normalized matrix table with Transcripts Per Kilobase TPM for every gene and every sample", "eosinophils", null, "Whole larvae were ground and digested into cell suspensions. The cell suspensions were then analyzed with FACS and the eGFP+ cells 500 cells for each sample were sorted into lysis buffer. The lysates were directly applied to reverse transcription and amplification. Enriched cDNA were then fragmented adpator tagged and purified for further sequencing.", null, "strain:AB strain|tissue:whole larvae|genotype:cebp1 / |transgene:Tgeslec:eGFP", "GSM7854234", "GSM7854234: cebp1 mut eos 2; Danio rerio; RNA Seq", "GSM7854234 r1", "GSM7854234", "1", "Whole larvae were ground and digested into cell suspensions. The cell suspensions were then analyzed with FACS and the eGFP+ cells 500 cells for each sample were sorted into lysis buffer. The lysates were directly applied to reverse transcription and amplification. Enriched cDNA were then fragmented adpator tagged and purified for further sequencing.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP467949", null, "loader:fastq load.py", "M2_2.fq.gz M2_1.fq.gz", "fastq fastq", 6104680800.0, 20348936.0, "GSM7854234 r1", "0:150 1:150", "A:1804058925;C:1198439018;G:1326225576;T:1775930488;N:26793", 150, 150, null, null, 1804058925, 1198439018, 1326225576, 1775930488, 26793, "SRX22175825", "SRS19233327", "SRA1737851", "South China University of Technology", "South China University of Technology", 2, 0.8123, 0.81465, 0.42735, 0.42341, 0.78171, 0.77567, 0.46764, 0.65485, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "sc_generic", "single_cell_generic", "generic-scrnaseq-only", null, "China", "2023-10-23", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [28618, "SRR26471897", "SRX22175824", "SRS19233325", "SRP467949", "PRJNA1031141", "Cebp1 and Cebp\u00df transcriptional axis controls eosinophilopoiesis in zebrafish [bulkRNA Seq]", "GSE246037", "Transcriptome Analysis", "Eosinophils are well known to regulate host protection from parasites and have been reported to paticipate many other physiologic and pathologic processes. Understanding the role of eosinophils in these processes requires a better understanding of eosinophilopoiesis. Using a zebrafish model we have identified an eosinophil lineage specific marker eslec. Using this marker we have established a Tgeslec:eGFP reporter line which specifically labels zebrafish eosinophil lineage cells from early life through maturity. Spatial temporal analysis of eslec+ cells demonstrated organ distribution at the larval stage. By single cell RNA Seq of eslec+ cells tissue distributed eosinophils were found to have similar differentiation paths but different tissue specific expression profiles. Genetic analysis demonstrated a Cebp1 and Cebp\u00df transcriptional axis that regulated eosinophilopoiesis in which Cebp1 directly targeted cebpb to inhibit eosinophil differentiationthe commitment differentiation and maturation of the eosinophil lineage. In summary this study characterized eosinophil development in multiple dimensions including spatial temporal patterns expression profiles and genetic regulators. The results provide for a better understanding of eosinophilopoiesis. Overall design: For the RNA Seq analysis of eosinophils from different genotypes eslec:eGFP+ eosinophils were sorted from whole larvae 7 dpf and lysed. The lysates were directly applied to reverse transcription and amplification. Enriched cDNA were then fragmented adpator tagged and purified for further sequencing.", "parent bioproject:PRJNA814534", "pubmed:38280871", null, "cebp1 mut eos 1", "GSM7854233", null, "source name:eosinophils|strain:AB strain|tissue:whole larvae|genotype:cebp1 / |transgene:Tgeslec:eGFP|geo loc name:missing|collection date:missing", "cebp1 mut eos 1", "Post quality control the fastq files were mapped to the zebrafish genome with the \"STAR\" package. Mapped reads were annotated with the \"FeatureCounts\" package. Annotated reads were applied