metadata: run_metadata: 475 rows where technology = "smartseq" and tissue

475 rows where technology = "smartseq" and tissue_curation = "Tail"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	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.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.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
50632	50632	SRR8485426	SRX5021281	SRS4054046	SRP169118	PRJNA505837	Glucocorticoids inhibit macrophage differentiation towards a pro inflammatory phenotype upon wounding without xxx their migration	GSE122643	Transcriptome Analysis	Glucocorticoid drugs are widely used to treat immune related diseases but their use is limited by side effects and by resistance which especially occurs in macrophage dominated diseases. In order to improve glucocorticoid therapies more research is required into the mechanisms of glucocorticoid action. In the present study we have used a zebrafish model for inflammation to study glucocorticoid effects on the innate immune response. In zebrafish larvae the migration of neutrophils towards a site of injury is inhibited by the synthetic glucocorticoid beclomethasone while migration of macrophages is glucocorticoid resistant. RNA sequencing was done on on Fluorescence Activated Cell Sorting FACS sorted macrophages.The results show that the vast majority of the wounding induced transcriptional changes in these cells are inhibited by beclomethasone whereas a small subset is glucocorticoid insensitive. As a result beclomethasone decreases the number of macrophages that differentiate towards a pro inflammatory M1 phenotype which we demonstrated using a tnfa:eGFP F reporter line and analysis of macrophage morphology. We conclude that the glucocorticoid resistance of the wounding induced macrophage migration is due to the insensitivity of the induction of macrophage specific chemoattractants to glucocorticoid inhibition which may explain the relative resistance of macrophage dominated diseases to glucocorticoid therapy. However the induction of pro inflammatory genes in macrophages is strongly attenuated which inhibits their differentiation to an M1 phenotype. Overall design: post anesthesia with 0.02% aminobenzoic acid ethyl ester tricaine Sigma Aldrich the tails of 3 dpf dpf embryos were partially amputated with a 1mm sapphire blade World Precision Instruments on 2% agarose coated Petri dishes under a Leica M165C stereomicroscope Chatzopoulou et al. 2016. Amputated and non amputated control embryos were pretreated for 2 hours with 25 µM beclomethasone Sigma Aldrich or vehicle 0.05% dimethyl sulfoxide DMSO …	pubmed:31072958	control amputated rep3	GSM3477138	tissue:3dpf zebrafish embryo treated with vehicle tail amputated\|drug treatment:0.05% DMSO in egg water\|tail amputation:tail amputated\|developmental stage:3dpf	control amputated rep3	Image analysis and base calling were done by the Illumina HCS version 2.2.68 and RTA version 1.18.66. cDNA sequencing data were analyzed by mapping the reads to the Danio rerio GRCz10 reference genome with annotation version 80 using Tophat v2.1.0. The DESeq v1.26.0 R package was used to test for differential expression. Before each analysis the genes with low reads were removed i.e. those genes for which the sum of reads from three replicates of the analyzed two groups was lower than 30. The output data were used for transcriptome analysis. Genome build: RNAseq reads from individual samples were mapped against D. rerio GRCz10.80 Supplementary files format and content: tab separated values files include id and reads for each gene	3dpf zebrafish embryo treated with vehicle tail amputated	post anesthesia with 0.02% aminobenzoic acid ethyl ester tricaine Sigma Aldrich the tails of 3 dpf dpf embryos were partially amputated Figure 1A with a 1mm sapphire blade World Precision Instruments on 2% agarose coated Petri dishes under a Leica M165C stereomicroscope Chatzopoulou et al. 2016. Amputated and non amputated control embryos were pretreated for 2 hours with 25 μM beclomethasone Sigma Aldrich or vehicle 0.05% dimethyl sulfoxide DMSO in egg water prior to amputation and received the same treatment post the amputation.	Macrophages were sorted from Tgmpeg1.4:mCherry F embryos as previously described Rougeot et al. 2014; Zakrzewska et al. 2010. Dissociation was performed with 100 150 embryos for each sample at 4 hours post amputation hpa using Liberase TL Roche and stopped by adding Fetal Calf Serum FCS to a final concentration of 10%. Isolated cells were resuspended in Dulbecco’s PBS DPBS and filtered through a 40 μm cell strainer. Actinomycin D Sigma Aldrich was added final concentration of 1 µg/ml to each step to inhibit transcription. Macrophages were sorted based on their red fluorescent signal using a FACSAria III cell sorter BD Biosciences. The sorted cells were collected in QIAzol lysis reagent Qiagen for RNA isolation. Extracted total RNA was amplified using the SMART seq V4 kit Clontech for sequencing. The RNA seq libraries generated with the SMART seq V4 kit were sequenced using an Illumina HiSeq 2500 instrument according to the manufacturer’s instructions with a read length of 50 nucleotides	Zebrafish were maintained and handled according to the guidelines from the Zebrafish Model Organism Database http://zfin.org and in compliance with the directives of the local animal welfare committee of Leiden University. They were exposed to a 14 hours light and 10 hours dark cycle to maintain circadian rhythmicity. Fertilization was performed by natural spawning at the beginning of the light period. Eggs were collected and raised at 28°C in egg water 60 µg/ml Instant Ocean sea salts and 0.0025% methylene blue.	drug treatment:0.05% DMSO in egg water\|tail amputation:tail amputated\|developmental stage:3dpf	GSM3477138	GSM3477138: control amputated rep3; Danio rerio; RNA Seq	GSM3477138	1	Macrophages were sorted from Tgmpeg1.4:mCherry F embryos as previously described Rougeot et al. 2014; Zakrzewska et al. 2010. Dissociation was performed with 100 150 embryos for each sample at 4 hours post amputation hpa using Liberase TL Roche and stopped by adding Fetal Calf Serum FCS to a final concentration of 10%. Isolated cells were resuspended in Dulbeccoâ??s PBS DPBS and filtered through a 40 Î¼m cell strainer. Actinomycin D Sigma Aldrich was added final concentration of 1 Âµg/ml to each step to inhibit transcription. Macrophages were sorted based on their red fluorescent signal using a FACSAria III cell sorter BD Biosciences. The sorted cells were collected in QIAzol lysis reagent Qiagen for RNA isolation. Extracted total RNA was amplified using the SMART seq V4 kit Clontech for sequencing. The RNA seq libraries generated with the SMART seq V4 kit were sequenced using an Illumina HiSeq 2500 instrument according to the manufacturerâ??s instructions with a read length of 50 nucleotides	GEO Accession:GSM3477138	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP169118	ZFG-16-07_24_19304_GTGGCC_L001_R1_001.fastq.gz	fastq	316229886.0	6200586.0	GSM3477138 r11	0:51	A:82355299;C:77071091;G:75965728;T:80825106;N:12662	51		82355299	77071091	75965728	80825106	12662	SRX5021281	SRS4054046	SRA811328	GEO	Leiden University	1	0.94871		0.02989		0.73054		0.45203		51		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	Netherlands	2018-11-16	Larval	Larval	Tail	Multi-system
50633	50633	SRR8485427	SRX5021281	SRS4054046	SRP169118	PRJNA505837	Glucocorticoids inhibit macrophage differentiation towards a pro inflammatory phenotype upon wounding without xxx their migration	GSE122643	Transcriptome Analysis	Glucocorticoid drugs are widely used to treat immune related diseases but their use is limited by side effects and by resistance which especially occurs in macrophage dominated diseases. In order to improve glucocorticoid therapies more research is required into the mechanisms of glucocorticoid action. In the present study we have used a zebrafish model for inflammation to study glucocorticoid effects on the innate immune response. In zebrafish larvae the migration of neutrophils towards a site of injury is inhibited by the synthetic glucocorticoid beclomethasone while migration of macrophages is glucocorticoid resistant. RNA sequencing was done on on Fluorescence Activated Cell Sorting FACS sorted macrophages.The results show that the vast majority of the wounding induced transcriptional changes in these cells are inhibited by beclomethasone whereas a small subset is glucocorticoid insensitive. As a result beclomethasone decreases the number of macrophages that differentiate towards a pro inflammatory M1 phenotype which we demonstrated using a tnfa:eGFP F reporter line and analysis of macrophage morphology. We conclude that the glucocorticoid resistance of the wounding induced macrophage migration is due to the insensitivity of the induction of macrophage specific chemoattractants to glucocorticoid inhibition which may explain the relative resistance of macrophage dominated diseases to glucocorticoid therapy. However the induction of pro inflammatory genes in macrophages is strongly attenuated which inhibits their differentiation to an M1 phenotype. Overall design: post anesthesia with 0.02% aminobenzoic acid ethyl ester tricaine Sigma Aldrich the tails of 3 dpf dpf embryos were partially amputated with a 1mm sapphire blade World Precision Instruments on 2% agarose coated Petri dishes under a Leica M165C stereomicroscope Chatzopoulou et al. 2016. Amputated and non amputated control embryos were pretreated for 2 hours with 25 µM beclomethasone Sigma Aldrich or vehicle 0.05% dimethyl sulfoxide DMSO …	pubmed:31072958	control amputated rep3	GSM3477138	tissue:3dpf zebrafish embryo treated with vehicle tail amputated\|drug treatment:0.05% DMSO in egg water\|tail amputation:tail amputated\|developmental stage:3dpf	control amputated rep3	Image analysis and base calling were done by the Illumina HCS version 2.2.68 and RTA version 1.18.66. cDNA sequencing data were analyzed by mapping the reads to the Danio rerio GRCz10 reference genome with annotation version 80 using Tophat v2.1.0. The DESeq v1.26.0 R package was used to test for differential expression. Before each analysis the genes with low reads were removed i.e. those genes for which the sum of reads from three replicates of the analyzed two groups was lower than 30. The output data were used for transcriptome analysis. Genome build: RNAseq reads from individual samples were mapped against D. rerio GRCz10.80 Supplementary files format and content: tab separated values files include id and reads for each gene	3dpf zebrafish embryo treated with vehicle tail amputated	post anesthesia with 0.02% aminobenzoic acid ethyl ester tricaine Sigma Aldrich the tails of 3 dpf dpf embryos were partially amputated Figure 1A with a 1mm sapphire blade World Precision Instruments on 2% agarose coated Petri dishes under a Leica M165C stereomicroscope Chatzopoulou et al. 2016. Amputated and non amputated control embryos were pretreated for 2 hours with 25 μM beclomethasone Sigma Aldrich or vehicle 0.05% dimethyl sulfoxide DMSO in egg water prior to amputation and received the same treatment post the amputation.	Macrophages were sorted from Tgmpeg1.4:mCherry F embryos as previously described Rougeot et al. 2014; Zakrzewska et al. 2010. Dissociation was performed with 100 150 embryos for each sample at 4 hours post amputation hpa using Liberase TL Roche and stopped by adding Fetal Calf Serum FCS to a final concentration of 10%. Isolated cells were resuspended in Dulbecco’s PBS DPBS and filtered through a 40 μm cell strainer. Actinomycin D Sigma Aldrich was added final concentration of 1 µg/ml to each step to inhibit transcription. Macrophages were sorted based on their red fluorescent signal using a FACSAria III cell sorter BD Biosciences. The sorted cells were collected in QIAzol lysis reagent Qiagen for RNA isolation. Extracted total RNA was amplified using the SMART seq V4 kit Clontech for sequencing. The RNA seq libraries generated with the SMART seq V4 kit were sequenced using an Illumina HiSeq 2500 instrument according to the manufacturer’s instructions with a read length of 50 nucleotides	Zebrafish were maintained and handled according to the guidelines from the Zebrafish Model Organism Database http://zfin.org and in compliance with the directives of the local animal welfare committee of Leiden University. They were exposed to a 14 hours light and 10 hours dark cycle to maintain circadian rhythmicity. Fertilization was performed by natural spawning at the beginning of the light period. Eggs were collected and raised at 28°C in egg water 60 µg/ml Instant Ocean sea salts and 0.0025% methylene blue.	drug treatment:0.05% DMSO in egg water\|tail amputation:tail amputated\|developmental stage:3dpf	GSM3477138	GSM3477138: control amputated rep3; Danio rerio; RNA Seq	GSM3477138	1	Macrophages were sorted from Tgmpeg1.4:mCherry F embryos as previously described Rougeot et al. 2014; Zakrzewska et al. 2010. Dissociation was performed with 100 150 embryos for each sample at 4 hours post amputation hpa using Liberase TL Roche and stopped by adding Fetal Calf Serum FCS to a final concentration of 10%. Isolated cells were resuspended in Dulbeccoâ??s PBS DPBS and filtered through a 40 Î¼m cell strainer. Actinomycin D Sigma Aldrich was added final concentration of 1 Âµg/ml to each step to inhibit transcription. Macrophages were sorted based on their red fluorescent signal using a FACSAria III cell sorter BD Biosciences. The sorted cells were collected in QIAzol lysis reagent Qiagen for RNA isolation. Extracted total RNA was amplified using the SMART seq V4 kit Clontech for sequencing. The RNA seq libraries generated with the SMART seq V4 kit were sequenced using an Illumina HiSeq 2500 instrument according to the manufacturerâ??s instructions with a read length of 50 nucleotides	GEO Accession:GSM3477138	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP169118	ZFG-16-07_24_19304_GTGGCC_L002_R1_001.fastq.gz	fastq	309190917.0	6062567.0	GSM3477138 r2	0:51	A:80504238;C:75359982;G:74246868;T:79039195;N:40634	51		80504238	75359982	74246868	79039195	40634	SRX5021281	SRS4054046	SRA811328	GEO	Leiden University	1	0.94805		0.02936		0.73093		0.4484		51		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	Netherlands	2018-11-16	Larval	Larval	Tail	Multi-system
