metadata: run_metadata: 938 rows where experiment.library_source = "TRANSCRIPTOMIC", experiment.library_strategy = "RNA-Seq" and technology = "celseq"

938 rows where experiment.library_source = "TRANSCRIPTOMIC", experiment.library_strategy = "RNA-Seq" and technology = "celseq"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.attributes	study.PMIDs	sample.title	sample.alias	sample.attributes	GEOsample.title	GEOsample.dataprocessing	GEOsample.source	GEOsample.treatmentprotocol	GEOsample.extractprotocol	GEOsample.growthprotocol	GEOsample.characteristics	GEOsample.accession	experiment.title	experiment.alias	experiment.library_name	experiment.design_description	experiment.library_construction_protocol	experiment.attributes	experiment.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	experiment.study_ref	run.attributes	run.filename	run.semantic_name	run.total_bases	run.total_spots	run.alias	run.read_lengths	run.base_counts	run.r1_length	run.r2_length	run.Acount	run.Ccount	run.Gcount	run.Tcount	run.Ncount	run.experiment	run.pool_member	submission.accession	submission.srasource	submission.bioprojectsource	seqdetective.n_mates	seqdetective.mapping_rate.mate1	seqdetective.mapping_rate.mate2	seqdetective.nofeature_rate.mate1	seqdetective.nofeature_rate.mate2	seqdetective.sparsity.mate1	seqdetective.sparsity.mate2	seqdetective.pos_strand_rate.mate1	seqdetective.pos_strand_rate.mate2	seqdetective.readlen.mate1	seqdetective.readlen.mate2	seqdetective.judgement.mate1	seqdetective.judgement.mate2	seqdetective.judgement.reason	platform_family	instrument_generation	read_bias	selection_class	prep_kit	sc_or_bulk	tech_class	technology	submission.bioprojectsource.country	earliest_date	devstage_curation	devstage_curation_coarse	tissue_curation	tissue_curation_coarse
30508	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/ß catenin signalling gradient which acts as a morphogen to establish embryonic anterior posterior patterning revealed that unfit cells with abnormal Wnt/ß 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/ß 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: ß catCA constitutive active form of ß catenin expressing GFP+ cells or ßcatCA unexpressing GFP cells from ß catCA mosaically introduced zebrafish early embryos were sorted by FACS cell sorter. Total RNAs were extracted and analyzed by RNA seq.		pubmed:39546611	Mosaic GFP control GFP min lot2	GSM8042248	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		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.		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.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 1500	SRP486518		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		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		0.20207		0.86143		0.54661		36		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Japan	2024-01-29	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
30509	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/ß catenin signalling gradient which acts as a morphogen to establish embryonic anterior posterior patterning revealed that unfit cells with abnormal Wnt/ß 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/ß 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: ß catCA constitutive active form of ß catenin expressing GFP+ cells or ßcatCA unexpressing GFP cells from ß catCA mosaically introduced zebrafish early embryos were sorted by FACS cell sorter. Total RNAs were extracted and analyzed by RNA seq.		pubmed:39546611	Mosaic GFP control GFP min lot1	GSM8042247	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		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.		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.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 1500	SRP486518		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		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		0.17754		0.8619		0.61474		36		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Japan	2024-01-29	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
30510	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/ß catenin signalling gradient which acts as a morphogen to establish embryonic anterior posterior patterning revealed that unfit cells with abnormal Wnt/ß 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/ß 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: ß catCA constitutive active form of ß catenin expressing GFP+ cells or ßcatCA unexpressing GFP cells from ß catCA mosaically introduced zebrafish early embryos were sorted by FACS cell sorter. Total RNAs were extracted and analyzed by RNA seq.		pubmed:39546611	Mosaic beta catCA GFP min lot2	GSM8042246	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		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.		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.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 1500	SRP486518		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		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		0.28434		0.95371		0.61551		36		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Japan	2024-01-29	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
30511	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/ß catenin signalling gradient which acts as a morphogen to establish embryonic anterior posterior patterning revealed that unfit cells with abnormal Wnt/ß 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/ß 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: ß catCA constitutive active form of ß catenin expressing GFP+ cells or ßcatCA unexpressing GFP cells from ß catCA mosaically introduced zebrafish early embryos were sorted by FACS cell sorter. Total RNAs were extracted and analyzed by RNA seq.		pubmed:39546611	Mosaic beta catCA GFP min lot1	GSM8042245	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		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.		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.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 1500	SRP486518		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		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		0.16823		0.84774		0.64548		36		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Japan	2024-01-29	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
33075	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: Fundaçåo para a Ciência e Tecnologia FCT Portugal		pubmed:38925414	Neutrophils mpx+ 8 xxx post injury AMD3100 biol rep 3	GSM8369980	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 28.5ºC 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 28.5ºC 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 28.5ºC 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		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP517033		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		122562825	62219285	75539895	86775172	65703	SRX25158199	SRS21848821	SRA1913211	Instituto de Medicina Molecular	Instituto de Medicina Molecular												B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Portugal	2024-06-29	Larval	Larval	Blood	Hematopoietic System
33076	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: Fundaçåo para a Ciência e Tecnologia FCT Portugal		pubmed:38925414	Neutrophils mpx+ 8 xxx post injury AMD3100 biol rep 3	GSM8369980	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 28.5ºC 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 28.5ºC 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 28.5ºC 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		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP517033		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		120149623	60854408	75192893	84703966	53370	SRX25158199	SRS21848821	SRA1913211	Instituto de Medicina Molecular	Instituto de Medicina Molecular												B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Portugal	2024-06-29	Larval	Larval	Blood	Hematopoietic System
33077	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: Fundaçåo para a Ciência e Tecnologia FCT Portugal		pubmed:38925414	Neutrophils mpx+ 8 xxx post injury AMD3100 biol rep 3	GSM8369980	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 28.5ºC 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 28.5ºC 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 28.5ºC 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		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP517033		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		124352905	63078724	76291828	87988386	37317	SRX25158199	SRS21848821	SRA1913211	Instituto de Medicina Molecular	Instituto de Medicina Molecular												B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Portugal	2024-06-29	Larval	Larval	Blood	Hematopoietic System
33078	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: Fundaçåo para a Ciência e Tecnologia FCT Portugal		pubmed:38925414	Neutrophils mpx+ 8 xxx post injury AMD3100 biol rep 3	GSM8369980	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 28.5ºC 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 28.5ºC 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 28.5ºC 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		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP517033		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		121803902	61651407	75900430	85843789	26192	SRX25158199	SRS21848821	SRA1913211	Instituto de Medicina Molecular	Instituto de Medicina Molecular												B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Portugal	2024-06-29	Larval	Larval	Blood	Hematopoietic System
33079	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: Fundaçåo para a Ciência e Tecnologia FCT Portugal		pubmed:38925414	Neutrophils mpx+ 8 xxx post injury AMD3100 biol rep 2	GSM8369979	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 28.5ºC 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 28.5ºC 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 28.5ºC 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		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP517033		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		55569742	28678683	33264744	41953354	31117	SRX25158198	SRS21848820	SRA1913211	Instituto de Medicina Molecular	Instituto de Medicina Molecular												B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Portugal	2024-06-29	Larval	Larval	Blood	Hematopoietic System