to the \"DESeq2\" package for differential expressed genes analysis. The sample to sample distance heatmaps were generated by \"pheatmap\" with the output of \"DESeq2\". The gene expression heatmaps were generated by \"pheatmap\" with the Z score of the TPM matrix. Assembly: GRCz11 Supplementary files format and content: Normalized matrix table with Transcripts Per Kilobase TPM for every gene and every sample", "eosinophils", null, "Whole larvae were ground and digested into cell suspensions. The cell suspensions were then analyzed with FACS and the eGFP+ cells 500 cells for each sample were sorted into lysis buffer. The lysates were directly applied to reverse transcription and amplification. Enriched cDNA were then fragmented adpator tagged and purified for further sequencing.", null, "strain:AB strain|tissue:whole larvae|genotype:cebp1 / |transgene:Tgeslec:eGFP", "GSM7854233", "GSM7854233: cebp1 mut eos 1; Danio rerio; RNA Seq", "GSM7854233 r1", "GSM7854233", "1", "Whole larvae were ground and digested into cell suspensions. The cell suspensions were then analyzed with FACS and the eGFP+ cells 500 cells for each sample were sorted into lysis buffer. The lysates were directly applied to reverse transcription and amplification. Enriched cDNA were then fragmented adpator tagged and purified for further sequencing.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP467949", null, "loader:fastq load.py", "M1_1.fq.gz M1_2.fq.gz", "fastq fastq", 6409092000.0, 21363640.0, "GSM7854233 r1", "0:150 1:150", "A:1887432519;C:1294546709;G:1354360945;T:1872720156;N:31671", 150, 150, null, null, 1887432519, 1294546709, 1354360945, 1872720156, 31671, "SRX22175824", "SRS19233325", "SRA1737851", "South China University of Technology", "South China University of Technology", 2, 0.84504, 0.84611, 0.39473, 0.39207, 0.76319, 0.75767, 0.63936, 0.62743, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "sc_generic", "single_cell_generic", "generic-scrnaseq-only", null, "China", "2023-10-23", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [73913, "SRR23284054", "SRX19227385", "SRS16633552", "SRP420237", "PRJNA929924", "A single cell map of maternal and zygotic mRNA dynamics during cell type specification in zebrafish embryos [SLAM seq]", "GSE224113", "Other", "During early embryogenesis embryos undergo a massive degradation of maternally inherited mRNAs and produce new zygotic transcripts. This maternal to zygotic transition requires a tight interplay of mRNA transcription and degradation but distinguishing their unique contributions remains a challenge. Here we dissect gene regulation during the zebrafish maternal to zygotic transition by combining single cell RNA sequencing with RNA metabolic labeling and nucleotide conversion within zebrafish embryos. We decompose single cell transcriptomes into their new zygotic and old maternal mRNA components and elicit critical information on gene regulation as it unfolds over both time and space. We show that most cell type restricted expression arises by zygotic transcription but distinguish a specific role for maternal transcripts in defining germ cell and enveloping layer identity two earliest specified cell identities. We recover the underlying replacement between maternal and zygotic copies of embryonic genes with a relatively constant overall mRNA level and associate a fast replacement with genes that has a restricted zygotic expression in either cell type or time. Our study provides a valuable resource to investigate maternal and zygotic transcriptomes and reveals post transcriptional events that control gene regulation during early embryogenesis. Overall design: SLAM seq zebrafish embryos 1hpf and 6hpf 2 technical replicates", "parent bioproject:PRJNA933118", "pubmed:37131717;pubmed:38600066", null, "zebrafish embryo 6hpf rep2", "GSM7012036", null, "source name:whole embryo|tissue:whole embryo|genotype:AB/TL|treatment:4sU injection|time:6hpf|geo loc name:missing|collection date:missing", "zebrafish