50634	50634	SRR8485424	SRX5021280	SRS4054045	SRP169118	PRJNA505837	Glucocorticoids inhibit macrophage differentiation towards a pro inflammatory phenotype upon wounding without xxx their migration	GSE122643	Transcriptome Analysis	Glucocorticoid drugs are widely used to treat immune related diseases but their use is limited by side effects and by resistance which especially occurs in macrophage dominated diseases. In order to improve glucocorticoid therapies more research is required into the mechanisms of glucocorticoid action. In the present study we have used a zebrafish model for inflammation to study glucocorticoid effects on the innate immune response. In zebrafish larvae the migration of neutrophils towards a site of injury is inhibited by the synthetic glucocorticoid beclomethasone while migration of macrophages is glucocorticoid resistant. RNA sequencing was done on on Fluorescence Activated Cell Sorting FACS sorted macrophages.The results show that the vast majority of the wounding induced transcriptional changes in these cells are inhibited by beclomethasone whereas a small subset is glucocorticoid insensitive. As a result beclomethasone decreases the number of macrophages that differentiate towards a pro inflammatory M1 phenotype which we demonstrated using a tnfa:eGFP F reporter line and analysis of macrophage morphology. We conclude that the glucocorticoid resistance of the wounding induced macrophage migration is due to the insensitivity of the induction of macrophage specific chemoattractants to glucocorticoid inhibition which may explain the relative resistance of macrophage dominated diseases to glucocorticoid therapy. However the induction of pro inflammatory genes in macrophages is strongly attenuated which inhibits their differentiation to an M1 phenotype. Overall design: post anesthesia with 0.02% aminobenzoic acid ethyl ester tricaine Sigma Aldrich the tails of 3 dpf dpf embryos were partially amputated with a 1mm sapphire blade World Precision Instruments on 2% agarose coated Petri dishes under a Leica M165C stereomicroscope Chatzopoulou et al. 2016. Amputated and non amputated control embryos were pretreated for 2 hours with 25 µM beclomethasone Sigma Aldrich or vehicle 0.05% dimethyl sulfoxide DMSO …	pubmed:31072958	beclo treated amputated rep3	GSM3477137	tissue:3dpf zebrafish embryo treated with beclomethas1 tail amputated\|drug treatment:25uM beclomethas1 in egg water\|tail amputation:tail amputated\|developmental stage:3dpf	beclo treated amputated rep3	Image analysis and base calling were done by the Illumina HCS version 2.2.68 and RTA version 1.18.66. cDNA sequencing data were analyzed by mapping the reads to the Danio rerio GRCz10 reference genome with annotation version 80 using Tophat v2.1.0. The DESeq v1.26.0 R package was used to test for differential expression. Before each analysis the genes with low reads were removed i.e. those genes for which the sum of reads from three replicates of the analyzed two groups was lower than 30. The output data were used for transcriptome analysis. Genome build: RNAseq reads from individual samples were mapped against D. rerio GRCz10.80 Supplementary files format and content: tab separated values files include id and reads for each gene	3dpf zebrafish embryo treated with beclomethasone tail amputated	post anesthesia with 0.02% aminobenzoic acid ethyl ester tricaine Sigma Aldrich the tails of 3 dpf dpf embryos were partially amputated Figure 1A with a 1mm sapphire blade World Precision Instruments on 2% agarose coated Petri dishes under a Leica M165C stereomicroscope Chatzopoulou et al. 2016. Amputated and non amputated control embryos were pretreated for 2 hours with 25 μM beclomethasone Sigma Aldrich or vehicle 0.05% dimethyl sulfoxide DMSO in egg water prior to amputation and received the same treatment post the amputation.	Macrophages were sorted from Tgmpeg1.4:mCherry F embryos as previously described Rougeot et al. 2014; Zakrzewska et al. 2010. Dissociation was performed with 100 150 embryos for each sample at 4 hours post amputation hpa using Liberase TL Roche and stopped by adding Fetal Calf Serum FCS to a final concentration of 10%. Isolated cells were resuspended in Dulbecco’s PBS DPBS and filtered through a 40 μm cell strainer. Actinomycin D Sigma Aldrich was added final concentration of 1 µg/ml to each step to inhibit transcription. Macrophages were sorted based on their red fluorescent signal using a FACSAria III cell sorter BD Biosciences. The sorted cells were collected in QIAzol lysis reagent Qiagen for RNA isolation. Extracted total RNA was amplified using the SMART seq V4 kit Clontech for sequencing. The RNA seq libraries generated with the SMART seq V4 kit were sequenced using an Illumina HiSeq 2500 instrument according to the manufacturer’s instructions with a read length of 50 nucleotides	Zebrafish were maintained and handled according to the guidelines from the Zebrafish Model Organism Database http://zfin.org and in compliance with the directives of the local animal welfare committee of Leiden University. They were exposed to a 14 hours light and 10 hours dark cycle to maintain circadian rhythmicity. Fertilization was performed by natural spawning at the beginning of the light period. Eggs were collected and raised at 28°C in egg water 60 µg/ml Instant Ocean sea salts and 0.0025% methylene blue.	drug treatment:25uM beclomethas1 in egg water\|tail amputation:tail amputated\|developmental stage:3dpf	GSM3477137	GSM3477137: beclo treated amputated rep3; Danio rerio; RNA Seq	GSM3477137	1	Macrophages were sorted from Tgmpeg1.4:mCherry F embryos as previously described Rougeot et al. 2014; Zakrzewska et al. 2010. Dissociation was performed with 100 150 embryos for each sample at 4 hours post amputation hpa using Liberase TL Roche and stopped by adding Fetal Calf Serum FCS to a final concentration of 10%. Isolated cells were resuspended in Dulbeccoâ??s PBS DPBS and filtered through a 40 Î¼m cell strainer. Actinomycin D Sigma Aldrich was added final concentration of 1 Âµg/ml to each step to inhibit transcription. Macrophages were sorted based on their red fluorescent signal using a FACSAria III cell sorter BD Biosciences. The sorted cells were collected in QIAzol lysis reagent Qiagen for RNA isolation. Extracted total RNA was amplified using the SMART seq V4 kit Clontech for sequencing. The RNA seq libraries generated with the SMART seq V4 kit were sequenced using an Illumina HiSeq 2500 instrument according to the manufacturerâ??s instructions with a read length of 50 nucleotides	GEO Accession:GSM3477137	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP169118	ZFG-16-07_23_19303_GGCTAC_L001_R1_001.fastq.gz	fastq	304235400.0	5965400.0	GSM3477137 r11	0:51	A:82653109;C:70694491;G:69477943;T:81398355;N:11502	51		82653109	70694491	69477943	81398355	11502	SRX5021280	SRS4054045	SRA811328	GEO	Leiden University	1	0.9339		0.09664		0.68489		0.45271		51		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	Netherlands	2018-11-16	Larval	Larval	Tail	Multi-system
50635	50635	SRR8485425	SRX5021280	SRS4054045	SRP169118	PRJNA505837	Glucocorticoids inhibit macrophage differentiation towards a pro inflammatory phenotype upon wounding without xxx their migration	GSE122643	Transcriptome Analysis	Glucocorticoid drugs are widely used to treat immune related diseases but their use is limited by side effects and by resistance which especially occurs in macrophage dominated diseases. In order to improve glucocorticoid therapies more research is required into the mechanisms of glucocorticoid action. In the present study we have used a zebrafish model for inflammation to study glucocorticoid effects on the innate immune response. In zebrafish larvae the migration of neutrophils towards a site of injury is inhibited by the synthetic glucocorticoid beclomethasone while migration of macrophages is glucocorticoid resistant. RNA sequencing was done on on Fluorescence Activated Cell Sorting FACS sorted macrophages.The results show that the vast majority of the wounding induced transcriptional changes in these cells are inhibited by beclomethasone whereas a small subset is glucocorticoid insensitive. As a result beclomethasone decreases the number of macrophages that differentiate towards a pro inflammatory M1 phenotype which we demonstrated using a tnfa:eGFP F reporter line and analysis of macrophage morphology. We conclude that the glucocorticoid resistance of the wounding induced macrophage migration is due to the insensitivity of the induction of macrophage specific chemoattractants to glucocorticoid inhibition which may explain the relative resistance of macrophage dominated diseases to glucocorticoid therapy. However the induction of pro inflammatory genes in macrophages is strongly attenuated which inhibits their differentiation to an M1 phenotype. Overall design: post anesthesia with 0.02% aminobenzoic acid ethyl ester tricaine Sigma Aldrich the tails of 3 dpf dpf embryos were partially amputated with a 1mm sapphire blade World Precision Instruments on 2% agarose coated Petri dishes under a Leica M165C stereomicroscope Chatzopoulou et al. 2016. Amputated and non amputated control embryos were pretreated for 2 hours with 25 µM beclomethasone Sigma Aldrich or vehicle 0.05% dimethyl sulfoxide DMSO …	pubmed:31072958	beclo treated amputated rep3	GSM3477137	tissue:3dpf zebrafish embryo treated with beclomethas1 tail amputated\|drug treatment:25uM beclomethas1 in egg water\|tail amputation:tail amputated\|developmental stage:3dpf	beclo treated amputated rep3	Image analysis and base calling were done by the Illumina HCS version 2.2.68 and RTA version 1.18.66. cDNA sequencing data were analyzed by mapping the reads to the Danio rerio GRCz10 reference genome with annotation version 80 using Tophat v2.1.0. The DESeq v1.26.0 R package was used to test for differential expression. Before each analysis the genes with low reads were removed i.e. those genes for which the sum of reads from three replicates of the analyzed two groups was lower than 30. The output data were used for transcriptome analysis. Genome build: RNAseq reads from individual samples were mapped against D. rerio GRCz10.80 Supplementary files format and content: tab separated values files include id and reads for each gene	3dpf zebrafish embryo treated with beclomethasone tail amputated	post anesthesia with 0.02% aminobenzoic acid ethyl ester tricaine Sigma Aldrich the tails of 3 dpf dpf embryos were partially amputated Figure 1A with a 1mm sapphire blade World Precision Instruments on 2% agarose coated Petri dishes under a Leica M165C stereomicroscope Chatzopoulou et al. 2016. Amputated and non amputated control embryos were pretreated for 2 hours with 25 μM beclomethasone Sigma Aldrich or vehicle 0.05% dimethyl sulfoxide DMSO in egg water prior to amputation and received the same treatment post the amputation.	Macrophages were sorted from Tgmpeg1.4:mCherry F embryos as previously described Rougeot et al. 2014; Zakrzewska et al. 2010. Dissociation was performed with 100 150 embryos for each sample at 4 hours post amputation hpa using Liberase TL Roche and stopped by adding Fetal Calf Serum FCS to a final concentration of 10%. Isolated cells were resuspended in Dulbecco’s PBS DPBS and filtered through a 40 μm cell strainer. Actinomycin D Sigma Aldrich was added final concentration of 1 µg/ml to each step to inhibit transcription. Macrophages were sorted based on their red fluorescent signal using a FACSAria III cell sorter BD Biosciences. The sorted cells were collected in QIAzol lysis reagent Qiagen for RNA isolation. Extracted total RNA was amplified using the SMART seq V4 kit Clontech for sequencing. The RNA seq libraries generated with the SMART seq V4 kit were sequenced using an Illumina HiSeq 2500 instrument according to the manufacturer’s instructions with a read length of 50 nucleotides	Zebrafish were maintained and handled according to the guidelines from the Zebrafish Model Organism Database http://zfin.org and in compliance with the directives of the local animal welfare committee of Leiden University. They were exposed to a 14 hours light and 10 hours dark cycle to maintain circadian rhythmicity. Fertilization was performed by natural spawning at the beginning of the light period. Eggs were collected and raised at 28°C in egg water 60 µg/ml Instant Ocean sea salts and 0.0025% methylene blue.	drug treatment:25uM beclomethas1 in egg water\|tail amputation:tail amputated\|developmental stage:3dpf	GSM3477137	GSM3477137: beclo treated amputated rep3; Danio rerio; RNA Seq	GSM3477137	1	Macrophages were sorted from Tgmpeg1.4:mCherry F embryos as previously described Rougeot et al. 2014; Zakrzewska et al. 2010. Dissociation was performed with 100 150 embryos for each sample at 4 hours post amputation hpa using Liberase TL Roche and stopped by adding Fetal Calf Serum FCS to a final concentration of 10%. Isolated cells were resuspended in Dulbeccoâ??s PBS DPBS and filtered through a 40 Î¼m cell strainer. Actinomycin D Sigma Aldrich was added final concentration of 1 Âµg/ml to each step to inhibit transcription. Macrophages were sorted based on their red fluorescent signal using a FACSAria III cell sorter BD Biosciences. The sorted cells were collected in QIAzol lysis reagent Qiagen for RNA isolation. Extracted total RNA was amplified using the SMART seq V4 kit Clontech for sequencing. The RNA seq libraries generated with the SMART seq V4 kit were sequenced using an Illumina HiSeq 2500 instrument according to the manufacturerâ??s instructions with a read length of 50 nucleotides	GEO Accession:GSM3477137	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP169118	ZFG-16-07_23_19303_GGCTAC_L002_R1_001.fastq.gz	fastq	298373154.0	5850454.0	GSM3477137 r2	0:51	A:81020901;C:69369228;G:68135781;T:79807628;N:39616	51		81020901	69369228	68135781	79807628	39616	SRX5021280	SRS4054045	SRA811328	GEO	Leiden University	1	0.9337		0.09688		0.68247		0.45194		51		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	Netherlands	2018-11-16	Larval	Larval	Tail	Multi-system