33080	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: Fundaçåo para a Ciência e Tecnologia FCT Portugal		pubmed:38925414	Neutrophils mpx+ 8 xxx post injury AMD3100 biol rep 2	GSM8369979	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 28.5ºC 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 28.5ºC 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 28.5ºC 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		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP517033		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		54428858	28027289	33149650	40918247	25196	SRX25158198	SRS21848820	SRA1913211	Instituto de Medicina Molecular	Instituto de Medicina Molecular												B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Portugal	2024-06-29	Larval	Larval	Blood	Hematopoietic System
33081	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: Fundaçåo para a Ciência e Tecnologia FCT Portugal		pubmed:38925414	Neutrophils mpx+ 8 xxx post injury AMD3100 biol rep 2	GSM8369979	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 28.5ºC 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 28.5ºC 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 28.5ºC 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		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP517033		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		56425187	29084972	33637112	42570603	17406	SRX25158198	SRS21848820	SRA1913211	Instituto de Medicina Molecular	Instituto de Medicina Molecular												B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Portugal	2024-06-29	Larval	Larval	Blood	Hematopoietic System
33082	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: Fundaçåo para a Ciência e Tecnologia FCT Portugal		pubmed:38925414	Neutrophils mpx+ 8 xxx post injury AMD3100 biol rep 2	GSM8369979	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 28.5ºC 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 28.5ºC 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 28.5ºC 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		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP517033		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		55213721	28430013	33462307	41503213	12266	SRX25158198	SRS21848820	SRA1913211	Instituto de Medicina Molecular	Instituto de Medicina Molecular												B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Portugal	2024-06-29	Larval	Larval	Blood	Hematopoietic System
33083	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: Fundaçåo para a Ciência e Tecnologia FCT Portugal		pubmed:38925414	Neutrophils mpx+ 8 xxx post injury AMD3100 biol rep 1	GSM8369978	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 28.5ºC 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 28.5ºC 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 28.5ºC 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		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP517033		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		17756825	7540147	9311367	9746444	8257	SRX25158197	SRS21848819	SRA1913211	Instituto de Medicina Molecular	Instituto de Medicina Molecular												B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Portugal	2024-06-29	Larval	Larval	Blood	Hematopoietic System
33084	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: Fundaçåo para a Ciência e Tecnologia FCT Portugal		pubmed:38925414	Neutrophils mpx+ 8 xxx post injury AMD3100 biol rep 1	GSM8369978	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 28.5ºC 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 28.5ºC 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 28.5ºC 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		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP517033		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		17376442	7355139	9244019	9468455	6745	SRX25158197	SRS21848819	SRA1913211	Instituto de Medicina Molecular	Instituto de Medicina Molecular												B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Portugal	2024-06-29	Larval	Larval	Blood	Hematopoietic System
33085	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: Fundaçåo para a Ciência e Tecnologia FCT Portugal		pubmed:38925414	Neutrophils mpx+ 8 xxx post injury AMD3100 biol rep 1	GSM8369978	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 28.5ºC 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 28.5ºC 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 28.5ºC 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		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP517033		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		17988707	7600964	9362568	9839285	4356	SRX25158197	SRS21848819	SRA1913211	Instituto de Medicina Molecular	Instituto de Medicina Molecular												B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Portugal	2024-06-29	Larval	Larval	Blood	Hematopoietic System
33086	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: Fundaçåo para a Ciência e Tecnologia FCT Portugal		pubmed:38925414	Neutrophils mpx+ 8 xxx post injury AMD3100 biol rep 1	GSM8369978	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 28.5ºC 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 28.5ºC 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 28.5ºC 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		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP517033		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		17608648	7492643	9327676	9628642	3331	SRX25158197	SRS21848819	SRA1913211	Instituto de Medicina Molecular	Instituto de Medicina Molecular												B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Portugal	2024-06-29	Larval	Larval	Blood	Hematopoietic System
33087	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: Fundaçåo para a Ciência e Tecnologia FCT Portugal		pubmed:38925414	Neutrophils mpx+ uninjured AMD3100 biol rep 3	GSM8369977	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 28.5ºC 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 28.5ºC 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 28.5ºC 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		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP517033		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		41373215	21759509	21832537	30061744	21135	SRX25158196	SRS21848818	SRA1913211	Instituto de Medicina Molecular	Instituto de Medicina Molecular												B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Portugal	2024-06-29	Larval	Larval	Blood	Hematopoietic System
33088	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: Fundaçåo para a Ciência e Tecnologia FCT Portugal		pubmed:38925414	Neutrophils mpx+ uninjured AMD3100 biol rep 3	GSM8369977	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 28.5ºC 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 28.5ºC 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 28.5ºC 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		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP517033		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		40482360	21287713	21750928	29306465	17594	SRX25158196	SRS21848818	SRA1913211	Instituto de Medicina Molecular	Instituto de Medicina Molecular												B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Portugal	2024-06-29	Larval	Larval	Blood	Hematopoietic System
33089	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: Fundaçåo para a Ciência e Tecnologia FCT Portugal		pubmed:38925414	Neutrophils mpx+ uninjured AMD3100 biol rep 3	GSM8369977	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 28.5ºC 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 28.5ºC 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 28.5ºC 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		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP517033		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		42022776	22106040	22075778	30479513	12473	SRX25158196	SRS21848818	SRA1913211	Instituto de Medicina Molecular	Instituto de Medicina Molecular												B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Portugal	2024-06-29	Larval	Larval	Blood	Hematopoietic System
33090	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: Fundaçåo para a Ciência e Tecnologia FCT Portugal		pubmed:38925414	Neutrophils mpx+ uninjured AMD3100 biol rep 3	GSM8369977	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 28.5ºC 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 28.5ºC 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 28.5ºC 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		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP517033		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		41132105	21578779	21934073	29681512	8511	SRX25158196	SRS21848818	SRA1913211	Instituto de Medicina Molecular	Instituto de Medicina Molecular												B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Portugal	2024-06-29	Larval	Larval	Blood	Hematopoietic System
33091	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: Fundaçåo para a Ciência e Tecnologia FCT Portugal		pubmed:38925414	Neutrophils mpx+ uninjured AMD3100 biol rep 2	GSM8369976	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 28.5ºC 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 28.5ºC 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 28.5ºC 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		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP517033		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		124800871	65627966	72434440	91152029	70074	SRX25158195	SRS21848817	SRA1913211	Instituto de Medicina Molecular	Instituto de Medicina Molecular												B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Portugal	2024-06-29	Larval	Larval	Blood	Hematopoietic System
33092	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: Fundaçåo para a Ciência e Tecnologia FCT Portugal		pubmed:38925414	Neutrophils mpx+ uninjured AMD3100 biol rep 2	GSM8369976	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 28.5ºC 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 28.5ºC 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 28.5ºC 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		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP517033		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		122147080	64042522	72135325	88869927	55506	SRX25158195	SRS21848817	SRA1913211	Instituto de Medicina Molecular	Instituto de Medicina Molecular												B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Portugal	2024-06-29	Larval	Larval	Blood	Hematopoietic System