embryo 6hpf rep2", "Sequence reads were trimmed for adaptor sequence using cutadapt Trimmed sequence reads were mapped to GRCz11 using STAR Read count extraction and NTR calculation were performed using GRAND SLAM Assembly: GRCz11/102 Supplementary files format and content: tab delimited text file includes readcount and NTR %new RNA for each Sample Library strategy: SLAM seq", "whole embryo", "20mM 4sU injection at 1 cell stage RNA was treated with Iodoacetamide to induce T to C conversions", "Total RNA was isolated using tri reagent Sigma T9424 and quantified using nanodrop polyA+RNA: Indexed RNA Seq libraries were prepared from 500 ng total RNA using the KAPA Stranded mRNA Seq Kit Kapa Biosystems Inc. according to the manufacturer\u2019s protocol. Libraries were size selected with SPRI beads and quantified by QuBIT Life Technologies. Average size of 300\u2009bp was determined by TapeStation Agilent Technologies USA. Libraries are then sequenced using an Illumina Nextseq500 sequencer. total RNA: indexed RNA Seq libraries for each sample were generated from total RNA using the Illumina RiboZeroHuman/Mouse/Rat kit following the manufacturer\u2019s instructions. Libraries were size selected with SPRI beads and quantified by QuBIT Life Technologies. Libraries are then sequenced using an Illumina Novaseq sequencer.", null, "tissue:whole embryo|genotype:AB/TL|treatment:4sU injection|time:6hpf", "GSM7012036", "GSM7012036: zebrafish embryo 6hpf rep2; Danio rerio; RNA Seq", "GSM7012036 r1", "GSM7012036", "1", "Total RNA was isolated using tri reagent Sigma T9424 and quantified using nanodrop polyA+RNA: Indexed RNA Seq libraries were prepared from 500 ng total RNA using the KAPA Stranded mRNA Seq Kit Kapa Biosystems Inc. according to the manufacturer's protocol. Libraries were size selected with SPRI beads and quantified by QuBIT Life Technologies. Average size of 300\u2009bp was determined by TapeStation Agilent Technologies USA. Libraries are then sequenced using an Illumina Nextseq500 sequencer. total RNA: indexed RNA Seq libraries for each sample were generated from total RNA using the Illumina RiboZeroHuman/Mouse/Rat kit following the manufacturer's instructions. Libraries were size selected with SPRI beads and quantified by QuBIT Life Technologies. Libraries are then sequenced using an Illumina Novaseq sequencer.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP420237", null, "loader:fastq load.py", "nextseq_20220515_slam_120122_6hr_S20_R1_001.fastq.gz", "fastq", 1231038044.0, 16197869.0, "GSM7012036 r1", "0:76", "A:287858332;C:300689662;G:294179125;T:348288250;N:22675", 76, null, null, null, 287858332, 300689662, 294179125, 348288250, 22675, "SRX19227385", "SRS16633552", "SRA1587567", "Hebrew University of Jerusalem", "Hebrew University of Jerusalem", 1, 0.91125, null, 0.06969, null, 0.75538, null, 0.55355, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "poly_a", "ribozero", "sc_generic", "single_cell_generic", "generic-scrnaseq-only", null, "Israel", "2023-01-31", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [73914, "SRR23284055", "SRX19227384", "SRS16633551", "SRP420237", "PRJNA929924", "A single cell map of maternal and zygotic mRNA dynamics during cell type specification in zebrafish embryos [SLAM seq]", "GSE224113", "Other", "During early embryogenesis embryos undergo a massive degradation of maternally inherited mRNAs and produce new zygotic transcripts. This maternal to zygotic transition requires a tight interplay of mRNA transcription and degradation but distinguishing their unique contributions remains a challenge. Here we dissect gene regulation during the zebrafish maternal to zygotic transition by combining single cell RNA sequencing with RNA metabolic labeling and nucleotide conversion within zebrafish embryos. We decompose single cell transcriptomes into their new zygotic and old maternal mRNA components and elicit critical information on gene regulation as it unfolds over both time and space. We show