50640	50640	SRR8485418	SRX5021277	SRS4054042	SRP169118	PRJNA505837	Glucocorticoids inhibit macrophage differentiation towards a pro inflammatory phenotype upon wounding without xxx their migration	GSE122643	Transcriptome Analysis	Glucocorticoid drugs are widely used to treat immune related diseases but their use is limited by side effects and by resistance which especially occurs in macrophage dominated diseases. In order to improve glucocorticoid therapies more research is required into the mechanisms of glucocorticoid action. In the present study we have used a zebrafish model for inflammation to study glucocorticoid effects on the innate immune response. In zebrafish larvae the migration of neutrophils towards a site of injury is inhibited by the synthetic glucocorticoid beclomethasone while migration of macrophages is glucocorticoid resistant. RNA sequencing was done on on Fluorescence Activated Cell Sorting FACS sorted macrophages.The results show that the vast majority of the wounding induced transcriptional changes in these cells are inhibited by beclomethasone whereas a small subset is glucocorticoid insensitive. As a result beclomethasone decreases the number of macrophages that differentiate towards a pro inflammatory M1 phenotype which we demonstrated using a tnfa:eGFP F reporter line and analysis of macrophage morphology. We conclude that the glucocorticoid resistance of the wounding induced macrophage migration is due to the insensitivity of the induction of macrophage specific chemoattractants to glucocorticoid inhibition which may explain the relative resistance of macrophage dominated diseases to glucocorticoid therapy. However the induction of pro inflammatory genes in macrophages is strongly attenuated which inhibits their differentiation to an M1 phenotype. Overall design: post anesthesia with 0.02% aminobenzoic acid ethyl ester tricaine Sigma Aldrich the tails of 3 dpf dpf embryos were partially amputated with a 1mm sapphire blade World Precision Instruments on 2% agarose coated Petri dishes under a Leica M165C stereomicroscope Chatzopoulou et al. 2016. Amputated and non amputated control embryos were pretreated for 2 hours with 25 µM beclomethasone Sigma Aldrich or vehicle 0.05% dimethyl sulfoxide DMSO …	pubmed:31072958	control amputated rep2	GSM3477134	tissue:3dpf zebrafish embryo treated with vehicle tail amputated\|drug treatment:0.05% DMSO in egg water\|tail amputation:tail amputated\|developmental stage:3dpf	control amputated rep2	Image analysis and base calling were done by the Illumina HCS version 2.2.68 and RTA version 1.18.66. cDNA sequencing data were analyzed by mapping the reads to the Danio rerio GRCz10 reference genome with annotation version 80 using Tophat v2.1.0. The DESeq v1.26.0 R package was used to test for differential expression. Before each analysis the genes with low reads were removed i.e. those genes for which the sum of reads from three replicates of the analyzed two groups was lower than 30. The output data were used for transcriptome analysis. Genome build: RNAseq reads from individual samples were mapped against D. rerio GRCz10.80 Supplementary files format and content: tab separated values files include id and reads for each gene	3dpf zebrafish embryo treated with vehicle tail amputated	post anesthesia with 0.02% aminobenzoic acid ethyl ester tricaine Sigma Aldrich the tails of 3 dpf dpf embryos were partially amputated Figure 1A with a 1mm sapphire blade World Precision Instruments on 2% agarose coated Petri dishes under a Leica M165C stereomicroscope Chatzopoulou et al. 2016. Amputated and non amputated control embryos were pretreated for 2 hours with 25 μM beclomethasone Sigma Aldrich or vehicle 0.05% dimethyl sulfoxide DMSO in egg water prior to amputation and received the same treatment post the amputation.	Macrophages were sorted from Tgmpeg1.4:mCherry F embryos as previously described Rougeot et al. 2014; Zakrzewska et al. 2010. Dissociation was performed with 100 150 embryos for each sample at 4 hours post amputation hpa using Liberase TL Roche and stopped by adding Fetal Calf Serum FCS to a final concentration of 10%. Isolated cells were resuspended in Dulbecco’s PBS DPBS and filtered through a 40 μm cell strainer. Actinomycin D Sigma Aldrich was added final concentration of 1 µg/ml to each step to inhibit transcription. Macrophages were sorted based on their red fluorescent signal using a FACSAria III cell sorter BD Biosciences. The sorted cells were collected in QIAzol lysis reagent Qiagen for RNA isolation. Extracted total RNA was amplified using the SMART seq V4 kit Clontech for sequencing. The RNA seq libraries generated with the SMART seq V4 kit were sequenced using an Illumina HiSeq 2500 instrument according to the manufacturer’s instructions with a read length of 50 nucleotides	Zebrafish were maintained and handled according to the guidelines from the Zebrafish Model Organism Database http://zfin.org and in compliance with the directives of the local animal welfare committee of Leiden University. They were exposed to a 14 hours light and 10 hours dark cycle to maintain circadian rhythmicity. Fertilization was performed by natural spawning at the beginning of the light period. Eggs were collected and raised at 28°C in egg water 60 µg/ml Instant Ocean sea salts and 0.0025% methylene blue.	drug treatment:0.05% DMSO in egg water\|tail amputation:tail amputated\|developmental stage:3dpf	GSM3477134	GSM3477134: control amputated rep2; Danio rerio; RNA Seq	GSM3477134	1	Macrophages were sorted from Tgmpeg1.4:mCherry F embryos as previously described Rougeot et al. 2014; Zakrzewska et al. 2010. Dissociation was performed with 100 150 embryos for each sample at 4 hours post amputation hpa using Liberase TL Roche and stopped by adding Fetal Calf Serum FCS to a final concentration of 10%. Isolated cells were resuspended in Dulbeccoâ??s PBS DPBS and filtered through a 40 Î¼m cell strainer. Actinomycin D Sigma Aldrich was added final concentration of 1 Âµg/ml to each step to inhibit transcription. Macrophages were sorted based on their red fluorescent signal using a FACSAria III cell sorter BD Biosciences. The sorted cells were collected in QIAzol lysis reagent Qiagen for RNA isolation. Extracted total RNA was amplified using the SMART seq V4 kit Clontech for sequencing. The RNA seq libraries generated with the SMART seq V4 kit were sequenced using an Illumina HiSeq 2500 instrument according to the manufacturerâ??s instructions with a read length of 50 nucleotides	GEO Accession:GSM3477134	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP169118	ZFG-16-07_16_19296_CTTGTA_L001_R1_001.fastq.gz	fastq	328044852.0	6432252.0	GSM3477134 r11	0:51	A:89623409;C:76183012;G:74936256;T:87289316;N:12859	51		89623409	76183012	74936256	87289316	12859	SRX5021277	SRS4054042	SRA811328	GEO	Leiden University	1	0.93376		0.05224		0.73217		0.46402		51		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	Netherlands	2018-11-16	Larval	Larval	Tail	Multi-system
50641	50641	SRR8485419	SRX5021277	SRS4054042	SRP169118	PRJNA505837	Glucocorticoids inhibit macrophage differentiation towards a pro inflammatory phenotype upon wounding without xxx their migration	GSE122643	Transcriptome Analysis	Glucocorticoid drugs are widely used to treat immune related diseases but their use is limited by side effects and by resistance which especially occurs in macrophage dominated diseases. In order to improve glucocorticoid therapies more research is required into the mechanisms of glucocorticoid action. In the present study we have used a zebrafish model for inflammation to study glucocorticoid effects on the innate immune response. In zebrafish larvae the migration of neutrophils towards a site of injury is inhibited by the synthetic glucocorticoid beclomethasone while migration of macrophages is glucocorticoid resistant. RNA sequencing was done on on Fluorescence Activated Cell Sorting FACS sorted macrophages.The results show that the vast majority of the wounding induced transcriptional changes in these cells are inhibited by beclomethasone whereas a small subset is glucocorticoid insensitive. As a result beclomethasone decreases the number of macrophages that differentiate towards a pro inflammatory M1 phenotype which we demonstrated using a tnfa:eGFP F reporter line and analysis of macrophage morphology. We conclude that the glucocorticoid resistance of the wounding induced macrophage migration is due to the insensitivity of the induction of macrophage specific chemoattractants to glucocorticoid inhibition which may explain the relative resistance of macrophage dominated diseases to glucocorticoid therapy. However the induction of pro inflammatory genes in macrophages is strongly attenuated which inhibits their differentiation to an M1 phenotype. Overall design: post anesthesia with 0.02% aminobenzoic acid ethyl ester tricaine Sigma Aldrich the tails of 3 dpf dpf embryos were partially amputated with a 1mm sapphire blade World Precision Instruments on 2% agarose coated Petri dishes under a Leica M165C stereomicroscope Chatzopoulou et al. 2016. Amputated and non amputated control embryos were pretreated for 2 hours with 25 µM beclomethasone Sigma Aldrich or vehicle 0.05% dimethyl sulfoxide DMSO …	pubmed:31072958	control amputated rep2	GSM3477134	tissue:3dpf zebrafish embryo treated with vehicle tail amputated\|drug treatment:0.05% DMSO in egg water\|tail amputation:tail amputated\|developmental stage:3dpf	control amputated rep2	Image analysis and base calling were done by the Illumina HCS version 2.2.68 and RTA version 1.18.66. cDNA sequencing data were analyzed by mapping the reads to the Danio rerio GRCz10 reference genome with annotation version 80 using Tophat v2.1.0. The DESeq v1.26.0 R package was used to test for differential expression. Before each analysis the genes with low reads were removed i.e. those genes for which the sum of reads from three replicates of the analyzed two groups was lower than 30. The output data were used for transcriptome analysis. Genome build: RNAseq reads from individual samples were mapped against D. rerio GRCz10.80 Supplementary files format and content: tab separated values files include id and reads for each gene	3dpf zebrafish embryo treated with vehicle tail amputated	post anesthesia with 0.02% aminobenzoic acid ethyl ester tricaine Sigma Aldrich the tails of 3 dpf dpf embryos were partially amputated Figure 1A with a 1mm sapphire blade World Precision Instruments on 2% agarose coated Petri dishes under a Leica M165C stereomicroscope Chatzopoulou et al. 2016. Amputated and non amputated control embryos were pretreated for 2 hours with 25 μM beclomethasone Sigma Aldrich or vehicle 0.05% dimethyl sulfoxide DMSO in egg water prior to amputation and received the same treatment post the amputation.	Macrophages were sorted from Tgmpeg1.4:mCherry F embryos as previously described Rougeot et al. 2014; Zakrzewska et al. 2010. Dissociation was performed with 100 150 embryos for each sample at 4 hours post amputation hpa using Liberase TL Roche and stopped by adding Fetal Calf Serum FCS to a final concentration of 10%. Isolated cells were resuspended in Dulbecco’s PBS DPBS and filtered through a 40 μm cell strainer. Actinomycin D Sigma Aldrich was added final concentration of 1 µg/ml to each step to inhibit transcription. Macrophages were sorted based on their red fluorescent signal using a FACSAria III cell sorter BD Biosciences. The sorted cells were collected in QIAzol lysis reagent Qiagen for RNA isolation. Extracted total RNA was amplified using the SMART seq V4 kit Clontech for sequencing. The RNA seq libraries generated with the SMART seq V4 kit were sequenced using an Illumina HiSeq 2500 instrument according to the manufacturer’s instructions with a read length of 50 nucleotides	Zebrafish were maintained and handled according to the guidelines from the Zebrafish Model Organism Database http://zfin.org and in compliance with the directives of the local animal welfare committee of Leiden University. They were exposed to a 14 hours light and 10 hours dark cycle to maintain circadian rhythmicity. Fertilization was performed by natural spawning at the beginning of the light period. Eggs were collected and raised at 28°C in egg water 60 µg/ml Instant Ocean sea salts and 0.0025% methylene blue.	drug treatment:0.05% DMSO in egg water\|tail amputation:tail amputated\|developmental stage:3dpf	GSM3477134	GSM3477134: control amputated rep2; Danio rerio; RNA Seq	GSM3477134	1	Macrophages were sorted from Tgmpeg1.4:mCherry F embryos as previously described Rougeot et al. 2014; Zakrzewska et al. 2010. Dissociation was performed with 100 150 embryos for each sample at 4 hours post amputation hpa using Liberase TL Roche and stopped by adding Fetal Calf Serum FCS to a final concentration of 10%. Isolated cells were resuspended in Dulbeccoâ??s PBS DPBS and filtered through a 40 Î¼m cell strainer. Actinomycin D Sigma Aldrich was added final concentration of 1 Âµg/ml to each step to inhibit transcription. Macrophages were sorted based on their red fluorescent signal using a FACSAria III cell sorter BD Biosciences. The sorted cells were collected in QIAzol lysis reagent Qiagen for RNA isolation. Extracted total RNA was amplified using the SMART seq V4 kit Clontech for sequencing. The RNA seq libraries generated with the SMART seq V4 kit were sequenced using an Illumina HiSeq 2500 instrument according to the manufacturerâ??s instructions with a read length of 50 nucleotides	GEO Accession:GSM3477134	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP169118	ZFG-16-07_16_19296_CTTGTA_L002_R1_001.fastq.gz	fastq	320708808.0	6288408.0	GSM3477134 r2	0:51	A:87602833;C:74503669;G:73249831;T:85307256;N:45219	51		87602833	74503669	73249831	85307256	45219	SRX5021277	SRS4054042	SRA811328	GEO	Leiden University	1	0.93388		0.05162		0.73064		0.46443		51		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	Netherlands	2018-11-16	Larval	Larval	Tail	Multi-system
50642	50642	SRR8485416	SRX5021276	SRS4054041	SRP169118	PRJNA505837	Glucocorticoids inhibit macrophage differentiation towards a pro inflammatory phenotype upon wounding without xxx their migration	GSE122643	Transcriptome Analysis	Glucocorticoid drugs are widely used to treat immune related diseases but their use is limited by side effects and by resistance which especially occurs in macrophage dominated diseases. In order to improve glucocorticoid therapies more research is required into the mechanisms of glucocorticoid action. In the present study we have used a zebrafish model for inflammation to study glucocorticoid effects on the innate immune response. In zebrafish larvae the migration of neutrophils towards a site of injury is inhibited by the synthetic glucocorticoid beclomethasone while migration of macrophages is glucocorticoid resistant. RNA sequencing was done on on Fluorescence Activated Cell Sorting FACS sorted macrophages.The results show that the vast majority of the wounding induced transcriptional changes in these cells are inhibited by beclomethasone whereas a small subset is glucocorticoid insensitive. As a result beclomethasone decreases the number of macrophages that differentiate towards a pro inflammatory M1 phenotype which we demonstrated using a tnfa:eGFP F reporter line and analysis of macrophage morphology. We conclude that the glucocorticoid resistance of the wounding induced macrophage migration is due to the insensitivity of the induction of macrophage specific chemoattractants to glucocorticoid inhibition which may explain the relative resistance of macrophage dominated diseases to glucocorticoid therapy. However the induction of pro inflammatory genes in macrophages is strongly attenuated which inhibits their differentiation to an M1 phenotype. Overall design: post anesthesia with 0.02% aminobenzoic acid ethyl ester tricaine Sigma Aldrich the tails of 3 dpf dpf embryos were partially amputated with a 1mm sapphire blade World Precision Instruments on 2% agarose coated Petri dishes under a Leica M165C stereomicroscope Chatzopoulou et al. 2016. Amputated and non amputated control embryos were pretreated for 2 hours with 25 µM beclomethasone Sigma Aldrich or vehicle 0.05% dimethyl sulfoxide DMSO …	pubmed:31072958	beclo treated amputated rep2	GSM3477133	tissue:3dpf zebrafish embryo treated with beclomethas1 tail amputated\|drug treatment:25uM beclomethas1 in egg water\|tail amputation:tail amputated\|developmental stage:3dpf	beclo treated amputated rep2	Image analysis and base calling were done by the Illumina HCS version 2.2.68 and RTA version 1.18.66. cDNA sequencing data were analyzed by mapping the reads to the Danio rerio GRCz10 reference genome with annotation version 80 using Tophat v2.1.0. The DESeq v1.26.0 R package was used to test for differential expression. Before each analysis the genes with low reads were removed i.e. those genes for which the sum of reads from three replicates of the analyzed two groups was lower than 30. The output data were used for transcriptome analysis. Genome build: RNAseq reads from individual samples were mapped against D. rerio GRCz10.80 Supplementary files format and content: tab separated values files include id and reads for each gene	3dpf zebrafish embryo treated with beclomethasone tail amputated	post anesthesia with 0.02% aminobenzoic acid ethyl ester tricaine Sigma Aldrich the tails of 3 dpf dpf embryos were partially amputated Figure 1A with a 1mm sapphire blade World Precision Instruments on 2% agarose coated Petri dishes under a Leica M165C stereomicroscope Chatzopoulou et al. 2016. Amputated and non amputated control embryos were pretreated for 2 hours with 25 μM beclomethasone Sigma Aldrich or vehicle 0.05% dimethyl sulfoxide DMSO in egg water prior to amputation and received the same treatment post the amputation.	