33093	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: Fundaçåo para a Ciência e Tecnologia FCT Portugal		pubmed:38925414	Neutrophils mpx+ uninjured AMD3100 biol rep 2	GSM8369976	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 28.5ºC 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 28.5ºC 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 28.5ºC 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		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP517033		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		126636264	66527902	73214426	92445348	38640	SRX25158195	SRS21848817	SRA1913211	Instituto de Medicina Molecular	Instituto de Medicina Molecular												B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Portugal	2024-06-29	Larval	Larval	Blood	Hematopoietic System
33094	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: Fundaçåo para a Ciência e Tecnologia FCT Portugal		pubmed:38925414	Neutrophils mpx+ uninjured AMD3100 biol rep 2	GSM8369976	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 28.5ºC 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 28.5ºC 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 28.5ºC 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		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP517033		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		123921807	64956560	72828989	90107944	27820	SRX25158195	SRS21848817	SRA1913211	Instituto de Medicina Molecular	Instituto de Medicina Molecular												B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Portugal	2024-06-29	Larval	Larval	Blood	Hematopoietic System
33095	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: Fundaçåo para a Ciência e Tecnologia FCT Portugal		pubmed:38925414	Neutrophils mpx+ uninjured AMD3100 biol rep 1	GSM8369975	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 28.5ºC 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 28.5ºC 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 28.5ºC 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		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP517033		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		37215898	18610797	18111317	26774380	19988	SRX25158194	SRS21848816	SRA1913211	Instituto de Medicina Molecular	Instituto de Medicina Molecular												B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Portugal	2024-06-29	Larval	Larval	Blood	Hematopoietic System
33096	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: Fundaçåo para a Ciência e Tecnologia FCT Portugal		pubmed:38925414	Neutrophils mpx+ uninjured AMD3100 biol rep 1	GSM8369975	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 28.5ºC 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 28.5ºC 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 28.5ºC 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		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP517033		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		36388012	18195984	18122717	26108692	15455	SRX25158194	SRS21848816	SRA1913211	Instituto de Medicina Molecular	Instituto de Medicina Molecular												B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Portugal	2024-06-29	Larval	Larval	Blood	Hematopoietic System
33097	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: Fundaçåo para a Ciência e Tecnologia FCT Portugal		pubmed:38925414	Neutrophils mpx+ uninjured AMD3100 biol rep 1	GSM8369975	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 28.5ºC 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 28.5ºC 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 28.5ºC 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		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP517033		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		37811843	18928051	18347174	27179477	11015	SRX25158194	SRS21848816	SRA1913211	Instituto de Medicina Molecular	Instituto de Medicina Molecular												B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Portugal	2024-06-29	Larval	Larval	Blood	Hematopoietic System
33098	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: Fundaçåo para a Ciência e Tecnologia FCT Portugal		pubmed:38925414	Neutrophils mpx+ uninjured AMD3100 biol rep 1	GSM8369975	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 28.5ºC 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 28.5ºC 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 28.5ºC 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		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP517033		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		37032383	18500721	18308236	26522753	7747	SRX25158194	SRS21848816	SRA1913211	Instituto de Medicina Molecular	Instituto de Medicina Molecular												B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Portugal	2024-06-29	Larval	Larval	Blood	Hematopoietic System
33099	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: Fundaçåo para a Ciência e Tecnologia FCT Portugal		pubmed:38925414	Neutrophils mpx+ 8 xxx post injury DMSO biol rep 3	GSM8369974	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 28.5ºC 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 28.5ºC 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 28.5ºC 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		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP517033		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		58227035	29120167	33153372	41186362	30584	SRX25158193	SRS21848815	SRA1913211	Instituto de Medicina Molecular	Instituto de Medicina Molecular												B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Portugal	2024-06-29	Larval	Larval	Blood	Hematopoietic System
33100	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: Fundaçåo para a Ciência e Tecnologia FCT Portugal		pubmed:38925414	Neutrophils mpx+ 8 xxx post injury DMSO biol rep 3	GSM8369974	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 28.5ºC 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 28.5ºC 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 28.5ºC 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		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP517033		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		57059029	28475827	33090143	40160441	25020	SRX25158193	SRS21848815	SRA1913211	Instituto de Medicina Molecular	Instituto de Medicina Molecular												B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Portugal	2024-06-29	Larval	Larval	Blood	Hematopoietic System
33101	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: Fundaçåo para a Ciência e Tecnologia FCT Portugal		pubmed:38925414	Neutrophils mpx+ 8 xxx post injury DMSO biol rep 3	GSM8369974	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 28.5ºC 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 28.5ºC 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 28.5ºC 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		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP517033		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		59164760	29564845	33567677	41822336	16982	SRX25158193	SRS21848815	SRA1913211	Instituto de Medicina Molecular	Instituto de Medicina Molecular												B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Portugal	2024-06-29	Larval	Larval	Blood	Hematopoietic System
33102	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: Fundaçåo para a Ciência e Tecnologia FCT Portugal		pubmed:38925414	Neutrophils mpx+ 8 xxx post injury DMSO biol rep 3	GSM8369974	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 28.5ºC 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 28.5ºC 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 28.5ºC 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		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP517033		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		57905646	28872433	33402085	40746636	12940	SRX25158193	SRS21848815	SRA1913211	Instituto de Medicina Molecular	Instituto de Medicina Molecular												B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Portugal	2024-06-29	Larval	Larval	Blood	Hematopoietic System
33103	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: Fundaçåo para a Ciência e Tecnologia FCT Portugal		pubmed:38925414	Neutrophils mpx+ 8 xxx post injury DMSO biol rep 2	GSM8369973	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 28.5ºC 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 28.5ºC 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 28.5ºC 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		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP517033		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		113302890	53832811	54274745	73429183	57131	SRX25158192	SRS21848814	SRA1913211	Instituto de Medicina Molecular	Instituto de Medicina Molecular												B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Portugal	2024-06-29	Larval	Larval	Blood	Hematopoietic System
33104	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: Fundaçåo para a Ciência e Tecnologia FCT Portugal		pubmed:38925414	Neutrophils mpx+ 8 xxx post injury DMSO biol rep 2	GSM8369973	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 28.5ºC 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 28.5ºC 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 28.5ºC 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		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP517033		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		111138289	52646716	54190664	71637241	45910	SRX25158192	SRS21848814	SRA1913211	Instituto de Medicina Molecular	Instituto de Medicina Molecular												B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Portugal	2024-06-29	Larval	Larval	Blood	Hematopoietic System