that most cell type restricted expression arises by zygotic transcription but distinguish a specific role for maternal transcripts in defining germ cell and enveloping layer identity two earliest specified cell identities. We recover the underlying replacement between maternal and zygotic copies of embryonic genes with a relatively constant overall mRNA level and associate a fast replacement with genes that has a restricted zygotic expression in either cell type or time. Our study provides a valuable resource to investigate maternal and zygotic transcriptomes and reveals post transcriptional events that control gene regulation during early embryogenesis. Overall design: SLAM seq zebrafish embryos 1hpf and 6hpf 2 technical replicates", "parent bioproject:PRJNA933118", "pubmed:37131717;pubmed:38600066", null, "zebrafish embryo 1hpf rep2", "GSM7012035", null, "source name:whole embryo|tissue:whole embryo|genotype:AB/TL|treatment:4sU injection|time:1hpf|geo loc name:missing|collection date:missing", "zebrafish embryo 1hpf rep2", "Sequence reads were trimmed for adaptor sequence using cutadapt Trimmed sequence reads were mapped to GRCz11 using STAR Read count extraction and NTR calculation were performed using GRAND SLAM Assembly: GRCz11/102 Supplementary files format and content: tab delimited text file includes readcount and NTR %new RNA for each Sample Library strategy: SLAM seq", "whole embryo", "20mM 4sU injection at 1 cell stage RNA was treated with Iodoacetamide to induce T to C conversions", "Total RNA was isolated using tri reagent Sigma T9424 and quantified using nanodrop polyA+RNA: Indexed RNA Seq libraries were prepared from 500 ng total RNA using the KAPA Stranded mRNA Seq Kit Kapa Biosystems Inc. according to the manufacturer\u2019s protocol. Libraries were size selected with SPRI beads and quantified by QuBIT Life Technologies. Average size of 300\u2009bp was determined by TapeStation Agilent Technologies USA. Libraries are then sequenced using an Illumina Nextseq500 sequencer. total RNA: indexed RNA Seq libraries for each sample were generated from total RNA using the Illumina RiboZeroHuman/Mouse/Rat kit following the manufacturer\u2019s instructions. Libraries were size selected with SPRI beads and quantified by QuBIT Life Technologies. Libraries are then sequenced using an Illumina Novaseq sequencer.", null, "tissue:whole embryo|genotype:AB/TL|treatment:4sU injection|time:1hpf", "GSM7012035", "GSM7012035: zebrafish embryo 1hpf rep2; Danio rerio; RNA Seq", "GSM7012035 r1", "GSM7012035", "1", "Total RNA was isolated using tri reagent Sigma T9424 and quantified using nanodrop polyA+RNA: Indexed RNA Seq libraries were prepared from 500 ng total RNA using the KAPA Stranded mRNA Seq Kit Kapa Biosystems Inc. according to the manufacturer's protocol. Libraries were size selected with SPRI beads and quantified by QuBIT Life Technologies. Average size of 300\u2009bp was determined by TapeStation Agilent Technologies USA. Libraries are then sequenced using an Illumina Nextseq500 sequencer. total RNA: indexed RNA Seq libraries for each sample were generated from total RNA using the Illumina RiboZeroHuman/Mouse/Rat kit following the manufacturer's instructions. Libraries were size selected with SPRI beads and quantified by QuBIT Life Technologies. Libraries are then sequenced using an Illumina Novaseq sequencer.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP420237", null, "loader:fastq load.py", "nextseq_20220515_slam_120122_1hr_S19_R1_001.fastq.gz", "fastq", 988543704.0, 13007154.0, "GSM7012035 r1", "0:76", "A:237897735;C:241764496;G:233504938;T:275357752;N:18783", 76, null, null, null, 237897735, 241764496, 233504938, 275357752, 18783, "SRX19227384", "SRS16633551", "SRA1587567", "Hebrew University of Jerusalem", "Hebrew University of Jerusalem", 1, 0.93827, null, 0.03581, null, 0.78027, null, 0.53364, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "poly_a", "ribozero", "sc_generic", "single_cell_generic", "generic-scrnaseq-only", null, "Israel", "2023-01-31", "Cleavage", "Embryo", "Whole