Macrophages were sorted from Tgmpeg1.4:mCherry F embryos as previously described Rougeot et al. 2014; Zakrzewska et al. 2010. Dissociation was performed with 100 150 embryos for each sample at 4 hours post amputation hpa using Liberase TL Roche and stopped by adding Fetal Calf Serum FCS to a final concentration of 10%. Isolated cells were resuspended in Dulbecco’s PBS DPBS and filtered through a 40 μm cell strainer. Actinomycin D Sigma Aldrich was added final concentration of 1 µg/ml to each step to inhibit transcription. Macrophages were sorted based on their red fluorescent signal using a FACSAria III cell sorter BD Biosciences. The sorted cells were collected in QIAzol lysis reagent Qiagen for RNA isolation. Extracted total RNA was amplified using the SMART seq V4 kit Clontech for sequencing. The RNA seq libraries generated with the SMART seq V4 kit were sequenced using an Illumina HiSeq 2500 instrument according to the manufacturer’s instructions with a read length of 50 nucleotides	Zebrafish were maintained and handled according to the guidelines from the Zebrafish Model Organism Database http://zfin.org and in compliance with the directives of the local animal welfare committee of Leiden University. They were exposed to a 14 hours light and 10 hours dark cycle to maintain circadian rhythmicity. Fertilization was performed by natural spawning at the beginning of the light period. Eggs were collected and raised at 28°C in egg water 60 µg/ml Instant Ocean sea salts and 0.0025% methylene blue.	drug treatment:25uM beclomethas1 in egg water\|tail amputation:tail amputated\|developmental stage:3dpf	GSM3477133	GSM3477133: beclo treated amputated rep2; Danio rerio; RNA Seq	GSM3477133	1	Macrophages were sorted from Tgmpeg1.4:mCherry F embryos as previously described Rougeot et al. 2014; Zakrzewska et al. 2010. Dissociation was performed with 100 150 embryos for each sample at 4 hours post amputation hpa using Liberase TL Roche and stopped by adding Fetal Calf Serum FCS to a final concentration of 10%. Isolated cells were resuspended in Dulbeccoâ??s PBS DPBS and filtered through a 40 Î¼m cell strainer. Actinomycin D Sigma Aldrich was added final concentration of 1 Âµg/ml to each step to inhibit transcription. Macrophages were sorted based on their red fluorescent signal using a FACSAria III cell sorter BD Biosciences. The sorted cells were collected in QIAzol lysis reagent Qiagen for RNA isolation. Extracted total RNA was amplified using the SMART seq V4 kit Clontech for sequencing. The RNA seq libraries generated with the SMART seq V4 kit were sequenced using an Illumina HiSeq 2500 instrument according to the manufacturerâ??s instructions with a read length of 50 nucleotides	GEO Accession:GSM3477133	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP169118	ZFG-16-07_15_19295_TGACCA_L001_R1_001.fastq.gz	fastq	298483008.0	5852608.0	GSM3477133 r11	0:51	A:81892953;C:68642687;G:67201892;T:80733415;N:12061	51		81892953	68642687	67201892	80733415	12061	SRX5021276	SRS4054041	SRA811328	GEO	Leiden University	1	0.93509		0.09108		0.68785		0.47874		51		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	Netherlands	2018-11-16	Larval	Larval	Tail	Multi-system
50643	50643	SRR8485417	SRX5021276	SRS4054041	SRP169118	PRJNA505837	Glucocorticoids inhibit macrophage differentiation towards a pro inflammatory phenotype upon wounding without xxx their migration	GSE122643	Transcriptome Analysis	Glucocorticoid drugs are widely used to treat immune related diseases but their use is limited by side effects and by resistance which especially occurs in macrophage dominated diseases. In order to improve glucocorticoid therapies more research is required into the mechanisms of glucocorticoid action. In the present study we have used a zebrafish model for inflammation to study glucocorticoid effects on the innate immune response. In zebrafish larvae the migration of neutrophils towards a site of injury is inhibited by the synthetic glucocorticoid beclomethasone while migration of macrophages is glucocorticoid resistant. RNA sequencing was done on on Fluorescence Activated Cell Sorting FACS sorted macrophages.The results show that the vast majority of the wounding induced transcriptional changes in these cells are inhibited by beclomethasone whereas a small subset is glucocorticoid insensitive. As a result beclomethasone decreases the number of macrophages that differentiate towards a pro inflammatory M1 phenotype which we demonstrated using a tnfa:eGFP F reporter line and analysis of macrophage morphology. We conclude that the glucocorticoid resistance of the wounding induced macrophage migration is due to the insensitivity of the induction of macrophage specific chemoattractants to glucocorticoid inhibition which may explain the relative resistance of macrophage dominated diseases to glucocorticoid therapy. However the induction of pro inflammatory genes in macrophages is strongly attenuated which inhibits their differentiation to an M1 phenotype. Overall design: post anesthesia with 0.02% aminobenzoic acid ethyl ester tricaine Sigma Aldrich the tails of 3 dpf dpf embryos were partially amputated with a 1mm sapphire blade World Precision Instruments on 2% agarose coated Petri dishes under a Leica M165C stereomicroscope Chatzopoulou et al. 2016. Amputated and non amputated control embryos were pretreated for 2 hours with 25 µM beclomethasone Sigma Aldrich or vehicle 0.05% dimethyl sulfoxide DMSO …	pubmed:31072958	beclo treated amputated rep2	GSM3477133	tissue:3dpf zebrafish embryo treated with beclomethas1 tail amputated\|drug treatment:25uM beclomethas1 in egg water\|tail amputation:tail amputated\|developmental stage:3dpf	beclo treated amputated rep2	Image analysis and base calling were done by the Illumina HCS version 2.2.68 and RTA version 1.18.66. cDNA sequencing data were analyzed by mapping the reads to the Danio rerio GRCz10 reference genome with annotation version 80 using Tophat v2.1.0. The DESeq v1.26.0 R package was used to test for differential expression. Before each analysis the genes with low reads were removed i.e. those genes for which the sum of reads from three replicates of the analyzed two groups was lower than 30. The output data were used for transcriptome analysis. Genome build: RNAseq reads from individual samples were mapped against D. rerio GRCz10.80 Supplementary files format and content: tab separated values files include id and reads for each gene	3dpf zebrafish embryo treated with beclomethasone tail amputated	post anesthesia with 0.02% aminobenzoic acid ethyl ester tricaine Sigma Aldrich the tails of 3 dpf dpf embryos were partially amputated Figure 1A with a 1mm sapphire blade World Precision Instruments on 2% agarose coated Petri dishes under a Leica M165C stereomicroscope Chatzopoulou et al. 2016. Amputated and non amputated control embryos were pretreated for 2 hours with 25 μM beclomethasone Sigma Aldrich or vehicle 0.05% dimethyl sulfoxide DMSO in egg water prior to amputation and received the same treatment post the amputation.	Macrophages were sorted from Tgmpeg1.4:mCherry F embryos as previously described Rougeot et al. 2014; Zakrzewska et al. 2010. Dissociation was performed with 100 150 embryos for each sample at 4 hours post amputation hpa using Liberase TL Roche and stopped by adding Fetal Calf Serum FCS to a final concentration of 10%. Isolated cells were resuspended in Dulbecco’s PBS DPBS and filtered through a 40 μm cell strainer. Actinomycin D Sigma Aldrich was added final concentration of 1 µg/ml to each step to inhibit transcription. Macrophages were sorted based on their red fluorescent signal using a FACSAria III cell sorter BD Biosciences. The sorted cells were collected in QIAzol lysis reagent Qiagen for RNA isolation. Extracted total RNA was amplified using the SMART seq V4 kit Clontech for sequencing. The RNA seq libraries generated with the SMART seq V4 kit were sequenced using an Illumina HiSeq 2500 instrument according to the manufacturer’s instructions with a read length of 50 nucleotides	Zebrafish were maintained and handled according to the guidelines from the Zebrafish Model Organism Database http://zfin.org and in compliance with the directives of the local animal welfare committee of Leiden University. They were exposed to a 14 hours light and 10 hours dark cycle to maintain circadian rhythmicity. Fertilization was performed by natural spawning at the beginning of the light period. Eggs were collected and raised at 28°C in egg water 60 µg/ml Instant Ocean sea salts and 0.0025% methylene blue.	drug treatment:25uM beclomethas1 in egg water\|tail amputation:tail amputated\|developmental stage:3dpf	GSM3477133	GSM3477133: beclo treated amputated rep2; Danio rerio; RNA Seq	GSM3477133	1	Macrophages were sorted from Tgmpeg1.4:mCherry F embryos as previously described Rougeot et al. 2014; Zakrzewska et al. 2010. Dissociation was performed with 100 150 embryos for each sample at 4 hours post amputation hpa using Liberase TL Roche and stopped by adding Fetal Calf Serum FCS to a final concentration of 10%. Isolated cells were resuspended in Dulbeccoâ??s PBS DPBS and filtered through a 40 Î¼m cell strainer. Actinomycin D Sigma Aldrich was added final concentration of 1 Âµg/ml to each step to inhibit transcription. Macrophages were sorted based on their red fluorescent signal using a FACSAria III cell sorter BD Biosciences. The sorted cells were collected in QIAzol lysis reagent Qiagen for RNA isolation. Extracted total RNA was amplified using the SMART seq V4 kit Clontech for sequencing. The RNA seq libraries generated with the SMART seq V4 kit were sequenced using an Illumina HiSeq 2500 instrument according to the manufacturerâ??s instructions with a read length of 50 nucleotides	GEO Accession:GSM3477133	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP169118	ZFG-16-07_15_19295_TGACCA_L002_R1_001.fastq.gz	fastq	291739890.0	5720390.0	GSM3477133 r2	0:51	A:80006138;C:67116448;G:65686679;T:78890561;N:40064	51		80006138	67116448	65686679	78890561	40064	SRX5021276	SRS4054041	SRA811328	GEO	Leiden University	1	0.93405		0.09006		0.68897		0.47001		51		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	Netherlands	2018-11-16	Larval	Larval	Tail	Multi-system
50648	50648	SRR8485410	SRX5021273	SRS4054038	SRP169118	PRJNA505837	Glucocorticoids inhibit macrophage differentiation towards a pro inflammatory phenotype upon wounding without xxx their migration	GSE122643	Transcriptome Analysis	Glucocorticoid drugs are widely used to treat immune related diseases but their use is limited by side effects and by resistance which especially occurs in macrophage dominated diseases. In order to improve glucocorticoid therapies more research is required into the mechanisms of glucocorticoid action. In the present study we have used a zebrafish model for inflammation to study glucocorticoid effects on the innate immune response. In zebrafish larvae the migration of neutrophils towards a site of injury is inhibited by the synthetic glucocorticoid beclomethasone while migration of macrophages is glucocorticoid resistant. RNA sequencing was done on on Fluorescence Activated Cell Sorting FACS sorted macrophages.The results show that the vast majority of the wounding induced transcriptional changes in these cells are inhibited by beclomethasone whereas a small subset is glucocorticoid insensitive. As a result beclomethasone decreases the number of macrophages that differentiate towards a pro inflammatory M1 phenotype which we demonstrated using a tnfa:eGFP F reporter line and analysis of macrophage morphology. We conclude that the glucocorticoid resistance of the wounding induced macrophage migration is due to the insensitivity of the induction of macrophage specific chemoattractants to glucocorticoid inhibition which may explain the relative resistance of macrophage dominated diseases to glucocorticoid therapy. However the induction of pro inflammatory genes in macrophages is strongly attenuated which inhibits their differentiation to an M1 phenotype. Overall design: post anesthesia with 0.02% aminobenzoic acid ethyl ester tricaine Sigma Aldrich the tails of 3 dpf dpf embryos were partially amputated with a 1mm sapphire blade World Precision Instruments on 2% agarose coated Petri dishes under a Leica M165C stereomicroscope Chatzopoulou et al. 2016. Amputated and non amputated control embryos were pretreated for 2 hours with 25 µM beclomethasone Sigma Aldrich or vehicle 0.05% dimethyl sulfoxide DMSO …	pubmed:31072958	control amputated rep1	GSM3477130	tissue:3dpf zebrafish embryo treated with vehicle tail amputated\|drug treatment:0.05% DMSO in egg water\|tail amputation:tail amputated\|developmental stage:3dpf	control amputated rep1	Image analysis and base calling were done by the Illumina HCS version 2.2.68 and RTA version 1.18.66. cDNA sequencing data were analyzed by mapping the reads to the Danio rerio GRCz10 reference genome with annotation version 80 using Tophat v2.1.0. The DESeq v1.26.0 R package was used to test for differential expression. Before each analysis the genes with low reads were removed i.e. those genes for which the sum of reads from three replicates of the analyzed two groups was lower than 30. The output data were used for transcriptome analysis. Genome build: RNAseq reads from individual samples were mapped against D. rerio GRCz10.80 Supplementary files format and content: tab separated values files include id and reads for each gene	3dpf zebrafish embryo treated with vehicle tail amputated	post anesthesia with 0.02% aminobenzoic acid ethyl ester tricaine Sigma Aldrich the tails of 3 dpf dpf embryos were partially amputated Figure 1A with a 1mm sapphire blade World Precision Instruments on 2% agarose coated Petri dishes under a Leica M165C stereomicroscope Chatzopoulou et al. 2016. Amputated and non amputated control embryos were pretreated for 2 hours with 25 μM beclomethasone Sigma Aldrich or vehicle 0.05% dimethyl sulfoxide DMSO in egg water prior to amputation and received the same treatment post the amputation.	