33105	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: Fundaçåo para a Ciência e Tecnologia FCT Portugal		pubmed:38925414	Neutrophils mpx+ 8 xxx post injury DMSO biol rep 2	GSM8369973	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 28.5ºC 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 28.5ºC 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 28.5ºC 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		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP517033		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		115247052	54662821	54854607	74494831	31489	SRX25158192	SRS21848814	SRA1913211	Instituto de Medicina Molecular	Instituto de Medicina Molecular												B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Portugal	2024-06-29	Larval	Larval	Blood	Hematopoietic System
33106	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: Fundaçåo para a Ciência e Tecnologia FCT Portugal		pubmed:38925414	Neutrophils mpx+ 8 xxx post injury DMSO biol rep 2	GSM8369973	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 28.5ºC 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 28.5ºC 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 28.5ºC 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		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP517033		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		113032051	53520496	54754695	72762244	22434	SRX25158192	SRS21848814	SRA1913211	Instituto de Medicina Molecular	Instituto de Medicina Molecular												B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Portugal	2024-06-29	Larval	Larval	Blood	Hematopoietic System
33107	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: Fundaçåo para a Ciência e Tecnologia FCT Portugal		pubmed:38925414	Neutrophils mpx+ 8 xxx post injury DMSO biol rep 1	GSM8369972	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 28.5ºC 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 28.5ºC 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 28.5ºC 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		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP517033		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		29052800	15106261	15344010	20023888	15641	SRX25158191	SRS21848813	SRA1913211	Instituto de Medicina Molecular	Instituto de Medicina Molecular												B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Portugal	2024-06-29	Larval	Larval	Blood	Hematopoietic System
33108	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: Fundaçåo para a Ciência e Tecnologia FCT Portugal		pubmed:38925414	Neutrophils mpx+ 8 xxx post injury DMSO biol rep 1	GSM8369972	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 28.5ºC 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 28.5ºC 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 28.5ºC 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		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP517033		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		28490299	14795977	15298357	19554765	11442	SRX25158191	SRS21848813	SRA1913211	Instituto de Medicina Molecular	Instituto de Medicina Molecular												B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Portugal	2024-06-29	Larval	Larval	Blood	Hematopoietic System
33109	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: Fundaçåo para a Ciência e Tecnologia FCT Portugal		pubmed:38925414	Neutrophils mpx+ 8 xxx post injury DMSO biol rep 1	GSM8369972	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 28.5ºC 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 28.5ºC 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 28.5ºC 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		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP517033		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		29548150	15350378	15486892	20325654	8066	SRX25158191	SRS21848813	SRA1913211	Instituto de Medicina Molecular	Instituto de Medicina Molecular												B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Portugal	2024-06-29	Larval	Larval	Blood	Hematopoietic System
33110	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: Fundaçåo para a Ciência e Tecnologia FCT Portugal		pubmed:38925414	Neutrophils mpx+ 8 xxx post injury DMSO biol rep 1	GSM8369972	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 28.5ºC 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 28.5ºC 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 28.5ºC 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		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP517033		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		28874779	14986197	15407453	19795922	6409	SRX25158191	SRS21848813	SRA1913211	Instituto de Medicina Molecular	Instituto de Medicina Molecular												B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Portugal	2024-06-29	Larval	Larval	Blood	Hematopoietic System
33111	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: Fundaçåo para a Ciência e Tecnologia FCT Portugal		pubmed:38925414	Neutrophils mpx+ uninjured DMSO biol rep 3	GSM8369971	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 28.5ºC 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 28.5ºC 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 28.5ºC 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		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP517033		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		65842196	33929963	37226765	45358269	34407	SRX25158190	SRS21848812	SRA1913211	Instituto de Medicina Molecular	Instituto de Medicina Molecular												B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Portugal	2024-06-29	Larval	Larval	Blood	Hematopoietic System
33112	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: Fundaçåo para a Ciência e Tecnologia FCT Portugal		pubmed:38925414	Neutrophils mpx+ uninjured DMSO biol rep 3	GSM8369971	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 28.5ºC 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 28.5ºC 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 28.5ºC 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		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP517033		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		64544585	33163305	37078756	44266486	28508	SRX25158190	SRS21848812	SRA1913211	Instituto de Medicina Molecular	Instituto de Medicina Molecular												B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Portugal	2024-06-29	Larval	Larval	Blood	Hematopoietic System
33113	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: Fundaçåo para a Ciência e Tecnologia FCT Portugal		pubmed:38925414	Neutrophils mpx+ uninjured DMSO biol rep 3	GSM8369971	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 28.5ºC 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 28.5ºC 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 28.5ºC 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		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP517033		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		66919946	34450944	37652300	46025841	19709	SRX25158190	SRS21848812	SRA1913211	Instituto de Medicina Molecular	Instituto de Medicina Molecular												B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Portugal	2024-06-29	Larval	Larval	Blood	Hematopoietic System
33114	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: Fundaçåo para a Ciência e Tecnologia FCT Portugal		pubmed:38925414	Neutrophils mpx+ uninjured DMSO biol rep 3	GSM8369971	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 28.5ºC 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 28.5ºC 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 28.5ºC 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		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP517033		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		65513514	33675079	37432606	44872485	14056	SRX25158190	SRS21848812	SRA1913211	Instituto de Medicina Molecular	Instituto de Medicina Molecular												B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Portugal	2024-06-29	Larval	Larval	Blood	Hematopoietic System
33115	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: Fundaçåo para a Ciência e Tecnologia FCT Portugal		pubmed:38925414	Neutrophils mpx+ uninjured DMSO biol rep 2	GSM8369970	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 28.5ºC 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 28.5ºC 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 28.5ºC 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		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP517033		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		16928569	8492491	9006326	11358172	9202	SRX25158189	SRS21848811	SRA1913211	Instituto de Medicina Molecular	Instituto de Medicina Molecular												B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Portugal	2024-06-29	Larval	Larval	Blood	Hematopoietic System
33116	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: Fundaçåo para a Ciência e Tecnologia FCT Portugal		pubmed:38925414	Neutrophils mpx+ uninjured DMSO biol rep 2	GSM8369970	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 28.5ºC 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 28.5ºC 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 28.5ºC 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		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP517033		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		16608407	8309766	8990622	11094414	6751	SRX25158189	SRS21848811	SRA1913211	Instituto de Medicina Molecular	Instituto de Medicina Molecular												B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Portugal	2024-06-29	Larval	Larval	Blood	Hematopoietic System
33117	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: Fundaçåo para a Ciência e Tecnologia FCT Portugal		pubmed:38925414	Neutrophils mpx+ uninjured DMSO biol rep 2	GSM8369970	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 28.5ºC 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 28.5ºC 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 28.5ºC 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		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP517033		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		17217451	8640544	9146095	11557146	4644	SRX25158189	SRS21848811	SRA1913211	Instituto de Medicina Molecular	Instituto de Medicina Molecular												B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Portugal	2024-06-29	Larval	Larval	Blood	Hematopoietic System