Organism", "All anatomical structures"], [73915, "SRR23284056", "SRX19227383", "SRS16633550", "SRP420237", "PRJNA929924", "A single cell map of maternal and zygotic mRNA dynamics during cell type specification in zebrafish embryos [SLAM seq]", "GSE224113", "Other", "During early embryogenesis embryos undergo a massive degradation of maternally inherited mRNAs and produce new zygotic transcripts. This maternal to zygotic transition requires a tight interplay of mRNA transcription and degradation but distinguishing their unique contributions remains a challenge. Here we dissect gene regulation during the zebrafish maternal to zygotic transition by combining single cell RNA sequencing with RNA metabolic labeling and nucleotide conversion within zebrafish embryos. We decompose single cell transcriptomes into their new zygotic and old maternal mRNA components and elicit critical information on gene regulation as it unfolds over both time and space. We show that most cell type restricted expression arises by zygotic transcription but distinguish a specific role for maternal transcripts in defining germ cell and enveloping layer identity two earliest specified cell identities. We recover the underlying replacement between maternal and zygotic copies of embryonic genes with a relatively constant overall mRNA level and associate a fast replacement with genes that has a restricted zygotic expression in either cell type or time. Our study provides a valuable resource to investigate maternal and zygotic transcriptomes and reveals post transcriptional events that control gene regulation during early embryogenesis. Overall design: SLAM seq zebrafish embryos 1hpf and 6hpf 2 technical replicates", "parent bioproject:PRJNA933118", "pubmed:37131717;pubmed:38600066", null, "zebrafish embryo 6hpf rep1", "GSM7012034", null, "source name:whole embryo|tissue:whole embryo|genotype:AB/TL|treatment:4sU injection|time:6hpf|geo loc name:missing|collection date:missing", "zebrafish embryo 6hpf rep1", "Sequence reads were trimmed for adaptor sequence using cutadapt Trimmed sequence reads were mapped to GRCz11 using STAR Read count extraction and NTR calculation were performed using GRAND SLAM Assembly: GRCz11/102 Supplementary files format and content: tab delimited text file includes readcount and NTR %new RNA for each Sample Library strategy: SLAM seq", "whole embryo", "20mM 4sU injection at 1 cell stage RNA was treated with Iodoacetamide to induce T to C conversions", "Total RNA was isolated using tri reagent Sigma T9424 and quantified using nanodrop polyA+RNA: Indexed RNA Seq libraries were prepared from 500 ng total RNA using the KAPA Stranded mRNA Seq Kit Kapa Biosystems Inc. according to the manufacturer\u2019s protocol. Libraries were size selected with SPRI beads and quantified by QuBIT Life Technologies. Average size of 300\u2009bp was determined by TapeStation Agilent Technologies USA. Libraries are then sequenced using an Illumina Nextseq500 sequencer. total RNA: indexed RNA Seq libraries for each sample were generated from total RNA using the Illumina RiboZeroHuman/Mouse/Rat kit following the manufacturer\u2019s instructions. Libraries were size selected with SPRI beads and quantified by QuBIT Life Technologies. Libraries are then sequenced using an Illumina Novaseq sequencer.", null, "tissue:whole embryo|genotype:AB/TL|treatment:4sU injection|time:6hpf", "GSM7012034", "GSM7012034: zebrafish embryo 6hpf rep1; Danio rerio; RNA Seq", "GSM7012034 r1", "GSM7012034", "1", "Total RNA was isolated using tri reagent Sigma T9424 and quantified using nanodrop polyA+RNA: Indexed RNA Seq libraries were prepared from 500 ng total RNA using the KAPA Stranded mRNA Seq Kit Kapa Biosystems Inc. according to the manufacturer's protocol. Libraries were size selected with SPRI beads and quantified by QuBIT Life Technologies. Average size of 300\u2009bp was determined by TapeStation Agilent Technologies USA. Libraries are then sequenced using an Illumina Nextseq500 sequencer. total RNA: indexed RNA Seq libraries for each sample were generated from total RNA using the Illumina RiboZeroHuman/Mouse/Rat kit following the manufacturer's instructions. Libraries were size selected with SPRI beads and quantified by QuBIT Life Technologies. Libraries are then sequenced using an Illumina Novaseq sequencer.