{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where experiment.library_selection = \"cDNA\", experiment.library_source = \"TRANSCRIPTOMIC\" and technology = \"celseq\"", "rows": [[30508, "SRR27764648", "SRX23429609", "SRS20284060", "SRP486518", "PRJNA1070582", "Gene expression profile of neighboring cells of cells with unfit Wnt morphogen gradient during cell competition", "GSE254439", "Transcriptome Analysis", "Morphogen signalling forms an activity gradient and instructs cell identities in a signalling strength dependent manner to pattern developing tissues. However  developing tissues also undergo dynamic morphogenesis  which may produce cells with unfit morphogen signalling and consequent noisy morphogen gradient. Here we show that a cell competition related system corrects such noisy morphogen gradients. Zebrafish imaging analyses of the Wnt/\u00df catenin signalling gradient  which acts as a morphogen to establish embryonic anterior posterior patterning  revealed that unfit cells with abnormal Wnt/\u00df catenin activity spontaneously appear and produce noise in the gradient. Communication between unfit and neighbouring fit cells via cadherin proteins stimulates apoptosis of the unfit cells by activating Smad signalling and reactive oxygen species production. This unfit cell elimination is required for proper Wnt/\u00df catenin gradient formation and consequent anterior posterior patterning. Because this gradient controls patterning not only in the embryo but also in adult tissues  this system may support tissue robustness and disease prevention. Overall design: \u00df catCA constitutive active form of \u00df catenin expressing GFP+ cells  or \u00dfcatCA unexpressing GFP  cells from \u00df catCA mosaically introduced zebrafish early embryos were sorted by FACS cell sorter. Total RNAs were extracted and analyzed by RNA seq.", null, "pubmed:39546611", null, "Mosaic GFP control GFP min lot2", "GSM8042248", null, "source name:early embryonic cell|strain:AB|tissue:early embryonic cell|developmental stage:9 hpf loc name:missing|collection date:missing", "Mosaic GFP control GFP min lot2", "Sequenced reads were mapped to the GRCz10 reference genome using Bowtie2 ver. 2.3.1. UMI counts were extracted per HTSeq ver. 0.6.1 from the CEL Seq2 pipeline. Assembly: GRCz10 Supplementary files format and content: Tab delimited text file for expression data normalized by regularized logarithm.", "early embryonic cell", null, "Cells were dissolved in TRIzol reagent Invitrogen and extracted. Samples were prepared according to the CEL Seq2 protocol described in Hashimshony et al. Geneome Biology 2016. Libraries preparation was performed according to the published CEL Seq2 protocol.", null, "strain:AB|tissue:early embryonic cell|developmental stage:9 hpf", "GSM8042248", "GSM8042248: Mosaic GFP control GFP min lot2; Danio rerio; RNA Seq", "GSM8042248 r1", "GSM8042248", "1", "Cells were dissolved in TRIzol reagent Invitrogen and extracted. Samples were prepared according to the CEL Seq2 protocol described in Hashimshony et al. Geneome Biology 2016. Libraries preparation was performed according to the published CEL Seq2 protocol.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 1500", null, "SRP486518", null, null, "Mosaic_GFP_control_GFP_min_lot2.fastq.gz", "fastq", 7474464.0, 207624.0, "GSM8042248 r1", "0:36", "A:1796571;C:1274347;G:1548876;T:2854637;N:33", 36, null, null, null, 1796571, 1274347, 1548876, 2854637, 33, "SRX23429609", "SRS20284060", "SRA1793856", "Department of Homeostatic Regulation, Research Institute for Microbial Diseases, Osaka University", "Department of Homeostatic Regulation, Research Institute for Microbial Diseases, Osaka University", 1, 0.82922, null, 0.20207, null, 0.86143, null, 0.54661, null, 36, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Japan", "2024-01-29", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [30509, "SRR27764649", "SRX23429608", "SRS20284059", "SRP486518", "PRJNA1070582", "Gene expression profile of neighboring cells of cells with unfit Wnt morphogen gradient during cell competition", "GSE254439", "Transcriptome Analysis", "Morphogen signalling forms an activity gradient and instructs cell identities in a signalling strength dependent manner to pattern developing tissues. However  developing tissues also undergo dynamic morphogenesis  which may produce cells with unfit morphogen signalling and consequent noisy morphogen gradient. Here we show that a cell competition related system corrects such noisy morphogen gradients. Zebrafish imaging analyses of the Wnt/\u00df catenin signalling gradient  which acts as a morphogen to establish embryonic anterior posterior patterning  revealed that unfit cells with abnormal Wnt/\u00df catenin activity spontaneously appear and produce noise in the gradient. Communication between unfit and neighbouring fit cells via cadherin proteins stimulates apoptosis of the unfit cells by activating Smad signalling and reactive oxygen species production. This unfit cell elimination is required for proper Wnt/\u00df catenin gradient formation and consequent anterior posterior patterning. Because this gradient controls patterning not only in the embryo but also in adult tissues  this system may support tissue robustness and disease prevention. Overall design: \u00df catCA constitutive active form of \u00df catenin expressing GFP+ cells  or \u00dfcatCA unexpressing GFP  cells from \u00df catCA mosaically introduced zebrafish early embryos were sorted by FACS cell sorter. Total RNAs were extracted and analyzed by RNA seq.", null, "pubmed:39546611", null, "Mosaic GFP control GFP min lot1", "GSM8042247", null, "source name:early embryonic cell|strain:AB|tissue:early embryonic cell|developmental stage:9 hpf loc name:missing|collection date:missing", "Mosaic GFP control GFP min lot1", "Sequenced reads were mapped to the GRCz10 reference genome using Bowtie2 ver. 2.3.1. UMI counts were extracted per HTSeq ver. 0.6.1 from the CEL Seq2 pipeline. Assembly: GRCz10 Supplementary files format and content: Tab delimited text file for expression data normalized by regularized logarithm.", "early embryonic cell", null, "Cells were dissolved in TRIzol reagent Invitrogen and extracted. Samples were prepared according to the CEL Seq2 protocol described in Hashimshony et al. Geneome Biology 2016. Libraries preparation was performed according to the published CEL Seq2 protocol.", null, "strain:AB|tissue:early embryonic cell|developmental stage:9 hpf", "GSM8042247", "GSM8042247: Mosaic GFP control GFP min lot1; Danio rerio; RNA Seq", "GSM8042247 r1", "GSM8042247", "1", "Cells were dissolved in TRIzol reagent Invitrogen and extracted. Samples were prepared according to the CEL Seq2 protocol described in Hashimshony et al. Geneome Biology 2016. Libraries preparation was performed according to the published CEL Seq2 protocol.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 1500", null, "SRP486518", null, null, "Mosaic_GFP_control_GFP_min_lot1.fastq.gz", "fastq", 8256240.0, 229340.0, "GSM8042247 r1", "0:36", "A:1947003;C:1345938;G:1692065;T:3271133;N:101", 36, null, null, null, 1947003, 1345938, 1692065, 3271133, 101, "SRX23429608", "SRS20284059", "SRA1793856", "Department of Homeostatic Regulation, Research Institute for Microbial Diseases, Osaka University", "Department of Homeostatic Regulation, Research Institute for Microbial Diseases, Osaka University", 1, 0.83305, null, 0.17754, null, 0.8619, null, 0.61474, null, 36, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Japan", "2024-01-29", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [30510, "SRR27764650", "SRX23429607", "SRS20284058", "SRP486518", "PRJNA1070582", "Gene expression profile of neighboring cells of cells with unfit Wnt morphogen gradient during cell competition", "GSE254439", "Transcriptome Analysis", "Morphogen signalling forms an activity gradient and instructs cell identities in a signalling strength dependent manner to pattern developing tissues. However  developing tissues also undergo dynamic morphogenesis  which may produce cells with unfit morphogen signalling and consequent noisy morphogen gradient. Here we show that a cell competition related system corrects such noisy morphogen gradients. Zebrafish imaging analyses of the Wnt/\u00df catenin signalling gradient  which acts as a morphogen to establish embryonic anterior posterior patterning  revealed that unfit cells with abnormal Wnt/\u00df catenin activity spontaneously appear and produce noise in the gradient. Communication between unfit and neighbouring fit cells via cadherin proteins stimulates apoptosis of the unfit cells by activating Smad signalling and reactive oxygen species production. This unfit cell elimination is required for proper Wnt/\u00df catenin gradient formation and consequent anterior posterior patterning. Because this gradient controls patterning not only in the embryo but also in adult tissues  this system may support tissue robustness and disease prevention. Overall design: \u00df catCA constitutive active form of \u00df catenin expressing GFP+ cells  or \u00dfcatCA unexpressing GFP  cells from \u00df catCA mosaically introduced zebrafish early embryos were sorted by FACS cell sorter. Total RNAs were extracted and analyzed by RNA seq.", null, "pubmed:39546611", null, "Mosaic beta catCA GFP min lot2", "GSM8042246", null, "source name:early embryonic cell|strain:AB|tissue:early embryonic cell|developmental stage:9 hpf loc name:missing|collection date:missing", "Mosaic beta catCA GFP min lot2", "Sequenced reads were mapped to the GRCz10 reference genome using Bowtie2 ver. 2.3.1. UMI counts were extracted per HTSeq ver. 0.6.1 from the CEL Seq2 pipeline. Assembly: GRCz10 Supplementary files format and content: Tab delimited text file for expression data normalized by regularized logarithm.", "early embryonic cell", null, "Cells were dissolved in TRIzol reagent Invitrogen and extracted. Samples were prepared according to the CEL Seq2 protocol described in Hashimshony et al. Geneome Biology 2016. Libraries preparation was performed according to the published CEL Seq2 protocol.", null, "strain:AB|tissue:early embryonic cell|developmental stage:9 hpf", "GSM8042246", "GSM8042246: Mosaic beta catCA GFP min lot2; Danio rerio; RNA Seq", "GSM8042246 r1", "GSM8042246", "1", "Cells were dissolved in TRIzol reagent Invitrogen and extracted. Samples were prepared according to the CEL Seq2 protocol described in Hashimshony et al. Geneome Biology 2016. Libraries preparation was performed according to the published CEL Seq2 protocol.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 1500", null, "SRP486518", null, null, "Mosaic_beta-catCA_GFP_min_lot2.fastq.gz", "fastq", 856836.0, 23801.0, "GSM8042246 r1", "0:36", "A:217589;C:147419;G:175612;T:316201;N:15", 36, null, null, null, 217589, 147419, 175612, 316201, 15, "SRX23429607", "SRS20284058", "SRA1793856", "Department of Homeostatic Regulation, Research Institute for Microbial Diseases, Osaka University", "Department of Homeostatic Regulation, Research Institute for Microbial Diseases, Osaka University", 1, 0.82481, null, 0.28434, null, 0.95371, null, 0.61551, null, 36, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Japan", "2024-01-29", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [30511, "SRR27764651", "SRX23429606", "SRS20284057", "SRP486518", "PRJNA1070582", "Gene expression profile of neighboring cells of cells with unfit Wnt morphogen gradient during cell competition", "GSE254439", "Transcriptome Analysis", "Morphogen signalling forms an activity gradient and instructs cell identities in a signalling strength dependent manner to pattern developing tissues. However  developing tissues also undergo dynamic morphogenesis  which may produce cells with unfit morphogen signalling and consequent noisy morphogen gradient. Here we show that a cell competition related system corrects such noisy morphogen gradients. Zebrafish imaging analyses of the Wnt/\u00df catenin signalling gradient  which acts as a morphogen to establish embryonic anterior posterior patterning  revealed that unfit cells with abnormal Wnt/\u00df catenin activity spontaneously appear and produce noise in the gradient. Communication between unfit and neighbouring fit cells via cadherin proteins stimulates apoptosis of the unfit cells by activating Smad signalling and reactive oxygen species production. This unfit cell elimination is required for proper Wnt/\u00df catenin gradient formation and consequent anterior posterior patterning. Because this gradient controls patterning not only in the embryo but also in adult tissues  this system may support tissue robustness and disease prevention. Overall design: \u00df catCA constitutive active form of \u00df catenin expressing GFP+ cells  or \u00dfcatCA unexpressing GFP  cells from \u00df catCA mosaically introduced zebrafish early embryos were sorted by FACS cell sorter. Total RNAs were extracted and analyzed by RNA seq.", null, "pubmed:39546611", null, "Mosaic beta catCA GFP min lot1", "GSM8042245", null, "source name:early embryonic cell|strain:AB|tissue:early embryonic cell|developmental stage:9 hpf loc name:missing|collection date:missing", "Mosaic beta catCA GFP min lot1", "Sequenced reads were mapped to the GRCz10 reference genome using Bowtie2 ver. 2.3.1. UMI counts were extracted per HTSeq ver. 0.6.1 from the CEL Seq2 pipeline. Assembly: GRCz10 Supplementary files format and content: Tab delimited text file for expression data normalized by regularized logarithm.", "early embryonic cell", null, "Cells were dissolved in TRIzol reagent Invitrogen and extracted. Samples were prepared according to the CEL Seq2 protocol described in Hashimshony et al. Geneome Biology 2016. Libraries preparation was performed according to the published CEL Seq2 protocol.", null, "strain:AB|tissue:early embryonic cell|developmental stage:9 hpf", "GSM8042245", "GSM8042245: Mosaic beta catCA GFP min lot1; Danio rerio; RNA Seq", "GSM8042245 r1", "GSM8042245", "1", "Cells were dissolved in TRIzol reagent Invitrogen and extracted. Samples were prepared according to the CEL Seq2 protocol described in Hashimshony et al. Geneome Biology 2016. Libraries preparation was performed according to the published CEL Seq2 protocol.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 1500", null, "SRP486518", null, null, "Mosaic_beta-catCA_GFP_min_lot1.fastq.gz", "fastq", 7181388.0, 199483.0, "GSM8042245 r1", "0:36", "A:1744919;C:1207643;G:1456829;T:2771919;N:78", 36, null, null, null, 1744919, 1207643, 1456829, 2771919, 78, "SRX23429606", "SRS20284057", "SRA1793856", "Department of Homeostatic Regulation, Research Institute for Microbial Diseases, Osaka University", "Department of Homeostatic Regulation, Research Institute for Microbial Diseases, Osaka University", 1, 0.83629, null, 0.16823, null, 0.84774, null, 0.64548, null, 36, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Japan", "2024-01-29", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [33075, "SRR29654109", "SRX25158199", "SRS21848821", "SRP517033", "PRJNA1129880", "Neutrophil immune profile guides spinal cord regeneration in zebrafish", "GSE271113", "Transcriptome Analysis", "Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet  their role in the repair process  particularly in a regenerative context  remains largely unknown. Here  we show that  promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely  blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether  these findings provide new insights into the role of neutrophils in spinal cord regeneration  emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition  we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100  and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Funda\u00e7\u00e5o para a Ci\u00eancia e Tecnologia FCT  Portugal", null, "pubmed:38925414", null, "Neutrophils mpx+  8 xxx post injury  AMD3100  biol rep 3", "GSM8369980", null, "tissue:Neutrophils mpx:GFP+|cell type:Neutrophils mpx:GFP+|treatment:8 xxx post injury AMD3100|geo loc name:missing|collection date:missing", "Neutrophils mpx+  8 xxx post injury  AMD3100  biol rep 3", "Libraries were paired end sequenced on a Nextseq 500 Illumina  high output  with a 1x75 bp Illumina Kit Read 1: 26 cycles  index read: 6 cycles  Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded.  Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script", "Neutrophils mpx:GFP+", "At 3 dpf  larvae were anesthetized in 0.5 mM tricaine. Subsequenclty  the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next  larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", "Zebrafish embryos were raised at 28.5\u00baC in E3 media with Methylene blue", "cell type:Neutrophils mpx:GFP+|treatment:8 xxx post injury AMD3100", "GSM8369980", "GSM8369980: Neutrophils mpx+  8 xxx post injury  AMD3100  biol rep 3; Danio rerio; RNA Seq", "GSM8369980 r1", "GSM8369980", "1", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP517033", null, null, "IMM-CT-b001_HW5F2BGXN_S6_L001_8hpi_AMD_-016_cbc.fastq.gz", "fastq", 347162880.0, 5786048.0, "GSM8369980 r1", "0:60", "A:122562825;C:62219285;G:75539895;T:86775172;N:65703", 60, null, null, null, 122562825, 62219285, 75539895, 86775172, 65703, "SRX25158199", "SRS21848821", "SRA1913211", "Instituto de Medicina Molecular", "Instituto de Medicina Molecular", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Portugal", "2024-06-29", "Larval", "Larval", "Blood", "Hematopoietic System"], [33076, "SRR29654110", "SRX25158199", "SRS21848821", "SRP517033", "PRJNA1129880", "Neutrophil immune profile guides spinal cord regeneration in zebrafish", "GSE271113", "Transcriptome Analysis", "Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet  their role in the repair process  particularly in a regenerative context  remains largely unknown. Here  we show that  promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely  blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether  these findings provide new insights into the role of neutrophils in spinal cord regeneration  emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition  we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100  and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Funda\u00e7\u00e5o para a Ci\u00eancia e Tecnologia FCT  Portugal", null, "pubmed:38925414", null, "Neutrophils mpx+  8 xxx post injury  AMD3100  biol rep 3", "GSM8369980", null, "tissue:Neutrophils mpx:GFP+|cell type:Neutrophils mpx:GFP+|treatment:8 xxx post injury AMD3100|geo loc name:missing|collection date:missing", "Neutrophils mpx+  8 xxx post injury  AMD3100  biol rep 3", "Libraries were paired end sequenced on a Nextseq 500 Illumina  high output  with a 1x75 bp Illumina Kit Read 1: 26 cycles  index read: 6 cycles  Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded.  Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script", "Neutrophils mpx:GFP+", "At 3 dpf  larvae were anesthetized in 0.5 mM tricaine. Subsequenclty  the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next  larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", "Zebrafish embryos were raised at 28.5\u00baC in E3 media with Methylene blue", "cell type:Neutrophils mpx:GFP+|treatment:8 xxx post injury AMD3100", "GSM8369980", "GSM8369980: Neutrophils mpx+  8 xxx post injury  AMD3100  biol rep 3; Danio rerio; RNA Seq", "GSM8369980 r1", "GSM8369980", "1", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP517033", null, null, "IMM-CT-b001_HW5F2BGXN_S6_L002_8hpi_AMD_-016_cbc.fastq.gz", "fastq", 340954260.0, 5682571.0, "GSM8369980 r2", "0:60", "A:120149623;C:60854408;G:75192893;T:84703966;N:53370", 60, null, null, null, 120149623, 60854408, 75192893, 84703966, 53370, "SRX25158199", "SRS21848821", "SRA1913211", "Instituto de Medicina Molecular", "Instituto de Medicina Molecular", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Portugal", "2024-06-29", "Larval", "Larval", "Blood", "Hematopoietic System"], [33077, "SRR29654111", "SRX25158199", "SRS21848821", "SRP517033", "PRJNA1129880", "Neutrophil immune profile guides spinal cord regeneration in zebrafish", "GSE271113", "Transcriptome Analysis", "Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet  their role in the repair process  particularly in a regenerative context  remains largely unknown. Here  we show that  promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely  blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether  these findings provide new insights into the role of neutrophils in spinal cord regeneration  emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition  we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100  and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Funda\u00e7\u00e5o para a Ci\u00eancia e Tecnologia FCT  Portugal", null, "pubmed:38925414", null, "Neutrophils mpx+  8 xxx post injury  AMD3100  biol rep 3", "GSM8369980", null, "tissue:Neutrophils mpx:GFP+|cell type:Neutrophils mpx:GFP+|treatment:8 xxx post injury AMD3100|geo loc name:missing|collection date:missing", "Neutrophils mpx+  8 xxx post injury  AMD3100  biol rep 3", "Libraries were paired end sequenced on a Nextseq 500 Illumina  high output  with a 1x75 bp Illumina Kit Read 1: 26 cycles  index read: 6 cycles  Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded.  Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script", "Neutrophils mpx:GFP+", "At 3 dpf  larvae were anesthetized in 0.5 mM tricaine. Subsequenclty  the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next  larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", "Zebrafish embryos were raised at 28.5\u00baC in E3 media with Methylene blue", "cell type:Neutrophils mpx:GFP+|treatment:8 xxx post injury AMD3100", "GSM8369980", "GSM8369980: Neutrophils mpx+  8 xxx post injury  AMD3100  biol rep 3; Danio rerio; RNA Seq", "GSM8369980 r1", "GSM8369980", "1", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP517033", null, null, "IMM-CT-b001_HW5F2BGXN_S6_L003_8hpi_AMD_-016_cbc.fastq.gz", "fastq", 351749160.0, 5862486.0, "GSM8369980 r3", "0:60", "A:124352905;C:63078724;G:76291828;T:87988386;N:37317", 60, null, null, null, 124352905, 63078724, 76291828, 87988386, 37317, "SRX25158199", "SRS21848821", "SRA1913211", "Instituto de Medicina Molecular", "Instituto de Medicina Molecular", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Portugal", "2024-06-29", "Larval", "Larval", "Blood", "Hematopoietic System"], [33078, "SRR29654112", "SRX25158199", "SRS21848821", "SRP517033", "PRJNA1129880", "Neutrophil immune profile guides spinal cord regeneration in zebrafish", "GSE271113", "Transcriptome Analysis", "Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet  their role in the repair process  particularly in a regenerative context  remains largely unknown. Here  we show that  promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely  blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether  these findings provide new insights into the role of neutrophils in spinal cord regeneration  emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition  we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100  and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Funda\u00e7\u00e5o para a Ci\u00eancia e Tecnologia FCT  Portugal", null, "pubmed:38925414", null, "Neutrophils mpx+  8 xxx post injury  AMD3100  biol rep 3", "GSM8369980", null, "tissue:Neutrophils mpx:GFP+|cell type:Neutrophils mpx:GFP+|treatment:8 xxx post injury AMD3100|geo loc name:missing|collection date:missing", "Neutrophils mpx+  8 xxx post injury  AMD3100  biol rep 3", "Libraries were paired end sequenced on a Nextseq 500 Illumina  high output  with a 1x75 bp Illumina Kit Read 1: 26 cycles  index read: 6 cycles  Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded.  Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script", "Neutrophils mpx:GFP+", "At 3 dpf  larvae were anesthetized in 0.5 mM tricaine. Subsequenclty  the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next  larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", "Zebrafish embryos were raised at 28.5\u00baC in E3 media with Methylene blue", "cell type:Neutrophils mpx:GFP+|treatment:8 xxx post injury AMD3100", "GSM8369980", "GSM8369980: Neutrophils mpx+  8 xxx post injury  AMD3100  biol rep 3; Danio rerio; RNA Seq", "GSM8369980 r1", "GSM8369980", "1", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP517033", null, null, "IMM-CT-b001_HW5F2BGXN_S6_L004_8hpi_AMD_-016_cbc.fastq.gz", "fastq", 345225720.0, 5753762.0, "GSM8369980 r4", "0:60", "A:121803902;C:61651407;G:75900430;T:85843789;N:26192", 60, null, null, null, 121803902, 61651407, 75900430, 85843789, 26192, "SRX25158199", "SRS21848821", "SRA1913211", "Instituto de Medicina Molecular", "Instituto de Medicina Molecular", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Portugal", "2024-06-29", "Larval", "Larval", "Blood", "Hematopoietic System"], [33079, "SRR29654113", "SRX25158198", "SRS21848820", "SRP517033", "PRJNA1129880", "Neutrophil immune profile guides spinal cord regeneration in zebrafish", "GSE271113", "Transcriptome Analysis", "Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet  their role in the repair process  particularly in a regenerative context  remains largely unknown. Here  we show that  promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely  blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether  these findings provide new insights into the role of neutrophils in spinal cord regeneration  emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition  we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100  and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Funda\u00e7\u00e5o para a Ci\u00eancia e Tecnologia FCT  Portugal", null, "pubmed:38925414", null, "Neutrophils mpx+  8 xxx post injury  AMD3100  biol rep 2", "GSM8369979", null, "tissue:Neutrophils mpx:GFP+|cell type:Neutrophils mpx:GFP+|treatment:8 xxx post injury AMD3100|geo loc name:missing|collection date:missing", "Neutrophils mpx+  8 xxx post injury  AMD3100  biol rep 2", "Libraries were paired end sequenced on a Nextseq 500 Illumina  high output  with a 1x75 bp Illumina Kit Read 1: 26 cycles  index read: 6 cycles  Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded.  Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script", "Neutrophils mpx:GFP+", "At 3 dpf  larvae were anesthetized in 0.5 mM tricaine. Subsequenclty  the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next  larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", "Zebrafish embryos were raised at 28.5\u00baC in E3 media with Methylene blue", "cell type:Neutrophils mpx:GFP+|treatment:8 xxx post injury AMD3100", "GSM8369979", "GSM8369979: Neutrophils mpx+  8 xxx post injury  AMD3100  biol rep 2; Danio rerio; RNA Seq", "GSM8369979 r1", "GSM8369979", "1", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP517033", null, null, "IMM-CT-b001_HW5F2BGXN_S6_L001_8hpi_AMD_-015_cbc.fastq.gz", "fastq", 159497640.0, 2658294.0, "GSM8369979 r1", "0:60", "A:55569742;C:28678683;G:33264744;T:41953354;N:31117", 60, null, null, null, 55569742, 28678683, 33264744, 41953354, 31117, "SRX25158198", "SRS21848820", "SRA1913211", "Instituto de Medicina Molecular", "Instituto de Medicina Molecular", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Portugal", "2024-06-29", "Larval", "Larval", "Blood", "Hematopoietic System"], [33080, "SRR29654114", "SRX25158198", "SRS21848820", "SRP517033", "PRJNA1129880", "Neutrophil immune profile guides spinal cord regeneration in zebrafish", "GSE271113", "Transcriptome Analysis", "Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet  their role in the repair process  particularly in a regenerative context  remains largely unknown. Here  we show that  promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely  blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether  these findings provide new insights into the role of neutrophils in spinal cord regeneration  emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition  we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100  and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Funda\u00e7\u00e5o para a Ci\u00eancia e Tecnologia FCT  Portugal", null, "pubmed:38925414", null, "Neutrophils mpx+  8 xxx post injury  AMD3100  biol rep 2", "GSM8369979", null, "tissue:Neutrophils mpx:GFP+|cell type:Neutrophils mpx:GFP+|treatment:8 xxx post injury AMD3100|geo loc name:missing|collection date:missing", "Neutrophils mpx+  8 xxx post injury  AMD3100  biol rep 2", "Libraries were paired end sequenced on a Nextseq 500 Illumina  high output  with a 1x75 bp Illumina Kit Read 1: 26 cycles  index read: 6 cycles  Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded.  Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script", "Neutrophils mpx:GFP+", "At 3 dpf  larvae were anesthetized in 0.5 mM tricaine. Subsequenclty  the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next  larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", "Zebrafish embryos were raised at 28.5\u00baC in E3 media with Methylene blue", "cell type:Neutrophils mpx:GFP+|treatment:8 xxx post injury AMD3100", "GSM8369979", "GSM8369979: Neutrophils mpx+  8 xxx post injury  AMD3100  biol rep 2; Danio rerio; RNA Seq", "GSM8369979 r1", "GSM8369979", "1", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP517033", null, null, "IMM-CT-b001_HW5F2BGXN_S6_L002_8hpi_AMD_-015_cbc.fastq.gz", "fastq", 156549240.0, 2609154.0, "GSM8369979 r2", "0:60", "A:54428858;C:28027289;G:33149650;T:40918247;N:25196", 60, null, null, null, 54428858, 28027289, 33149650, 40918247, 25196, "SRX25158198", "SRS21848820", "SRA1913211", "Instituto de Medicina Molecular", "Instituto de Medicina Molecular", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Portugal", "2024-06-29", "Larval", "Larval", "Blood", "Hematopoietic System"], [33081, "SRR29654115", "SRX25158198", "SRS21848820", "SRP517033", "PRJNA1129880", "Neutrophil immune profile guides spinal cord regeneration in zebrafish", "GSE271113", "Transcriptome Analysis", "Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet  their role in the repair process  particularly in a regenerative context  remains largely unknown. Here  we show that  promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely  blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether  these findings provide new insights into the role of neutrophils in spinal cord regeneration  emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition  we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100  and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Funda\u00e7\u00e5o para a Ci\u00eancia e Tecnologia FCT  Portugal", null, "pubmed:38925414", null, "Neutrophils mpx+  8 xxx post injury  AMD3100  biol rep 2", "GSM8369979", null, "tissue:Neutrophils mpx:GFP+|cell type:Neutrophils mpx:GFP+|treatment:8 xxx post injury AMD3100|geo loc name:missing|collection date:missing", "Neutrophils mpx+  8 xxx post injury  AMD3100  biol rep 2", "Libraries were paired end sequenced on a Nextseq 500 Illumina  high output  with a 1x75 bp Illumina Kit Read 1: 26 cycles  index read: 6 cycles  Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded.  Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script", "Neutrophils mpx:GFP+", "At 3 dpf  larvae were anesthetized in 0.5 mM tricaine. Subsequenclty  the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next  larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", "Zebrafish embryos were raised at 28.5\u00baC in E3 media with Methylene blue", "cell type:Neutrophils mpx:GFP+|treatment:8 xxx post injury AMD3100", "GSM8369979", "GSM8369979: Neutrophils mpx+  8 xxx post injury  AMD3100  biol rep 2; Danio rerio; RNA Seq", "GSM8369979 r1", "GSM8369979", "1", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP517033", null, null, "IMM-CT-b001_HW5F2BGXN_S6_L003_8hpi_AMD_-015_cbc.fastq.gz", "fastq", 161735280.0, 2695588.0, "GSM8369979 r3", "0:60", "A:56425187;C:29084972;G:33637112;T:42570603;N:17406", 60, null, null, null, 56425187, 29084972, 33637112, 42570603, 17406, "SRX25158198", "SRS21848820", "SRA1913211", "Instituto de Medicina Molecular", "Instituto de Medicina Molecular", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Portugal", "2024-06-29", "Larval", "Larval", "Blood", "Hematopoietic System"], [33082, "SRR29654116", "SRX25158198", "SRS21848820", "SRP517033", "PRJNA1129880", "Neutrophil immune profile guides spinal cord regeneration in zebrafish", "GSE271113", "Transcriptome Analysis", "Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet  their role in the repair process  particularly in a regenerative context  remains largely unknown. Here  we show that  promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely  blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether  these findings provide new insights into the role of neutrophils in spinal cord regeneration  emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition  we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100  and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Funda\u00e7\u00e5o para a Ci\u00eancia e Tecnologia FCT  Portugal", null, "pubmed:38925414", null, "Neutrophils mpx+  8 xxx post injury  AMD3100  biol rep 2", "GSM8369979", null, "tissue:Neutrophils mpx:GFP+|cell type:Neutrophils mpx:GFP+|treatment:8 xxx post injury AMD3100|geo loc name:missing|collection date:missing", "Neutrophils mpx+  8 xxx post injury  AMD3100  biol rep 2", "Libraries were paired end sequenced on a Nextseq 500 Illumina  high output  with a 1x75 bp Illumina Kit Read 1: 26 cycles  index read: 6 cycles  Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded.  Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script", "Neutrophils mpx:GFP+", "At 3 dpf  larvae were anesthetized in 0.5 mM tricaine. Subsequenclty  the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next  larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", "Zebrafish embryos were raised at 28.5\u00baC in E3 media with Methylene blue", "cell type:Neutrophils mpx:GFP+|treatment:8 xxx post injury AMD3100", "GSM8369979", "GSM8369979: Neutrophils mpx+  8 xxx post injury  AMD3100  biol rep 2; Danio rerio; RNA Seq", "GSM8369979 r1", "GSM8369979", "1", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP517033", null, null, "IMM-CT-b001_HW5F2BGXN_S6_L004_8hpi_AMD_-015_cbc.fastq.gz", "fastq", 158621520.0, 2643692.0, "GSM8369979 r4", "0:60", "A:55213721;C:28430013;G:33462307;T:41503213;N:12266", 60, null, null, null, 55213721, 28430013, 33462307, 41503213, 12266, "SRX25158198", "SRS21848820", "SRA1913211", "Instituto de Medicina Molecular", "Instituto de Medicina Molecular", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Portugal", "2024-06-29", "Larval", "Larval", "Blood", "Hematopoietic System"], [33083, "SRR29654117", "SRX25158197", "SRS21848819", "SRP517033", "PRJNA1129880", "Neutrophil immune profile guides spinal cord regeneration in zebrafish", "GSE271113", "Transcriptome Analysis", "Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet  their role in the repair process  particularly in a regenerative context  remains largely unknown. Here  we show that  promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely  blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether  these findings provide new insights into the role of neutrophils in spinal cord regeneration  emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition  we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100  and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Funda\u00e7\u00e5o para a Ci\u00eancia e Tecnologia FCT  Portugal", null, "pubmed:38925414", null, "Neutrophils mpx+  8 xxx post injury  AMD3100  biol rep 1", "GSM8369978", null, "tissue:Neutrophils mpx:GFP+|cell type:Neutrophils mpx:GFP+|treatment:8 xxx post injury AMD3100|geo loc name:missing|collection date:missing", "Neutrophils mpx+  8 xxx post injury  AMD3100  biol rep 1", "Libraries were paired end sequenced on a Nextseq 500 Illumina  high output  with a 1x75 bp Illumina Kit Read 1: 26 cycles  index read: 6 cycles  Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded.  Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script", "Neutrophils mpx:GFP+", "At 3 dpf  larvae were anesthetized in 0.5 mM tricaine. Subsequenclty  the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next  larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", "Zebrafish embryos were raised at 28.5\u00baC in E3 media with Methylene blue", "cell type:Neutrophils mpx:GFP+|treatment:8 xxx post injury AMD3100", "GSM8369978", "GSM8369978: Neutrophils mpx+  8 xxx post injury  AMD3100  biol rep 1; Danio rerio; RNA Seq", "GSM8369978 r1", "GSM8369978", "1", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP517033", null, null, "IMM-CT-b001_HW5F2BGXN_S6_L001_8hpi_AMD_-011_cbc.fastq.gz", "fastq", 44363040.0, 739384.0, "GSM8369978 r1", "0:60", "A:17756825;C:7540147;G:9311367;T:9746444;N:8257", 60, null, null, null, 17756825, 7540147, 9311367, 9746444, 8257, "SRX25158197", "SRS21848819", "SRA1913211", "Instituto de Medicina Molecular", "Instituto de Medicina Molecular", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Portugal", "2024-06-29", "Larval", "Larval", "Blood", "Hematopoietic System"], [33084, "SRR29654118", "SRX25158197", "SRS21848819", "SRP517033", "PRJNA1129880", "Neutrophil immune profile guides spinal cord regeneration in zebrafish", "GSE271113", "Transcriptome Analysis", "Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet  their role in the repair process  particularly in a regenerative context  remains largely unknown. Here  we show that  promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely  blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether  these findings provide new insights into the role of neutrophils in spinal cord regeneration  emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition  we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100  and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Funda\u00e7\u00e5o para a Ci\u00eancia e Tecnologia FCT  Portugal", null, "pubmed:38925414", null, "Neutrophils mpx+  8 xxx post injury  AMD3100  biol rep 1", "GSM8369978", null, "tissue:Neutrophils mpx:GFP+|cell type:Neutrophils mpx:GFP+|treatment:8 xxx post injury AMD3100|geo loc name:missing|collection date:missing", "Neutrophils mpx+  8 xxx post injury  AMD3100  biol rep 1", "Libraries were paired end sequenced on a Nextseq 500 Illumina  high output  with a 1x75 bp Illumina Kit Read 1: 26 cycles  index read: 6 cycles  Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded.  Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script", "Neutrophils mpx:GFP+", "At 3 dpf  larvae were anesthetized in 0.5 mM tricaine. Subsequenclty  the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next  larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", "Zebrafish embryos were raised at 28.5\u00baC in E3 media with Methylene blue", "cell type:Neutrophils mpx:GFP+|treatment:8 xxx post injury AMD3100", "GSM8369978", "GSM8369978: Neutrophils mpx+  8 xxx post injury  AMD3100  biol rep 1; Danio rerio; RNA Seq", "GSM8369978 r1", "GSM8369978", "1", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP517033", null, null, "IMM-CT-b001_HW5F2BGXN_S6_L002_8hpi_AMD_-011_cbc.fastq.gz", "fastq", 43450800.0, 724180.0, "GSM8369978 r2", "0:60", "A:17376442;C:7355139;G:9244019;T:9468455;N:6745", 60, null, null, null, 17376442, 7355139, 9244019, 9468455, 6745, "SRX25158197", "SRS21848819", "SRA1913211", "Instituto de Medicina Molecular", "Instituto de Medicina Molecular", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Portugal", "2024-06-29", "Larval", "Larval", "Blood", "Hematopoietic System"], [33085, "SRR29654119", "SRX25158197", "SRS21848819", "SRP517033", "PRJNA1129880", "Neutrophil immune profile guides spinal cord regeneration in zebrafish", "GSE271113", "Transcriptome Analysis", "Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet  their role in the repair process  particularly in a regenerative context  remains largely unknown. Here  we show that  promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely  blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether  these findings provide new insights into the role of neutrophils in spinal cord regeneration  emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition  we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100  and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Funda\u00e7\u00e5o para a Ci\u00eancia e Tecnologia FCT  Portugal", null, "pubmed:38925414", null, "Neutrophils mpx+  8 xxx post injury  AMD3100  biol rep 1", "GSM8369978", null, "tissue:Neutrophils mpx:GFP+|cell type:Neutrophils mpx:GFP+|treatment:8 xxx post injury AMD3100|geo loc name:missing|collection date:missing", "Neutrophils mpx+  8 xxx post injury  AMD3100  biol rep 1", "Libraries were paired end sequenced on a Nextseq 500 Illumina  high output  with a 1x75 bp Illumina Kit Read 1: 26 cycles  index read: 6 cycles  Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded.  Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script", "Neutrophils mpx:GFP+", "At 3 dpf  larvae were anesthetized in 0.5 mM tricaine. Subsequenclty  the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next  larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", "Zebrafish embryos were raised at 28.5\u00baC in E3 media with Methylene blue", "cell type:Neutrophils mpx:GFP+|treatment:8 xxx post injury AMD3100", "GSM8369978", "GSM8369978: Neutrophils mpx+  8 xxx post injury  AMD3100  biol rep 1; Danio rerio; RNA Seq", "GSM8369978 r1", "GSM8369978", "1", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP517033", null, null, "IMM-CT-b001_HW5F2BGXN_S6_L003_8hpi_AMD_-011_cbc.fastq.gz", "fastq", 44795880.0, 746598.0, "GSM8369978 r3", "0:60", "A:17988707;C:7600964;G:9362568;T:9839285;N:4356", 60, null, null, null, 17988707, 7600964, 9362568, 9839285, 4356, "SRX25158197", "SRS21848819", "SRA1913211", "Instituto de Medicina Molecular", "Instituto de Medicina Molecular", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Portugal", "2024-06-29", "Larval", "Larval", "Blood", "Hematopoietic System"], [33086, "SRR29654120", "SRX25158197", "SRS21848819", "SRP517033", "PRJNA1129880", "Neutrophil immune profile guides spinal cord regeneration in zebrafish", "GSE271113", "Transcriptome Analysis", "Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet  their role in the repair process  particularly in a regenerative context  remains largely unknown. Here  we show that  promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely  blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether  these findings provide new insights into the role of neutrophils in spinal cord regeneration  emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition  we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100  and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Funda\u00e7\u00e5o para a Ci\u00eancia e Tecnologia FCT  Portugal", null, "pubmed:38925414", null, "Neutrophils mpx+  8 xxx post injury  AMD3100  biol rep 1", "GSM8369978", null, "tissue:Neutrophils mpx:GFP+|cell type:Neutrophils mpx:GFP+|treatment:8 xxx post injury AMD3100|geo loc name:missing|collection date:missing", "Neutrophils mpx+  8 xxx post injury  AMD3100  biol rep 1", "Libraries were paired end sequenced on a Nextseq 500 Illumina  high output  with a 1x75 bp Illumina Kit Read 1: 26 cycles  index read: 6 cycles  Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded.  Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script", "Neutrophils mpx:GFP+", "At 3 dpf  larvae were anesthetized in 0.5 mM tricaine. Subsequenclty  the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next  larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", "Zebrafish embryos were raised at 28.5\u00baC in E3 media with Methylene blue", "cell type:Neutrophils mpx:GFP+|treatment:8 xxx post injury AMD3100", "GSM8369978", "GSM8369978: Neutrophils mpx+  8 xxx post injury  AMD3100  biol rep 1; Danio rerio; RNA Seq", "GSM8369978 r1", "GSM8369978", "1", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP517033", null, null, "IMM-CT-b001_HW5F2BGXN_S6_L004_8hpi_AMD_-011_cbc.fastq.gz", "fastq", 44060940.0, 734349.0, "GSM8369978 r4", "0:60", "A:17608648;C:7492643;G:9327676;T:9628642;N:3331", 60, null, null, null, 17608648, 7492643, 9327676, 9628642, 3331, "SRX25158197", "SRS21848819", "SRA1913211", "Instituto de Medicina Molecular", "Instituto de Medicina Molecular", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Portugal", "2024-06-29", "Larval", "Larval", "Blood", "Hematopoietic System"], [33087, "SRR29654121", "SRX25158196", "SRS21848818", "SRP517033", "PRJNA1129880", "Neutrophil immune profile guides spinal cord regeneration in zebrafish", "GSE271113", "Transcriptome Analysis", "Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet  their role in the repair process  particularly in a regenerative context  remains largely unknown. Here  we show that  promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely  blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether  these findings provide new insights into the role of neutrophils in spinal cord regeneration  emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition  we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100  and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Funda\u00e7\u00e5o para a Ci\u00eancia e Tecnologia FCT  Portugal", null, "pubmed:38925414", null, "Neutrophils mpx+  uninjured  AMD3100  biol rep 3", "GSM8369977", null, "tissue:Neutrophils mpx:GFP+|cell type:Neutrophils mpx:GFP+|treatment:uninjured AMD3100|geo loc name:missing|collection date:missing", "Neutrophils mpx+  uninjured  AMD3100  biol rep 3", "Libraries were paired end sequenced on a Nextseq 500 Illumina  high output  with a 1x75 bp Illumina Kit Read 1: 26 cycles  index read: 6 cycles  Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded.  Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script", "Neutrophils mpx:GFP+", "At 3 dpf  larvae were anesthetized in 0.5 mM tricaine. Subsequenclty  the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next  larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", "Zebrafish embryos were raised at 28.5\u00baC in E3 media with Methylene blue", "cell type:Neutrophils mpx:GFP+|treatment:uninjured AMD3100", "GSM8369977", "GSM8369977: Neutrophils mpx+  uninjured  AMD3100  biol rep 3; Danio rerio; RNA Seq", "GSM8369977 r1", "GSM8369977", "1", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP517033", null, null, "IMM-CT-b001_HW5F2BGXN_S6_L001_Uninjured_AMD_-014_cbc.fastq.gz", "fastq", 115048140.0, 1917469.0, "GSM8369977 r1", "0:60", "A:41373215;C:21759509;G:21832537;T:30061744;N:21135", 60, null, null, null, 41373215, 21759509, 21832537, 30061744, 21135, "SRX25158196", "SRS21848818", "SRA1913211", "Instituto de Medicina Molecular", "Instituto de Medicina Molecular", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Portugal", "2024-06-29", "Larval", "Larval", "Blood", "Hematopoietic System"], [33088, "SRR29654122", "SRX25158196", "SRS21848818", "SRP517033", "PRJNA1129880", "Neutrophil immune profile guides spinal cord regeneration in zebrafish", "GSE271113", "Transcriptome Analysis", "Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet  their role in the repair process  particularly in a regenerative context  remains largely unknown. Here  we show that  promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely  blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether  these findings provide new insights into the role of neutrophils in spinal cord regeneration  emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition  we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100  and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Funda\u00e7\u00e5o para a Ci\u00eancia e Tecnologia FCT  Portugal", null, "pubmed:38925414", null, "Neutrophils mpx+  uninjured  AMD3100  biol rep 3", "GSM8369977", null, "tissue:Neutrophils mpx:GFP+|cell type:Neutrophils mpx:GFP+|treatment:uninjured AMD3100|geo loc name:missing|collection date:missing", "Neutrophils mpx+  uninjured  AMD3100  biol rep 3", "Libraries were paired end sequenced on a Nextseq 500 Illumina  high output  with a 1x75 bp Illumina Kit Read 1: 26 cycles  index read: 6 cycles  Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded.  Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script", "Neutrophils mpx:GFP+", "At 3 dpf  larvae were anesthetized in 0.5 mM tricaine. Subsequenclty  the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next  larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", "Zebrafish embryos were raised at 28.5\u00baC in E3 media with Methylene blue", "cell type:Neutrophils mpx:GFP+|treatment:uninjured AMD3100", "GSM8369977", "GSM8369977: Neutrophils mpx+  uninjured  AMD3100  biol rep 3; Danio rerio; RNA Seq", "GSM8369977 r1", "GSM8369977", "1", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP517033", null, null, "IMM-CT-b001_HW5F2BGXN_S6_L002_Uninjured_AMD_-014_cbc.fastq.gz", "fastq", 112845060.0, 1880751.0, "GSM8369977 r2", "0:60", "A:40482360;C:21287713;G:21750928;T:29306465;N:17594", 60, null, null, null, 40482360, 21287713, 21750928, 29306465, 17594, "SRX25158196", "SRS21848818", "SRA1913211", "Instituto de Medicina Molecular", "Instituto de Medicina Molecular", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Portugal", "2024-06-29", "Larval", "Larval", "Blood", "Hematopoietic System"], [33089, "SRR29654123", "SRX25158196", "SRS21848818", "SRP517033", "PRJNA1129880", "Neutrophil immune profile guides spinal cord regeneration in zebrafish", "GSE271113", "Transcriptome Analysis", "Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet  their role in the repair process  particularly in a regenerative context  remains largely unknown. Here  we show that  promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely  blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether  these findings provide new insights into the role of neutrophils in spinal cord regeneration  emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition  we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100  and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Funda\u00e7\u00e5o para a Ci\u00eancia e Tecnologia FCT  Portugal", null, "pubmed:38925414", null, "Neutrophils mpx+  uninjured  AMD3100  biol rep 3", "GSM8369977", null, "tissue:Neutrophils mpx:GFP+|cell type:Neutrophils mpx:GFP+|treatment:uninjured AMD3100|geo loc name:missing|collection date:missing", "Neutrophils mpx+  uninjured  AMD3100  biol rep 3", "Libraries were paired end sequenced on a Nextseq 500 Illumina  high output  with a 1x75 bp Illumina Kit Read 1: 26 cycles  index read: 6 cycles  Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded.  Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script", "Neutrophils mpx:GFP+", "At 3 dpf  larvae were anesthetized in 0.5 mM tricaine. Subsequenclty  the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next  larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", "Zebrafish embryos were raised at 28.5\u00baC in E3 media with Methylene blue", "cell type:Neutrophils mpx:GFP+|treatment:uninjured AMD3100", "GSM8369977", "GSM8369977: Neutrophils mpx+  uninjured  AMD3100  biol rep 3; Danio rerio; RNA Seq", "GSM8369977 r1", "GSM8369977", "1", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP517033", null, null, "IMM-CT-b001_HW5F2BGXN_S6_L003_Uninjured_AMD_-014_cbc.fastq.gz", "fastq", 116696580.0, 1944943.0, "GSM8369977 r3", "0:60", "A:42022776;C:22106040;G:22075778;T:30479513;N:12473", 60, null, null, null, 42022776, 22106040, 22075778, 30479513, 12473, "SRX25158196", "SRS21848818", "SRA1913211", "Instituto de Medicina Molecular", "Instituto de Medicina Molecular", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Portugal", "2024-06-29", "Larval", "Larval", "Blood", "Hematopoietic System"], [33090, "SRR29654124", "SRX25158196", "SRS21848818", "SRP517033", "PRJNA1129880", "Neutrophil immune profile guides spinal cord regeneration in zebrafish", "GSE271113", "Transcriptome Analysis", "Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet  their role in the repair process  particularly in a regenerative context  remains largely unknown. Here  we show that  promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely  blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether  these findings provide new insights into the role of neutrophils in spinal cord regeneration  emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition  we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100  and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Funda\u00e7\u00e5o para a Ci\u00eancia e Tecnologia FCT  Portugal", null, "pubmed:38925414", null, "Neutrophils mpx+  uninjured  AMD3100  biol rep 3", "GSM8369977", null, "tissue:Neutrophils mpx:GFP+|cell type:Neutrophils mpx:GFP+|treatment:uninjured AMD3100|geo loc name:missing|collection date:missing", "Neutrophils mpx+  uninjured  AMD3100  biol rep 3", "Libraries were paired end sequenced on a Nextseq 500 Illumina  high output  with a 1x75 bp Illumina Kit Read 1: 26 cycles  index read: 6 cycles  Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded.  Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script", "Neutrophils mpx:GFP+", "At 3 dpf  larvae were anesthetized in 0.5 mM tricaine. Subsequenclty  the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next  larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", "Zebrafish embryos were raised at 28.5\u00baC in E3 media with Methylene blue", "cell type:Neutrophils mpx:GFP+|treatment:uninjured AMD3100", "GSM8369977", "GSM8369977: Neutrophils mpx+  uninjured  AMD3100  biol rep 3; Danio rerio; RNA Seq", "GSM8369977 r1", "GSM8369977", "1", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP517033", null, null, "IMM-CT-b001_HW5F2BGXN_S6_L004_Uninjured_AMD_-014_cbc.fastq.gz", "fastq", 114334980.0, 1905583.0, "GSM8369977 r4", "0:60", "A:41132105;C:21578779;G:21934073;T:29681512;N:8511", 60, null, null, null, 41132105, 21578779, 21934073, 29681512, 8511, "SRX25158196", "SRS21848818", "SRA1913211", "Instituto de Medicina Molecular", "Instituto de Medicina Molecular", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Portugal", "2024-06-29", "Larval", "Larval", "Blood", "Hematopoietic System"], [33091, "SRR29654125", "SRX25158195", "SRS21848817", "SRP517033", "PRJNA1129880", "Neutrophil immune profile guides spinal cord regeneration in zebrafish", "GSE271113", "Transcriptome Analysis", "Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet  their role in the repair process  particularly in a regenerative context  remains largely unknown. Here  we show that  promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely  blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether  these findings provide new insights into the role of neutrophils in spinal cord regeneration  emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition  we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100  and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Funda\u00e7\u00e5o para a Ci\u00eancia e Tecnologia FCT  Portugal", null, "pubmed:38925414", null, "Neutrophils mpx+  uninjured  AMD3100  biol rep 2", "GSM8369976", null, "tissue:Neutrophils mpx:GFP+|cell type:Neutrophils mpx:GFP+|treatment:uninjured AMD3100|geo loc name:missing|collection date:missing", "Neutrophils mpx+  uninjured  AMD3100  biol rep 2", "Libraries were paired end sequenced on a Nextseq 500 Illumina  high output  with a 1x75 bp Illumina Kit Read 1: 26 cycles  index read: 6 cycles  Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded.  Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script", "Neutrophils mpx:GFP+", "At 3 dpf  larvae were anesthetized in 0.5 mM tricaine. Subsequenclty  the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next  larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", "Zebrafish embryos were raised at 28.5\u00baC in E3 media with Methylene blue", "cell type:Neutrophils mpx:GFP+|treatment:uninjured AMD3100", "GSM8369976", "GSM8369976: Neutrophils mpx+  uninjured  AMD3100  biol rep 2; Danio rerio; RNA Seq", "GSM8369976 r1", "GSM8369976", "1", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP517033", null, null, "IMM-CT-b001_HW5F2BGXN_S6_L001_Uninjured_AMD_-013_cbc.fastq.gz", "fastq", 354085380.0, 5901423.0, "GSM8369976 r1", "0:60", "A:124800871;C:65627966;G:72434440;T:91152029;N:70074", 60, null, null, null, 124800871, 65627966, 72434440, 91152029, 70074, "SRX25158195", "SRS21848817", "SRA1913211", "Instituto de Medicina Molecular", "Instituto de Medicina Molecular", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Portugal", "2024-06-29", "Larval", "Larval", "Blood", "Hematopoietic System"], [33092, "SRR29654126", "SRX25158195", "SRS21848817", "SRP517033", "PRJNA1129880", "Neutrophil immune profile guides spinal cord regeneration in zebrafish", "GSE271113", "Transcriptome Analysis", "Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet  their role in the repair process  particularly in a regenerative context  remains largely unknown. Here  we show that  promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely  blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether  these findings provide new insights into the role of neutrophils in spinal cord regeneration  emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition  we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100  and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Funda\u00e7\u00e5o para a Ci\u00eancia e Tecnologia FCT  Portugal", null, "pubmed:38925414", null, "Neutrophils mpx+  uninjured  AMD3100  biol rep 2", "GSM8369976", null, "tissue:Neutrophils mpx:GFP+|cell type:Neutrophils mpx:GFP+|treatment:uninjured AMD3100|geo loc name:missing|collection date:missing", "Neutrophils mpx+  uninjured  AMD3100  biol rep 2", "Libraries were paired end sequenced on a Nextseq 500 Illumina  high output  with a 1x75 bp Illumina Kit Read 1: 26 cycles  index read: 6 cycles  Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded.  Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script", "Neutrophils mpx:GFP+", "At 3 dpf  larvae were anesthetized in 0.5 mM tricaine. Subsequenclty  the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next  larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", "Zebrafish embryos were raised at 28.5\u00baC in E3 media with Methylene blue", "cell type:Neutrophils mpx:GFP+|treatment:uninjured AMD3100", "GSM8369976", "GSM8369976: Neutrophils mpx+  uninjured  AMD3100  biol rep 2; Danio rerio; RNA Seq", "GSM8369976 r1", "GSM8369976", "1", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP517033", null, null, "IMM-CT-b001_HW5F2BGXN_S6_L002_Uninjured_AMD_-013_cbc.fastq.gz", "fastq", 347250360.0, 5787506.0, "GSM8369976 r2", "0:60", "A:122147080;C:64042522;G:72135325;T:88869927;N:55506", 60, null, null, null, 122147080, 64042522, 72135325, 88869927, 55506, "SRX25158195", "SRS21848817", "SRA1913211", "Instituto de Medicina Molecular", "Instituto de Medicina Molecular", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Portugal", "2024-06-29", "Larval", "Larval", "Blood", "Hematopoietic System"], [33093, "SRR29654127", "SRX25158195", "SRS21848817", "SRP517033", "PRJNA1129880", "Neutrophil immune profile guides spinal cord regeneration in zebrafish", "GSE271113", "Transcriptome Analysis", "Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet  their role in the repair process  particularly in a regenerative context  remains largely unknown. Here  we show that  promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely  blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether  these findings provide new insights into the role of neutrophils in spinal cord regeneration  emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition  we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100  and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Funda\u00e7\u00e5o para a Ci\u00eancia e Tecnologia FCT  Portugal", null, "pubmed:38925414", null, "Neutrophils mpx+  uninjured  AMD3100  biol rep 2", "GSM8369976", null, "tissue:Neutrophils mpx:GFP+|cell type:Neutrophils mpx:GFP+|treatment:uninjured AMD3100|geo loc name:missing|collection date:missing", "Neutrophils mpx+  uninjured  AMD3100  biol rep 2", "Libraries were paired end sequenced on a Nextseq 500 Illumina  high output  with a 1x75 bp Illumina Kit Read 1: 26 cycles  index read: 6 cycles  Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded.  Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script", "Neutrophils mpx:GFP+", "At 3 dpf  larvae were anesthetized in 0.5 mM tricaine. Subsequenclty  the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next  larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", "Zebrafish embryos were raised at 28.5\u00baC in E3 media with Methylene blue", "cell type:Neutrophils mpx:GFP+|treatment:uninjured AMD3100", "GSM8369976", "GSM8369976: Neutrophils mpx+  uninjured  AMD3100  biol rep 2; Danio rerio; RNA Seq", "GSM8369976 r1", "GSM8369976", "1", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP517033", null, null, "IMM-CT-b001_HW5F2BGXN_S6_L003_Uninjured_AMD_-013_cbc.fastq.gz", "fastq", 358862580.0, 5981043.0, "GSM8369976 r3", "0:60", "A:126636264;C:66527902;G:73214426;T:92445348;N:38640", 60, null, null, null, 126636264, 66527902, 73214426, 92445348, 38640, "SRX25158195", "SRS21848817", "SRA1913211", "Instituto de Medicina Molecular", "Instituto de Medicina Molecular", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Portugal", "2024-06-29", "Larval", "Larval", "Blood", "Hematopoietic System"], [33094, "SRR29654128", "SRX25158195", "SRS21848817", "SRP517033", "PRJNA1129880", "Neutrophil immune profile guides spinal cord regeneration in zebrafish", "GSE271113", "Transcriptome Analysis", "Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet  their role in the repair process  particularly in a regenerative context  remains largely unknown. Here  we show that  promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely  blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether  these findings provide new insights into the role of neutrophils in spinal cord regeneration  emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition  we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100  and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Funda\u00e7\u00e5o para a Ci\u00eancia e Tecnologia FCT  Portugal", null, "pubmed:38925414", null, "Neutrophils mpx+  uninjured  AMD3100  biol rep 2", "GSM8369976", null, "tissue:Neutrophils mpx:GFP+|cell type:Neutrophils mpx:GFP+|treatment:uninjured AMD3100|geo loc name:missing|collection date:missing", "Neutrophils mpx+  uninjured  AMD3100  biol rep 2", "Libraries were paired end sequenced on a Nextseq 500 Illumina  high output  with a 1x75 bp Illumina Kit Read 1: 26 cycles  index read: 6 cycles  Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded.  Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script", "Neutrophils mpx:GFP+", "At 3 dpf  larvae were anesthetized in 0.5 mM tricaine. Subsequenclty  the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next  larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", "Zebrafish embryos were raised at 28.5\u00baC in E3 media with Methylene blue", "cell type:Neutrophils mpx:GFP+|treatment:uninjured AMD3100", "GSM8369976", "GSM8369976: Neutrophils mpx+  uninjured  AMD3100  biol rep 2; Danio rerio; RNA Seq", "GSM8369976 r1", "GSM8369976", "1", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP517033", null, null, "IMM-CT-b001_HW5F2BGXN_S6_L004_Uninjured_AMD_-013_cbc.fastq.gz", "fastq", 351843120.0, 5864052.0, "GSM8369976 r4", "0:60", "A:123921807;C:64956560;G:72828989;T:90107944;N:27820", 60, null, null, null, 123921807, 64956560, 72828989, 90107944, 27820, "SRX25158195", "SRS21848817", "SRA1913211", "Instituto de Medicina Molecular", "Instituto de Medicina Molecular", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Portugal", "2024-06-29", "Larval", "Larval", "Blood", "Hematopoietic System"], [33095, "SRR29654129", "SRX25158194", "SRS21848816", "SRP517033", "PRJNA1129880", "Neutrophil immune profile guides spinal cord regeneration in zebrafish", "GSE271113", "Transcriptome Analysis", "Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet  their role in the repair process  particularly in a regenerative context  remains largely unknown. Here  we show that  promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely  blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether  these findings provide new insights into the role of neutrophils in spinal cord regeneration  emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition  we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100  and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Funda\u00e7\u00e5o para a Ci\u00eancia e Tecnologia FCT  Portugal", null, "pubmed:38925414", null, "Neutrophils mpx+  uninjured  AMD3100  biol rep 1", "GSM8369975", null, "tissue:Neutrophils mpx:GFP+|cell type:Neutrophils mpx:GFP+|treatment:uninjured AMD3100|geo loc name:missing|collection date:missing", "Neutrophils mpx+  uninjured  AMD3100  biol rep 1", "Libraries were paired end sequenced on a Nextseq 500 Illumina  high output  with a 1x75 bp Illumina Kit Read 1: 26 cycles  index read: 6 cycles  Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded.  Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script", "Neutrophils mpx:GFP+", "At 3 dpf  larvae were anesthetized in 0.5 mM tricaine. Subsequenclty  the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next  larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", "Zebrafish embryos were raised at 28.5\u00baC in E3 media with Methylene blue", "cell type:Neutrophils mpx:GFP+|treatment:uninjured AMD3100", "GSM8369975", "GSM8369975: Neutrophils mpx+  uninjured  AMD3100  biol rep 1; Danio rerio; RNA Seq", "GSM8369975 r1", "GSM8369975", "1", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP517033", null, null, "IMM-CT-b001_HW5F2BGXN_S6_L001_Uninjured_AMD_-010_cbc.fastq.gz", "fastq", 100732380.0, 1678873.0, "GSM8369975 r1", "0:60", "A:37215898;C:18610797;G:18111317;T:26774380;N:19988", 60, null, null, null, 37215898, 18610797, 18111317, 26774380, 19988, "SRX25158194", "SRS21848816", "SRA1913211", "Instituto de Medicina Molecular", "Instituto de Medicina Molecular", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Portugal", "2024-06-29", "Larval", "Larval", "Blood", "Hematopoietic System"], [33096, "SRR29654130", "SRX25158194", "SRS21848816", "SRP517033", "PRJNA1129880", "Neutrophil immune profile guides spinal cord regeneration in zebrafish", "GSE271113", "Transcriptome Analysis", "Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet  their role in the repair process  particularly in a regenerative context  remains largely unknown. Here  we show that  promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely  blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether  these findings provide new insights into the role of neutrophils in spinal cord regeneration  emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition  we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100  and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Funda\u00e7\u00e5o para a Ci\u00eancia e Tecnologia FCT  Portugal", null, "pubmed:38925414", null, "Neutrophils mpx+  uninjured  AMD3100  biol rep 1", "GSM8369975", null, "tissue:Neutrophils mpx:GFP+|cell type:Neutrophils mpx:GFP+|treatment:uninjured AMD3100|geo loc name:missing|collection date:missing", "Neutrophils mpx+  uninjured  AMD3100  biol rep 1", "Libraries were paired end sequenced on a Nextseq 500 Illumina  high output  with a 1x75 bp Illumina Kit Read 1: 26 cycles  index read: 6 cycles  Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded.  Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script", "Neutrophils mpx:GFP+", "At 3 dpf  larvae were anesthetized in 0.5 mM tricaine. Subsequenclty  the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next  larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", "Zebrafish embryos were raised at 28.5\u00baC in E3 media with Methylene blue", "cell type:Neutrophils mpx:GFP+|treatment:uninjured AMD3100", "GSM8369975", "GSM8369975: Neutrophils mpx+  uninjured  AMD3100  biol rep 1; Danio rerio; RNA Seq", "GSM8369975 r1", "GSM8369975", "1", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP517033", null, null, "IMM-CT-b001_HW5F2BGXN_S6_L002_Uninjured_AMD_-010_cbc.fastq.gz", "fastq", 98830860.0, 1647181.0, "GSM8369975 r2", "0:60", "A:36388012;C:18195984;G:18122717;T:26108692;N:15455", 60, null, null, null, 36388012, 18195984, 18122717, 26108692, 15455, "SRX25158194", "SRS21848816", "SRA1913211", "Instituto de Medicina Molecular", "Instituto de Medicina Molecular", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Portugal", "2024-06-29", "Larval", "Larval", "Blood", "Hematopoietic System"], [33097, "SRR29654131", "SRX25158194", "SRS21848816", "SRP517033", "PRJNA1129880", "Neutrophil immune profile guides spinal cord regeneration in zebrafish", "GSE271113", "Transcriptome Analysis", "Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet  their role in the repair process  particularly in a regenerative context  remains largely unknown. Here  we show that  promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely  blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether  these findings provide new insights into the role of neutrophils in spinal cord regeneration  emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition  we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100  and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Funda\u00e7\u00e5o para a Ci\u00eancia e Tecnologia FCT  Portugal", null, "pubmed:38925414", null, "Neutrophils mpx+  uninjured  AMD3100  biol rep 1", "GSM8369975", null, "tissue:Neutrophils mpx:GFP+|cell type:Neutrophils mpx:GFP+|treatment:uninjured AMD3100|geo loc name:missing|collection date:missing", "Neutrophils mpx+  uninjured  AMD3100  biol rep 1", "Libraries were paired end sequenced on a Nextseq 500 Illumina  high output  with a 1x75 bp Illumina Kit Read 1: 26 cycles  index read: 6 cycles  Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded.  Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script", "Neutrophils mpx:GFP+", "At 3 dpf  larvae were anesthetized in 0.5 mM tricaine. Subsequenclty  the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next  larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", "Zebrafish embryos were raised at 28.5\u00baC in E3 media with Methylene blue", "cell type:Neutrophils mpx:GFP+|treatment:uninjured AMD3100", "GSM8369975", "GSM8369975: Neutrophils mpx+  uninjured  AMD3100  biol rep 1; Danio rerio; RNA Seq", "GSM8369975 r1", "GSM8369975", "1", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP517033", null, null, "IMM-CT-b001_HW5F2BGXN_S6_L003_Uninjured_AMD_-010_cbc.fastq.gz", "fastq", 102277560.0, 1704626.0, "GSM8369975 r3", "0:60", "A:37811843;C:18928051;G:18347174;T:27179477;N:11015", 60, null, null, null, 37811843, 18928051, 18347174, 27179477, 11015, "SRX25158194", "SRS21848816", "SRA1913211", "Instituto de Medicina Molecular", "Instituto de Medicina Molecular", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Portugal", "2024-06-29", "Larval", "Larval", "Blood", "Hematopoietic System"], [33098, "SRR29654132", "SRX25158194", "SRS21848816", "SRP517033", "PRJNA1129880", "Neutrophil immune profile guides spinal cord regeneration in zebrafish", "GSE271113", "Transcriptome Analysis", "Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet  their role in the repair process  particularly in a regenerative context  remains largely unknown. Here  we show that  promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely  blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether  these findings provide new insights into the role of neutrophils in spinal cord regeneration  emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition  we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100  and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Funda\u00e7\u00e5o para a Ci\u00eancia e Tecnologia FCT  Portugal", null, "pubmed:38925414", null, "Neutrophils mpx+  uninjured  AMD3100  biol rep 1", "GSM8369975", null, "tissue:Neutrophils mpx:GFP+|cell type:Neutrophils mpx:GFP+|treatment:uninjured AMD3100|geo loc name:missing|collection date:missing", "Neutrophils mpx+  uninjured  AMD3100  biol rep 1", "Libraries were paired end sequenced on a Nextseq 500 Illumina  high output  with a 1x75 bp Illumina Kit Read 1: 26 cycles  index read: 6 cycles  Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded.  Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script", "Neutrophils mpx:GFP+", "At 3 dpf  larvae were anesthetized in 0.5 mM tricaine. Subsequenclty  the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next  larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", "Zebrafish embryos were raised at 28.5\u00baC in E3 media with Methylene blue", "cell type:Neutrophils mpx:GFP+|treatment:uninjured AMD3100", "GSM8369975", "GSM8369975: Neutrophils mpx+  uninjured  AMD3100  biol rep 1; Danio rerio; RNA Seq", "GSM8369975 r1", "GSM8369975", "1", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP517033", null, null, "IMM-CT-b001_HW5F2BGXN_S6_L004_Uninjured_AMD_-010_cbc.fastq.gz", "fastq", 100371840.0, 1672864.0, "GSM8369975 r4", "0:60", "A:37032383;C:18500721;G:18308236;T:26522753;N:7747", 60, null, null, null, 37032383, 18500721, 18308236, 26522753, 7747, "SRX25158194", "SRS21848816", "SRA1913211", "Instituto de Medicina Molecular", "Instituto de Medicina Molecular", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Portugal", "2024-06-29", "Larval", "Larval", "Blood", "Hematopoietic System"], [33099, "SRR29654133", "SRX25158193", "SRS21848815", "SRP517033", "PRJNA1129880", "Neutrophil immune profile guides spinal cord regeneration in zebrafish", "GSE271113", "Transcriptome Analysis", "Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet  their role in the repair process  particularly in a regenerative context  remains largely unknown. Here  we show that  promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely  blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether  these findings provide new insights into the role of neutrophils in spinal cord regeneration  emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition  we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100  and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Funda\u00e7\u00e5o para a Ci\u00eancia e Tecnologia FCT  Portugal", null, "pubmed:38925414", null, "Neutrophils mpx+  8 xxx post injury  DMSO  biol rep 3", "GSM8369974", null, "tissue:Neutrophils mpx:GFP+|cell type:Neutrophils mpx:GFP+|treatment:8 xxx post injury DMSO|geo loc name:missing|collection date:missing", "Neutrophils mpx+  8 xxx post injury  DMSO  biol rep 3", "Libraries were paired end sequenced on a Nextseq 500 Illumina  high output  with a 1x75 bp Illumina Kit Read 1: 26 cycles  index read: 6 cycles  Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded.  Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script", "Neutrophils mpx:GFP+", "At 3 dpf  larvae were anesthetized in 0.5 mM tricaine. Subsequenclty  the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next  larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", "Zebrafish embryos were raised at 28.5\u00baC in E3 media with Methylene blue", "cell type:Neutrophils mpx:GFP+|treatment:8 xxx post injury DMSO", "GSM8369974", "GSM8369974: Neutrophils mpx+  8 xxx post injury  DMSO  biol rep 3; Danio rerio; RNA Seq", "GSM8369974 r1", "GSM8369974", "1", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP517033", null, null, "IMM-CT-b001_HW5F2BGXN_S6_L001_8hpi_DMSO_-008_cbc.fastq.gz", "fastq", 161717520.0, 2695292.0, "GSM8369974 r1", "0:60", "A:58227035;C:29120167;G:33153372;T:41186362;N:30584", 60, null, null, null, 58227035, 29120167, 33153372, 41186362, 30584, "SRX25158193", "SRS21848815", "SRA1913211", "Instituto de Medicina Molecular", "Instituto de Medicina Molecular", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Portugal", "2024-06-29", "Larval", "Larval", "Blood", "Hematopoietic System"], [33100, "SRR29654134", "SRX25158193", "SRS21848815", "SRP517033", "PRJNA1129880", "Neutrophil immune profile guides spinal cord regeneration in zebrafish", "GSE271113", "Transcriptome Analysis", "Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet  their role in the repair process  particularly in a regenerative context  remains largely unknown. Here  we show that  promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely  blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether  these findings provide new insights into the role of neutrophils in spinal cord regeneration  emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition  we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100  and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Funda\u00e7\u00e5o para a Ci\u00eancia e Tecnologia FCT  Portugal", null, "pubmed:38925414", null, "Neutrophils mpx+  8 xxx post injury  DMSO  biol rep 3", "GSM8369974", null, "tissue:Neutrophils mpx:GFP+|cell type:Neutrophils mpx:GFP+|treatment:8 xxx post injury DMSO|geo loc name:missing|collection date:missing", "Neutrophils mpx+  8 xxx post injury  DMSO  biol rep 3", "Libraries were paired end sequenced on a Nextseq 500 Illumina  high output  with a 1x75 bp Illumina Kit Read 1: 26 cycles  index read: 6 cycles  Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded.  Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script", "Neutrophils mpx:GFP+", "At 3 dpf  larvae were anesthetized in 0.5 mM tricaine. Subsequenclty  the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next  larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", "Zebrafish embryos were raised at 28.5\u00baC in E3 media with Methylene blue", "cell type:Neutrophils mpx:GFP+|treatment:8 xxx post injury DMSO", "GSM8369974", "GSM8369974: Neutrophils mpx+  8 xxx post injury  DMSO  biol rep 3; Danio rerio; RNA Seq", "GSM8369974 r1", "GSM8369974", "1", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP517033", null, null, "IMM-CT-b001_HW5F2BGXN_S6_L002_8hpi_DMSO_-008_cbc.fastq.gz", "fastq", 158810460.0, 2646841.0, "GSM8369974 r2", "0:60", "A:57059029;C:28475827;G:33090143;T:40160441;N:25020", 60, null, null, null, 57059029, 28475827, 33090143, 40160441, 25020, "SRX25158193", "SRS21848815", "SRA1913211", "Instituto de Medicina Molecular", "Instituto de Medicina Molecular", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Portugal", "2024-06-29", "Larval", "Larval", "Blood", "Hematopoietic System"], [33101, "SRR29654135", "SRX25158193", "SRS21848815", "SRP517033", "PRJNA1129880", "Neutrophil immune profile guides spinal cord regeneration in zebrafish", "GSE271113", "Transcriptome Analysis", "Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet  their role in the repair process  particularly in a regenerative context  remains largely unknown. Here  we show that  promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely  blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether  these findings provide new insights into the role of neutrophils in spinal cord regeneration  emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition  we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100  and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Funda\u00e7\u00e5o para a Ci\u00eancia e Tecnologia FCT  Portugal", null, "pubmed:38925414", null, "Neutrophils mpx+  8 xxx post injury  DMSO  biol rep 3", "GSM8369974", null, "tissue:Neutrophils mpx:GFP+|cell type:Neutrophils mpx:GFP+|treatment:8 xxx post injury DMSO|geo loc name:missing|collection date:missing", "Neutrophils mpx+  8 xxx post injury  DMSO  biol rep 3", "Libraries were paired end sequenced on a Nextseq 500 Illumina  high output  with a 1x75 bp Illumina Kit Read 1: 26 cycles  index read: 6 cycles  Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded.  Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script", "Neutrophils mpx:GFP+", "At 3 dpf  larvae were anesthetized in 0.5 mM tricaine. Subsequenclty  the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next  larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", "Zebrafish embryos were raised at 28.5\u00baC in E3 media with Methylene blue", "cell type:Neutrophils mpx:GFP+|treatment:8 xxx post injury DMSO", "GSM8369974", "GSM8369974: Neutrophils mpx+  8 xxx post injury  DMSO  biol rep 3; Danio rerio; RNA Seq", "GSM8369974 r1", "GSM8369974", "1", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP517033", null, null, "IMM-CT-b001_HW5F2BGXN_S6_L003_8hpi_DMSO_-008_cbc.fastq.gz", "fastq", 164136600.0, 2735610.0, "GSM8369974 r3", "0:60", "A:59164760;C:29564845;G:33567677;T:41822336;N:16982", 60, null, null, null, 59164760, 29564845, 33567677, 41822336, 16982, "SRX25158193", "SRS21848815", "SRA1913211", "Instituto de Medicina Molecular", "Instituto de Medicina Molecular", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Portugal", "2024-06-29", "Larval", "Larval", "Blood", "Hematopoietic System"], [33102, "SRR29654136", "SRX25158193", "SRS21848815", "SRP517033", "PRJNA1129880", "Neutrophil immune profile guides spinal cord regeneration in zebrafish", "GSE271113", "Transcriptome Analysis", "Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet  their role in the repair process  particularly in a regenerative context  remains largely unknown. Here  we show that  promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely  blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether  these findings provide new insights into the role of neutrophils in spinal cord regeneration  emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition  we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100  and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Funda\u00e7\u00e5o para a Ci\u00eancia e Tecnologia FCT  Portugal", null, "pubmed:38925414", null, "Neutrophils mpx+  8 xxx post injury  DMSO  biol rep 3", "GSM8369974", null, "tissue:Neutrophils mpx:GFP+|cell type:Neutrophils mpx:GFP+|treatment:8 xxx post injury DMSO|geo loc name:missing|collection date:missing", "Neutrophils mpx+  8 xxx post injury  DMSO  biol rep 3", "Libraries were paired end sequenced on a Nextseq 500 Illumina  high output  with a 1x75 bp Illumina Kit Read 1: 26 cycles  index read: 6 cycles  Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded.  Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script", "Neutrophils mpx:GFP+", "At 3 dpf  larvae were anesthetized in 0.5 mM tricaine. Subsequenclty  the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next  larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", "Zebrafish embryos were raised at 28.5\u00baC in E3 media with Methylene blue", "cell type:Neutrophils mpx:GFP+|treatment:8 xxx post injury DMSO", "GSM8369974", "GSM8369974: Neutrophils mpx+  8 xxx post injury  DMSO  biol rep 3; Danio rerio; RNA Seq", "GSM8369974 r1", "GSM8369974", "1", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP517033", null, null, "IMM-CT-b001_HW5F2BGXN_S6_L004_8hpi_DMSO_-008_cbc.fastq.gz", "fastq", 160939740.0, 2682329.0, "GSM8369974 r4", "0:60", "A:57905646;C:28872433;G:33402085;T:40746636;N:12940", 60, null, null, null, 57905646, 28872433, 33402085, 40746636, 12940, "SRX25158193", "SRS21848815", "SRA1913211", "Instituto de Medicina Molecular", "Instituto de Medicina Molecular", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Portugal", "2024-06-29", "Larval", "Larval", "Blood", "Hematopoietic System"], [33103, "SRR29654137", "SRX25158192", "SRS21848814", "SRP517033", "PRJNA1129880", "Neutrophil immune profile guides spinal cord regeneration in zebrafish", "GSE271113", "Transcriptome Analysis", "Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet  their role in the repair process  particularly in a regenerative context  remains largely unknown. Here  we show that  promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely  blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether  these findings provide new insights into the role of neutrophils in spinal cord regeneration  emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition  we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100  and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Funda\u00e7\u00e5o para a Ci\u00eancia e Tecnologia FCT  Portugal", null, "pubmed:38925414", null, "Neutrophils mpx+  8 xxx post injury  DMSO  biol rep 2", "GSM8369973", null, "tissue:Neutrophils mpx:GFP+|cell type:Neutrophils mpx:GFP+|treatment:8 xxx post injury DMSO|geo loc name:missing|collection date:missing", "Neutrophils mpx+  8 xxx post injury  DMSO  biol rep 2", "Libraries were paired end sequenced on a Nextseq 500 Illumina  high output  with a 1x75 bp Illumina Kit Read 1: 26 cycles  index read: 6 cycles  Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded.  Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script", "Neutrophils mpx:GFP+", "At 3 dpf  larvae were anesthetized in 0.5 mM tricaine. Subsequenclty  the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next  larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", "Zebrafish embryos were raised at 28.5\u00baC in E3 media with Methylene blue", "cell type:Neutrophils mpx:GFP+|treatment:8 xxx post injury DMSO", "GSM8369973", "GSM8369973: Neutrophils mpx+  8 xxx post injury  DMSO  biol rep 2; Danio rerio; RNA Seq", "GSM8369973 r1", "GSM8369973", "1", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP517033", null, null, "IMM-CT-b001_HW5F2BGXN_S6_L001_8hpi_DMSO_-005_cbc.fastq.gz", "fastq", 294896760.0, 4914946.0, "GSM8369973 r1", "0:60", "A:113302890;C:53832811;G:54274745;T:73429183;N:57131", 60, null, null, null, 113302890, 53832811, 54274745, 73429183, 57131, "SRX25158192", "SRS21848814", "SRA1913211", "Instituto de Medicina Molecular", "Instituto de Medicina Molecular", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Portugal", "2024-06-29", "Larval", "Larval", "Blood", "Hematopoietic System"], [33104, "SRR29654138", "SRX25158192", "SRS21848814", "SRP517033", "PRJNA1129880", "Neutrophil immune profile guides spinal cord regeneration in zebrafish", "GSE271113", "Transcriptome Analysis", "Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet  their role in the repair process  particularly in a regenerative context  remains largely unknown. Here  we show that  promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely  blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether  these findings provide new insights into the role of neutrophils in spinal cord regeneration  emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition  we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100  and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Funda\u00e7\u00e5o para a Ci\u00eancia e Tecnologia FCT  Portugal", null, "pubmed:38925414", null, "Neutrophils mpx+  8 xxx post injury  DMSO  biol rep 2", "GSM8369973", null, "tissue:Neutrophils mpx:GFP+|cell type:Neutrophils mpx:GFP+|treatment:8 xxx post injury DMSO|geo loc name:missing|collection date:missing", "Neutrophils mpx+  8 xxx post injury  DMSO  biol rep 2", "Libraries were paired end sequenced on a Nextseq 500 Illumina  high output  with a 1x75 bp Illumina Kit Read 1: 26 cycles  index read: 6 cycles  Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded.  Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script", "Neutrophils mpx:GFP+", "At 3 dpf  larvae were anesthetized in 0.5 mM tricaine. Subsequenclty  the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next  larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", "Zebrafish embryos were raised at 28.5\u00baC in E3 media with Methylene blue", "cell type:Neutrophils mpx:GFP+|treatment:8 xxx post injury DMSO", "GSM8369973", "GSM8369973: Neutrophils mpx+  8 xxx post injury  DMSO  biol rep 2; Danio rerio; RNA Seq", "GSM8369973 r1", "GSM8369973", "1", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP517033", null, null, "IMM-CT-b001_HW5F2BGXN_S6_L002_8hpi_DMSO_-005_cbc.fastq.gz", "fastq", 289658820.0, 4827647.0, "GSM8369973 r2", "0:60", "A:111138289;C:52646716;G:54190664;T:71637241;N:45910", 60, null, null, null, 111138289, 52646716, 54190664, 71637241, 45910, "SRX25158192", "SRS21848814", "SRA1913211", "Instituto de Medicina Molecular", "Instituto de Medicina Molecular", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Portugal", "2024-06-29", "Larval", "Larval", "Blood", "Hematopoietic System"], [33105, "SRR29654139", "SRX25158192", "SRS21848814", "SRP517033", "PRJNA1129880", "Neutrophil immune profile guides spinal cord regeneration in zebrafish", "GSE271113", "Transcriptome Analysis", "Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet  their role in the repair process  particularly in a regenerative context  remains largely unknown. Here  we show that  promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely  blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether  these findings provide new insights into the role of neutrophils in spinal cord regeneration  emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition  we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100  and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Funda\u00e7\u00e5o para a Ci\u00eancia e Tecnologia FCT  Portugal", null, "pubmed:38925414", null, "Neutrophils mpx+  8 xxx post injury  DMSO  biol rep 2", "GSM8369973", null, "tissue:Neutrophils mpx:GFP+|cell type:Neutrophils mpx:GFP+|treatment:8 xxx post injury DMSO|geo loc name:missing|collection date:missing", "Neutrophils mpx+  8 xxx post injury  DMSO  biol rep 2", "Libraries were paired end sequenced on a Nextseq 500 Illumina  high output  with a 1x75 bp Illumina Kit Read 1: 26 cycles  index read: 6 cycles  Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded.  Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script", "Neutrophils mpx:GFP+", "At 3 dpf  larvae were anesthetized in 0.5 mM tricaine. Subsequenclty  the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next  larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", "Zebrafish embryos were raised at 28.5\u00baC in E3 media with Methylene blue", "cell type:Neutrophils mpx:GFP+|treatment:8 xxx post injury DMSO", "GSM8369973", "GSM8369973: Neutrophils mpx+  8 xxx post injury  DMSO  biol rep 2; Danio rerio; RNA Seq", "GSM8369973 r1", "GSM8369973", "1", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP517033", null, null, "IMM-CT-b001_HW5F2BGXN_S6_L003_8hpi_DMSO_-005_cbc.fastq.gz", "fastq", 299290800.0, 4988180.0, "GSM8369973 r3", "0:60", "A:115247052;C:54662821;G:54854607;T:74494831;N:31489", 60, null, null, null, 115247052, 54662821, 54854607, 74494831, 31489, "SRX25158192", "SRS21848814", "SRA1913211", "Instituto de Medicina Molecular", "Instituto de Medicina Molecular", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Portugal", "2024-06-29", "Larval", "Larval", "Blood", "Hematopoietic System"], [33106, "SRR29654140", "SRX25158192", "SRS21848814", "SRP517033", "PRJNA1129880", "Neutrophil immune profile guides spinal cord regeneration in zebrafish", "GSE271113", "Transcriptome Analysis", "Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet  their role in the repair process  particularly in a regenerative context  remains largely unknown. Here  we show that  promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely  blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether  these findings provide new insights into the role of neutrophils in spinal cord regeneration  emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition  we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100  and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Funda\u00e7\u00e5o para a Ci\u00eancia e Tecnologia FCT  Portugal", null, "pubmed:38925414", null, "Neutrophils mpx+  8 xxx post injury  DMSO  biol rep 2", "GSM8369973", null, "tissue:Neutrophils mpx:GFP+|cell type:Neutrophils mpx:GFP+|treatment:8 xxx post injury DMSO|geo loc name:missing|collection date:missing", "Neutrophils mpx+  8 xxx post injury  DMSO  biol rep 2", "Libraries were paired end sequenced on a Nextseq 500 Illumina  high output  with a 1x75 bp Illumina Kit Read 1: 26 cycles  index read: 6 cycles  Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded.  Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script", "Neutrophils mpx:GFP+", "At 3 dpf  larvae were anesthetized in 0.5 mM tricaine. Subsequenclty  the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next  larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", "Zebrafish embryos were raised at 28.5\u00baC in E3 media with Methylene blue", "cell type:Neutrophils mpx:GFP+|treatment:8 xxx post injury DMSO", "GSM8369973", "GSM8369973: Neutrophils mpx+  8 xxx post injury  DMSO  biol rep 2; Danio rerio; RNA Seq", "GSM8369973 r1", "GSM8369973", "1", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP517033", null, null, "IMM-CT-b001_HW5F2BGXN_S6_L004_8hpi_DMSO_-005_cbc.fastq.gz", "fastq", 294091920.0, 4901532.0, "GSM8369973 r4", "0:60", "A:113032051;C:53520496;G:54754695;T:72762244;N:22434", 60, null, null, null, 113032051, 53520496, 54754695, 72762244, 22434, "SRX25158192", "SRS21848814", "SRA1913211", "Instituto de Medicina Molecular", "Instituto de Medicina Molecular", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Portugal", "2024-06-29", "Larval", "Larval", "Blood", "Hematopoietic System"], [33107, "SRR29654141", "SRX25158191", "SRS21848813", "SRP517033", "PRJNA1129880", "Neutrophil immune profile guides spinal cord regeneration in zebrafish", "GSE271113", "Transcriptome Analysis", "Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet  their role in the repair process  particularly in a regenerative context  remains largely unknown. Here  we show that  promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely  blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether  these findings provide new insights into the role of neutrophils in spinal cord regeneration  emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition  we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100  and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Funda\u00e7\u00e5o para a Ci\u00eancia e Tecnologia FCT  Portugal", null, "pubmed:38925414", null, "Neutrophils mpx+  8 xxx post injury  DMSO  biol rep 1", "GSM8369972", null, "tissue:Neutrophils mpx:GFP+|cell type:Neutrophils mpx:GFP+|treatment:8 xxx post injury DMSO|geo loc name:missing|collection date:missing", "Neutrophils mpx+  8 xxx post injury  DMSO  biol rep 1", "Libraries were paired end sequenced on a Nextseq 500 Illumina  high output  with a 1x75 bp Illumina Kit Read 1: 26 cycles  index read: 6 cycles  Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded.  Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script", "Neutrophils mpx:GFP+", "At 3 dpf  larvae were anesthetized in 0.5 mM tricaine. Subsequenclty  the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next  larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", "Zebrafish embryos were raised at 28.5\u00baC in E3 media with Methylene blue", "cell type:Neutrophils mpx:GFP+|treatment:8 xxx post injury DMSO", "GSM8369972", "GSM8369972: Neutrophils mpx+  8 xxx post injury  DMSO  biol rep 1; Danio rerio; RNA Seq", "GSM8369972 r1", "GSM8369972", "1", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP517033", null, null, "IMM-CT-b001_HW5F2BGXN_S6_L001_8hpi_DMSO_-004_cbc.fastq.gz", "fastq", 79542600.0, 1325710.0, "GSM8369972 r1", "0:60", "A:29052800;C:15106261;G:15344010;T:20023888;N:15641", 60, null, null, null, 29052800, 15106261, 15344010, 20023888, 15641, "SRX25158191", "SRS21848813", "SRA1913211", "Instituto de Medicina Molecular", "Instituto de Medicina Molecular", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Portugal", "2024-06-29", "Larval", "Larval", "Blood", "Hematopoietic System"], [33108, "SRR29654142", "SRX25158191", "SRS21848813", "SRP517033", "PRJNA1129880", "Neutrophil immune profile guides spinal cord regeneration in zebrafish", "GSE271113", "Transcriptome Analysis", "Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet  their role in the repair process  particularly in a regenerative context  remains largely unknown. Here  we show that  promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely  blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether  these findings provide new insights into the role of neutrophils in spinal cord regeneration  emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition  we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100  and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Funda\u00e7\u00e5o para a Ci\u00eancia e Tecnologia FCT  Portugal", null, "pubmed:38925414", null, "Neutrophils mpx+  8 xxx post injury  DMSO  biol rep 1", "GSM8369972", null, "tissue:Neutrophils mpx:GFP+|cell type:Neutrophils mpx:GFP+|treatment:8 xxx post injury DMSO|geo loc name:missing|collection date:missing", "Neutrophils mpx+  8 xxx post injury  DMSO  biol rep 1", "Libraries were paired end sequenced on a Nextseq 500 Illumina  high output  with a 1x75 bp Illumina Kit Read 1: 26 cycles  index read: 6 cycles  Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded.  Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script", "Neutrophils mpx:GFP+", "At 3 dpf  larvae were anesthetized in 0.5 mM tricaine. Subsequenclty  the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next  larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", "Zebrafish embryos were raised at 28.5\u00baC in E3 media with Methylene blue", "cell type:Neutrophils mpx:GFP+|treatment:8 xxx post injury DMSO", "GSM8369972", "GSM8369972: Neutrophils mpx+  8 xxx post injury  DMSO  biol rep 1; Danio rerio; RNA Seq", "GSM8369972 r1", "GSM8369972", "1", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP517033", null, null, "IMM-CT-b001_HW5F2BGXN_S6_L002_8hpi_DMSO_-004_cbc.fastq.gz", "fastq", 78150840.0, 1302514.0, "GSM8369972 r2", "0:60", "A:28490299;C:14795977;G:15298357;T:19554765;N:11442", 60, null, null, null, 28490299, 14795977, 15298357, 19554765, 11442, "SRX25158191", "SRS21848813", "SRA1913211", "Instituto de Medicina Molecular", "Instituto de Medicina Molecular", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Portugal", "2024-06-29", "Larval", "Larval", "Blood", "Hematopoietic System"], [33109, "SRR29654143", "SRX25158191", "SRS21848813", "SRP517033", "PRJNA1129880", "Neutrophil immune profile guides spinal cord regeneration in zebrafish", "GSE271113", "Transcriptome Analysis", "Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet  their role in the repair process  particularly in a regenerative context  remains largely unknown. Here  we show that  promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely  blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether  these findings provide new insights into the role of neutrophils in spinal cord regeneration  emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition  we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100  and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Funda\u00e7\u00e5o para a Ci\u00eancia e Tecnologia FCT  Portugal", null, "pubmed:38925414", null, "Neutrophils mpx+  8 xxx post injury  DMSO  biol rep 1", "GSM8369972", null, "tissue:Neutrophils mpx:GFP+|cell type:Neutrophils mpx:GFP+|treatment:8 xxx post injury DMSO|geo loc name:missing|collection date:missing", "Neutrophils mpx+  8 xxx post injury  DMSO  biol rep 1", "Libraries were paired end sequenced on a Nextseq 500 Illumina  high output  with a 1x75 bp Illumina Kit Read 1: 26 cycles  index read: 6 cycles  Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded.  Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script", "Neutrophils mpx:GFP+", "At 3 dpf  larvae were anesthetized in 0.5 mM tricaine. Subsequenclty  the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next  larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", "Zebrafish embryos were raised at 28.5\u00baC in E3 media with Methylene blue", "cell type:Neutrophils mpx:GFP+|treatment:8 xxx post injury DMSO", "GSM8369972", "GSM8369972: Neutrophils mpx+  8 xxx post injury  DMSO  biol rep 1; Danio rerio; RNA Seq", "GSM8369972 r1", "GSM8369972", "1", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP517033", null, null, "IMM-CT-b001_HW5F2BGXN_S6_L003_8hpi_DMSO_-004_cbc.fastq.gz", "fastq", 80719140.0, 1345319.0, "GSM8369972 r3", "0:60", "A:29548150;C:15350378;G:15486892;T:20325654;N:8066", 60, null, null, null, 29548150, 15350378, 15486892, 20325654, 8066, "SRX25158191", "SRS21848813", "SRA1913211", "Instituto de Medicina Molecular", "Instituto de Medicina Molecular", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Portugal", "2024-06-29", "Larval", "Larval", "Blood", "Hematopoietic System"], [33110, "SRR29654144", "SRX25158191", "SRS21848813", "SRP517033", "PRJNA1129880", "Neutrophil immune profile guides spinal cord regeneration in zebrafish", "GSE271113", "Transcriptome Analysis", "Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet  their role in the repair process  particularly in a regenerative context  remains largely unknown. Here  we show that  promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely  blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether  these findings provide new insights into the role of neutrophils in spinal cord regeneration  emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition  we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100  and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Funda\u00e7\u00e5o para a Ci\u00eancia e Tecnologia FCT  Portugal", null, "pubmed:38925414", null, "Neutrophils mpx+  8 xxx post injury  DMSO  biol rep 1", "GSM8369972", null, "tissue:Neutrophils mpx:GFP+|cell type:Neutrophils mpx:GFP+|treatment:8 xxx post injury DMSO|geo loc name:missing|collection date:missing", "Neutrophils mpx+  8 xxx post injury  DMSO  biol rep 1", "Libraries were paired end sequenced on a Nextseq 500 Illumina  high output  with a 1x75 bp Illumina Kit Read 1: 26 cycles  index read: 6 cycles  Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded.  Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script", "Neutrophils mpx:GFP+", "At 3 dpf  larvae were anesthetized in 0.5 mM tricaine. Subsequenclty  the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next  larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", "Zebrafish embryos were raised at 28.5\u00baC in E3 media with Methylene blue", "cell type:Neutrophils mpx:GFP+|treatment:8 xxx post injury DMSO", "GSM8369972", "GSM8369972: Neutrophils mpx+  8 xxx post injury  DMSO  biol rep 1; Danio rerio; RNA Seq", "GSM8369972 r1", "GSM8369972", "1", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP517033", null, null, "IMM-CT-b001_HW5F2BGXN_S6_L004_8hpi_DMSO_-004_cbc.fastq.gz", "fastq", 79070760.0, 1317846.0, "GSM8369972 r4", "0:60", "A:28874779;C:14986197;G:15407453;T:19795922;N:6409", 60, null, null, null, 28874779, 14986197, 15407453, 19795922, 6409, "SRX25158191", "SRS21848813", "SRA1913211", "Instituto de Medicina Molecular", "Instituto de Medicina Molecular", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Portugal", "2024-06-29", "Larval", "Larval", "Blood", "Hematopoietic System"], [33111, "SRR29654145", "SRX25158190", "SRS21848812", "SRP517033", "PRJNA1129880", "Neutrophil immune profile guides spinal cord regeneration in zebrafish", "GSE271113", "Transcriptome Analysis", "Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet  their role in the repair process  particularly in a regenerative context  remains largely unknown. Here  we show that  promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely  blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether  these findings provide new insights into the role of neutrophils in spinal cord regeneration  emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition  we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100  and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Funda\u00e7\u00e5o para a Ci\u00eancia e Tecnologia FCT  Portugal", null, "pubmed:38925414", null, "Neutrophils mpx+  uninjured  DMSO  biol rep 3", "GSM8369971", null, "tissue:Neutrophils mpx:GFP+|cell type:Neutrophils mpx:GFP+|treatment:uninjured DMSO|geo loc name:missing|collection date:missing", "Neutrophils mpx+  uninjured  DMSO  biol rep 3", "Libraries were paired end sequenced on a Nextseq 500 Illumina  high output  with a 1x75 bp Illumina Kit Read 1: 26 cycles  index read: 6 cycles  Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded.  Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script", "Neutrophils mpx:GFP+", "At 3 dpf  larvae were anesthetized in 0.5 mM tricaine. Subsequenclty  the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next  larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", "Zebrafish embryos were raised at 28.5\u00baC in E3 media with Methylene blue", "cell type:Neutrophils mpx:GFP+|treatment:uninjured DMSO", "GSM8369971", "GSM8369971: Neutrophils mpx+  uninjured  DMSO  biol rep 3; Danio rerio; RNA Seq", "GSM8369971 r1", "GSM8369971", "1", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP517033", null, null, "IMM-CT-b001_HW5F2BGXN_S6_L001_Uninjured_DMSO_-009_cbc.fastq.gz", "fastq", 182391600.0, 3039860.0, "GSM8369971 r1", "0:60", "A:65842196;C:33929963;G:37226765;T:45358269;N:34407", 60, null, null, null, 65842196, 33929963, 37226765, 45358269, 34407, "SRX25158190", "SRS21848812", "SRA1913211", "Instituto de Medicina Molecular", "Instituto de Medicina Molecular", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Portugal", "2024-06-29", "Larval", "Larval", "Blood", "Hematopoietic System"], [33112, "SRR29654146", "SRX25158190", "SRS21848812", "SRP517033", "PRJNA1129880", "Neutrophil immune profile guides spinal cord regeneration in zebrafish", "GSE271113", "Transcriptome Analysis", "Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet  their role in the repair process  particularly in a regenerative context  remains largely unknown. Here  we show that  promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely  blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether  these findings provide new insights into the role of neutrophils in spinal cord regeneration  emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition  we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100  and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Funda\u00e7\u00e5o para a Ci\u00eancia e Tecnologia FCT  Portugal", null, "pubmed:38925414", null, "Neutrophils mpx+  uninjured  DMSO  biol rep 3", "GSM8369971", null, "tissue:Neutrophils mpx:GFP+|cell type:Neutrophils mpx:GFP+|treatment:uninjured DMSO|geo loc name:missing|collection date:missing", "Neutrophils mpx+  uninjured  DMSO  biol rep 3", "Libraries were paired end sequenced on a Nextseq 500 Illumina  high output  with a 1x75 bp Illumina Kit Read 1: 26 cycles  index read: 6 cycles  Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded.  Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script", "Neutrophils mpx:GFP+", "At 3 dpf  larvae were anesthetized in 0.5 mM tricaine. Subsequenclty  the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next  larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", "Zebrafish embryos were raised at 28.5\u00baC in E3 media with Methylene blue", "cell type:Neutrophils mpx:GFP+|treatment:uninjured DMSO", "GSM8369971", "GSM8369971: Neutrophils mpx+  uninjured  DMSO  biol rep 3; Danio rerio; RNA Seq", "GSM8369971 r1", "GSM8369971", "1", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP517033", null, null, "IMM-CT-b001_HW5F2BGXN_S6_L002_Uninjured_DMSO_-009_cbc.fastq.gz", "fastq", 179081640.0, 2984694.0, "GSM8369971 r2", "0:60", "A:64544585;C:33163305;G:37078756;T:44266486;N:28508", 60, null, null, null, 64544585, 33163305, 37078756, 44266486, 28508, "SRX25158190", "SRS21848812", "SRA1913211", "Instituto de Medicina Molecular", "Instituto de Medicina Molecular", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Portugal", "2024-06-29", "Larval", "Larval", "Blood", "Hematopoietic System"], [33113, "SRR29654147", "SRX25158190", "SRS21848812", "SRP517033", "PRJNA1129880", "Neutrophil immune profile guides spinal cord regeneration in zebrafish", "GSE271113", "Transcriptome Analysis", "Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet  their role in the repair process  particularly in a regenerative context  remains largely unknown. Here  we show that  promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely  blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether  these findings provide new insights into the role of neutrophils in spinal cord regeneration  emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition  we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100  and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Funda\u00e7\u00e5o para a Ci\u00eancia e Tecnologia FCT  Portugal", null, "pubmed:38925414", null, "Neutrophils mpx+  uninjured  DMSO  biol rep 3", "GSM8369971", null, "tissue:Neutrophils mpx:GFP+|cell type:Neutrophils mpx:GFP+|treatment:uninjured DMSO|geo loc name:missing|collection date:missing", "Neutrophils mpx+  uninjured  DMSO  biol rep 3", "Libraries were paired end sequenced on a Nextseq 500 Illumina  high output  with a 1x75 bp Illumina Kit Read 1: 26 cycles  index read: 6 cycles  Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded.  Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script", "Neutrophils mpx:GFP+", "At 3 dpf  larvae were anesthetized in 0.5 mM tricaine. Subsequenclty  the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next  larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", "Zebrafish embryos were raised at 28.5\u00baC in E3 media with Methylene blue", "cell type:Neutrophils mpx:GFP+|treatment:uninjured DMSO", "GSM8369971", "GSM8369971: Neutrophils mpx+  uninjured  DMSO  biol rep 3; Danio rerio; RNA Seq", "GSM8369971 r1", "GSM8369971", "1", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP517033", null, null, "IMM-CT-b001_HW5F2BGXN_S6_L003_Uninjured_DMSO_-009_cbc.fastq.gz", "fastq", 185068740.0, 3084479.0, "GSM8369971 r3", "0:60", "A:66919946;C:34450944;G:37652300;T:46025841;N:19709", 60, null, null, null, 66919946, 34450944, 37652300, 46025841, 19709, "SRX25158190", "SRS21848812", "SRA1913211", "Instituto de Medicina Molecular", "Instituto de Medicina Molecular", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Portugal", "2024-06-29", "Larval", "Larval", "Blood", "Hematopoietic System"], [33114, "SRR29654148", "SRX25158190", "SRS21848812", "SRP517033", "PRJNA1129880", "Neutrophil immune profile guides spinal cord regeneration in zebrafish", "GSE271113", "Transcriptome Analysis", "Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet  their role in the repair process  particularly in a regenerative context  remains largely unknown. Here  we show that  promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely  blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether  these findings provide new insights into the role of neutrophils in spinal cord regeneration  emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition  we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100  and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Funda\u00e7\u00e5o para a Ci\u00eancia e Tecnologia FCT  Portugal", null, "pubmed:38925414", null, "Neutrophils mpx+  uninjured  DMSO  biol rep 3", "GSM8369971", null, "tissue:Neutrophils mpx:GFP+|cell type:Neutrophils mpx:GFP+|treatment:uninjured DMSO|geo loc name:missing|collection date:missing", "Neutrophils mpx+  uninjured  DMSO  biol rep 3", "Libraries were paired end sequenced on a Nextseq 500 Illumina  high output  with a 1x75 bp Illumina Kit Read 1: 26 cycles  index read: 6 cycles  Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded.  Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script", "Neutrophils mpx:GFP+", "At 3 dpf  larvae were anesthetized in 0.5 mM tricaine. Subsequenclty  the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next  larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", "Zebrafish embryos were raised at 28.5\u00baC in E3 media with Methylene blue", "cell type:Neutrophils mpx:GFP+|treatment:uninjured DMSO", "GSM8369971", "GSM8369971: Neutrophils mpx+  uninjured  DMSO  biol rep 3; Danio rerio; RNA Seq", "GSM8369971 r1", "GSM8369971", "1", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP517033", null, null, "IMM-CT-b001_HW5F2BGXN_S6_L004_Uninjured_DMSO_-009_cbc.fastq.gz", "fastq", 181507740.0, 3025129.0, "GSM8369971 r4", "0:60", "A:65513514;C:33675079;G:37432606;T:44872485;N:14056", 60, null, null, null, 65513514, 33675079, 37432606, 44872485, 14056, "SRX25158190", "SRS21848812", "SRA1913211", "Instituto de Medicina Molecular", "Instituto de Medicina Molecular", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Portugal", "2024-06-29", "Larval", "Larval", "Blood", "Hematopoietic System"], [33115, "SRR29654149", "SRX25158189", "SRS21848811", "SRP517033", "PRJNA1129880", "Neutrophil immune profile guides spinal cord regeneration in zebrafish", "GSE271113", "Transcriptome Analysis", "Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet  their role in the repair process  particularly in a regenerative context  remains largely unknown. Here  we show that  promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely  blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether  these findings provide new insights into the role of neutrophils in spinal cord regeneration  emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition  we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100  and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Funda\u00e7\u00e5o para a Ci\u00eancia e Tecnologia FCT  Portugal", null, "pubmed:38925414", null, "Neutrophils mpx+  uninjured  DMSO  biol rep 2", "GSM8369970", null, "tissue:Neutrophils mpx:GFP+|cell type:Neutrophils mpx:GFP+|treatment:uninjured DMSO|geo loc name:missing|collection date:missing", "Neutrophils mpx+  uninjured  DMSO  biol rep 2", "Libraries were paired end sequenced on a Nextseq 500 Illumina  high output  with a 1x75 bp Illumina Kit Read 1: 26 cycles  index read: 6 cycles  Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded.  Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script", "Neutrophils mpx:GFP+", "At 3 dpf  larvae were anesthetized in 0.5 mM tricaine. Subsequenclty  the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next  larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", "Zebrafish embryos were raised at 28.5\u00baC in E3 media with Methylene blue", "cell type:Neutrophils mpx:GFP+|treatment:uninjured DMSO", "GSM8369970", "GSM8369970: Neutrophils mpx+  uninjured  DMSO  biol rep 2; Danio rerio; RNA Seq", "GSM8369970 r1", "GSM8369970", "1", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP517033", null, null, "IMM-CT-b001_HW5F2BGXN_S6_L001_Uninjured_DMSO_-006_cbc.fastq.gz", "fastq", 45794760.0, 763246.0, "GSM8369970 r1", "0:60", "A:16928569;C:8492491;G:9006326;T:11358172;N:9202", 60, null, null, null, 16928569, 8492491, 9006326, 11358172, 9202, "SRX25158189", "SRS21848811", "SRA1913211", "Instituto de Medicina Molecular", "Instituto de Medicina Molecular", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Portugal", "2024-06-29", "Larval", "Larval", "Blood", "Hematopoietic System"], [33116, "SRR29654150", "SRX25158189", "SRS21848811", "SRP517033", "PRJNA1129880", "Neutrophil immune profile guides spinal cord regeneration in zebrafish", "GSE271113", "Transcriptome Analysis", "Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet  their role in the repair process  particularly in a regenerative context  remains largely unknown. Here  we show that  promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely  blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether  these findings provide new insights into the role of neutrophils in spinal cord regeneration  emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition  we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100  and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Funda\u00e7\u00e5o para a Ci\u00eancia e Tecnologia FCT  Portugal", null, "pubmed:38925414", null, "Neutrophils mpx+  uninjured  DMSO  biol rep 2", "GSM8369970", null, "tissue:Neutrophils mpx:GFP+|cell type:Neutrophils mpx:GFP+|treatment:uninjured DMSO|geo loc name:missing|collection date:missing", "Neutrophils mpx+  uninjured  DMSO  biol rep 2", "Libraries were paired end sequenced on a Nextseq 500 Illumina  high output  with a 1x75 bp Illumina Kit Read 1: 26 cycles  index read: 6 cycles  Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded.  Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script", "Neutrophils mpx:GFP+", "At 3 dpf  larvae were anesthetized in 0.5 mM tricaine. Subsequenclty  the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next  larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", "Zebrafish embryos were raised at 28.5\u00baC in E3 media with Methylene blue", "cell type:Neutrophils mpx:GFP+|treatment:uninjured DMSO", "GSM8369970", "GSM8369970: Neutrophils mpx+  uninjured  DMSO  biol rep 2; Danio rerio; RNA Seq", "GSM8369970 r1", "GSM8369970", "1", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP517033", null, null, "IMM-CT-b001_HW5F2BGXN_S6_L002_Uninjured_DMSO_-006_cbc.fastq.gz", "fastq", 45009960.0, 750166.0, "GSM8369970 r2", "0:60", "A:16608407;C:8309766;G:8990622;T:11094414;N:6751", 60, null, null, null, 16608407, 8309766, 8990622, 11094414, 6751, "SRX25158189", "SRS21848811", "SRA1913211", "Instituto de Medicina Molecular", "Instituto de Medicina Molecular", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Portugal", "2024-06-29", "Larval", "Larval", "Blood", "Hematopoietic System"], [33117, "SRR29654151", "SRX25158189", "SRS21848811", "SRP517033", "PRJNA1129880", "Neutrophil immune profile guides spinal cord regeneration in zebrafish", "GSE271113", "Transcriptome Analysis", "Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet  their role in the repair process  particularly in a regenerative context  remains largely unknown. Here  we show that  promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely  blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether  these findings provide new insights into the role of neutrophils in spinal cord regeneration  emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition  we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100  and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Funda\u00e7\u00e5o para a Ci\u00eancia e Tecnologia FCT  Portugal", null, "pubmed:38925414", null, "Neutrophils mpx+  uninjured  DMSO  biol rep 2", "GSM8369970", null, "tissue:Neutrophils mpx:GFP+|cell type:Neutrophils mpx:GFP+|treatment:uninjured DMSO|geo loc name:missing|collection date:missing", "Neutrophils mpx+  uninjured  DMSO  biol rep 2", "Libraries were paired end sequenced on a Nextseq 500 Illumina  high output  with a 1x75 bp Illumina Kit Read 1: 26 cycles  index read: 6 cycles  Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded.  Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script", "Neutrophils mpx:GFP+", "At 3 dpf  larvae were anesthetized in 0.5 mM tricaine. Subsequenclty  the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next  larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", "Zebrafish embryos were raised at 28.5\u00baC in E3 media with Methylene blue", "cell type:Neutrophils mpx:GFP+|treatment:uninjured DMSO", "GSM8369970", "GSM8369970: Neutrophils mpx+  uninjured  DMSO  biol rep 2; Danio rerio; RNA Seq", "GSM8369970 r1", "GSM8369970", "1", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP517033", null, null, "IMM-CT-b001_HW5F2BGXN_S6_L003_Uninjured_DMSO_-006_cbc.fastq.gz", "fastq", 46565880.0, 776098.0, "GSM8369970 r3", "0:60", "A:17217451;C:8640544;G:9146095;T:11557146;N:4644", 60, null, null, null, 17217451, 8640544, 9146095, 11557146, 4644, "SRX25158189", "SRS21848811", "SRA1913211", "Instituto de Medicina Molecular", "Instituto de Medicina Molecular", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Portugal", "2024-06-29", "Larval", "Larval", "Blood", "Hematopoietic System"], [33118, "SRR29654152", "SRX25158189", "SRS21848811", "SRP517033", "PRJNA1129880", "Neutrophil immune profile guides spinal cord regeneration in zebrafish", "GSE271113", "Transcriptome Analysis", "Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet  their role in the repair process  particularly in a regenerative context  remains largely unknown. Here  we show that  promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely  blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether  these findings provide new insights into the role of neutrophils in spinal cord regeneration  emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition  we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100  and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Funda\u00e7\u00e5o para a Ci\u00eancia e Tecnologia FCT  Portugal", null, "pubmed:38925414", null, "Neutrophils mpx+  uninjured  DMSO  biol rep 2", "GSM8369970", null, "tissue:Neutrophils mpx:GFP+|cell type:Neutrophils mpx:GFP+|treatment:uninjured DMSO|geo loc name:missing|collection date:missing", "Neutrophils mpx+  uninjured  DMSO  biol rep 2", "Libraries were paired end sequenced on a Nextseq 500 Illumina  high output  with a 1x75 bp Illumina Kit Read 1: 26 cycles  index read: 6 cycles  Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded.  Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script", "Neutrophils mpx:GFP+", "At 3 dpf  larvae were anesthetized in 0.5 mM tricaine. Subsequenclty  the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next  larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", "Zebrafish embryos were raised at 28.5\u00baC in E3 media with Methylene blue", "cell type:Neutrophils mpx:GFP+|treatment:uninjured DMSO", "GSM8369970", "GSM8369970: Neutrophils mpx+  uninjured  DMSO  biol rep 2; Danio rerio; RNA Seq", "GSM8369970 r1", "GSM8369970", "1", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP517033", null, null, "IMM-CT-b001_HW5F2BGXN_S6_L004_Uninjured_DMSO_-006_cbc.fastq.gz", "fastq", 45624660.0, 760411.0, "GSM8369970 r4", "0:60", "A:16852187;C:8431444;G:9090234;T:11246907;N:3888", 60, null, null, null, 16852187, 8431444, 9090234, 11246907, 3888, "SRX25158189", "SRS21848811", "SRA1913211", "Instituto de Medicina Molecular", "Instituto de Medicina Molecular", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Portugal", "2024-06-29", "Larval", "Larval", "Blood", "Hematopoietic System"], [33119, "SRR29654153", "SRX25158188", "SRS21848810", "SRP517033", "PRJNA1129880", "Neutrophil immune profile guides spinal cord regeneration in zebrafish", "GSE271113", "Transcriptome Analysis", "Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet  their role in the repair process  particularly in a regenerative context  remains largely unknown. Here  we show that  promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely  blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether  these findings provide new insights into the role of neutrophils in spinal cord regeneration  emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition  we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100  and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Funda\u00e7\u00e5o para a Ci\u00eancia e Tecnologia FCT  Portugal", null, "pubmed:38925414", null, "Neutrophils mpx+  uninjured  DMSO  biol rep 1", "GSM8369969", null, "tissue:Neutrophils mpx:GFP+|cell type:Neutrophils mpx:GFP+|treatment:uninjured DMSO|geo loc name:missing|collection date:missing", "Neutrophils mpx+  uninjured  DMSO  biol rep 1", "Libraries were paired end sequenced on a Nextseq 500 Illumina  high output  with a 1x75 bp Illumina Kit Read 1: 26 cycles  index read: 6 cycles  Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded.  Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script", "Neutrophils mpx:GFP+", "At 3 dpf  larvae were anesthetized in 0.5 mM tricaine. Subsequenclty  the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next  larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", "Zebrafish embryos were raised at 28.5\u00baC in E3 media with Methylene blue", "cell type:Neutrophils mpx:GFP+|treatment:uninjured DMSO", "GSM8369969", "GSM8369969: Neutrophils mpx+  uninjured  DMSO  biol rep 1; Danio rerio; RNA Seq", "GSM8369969 r1", "GSM8369969", "1", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP517033", null, null, "IMM-CT-b001_HW5F2BGXN_S6_L001_Uninjured_DMSO_-003_cbc.fastq.gz", "fastq", 55867380.0, 931123.0, "GSM8369969 r1", "0:60", "A:20680346;C:10254613;G:10895370;T:14026951;N:10100", 60, null, null, null, 20680346, 10254613, 10895370, 14026951, 10100, "SRX25158188", "SRS21848810", "SRA1913211", "Instituto de Medicina Molecular", "Instituto de Medicina Molecular", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Portugal", "2024-06-29", "Larval", "Larval", "Blood", "Hematopoietic System"], [33120, "SRR29654154", "SRX25158188", "SRS21848810", "SRP517033", "PRJNA1129880", "Neutrophil immune profile guides spinal cord regeneration in zebrafish", "GSE271113", "Transcriptome Analysis", "Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet  their role in the repair process  particularly in a regenerative context  remains largely unknown. Here  we show that  promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely  blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether  these findings provide new insights into the role of neutrophils in spinal cord regeneration  emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition  we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100  and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Funda\u00e7\u00e5o para a Ci\u00eancia e Tecnologia FCT  Portugal", null, "pubmed:38925414", null, "Neutrophils mpx+  uninjured  DMSO  biol rep 1", "GSM8369969", null, "tissue:Neutrophils mpx:GFP+|cell type:Neutrophils mpx:GFP+|treatment:uninjured DMSO|geo loc name:missing|collection date:missing", "Neutrophils mpx+  uninjured  DMSO  biol rep 1", "Libraries were paired end sequenced on a Nextseq 500 Illumina  high output  with a 1x75 bp Illumina Kit Read 1: 26 cycles  index read: 6 cycles  Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded.  Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script", "Neutrophils mpx:GFP+", "At 3 dpf  larvae were anesthetized in 0.5 mM tricaine. Subsequenclty  the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next  larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", "Zebrafish embryos were raised at 28.5\u00baC in E3 media with Methylene blue", "cell type:Neutrophils mpx:GFP+|treatment:uninjured DMSO", "GSM8369969", "GSM8369969: Neutrophils mpx+  uninjured  DMSO  biol rep 1; Danio rerio; RNA Seq", "GSM8369969 r1", "GSM8369969", "1", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP517033", null, null, "IMM-CT-b001_HW5F2BGXN_S6_L002_Uninjured_DMSO_-003_cbc.fastq.gz", "fastq", 54889080.0, 914818.0, "GSM8369969 r2", "0:60", "A:20264110;C:10026239;G:10861715;T:13728039;N:8977", 60, null, null, null, 20264110, 10026239, 10861715, 13728039, 8977, "SRX25158188", "SRS21848810", "SRA1913211", "Instituto de Medicina Molecular", "Instituto de Medicina Molecular", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Portugal", "2024-06-29", "Larval", "Larval", "Blood", "Hematopoietic System"], [33121, "SRR29654155", "SRX25158188", "SRS21848810", "SRP517033", "PRJNA1129880", "Neutrophil immune profile guides spinal cord regeneration in zebrafish", "GSE271113", "Transcriptome Analysis", "Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet  their role in the repair process  particularly in a regenerative context  remains largely unknown. Here  we show that  promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely  blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether  these findings provide new insights into the role of neutrophils in spinal cord regeneration  emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition  we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100  and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Funda\u00e7\u00e5o para a Ci\u00eancia e Tecnologia FCT  Portugal", null, "pubmed:38925414", null, "Neutrophils mpx+  uninjured  DMSO  biol rep 1", "GSM8369969", null, "tissue:Neutrophils mpx:GFP+|cell type:Neutrophils mpx:GFP+|treatment:uninjured DMSO|geo loc name:missing|collection date:missing", "Neutrophils mpx+  uninjured  DMSO  biol rep 1", "Libraries were paired end sequenced on a Nextseq 500 Illumina  high output  with a 1x75 bp Illumina Kit Read 1: 26 cycles  index read: 6 cycles  Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded.  Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script", "Neutrophils mpx:GFP+", "At 3 dpf  larvae were anesthetized in 0.5 mM tricaine. Subsequenclty  the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next  larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", "Zebrafish embryos were raised at 28.5\u00baC in E3 media with Methylene blue", "cell type:Neutrophils mpx:GFP+|treatment:uninjured DMSO", "GSM8369969", "GSM8369969: Neutrophils mpx+  uninjured  DMSO  biol rep 1; Danio rerio; RNA Seq", "GSM8369969 r1", "GSM8369969", "1", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP517033", null, null, "IMM-CT-b001_HW5F2BGXN_S6_L003_Uninjured_DMSO_-003_cbc.fastq.gz", "fastq", 56764440.0, 946074.0, "GSM8369969 r3", "0:60", "A:21036899;C:10416984;G:11027830;T:14275499;N:7228", 60, null, null, null, 21036899, 10416984, 11027830, 14275499, 7228, "SRX25158188", "SRS21848810", "SRA1913211", "Instituto de Medicina Molecular", "Instituto de Medicina Molecular", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Portugal", "2024-06-29", "Larval", "Larval", "Blood", "Hematopoietic System"], [33122, "SRR29654156", "SRX25158188", "SRS21848810", "SRP517033", "PRJNA1129880", "Neutrophil immune profile guides spinal cord regeneration in zebrafish", "GSE271113", "Transcriptome Analysis", "Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet  their role in the repair process  particularly in a regenerative context  remains largely unknown. Here  we show that  promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely  blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether  these findings provide new insights into the role of neutrophils in spinal cord regeneration  emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition  we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100  and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Funda\u00e7\u00e5o para a Ci\u00eancia e Tecnologia FCT  Portugal", null, "pubmed:38925414", null, "Neutrophils mpx+  uninjured  DMSO  biol rep 1", "GSM8369969", null, "tissue:Neutrophils mpx:GFP+|cell type:Neutrophils mpx:GFP+|treatment:uninjured DMSO|geo loc name:missing|collection date:missing", "Neutrophils mpx+  uninjured  DMSO  biol rep 1", "Libraries were paired end sequenced on a Nextseq 500 Illumina  high output  with a 1x75 bp Illumina Kit Read 1: 26 cycles  index read: 6 cycles  Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded.  Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script", "Neutrophils mpx:GFP+", "At 3 dpf  larvae were anesthetized in 0.5 mM tricaine. Subsequenclty  the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next  larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", "Zebrafish embryos were raised at 28.5\u00baC in E3 media with Methylene blue", "cell type:Neutrophils mpx:GFP+|treatment:uninjured DMSO", "GSM8369969", "GSM8369969: Neutrophils mpx+  uninjured  DMSO  biol rep 1; Danio rerio; RNA Seq", "GSM8369969 r1", "GSM8369969", "1", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP517033", null, null, "IMM-CT-b001_HW5F2BGXN_S6_L004_Uninjured_DMSO_-003_cbc.fastq.gz", "fastq", 55531080.0, 925518.0, "GSM8369969 r4", "0:60", "A:20538193;C:10150017;G:10949669;T:13888674;N:4527", 60, null, null, null, 20538193, 10150017, 10949669, 13888674, 4527, "SRX25158188", "SRS21848810", "SRA1913211", "Instituto de Medicina Molecular", "Instituto de Medicina Molecular", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Portugal", "2024-06-29", "Larval", "Larval", "Blood", "Hematopoietic System"], [38073, "SRR1531483", "SRX665263", "SRS670077", "SRP045064", "PRJNA256975", "Genome wide RNA tomography in the zebrafish embryo", "GSE59873", "Other", "Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes  they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches  using for example in situ hybridization  can provide spatial information about gene expression  but are limited to analyzing one or a few genes at a time. Here  we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly  our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage  10 somites  15 somites  18 somites and mouse forelimbs E10.5  we cryosectioned samples  extracted RNA from the individual sections  and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.", null, "pubmed:25417113", null, "18 somites stage  straightened  secti1d tail to head", "GSM1448820", null, "tissue:deyolked embryo  head removed|Stage:18 somites|sectioning direction:tail to head|section thickness:24 \u00b5m|embedding strategy:deyolked and straightened embryo", "18 somites stage  straightened  secti1d tail to head", "Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections", "deyolked embryo  head removed", "Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned  and individual slices were transferred to Eppendorf tubes on dry ice.", "RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012", null, "Stage:18 somites|sectioning direction:tail to head|section thickness:24 \u00b5m|embedding strategy:deyolked and straightened embryo", "GSM1448820", "GSM1448820: 18 somites stage  straightened  secti1d tail to head; Danio rerio; RNA Seq", "GSM1448820", null, "1", "RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012", "GEO Accession:GSM1448820", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP045064", null, null, "dr_18ss_TH_R2.fastq.gz dr_18ss_TH_R1.fastq.gz", "fastq fastq", 15779230884.0, 154698342.0, "GSM1448820 r1", "0:51 1:51", "A:3451000604;C:2392800593;G:2522666152;T:7412137093;N:626442", 51, 51, null, null, 3451000604, 2392800593, 2522666152, 7412137093, 626442, "SRX665263", "SRS670077", "SRA177126", "GEO", "Hubrecht Institute", 2, 0.11555, 0.70031, 0.08647, 0.12212, 0.98238, 0.78946, 0.48905, 0.5514, 51, 51, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2014-07-29", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38074, "SRR1531482", "SRX665262", "SRS670076", "SRP045064", "PRJNA256975", "Genome wide RNA tomography in the zebrafish embryo", "GSE59873", "Other", "Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes  they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches  using for example in situ hybridization  can provide spatial information about gene expression  but are limited to analyzing one or a few genes at a time. Here  we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly  our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage  10 somites  15 somites  18 somites and mouse forelimbs E10.5  we cryosectioned samples  extracted RNA from the individual sections  and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.", null, "pubmed:25417113", null, "15 somites stage  straightened  secti1d tail to head  replicate", "GSM1448819", null, "tissue:deyolked embryo|Stage:15 somites|sectioning direction:tail to head|section thickness:18 \u00b5m|embedding strategy:deyolked and straightened embryo", "15 somites stage  straightened  secti1d tail to head  replicate", "Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections", "deyolked embryo", "Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned  and individual slices were transferred to Eppendorf tubes on dry ice.", "RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012", null, "Stage:15 somites|sectioning direction:tail to head|section thickness:18 \u00b5m|embedding strategy:deyolked and straightened embryo", "GSM1448819", "GSM1448819: 15 somites stage  straightened  secti1d tail to head  replicate; Danio rerio; RNA Seq", "GSM1448819", null, "1", "RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012", "GEO Accession:GSM1448819", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP045064", null, null, "dr_15ss_TH2_R2.fastq.gz dr_15ss_TH2_R1.fastq.gz", "fastq fastq", 4502603442.0, 44143171.0, "GSM1448819 r1", "0:51 1:51", "A:1010801791;C:688133305;G:712006267;T:2047960758;N:43701321", 51, 51, null, null, 1010801791, 688133305, 712006267, 2047960758, 43701321, "SRX665262", "SRS670076", "SRA177126", "GEO", "Hubrecht Institute", 2, 0.0903, 0.78618, 0.08054, 0.12953, 0.98703, 0.78046, 0.53574, 0.52775, 51, 51, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2014-07-29", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38075, "SRR1531481", "SRX665261", "SRS670075", "SRP045064", "PRJNA256975", "Genome wide RNA tomography in the zebrafish embryo", "GSE59873", "Other", "Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes  they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches  using for example in situ hybridization  can provide spatial information about gene expression  but are limited to analyzing one or a few genes at a time. Here  we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly  our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage  10 somites  15 somites  18 somites and mouse forelimbs E10.5  we cryosectioned samples  extracted RNA from the individual sections  and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.", null, "pubmed:25417113", null, "sections 97 108 for samples dr 15ss TH and dr 15ss HT", "GSM1448818", null, "tissue:deyolked embryo|Stage:15 somites|sectioning direction:head to tail and tail to head|section thickness:18 \u00b5m|embedding strategy:deyolked and straightened embryo", "sections 97 108 for samples dr 15ss TH and dr 15ss HT", "Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections", "deyolked embryo", "Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned  and individual slices were transferred to Eppendorf tubes on dry ice.", "RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012", null, "Stage:15 somites|sectioning direction:head to tail and tail to head|section thickness:18 \u00b5m|embedding strategy:deyolked and straightened embryo", "GSM1448818", "GSM1448818: sections 97 108 for samples dr 15ss TH and dr 15ss HT; Danio rerio; RNA Seq", "GSM1448818", null, "1", "RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012", "GEO Accession:GSM1448818", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP045064", null, null, "dr_15ss_TH97-108_HT97-108_R2.fastq.gz dr_15ss_TH97-108_HT97-108_R1.fastq.gz", "fastq fastq", 472071606.0, 4628153.0, "GSM1448818 r1", "0:51 1:51", "A:108013079;C:76852222;G:73612321;T:208300498;N:5293486", 51, 51, null, null, 108013079, 76852222, 73612321, 208300498, 5293486, "SRX665261", "SRS670075", "SRA177126", "GEO", "Hubrecht Institute", 2, 0.06997, 0.71056, 0.06103, 0.12966, 0.9865, 0.79446, 0.53118, 0.53673, 51, 51, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2014-07-29", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38076, "SRR1531480", "SRX665260", "SRS670074", "SRP045064", "PRJNA256975", "Genome wide RNA tomography in the zebrafish embryo", "GSE59873", "Other", "Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes  they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches  using for example in situ hybridization  can provide spatial information about gene expression  but are limited to analyzing one or a few genes at a time. Here  we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly  our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage  10 somites  15 somites  18 somites and mouse forelimbs E10.5  we cryosectioned samples  extracted RNA from the individual sections  and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.", null, "pubmed:25417113", null, "15 somites stage  straightened  secti1d tail to head", "GSM1448817", null, "tissue:deyolked embryo|Stage:15 somites|sectioning direction:tail to head|section thickness:18 \u00b5m|embedding strategy:deyolked and straightened embryo", "15 somites stage  straightened  secti1d tail to head", "Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections", "deyolked embryo", "Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned  and individual slices were transferred to Eppendorf tubes on dry ice.", "RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012", null, "Stage:15 somites|sectioning direction:tail to head|section thickness:18 \u00b5m|embedding strategy:deyolked and straightened embryo", "GSM1448817", "GSM1448817: 15 somites stage  straightened  secti1d tail to head; Danio rerio; RNA Seq", "GSM1448817", null, "1", "RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012", "GEO Accession:GSM1448817", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP045064", null, null, "dr_15ss_TH_R1.fastq.gz dr_15ss_TH_R2.fastq.gz", "fastq fastq", 3381229314.0, 33149307.0, "GSM1448817 r1", "0:51 1:51", "A:806003850;C:517726785;G:527487361;T:1491678004;N:38333314", 51, 51, null, null, 806003850, 517726785, 527487361, 1491678004, 38333314, "SRX665260", "SRS670074", "SRA177126", "GEO", "Hubrecht Institute", 2, 0.06812, 0.69273, 0.05849, 0.1511, 0.98502, 0.7834, 0.47808, 0.53868, 51, 51, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2014-07-29", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38077, "SRR1531479", "SRX665259", "SRS670073", "SRP045064", "PRJNA256975", "Genome wide RNA tomography in the zebrafish embryo", "GSE59873", "Other", "Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes  they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches  using for example in situ hybridization  can provide spatial information about gene expression  but are limited to analyzing one or a few genes at a time. Here  we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly  our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage  10 somites  15 somites  18 somites and mouse forelimbs E10.5  we cryosectioned samples  extracted RNA from the individual sections  and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.", null, "pubmed:25417113", null, "15 somites stage  straightened  secti1d head to tail", "GSM1448816", null, "tissue:deyolked embryo|Stage:15 somites|sectioning direction:head to tail|section thickness:18 \u00b5m|embedding strategy:deyolked and straightened embryo", "15 somites stage  straightened  secti1d head to tail", "Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections", "deyolked embryo", "Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned  and individual slices were transferred to Eppendorf tubes on dry ice.", "RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012", null, "Stage:15 somites|sectioning direction:head to tail|section thickness:18 \u00b5m|embedding strategy:deyolked and straightened embryo", "GSM1448816", "GSM1448816: 15 somites stage  straightened  secti1d head to tail; Danio rerio; RNA Seq", "GSM1448816", null, "1", "RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012", "GEO Accession:GSM1448816", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP045064", null, null, "dr_15ss_HT_R1.fastq.gz dr_15ss_HT_R2.fastq.gz", "fastq fastq", 3476174076.0, 34080138.0, "GSM1448816 r1", "0:51 1:51", "A:800519794;C:540890287;G:554165272;T:1542680760;N:37917963", 51, 51, null, null, 800519794, 540890287, 554165272, 1542680760, 37917963, "SRX665259", "SRS670073", "SRA177126", "GEO", "Hubrecht Institute", 2, 0.06769, 0.70036, 0.05945, 0.13184, 0.98849, 0.79026, 0.50058, 0.57003, 51, 51, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2014-07-29", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38078, "SRR1531477", "SRX665258", "SRS670072", "SRP045064", "PRJNA256975", "Genome wide RNA tomography in the zebrafish embryo", "GSE59873", "Other", "Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes  they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches  using for example in situ hybridization  can provide spatial information about gene expression  but are limited to analyzing one or a few genes at a time. Here  we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly  our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage  10 somites  15 somites  18 somites and mouse forelimbs E10.5  we cryosectioned samples  extracted RNA from the individual sections  and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.", null, "pubmed:25417113", null, "15 somite stage  secti1d from right to left", "GSM1448815", null, "tissue:whole embryo|Stage:15 somites|sectioning direction:right left|section thickness:18 \u00b5m|embedding strategy:intact embryo", "15 somite stage  secti1d from right to left", "Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections", "whole embryo", "Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned  and individual slices were transferred to Eppendorf tubes on dry ice.", "RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012", null, "Stage:15 somites|sectioning direction:right left|section thickness:18 \u00b5m|embedding strategy:intact embryo", "GSM1448815", "GSM1448815: 15 somite stage  secti1d from right to left; Danio rerio; RNA Seq", "GSM1448815", null, "1", "RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012", "GEO Accession:GSM1448815", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP045064", null, null, "dr_15ss_RL_R1.fastq.gz dr_15ss_RL_R2.fastq.gz", "fastq fastq", 3840123336.0, 37648268.0, "GSM1448815 r1", "0:51 1:51", "A:915153174;C:577478134;G:648196113;T:1695635476;N:3660439", 51, 51, null, null, 915153174, 577478134, 648196113, 1695635476, 3660439, "SRX665258", "SRS670072", "SRA177126", "GEO", "Hubrecht Institute", 2, 0.05313, 0.71589, 0.0419, 0.15174, 0.97717, 0.77484, 0.5218, 0.45828, 51, 51, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2014-07-29", "Segmentation", "Embryo", "Whole Organism", "All anatomical structures"], [38079, "SRR1531478", "SRX665258", "SRS670072", "SRP045064", "PRJNA256975", "Genome wide RNA tomography in the zebrafish embryo", "GSE59873", "Other", "Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes  they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches  using for example in situ hybridization  can provide spatial information about gene expression  but are limited to analyzing one or a few genes at a time. Here  we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly  our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage  10 somites  15 somites  18 somites and mouse forelimbs E10.5  we cryosectioned samples  extracted RNA from the individual sections  and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.", null, "pubmed:25417113", null, "15 somite stage  secti1d from right to left", "GSM1448815", null, "tissue:whole embryo|Stage:15 somites|sectioning direction:right left|section thickness:18 \u00b5m|embedding strategy:intact embryo", "15 somite stage  secti1d from right to left", "Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections", "whole embryo", "Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned  and individual slices were transferred to Eppendorf tubes on dry ice.", "RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012", null, "Stage:15 somites|sectioning direction:right left|section thickness:18 \u00b5m|embedding strategy:intact embryo", "GSM1448815", "GSM1448815: 15 somite stage  secti1d from right to left; Danio rerio; RNA Seq", "GSM1448815", null, "1", "RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012", "GEO Accession:GSM1448815", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP045064", null, "instrument model:Illumina MiSeq", "miseq_dr_15ss_RL_R1.fastq.gz miseq_dr_15ss_RL_R2.fastq.gz", "fastq fastq", 619303490.0, 1235999.0, "GSM1448815 r2", "0:251 1:250.06", "A:196814024;C:126079066;G:111585151;T:184825248;N:1", 251, 250, null, null, 196814024, 126079066, 111585151, 184825248, 1, "SRX665258", "SRS670072", "SRA177126", "GEO", "Hubrecht Institute", 2, 0.37674, 0.6743, 0.06734, 0.08523, 0.92516, 0.86196, 0.56151, 0.54745, 251, 251, "B", "B", "mate1-mate2 similar by mapping diff", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2014-07-29", "Segmentation", "Embryo", "Whole Organism", "All anatomical structures"], [38080, "SRR1531475", "SRX665257", "SRS670070", "SRP045064", "PRJNA256975", "Genome wide RNA tomography in the zebrafish embryo", "GSE59873", "Other", "Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes  they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches  using for example in situ hybridization  can provide spatial information about gene expression  but are limited to analyzing one or a few genes at a time. Here  we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly  our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage  10 somites  15 somites  18 somites and mouse forelimbs E10.5  we cryosectioned samples  extracted RNA from the individual sections  and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.", null, "pubmed:25417113", null, "15 somite stage  secti1d from left to right", "GSM1448814", null, "tissue:whole embryo|Stage:15 somites|sectioning direction:left right|section thickness:18 \u00b5m|embedding strategy:intact embryo", "15 somite stage  secti1d from left to right", "Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections", "whole embryo", "Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned  and individual slices were transferred to Eppendorf tubes on dry ice.", "RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012", null, "Stage:15 somites|sectioning direction:left right|section thickness:18 \u00b5m|embedding strategy:intact embryo", "GSM1448814", "GSM1448814: 15 somite stage  secti1d from left to right; Danio rerio; RNA Seq", "GSM1448814", null, "1", "RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012", "GEO Accession:GSM1448814", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP045064", null, null, "dr_15ss_LR_R2.fastq.gz dr_15ss_LR_R1.fastq.gz", "fastq fastq", 2077803342.0, 20370621.0, "GSM1448814 r1", "0:51 1:51", "A:487276259;C:320933398;G:342175116;T:925418636;N:1999933", 51, 51, null, null, 487276259, 320933398, 342175116, 925418636, 1999933, "SRX665257", "SRS670070", "SRA177126", "GEO", "Hubrecht Institute", 2, 0.04544, 0.77533, 0.03741, 0.15439, 0.98435, 0.77662, 0.56397, 0.57005, 51, 51, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2014-07-29", "Segmentation", "Embryo", "Whole Organism", "All anatomical structures"], [38081, "SRR1531476", "SRX665257", "SRS670070", "SRP045064", "PRJNA256975", "Genome wide RNA tomography in the zebrafish embryo", "GSE59873", "Other", "Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes  they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches  using for example in situ hybridization  can provide spatial information about gene expression  but are limited to analyzing one or a few genes at a time. Here  we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly  our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage  10 somites  15 somites  18 somites and mouse forelimbs E10.5  we cryosectioned samples  extracted RNA from the individual sections  and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.", null, "pubmed:25417113", null, "15 somite stage  secti1d from left to right", "GSM1448814", null, "tissue:whole embryo|Stage:15 somites|sectioning direction:left right|section thickness:18 \u00b5m|embedding strategy:intact embryo", "15 somite stage  secti1d from left to right", "Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections", "whole embryo", "Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned  and individual slices were transferred to Eppendorf tubes on dry ice.", "RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012", null, "Stage:15 somites|sectioning direction:left right|section thickness:18 \u00b5m|embedding strategy:intact embryo", "GSM1448814", "GSM1448814: 15 somite stage  secti1d from left to right; Danio rerio; RNA Seq", "GSM1448814", null, "1", "RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012", "GEO Accession:GSM1448814", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP045064", null, "instrument model:Illumina MiSeq", "miseq_dr_15ss_LR_R1.fastq.gz miseq_dr_15ss_LR_R2.fastq.gz", "fastq fastq", 648479770.0, 1294232.0, "GSM1448814 r2", "0:251 1:250.05", "A:208271519;C:133135452;G:114142609;T:192930139;N:51", 251, 250, null, null, 208271519, 133135452, 114142609, 192930139, 51, "SRX665257", "SRS670070", "SRA177126", "GEO", "Hubrecht Institute", 