Macrophages were sorted from Tgmpeg1.4:mCherry F embryos as previously described Rougeot et al. 2014; Zakrzewska et al. 2010. Dissociation was performed with 100 150 embryos for each sample at 4 hours post amputation hpa using Liberase TL Roche and stopped by adding Fetal Calf Serum FCS to a final concentration of 10%. Isolated cells were resuspended in Dulbecco’s PBS DPBS and filtered through a 40 μm cell strainer. Actinomycin D Sigma Aldrich was added final concentration of 1 µg/ml to each step to inhibit transcription. Macrophages were sorted based on their red fluorescent signal using a FACSAria III cell sorter BD Biosciences. The sorted cells were collected in QIAzol lysis reagent Qiagen for RNA isolation. Extracted total RNA was amplified using the SMART seq V4 kit Clontech for sequencing. The RNA seq libraries generated with the SMART seq V4 kit were sequenced using an Illumina HiSeq 2500 instrument according to the manufacturer’s instructions with a read length of 50 nucleotides	Zebrafish were maintained and handled according to the guidelines from the Zebrafish Model Organism Database http://zfin.org and in compliance with the directives of the local animal welfare committee of Leiden University. They were exposed to a 14 hours light and 10 hours dark cycle to maintain circadian rhythmicity. Fertilization was performed by natural spawning at the beginning of the light period. Eggs were collected and raised at 28°C in egg water 60 µg/ml Instant Ocean sea salts and 0.0025% methylene blue.	drug treatment:0.05% DMSO in egg water\|tail amputation:tail amputated\|developmental stage:3dpf	GSM3477130	GSM3477130: control amputated rep1; Danio rerio; RNA Seq	GSM3477130	1	Macrophages were sorted from Tgmpeg1.4:mCherry F embryos as previously described Rougeot et al. 2014; Zakrzewska et al. 2010. Dissociation was performed with 100 150 embryos for each sample at 4 hours post amputation hpa using Liberase TL Roche and stopped by adding Fetal Calf Serum FCS to a final concentration of 10%. Isolated cells were resuspended in Dulbeccoâ??s PBS DPBS and filtered through a 40 Î¼m cell strainer. Actinomycin D Sigma Aldrich was added final concentration of 1 Âµg/ml to each step to inhibit transcription. Macrophages were sorted based on their red fluorescent signal using a FACSAria III cell sorter BD Biosciences. The sorted cells were collected in QIAzol lysis reagent Qiagen for RNA isolation. Extracted total RNA was amplified using the SMART seq V4 kit Clontech for sequencing. The RNA seq libraries generated with the SMART seq V4 kit were sequenced using an Illumina HiSeq 2500 instrument according to the manufacturerâ??s instructions with a read length of 50 nucleotides	GEO Accession:GSM3477130	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP169118			485992821.0	9529271.0	GSM3477130 r11	0:51	A:134082582;C:111125846;G:108604274;T:131898648;N:281471	51		134082582	111125846	108604274	131898648	281471	SRX5021273	SRS4054038	SRA811328	GEO	Leiden University	1	0.934		0.085		0.69246		0.46718		51		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	Netherlands	2018-11-16	Larval	Larval	Tail	Multi-system
50649	50649	SRR8485411	SRX5021273	SRS4054038	SRP169118	PRJNA505837	Glucocorticoids inhibit macrophage differentiation towards a pro inflammatory phenotype upon wounding without xxx their migration	GSE122643	Transcriptome Analysis	Glucocorticoid drugs are widely used to treat immune related diseases but their use is limited by side effects and by resistance which especially occurs in macrophage dominated diseases. In order to improve glucocorticoid therapies more research is required into the mechanisms of glucocorticoid action. In the present study we have used a zebrafish model for inflammation to study glucocorticoid effects on the innate immune response. In zebrafish larvae the migration of neutrophils towards a site of injury is inhibited by the synthetic glucocorticoid beclomethasone while migration of macrophages is glucocorticoid resistant. RNA sequencing was done on on Fluorescence Activated Cell Sorting FACS sorted macrophages.The results show that the vast majority of the wounding induced transcriptional changes in these cells are inhibited by beclomethasone whereas a small subset is glucocorticoid insensitive. As a result beclomethasone decreases the number of macrophages that differentiate towards a pro inflammatory M1 phenotype which we demonstrated using a tnfa:eGFP F reporter line and analysis of macrophage morphology. We conclude that the glucocorticoid resistance of the wounding induced macrophage migration is due to the insensitivity of the induction of macrophage specific chemoattractants to glucocorticoid inhibition which may explain the relative resistance of macrophage dominated diseases to glucocorticoid therapy. However the induction of pro inflammatory genes in macrophages is strongly attenuated which inhibits their differentiation to an M1 phenotype. Overall design: post anesthesia with 0.02% aminobenzoic acid ethyl ester tricaine Sigma Aldrich the tails of 3 dpf dpf embryos were partially amputated with a 1mm sapphire blade World Precision Instruments on 2% agarose coated Petri dishes under a Leica M165C stereomicroscope Chatzopoulou et al. 2016. Amputated and non amputated control embryos were pretreated for 2 hours with 25 µM beclomethasone Sigma Aldrich or vehicle 0.05% dimethyl sulfoxide DMSO …	pubmed:31072958	control amputated rep1	GSM3477130	tissue:3dpf zebrafish embryo treated with vehicle tail amputated\|drug treatment:0.05% DMSO in egg water\|tail amputation:tail amputated\|developmental stage:3dpf	control amputated rep1	Image analysis and base calling were done by the Illumina HCS version 2.2.68 and RTA version 1.18.66. cDNA sequencing data were analyzed by mapping the reads to the Danio rerio GRCz10 reference genome with annotation version 80 using Tophat v2.1.0. The DESeq v1.26.0 R package was used to test for differential expression. Before each analysis the genes with low reads were removed i.e. those genes for which the sum of reads from three replicates of the analyzed two groups was lower than 30. The output data were used for transcriptome analysis. Genome build: RNAseq reads from individual samples were mapped against D. rerio GRCz10.80 Supplementary files format and content: tab separated values files include id and reads for each gene	3dpf zebrafish embryo treated with vehicle tail amputated	post anesthesia with 0.02% aminobenzoic acid ethyl ester tricaine Sigma Aldrich the tails of 3 dpf dpf embryos were partially amputated Figure 1A with a 1mm sapphire blade World Precision Instruments on 2% agarose coated Petri dishes under a Leica M165C stereomicroscope Chatzopoulou et al. 2016. Amputated and non amputated control embryos were pretreated for 2 hours with 25 μM beclomethasone Sigma Aldrich or vehicle 0.05% dimethyl sulfoxide DMSO in egg water prior to amputation and received the same treatment post the amputation.	Macrophages were sorted from Tgmpeg1.4:mCherry F embryos as previously described Rougeot et al. 2014; Zakrzewska et al. 2010. Dissociation was performed with 100 150 embryos for each sample at 4 hours post amputation hpa using Liberase TL Roche and stopped by adding Fetal Calf Serum FCS to a final concentration of 10%. Isolated cells were resuspended in Dulbecco’s PBS DPBS and filtered through a 40 μm cell strainer. Actinomycin D Sigma Aldrich was added final concentration of 1 µg/ml to each step to inhibit transcription. Macrophages were sorted based on their red fluorescent signal using a FACSAria III cell sorter BD Biosciences. The sorted cells were collected in QIAzol lysis reagent Qiagen for RNA isolation. Extracted total RNA was amplified using the SMART seq V4 kit Clontech for sequencing. The RNA seq libraries generated with the SMART seq V4 kit were sequenced using an Illumina HiSeq 2500 instrument according to the manufacturer’s instructions with a read length of 50 nucleotides	Zebrafish were maintained and handled according to the guidelines from the Zebrafish Model Organism Database http://zfin.org and in compliance with the directives of the local animal welfare committee of Leiden University. They were exposed to a 14 hours light and 10 hours dark cycle to maintain circadian rhythmicity. Fertilization was performed by natural spawning at the beginning of the light period. Eggs were collected and raised at 28°C in egg water 60 µg/ml Instant Ocean sea salts and 0.0025% methylene blue.	drug treatment:0.05% DMSO in egg water\|tail amputation:tail amputated\|developmental stage:3dpf	GSM3477130	GSM3477130: control amputated rep1; Danio rerio; RNA Seq	GSM3477130	1	Macrophages were sorted from Tgmpeg1.4:mCherry F embryos as previously described Rougeot et al. 2014; Zakrzewska et al. 2010. Dissociation was performed with 100 150 embryos for each sample at 4 hours post amputation hpa using Liberase TL Roche and stopped by adding Fetal Calf Serum FCS to a final concentration of 10%. Isolated cells were resuspended in Dulbeccoâ??s PBS DPBS and filtered through a 40 Î¼m cell strainer. Actinomycin D Sigma Aldrich was added final concentration of 1 Âµg/ml to each step to inhibit transcription. Macrophages were sorted based on their red fluorescent signal using a FACSAria III cell sorter BD Biosciences. The sorted cells were collected in QIAzol lysis reagent Qiagen for RNA isolation. Extracted total RNA was amplified using the SMART seq V4 kit Clontech for sequencing. The RNA seq libraries generated with the SMART seq V4 kit were sequenced using an Illumina HiSeq 2500 instrument according to the manufacturerâ??s instructions with a read length of 50 nucleotides	GEO Accession:GSM3477130	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP169118	ZFG-16-07_8_19277_GATCAG_L002_R1_001.fastq.gz	fastq	504186102.0	9886002.0	GSM3477130 r2	0:51	A:139181704;C:115283021;G:112688512;T:136874289;N:158576	51		139181704	115283021	112688512	136874289	158576	SRX5021273	SRS4054038	SRA811328	GEO	Leiden University	1	0.93371		0.08483		0.69378		0.46833		51		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	Netherlands	2018-11-16	Larval	Larval	Tail	Multi-system
50650	50650	SRR8485408	SRX5021272	SRS4054037	SRP169118	PRJNA505837	Glucocorticoids inhibit macrophage differentiation towards a pro inflammatory phenotype upon wounding without xxx their migration	GSE122643	Transcriptome Analysis	Glucocorticoid drugs are widely used to treat immune related diseases but their use is limited by side effects and by resistance which especially occurs in macrophage dominated diseases. In order to improve glucocorticoid therapies more research is required into the mechanisms of glucocorticoid action. In the present study we have used a zebrafish model for inflammation to study glucocorticoid effects on the innate immune response. In zebrafish larvae the migration of neutrophils towards a site of injury is inhibited by the synthetic glucocorticoid beclomethasone while migration of macrophages is glucocorticoid resistant. RNA sequencing was done on on Fluorescence Activated Cell Sorting FACS sorted macrophages.The results show that the vast majority of the wounding induced transcriptional changes in these cells are inhibited by beclomethasone whereas a small subset is glucocorticoid insensitive. As a result beclomethasone decreases the number of macrophages that differentiate towards a pro inflammatory M1 phenotype which we demonstrated using a tnfa:eGFP F reporter line and analysis of macrophage morphology. We conclude that the glucocorticoid resistance of the wounding induced macrophage migration is due to the insensitivity of the induction of macrophage specific chemoattractants to glucocorticoid inhibition which may explain the relative resistance of macrophage dominated diseases to glucocorticoid therapy. However the induction of pro inflammatory genes in macrophages is strongly attenuated which inhibits their differentiation to an M1 phenotype. Overall design: post anesthesia with 0.02% aminobenzoic acid ethyl ester tricaine Sigma Aldrich the tails of 3 dpf dpf embryos were partially amputated with a 1mm sapphire blade World Precision Instruments on 2% agarose coated Petri dishes under a Leica M165C stereomicroscope Chatzopoulou et al. 2016. Amputated and non amputated control embryos were pretreated for 2 hours with 25 µM beclomethasone Sigma Aldrich or vehicle 0.05% dimethyl sulfoxide DMSO …	pubmed:31072958	beclo treated amputated rep1	GSM3477129	tissue:3dpf zebrafish embryo treated with beclomethas1 tail amputated\|drug treatment:25uM beclomethas1 in egg water\|tail amputation:tail amputated\|developmental stage:3dpf	beclo treated amputated rep1	Image analysis and base calling were done by the Illumina HCS version 2.2.68 and RTA version 1.18.66. cDNA sequencing data were analyzed by mapping the reads to the Danio rerio GRCz10 reference genome with annotation version 80 using Tophat v2.1.0. The DESeq v1.26.0 R package was used to test for differential expression. Before each analysis the genes with low reads were removed i.e. those genes for which the sum of reads from three replicates of the analyzed two groups was lower than 30. The output data were used for transcriptome analysis. Genome build: RNAseq reads from individual samples were mapped against D. rerio GRCz10.80 Supplementary files format and content: tab separated values files include id and reads for each gene	3dpf zebrafish embryo treated with beclomethasone tail amputated	post anesthesia with 0.02% aminobenzoic acid ethyl ester tricaine Sigma Aldrich the tails of 3 dpf dpf embryos were partially amputated Figure 1A with a 1mm sapphire blade World Precision Instruments on 2% agarose coated Petri dishes under a Leica M165C stereomicroscope Chatzopoulou et al. 2016. Amputated and non amputated control embryos were pretreated for 2 hours with 25 μM beclomethasone Sigma Aldrich or vehicle 0.05% dimethyl sulfoxide DMSO in egg water prior to amputation and received the same treatment post the amputation.	