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP420237", null, "loader:fastq load.py", "novaseq_20220630_slam_120122_6h_1.fastq.gz novaseq_20220630_slam_120122_6h_2.fastq.gz", "fastq fastq", 7578082116.0, 37515258.0, "GSM7012034 r1", "0:101 1:101", "A:1938942537;C:1836634013;G:1866966085;T:1935520946;N:18535", 101, 101, null, null, 1938942537, 1836634013, 1866966085, 1935520946, 18535, "SRX19227383", "SRS16633550", "SRA1587567", "Hebrew University of Jerusalem", "Hebrew University of Jerusalem", 2, 0.86852, 0.87284, 0.11981, 0.11692, 0.7571, 0.75702, 0.63941, 0.63601, 101, 101, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "ribozero", "sc_generic", "single_cell_generic", "generic-scrnaseq-only", null, "Israel", "2023-01-31", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [73916, "SRR23284057", "SRX19227382", "SRS16633549", "SRP420237", "PRJNA929924", "A single cell map of maternal and zygotic mRNA dynamics during cell type specification in zebrafish embryos [SLAM seq]", "GSE224113", "Other", "During early embryogenesis embryos undergo a massive degradation of maternally inherited mRNAs and produce new zygotic transcripts. This maternal to zygotic transition requires a tight interplay of mRNA transcription and degradation but distinguishing their unique contributions remains a challenge. Here we dissect gene regulation during the zebrafish maternal to zygotic transition by combining single cell RNA sequencing with RNA metabolic labeling and nucleotide conversion within zebrafish embryos. We decompose single cell transcriptomes into their new zygotic and old maternal mRNA components and elicit critical information on gene regulation as it unfolds over both time and space. We show that most cell type restricted expression arises by zygotic transcription but distinguish a specific role for maternal transcripts in defining germ cell and enveloping layer identity two earliest specified cell identities. We recover the underlying replacement between maternal and zygotic copies of embryonic genes with a relatively constant overall mRNA level and associate a fast replacement with genes that has a restricted zygotic expression in either cell type or time. Our study provides a valuable resource to investigate maternal and zygotic transcriptomes and reveals post transcriptional events that control gene regulation during early embryogenesis. Overall design: SLAM seq zebrafish embryos 1hpf and 6hpf 2 technical replicates", "parent bioproject:PRJNA933118", "pubmed:37131717;pubmed:38600066", null, "zebrafish embryo 1hpf rep1", "GSM7012033", null, "source name:whole embryo|tissue:whole embryo|genotype:AB/TL|treatment:4sU injection|time:1hpf|geo loc name:missing|collection date:missing", "zebrafish embryo 1hpf rep1", "Sequence reads were trimmed for adaptor sequence using cutadapt Trimmed sequence reads were mapped to GRCz11 using STAR Read count extraction and NTR calculation were performed using GRAND SLAM Assembly: GRCz11/102 Supplementary files format and content: tab delimited text file includes readcount and NTR %new RNA for each Sample Library strategy: SLAM seq", "whole embryo", "20mM 4sU injection at 1 cell stage RNA was treated with Iodoacetamide to induce T to C conversions", "Total RNA was isolated using tri reagent Sigma T9424 and quantified using nanodrop polyA+RNA: Indexed RNA Seq libraries were prepared from 500 ng total RNA using the KAPA Stranded mRNA Seq Kit Kapa Biosystems Inc. according to the manufacturer\u2019s protocol. Libraries were size selected with SPRI beads and quantified by QuBIT Life Technologies. Average