2, 0.34992, 0.64011, 0.08713, 0.16967, 0.92103, 0.83853, 0.54292, 0.52547, 251, 250, "B", "B", "mate1-mate2 similar by mapping diff", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2014-07-29", "Segmentation", "Embryo", "Whole Organism", "All anatomical structures"], [38082, "SRR1531473", "SRX665256", "SRS670071", "SRP045064", "PRJNA256975", "Genome wide RNA tomography in the zebrafish embryo", "GSE59873", "Other", "Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes  they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches  using for example in situ hybridization  can provide spatial information about gene expression  but are limited to analyzing one or a few genes at a time. Here  we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly  our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage  10 somites  15 somites  18 somites and mouse forelimbs E10.5  we cryosectioned samples  extracted RNA from the individual sections  and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.", null, "pubmed:25417113", null, "15 somite stage  secti1d from dorsal to ventral end", "GSM1448813", null, "tissue:whole embryo|Stage:15 somites|sectioning direction:dorsal ventral|section thickness:18 \u00b5m|embedding strategy:intact embryo", "15 somite stage  secti1d from dorsal to ventral end", "Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections", "whole embryo", "Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned  and individual slices were transferred to Eppendorf tubes on dry ice.", "RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012", null, "Stage:15 somites|sectioning direction:dorsal ventral|section thickness:18 \u00b5m|embedding strategy:intact embryo", "GSM1448813", "GSM1448813: 15 somite stage  secti1d from dorsal to ventral end; Danio rerio; RNA Seq", "GSM1448813", null, "1", "RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012", "GEO Accession:GSM1448813", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP045064", null, null, "dr_15ss_DV_R1.fastq.gz dr_15ss_DV_R2.fastq.gz", "fastq fastq", 2516804610.0, 24674555.0, "GSM1448813 r1", "0:51 1:51", "A:579818006;C:406550753;G:379205422;T:1129932140;N:21298289", 51, 51, null, null, 579818006, 406550753, 379205422, 1129932140, 21298289, "SRX665256", "SRS670071", "SRA177126", "GEO", "Hubrecht Institute", 2, 0.04189, 0.74891, 0.03368, 0.12625, 0.98695, 0.78423, 0.46823, 0.53429, 51, 51, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2014-07-29", "Segmentation", "Embryo", "Whole Organism", "All anatomical structures"], [38083, "SRR1531474", "SRX665256", "SRS670071", "SRP045064", "PRJNA256975", "Genome wide RNA tomography in the zebrafish embryo", "GSE59873", "Other", "Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes  they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches  using for example in situ hybridization  can provide spatial information about gene expression  but are limited to analyzing one or a few genes at a time. Here  we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly  our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage  10 somites  15 somites  18 somites and mouse forelimbs E10.5  we cryosectioned samples  extracted RNA from the individual sections  and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.", null, "pubmed:25417113", null, "15 somite stage  secti1d from dorsal to ventral end", "GSM1448813", null, "tissue:whole embryo|Stage:15 somites|sectioning direction:dorsal ventral|section thickness:18 \u00b5m|embedding strategy:intact embryo", "15 somite stage  secti1d from dorsal to ventral end", "Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections", "whole embryo", "Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned  and individual slices were transferred to Eppendorf tubes on dry ice.", "RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012", null, "Stage:15 somites|sectioning direction:dorsal ventral|section thickness:18 \u00b5m|embedding strategy:intact embryo", "GSM1448813", "GSM1448813: 15 somite stage  secti1d from dorsal to ventral end; Danio rerio; RNA Seq", "GSM1448813", null, "1", "RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012", "GEO Accession:GSM1448813", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP045064", null, "instrument model:Illumina MiSeq", "miseq_dr_15ss_DV_R1.fastq.gz miseq_dr_15ss_DV_R2.fastq.gz", "fastq fastq", 1831352383.0, 3654695.0, "GSM1448813 r2", "0:251 1:250.10", "A:593055798;C:392880040;G:312965357;T:532451118;N:70", 251, 250, null, null, 593055798, 392880040, 312965357, 532451118, 70, "SRX665256", "SRS670071", "SRA177126", "GEO", "Hubrecht Institute", 2, 0.27976, 0.58087, 0.05423, 0.08127, 0.93943, 0.88868, 0.51246, 0.50653, 251, 251, "B", "B", "mate1-mate2 similar by mapping diff", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2014-07-29", "Segmentation", "Embryo", "Whole Organism", "All anatomical structures"], [38084, "SRR1531471", "SRX665255", "SRS670069", "SRP045064", "PRJNA256975", "Genome wide RNA tomography in the zebrafish embryo", "GSE59873", "Other", "Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes  they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches  using for example in situ hybridization  can provide spatial information about gene expression  but are limited to analyzing one or a few genes at a time. Here  we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly  our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage  10 somites  15 somites  18 somites and mouse forelimbs E10.5  we cryosectioned samples  extracted RNA from the individual sections  and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.", null, "pubmed:25417113", null, "15 somite stage  secti1d from ventral to dorsal end", "GSM1448812", null, "tissue:whole embryo|Stage:15 somites|sectioning direction:ventral dorsal|section thickness:18 \u00b5m|embedding strategy:intact embryo", "15 somite stage  secti1d from ventral to dorsal end", "Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections", "whole embryo", "Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned  and individual slices were transferred to Eppendorf tubes on dry ice.", "RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012", null, "Stage:15 somites|sectioning direction:ventral dorsal|section thickness:18 \u00b5m|embedding strategy:intact embryo", "GSM1448812", "GSM1448812: 15 somite stage  secti1d from ventral to dorsal end; Danio rerio; RNA Seq", "GSM1448812", null, "1", "RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012", "GEO Accession:GSM1448812", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP045064", null, null, "dr_15ss_VD_R1.fastq.gz dr_15ss_VD_R2.fastq.gz", "fastq fastq", 1673808678.0, 16409889.0, "GSM1448812 r1", "0:51 1:51", "A:397744759;C:269067687;G:250815180;T:740808813;N:15372239", 51, 51, null, null, 397744759, 269067687, 250815180, 740808813, 15372239, "SRX665255", "SRS670069", "SRA177126", "GEO", "Hubrecht Institute", 2, 0.05917, 0.69313, 0.0499, 0.19364, 0.98364, 0.78232, 0.54626, 0.5434, 51, 51, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2014-07-29", "Segmentation", "Embryo", "Whole Organism", "All anatomical structures"], [38085, "SRR1531472", "SRX665255", "SRS670069", "SRP045064", "PRJNA256975", "Genome wide RNA tomography in the zebrafish embryo", "GSE59873", "Other", "Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes  they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches  using for example in situ hybridization  can provide spatial information about gene expression  but are limited to analyzing one or a few genes at a time. Here  we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly  our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage  10 somites  15 somites  18 somites and mouse forelimbs E10.5  we cryosectioned samples  extracted RNA from the individual sections  and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.", null, "pubmed:25417113", null, "15 somite stage  secti1d from ventral to dorsal end", "GSM1448812", null, "tissue:whole embryo|Stage:15 somites|sectioning direction:ventral dorsal|section thickness:18 \u00b5m|embedding strategy:intact embryo", "15 somite stage  secti1d from ventral to dorsal end", "Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections", "whole embryo", "Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned  and individual slices were transferred to Eppendorf tubes on dry ice.", "RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012", null, "Stage:15 somites|sectioning direction:ventral dorsal|section thickness:18 \u00b5m|embedding strategy:intact embryo", "GSM1448812", "GSM1448812: 15 somite stage  secti1d from ventral to dorsal end; Danio rerio; RNA Seq", "GSM1448812", null, "1", "RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012", "GEO Accession:GSM1448812", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP045064", null, "instrument model:Illumina MiSeq", "miseq_dr_15ss_VD_R2.fastq.gz miseq_dr_15ss_VD_R1.fastq.gz", "fastq fastq", 587520609.0, 1172567.0, "GSM1448812 r2", "0:251 1:250.06", "A:194391951;C:123162952;G:98682047;T:171283648;N:11", 251, 250, null, null, 194391951, 123162952, 98682047, 171283648, 11, "SRX665255", "SRS670069", "SRA177126", "GEO", "Hubrecht Institute", 2, 0.25906, 0.51091, 0.10052, 0.13544, 0.94274, 0.90015, 0.54255, 0.53365, 251, 251, "B", "B", "mate1-mate2 similar by mapping diff", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2014-07-29", "Segmentation", "Embryo", "Whole Organism", "All anatomical structures"], [38086, "SRR1531470", "SRX665254", "SRS670068", "SRP045064", "PRJNA256975", "Genome wide RNA tomography in the zebrafish embryo", "GSE59873", "Other", "Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes  they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches  using for example in situ hybridization  can provide spatial information about gene expression  but are limited to analyzing one or a few genes at a time. Here  we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly  our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage  10 somites  15 somites  18 somites and mouse forelimbs E10.5  we cryosectioned samples  extracted RNA from the individual sections  and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.", null, "pubmed:25417113", null, "15 somite stage  secti1d from posterior to anterior end", "GSM1448811", null, "tissue:whole embryo|Stage:15 somites|sectioning direction:posterior anterior|section thickness:18 \u00b5m|embedding strategy:intact embryo", "15 somite stage  secti1d from posterior to anterior end", "Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections", "whole embryo", "Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned  and individual slices were transferred to Eppendorf tubes on dry ice.", "RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012", null, "Stage:15 somites|sectioning direction:posterior anterior|section thickness:18 \u00b5m|embedding strategy:intact embryo", "GSM1448811", "GSM1448811: 15 somite stage  secti1d from posterior to anterior end; Danio rerio; RNA Seq", "GSM1448811", null, "1", "RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012", "GEO Accession:GSM1448811", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP045064", null, null, "dr_15ss_PA_R2.fastq.gz dr_15ss_PA_R1.fastq.gz", "fastq fastq", 2483143794.0, 24344547.0, "GSM1448811 r1", "0:51 1:51", "A:563038776;C:400378151;G:372280878;T:1126633332;N:20812657", 51, 51, null, null, 563038776, 400378151, 372280878, 1126633332, 20812657, "SRX665254", "SRS670068", "SRA177126", "GEO", "Hubrecht Institute", 2, 0.04278, 0.78001, 0.03367, 0.11539, 0.98727, 0.77865, 0.49734, 0.53041, 51, 51, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2014-07-29", "Segmentation", "Embryo", "Whole Organism", "All anatomical structures"], [38087, "SRR1531469", "SRX665253", "SRS670067", "SRP045064", "PRJNA256975", "Genome wide RNA tomography in the zebrafish embryo", "GSE59873", "Other", "Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes  they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches  using for example in situ hybridization  can provide spatial information about gene expression  but are limited to analyzing one or a few genes at a time. Here  we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly  our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage  10 somites  15 somites  18 somites and mouse forelimbs E10.5  we cryosectioned samples  extracted RNA from the individual sections  and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.", null, "pubmed:25417113", null, "15 somite stage  secti1d from anterior to posterior end", "GSM1448810", null, "tissue:whole embryo|Stage:15 somites|sectioning direction:anterior posterior|section thickness:18 \u00b5m|embedding strategy:intact embryo", "15 somite stage  secti1d from anterior to posterior end", "Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections", "whole embryo", "Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned  and individual slices were transferred to Eppendorf tubes on dry ice.", "RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012", null, "Stage:15 somites|sectioning direction:anterior posterior|section thickness:18 \u00b5m|embedding strategy:intact embryo", "GSM1448810", "GSM1448810: 15 somite stage  secti1d from anterior to posterior end; Danio rerio; RNA Seq", "GSM1448810", null, "1", "RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012", "GEO Accession:GSM1448810", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP045064", null, null, "dr_15ss_AP_R2.fastq.gz dr_15ss_AP_R1.fastq.gz", "fastq fastq", 3436281570.0, 33689035.0, "GSM1448810 r1", "0:51 1:51", "A:794842891;C:552474558;G:514289189;T:1545720661;N:28954271", 51, 51, null, null, 794842891, 552474558, 514289189, 1545720661, 28954271, "SRX665253", "SRS670067", "SRA177126", "GEO", "Hubrecht Institute", 2, 0.04616, 0.72787, 0.03714, 0.11902, 0.98636, 0.78372, 0.50428, 0.54252, 51, 51, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2014-07-29", "Segmentation", "Embryo", "Whole Organism", "All anatomical structures"], [38088, "SRR1531468", "SRX665252", "SRS670066", "SRP045064", "PRJNA256975", "Genome wide RNA tomography in the zebrafish embryo", "GSE59873", "Other", "Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes  they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches  using for example in situ hybridization  can provide spatial information about gene expression  but are limited to analyzing one or a few genes at a time. Here  we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly  our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage  10 somites  15 somites  18 somites and mouse forelimbs E10.5  we cryosectioned samples  extracted RNA from the individual sections  and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.", null, "pubmed:25417113", null, "10 somite stage  secti1d from right to left", "GSM1448809", null, "tissue:whole embryo|Stage:10 somites|sectioning direction:right left|section thickness:18 \u00b5m|embedding strategy:intact embryo", "10 somite stage  secti1d from right to left", "Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections", "whole embryo", "Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned  and individual slices were transferred to Eppendorf tubes on dry ice.", "RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012", null, "Stage:10 somites|sectioning direction:right left|section thickness:18 \u00b5m|embedding strategy:intact embryo", "GSM1448809", "GSM1448809: 10 somite stage  secti1d from right to left; Danio rerio; RNA Seq", "GSM1448809", null, "1", "RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012", "GEO Accession:GSM1448809", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP045064", null, null, "dr_10ss_RL_R2.fastq.gz dr_10ss_RL_R1.fastq.gz", "fastq fastq", 2058025848.0, 20176724.0, "GSM1448809 r1", "0:51 1:51", "A:466388690;C:327195544;G:324646168;T:921984274;N:17811172", 51, 51, null, null, 466388690, 327195544, 324646168, 921984274, 17811172, "SRX665252", "SRS670066", "SRA177126", "GEO", "Hubrecht Institute", 2, 0.03352, 0.82842, 0.02775, 0.10176, 0.99019, 0.7878, 0.56827, 0.53664, 51, 51, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2014-07-29", "Segmentation", "Embryo", "Whole Organism", "All anatomical structures"], [38089, "SRR1531467", "SRX665251", "SRS670065", "SRP045064", "PRJNA256975", "Genome wide RNA tomography in the zebrafish embryo", "GSE59873", "Other", "Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes  they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches  using for example in situ hybridization  can provide spatial information about gene expression  but are limited to analyzing one or a few genes at a time. Here  we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly  our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage  10 somites  15 somites  18 somites and mouse forelimbs E10.5  we cryosectioned samples  extracted RNA from the individual sections  and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.", null, "pubmed:25417113", null, "10 somite stage  secti1d from left to right", "GSM1448808", null, "tissue:whole embryo|Stage:10 somites|sectioning direction:left right|section thickness:18 \u00b5m|embedding strategy:intact embryo", "10 somite stage  secti1d from left to right", "Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections", "whole embryo", "Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned  and individual slices were transferred to Eppendorf tubes on dry ice.", "RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012", null, "Stage:10 somites|sectioning direction:left right|section thickness:18 \u00b5m|embedding strategy:intact embryo", "GSM1448808", "GSM1448808: 10 somite stage  secti1d from left to right; Danio rerio; RNA Seq", "GSM1448808", null, "1", "RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012", "GEO Accession:GSM1448808", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP045064", null, null, "dr_10ss_LR_R1.fastq.gz dr_10ss_LR_R2.fastq.gz", "fastq fastq", 2372600886.0, 23260793.0, "GSM1448808 r1", "0:51 1:51", "A:539978604;C:369014393;G:373430985;T:1069557826;N:20619078", 51, 51, null, null, 539978604, 369014393, 373430985, 1069557826, 20619078, "SRX665251", "SRS670065", "SRA177126", "GEO", "Hubrecht Institute", 2, 0.04947, 0.82594, 0.04114, 0.11817, 0.98703, 0.77727, 0.5181, 0.46105, 51, 51, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2014-07-29", "Segmentation", "Embryo", "Whole Organism", "All anatomical structures"], [38090, "SRR1531465", "SRX665250", "SRS670064", "SRP045064", "PRJNA256975", "Genome wide RNA tomography in the zebrafish embryo", "GSE59873", "Other", "Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes  they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches  using for example in situ hybridization  can provide spatial information about gene expression  but are limited to analyzing one or a few genes at a time. Here  we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly  our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage  10 somites  15 somites  18 somites and mouse forelimbs E10.5  we cryosectioned samples  extracted RNA from the individual sections  and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.", null, "pubmed:25417113", null, "10 somite stage  secti1d from dorsal to ventral end", "GSM1448807", null, "tissue:whole embryo|Stage:10 somites|sectioning direction:dorsal ventral|section thickness:18 \u00b5m|embedding strategy:intact embryo", "10 somite stage  secti1d from dorsal to ventral end", "Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections", "whole embryo", "Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned  and individual slices were transferred to Eppendorf tubes on dry ice.", "RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012", null, "Stage:10 somites|sectioning direction:dorsal ventral|section thickness:18 \u00b5m|embedding strategy:intact embryo", "GSM1448807", "GSM1448807: 10 somite stage  secti1d from dorsal to ventral end; Danio rerio; RNA Seq", "GSM1448807", null, "1", "RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012", "GEO Accession:GSM1448807", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP045064", null, null, "dr_10ss_DV_R1.fastq.gz dr_10ss_DV_R2.fastq.gz", "fastq fastq", 4808137200.0, 47138600.0, "GSM1448807 r1", "0:51 1:51", "A:1069537756;C:773357615;G:788490520;T:2131916220;N:44835089", 51, 51, null, null, 1069537756, 773357615, 788490520, 2131916220, 44835089, "SRX665250", "SRS670064", "SRA177126", "GEO", "Hubrecht Institute", 2, 0.05336, 0.7348, 0.04376, 0.11098, 0.98311, 0.78829, 0.55869, 0.5169, 51, 51, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2014-07-29", "Segmentation", "Embryo", "Whole Organism", "All anatomical structures"], [38091, "SRR1531466", "SRX665250", "SRS670064", "SRP045064", "PRJNA256975", "Genome wide RNA tomography in the zebrafish embryo", "GSE59873", "Other", "Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes  they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches  using for example in situ hybridization  can provide spatial information about gene expression  but are limited to analyzing one or a few genes at a time. Here  we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly  our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage  10 somites  15 somites  18 somites and mouse forelimbs E10.5  we cryosectioned samples  extracted RNA from the individual sections  and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.", null, "pubmed:25417113", null, "10 somite stage  secti1d from dorsal to ventral end", "GSM1448807", null, "tissue:whole embryo|Stage:10 somites|sectioning direction:dorsal ventral|section thickness:18 \u00b5m|embedding strategy:intact embryo", "10 somite stage  secti1d from dorsal to ventral end", "Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections", "whole embryo", "Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned  and individual slices were transferred to Eppendorf tubes on dry ice.", "RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012", null, "Stage:10 somites|sectioning direction:dorsal ventral|section thickness:18 \u00b5m|embedding strategy:intact embryo", "GSM1448807", "GSM1448807: 10 somite stage  secti1d from dorsal to ventral end; Danio rerio; RNA Seq", "GSM1448807", null, "1", "RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012", "GEO Accession:GSM1448807", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP045064", null, "instrument model:Illumina MiSeq", "miseq_dr_10ss_DV_R1.fastq.gz miseq_dr_10ss_DV_R2.fastq.gz", "fastq fastq", 981031778.0, 1957880.0, "GSM1448807 r2", "0:251 1:250.07", "A:318017696;C:204637111;G:170546834;T:287830124;N:13", 251, 250, null, null, 318017696, 204637111, 170546834, 287830124, 13, "SRX665250", "SRS670064", "SRA177126", "GEO", "Hubrecht Institute", 2, 0.28421, 0.5957, 0.04748, 0.07361, 0.93917, 0.88298, 0.53618, 0.53493, 251, 251, "B", "B", "mate1-mate2 similar by mapping diff", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2014-07-29", "Segmentation", "Embryo", "Whole Organism", "All anatomical structures"], [38092, "SRR1531463", "SRX665249", "SRS670063", "SRP045064", "PRJNA256975", "Genome wide RNA tomography in the zebrafish embryo", "GSE59873", "Other", "Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes  they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches  using for example in situ hybridization  can provide spatial information about gene expression  but are limited to analyzing one or a few genes at a time. Here  we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly  our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage  10 somites  15 somites  18 somites and mouse forelimbs E10.5  we cryosectioned samples  extracted RNA from the individual sections  and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.", null, "pubmed:25417113", null, "10 somite stage  secti1d from ventral to dorsal end", "GSM1448806", null, "tissue:whole embryo|Stage:10 somites|sectioning direction:ventral dorsal|section thickness:18 \u00b5m|embedding strategy:intact embryo", "10 somite stage  secti1d from ventral to dorsal end", "Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections", "whole embryo", "Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned  and individual slices were transferred to Eppendorf tubes on dry ice.", "RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012", null, "Stage:10 somites|sectioning direction:ventral dorsal|section thickness:18 \u00b5m|embedding strategy:intact embryo", "GSM1448806", "GSM1448806: 10 somite stage  secti1d from ventral to dorsal end; Danio rerio; RNA Seq", "GSM1448806", null, "1", "RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012", "GEO Accession:GSM1448806", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP045064", null, null, "dr_10ss_VD_R1.fastq.gz dr_10ss_VD_R2.fastq.gz", "fastq fastq", 4042242048.0, 39629824.0, "GSM1448806 r1", "0:51 1:51", "A:880941046;C:636899286;G:642176352;T:1845085169;N:37140195", 51, 51, null, null, 880941046, 636899286, 642176352, 1845085169, 37140195, "SRX665249", "SRS670063", "SRA177126", "GEO", "Hubrecht Institute", 2, 0.04898, 0.80518, 0.04234, 0.10309, 0.99044, 0.78437, 0.4974, 0.53264, 51, 51, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2014-07-29", "Segmentation", "Embryo", "Whole Organism", "All anatomical structures"], [38093, "SRR1531464", "SRX665249", "SRS670063", "SRP045064", "PRJNA256975", "Genome wide RNA tomography in the zebrafish embryo", "GSE59873", "Other", "Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes  they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches  using for example in situ hybridization  can provide spatial information about gene expression  but are limited to analyzing one or a few genes at a time. Here  we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly  our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage  10 somites  15 somites  18 somites and mouse forelimbs E10.5  we cryosectioned samples  extracted RNA from the individual sections  and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.", null, "pubmed:25417113", null, "10 somite stage  secti1d from ventral to dorsal end", "GSM1448806", null, "tissue:whole embryo|Stage:10 somites|sectioning direction:ventral dorsal|section thickness:18 \u00b5m|embedding strategy:intact embryo", "10 somite stage  secti1d from ventral to dorsal end", "Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections", "whole embryo", "Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned  and individual slices were transferred to Eppendorf tubes on dry ice.", "RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012", null, "Stage:10 somites|sectioning direction:ventral dorsal|section thickness:18 \u00b5m|embedding strategy:intact embryo", "GSM1448806", "GSM1448806: 10 somite stage  secti1d from ventral to dorsal end; Danio rerio; RNA Seq", "GSM1448806", null, "1", "RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012", "GEO Accession:GSM1448806", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP045064", null, "instrument model:Illumina MiSeq", "miseq_dr_10ss_VD_R1.fastq.gz miseq_dr_10ss_VD_R2.fastq.gz", "fastq fastq", 738071470.0, 1473056.0, "GSM1448806 r2", "0:251 1:250.05", "A:241662059;C:148514183;G:127467910;T:220427298;N:20", 251, 250, null, null, 241662059, 148514183, 127467910, 220427298, 20, "SRX665249", "SRS670063", "SRA177126", "GEO", "Hubrecht Institute", 2, 0.33554, 0.65168, 0.04798, 0.07375, 0.93334, 0.87121, 0.53425, 0.51721, 251, 251, "B", "B", "mate1-mate2 similar by mapping diff", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2014-07-29", "Segmentation", "Embryo", "Whole Organism", "All anatomical structures"], [38094, "SRR1531461", "SRX665248", "SRS670062", "SRP045064", "PRJNA256975", "Genome wide RNA tomography in the zebrafish embryo", "GSE59873", "Other", "Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes  they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches  using for example in situ hybridization  can provide spatial information about gene expression  but are limited to analyzing one or a few genes at a time. Here  we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly  our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage  10 somites  15 somites  18 somites and mouse forelimbs E10.5  we cryosectioned samples  extracted RNA from the individual sections  and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.", null, "pubmed:25417113", null, "10 somite stage  secti1d from posterior to anterior end", "GSM1448805", null, "tissue:whole embryo|Stage:10 somites|sectioning direction:anterior posterior|section thickness:18 \u00b5m|embedding strategy:intact embryo", "10 somite stage  secti1d from posterior to anterior end", "Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections", "whole embryo", "Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned  and individual slices were transferred to Eppendorf tubes on dry ice.", "RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012", null, "Stage:10 somites|sectioning direction:anterior posterior|section thickness:18 \u00b5m|embedding strategy:intact embryo", "GSM1448805", "GSM1448805: 10 somite stage  secti1d from posterior to anterior end; Danio rerio; RNA Seq", "GSM1448805", null, "1", "RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012", "GEO Accession:GSM1448805", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP045064", null, null, "dr_10ss_PA_R1.fastq.gz dr_10ss_PA_R2.fastq.gz", "fastq fastq", 4759203720.0, 46658860.0, "GSM1448805 r1", "0:51 1:51", "A:1044025561;C:745846492;G:761494052;T:2164007108;N:43830507", 51, 51, null, null, 1044025561, 745846492, 761494052, 2164007108, 43830507, "SRX665248", "SRS670062", "SRA177126", "GEO", "Hubrecht Institute", 2, 0.04594, 0.81204, 0.0388, 0.10992, 0.98938, 0.78244, 0.51272, 0.52639, 51, 51, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2014-07-29", "Segmentation", "Embryo", "Whole Organism", "All anatomical structures"], [38095, "SRR1531462", "SRX665248", "SRS670062", "SRP045064", "PRJNA256975", "Genome wide RNA tomography in the zebrafish embryo", "GSE59873", "Other", "Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes  they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches  using for example in situ hybridization  can provide spatial information about gene expression  but are limited to analyzing one or a few genes at a time. Here  we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly  our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage  10 somites  15 somites  18 somites and mouse forelimbs E10.5  we cryosectioned samples  extracted RNA from the individual sections  and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.", null, "pubmed:25417113", null, "10 somite stage  secti1d from posterior to anterior end", "GSM1448805", null, "tissue:whole embryo|Stage:10 somites|sectioning direction:anterior posterior|section thickness:18 \u00b5m|embedding strategy:intact embryo", "10 somite stage  secti1d from posterior to anterior end", "Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections", "whole embryo", "Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned  and individual slices were transferred to Eppendorf tubes on dry ice.", "RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012", null, "Stage:10 somites|sectioning direction:anterior posterior|section thickness:18 \u00b5m|embedding strategy:intact embryo", "GSM1448805", "GSM1448805: 10 somite stage  secti1d from posterior to anterior end; Danio rerio; RNA Seq", "GSM1448805", null, "1", "RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012", "GEO Accession:GSM1448805", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP045064", null, "instrument model:Illumina MiSeq", "miseq_dr_10ss_PA_R2.fastq.gz miseq_dr_10ss_PA_R1.fastq.gz", "fastq fastq", 923948352.0, 1843960.0, "GSM1448805 r2", "0:251 1:250.07", "A:301981474;C:189568545;G:157916393;T:274481921;N:19", 251, 250, null, null, 301981474, 189568545, 157916393, 274481921, 19, "SRX665248", "SRS670062", "SRA177126", "GEO", "Hubrecht Institute", 2, 0.33803, 0.65569, 0.05131, 0.07917, 0.93419, 0.87355, 0.4399, 0.52526, 251, 251, "B", "B", "mate1-mate2 similar by mapping diff", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2014-07-29", "Segmentation", "Embryo", "Whole Organism", "All anatomical structures"], [38096, "SRR1531460", "SRX665247", "SRS670061", "SRP045064", "PRJNA256975", "Genome wide RNA tomography in the zebrafish embryo", "GSE59873", "Other", "Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes  they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches  using for example in situ hybridization  can provide spatial information about gene expression  but are limited to analyzing one or a few genes at a time. Here  we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly  our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage  10 somites  15 somites  18 somites and mouse forelimbs E10.5  we cryosectioned samples  extracted RNA from the individual sections  and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.", null, "pubmed:25417113", null, "10 somite stage  secti1d from anterior to posterior end  replicate", "GSM1448804", null, "tissue:whole embryo|Stage:10 somites|sectioning direction:anterior posterior|section thickness:18 \u00b5m|embedding strategy:intact embryo", "10 somite stage  secti1d from anterior to posterior end  replicate", "Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections", "whole embryo", "Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned  and individual slices were transferred to Eppendorf tubes on dry ice.", "RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012", null, "Stage:10 somites|sectioning direction:anterior posterior|section thickness:18 \u00b5m|embedding strategy:intact embryo", "GSM1448804", "GSM1448804: 10 somite stage  secti1d from anterior to posterior end  replicate; Danio rerio; RNA Seq", "GSM1448804", null, "1", "RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012", "GEO Accession:GSM1448804", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP045064", null, null, "dr_10ss_AP2_R1.fastq.gz dr_10ss_AP2_R2.fastq.gz", "fastq fastq", 2096761878.0, 20556489.0, "GSM1448804 r1", "0:51 1:51", "A:486131317;C:330426143;G:323887100;T:938024368;N:18292950", 51, 51, null, null, 486131317, 330426143, 323887100, 938024368, 18292950, "SRX665247", "SRS670061", "SRA177126", "GEO", "Hubrecht Institute", 2, 0.0484, 0.78914, 0.0396, 0.12303, 0.9866, 0.78234, 0.53395, 0.53422, 51, 51, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2014-07-29", "Segmentation", "Embryo", "Whole Organism", "All anatomical structures"], [38097, "SRR1531458", "SRX665246", "SRS670060", "SRP045064", "PRJNA256975", "Genome wide RNA tomography in the zebrafish embryo", "GSE59873", "Other", "Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes  they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches  using for example in situ hybridization  can provide spatial information about gene expression  but are limited to analyzing one or a few genes at a time. Here  we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly  our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage  10 somites  15 somites  18 somites and mouse forelimbs E10.5  we cryosectioned samples  extracted RNA from the individual sections  and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.", null, "pubmed:25417113", null, "10 somite stage  secti1d from anterior to posterior end", "GSM1448803", null, "tissue:whole embryo|Stage:10 somites|sectioning direction:anterior posterior|section thickness:18 \u00b5m|embedding strategy:intact embryo", "10 somite stage  secti1d from anterior to posterior end", "Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections", "whole embryo", "Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned  and individual slices were transferred to Eppendorf tubes on dry ice.", "RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012", null, "Stage:10 somites|sectioning direction:anterior posterior|section thickness:18 \u00b5m|embedding strategy:intact embryo", "GSM1448803", "GSM1448803: 10 somite stage  secti1d from anterior to posterior end; Danio rerio; RNA Seq", "GSM1448803", null, "1", "RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012", "GEO Accession:GSM1448803", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP045064", null, null, "dr_10ss_AP_R2.fastq.gz dr_10ss_AP_R1.fastq.gz", "fastq fastq", 3873169500.0, 37972250.0, "GSM1448803 r1", "0:51 1:51", "A:844434990;C:614503150;G:615061181;T:1763736099;N:35434080", 51, 51, null, null, 844434990, 614503150, 615061181, 1763736099, 35434080, "SRX665246", "SRS670060", "SRA177126", "GEO", "Hubrecht Institute", 2, 0.0354, 0.81065, 0.02893, 0.12263, 0.98944, 0.77386, 0.52631, 0.52007, 51, 51, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2014-07-29", "Segmentation", "Embryo", "Whole Organism", "All anatomical structures"], [38098, "SRR1531459", "SRX665246", "SRS670060", "SRP045064", "PRJNA256975", "Genome wide RNA tomography in the zebrafish embryo", "GSE59873", "Other", "Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes  they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches  using for example in situ hybridization  can provide spatial information about gene expression  but are limited to analyzing one or a few genes at a time. Here  we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly  our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage  10 somites  15 somites  18 somites and mouse forelimbs E10.5  we cryosectioned samples  extracted RNA from the individual sections  and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.", null, "pubmed:25417113", null, "10 somite stage  secti1d from anterior to posterior end", "GSM1448803", null, "tissue:whole embryo|Stage:10 somites|sectioning direction:anterior posterior|section thickness:18 \u00b5m|embedding strategy:intact embryo", "10 somite stage  secti1d from anterior to posterior end", "Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections", "whole embryo", "Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned  and individual slices were transferred to Eppendorf tubes on dry ice.", "RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012", null, "Stage:10 somites|sectioning direction:anterior posterior|section thickness:18 \u00b5m|embedding strategy:intact embryo", "GSM1448803", "GSM1448803: 10 somite stage  secti1d from anterior to posterior end; Danio rerio; RNA Seq", "GSM1448803", null, "1", "RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012", "GEO Accession:GSM1448803", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP045064", null, "instrument model:Illumina MiSeq", "miseq_dr_10ss_AP_R1.fastq.gz miseq_dr_10ss_AP_R2.fastq.gz", "fastq fastq", 496084013.0, 990096.0, "GSM1448803 r2", "0:251 1:250.05", "A:161790706;C:99237964;G:85634725;T:149420610;N:8", 251, 250, null, null, 161790706, 99237964, 85634725, 149420610, 8, "SRX665246", "SRS670060", "SRA177126", "GEO", "Hubrecht Institute", 2, 0.35483, 0.66804, 0.06659, 0.09269, 0.92699, 0.86113, 0.53381, 0.51797, 251, 251, "B", "B", "mate1-mate2 similar by mapping diff", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2014-07-29", "Segmentation", "Embryo", "Whole Organism", "All anatomical structures"], [38099, "SRR1531457", "SRX665245", "SRS670059", "SRP045064", "PRJNA256975", "Genome wide RNA tomography in the zebrafish embryo", "GSE59873", "Other", "Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes  they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches  using for example in situ hybridization  can provide spatial information about gene expression  but are limited to analyzing one or a few genes at a time. Here  we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly  our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage  10 somites  15 somites  18 somites and mouse forelimbs E10.5  we cryosectioned samples  extracted RNA from the individual sections  and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.", null, "pubmed:25417113", null, "shield stage  secti1d from dorsal to ventral end  replicate", "GSM1448802", null, "tissue:whole embryo|Stage:shield stage|sectioning direction:dorsal ventral|section thickness:18 \u00b5m|embedding strategy:intact embryo", "shield stage  secti1d from dorsal to ventral end  replicate", "Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections", "whole embryo", "Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned  and individual slices were transferred to Eppendorf tubes on dry ice.", "RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012", null, "Stage:shield stage|sectioning direction:dorsal ventral|section thickness:18 \u00b5m|embedding strategy:intact embryo", "GSM1448802", "GSM1448802: shield stage  secti1d from dorsal to ventral end  replicate; Danio rerio; RNA Seq", "GSM1448802", null, "1", "RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012", "GEO Accession:GSM1448802", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP045064", null, null, "dr_shield_DV2_R2.fastq.gz dr_shield_DV2_R1.fastq.gz", "fastq fastq", 2735350014.0, 26817157.0, "GSM1448802 r1", "0:51 1:51", "A:650077339;C:412458828;G:411687121;T:1237686190;N:23440536", 51, 51, null, null, 650077339, 412458828, 411687121, 1237686190, 23440536, "SRX665245", "SRS670059", "SRA177126", "GEO", "Hubrecht Institute", 2, 0.02556, 0.75175, 0.01912, 0.10697, 0.99076, 0.79819, 0.54093, 0.55229, 51, 51, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2014-07-29", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [38100, "SRR1531455", "SRX665244", "SRS670058", "SRP045064", "PRJNA256975", "Genome wide RNA tomography in the zebrafish embryo", "GSE59873", "Other", "Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes  they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches  using for example in situ hybridization  can provide spatial information about gene expression  but are limited to analyzing one or a few genes at a time. Here  we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly  our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage  10 somites  15 somites  18 somites and mouse forelimbs E10.5  we cryosectioned samples  extracted RNA from the individual sections  and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.", null, "pubmed:25417113", null, "shield stage  secti1d from dorsal to ventral end", "GSM1448801", null, "tissue:whole embryo|Stage:shield stage|sectioning direction:dorsal ventral|section thickness:18 \u00b5m|embedding strategy:intact embryo", "shield stage  secti1d from dorsal to ventral end", "Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections", "whole embryo", "Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned  and individual slices were transferred to Eppendorf tubes on dry ice.", "RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012", null, "Stage:shield stage|sectioning direction:dorsal ventral|section thickness:18 \u00b5m|embedding strategy:intact embryo", "GSM1448801", "GSM1448801: shield stage  secti1d from dorsal to ventral end; Danio rerio; RNA Seq", "GSM1448801", null, "1", "RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012", "GEO Accession:GSM1448801", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP045064", null, null, "dr_shield_DV_R1.fastq.gz dr_shield_DV_R2.fastq.gz", "fastq fastq", 1605318738.0, 15738419.0, "GSM1448801 r1", "0:51 1:51", "A:361176217;C:248822696;G:253372108;T:726629351;N:15318366", 51, 51, null, null, 361176217, 248822696, 253372108, 726629351, 15318366, "SRX665244", "SRS670058", "SRA177126", "GEO", "Hubrecht Institute", 2, 0.02633, 0.68496, 0.02344, 0.10104, 0.99638, 0.80006, 0.46031, 0.57655, 51, 51, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2014-07-29", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [38101, "SRR1531456", "SRX665244", "SRS670058", "SRP045064", "PRJNA256975", "Genome wide RNA tomography in the zebrafish embryo", "GSE59873", "Other", "Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes  they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches  using for example in situ hybridization  can provide spatial information about gene expression  but are limited to analyzing one or a few genes at a time. Here  we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly  our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage  10 somites  15 somites  18 somites and mouse forelimbs E10.5  we cryosectioned samples  extracted RNA from the individual sections  and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.", null, "pubmed:25417113", null, "shield stage  secti1d from dorsal to ventral end", "GSM1448801", null, "tissue:whole embryo|Stage:shield stage|sectioning direction:dorsal ventral|section thickness:18 \u00b5m|embedding strategy:intact embryo", "shield stage  secti1d from dorsal to ventral end", "Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections", "whole embryo", "Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned  and individual slices were transferred to Eppendorf tubes on dry ice.", "RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012", null, "Stage:shield stage|sectioning direction:dorsal ventral|section thickness:18 \u00b5m|embedding strategy:intact embryo", "GSM1448801", "GSM1448801: shield stage  secti1d from dorsal to ventral end; Danio rerio; RNA Seq", "GSM1448801", null, "1", "RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012", "GEO Accession:GSM1448801", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP045064", null, "instrument model:Illumina MiSeq", "miseq_dr_shield_DV_R1.fastq.gz miseq_dr_shield_DV_R2.fastq.gz", "fastq fastq", 114907294.0, 229320.0, "GSM1448801 r2", "0:251 1:250.08", "A:37813553;C:24168661;G:19441624;T:33483456;N:0", 251, 250, null, null, 37813553, 24168661, 19441624, 33483456, 0, "SRX665244", "SRS670058", "SRA177126", "GEO", "Hubrecht Institute", 2, 0.26022, 0.46204, 0.03083, 0.05933, 0.94627, 0.89301, 0.56728, 0.55478, 251, 250, "B", "B", "mate1-mate2 similar by mapping diff", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2014-07-29", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [38102, "SRR1531453", "SRX665243", "SRS670056", "SRP045064", "PRJNA256975", "Genome wide RNA tomography in the zebrafish embryo", "GSE59873", "Other", "Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes  they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches  using for example in situ hybridization  can provide spatial information about gene expression  but are limited to analyzing one or a few genes at a time. Here  we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly  our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage  10 somites  15 somites  18 somites and mouse forelimbs E10.5  we cryosectioned samples  extracted RNA from the individual sections  and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.", null, "pubmed:25417113", null, "shield stage  secti1d from ventral to dorsal end", "GSM1448800", null, "tissue:whole embryo|Stage:shield stage|sectioning direction:ventral dorsal|section thickness:18 \u00b5m|embedding strategy:intact embryo", "shield stage  secti1d from ventral to dorsal end", "Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections", "whole embryo", "Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned  and individual slices were transferred to Eppendorf tubes on dry ice.", "RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  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Cell Reports  2012", "GEO Accession:GSM1448800", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP045064", null, null, "dr_shield_VD_R1.fastq.gz dr_shield_VD_R2.fastq.gz", "fastq fastq", 1840839492.0, 18047446.0, "GSM1448800 r1", "0:51 1:51", "A:421253850;C:292045914;G:295175858;T:814744774;N:17619096", 51, 51, null, null, 421253850, 292045914, 295175858, 814744774, 17619096, "SRX665243", "SRS670056", "SRA177126", "GEO", "Hubrecht Institute", 2, 0.01815, 0.6287, 0.01468, 0.09567, 0.99452, 0.80975, 0.5259, 0.58926, 51, 51, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2014-07-29", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [38103, "SRR1531454", "SRX665243", "SRS670056", "SRP045064", "PRJNA256975", "Genome wide RNA tomography in the zebrafish embryo", "GSE59873", "Other", "Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes  they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches  using for example in situ hybridization  can provide spatial information about gene expression  but are limited to analyzing one or a few genes at a time. Here  we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly  our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage  10 somites  15 somites  18 somites and mouse forelimbs E10.5  we cryosectioned samples  extracted RNA from the individual sections  and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.", null, "pubmed:25417113", null, "shield stage  secti1d from ventral to dorsal end", "GSM1448800", null, "tissue:whole embryo|Stage:shield stage|sectioning direction:ventral dorsal|section thickness:18 \u00b5m|embedding strategy:intact embryo", "shield stage  secti1d from ventral to dorsal end", "Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections", "whole embryo", "Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned  and individual slices were transferred to Eppendorf tubes on dry ice.", "RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012", null, "Stage:shield stage|sectioning direction:ventral dorsal|section thickness:18 \u00b5m|embedding strategy:intact embryo", "GSM1448800", "GSM1448800: shield stage  secti1d from ventral to dorsal end; Danio rerio; RNA Seq", "GSM1448800", null, "1", "RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012", "GEO Accession:GSM1448800", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP045064", null, "instrument model:Illumina MiSeq", "miseq_dr_shield_VD_R2.fastq.gz miseq_dr_shield_VD_R1.fastq.gz", "fastq fastq", 158531701.0, 316379.0, "GSM1448800 r2", null, null, null, null, null, null, null, null, null, null, null, "SRX665243", "SRS670056", "SRA177126", "GEO", "Hubrecht Institute", 2, 0.06803, 0.1733, 0.00916, 0.026, 0.94085, 0.88899, 0.58254, 0.5723, 251, 251, "B", "B", "mate1-mate2 similar by mapping diff", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2014-07-29", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [38104, "SRR1531451", "SRX665242", "SRS670055", "SRP045064", "PRJNA256975", "Genome wide RNA tomography in the zebrafish embryo", "GSE59873", "Other", "Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes  they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches  using for example in situ hybridization  can provide spatial information about gene expression  but are limited to analyzing one or a few genes at a time. Here  we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly  our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage  10 somites  15 somites  18 somites and mouse forelimbs E10.5  we cryosectioned samples  extracted RNA from the individual sections  and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.", null, "pubmed:25417113", null, "shield stage  secti1d from right to left", "GSM1448799", null, "tissue:whole embryo|Stage:shield stage|sectioning direction:right left|section thickness:18 \u00b5m|embedding strategy:intact embryo", "shield stage  secti1d from right to left", "Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections", "whole embryo", "Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned  and individual slices were transferred to Eppendorf tubes on dry ice.", "RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012", null, "Stage:shield stage|sectioning direction:right left|section thickness:18 \u00b5m|embedding strategy:intact embryo", "GSM1448799", "GSM1448799: shield stage  secti1d from right to left; Danio rerio; RNA Seq", "GSM1448799", null, "1", "RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012", "GEO Accession:GSM1448799", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP045064", null, null, "dr_shield_RL_R1.fastq.gz dr_shield_RL_R2.fastq.gz", "fastq fastq", 2003076918.0, 19638009.0, "GSM1448799 r1", "0:51 1:51", "A:457537608;C:308292947;G:312973612;T:905317961;N:18954790", 51, 51, null, null, 457537608, 308292947, 312973612, 905317961, 18954790, "SRX665242", "SRS670055", "SRA177126", "GEO", "Hubrecht Institute", 2, 0.02111, 0.7573, 0.01656, 0.11316, 0.99364, 0.8005, 0.4501, 0.59142, 51, 51, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2014-07-29", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [38105, "SRR1531452", "SRX665242", "SRS670055", "SRP045064", "PRJNA256975", "Genome wide RNA tomography in the zebrafish embryo", "GSE59873", "Other", "Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes  they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches  using for example in situ hybridization  can provide spatial information about gene expression  but are limited to analyzing one or a few genes at a time. Here  we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly  our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage  10 somites  15 somites  18 somites and mouse forelimbs E10.5  we cryosectioned samples  extracted RNA from the individual sections  and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.", null, "pubmed:25417113", null, "shield stage  secti1d from right to left", "GSM1448799", null, "tissue:whole embryo|Stage:shield stage|sectioning direction:right left|section thickness:18 \u00b5m|embedding strategy:intact embryo", "shield stage  secti1d from right to left", "Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections", "whole embryo", "Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned  and individual slices were transferred to Eppendorf tubes on dry ice.", "RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012", null, "Stage:shield stage|sectioning direction:right left|section thickness:18 \u00b5m|embedding strategy:intact embryo", "GSM1448799", "GSM1448799: shield stage  secti1d from right to left; Danio rerio; RNA Seq", "GSM1448799", null, "1", "RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012", "GEO Accession:GSM1448799", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP045064", null, "instrument model:Illumina MiSeq", "miseq_dr_shield_RL_R1.fastq.gz miseq_dr_shield_RL_R2.fastq.gz", "fastq fastq", 154180181.0, 307695.0, "GSM1448799 r2", "0:251 1:250.08", "A:50801230;C:32293099;G:25917988;T:45167860;N:4", 251, 250, null, null, 50801230, 32293099, 25917988, 45167860, 4, "SRX665242", "SRS670055", "SRA177126", "GEO", "Hubrecht Institute", 2, 0.31553, 0.64085, 0.03613, 0.06829, 0.94101, 0.8938, 0.60272, 0.58117, 251, 251, "B", "B", "mate1-mate2 similar by mapping diff", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2014-07-29", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [38106, "SRR1531449", "SRX665241", "SRS670053", "SRP045064", "PRJNA256975", "Genome wide RNA tomography in the zebrafish embryo", "GSE59873", "Other", "Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes  they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches  using for example in situ hybridization  can provide spatial information about gene expression  but are limited to analyzing one or a few genes at a time. Here  we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly  our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage  10 somites  15 somites  18 somites and mouse forelimbs E10.5  we cryosectioned samples  extracted RNA from the individual sections  and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.", null, "pubmed:25417113", null, "shield stage  secti1d from left to right", "GSM1448798", null, "tissue:whole embryo|Stage:shield stage|sectioning direction:left right|section thickness:18 \u00b5m|embedding strategy:intact embryo", "shield stage  secti1d from left to right", "Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections", "whole embryo", "Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned  and individual slices were transferred to Eppendorf tubes on dry ice.", "RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012", null, "Stage:shield stage|sectioning direction:left right|section thickness:18 \u00b5m|embedding strategy:intact embryo", "GSM1448798", "GSM1448798: shield stage  secti1d from left to right; Danio rerio; RNA Seq", "GSM1448798", null, "1", "RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012", "GEO Accession:GSM1448798", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP045064", null, null, "dr_shield_LR_R1.fastq.gz dr_shield_LR_R2.fastq.gz", "fastq fastq", 1755442542.0, 17210221.0, "GSM1448798 r1", "0:51 1:51", "A:401133098;C:265688355;G:264899378;T:807011867;N:16709844", 51, 51, null, null, 401133098, 265688355, 264899378, 807011867, 16709844, "SRX665241", "SRS670053", "SRA177126", "GEO", "Hubrecht Institute", 2, 0.02829, 0.71918, 0.02455, 0.14486, 0.99484, 0.79866, 0.50383, 0.57925, 51, 51, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2014-07-29", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [38107, "SRR1531450", "SRX665241", "SRS670053", "SRP045064", "PRJNA256975", "Genome wide RNA tomography in the zebrafish embryo", "GSE59873", "Other", "Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes  they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches  using for example in situ hybridization  can provide spatial information about gene expression  but are limited to analyzing one or a few genes at a time. Here  we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly  our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage  10 somites  15 somites  18 somites and mouse forelimbs E10.5  we cryosectioned samples  extracted RNA from the individual sections  and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.", null, "pubmed:25417113", null, "shield stage  secti1d from left to right", "GSM1448798", null, "tissue:whole embryo|Stage:shield stage|sectioning direction:left right|section thickness:18 \u00b5m|embedding strategy:intact embryo", "shield stage  secti1d from left to right", "Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections", "whole embryo", "Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned  and individual slices were transferred to Eppendorf tubes on dry ice.", "RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012", null, "Stage:shield stage|sectioning direction:left right|section thickness:18 \u00b5m|embedding strategy:intact embryo", "GSM1448798", "GSM1448798: shield stage  secti1d from left to right; Danio rerio; RNA Seq", "GSM1448798", null, "1", "RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012", "GEO Accession:GSM1448798", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP045064", null, "instrument model:Illumina MiSeq", "miseq_dr_shield_LR_R1.fastq.gz miseq_dr_shield_LR_R2.fastq.gz", "fastq fastq", 139755993.0, 278913.0, "GSM1448798 r2", "0:251 1:250.07", "A:46536591;C:28346077;G:23036783;T:41836538;N:4", 251, 250, null, null, 46536591, 28346077, 23036783, 41836538, 4, "SRX665241", "SRS670053", "SRA177126", "GEO", "Hubrecht Institute", 2, 0.27443, 0.57858, 0.06346, 0.09954, 0.94194, 0.89522, 0.55896, 0.56169, 251, 251, "B", "B", "mate1-mate2 similar by mapping diff", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2014-07-29", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [38108, "SRR1531448", "SRX665240", "SRS670054", "SRP045064", "PRJNA256975", "Genome wide RNA tomography in the zebrafish embryo", "GSE59873", "Other", "Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes  they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches  using for example in situ hybridization  can provide spatial information about gene expression  but are limited to analyzing one or a few genes at a time. Here  we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly  our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage  10 somites  15 somites  18 somites and mouse forelimbs E10.5  we cryosectioned samples  extracted RNA from the individual sections  and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.", null, "pubmed:25417113", null, "shield stage  secti1d from vegetal to animal pole  replicate", "GSM1448797", null, "tissue:whole embryo|Stage:shield stage|sectioning direction:vegetal animal|section thickness:18 \u00b5m|embedding strategy:intact embryo", "shield stage  secti1d from vegetal to animal pole  replicate", "Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections", "whole embryo", "Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned  and individual slices were transferred to Eppendorf tubes on dry ice.", "RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012", null, "Stage:shield stage|sectioning direction:vegetal animal|section thickness:18 \u00b5m|embedding strategy:intact embryo", "GSM1448797", "GSM1448797: shield stage  secti1d from vegetal to animal pole  replicate; Danio rerio; RNA Seq", "GSM1448797", null, "1", "RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012", "GEO