33118	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: Fundaçåo para a Ciência e Tecnologia FCT Portugal		pubmed:38925414	Neutrophils mpx+ uninjured DMSO biol rep 2	GSM8369970	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 28.5ºC 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 28.5ºC 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 28.5ºC 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		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP517033		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		16852187	8431444	9090234	11246907	3888	SRX25158189	SRS21848811	SRA1913211	Instituto de Medicina Molecular	Instituto de Medicina Molecular												B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Portugal	2024-06-29	Larval	Larval	Blood	Hematopoietic System
33119	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: Fundaçåo para a Ciência e Tecnologia FCT Portugal		pubmed:38925414	Neutrophils mpx+ uninjured DMSO biol rep 1	GSM8369969	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 28.5ºC 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 28.5ºC 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 28.5ºC 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		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP517033		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		20680346	10254613	10895370	14026951	10100	SRX25158188	SRS21848810	SRA1913211	Instituto de Medicina Molecular	Instituto de Medicina Molecular												B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Portugal	2024-06-29	Larval	Larval	Blood	Hematopoietic System
33120	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: Fundaçåo para a Ciência e Tecnologia FCT Portugal		pubmed:38925414	Neutrophils mpx+ uninjured DMSO biol rep 1	GSM8369969	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 28.5ºC 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 28.5ºC 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 28.5ºC 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		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP517033		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		20264110	10026239	10861715	13728039	8977	SRX25158188	SRS21848810	SRA1913211	Instituto de Medicina Molecular	Instituto de Medicina Molecular												B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Portugal	2024-06-29	Larval	Larval	Blood	Hematopoietic System
33121	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: Fundaçåo para a Ciência e Tecnologia FCT Portugal		pubmed:38925414	Neutrophils mpx+ uninjured DMSO biol rep 1	GSM8369969	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 28.5ºC 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 28.5ºC 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 28.5ºC 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		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP517033		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		21036899	10416984	11027830	14275499	7228	SRX25158188	SRS21848810	SRA1913211	Instituto de Medicina Molecular	Instituto de Medicina Molecular												B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Portugal	2024-06-29	Larval	Larval	Blood	Hematopoietic System
33122	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: Fundaçåo para a Ciência e Tecnologia FCT Portugal		pubmed:38925414	Neutrophils mpx+ uninjured DMSO biol rep 1	GSM8369969	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 28.5ºC 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 28.5ºC 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 28.5ºC 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		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP517033		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		20538193	10150017	10949669	13888674	4527	SRX25158188	SRS21848810	SRA1913211	Instituto de Medicina Molecular	Instituto de Medicina Molecular												B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Portugal	2024-06-29	Larval	Larval	Blood	Hematopoietic System
38073	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.		pubmed:25417113	18 somites stage straightened secti1d tail to head	GSM1448820	tissue:deyolked embryo head removed\|Stage:18 somites\|sectioning direction:tail to head\|section thickness:24 µm\|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		Stage:18 somites\|sectioning direction:tail to head\|section thickness:24 µm\|embedding strategy:deyolked and straightened embryo	GSM1448820	GSM1448820: 18 somites stage straightened secti1d tail to head; Danio rerio; RNA Seq	GSM1448820		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	SRP045064		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	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	Netherlands	2014-07-29	Segmentation	Embryo	Embryo Imprecise	All anatomical structures
38074	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.		pubmed:25417113	15 somites stage straightened secti1d tail to head replicate	GSM1448819	tissue:deyolked embryo\|Stage:15 somites\|sectioning direction:tail to head\|section thickness:18 µm\|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		Stage:15 somites\|sectioning direction:tail to head\|section thickness:18 µm\|embedding strategy:deyolked and straightened embryo	GSM1448819	GSM1448819: 15 somites stage straightened secti1d tail to head replicate; Danio rerio; RNA Seq	GSM1448819		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	SRP045064		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	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	Netherlands	2014-07-29	Segmentation	Embryo	Embryo Imprecise	All anatomical structures
38075	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.		pubmed:25417113	sections 97 108 for samples dr 15ss TH and dr 15ss HT	GSM1448818	tissue:deyolked embryo\|Stage:15 somites\|sectioning direction:head to tail and tail to head\|section thickness:18 µm\|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		Stage:15 somites\|sectioning direction:head to tail and tail to head\|section thickness:18 µm\|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		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	SRP045064		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	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	Netherlands	2014-07-29	Segmentation	Embryo	Embryo Imprecise	All anatomical structures
38076	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.		pubmed:25417113	15 somites stage straightened secti1d tail to head	GSM1448817	tissue:deyolked embryo\|Stage:15 somites\|sectioning direction:tail to head\|section thickness:18 µm\|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		Stage:15 somites\|sectioning direction:tail to head\|section thickness:18 µm\|embedding strategy:deyolked and straightened embryo	GSM1448817	GSM1448817: 15 somites stage straightened secti1d tail to head; Danio rerio; RNA Seq	GSM1448817		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	SRP045064		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	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	Netherlands	2014-07-29	Segmentation	Embryo	Embryo Imprecise	All anatomical structures
38077	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.		pubmed:25417113	15 somites stage straightened secti1d head to tail	GSM1448816	tissue:deyolked embryo\|Stage:15 somites\|sectioning direction:head to tail\|section thickness:18 µm\|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		Stage:15 somites\|sectioning direction:head to tail\|section thickness:18 µm\|embedding strategy:deyolked and straightened embryo	GSM1448816	GSM1448816: 15 somites stage straightened secti1d head to tail; Danio rerio; RNA Seq	GSM1448816		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	SRP045064		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	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	Netherlands	2014-07-29	Segmentation	Embryo	Embryo Imprecise	All anatomical structures
38078	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.		pubmed:25417113	15 somite stage secti1d from right to left	GSM1448815	tissue:whole embryo\|Stage:15 somites\|sectioning direction:right left\|section thickness:18 µm\|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		Stage:15 somites\|sectioning direction:right left\|section thickness:18 µm\|embedding strategy:intact embryo	GSM1448815	GSM1448815: 15 somite stage secti1d from right to left; Danio rerio; RNA Seq	GSM1448815		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	SRP045064		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	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	Netherlands	2014-07-29	Segmentation	Embryo	Whole Organism	All anatomical structures
38079	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.		pubmed:25417113	15 somite stage secti1d from right to left	GSM1448815	tissue:whole embryo\|Stage:15 somites\|sectioning direction:right left\|section thickness:18 µm\|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		Stage:15 somites\|sectioning direction:right left\|section thickness:18 µm\|embedding strategy:intact embryo	GSM1448815	GSM1448815: 15 somite stage secti1d from right to left; Danio rerio; RNA Seq	GSM1448815		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	SRP045064	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	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	Netherlands	2014-07-29	Segmentation	Embryo	Whole Organism	All anatomical structures
38080	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.		pubmed:25417113	15 somite stage secti1d from left to right	GSM1448814	tissue:whole embryo\|Stage:15 somites\|sectioning direction:left right\|section thickness:18 µm\|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		Stage:15 somites\|sectioning direction:left right\|section thickness:18 µm\|embedding strategy:intact embryo	GSM1448814	GSM1448814: 15 somite stage secti1d from left to right; Danio rerio; RNA Seq	GSM1448814		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	SRP045064		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	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	Netherlands	2014-07-29	Segmentation	Embryo	Whole Organism	All anatomical structures