Macrophages were sorted from Tgmpeg1.4:mCherry F embryos as previously described Rougeot et al. 2014; Zakrzewska et al. 2010. Dissociation was performed with 100 150 embryos for each sample at 4 hours post amputation hpa using Liberase TL Roche and stopped by adding Fetal Calf Serum FCS to a final concentration of 10%. Isolated cells were resuspended in Dulbecco’s PBS DPBS and filtered through a 40 μm cell strainer. Actinomycin D Sigma Aldrich was added final concentration of 1 µg/ml to each step to inhibit transcription. Macrophages were sorted based on their red fluorescent signal using a FACSAria III cell sorter BD Biosciences. The sorted cells were collected in QIAzol lysis reagent Qiagen for RNA isolation. Extracted total RNA was amplified using the SMART seq V4 kit Clontech for sequencing. The RNA seq libraries generated with the SMART seq V4 kit were sequenced using an Illumina HiSeq 2500 instrument according to the manufacturer’s instructions with a read length of 50 nucleotides	Zebrafish were maintained and handled according to the guidelines from the Zebrafish Model Organism Database http://zfin.org and in compliance with the directives of the local animal welfare committee of Leiden University. They were exposed to a 14 hours light and 10 hours dark cycle to maintain circadian rhythmicity. Fertilization was performed by natural spawning at the beginning of the light period. Eggs were collected and raised at 28°C in egg water 60 µg/ml Instant Ocean sea salts and 0.0025% methylene blue.	drug treatment:25uM beclomethas1 in egg water\|tail amputation:tail amputated\|developmental stage:3dpf	GSM3477129	GSM3477129: beclo treated amputated rep1; Danio rerio; RNA Seq	GSM3477129	1	Macrophages were sorted from Tgmpeg1.4:mCherry F embryos as previously described Rougeot et al. 2014; Zakrzewska et al. 2010. Dissociation was performed with 100 150 embryos for each sample at 4 hours post amputation hpa using Liberase TL Roche and stopped by adding Fetal Calf Serum FCS to a final concentration of 10%. Isolated cells were resuspended in Dulbeccoâ??s PBS DPBS and filtered through a 40 Î¼m cell strainer. Actinomycin D Sigma Aldrich was added final concentration of 1 Âµg/ml to each step to inhibit transcription. Macrophages were sorted based on their red fluorescent signal using a FACSAria III cell sorter BD Biosciences. The sorted cells were collected in QIAzol lysis reagent Qiagen for RNA isolation. Extracted total RNA was amplified using the SMART seq V4 kit Clontech for sequencing. The RNA seq libraries generated with the SMART seq V4 kit were sequenced using an Illumina HiSeq 2500 instrument according to the manufacturerâ??s instructions with a read length of 50 nucleotides	GEO Accession:GSM3477129	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP169118	ZFG-16-07_7_19276_ATGTCA_L001_R1_001.fastq.gz	fastq	372699891.0	7307841.0	GSM3477129 r11	0:51	A:102344955;C:85719514;G:84019859;T:100398430;N:217133	51		102344955	85719514	84019859	100398430	217133	SRX5021272	SRS4054037	SRA811328	GEO	Leiden University	1	0.93518		0.09741		0.70175		0.47813		51		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	Netherlands	2018-11-16	Larval	Larval	Tail	Multi-system
50651	50651	SRR8485409	SRX5021272	SRS4054037	SRP169118	PRJNA505837	Glucocorticoids inhibit macrophage differentiation towards a pro inflammatory phenotype upon wounding without xxx their migration	GSE122643	Transcriptome Analysis	Glucocorticoid drugs are widely used to treat immune related diseases but their use is limited by side effects and by resistance which especially occurs in macrophage dominated diseases. In order to improve glucocorticoid therapies more research is required into the mechanisms of glucocorticoid action. In the present study we have used a zebrafish model for inflammation to study glucocorticoid effects on the innate immune response. In zebrafish larvae the migration of neutrophils towards a site of injury is inhibited by the synthetic glucocorticoid beclomethasone while migration of macrophages is glucocorticoid resistant. RNA sequencing was done on on Fluorescence Activated Cell Sorting FACS sorted macrophages.The results show that the vast majority of the wounding induced transcriptional changes in these cells are inhibited by beclomethasone whereas a small subset is glucocorticoid insensitive. As a result beclomethasone decreases the number of macrophages that differentiate towards a pro inflammatory M1 phenotype which we demonstrated using a tnfa:eGFP F reporter line and analysis of macrophage morphology. We conclude that the glucocorticoid resistance of the wounding induced macrophage migration is due to the insensitivity of the induction of macrophage specific chemoattractants to glucocorticoid inhibition which may explain the relative resistance of macrophage dominated diseases to glucocorticoid therapy. However the induction of pro inflammatory genes in macrophages is strongly attenuated which inhibits their differentiation to an M1 phenotype. Overall design: post anesthesia with 0.02% aminobenzoic acid ethyl ester tricaine Sigma Aldrich the tails of 3 dpf dpf embryos were partially amputated with a 1mm sapphire blade World Precision Instruments on 2% agarose coated Petri dishes under a Leica M165C stereomicroscope Chatzopoulou et al. 2016. Amputated and non amputated control embryos were pretreated for 2 hours with 25 µM beclomethasone Sigma Aldrich or vehicle 0.05% dimethyl sulfoxide DMSO …	pubmed:31072958	beclo treated amputated rep1	GSM3477129	tissue:3dpf zebrafish embryo treated with beclomethas1 tail amputated\|drug treatment:25uM beclomethas1 in egg water\|tail amputation:tail amputated\|developmental stage:3dpf	beclo treated amputated rep1	Image analysis and base calling were done by the Illumina HCS version 2.2.68 and RTA version 1.18.66. cDNA sequencing data were analyzed by mapping the reads to the Danio rerio GRCz10 reference genome with annotation version 80 using Tophat v2.1.0. The DESeq v1.26.0 R package was used to test for differential expression. Before each analysis the genes with low reads were removed i.e. those genes for which the sum of reads from three replicates of the analyzed two groups was lower than 30. The output data were used for transcriptome analysis. Genome build: RNAseq reads from individual samples were mapped against D. rerio GRCz10.80 Supplementary files format and content: tab separated values files include id and reads for each gene	3dpf zebrafish embryo treated with beclomethasone tail amputated	post anesthesia with 0.02% aminobenzoic acid ethyl ester tricaine Sigma Aldrich the tails of 3 dpf dpf embryos were partially amputated Figure 1A with a 1mm sapphire blade World Precision Instruments on 2% agarose coated Petri dishes under a Leica M165C stereomicroscope Chatzopoulou et al. 2016. Amputated and non amputated control embryos were pretreated for 2 hours with 25 μM beclomethasone Sigma Aldrich or vehicle 0.05% dimethyl sulfoxide DMSO in egg water prior to amputation and received the same treatment post the amputation.	Macrophages were sorted from Tgmpeg1.4:mCherry F embryos as previously described Rougeot et al. 2014; Zakrzewska et al. 2010. Dissociation was performed with 100 150 embryos for each sample at 4 hours post amputation hpa using Liberase TL Roche and stopped by adding Fetal Calf Serum FCS to a final concentration of 10%. Isolated cells were resuspended in Dulbecco’s PBS DPBS and filtered through a 40 μm cell strainer. Actinomycin D Sigma Aldrich was added final concentration of 1 µg/ml to each step to inhibit transcription. Macrophages were sorted based on their red fluorescent signal using a FACSAria III cell sorter BD Biosciences. The sorted cells were collected in QIAzol lysis reagent Qiagen for RNA isolation. Extracted total RNA was amplified using the SMART seq V4 kit Clontech for sequencing. The RNA seq libraries generated with the SMART seq V4 kit were sequenced using an Illumina HiSeq 2500 instrument according to the manufacturer’s instructions with a read length of 50 nucleotides	Zebrafish were maintained and handled according to the guidelines from the Zebrafish Model Organism Database http://zfin.org and in compliance with the directives of the local animal welfare committee of Leiden University. They were exposed to a 14 hours light and 10 hours dark cycle to maintain circadian rhythmicity. Fertilization was performed by natural spawning at the beginning of the light period. Eggs were collected and raised at 28°C in egg water 60 µg/ml Instant Ocean sea salts and 0.0025% methylene blue.	drug treatment:25uM beclomethas1 in egg water\|tail amputation:tail amputated\|developmental stage:3dpf	GSM3477129	GSM3477129: beclo treated amputated rep1; Danio rerio; RNA Seq	GSM3477129	1	Macrophages were sorted from Tgmpeg1.4:mCherry F embryos as previously described Rougeot et al. 2014; Zakrzewska et al. 2010. Dissociation was performed with 100 150 embryos for each sample at 4 hours post amputation hpa using Liberase TL Roche and stopped by adding Fetal Calf Serum FCS to a final concentration of 10%. Isolated cells were resuspended in Dulbeccoâ??s PBS DPBS and filtered through a 40 Î¼m cell strainer. Actinomycin D Sigma Aldrich was added final concentration of 1 Âµg/ml to each step to inhibit transcription. Macrophages were sorted based on their red fluorescent signal using a FACSAria III cell sorter BD Biosciences. The sorted cells were collected in QIAzol lysis reagent Qiagen for RNA isolation. Extracted total RNA was amplified using the SMART seq V4 kit Clontech for sequencing. The RNA seq libraries generated with the SMART seq V4 kit were sequenced using an Illumina HiSeq 2500 instrument according to the manufacturerâ??s instructions with a read length of 50 nucleotides	GEO Accession:GSM3477129	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP169118			388225923.0	7612273.0	GSM3477129 r2	0:51	A:106661370;C:89296371;G:87541480;T:104603484;N:123218	51		106661370	89296371	87541480	104603484	123218	SRX5021272	SRS4054037	SRA811328	GEO	Leiden University	1	0.93449		0.09749		0.70264		0.47314		51		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	Netherlands	2018-11-16	Larval	Larval	Tail	Multi-system
54735	54735	SRR10151942	SRX6877449	SRS5413231	SRP222763	PRJNA572587	Characterization of T cells from the larval zebrafish tail via single cell RNAseq	GSE137770	Transcriptome Analysis	We report single cell RNA sequencing of cells from the Tglck:GFP larval zebrafish tail to identify cell types expressing the marker and to identify gene candidates related to T cell migration behaviors. We identified 330 putative T cells and 131 putative epithelial cells. Differential expression analysis between the two groups revealed genes related to actin cytoskeleton remodeling associated with the T cells in addition to canonical T and ubiquitous immune cell markers. Overall design: Single cells n=461 isolated from FACS of Tglck:GFP Danio rerio FITC+ were analyzed.	pubmed:32427565	lckgfp s383	GSM4087504	source name:Danio rerio tail\|line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	lckgfp s383	STAR 2.5 Htseq 0.8.0 htseq count m intersection nonempty nonunique all Genome build: GRCz10 Supplementary files format and content: Raw counts of numbers of reads aligned to each feature for each cell in tab separated format lckgfp counts.txt	Danio rerio tail	Liberase TL 100 ug/mL and manual trituration was used to dissociate tail tissue. Cells were FACS sorted FITC+	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018		line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	GSM4087504	GSM4087504: lckgfp s383; Danio rerio; RNA Seq	GSM4087504	1	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018	GEO Accession:GSM4087504	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP222763	lckgfp_s383_R1.fastq.gz lckgfp_s383_R2.fastq.gz	fastq fastq	234832600.0	1174163.0	GSM4087504 r1	0:100 1:100	A:73305400;C:48312945;G:46608604;T:66604424;N:1227	100	100	73305400	48312945	46608604	66604424	1227	SRX6877449	SRS5413231	SRA965286	GEO	Stanford University	2	0.75941	0.76379	0.1177	0.1196	0.97948	0.9793	0.67812	0.67194	100	100	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2019-09-20	Larval	Larval	Tail	Multi-system
54736	54736	SRR10151941	SRX6877448	SRS5413230	SRP222763	PRJNA572587	Characterization of T cells from the larval zebrafish tail via single cell RNAseq	GSE137770	Transcriptome Analysis	We report single cell RNA sequencing of cells from the Tglck:GFP larval zebrafish tail to identify cell types expressing the marker and to identify gene candidates related to T cell migration behaviors. We identified 330 putative T cells and 131 putative epithelial cells. Differential expression analysis between the two groups revealed genes related to actin cytoskeleton remodeling associated with the T cells in addition to canonical T and ubiquitous immune cell markers. Overall design: Single cells n=461 isolated from FACS of Tglck:GFP Danio rerio FITC+ were analyzed.	pubmed:32427565	lckgfp s382	GSM4087503	source name:Danio rerio tail\|line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	lckgfp s382	STAR 2.5 Htseq 0.8.0 htseq count m intersection nonempty nonunique all Genome build: GRCz10 Supplementary files format and content: Raw counts of numbers of reads aligned to each feature for each cell in tab separated format lckgfp counts.txt	Danio rerio tail	Liberase TL 100 ug/mL and manual trituration was used to dissociate tail tissue. Cells were FACS sorted FITC+	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018		line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	GSM4087503	GSM4087503: lckgfp s382; Danio rerio; RNA Seq	GSM4087503	1	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018	GEO Accession:GSM4087503	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP222763	lckgfp_s382_R1.fastq.gz lckgfp_s382_R2.fastq.gz	fastq fastq	231321400.0	1156607.0	GSM4087503 r1	0:100 1:100	A:74109121;C:45769344;G:44284415;T:67157279;N:1241	100	100	74109121	45769344	44284415	67157279	1241	SRX6877448	SRS5413230	SRA965286	GEO	Stanford University	2	0.71327	0.73209	0.11938	0.12294	0.98113	0.98121	0.67445	0.67189	100	100	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2019-09-20	Larval	Larval	Tail	Multi-system
54737	54737	SRR10151940	SRX6877447	SRS5413229	SRP222763	PRJNA572587	Characterization of T cells from the larval zebrafish tail via single cell RNAseq	GSE137770	Transcriptome Analysis	We report single cell RNA sequencing of cells from the Tglck:GFP larval zebrafish tail to identify cell types expressing the marker and to identify gene candidates related to T cell migration behaviors. We identified 330 putative T cells and 131 putative epithelial cells. Differential expression analysis between the two groups revealed genes related to actin cytoskeleton remodeling associated with the T cells in addition to canonical T and ubiquitous immune cell markers. Overall design: Single cells n=461 isolated from FACS of Tglck:GFP Danio rerio FITC+ were analyzed.	pubmed:32427565	lckgfp s381	GSM4087502	source name:Danio rerio tail\|line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	lckgfp s381	STAR 2.5 Htseq 0.8.0 htseq count m intersection nonempty nonunique all Genome build: GRCz10 Supplementary files format and content: Raw counts of numbers of reads aligned to each feature for each cell in tab separated format lckgfp counts.txt	Danio rerio tail	Liberase TL 100 ug/mL and manual trituration was used to dissociate tail tissue. Cells were FACS sorted FITC+	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018		line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	GSM4087502	GSM4087502: lckgfp s381; Danio rerio; RNA Seq	GSM4087502	1	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018	GEO Accession:GSM4087502	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP222763	lckgfp_s381_R1.fastq.gz lckgfp_s381_R2.fastq.gz	fastq fastq	245645600.0	1228228.0	GSM4087502 r1	0:100 1:100	A:73876655;C:46349996;G:46669257;T:78748704;N:988	100	100	73876655	46349996	46669257	78748704	988	SRX6877447	SRS5413229	SRA965286	GEO	Stanford University	2	0.84889	0.85255	0.24599	0.25118	0.9584	0.9586	0.60851	0.60597	100	100	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2019-09-20	Larval	Larval	Tail	Multi-system