Accession:GSM1448797", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP045064", null, null, "dr_shield_VA2_R1.fastq.gz dr_shield_VA2_R2.fastq.gz", "fastq fastq", 1962884532.0, 19243966.0, "GSM1448797 r1", "0:51 1:51", "A:449529690;C:292065368;G:287973067;T:916330652;N:16985755", 51, 51, null, null, 449529690, 292065368, 287973067, 916330652, 16985755, "SRX665240", "SRS670054", "SRA177126", "GEO", "Hubrecht Institute", 2, 0.04512, 0.77455, 0.03997, 0.11233, 0.99293, 0.78488, 0.50931, 0.5171, 51, 51, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2014-07-29", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [38109, "SRR1531446", "SRX665239", "SRS670057", "SRP045064", "PRJNA256975", "Genome wide RNA tomography in the zebrafish embryo", "GSE59873", "Other", "Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes  they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches  using for example in situ hybridization  can provide spatial information about gene expression  but are limited to analyzing one or a few genes at a time. Here  we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly  our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage  10 somites  15 somites  18 somites and mouse forelimbs E10.5  we cryosectioned samples  extracted RNA from the individual sections  and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.", null, "pubmed:25417113", null, "shield stage  secti1d from vegetal to animal pole", "GSM1448796", null, "tissue:whole embryo|Stage:shield stage|sectioning direction:vegetal animal|section thickness:18 \u00b5m|embedding strategy:intact embryo", "shield stage  secti1d from vegetal to animal pole", "Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections", "whole embryo", "Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned  and individual slices were transferred to Eppendorf tubes on dry ice.", "RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012", null, "Stage:shield stage|sectioning direction:vegetal animal|section thickness:18 \u00b5m|embedding strategy:intact embryo", "GSM1448796", "GSM1448796: shield stage  secti1d from vegetal to animal pole; Danio rerio; RNA Seq", "GSM1448796", null, "1", "RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012", "GEO Accession:GSM1448796", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP045064", null, null, "dr_shield_VA_R2.fastq.gz dr_shield_VA_R1.fastq.gz", "fastq fastq", 2367839934.0, 23214117.0, "GSM1448796 r1", "0:51 1:51", "A:544061124;C:369321045;G:383489434;T:1047897582;N:23070749", 51, 51, null, null, 544061124, 369321045, 383489434, 1047897582, 23070749, "SRX665239", "SRS670057", "SRA177126", "GEO", "Hubrecht Institute", 2, 0.02284, 0.57831, 0.0199, 0.08251, 0.99579, 0.81653, 0.4451, 0.5792, 51, 51, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2014-07-29", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [38110, "SRR1531447", "SRX665239", "SRS670057", "SRP045064", "PRJNA256975", "Genome wide RNA tomography in the zebrafish embryo", "GSE59873", "Other", "Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes  they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches  using for example in situ hybridization  can provide spatial information about gene expression  but are limited to analyzing one or a few genes at a time. Here  we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly  our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage  10 somites  15 somites  18 somites and mouse forelimbs E10.5  we cryosectioned samples  extracted RNA from the individual sections  and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.", null, "pubmed:25417113", null, "shield stage  secti1d from vegetal to animal pole", "GSM1448796", null, "tissue:whole embryo|Stage:shield stage|sectioning direction:vegetal animal|section thickness:18 \u00b5m|embedding strategy:intact embryo", "shield stage  secti1d from vegetal to animal pole", "Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections", "whole embryo", "Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned  and individual slices were transferred to Eppendorf tubes on dry ice.", "RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012", null, "Stage:shield stage|sectioning direction:vegetal animal|section thickness:18 \u00b5m|embedding strategy:intact embryo", "GSM1448796", "GSM1448796: shield stage  secti1d from vegetal to animal pole; Danio rerio; RNA Seq", "GSM1448796", null, "1", "RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012", "GEO Accession:GSM1448796", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP045064", null, "instrument model:Illumina MiSeq", "miseq_dr_shield_VA_R1.fastq.gz miseq_dr_shield_VA_R2.fastq.gz", "fastq fastq", 139677889.0, 278764.0, "GSM1448796 r2", "0:251 1:250.06", "A:45877333;C:29821713;G:24032460;T:39946380;N:3", 251, 250, null, null, 45877333, 29821713, 24032460, 39946380, 3, "SRX665239", "SRS670057", "SRA177126", "GEO", "Hubrecht Institute", 2, 0.21444, 0.33364, 0.02489, 0.04529, 0.95156, 0.901, 0.56549, 0.55749, 251, 251, "B", "B", "mate1-mate2 similar by mapping diff", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2014-07-29", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [38111, "SRR1531444", "SRX665238", "SRS670052", "SRP045064", "PRJNA256975", "Genome wide RNA tomography in the zebrafish embryo", "GSE59873", "Other", "Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes  they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches  using for example in situ hybridization  can provide spatial information about gene expression  but are limited to analyzing one or a few genes at a time. Here  we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly  our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage  10 somites  15 somites  18 somites and mouse forelimbs E10.5  we cryosectioned samples  extracted RNA from the individual sections  and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.", null, "pubmed:25417113", null, "shield stage  secti1d from animal to vegetal pole", "GSM1448795", null, "tissue:whole embryo|Stage:shield stage|sectioning direction:animal vegetal|section thickness:18 \u00b5m|embedding strategy:intact embryo", "shield stage  secti1d from animal to vegetal pole", "Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections", "whole embryo", "Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned  and individual slices were transferred to Eppendorf tubes on dry ice.", "RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012", null, "Stage:shield stage|sectioning direction:animal vegetal|section thickness:18 \u00b5m|embedding strategy:intact embryo", "GSM1448795", "GSM1448795: shield stage  secti1d from animal to vegetal pole; Danio rerio; RNA Seq", "GSM1448795", null, "1", "RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012", "GEO Accession:GSM1448795", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP045064", null, null, "dr_shield_AV_R1.fastq.gz dr_shield_AV_R2.fastq.gz", "fastq fastq", 2059615110.0, 20192305.0, "GSM1448795 r1", "0:51 1:51", "A:487942041;C:328047311;G:336282927;T:886836259;N:20506572", 51, 51, null, null, 487942041, 328047311, 336282927, 886836259, 20506572, "SRX665238", "SRS670052", "SRA177126", "GEO", "Hubrecht Institute", 2, 0.01633, 0.50842, 0.0136, 0.07269, 0.99541, 0.82183, 0.51242, 0.59281, 51, 51, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2014-07-29", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [38112, "SRR1531445", "SRX665238", "SRS670052", "SRP045064", "PRJNA256975", "Genome wide RNA tomography in the zebrafish embryo", "GSE59873", "Other", "Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes  they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches  using for example in situ hybridization  can provide spatial information about gene expression  but are limited to analyzing one or a few genes at a time. Here  we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly  our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage  10 somites  15 somites  18 somites and mouse forelimbs E10.5  we cryosectioned samples  extracted RNA from the individual sections  and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.", null, "pubmed:25417113", null, "shield stage  secti1d from animal to vegetal pole", "GSM1448795", null, "tissue:whole embryo|Stage:shield stage|sectioning direction:animal vegetal|section thickness:18 \u00b5m|embedding strategy:intact embryo", "shield stage  secti1d from animal to vegetal pole", "Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections", "whole embryo", "Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned  and individual slices were transferred to Eppendorf tubes on dry ice.", "RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012", null, "Stage:shield stage|sectioning direction:animal vegetal|section thickness:18 \u00b5m|embedding strategy:intact embryo", "GSM1448795", "GSM1448795: shield stage  secti1d from animal to vegetal pole; Danio rerio; RNA Seq", "GSM1448795", null, "1", "RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012", "GEO Accession:GSM1448795", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP045064", null, "instrument model:Illumina MiSeq", "miseq_dr_shield_AV_R1.fastq.gz miseq_dr_shield_AV_R2.fastq.gz", "fastq fastq", 176530873.0, 352271.0, "GSM1448795 r2", "0:251 1:250.12", "A:57029265;C:38838035;G:30065677;T:50597891;N:5", 251, 250, null, null, 57029265, 38838035, 30065677, 50597891, 5, "SRX665238", "SRS670052", "SRA177126", "GEO", "Hubrecht Institute", 2, 0.20318, 0.26844, 0.02342, 0.03751, 0.95499, 0.9069, 0.4325, 0.57102, 251, 251, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2014-07-29", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [38122, "SRR1555598", "SRX684706", "SRS687823", "SRP045679", "PRJNA258656", "Danio rerio high resolution developmental transcriptomic time course", "GSE60619", "Transcriptome Analysis", "Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This \u201cphylotypic stage\u201d has recently received support from transcriptome analyses  which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a \u2018zootypic\u2019 stage  however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum  including a segmented worm  a flatworm  a roundworm  a water bear  a fruitfly  a sea urchin  a zebrafish  a sea anemone  a sponge  and a comb jelly. For each species  we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly  we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation  and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes  also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples", "parent bioproject:PRJNA287810", "pubmed:26886793", null, "Metazome ZF timecourse sample 0106", "GSM1483841", null, "tissue:single embryo", "Metazome ZF timecourse sample 0106", "Libraries were sequenced on the Illumina HiSeq2000 according to standard  paired end sequencing  protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl  fastq cluster count 1234567890   mismatches 0   use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases   not required. CEL Seq Hashimshony  et a. 2012l demultiplexing of second mate  using first mate barcode  allowing no mismatches in barcode. bowtie2  version 2.1.0  against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix", "single embryo", null, "RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.", "zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute  Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.", "time min post fertilization:4240", "GSM1483841", "GSM1483841: Metazome ZF timecourse sample 0106; Danio rerio; RNA Seq", "GSM1483841", null, "1", "RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.", "GEO Accession:GSM1483841", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP045679", null, null, "Metazome_ZF_timecourse_sample_0106.fastq.gz", "fastq", 3911705.0, 111763.0, "GSM1483841 r1", "0:35", "A:1100064;C:790487;G:836206;T:1169251;N:15697", 35, null, null, null, 1100064, 790487, 836206, 1169251, 15697, "SRX684706", "SRS687823", "SRA179995", "GEO", "Yanai, Biology, Technion - Israel Institute of Technology", 1, 0.72414, null, 0.09461, null, 0.96725, null, 0.4942, null, 35, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Israel", "2014-08-21", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38123, "SRR1555597", "SRX684705", "SRS687821", "SRP045679", "PRJNA258656", "Danio rerio high resolution developmental transcriptomic time course", "GSE60619", "Transcriptome Analysis", "Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This \u201cphylotypic stage\u201d has recently received support from transcriptome analyses  which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a \u2018zootypic\u2019 stage  however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum  including a segmented worm  a flatworm  a roundworm  a water bear  a fruitfly  a sea urchin  a zebrafish  a sea anemone  a sponge  and a comb jelly. For each species  we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly  we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation  and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes  also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples", "parent bioproject:PRJNA287810", "pubmed:26886793", null, "Metazome ZF timecourse sample 0105", "GSM1483840", null, "tissue:single embryo", "Metazome ZF timecourse sample 0105", "Libraries were sequenced on the Illumina HiSeq2000 according to standard  paired end sequencing  protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl  fastq cluster count 1234567890   mismatches 0   use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases   not required. CEL Seq Hashimshony  et a. 2012l demultiplexing of second mate  using first mate barcode  allowing no mismatches in barcode. bowtie2  version 2.1.0  against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix", "single embryo", null, "RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.", "zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute  Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.", "time min post fertilization:4200", "GSM1483840", "GSM1483840: Metazome ZF timecourse sample 0105; Danio rerio; RNA Seq", "GSM1483840", null, "1", "RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.", "GEO Accession:GSM1483840", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP045679", null, null, "Metazome_ZF_timecourse_sample_0105.fastq.gz", "fastq", 32877145.0, 939347.0, "GSM1483840 r1", "0:35", "A:9524894;C:6625944;G:6696548;T:9953576;N:76183", 35, null, null, null, 9524894, 6625944, 6696548, 9953576, 76183, "SRX684705", "SRS687821", "SRA179995", "GEO", "Yanai, Biology, Technion - Israel Institute of Technology", 1, 0.74436, null, 0.07095, null, 0.88201, null, 0.47612, null, 35, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Israel", "2014-08-21", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38124, "SRR1555596", "SRX684704", "SRS687822", "SRP045679", "PRJNA258656", "Danio rerio high resolution developmental transcriptomic time course", "GSE60619", "Transcriptome Analysis", "Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This \u201cphylotypic stage\u201d has recently received support from transcriptome analyses  which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a \u2018zootypic\u2019 stage  however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum  including a segmented worm  a flatworm  a roundworm  a water bear  a fruitfly  a sea urchin  a zebrafish  a sea anemone  a sponge  and a comb jelly. For each species  we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly  we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation  and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes  also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples", "parent bioproject:PRJNA287810", "pubmed:26886793", null, "Metazome ZF timecourse sample 0104", "GSM1483839", null, "tissue:single embryo", "Metazome ZF timecourse sample 0104", "Libraries were sequenced on the Illumina HiSeq2000 according to standard  paired end sequencing  protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl  fastq cluster count 1234567890   mismatches 0   use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases   not required. CEL Seq Hashimshony  et a. 2012l demultiplexing of second mate  using first mate barcode  allowing no mismatches in barcode. bowtie2  version 2.1.0  against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix", "single embryo", null, "RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.", "zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute  Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.", "time min post fertilization:4160", "GSM1483839", "GSM1483839: Metazome ZF timecourse sample 0104; Danio rerio; RNA Seq", "GSM1483839", null, "1", "RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.", "GEO Accession:GSM1483839", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP045679", null, null, "Metazome_ZF_timecourse_sample_0104.fastq.gz", "fastq", 83810020.0, 2394572.0, "GSM1483839 r1", "0:35", "A:24075610;C:16799998;G:16694424;T:25967423;N:272565", 35, null, null, null, 24075610, 16799998, 16694424, 25967423, 272565, "SRX684704", "SRS687822", "SRA179995", "GEO", "Yanai, Biology, Technion - Israel Institute of Technology", 1, 0.7588, null, 0.07993, null, 0.84449, null, 0.49785, null, 35, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Israel", "2014-08-21", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38125, "SRR1555595", "SRX684703", "SRS687820", "SRP045679", "PRJNA258656", "Danio rerio high resolution developmental transcriptomic time course", "GSE60619", "Transcriptome Analysis", "Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This \u201cphylotypic stage\u201d has recently received support from transcriptome analyses  which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a \u2018zootypic\u2019 stage  however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum  including a segmented worm  a flatworm  a roundworm  a water bear  a fruitfly  a sea urchin  a zebrafish  a sea anemone  a sponge  and a comb jelly. For each species  we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly  we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation  and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes  also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples", "parent bioproject:PRJNA287810", "pubmed:26886793", null, "Metazome ZF timecourse sample 0103", "GSM1483838", null, "tissue:single embryo", "Metazome ZF timecourse sample 0103", "Libraries were sequenced on the Illumina HiSeq2000 according to standard  paired end sequencing  protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl  fastq cluster count 1234567890   mismatches 0   use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases   not required. CEL Seq Hashimshony  et a. 2012l demultiplexing of second mate  using first mate barcode  allowing no mismatches in barcode. bowtie2  version 2.1.0  against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix", "single embryo", null, "RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.", "zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute  Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.", "time min post fertilization:4120", "GSM1483838", "GSM1483838: Metazome ZF timecourse sample 0103; Danio rerio; RNA Seq", "GSM1483838", null, "1", "RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.", "GEO Accession:GSM1483838", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP045679", null, null, "Metazome_ZF_timecourse_sample_0103.fastq.gz", "fastq", 98206150.0, 2805890.0, "GSM1483838 r1", "0:35", "A:28361916;C:19232789;G:19589483;T:30798968;N:222994", 35, null, null, null, 28361916, 19232789, 19589483, 30798968, 222994, "SRX684703", "SRS687820", "SRA179995", "GEO", "Yanai, Biology, Technion - Israel Institute of Technology", 1, 0.75509, null, 0.13429, null, 0.81117, null, 0.49102, null, 35, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Israel", "2014-08-21", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38126, "SRR1555594", "SRX684702", "SRS687819", "SRP045679", "PRJNA258656", "Danio rerio high resolution developmental transcriptomic time course", "GSE60619", "Transcriptome Analysis", "Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This \u201cphylotypic stage\u201d has recently received support from transcriptome analyses  which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a \u2018zootypic\u2019 stage  however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum  including a segmented worm  a flatworm  a roundworm  a water bear  a fruitfly  a sea urchin  a zebrafish  a sea anemone  a sponge  and a comb jelly. For each species  we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly  we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation  and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes  also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples", "parent bioproject:PRJNA287810", "pubmed:26886793", null, "Metazome ZF timecourse sample 0102", "GSM1483837", null, "tissue:single embryo", "Metazome ZF timecourse sample 0102", "Libraries were sequenced on the Illumina HiSeq2000 according to standard  paired end sequencing  protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl  fastq cluster count 1234567890   mismatches 0   use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases   not required. CEL Seq Hashimshony  et a. 2012l demultiplexing of second mate  using first mate barcode  allowing no mismatches in barcode. bowtie2  version 2.1.0  against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix", "single embryo", null, "RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.", "zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute  Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.", "time min post fertilization:4080", "GSM1483837", "GSM1483837: Metazome ZF timecourse sample 0102; Danio rerio; RNA Seq", "GSM1483837", null, "1", "RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.", "GEO Accession:GSM1483837", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP045679", null, null, "Metazome_ZF_timecourse_sample_0102.fastq.gz", "fastq", 192817835.0, 5509081.0, "GSM1483837 r1", "0:35", "A:55969077;C:36880901;G:37835921;T:61101558;N:1030378", 35, null, null, null, 55969077, 36880901, 37835921, 61101558, 1030378, "SRX684702", "SRS687819", "SRA179995", "GEO", "Yanai, Biology, Technion - Israel Institute of Technology", 1, 0.73387, null, 0.17245, null, 0.80164, null, 0.48657, null, 35, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Israel", "2014-08-21", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38127, "SRR1555593", "SRX684701", "SRS687818", "SRP045679", "PRJNA258656", "Danio rerio high resolution developmental transcriptomic time course", "GSE60619", "Transcriptome Analysis", "Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This \u201cphylotypic stage\u201d has recently received support from transcriptome analyses  which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a \u2018zootypic\u2019 stage  however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum  including a segmented worm  a flatworm  a roundworm  a water bear  a fruitfly  a sea urchin  a zebrafish  a sea anemone  a sponge  and a comb jelly. For each species  we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly  we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation  and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes  also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples", "parent bioproject:PRJNA287810", "pubmed:26886793", null, "Metazome ZF timecourse sample 0101", "GSM1483836", null, "tissue:single embryo", "Metazome ZF timecourse sample 0101", "Libraries were sequenced on the Illumina HiSeq2000 according to standard  paired end sequencing  protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl  fastq cluster count 1234567890   mismatches 0   use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases   not required. CEL Seq Hashimshony  et a. 2012l demultiplexing of second mate  using first mate barcode  allowing no mismatches in barcode. bowtie2  version 2.1.0  against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix", "single embryo", null, "RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.", "zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute  Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.", "time min post fertilization:4040", "GSM1483836", "GSM1483836: Metazome ZF timecourse sample 0101; Danio rerio; RNA Seq", "GSM1483836", null, "1", "RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.", "GEO Accession:GSM1483836", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP045679", null, null, "Metazome_ZF_timecourse_sample_0101.fastq.gz", "fastq", 374339455.0, 10695413.0, "GSM1483836 r1", "0:35", "A:112191846;C:73679996;G:73185024;T:114766825;N:515764", 35, null, null, null, 112191846, 73679996, 73185024, 114766825, 515764, "SRX684701", "SRS687818", "SRA179995", "GEO", "Yanai, Biology, Technion - Israel Institute of Technology", 1, 0.83131, null, 0.16618, null, 0.77812, null, 0.49895, null, 35, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Israel", "2014-08-21", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38128, "SRR1555592", "SRX684700", "SRS687816", "SRP045679", "PRJNA258656", "Danio rerio high resolution developmental transcriptomic time course", "GSE60619", "Transcriptome Analysis", "Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This \u201cphylotypic stage\u201d has recently received support from transcriptome analyses  which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a \u2018zootypic\u2019 stage  however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum  including a segmented worm  a flatworm  a roundworm  a water bear  a fruitfly  a sea urchin  a zebrafish  a sea anemone  a sponge  and a comb jelly. For each species  we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly  we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation  and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes  also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples", "parent bioproject:PRJNA287810", "pubmed:26886793", null, "Metazome ZF timecourse sample 0100", "GSM1483835", null, "tissue:single embryo", "Metazome ZF timecourse sample 0100", "Libraries were sequenced on the Illumina HiSeq2000 according to standard  paired end sequencing  protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl  fastq cluster count 1234567890   mismatches 0   use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases   not required. CEL Seq Hashimshony  et a. 2012l demultiplexing of second mate  using first mate barcode  allowing no mismatches in barcode. bowtie2  version 2.1.0  against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix", "single embryo", null, "RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.", "zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute  Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.", "time min post fertilization:4000", "GSM1483835", "GSM1483835: Metazome ZF timecourse sample 0100; Danio rerio; RNA Seq", "GSM1483835", null, "1", "RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.", "GEO Accession:GSM1483835", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP045679", null, null, "Metazome_ZF_timecourse_sample_0100.fastq.gz", "fastq", 15239420.0, 435412.0, "GSM1483835 r1", "0:35", "A:4361241;C:3088134;G:3269084;T:4498093;N:22868", 35, null, null, null, 4361241, 3088134, 3269084, 4498093, 22868, "SRX684700", "SRS687816", "SRA179995", "GEO", "Yanai, Biology, Technion - Israel Institute of Technology", 1, 0.7702, null, 0.17879, null, 0.92904, null, 0.505, null, 35, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Israel", "2014-08-21", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38129, "SRR1555591", "SRX684699", "SRS687817", "SRP045679", "PRJNA258656", "Danio rerio high resolution developmental transcriptomic time course", "GSE60619", "Transcriptome Analysis", "Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This \u201cphylotypic stage\u201d has recently received support from transcriptome analyses  which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a \u2018zootypic\u2019 stage  however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum  including a segmented worm  a flatworm  a roundworm  a water bear  a fruitfly  a sea urchin  a zebrafish  a sea anemone  a sponge  and a comb jelly. For each species  we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly  we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation  and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes  also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples", "parent bioproject:PRJNA287810", "pubmed:26886793", null, "Metazome ZF timecourse sample 0099", "GSM1483834", null, "tissue:single embryo", "Metazome ZF timecourse sample 0099", "Libraries were sequenced on the Illumina HiSeq2000 according to standard  paired end sequencing  protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl  fastq cluster count 1234567890   mismatches 0   use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases   not required. CEL Seq Hashimshony  et a. 2012l demultiplexing of second mate  using first mate barcode  allowing no mismatches in barcode. bowtie2  version 2.1.0  against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix", "single embryo", null, "RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.", "zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute  Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.", "time min post fertilization:3960", "GSM1483834", "GSM1483834: Metazome ZF timecourse sample 0099; Danio rerio; RNA Seq", "GSM1483834", null, "1", "RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.", "GEO Accession:GSM1483834", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP045679", null, null, "Metazome_ZF_timecourse_sample_0099.fastq.gz", "fastq", 284196500.0, 8119900.0, "GSM1483834 r1", "0:35", "A:81991733;C:57440756;G:58362818;T:86010858;N:390335", 35, null, null, null, 81991733, 57440756, 58362818, 86010858, 390335, "SRX684699", "SRS687817", "SRA179995", "GEO", "Yanai, Biology, Technion - Israel Institute of Technology", 1, 0.81284, null, 0.1715, null, 0.78468, null, 0.49472, null, 35, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Israel", "2014-08-21", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"]], "truncated": false, "filtered_table_rows_count": 938, "expanded_columns": [], "expandable_columns": [], "columns": ["rowid", "run.accession", "experiment.accession", 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