38081	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.		pubmed:25417113	15 somite stage secti1d from left to right	GSM1448814	tissue:whole embryo\|Stage:15 somites\|sectioning direction:left right\|section thickness:18 µm\|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		Stage:15 somites\|sectioning direction:left right\|section thickness:18 µm\|embedding strategy:intact embryo	GSM1448814	GSM1448814: 15 somite stage secti1d from left to right; Danio rerio; RNA Seq	GSM1448814		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	SRP045064	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	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	Netherlands	2014-07-29	Segmentation	Embryo	Whole Organism	All anatomical structures
38082	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.		pubmed:25417113	15 somite stage secti1d from dorsal to ventral end	GSM1448813	tissue:whole embryo\|Stage:15 somites\|sectioning direction:dorsal ventral\|section thickness:18 µm\|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		Stage:15 somites\|sectioning direction:dorsal ventral\|section thickness:18 µm\|embedding strategy:intact embryo	GSM1448813	GSM1448813: 15 somite stage secti1d from dorsal to ventral end; Danio rerio; RNA Seq	GSM1448813		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	SRP045064		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	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	Netherlands	2014-07-29	Segmentation	Embryo	Whole Organism	All anatomical structures
38083	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.		pubmed:25417113	15 somite stage secti1d from dorsal to ventral end	GSM1448813	tissue:whole embryo\|Stage:15 somites\|sectioning direction:dorsal ventral\|section thickness:18 µm\|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		Stage:15 somites\|sectioning direction:dorsal ventral\|section thickness:18 µm\|embedding strategy:intact embryo	GSM1448813	GSM1448813: 15 somite stage secti1d from dorsal to ventral end; Danio rerio; RNA Seq	GSM1448813		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	SRP045064	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	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	Netherlands	2014-07-29	Segmentation	Embryo	Whole Organism	All anatomical structures
38084	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.		pubmed:25417113	15 somite stage secti1d from ventral to dorsal end	GSM1448812	tissue:whole embryo\|Stage:15 somites\|sectioning direction:ventral dorsal\|section thickness:18 µm\|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		Stage:15 somites\|sectioning direction:ventral dorsal\|section thickness:18 µm\|embedding strategy:intact embryo	GSM1448812	GSM1448812: 15 somite stage secti1d from ventral to dorsal end; Danio rerio; RNA Seq	GSM1448812		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	SRP045064		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	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	Netherlands	2014-07-29	Segmentation	Embryo	Whole Organism	All anatomical structures
38085	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.		pubmed:25417113	15 somite stage secti1d from ventral to dorsal end	GSM1448812	tissue:whole embryo\|Stage:15 somites\|sectioning direction:ventral dorsal\|section thickness:18 µm\|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		Stage:15 somites\|sectioning direction:ventral dorsal\|section thickness:18 µm\|embedding strategy:intact embryo	GSM1448812	GSM1448812: 15 somite stage secti1d from ventral to dorsal end; Danio rerio; RNA Seq	GSM1448812		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	SRP045064	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	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	Netherlands	2014-07-29	Segmentation	Embryo	Whole Organism	All anatomical structures
38086	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.		pubmed:25417113	15 somite stage secti1d from posterior to anterior end	GSM1448811	tissue:whole embryo\|Stage:15 somites\|sectioning direction:posterior anterior\|section thickness:18 µm\|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		Stage:15 somites\|sectioning direction:posterior anterior\|section thickness:18 µm\|embedding strategy:intact embryo	GSM1448811	GSM1448811: 15 somite stage secti1d from posterior to anterior end; Danio rerio; RNA Seq	GSM1448811		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	SRP045064		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	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	Netherlands	2014-07-29	Segmentation	Embryo	Whole Organism	All anatomical structures
38087	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.		pubmed:25417113	15 somite stage secti1d from anterior to posterior end	GSM1448810	tissue:whole embryo\|Stage:15 somites\|sectioning direction:anterior posterior\|section thickness:18 µm\|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		Stage:15 somites\|sectioning direction:anterior posterior\|section thickness:18 µm\|embedding strategy:intact embryo	GSM1448810	GSM1448810: 15 somite stage secti1d from anterior to posterior end; Danio rerio; RNA Seq	GSM1448810		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	SRP045064		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	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	Netherlands	2014-07-29	Segmentation	Embryo	Whole Organism	All anatomical structures
38088	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.		pubmed:25417113	10 somite stage secti1d from right to left	GSM1448809	tissue:whole embryo\|Stage:10 somites\|sectioning direction:right left\|section thickness:18 µm\|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		Stage:10 somites\|sectioning direction:right left\|section thickness:18 µm\|embedding strategy:intact embryo	GSM1448809	GSM1448809: 10 somite stage secti1d from right to left; Danio rerio; RNA Seq	GSM1448809		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	SRP045064		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	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	Netherlands	2014-07-29	Segmentation	Embryo	Whole Organism	All anatomical structures
38089	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.		pubmed:25417113	10 somite stage secti1d from left to right	GSM1448808	tissue:whole embryo\|Stage:10 somites\|sectioning direction:left right\|section thickness:18 µm\|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		Stage:10 somites\|sectioning direction:left right\|section thickness:18 µm\|embedding strategy:intact embryo	GSM1448808	GSM1448808: 10 somite stage secti1d from left to right; Danio rerio; RNA Seq	GSM1448808		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	SRP045064		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	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	Netherlands	2014-07-29	Segmentation	Embryo	Whole Organism	All anatomical structures
38090	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.		pubmed:25417113	10 somite stage secti1d from dorsal to ventral end	GSM1448807	tissue:whole embryo\|Stage:10 somites\|sectioning direction:dorsal ventral\|section thickness:18 µm\|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		Stage:10 somites\|sectioning direction:dorsal ventral\|section thickness:18 µm\|embedding strategy:intact embryo	GSM1448807	GSM1448807: 10 somite stage secti1d from dorsal to ventral end; Danio rerio; RNA Seq	GSM1448807		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	SRP045064		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	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	Netherlands	2014-07-29	Segmentation	Embryo	Whole Organism	All anatomical structures
38091	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.		pubmed:25417113	10 somite stage secti1d from dorsal to ventral end	GSM1448807	tissue:whole embryo\|Stage:10 somites\|sectioning direction:dorsal ventral\|section thickness:18 µm\|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		Stage:10 somites\|sectioning direction:dorsal ventral\|section thickness:18 µm\|embedding strategy:intact embryo	GSM1448807	GSM1448807: 10 somite stage secti1d from dorsal to ventral end; Danio rerio; RNA Seq	GSM1448807		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	SRP045064	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	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	Netherlands	2014-07-29	Segmentation	Embryo	Whole Organism	All anatomical structures
38092	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.		pubmed:25417113	10 somite stage secti1d from ventral to dorsal end	GSM1448806	tissue:whole embryo\|Stage:10 somites\|sectioning direction:ventral dorsal\|section thickness:18 µm\|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		Stage:10 somites\|sectioning direction:ventral dorsal\|section thickness:18 µm\|embedding strategy:intact embryo	GSM1448806	GSM1448806: 10 somite stage secti1d from ventral to dorsal end; Danio rerio; RNA Seq	GSM1448806		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	SRP045064		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	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	Netherlands	2014-07-29	Segmentation	Embryo	Whole Organism	All anatomical structures
38093	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.		pubmed:25417113	10 somite stage secti1d from ventral to dorsal end	GSM1448806	tissue:whole embryo\|Stage:10 somites\|sectioning direction:ventral dorsal\|section thickness:18 µm\|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		Stage:10 somites\|sectioning direction:ventral dorsal\|section thickness:18 µm\|embedding strategy:intact embryo	GSM1448806	GSM1448806: 10 somite stage secti1d from ventral to dorsal end; Danio rerio; RNA Seq	GSM1448806		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	SRP045064	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	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	Netherlands	2014-07-29	Segmentation	Embryo	Whole Organism	All anatomical structures