54738	54738	SRR10151939	SRX6877446	SRS5413228	SRP222763	PRJNA572587	Characterization of T cells from the larval zebrafish tail via single cell RNAseq	GSE137770	Transcriptome Analysis	We report single cell RNA sequencing of cells from the Tglck:GFP larval zebrafish tail to identify cell types expressing the marker and to identify gene candidates related to T cell migration behaviors. We identified 330 putative T cells and 131 putative epithelial cells. Differential expression analysis between the two groups revealed genes related to actin cytoskeleton remodeling associated with the T cells in addition to canonical T and ubiquitous immune cell markers. Overall design: Single cells n=461 isolated from FACS of Tglck:GFP Danio rerio FITC+ were analyzed.	pubmed:32427565	lckgfp s380	GSM4087501	source name:Danio rerio tail\|line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	lckgfp s380	STAR 2.5 Htseq 0.8.0 htseq count m intersection nonempty nonunique all Genome build: GRCz10 Supplementary files format and content: Raw counts of numbers of reads aligned to each feature for each cell in tab separated format lckgfp counts.txt	Danio rerio tail	Liberase TL 100 ug/mL and manual trituration was used to dissociate tail tissue. Cells were FACS sorted FITC+	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018		line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	GSM4087501	GSM4087501: lckgfp s380; Danio rerio; RNA Seq	GSM4087501	1	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018	GEO Accession:GSM4087501	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP222763	lckgfp_s380_R1.fastq.gz lckgfp_s380_R2.fastq.gz	fastq fastq	392055200.0	1960276.0	GSM4087501 r1	0:100 1:100	A:118333309;C:79802020;G:77119877;T:116798071;N:1923	100	100	118333309	79802020	77119877	116798071	1923	SRX6877446	SRS5413228	SRA965286	GEO	Stanford University	2	0.78714	0.7986	0.11307	0.1166	0.94466	0.94505	0.72339	0.72034	100	100	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2019-09-20	Larval	Larval	Tail	Multi-system
54739	54739	SRR10151938	SRX6877445	SRS5413227	SRP222763	PRJNA572587	Characterization of T cells from the larval zebrafish tail via single cell RNAseq	GSE137770	Transcriptome Analysis	We report single cell RNA sequencing of cells from the Tglck:GFP larval zebrafish tail to identify cell types expressing the marker and to identify gene candidates related to T cell migration behaviors. We identified 330 putative T cells and 131 putative epithelial cells. Differential expression analysis between the two groups revealed genes related to actin cytoskeleton remodeling associated with the T cells in addition to canonical T and ubiquitous immune cell markers. Overall design: Single cells n=461 isolated from FACS of Tglck:GFP Danio rerio FITC+ were analyzed.	pubmed:32427565	lckgfp s379	GSM4087500	source name:Danio rerio tail\|line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	lckgfp s379	STAR 2.5 Htseq 0.8.0 htseq count m intersection nonempty nonunique all Genome build: GRCz10 Supplementary files format and content: Raw counts of numbers of reads aligned to each feature for each cell in tab separated format lckgfp counts.txt	Danio rerio tail	Liberase TL 100 ug/mL and manual trituration was used to dissociate tail tissue. Cells were FACS sorted FITC+	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018		line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	GSM4087500	GSM4087500: lckgfp s379; Danio rerio; RNA Seq	GSM4087500	1	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018	GEO Accession:GSM4087500	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP222763	lckgfp_s379_R1.fastq.gz lckgfp_s379_R2.fastq.gz	fastq fastq	1126607400.0	5633037.0	GSM4087500 r1	0:100 1:100	A:316942811;C:247242301;G:247434168;T:314982567;N:5553	100	100	316942811	247242301	247434168	314982567	5553	SRX6877445	SRS5413227	SRA965286	GEO	Stanford University	2	0.90628	0.90945	0.2181	0.22037	0.97964	0.97958	0.47443	0.49146	100	100	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2019-09-20	Larval	Larval	Tail	Multi-system
54740	54740	SRR10151937	SRX6877444	SRS5413226	SRP222763	PRJNA572587	Characterization of T cells from the larval zebrafish tail via single cell RNAseq	GSE137770	Transcriptome Analysis	We report single cell RNA sequencing of cells from the Tglck:GFP larval zebrafish tail to identify cell types expressing the marker and to identify gene candidates related to T cell migration behaviors. We identified 330 putative T cells and 131 putative epithelial cells. Differential expression analysis between the two groups revealed genes related to actin cytoskeleton remodeling associated with the T cells in addition to canonical T and ubiquitous immune cell markers. Overall design: Single cells n=461 isolated from FACS of Tglck:GFP Danio rerio FITC+ were analyzed.	pubmed:32427565	lckgfp s378	GSM4087499	source name:Danio rerio tail\|line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	lckgfp s378	STAR 2.5 Htseq 0.8.0 htseq count m intersection nonempty nonunique all Genome build: GRCz10 Supplementary files format and content: Raw counts of numbers of reads aligned to each feature for each cell in tab separated format lckgfp counts.txt	Danio rerio tail	Liberase TL 100 ug/mL and manual trituration was used to dissociate tail tissue. Cells were FACS sorted FITC+	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018		line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	GSM4087499	GSM4087499: lckgfp s378; Danio rerio; RNA Seq	GSM4087499	1	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018	GEO Accession:GSM4087499	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP222763	lckgfp_s378_R1.fastq.gz lckgfp_s378_R2.fastq.gz	fastq fastq	337111400.0	1685557.0	GSM4087499 r1	0:100 1:100	A:98638322;C:70570254;G:69961020;T:97940105;N:1699	100	100	98638322	70570254	69961020	97940105	1699	SRX6877444	SRS5413226	SRA965286	GEO	Stanford University	2	0.87386	0.87621	0.19517	0.19574	0.97443	0.97463	0.60077	0.60132	100	100	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2019-09-20	Larval	Larval	Tail	Multi-system
54741	54741	SRR10151936	SRX6877443	SRS5413225	SRP222763	PRJNA572587	Characterization of T cells from the larval zebrafish tail via single cell RNAseq	GSE137770	Transcriptome Analysis	We report single cell RNA sequencing of cells from the Tglck:GFP larval zebrafish tail to identify cell types expressing the marker and to identify gene candidates related to T cell migration behaviors. We identified 330 putative T cells and 131 putative epithelial cells. Differential expression analysis between the two groups revealed genes related to actin cytoskeleton remodeling associated with the T cells in addition to canonical T and ubiquitous immune cell markers. Overall design: Single cells n=461 isolated from FACS of Tglck:GFP Danio rerio FITC+ were analyzed.	pubmed:32427565	lckgfp s377	GSM4087498	source name:Danio rerio tail\|line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	lckgfp s377	STAR 2.5 Htseq 0.8.0 htseq count m intersection nonempty nonunique all Genome build: GRCz10 Supplementary files format and content: Raw counts of numbers of reads aligned to each feature for each cell in tab separated format lckgfp counts.txt	Danio rerio tail	Liberase TL 100 ug/mL and manual trituration was used to dissociate tail tissue. Cells were FACS sorted FITC+	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018		line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	GSM4087498	GSM4087498: lckgfp s377; Danio rerio; RNA Seq	GSM4087498	1	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018	GEO Accession:GSM4087498	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP222763	lckgfp_s377_R1.fastq.gz lckgfp_s377_R2.fastq.gz	fastq fastq	213595800.0	1067979.0	GSM4087498 r1	0:100 1:100	A:65929082;C:44373444;G:41959720;T:61332589;N:965	100	100	65929082	44373444	41959720	61332589	965	SRX6877443	SRS5413225	SRA965286	GEO	Stanford University	2	0.63317	0.65413	0.48755	0.50508	0.96426	0.96317	0.67368	0.66493	100	100	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2019-09-20	Larval	Larval	Tail	Multi-system
54742	54742	SRR10151935	SRX6877442	SRS5413224	SRP222763	PRJNA572587	Characterization of T cells from the larval zebrafish tail via single cell RNAseq	GSE137770	Transcriptome Analysis	We report single cell RNA sequencing of cells from the Tglck:GFP larval zebrafish tail to identify cell types expressing the marker and to identify gene candidates related to T cell migration behaviors. We identified 330 putative T cells and 131 putative epithelial cells. Differential expression analysis between the two groups revealed genes related to actin cytoskeleton remodeling associated with the T cells in addition to canonical T and ubiquitous immune cell markers. Overall design: Single cells n=461 isolated from FACS of Tglck:GFP Danio rerio FITC+ were analyzed.	pubmed:32427565	lckgfp s376	GSM4087497	source name:Danio rerio tail\|line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	lckgfp s376	STAR 2.5 Htseq 0.8.0 htseq count m intersection nonempty nonunique all Genome build: GRCz10 Supplementary files format and content: Raw counts of numbers of reads aligned to each feature for each cell in tab separated format lckgfp counts.txt	Danio rerio tail	Liberase TL 100 ug/mL and manual trituration was used to dissociate tail tissue. Cells were FACS sorted FITC+	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018		line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	GSM4087497	GSM4087497: lckgfp s376; Danio rerio; RNA Seq	GSM4087497	1	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018	GEO Accession:GSM4087497	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP222763	lckgfp_s376_R1.fastq.gz lckgfp_s376_R2.fastq.gz	fastq fastq	88560200.0	442801.0	GSM4087497 r1	0:100 1:100	A:28243730;C:14191830;G:14708934;T:31415270;N:436	100	100	28243730	14191830	14708934	31415270	436	SRX6877442	SRS5413224	SRA965286	GEO	Stanford University	2	0.71521	0.72283	0.5654	0.57182	0.92989	0.9317	0.531	0.52094	100	100	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2019-09-20	Larval	Larval	Tail	Multi-system
54743	54743	SRR10151934	SRX6877441	SRS5413223	SRP222763	PRJNA572587	Characterization of T cells from the larval zebrafish tail via single cell RNAseq	GSE137770	Transcriptome Analysis	We report single cell RNA sequencing of cells from the Tglck:GFP larval zebrafish tail to identify cell types expressing the marker and to identify gene candidates related to T cell migration behaviors. We identified 330 putative T cells and 131 putative epithelial cells. Differential expression analysis between the two groups revealed genes related to actin cytoskeleton remodeling associated with the T cells in addition to canonical T and ubiquitous immune cell markers. Overall design: Single cells n=461 isolated from FACS of Tglck:GFP Danio rerio FITC+ were analyzed.	pubmed:32427565	lckgfp s375	GSM4087496	source name:Danio rerio tail\|line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	lckgfp s375	STAR 2.5 Htseq 0.8.0 htseq count m intersection nonempty nonunique all Genome build: GRCz10 Supplementary files format and content: Raw counts of numbers of reads aligned to each feature for each cell in tab separated format lckgfp counts.txt	Danio rerio tail	Liberase TL 100 ug/mL and manual trituration was used to dissociate tail tissue. Cells were FACS sorted FITC+	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018		line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	GSM4087496	GSM4087496: lckgfp s375; Danio rerio; RNA Seq	GSM4087496	1	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018	GEO Accession:GSM4087496	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP222763	lckgfp_s375_R1.fastq.gz lckgfp_s375_R2.fastq.gz	fastq fastq	64991200.0	324956.0	GSM4087496 r1	0:100 1:100	A:22513291;C:12471508;G:11416691;T:18589412;N:298	100	100	22513291	12471508	11416691	18589412	298	SRX6877441	SRS5413223	SRA965286	GEO	Stanford University	2	0.5963	0.62806	0.27588	0.2908	0.9754	0.975	0.44766	0.44857	100	100	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2019-09-20	Larval	Larval	Tail	Multi-system
54744	54744	SRR10151933	SRX6877440	SRS5413222	SRP222763	PRJNA572587	Characterization of T cells from the larval zebrafish tail via single cell RNAseq	GSE137770	Transcriptome Analysis	We report single cell RNA sequencing of cells from the Tglck:GFP larval zebrafish tail to identify cell types expressing the marker and to identify gene candidates related to T cell migration behaviors. We identified 330 putative T cells and 131 putative epithelial cells. Differential expression analysis between the two groups revealed genes related to actin cytoskeleton remodeling associated with the T cells in addition to canonical T and ubiquitous immune cell markers. Overall design: Single cells n=461 isolated from FACS of Tglck:GFP Danio rerio FITC+ were analyzed.	pubmed:32427565	lckgfp s374	GSM4087495	source name:Danio rerio tail\|line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	lckgfp s374	STAR 2.5 Htseq 0.8.0 htseq count m intersection nonempty nonunique all Genome build: GRCz10 Supplementary files format and content: Raw counts of numbers of reads aligned to each feature for each cell in tab separated format lckgfp counts.txt	Danio rerio tail	Liberase TL 100 ug/mL and manual trituration was used to dissociate tail tissue. Cells were FACS sorted FITC+	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018		line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	GSM4087495	GSM4087495: lckgfp s374; Danio rerio; RNA Seq	GSM4087495	1	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018	GEO Accession:GSM4087495	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP222763	lckgfp_s374_R1.fastq.gz lckgfp_s374_R2.fastq.gz	fastq fastq	176144200.0	880721.0	GSM4087495 r1	0:100 1:100	A:53180935;C:37108779;G:35845658;T:50007992;N:836	100	100	53180935	37108779	35845658	50007992	836	SRX6877440	SRS5413222	SRA965286	GEO	Stanford University	2	0.76708	0.77852	0.13854	0.14107	0.98238	0.98283	0.66594	0.67246	100	100	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2019-09-20	Larval	Larval	Tail	Multi-system