size of 300\u2009bp was determined by TapeStation Agilent Technologies USA. Libraries are then sequenced using an Illumina Nextseq500 sequencer. total RNA: indexed RNA Seq libraries for each sample were generated from total RNA using the Illumina RiboZeroHuman/Mouse/Rat kit following the manufacturer\u2019s instructions. Libraries were size selected with SPRI beads and quantified by QuBIT Life Technologies. Libraries are then sequenced using an Illumina Novaseq sequencer.", null, "tissue:whole embryo|genotype:AB/TL|treatment:4sU injection|time:1hpf", "GSM7012033", "GSM7012033: zebrafish embryo 1hpf rep1; Danio rerio; RNA Seq", "GSM7012033 r1", "GSM7012033", "1", "Total RNA was isolated using tri reagent Sigma T9424 and quantified using nanodrop polyA+RNA: Indexed RNA Seq libraries were prepared from 500 ng total RNA using the KAPA Stranded mRNA Seq Kit Kapa Biosystems Inc. according to the manufacturer's protocol. Libraries were size selected with SPRI beads and quantified by QuBIT Life Technologies. Average size of 300\u2009bp was determined by TapeStation Agilent Technologies USA. Libraries are then sequenced using an Illumina Nextseq500 sequencer. total RNA: indexed RNA Seq libraries for each sample were generated from total RNA using the Illumina RiboZeroHuman/Mouse/Rat kit following the manufacturer's instructions. Libraries were size selected with SPRI beads and quantified by QuBIT Life Technologies. Libraries are then sequenced using an Illumina Novaseq sequencer.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP420237", null, "loader:fastq load.py", "novaseq_20220630_slam_120122_1h_1.fastq.gz novaseq_20220630_slam_120122_1h_2.fastq.gz", "fastq fastq", 7422864306.0, 36746853.0, "GSM7012033 r1", "0:101 1:101", "A:1927554601;C:1775023714;G:1801237102;T:1919030393;N:18496", 101, 101, null, null, 1927554601, 1775023714, 1801237102, 1919030393, 18496, "SRX19227382", "SRS16633549", "SRA1587567", "Hebrew University of Jerusalem", "Hebrew University of Jerusalem", 2, 0.91995, 0.92316, 0.05523, 0.05324, 0.7595, 0.75897, 0.57483, 0.57891, 101, 101, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "ribozero", "sc_generic", "single_cell_generic", "generic-scrnaseq-only", null, "Israel", "2023-01-31", "Cleavage", "Embryo", "Whole Organism", "All anatomical structures"], [74361, "SRR30639559", "SRX26061375", "SRS22630890", "SRP425398", "PRJNA940501", "Zebrahub: Multimodal Zebrafish Developmental Atlas", "PRJNA940501", "Other", "A single embryo single cell RNA seq developmental atlas of Zebrafish.", null, null, null, "TDR110", "TDR110 30sinternew EKW NA none 10x", null, "strain:EKW|isolate:single embryo|breed:siblings per timepoint|cultivar:not applicable|ecotype:not applicable|age:24 hpf|collection date:2022 11 30|geo loc name:USA: California San Francisco|sex:not determined|tissue:Whole embryo|replicate:4|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "TDR110", "TDR110 30sinternew EKW NA none 10x", "TDR110 30sinternew EKW NA none 10x", "single embryo dissociation", null, null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP425398", null, null, "TDR110_30sinternew_EKW_NA_none_10x_S8_L001_I1_001.fastq.gz TDR110_30sinternew_EKW_NA_none_10x_S8_L001_I2_001.fastq.gz 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null, null, null, null, null, null, null, null, null, null, null, "SRX26061375", null, "SRA1969971", "Chan Zuckerberg Biohub|Quantitative Cell Science", "Chan Zuckerberg Biohub", null, null, null, null, null, null, null, null, null, null, null, null, null, null, "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_generic", "generic-scrnaseq-only", null, "United States", "2024-09-11", "Pharyngula", "Embryo", "Whole Organism", "All anatomical structures"], [74362, "SRR30639560", "SRX26061374", "SRS22630889", "SRP425398", "PRJNA940501", "Zebrahub: Multimodal Zebrafish Developmental Atlas", "PRJNA940501", "Other", "A single embryo single cell RNA seq developmental atlas of Zebrafish.", null, null, null, "TDR108", "TDR108 