38094	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.		pubmed:25417113	10 somite stage secti1d from posterior to anterior end	GSM1448805	tissue:whole embryo\|Stage:10 somites\|sectioning direction:anterior posterior\|section thickness:18 µm\|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		Stage:10 somites\|sectioning direction:anterior posterior\|section thickness:18 µm\|embedding strategy:intact embryo	GSM1448805	GSM1448805: 10 somite stage secti1d from posterior to anterior end; Danio rerio; RNA Seq	GSM1448805		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	SRP045064		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	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	Netherlands	2014-07-29	Segmentation	Embryo	Whole Organism	All anatomical structures
38095	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.		pubmed:25417113	10 somite stage secti1d from posterior to anterior end	GSM1448805	tissue:whole embryo\|Stage:10 somites\|sectioning direction:anterior posterior\|section thickness:18 µm\|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		Stage:10 somites\|sectioning direction:anterior posterior\|section thickness:18 µm\|embedding strategy:intact embryo	GSM1448805	GSM1448805: 10 somite stage secti1d from posterior to anterior end; Danio rerio; RNA Seq	GSM1448805		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	SRP045064	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	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	Netherlands	2014-07-29	Segmentation	Embryo	Whole Organism	All anatomical structures
38096	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.		pubmed:25417113	10 somite stage secti1d from anterior to posterior end replicate	GSM1448804	tissue:whole embryo\|Stage:10 somites\|sectioning direction:anterior posterior\|section thickness:18 µm\|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		Stage:10 somites\|sectioning direction:anterior posterior\|section thickness:18 µm\|embedding strategy:intact embryo	GSM1448804	GSM1448804: 10 somite stage secti1d from anterior to posterior end replicate; Danio rerio; RNA Seq	GSM1448804		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	SRP045064		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	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	Netherlands	2014-07-29	Segmentation	Embryo	Whole Organism	All anatomical structures
38097	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.		pubmed:25417113	10 somite stage secti1d from anterior to posterior end	GSM1448803	tissue:whole embryo\|Stage:10 somites\|sectioning direction:anterior posterior\|section thickness:18 µm\|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		Stage:10 somites\|sectioning direction:anterior posterior\|section thickness:18 µm\|embedding strategy:intact embryo	GSM1448803	GSM1448803: 10 somite stage secti1d from anterior to posterior end; Danio rerio; RNA Seq	GSM1448803		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	SRP045064		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	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	Netherlands	2014-07-29	Segmentation	Embryo	Whole Organism	All anatomical structures
38098	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.		pubmed:25417113	10 somite stage secti1d from anterior to posterior end	GSM1448803	tissue:whole embryo\|Stage:10 somites\|sectioning direction:anterior posterior\|section thickness:18 µm\|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		Stage:10 somites\|sectioning direction:anterior posterior\|section thickness:18 µm\|embedding strategy:intact embryo	GSM1448803	GSM1448803: 10 somite stage secti1d from anterior to posterior end; Danio rerio; RNA Seq	GSM1448803		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	SRP045064	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	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	Netherlands	2014-07-29	Segmentation	Embryo	Whole Organism	All anatomical structures
38099	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.		pubmed:25417113	shield stage secti1d from dorsal to ventral end replicate	GSM1448802	tissue:whole embryo\|Stage:shield stage\|sectioning direction:dorsal ventral\|section thickness:18 µm\|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		Stage:shield stage\|sectioning direction:dorsal ventral\|section thickness:18 µm\|embedding strategy:intact embryo	GSM1448802	GSM1448802: shield stage secti1d from dorsal to ventral end replicate; Danio rerio; RNA Seq	GSM1448802		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	SRP045064		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	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	Netherlands	2014-07-29	Gastrula	Embryo	Whole Organism	All anatomical structures
38100	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.		pubmed:25417113	shield stage secti1d from dorsal to ventral end	GSM1448801	tissue:whole embryo\|Stage:shield stage\|sectioning direction:dorsal ventral\|section thickness:18 µm\|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		Stage:shield stage\|sectioning direction:dorsal ventral\|section thickness:18 µm\|embedding strategy:intact embryo	GSM1448801	GSM1448801: shield stage secti1d from dorsal to ventral end; Danio rerio; RNA Seq	GSM1448801		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	SRP045064		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	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	Netherlands	2014-07-29	Gastrula	Embryo	Whole Organism	All anatomical structures
38101	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.		pubmed:25417113	shield stage secti1d from dorsal to ventral end	GSM1448801	tissue:whole embryo\|Stage:shield stage\|sectioning direction:dorsal ventral\|section thickness:18 µm\|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		Stage:shield stage\|sectioning direction:dorsal ventral\|section thickness:18 µm\|embedding strategy:intact embryo	GSM1448801	GSM1448801: shield stage secti1d from dorsal to ventral end; Danio rerio; RNA Seq	GSM1448801		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	SRP045064	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	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	Netherlands	2014-07-29	Gastrula	Embryo	Whole Organism	All anatomical structures
38102	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.		pubmed:25417113	shield stage secti1d from ventral to dorsal end	GSM1448800	tissue:whole embryo\|Stage:shield stage\|sectioning direction:ventral dorsal\|section thickness:18 µm\|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		Stage:shield stage\|sectioning direction:ventral dorsal\|section thickness:18 µm\|embedding strategy:intact embryo	GSM1448800	GSM1448800: shield stage secti1d from ventral to dorsal end; Danio rerio; RNA Seq	GSM1448800		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	SRP045064		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	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	Netherlands	2014-07-29	Gastrula	Embryo	Whole Organism	All anatomical structures
38103	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.		pubmed:25417113	shield stage secti1d from ventral to dorsal end	GSM1448800	tissue:whole embryo\|Stage:shield stage\|sectioning direction:ventral dorsal\|section thickness:18 µm\|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		Stage:shield stage\|sectioning direction:ventral dorsal\|section thickness:18 µm\|embedding strategy:intact embryo	GSM1448800	GSM1448800: shield stage secti1d from ventral to dorsal end; Danio rerio; RNA Seq	GSM1448800		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	SRP045064	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										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	Netherlands	2014-07-29	Gastrula	Embryo	Whole Organism	All anatomical structures
38104	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.		pubmed:25417113	shield stage secti1d from right to left	GSM1448799	tissue:whole embryo\|Stage:shield stage\|sectioning direction:right left\|section thickness:18 µm\|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		Stage:shield stage\|sectioning direction:right left\|section thickness:18 µm\|embedding strategy:intact embryo	GSM1448799	GSM1448799: shield stage secti1d from right to left; Danio rerio; RNA Seq	GSM1448799		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	SRP045064		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	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	Netherlands	2014-07-29	Gastrula	Embryo	Whole Organism	All anatomical structures
38105	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.		pubmed:25417113	shield stage secti1d from right to left	GSM1448799	tissue:whole embryo\|Stage:shield stage\|sectioning direction:right left\|section thickness:18 µm\|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		Stage:shield stage\|sectioning direction:right left\|section thickness:18 µm\|embedding strategy:intact embryo	GSM1448799	GSM1448799: shield stage secti1d from right to left; Danio rerio; RNA Seq	GSM1448799		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	SRP045064	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	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	Netherlands	2014-07-29	Gastrula	Embryo	Whole Organism	All anatomical structures
38106	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.		pubmed:25417113	shield stage secti1d from left to right	GSM1448798	tissue:whole embryo\|Stage:shield stage\|sectioning direction:left right\|section thickness:18 µm\|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		Stage:shield stage\|sectioning direction:left right\|section thickness:18 µm\|embedding strategy:intact embryo	GSM1448798	GSM1448798: shield stage secti1d from left to right; Danio rerio; RNA Seq	GSM1448798		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	SRP045064		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	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	Netherlands	2014-07-29	Gastrula	Embryo	Whole Organism	All anatomical structures
38107	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.		pubmed:25417113	shield stage secti1d from left to right	GSM1448798	tissue:whole embryo\|Stage:shield stage\|sectioning direction:left right\|section thickness:18 µm\|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		Stage:shield stage\|sectioning direction:left right\|section thickness:18 µm\|embedding strategy:intact embryo	GSM1448798	GSM1448798: shield stage secti1d from left to right; Danio rerio; RNA Seq	GSM1448798		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	SRP045064	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	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	Netherlands	2014-07-29	Gastrula	Embryo	Whole Organism	All anatomical structures
38108	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.		pubmed:25417113	shield stage secti1d from vegetal to animal pole replicate	GSM1448797	tissue:whole embryo\|Stage:shield stage\|sectioning direction:vegetal animal\|section thickness:18 µm\|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		Stage:shield stage\|sectioning direction:vegetal animal\|section thickness:18 µm\|embedding strategy:intact embryo	GSM1448797	GSM1448797: shield stage secti1d from vegetal to animal pole replicate; Danio rerio; RNA Seq	GSM1448797		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	SRP045064		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	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	Netherlands	2014-07-29	Gastrula	Embryo	Whole Organism	All anatomical structures
38109	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.		pubmed:25417113	shield stage secti1d from vegetal to animal pole	GSM1448796	tissue:whole embryo\|Stage:shield stage\|sectioning direction:vegetal animal\|section thickness:18 µm\|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		Stage:shield stage\|sectioning direction:vegetal animal\|section thickness:18 µm\|embedding strategy:intact embryo	GSM1448796	GSM1448796: shield stage secti1d from vegetal to animal pole; Danio rerio; RNA Seq	GSM1448796		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	SRP045064		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	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	Netherlands	2014-07-29	Gastrula	Embryo	Whole Organism	All anatomical structures
38110	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.		pubmed:25417113	shield stage secti1d from vegetal to animal pole	GSM1448796	tissue:whole embryo\|Stage:shield stage\|sectioning direction:vegetal animal\|section thickness:18 µm\|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		Stage:shield stage\|sectioning direction:vegetal animal\|section thickness:18 µm\|embedding strategy:intact embryo	GSM1448796	GSM1448796: shield stage secti1d from vegetal to animal pole; Danio rerio; RNA Seq	GSM1448796		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	SRP045064	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	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	Netherlands	2014-07-29	Gastrula	Embryo	Whole Organism	All anatomical structures
38111	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.		pubmed:25417113	shield stage secti1d from animal to vegetal pole	GSM1448795	tissue:whole embryo\|Stage:shield stage\|sectioning direction:animal vegetal\|section thickness:18 µm\|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		Stage:shield stage\|sectioning direction:animal vegetal\|section thickness:18 µm\|embedding strategy:intact embryo	GSM1448795	GSM1448795: shield stage secti1d from animal to vegetal pole; Danio rerio; RNA Seq	GSM1448795		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	SRP045064		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	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	Netherlands	2014-07-29	Gastrula	Embryo	Whole Organism	All anatomical structures
38112	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.		pubmed:25417113	shield stage secti1d from animal to vegetal pole	GSM1448795	tissue:whole embryo\|Stage:shield stage\|sectioning direction:animal vegetal\|section thickness:18 µm\|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		Stage:shield stage\|sectioning direction:animal vegetal\|section thickness:18 µm\|embedding strategy:intact embryo	GSM1448795	GSM1448795: shield stage secti1d from animal to vegetal pole; Danio rerio; RNA Seq	GSM1448795		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	SRP045064	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	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	Netherlands	2014-07-29	Gastrula	Embryo	Whole Organism	All anatomical structures
38122	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 “phylotypic stage” 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 ‘zootypic’ 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	Metazome ZF timecourse sample 0106	GSM1483841	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		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		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	SRP045679		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		1100064	790487	836206	1169251	15697	SRX684706	SRS687823	SRA179995	GEO	Yanai, Biology, Technion - Israel Institute of Technology	1	0.72414		0.09461		0.96725		0.4942		35		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Israel	2014-08-21	Zygote	Embryo	Embryo Imprecise	All anatomical structures
38123	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 “phylotypic stage” 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 ‘zootypic’ 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	Metazome ZF timecourse sample 0105	GSM1483840	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		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		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	SRP045679		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		9524894	6625944	6696548	9953576	76183	SRX684705	SRS687821	SRA179995	GEO	Yanai, Biology, Technion - Israel Institute of Technology	1	0.74436		0.07095		0.88201		0.47612		35		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Israel	2014-08-21	Zygote	Embryo	Embryo Imprecise	All anatomical structures
38124	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 “phylotypic stage” 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 ‘zootypic’ 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	Metazome ZF timecourse sample 0104	GSM1483839	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		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		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	SRP045679		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		24075610	16799998	16694424	25967423	272565	SRX684704	SRS687822	SRA179995	GEO	Yanai, Biology, Technion - Israel Institute of Technology	1	0.7588		0.07993		0.84449		0.49785		35		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Israel	2014-08-21	Zygote	Embryo	Embryo Imprecise	All anatomical structures
38125	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 “phylotypic stage” 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 ‘zootypic’ 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	Metazome ZF timecourse sample 0103	GSM1483838	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		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		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	SRP045679		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		28361916	19232789	19589483	30798968	222994	SRX684703	SRS687820	SRA179995	GEO	Yanai, Biology, Technion - Israel Institute of Technology	1	0.75509		0.13429		0.81117		0.49102		35		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Israel	2014-08-21	Zygote	Embryo	Embryo Imprecise	All anatomical structures
38126	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 “phylotypic stage” 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 ‘zootypic’ 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	Metazome ZF timecourse sample 0102	GSM1483837	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		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		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	SRP045679		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		55969077	36880901	37835921	61101558	1030378	SRX684702	SRS687819	SRA179995	GEO	Yanai, Biology, Technion - Israel Institute of Technology	1	0.73387		0.17245		0.80164		0.48657		35		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Israel	2014-08-21	Zygote	Embryo	Embryo Imprecise	All anatomical structures
38127	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 “phylotypic stage” 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 ‘zootypic’ 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	Metazome ZF timecourse sample 0101	GSM1483836	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		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		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	SRP045679		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		112191846	73679996	73185024	114766825	515764	SRX684701	SRS687818	SRA179995	GEO	Yanai, Biology, Technion - Israel Institute of Technology	1	0.83131		0.16618		0.77812		0.49895		35		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Israel	2014-08-21	Zygote	Embryo	Embryo Imprecise	All anatomical structures
38128	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 “phylotypic stage” 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 ‘zootypic’ 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	Metazome ZF timecourse sample 0100	GSM1483835	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		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		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	SRP045679		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		4361241	3088134	3269084	4498093	22868	SRX684700	SRS687816	SRA179995	GEO	Yanai, Biology, Technion - Israel Institute of Technology	1	0.7702		0.17879		0.92904		0.505		35		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Israel	2014-08-21	Zygote	Embryo	Embryo Imprecise	All anatomical structures
38129	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 “phylotypic stage” 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 ‘zootypic’ 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	Metazome ZF timecourse sample 0099	GSM1483834	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		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		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	SRP045679		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		81991733	57440756	58362818	86010858	390335	SRX684699	SRS687817	SRA179995	GEO	Yanai, Biology, Technion - Israel Institute of Technology	1	0.81284		0.1715		0.78468		0.49472		35		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Israel	2014-08-21	Zygote	Embryo	Embryo Imprecise	All anatomical structures

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