30sinternew EKW NA none 10x", null, "strain:EKW|isolate:single embryo|breed:siblings per timepoint|cultivar:not applicable|ecotype:not applicable|age:24 hpf|collection date:2022 11 30|geo loc name:USA: California San Francisco|sex:not determined|tissue:Whole embryo|replicate:3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "TDR108", "TDR108 30sinternew EKW NA none 10x", "TDR108 30sinternew EKW NA none 10x", "single embryo dissociation", null, null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP425398", null, null, "TDR108_30sinternew_EKW_NA_none_10x_S7_L001_I1_001.fastq.gz TDR108_30sinternew_EKW_NA_none_10x_S7_L001_I2_001.fastq.gz TDR108_30sinternew_EKW_NA_none_10x_S7_L001_R1_001.fastq.gz TDR108_30sinternew_EKW_NA_none_10x_S7_L001_R2_001.fastq.gz TDR108_30sinternew_EKW_NA_none_10x_S7_L002_I1_001.fastq.gz TDR108_30sinternew_EKW_NA_none_10x_S7_L002_I2_001.fastq.gz TDR108_30sinternew_EKW_NA_none_10x_S7_L002_R1_001.fastq.gz TDR108_30sinternew_EKW_NA_none_10x_S7_L002_R2_001.fastq.gz TDR108_30sinternew_EKW_NA_none_10x_S7_L003_I1_001.fastq.gz TDR108_30sinternew_EKW_NA_none_10x_S7_L003_I2_001.fastq.gz TDR108_30sinternew_EKW_NA_none_10x_S7_L003_R1_001.fastq.gz TDR108_30sinternew_EKW_NA_none_10x_S7_L003_R2_001.fastq.gz TDR108_30sinternew_EKW_NA_none_10x_S7_L004_I1_001.fastq.gz TDR108_30sinternew_EKW_NA_none_10x_S7_L004_I2_001.fastq.gz TDR108_30sinternew_EKW_NA_none_10x_S7_L004_R1_001.fastq.gz TDR108_30sinternew_EKW_NA_none_10x_S7_L004_R2_001.fastq.gz", "fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq", null, null, "TDR108 30sinternew EKW NA none 10x S7 L001 I1 001.fastq.gz", null, null, null, null, null, null, null, null, null, null, null, "SRX26061374", null, "SRA1969971", "Chan Zuckerberg Biohub|Quantitative Cell Science", "Chan Zuckerberg Biohub", null, null, null, null, null, null, null, null, null, null, null, null, null, null, "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_generic", "generic-scrnaseq-only", null, "United States", "2024-09-11", "Pharyngula", "Embryo", "Whole Organism", "All anatomical structures"], [74363, "SRR30639561", "SRX26061373", "SRS22630888", "SRP425398", "PRJNA940501", "Zebrahub: Multimodal Zebrafish Developmental Atlas", "PRJNA940501", "Other", "A single embryo single cell RNA seq developmental atlas of Zebrafish.", null, null, null, "TDR107", "TDR107 30sinternew EKW NA none 10x", null, "strain:EKW|isolate:single embryo|breed:siblings per timepoint|cultivar:not applicable|ecotype:not applicable|age:24 hpf|collection date:2022 11 30|geo loc name:USA: California San Francisco|sex:not determined|tissue:Whole embryo|replicate:2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "TDR107", "TDR107 30sinternew EKW NA none 10x", "TDR107 30sinternew EKW NA none 10x", "single embryo dissociation", null, null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP425398", null, null, "TDR107_30sinternew_EKW_NA_none_10x_S6_L001_I1_001.fastq.gz 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"TDR107 30sinternew EKW NA none 10x S6 L001 I1 001.fastq.gz", null, null, null, null, null, null, null, null, null, null, null, "SRX26061373", null, "SRA1969971", "Chan Zuckerberg Biohub|Quantitative Cell Science", "Chan Zuckerberg Biohub", null, null, null, null, null, null, null, null, null, null, null, null, null, null, "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_generic", "generic-scrnaseq-only", null, "United States", "2024-09-11", "Pharyngula", "Embryo", "Whole Organism", "All anatomical structures"], [74364, "SRR30639562", "SRX26061372", "SRS22630887", "SRP425398", "PRJNA940501", "Zebrahub: Multimodal Zebrafish Developmental Atlas", "PRJNA940501", "Other", "A single embryo single cell RNA seq developmental atlas of Zebrafish.", null, null, null, "TDR106", "TDR106 30sinternew EKW NA none 10x", null, "strain:EKW|isolate:single embryo|breed:siblings per timepoint|cultivar:not applicable|ecotype:not applicable|age:24 hpf|collection 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