54745	54745	SRR10151932	SRX6877439	SRS5413221	SRP222763	PRJNA572587	Characterization of T cells from the larval zebrafish tail via single cell RNAseq	GSE137770	Transcriptome Analysis	We report single cell RNA sequencing of cells from the Tglck:GFP larval zebrafish tail to identify cell types expressing the marker and to identify gene candidates related to T cell migration behaviors. We identified 330 putative T cells and 131 putative epithelial cells. Differential expression analysis between the two groups revealed genes related to actin cytoskeleton remodeling associated with the T cells in addition to canonical T and ubiquitous immune cell markers. Overall design: Single cells n=461 isolated from FACS of Tglck:GFP Danio rerio FITC+ were analyzed.	pubmed:32427565	lckgfp s373	GSM4087494	source name:Danio rerio tail\|line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	lckgfp s373	STAR 2.5 Htseq 0.8.0 htseq count m intersection nonempty nonunique all Genome build: GRCz10 Supplementary files format and content: Raw counts of numbers of reads aligned to each feature for each cell in tab separated format lckgfp counts.txt	Danio rerio tail	Liberase TL 100 ug/mL and manual trituration was used to dissociate tail tissue. Cells were FACS sorted FITC+	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018		line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	GSM4087494	GSM4087494: lckgfp s373; Danio rerio; RNA Seq	GSM4087494	1	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018	GEO Accession:GSM4087494	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP222763	lckgfp_s373_R1.fastq.gz lckgfp_s373_R2.fastq.gz	fastq fastq	139717800.0	698589.0	GSM4087494 r1	0:100 1:100	A:42519883;C:25961082;G:25907850;T:45328266;N:719	100	100	42519883	25961082	25907850	45328266	719	SRX6877439	SRS5413221	SRA965286	GEO	Stanford University	2	0.75679	0.76819	0.28064	0.29002	0.97305	0.97273	0.56393	0.53945	100	100	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2019-09-20	Larval	Larval	Tail	Multi-system
54746	54746	SRR10151931	SRX6877438	SRS5413220	SRP222763	PRJNA572587	Characterization of T cells from the larval zebrafish tail via single cell RNAseq	GSE137770	Transcriptome Analysis	We report single cell RNA sequencing of cells from the Tglck:GFP larval zebrafish tail to identify cell types expressing the marker and to identify gene candidates related to T cell migration behaviors. We identified 330 putative T cells and 131 putative epithelial cells. Differential expression analysis between the two groups revealed genes related to actin cytoskeleton remodeling associated with the T cells in addition to canonical T and ubiquitous immune cell markers. Overall design: Single cells n=461 isolated from FACS of Tglck:GFP Danio rerio FITC+ were analyzed.	pubmed:32427565	lckgfp s372	GSM4087493	source name:Danio rerio tail\|line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	lckgfp s372	STAR 2.5 Htseq 0.8.0 htseq count m intersection nonempty nonunique all Genome build: GRCz10 Supplementary files format and content: Raw counts of numbers of reads aligned to each feature for each cell in tab separated format lckgfp counts.txt	Danio rerio tail	Liberase TL 100 ug/mL and manual trituration was used to dissociate tail tissue. Cells were FACS sorted FITC+	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018		line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	GSM4087493	GSM4087493: lckgfp s372; Danio rerio; RNA Seq	GSM4087493	1	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018	GEO Accession:GSM4087493	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP222763	lckgfp_s372_R1.fastq.gz lckgfp_s372_R2.fastq.gz	fastq fastq	446412600.0	2232063.0	GSM4087493 r1	0:100 1:100	A:128821576;C:93782508;G:93694322;T:130111961;N:2233	100	100	128821576	93782508	93694322	130111961	2233	SRX6877438	SRS5413220	SRA965286	GEO	Stanford University	2	0.89125	0.89493	0.23701	0.24011	0.9697	0.97005	0.53362	0.53735	100	100	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2019-09-20	Larval	Larval	Tail	Multi-system
54747	54747	SRR10151930	SRX6877437	SRS5413219	SRP222763	PRJNA572587	Characterization of T cells from the larval zebrafish tail via single cell RNAseq	GSE137770	Transcriptome Analysis	We report single cell RNA sequencing of cells from the Tglck:GFP larval zebrafish tail to identify cell types expressing the marker and to identify gene candidates related to T cell migration behaviors. We identified 330 putative T cells and 131 putative epithelial cells. Differential expression analysis between the two groups revealed genes related to actin cytoskeleton remodeling associated with the T cells in addition to canonical T and ubiquitous immune cell markers. Overall design: Single cells n=461 isolated from FACS of Tglck:GFP Danio rerio FITC+ were analyzed.	pubmed:32427565	lckgfp s371	GSM4087492	source name:Danio rerio tail\|line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	lckgfp s371	STAR 2.5 Htseq 0.8.0 htseq count m intersection nonempty nonunique all Genome build: GRCz10 Supplementary files format and content: Raw counts of numbers of reads aligned to each feature for each cell in tab separated format lckgfp counts.txt	Danio rerio tail	Liberase TL 100 ug/mL and manual trituration was used to dissociate tail tissue. Cells were FACS sorted FITC+	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018		line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	GSM4087492	GSM4087492: lckgfp s371; Danio rerio; RNA Seq	GSM4087492	1	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018	GEO Accession:GSM4087492	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP222763	lckgfp_s371_R1.fastq.gz lckgfp_s371_R2.fastq.gz	fastq fastq	339631800.0	1698159.0	GSM4087492 r1	0:100 1:100	A:98594117;C:68506566;G:69103975;T:103425575;N:1567	100	100	98594117	68506566	69103975	103425575	1567	SRX6877437	SRS5413219	SRA965286	GEO	Stanford University	2	0.84886	0.85388	0.19246	0.19436	0.95014	0.95012	0.54321	0.54848	100	100	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2019-09-20	Larval	Larval	Tail	Multi-system
54748	54748	SRR10151929	SRX6877436	SRS5413218	SRP222763	PRJNA572587	Characterization of T cells from the larval zebrafish tail via single cell RNAseq	GSE137770	Transcriptome Analysis	We report single cell RNA sequencing of cells from the Tglck:GFP larval zebrafish tail to identify cell types expressing the marker and to identify gene candidates related to T cell migration behaviors. We identified 330 putative T cells and 131 putative epithelial cells. Differential expression analysis between the two groups revealed genes related to actin cytoskeleton remodeling associated with the T cells in addition to canonical T and ubiquitous immune cell markers. Overall design: Single cells n=461 isolated from FACS of Tglck:GFP Danio rerio FITC+ were analyzed.	pubmed:32427565	lckgfp s370	GSM4087491	source name:Danio rerio tail\|line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	lckgfp s370	STAR 2.5 Htseq 0.8.0 htseq count m intersection nonempty nonunique all Genome build: GRCz10 Supplementary files format and content: Raw counts of numbers of reads aligned to each feature for each cell in tab separated format lckgfp counts.txt	Danio rerio tail	Liberase TL 100 ug/mL and manual trituration was used to dissociate tail tissue. Cells were FACS sorted FITC+	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018		line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	GSM4087491	GSM4087491: lckgfp s370; Danio rerio; RNA Seq	GSM4087491	1	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018	GEO Accession:GSM4087491	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP222763	lckgfp_s370_R1.fastq.gz lckgfp_s370_R2.fastq.gz	fastq fastq	87104400.0	435522.0	GSM4087491 r1	0:100 1:100	A:26443732;C:16935041;G:16826001;T:26899213;N:413	100	100	26443732	16935041	16826001	26899213	413	SRX6877436	SRS5413218	SRA965286	GEO	Stanford University	2	0.82125	0.82733	0.31193	0.31596	0.97453	0.97433	0.60892	0.61117	100	100	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2019-09-20	Larval	Larval	Tail	Multi-system
54749	54749	SRR10151928	SRX6877435	SRS5413217	SRP222763	PRJNA572587	Characterization of T cells from the larval zebrafish tail via single cell RNAseq	GSE137770	Transcriptome Analysis	We report single cell RNA sequencing of cells from the Tglck:GFP larval zebrafish tail to identify cell types expressing the marker and to identify gene candidates related to T cell migration behaviors. We identified 330 putative T cells and 131 putative epithelial cells. Differential expression analysis between the two groups revealed genes related to actin cytoskeleton remodeling associated with the T cells in addition to canonical T and ubiquitous immune cell markers. Overall design: Single cells n=461 isolated from FACS of Tglck:GFP Danio rerio FITC+ were analyzed.	pubmed:32427565	lckgfp s369	GSM4087490	source name:Danio rerio tail\|line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	lckgfp s369	STAR 2.5 Htseq 0.8.0 htseq count m intersection nonempty nonunique all Genome build: GRCz10 Supplementary files format and content: Raw counts of numbers of reads aligned to each feature for each cell in tab separated format lckgfp counts.txt	Danio rerio tail	Liberase TL 100 ug/mL and manual trituration was used to dissociate tail tissue. Cells were FACS sorted FITC+	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018		line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	GSM4087490	GSM4087490: lckgfp s369; Danio rerio; RNA Seq	GSM4087490	1	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018	GEO Accession:GSM4087490	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP222763	lckgfp_s369_R1.fastq.gz lckgfp_s369_R2.fastq.gz	fastq fastq	581275000.0	2906375.0	GSM4087490 r1	0:100 1:100	A:164842289;C:120994794;G:122636896;T:172798268;N:2753	100	100	164842289	120994794	122636896	172798268	2753	SRX6877435	SRS5413217	SRA965286	GEO	Stanford University	2	0.88299	0.88484	0.19686	0.19809	0.95436	0.95408	0.56675	0.57288	100	100	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2019-09-20	Larval	Larval	Tail	Multi-system
54750	54750	SRR10151927	SRX6877434	SRS5413216	SRP222763	PRJNA572587	Characterization of T cells from the larval zebrafish tail via single cell RNAseq	GSE137770	Transcriptome Analysis	We report single cell RNA sequencing of cells from the Tglck:GFP larval zebrafish tail to identify cell types expressing the marker and to identify gene candidates related to T cell migration behaviors. We identified 330 putative T cells and 131 putative epithelial cells. Differential expression analysis between the two groups revealed genes related to actin cytoskeleton remodeling associated with the T cells in addition to canonical T and ubiquitous immune cell markers. Overall design: Single cells n=461 isolated from FACS of Tglck:GFP Danio rerio FITC+ were analyzed.	pubmed:32427565	lckgfp s368	GSM4087489	source name:Danio rerio tail\|line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	lckgfp s368	STAR 2.5 Htseq 0.8.0 htseq count m intersection nonempty nonunique all Genome build: GRCz10 Supplementary files format and content: Raw counts of numbers of reads aligned to each feature for each cell in tab separated format lckgfp counts.txt	Danio rerio tail	Liberase TL 100 ug/mL and manual trituration was used to dissociate tail tissue. Cells were FACS sorted FITC+	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018		line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	GSM4087489	GSM4087489: lckgfp s368; Danio rerio; RNA Seq	GSM4087489	1	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018	GEO Accession:GSM4087489	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP222763	lckgfp_s368_R1.fastq.gz lckgfp_s368_R2.fastq.gz	fastq fastq	312312800.0	1561564.0	GSM4087489 r1	0:100 1:100	A:92531881;C:61673383;G:61568700;T:96537155;N:1681	100	100	92531881	61673383	61568700	96537155	1681	SRX6877434	SRS5413216	SRA965286	GEO	Stanford University	2	0.82667	0.83385	0.29498	0.29709	0.97344	0.97366	0.54305	0.54647	100	100	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2019-09-20	Larval	Larval	Tail	Multi-system
54751	54751	SRR10151926	SRX6877433	SRS5413215	SRP222763	PRJNA572587	Characterization of T cells from the larval zebrafish tail via single cell RNAseq	GSE137770	Transcriptome Analysis	We report single cell RNA sequencing of cells from the Tglck:GFP larval zebrafish tail to identify cell types expressing the marker and to identify gene candidates related to T cell migration behaviors. We identified 330 putative T cells and 131 putative epithelial cells. Differential expression analysis between the two groups revealed genes related to actin cytoskeleton remodeling associated with the T cells in addition to canonical T and ubiquitous immune cell markers. Overall design: Single cells n=461 isolated from FACS of Tglck:GFP Danio rerio FITC+ were analyzed.	pubmed:32427565	lckgfp s367	GSM4087488	source name:Danio rerio tail\|line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	lckgfp s367	STAR 2.5 Htseq 0.8.0 htseq count m intersection nonempty nonunique all Genome build: GRCz10 Supplementary files format and content: Raw counts of numbers of reads aligned to each feature for each cell in tab separated format lckgfp counts.txt	Danio rerio tail	Liberase TL 100 ug/mL and manual trituration was used to dissociate tail tissue. Cells were FACS sorted FITC+	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018		line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	GSM4087488	GSM4087488: lckgfp s367; Danio rerio; RNA Seq	GSM4087488	1	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018	GEO Accession:GSM4087488	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP222763	lckgfp_s367_R1.fastq.gz lckgfp_s367_R2.fastq.gz	fastq fastq	46265000.0	231325.0	GSM4087488 r1	0:100 1:100	A:13465697;C:8956151;G:9229542;T:14613421;N:189	100	100	13465697	8956151	9229542	14613421	189	SRX6877433	SRS5413215	SRA965286	GEO	Stanford University	2	0.84333	0.8365	0.28527	0.2816	0.97561	0.97469	0.52056	0.52116	100	100	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2019-09-20	Larval	Larval	Tail	Multi-system
54752	54752	SRR10151925	SRX6877432	SRS5413214	SRP222763	PRJNA572587	Characterization of T cells from the larval zebrafish tail via single cell RNAseq	GSE137770	Transcriptome Analysis	We report single cell RNA sequencing of cells from the Tglck:GFP larval zebrafish tail to identify cell types expressing the marker and to identify gene candidates related to T cell migration behaviors. We identified 330 putative T cells and 131 putative epithelial cells. Differential expression analysis between the two groups revealed genes related to actin cytoskeleton remodeling associated with the T cells in addition to canonical T and ubiquitous immune cell markers. Overall design: Single cells n=461 isolated from FACS of Tglck:GFP Danio rerio FITC+ were analyzed.	pubmed:32427565	lckgfp s366	GSM4087487	source name:Danio rerio tail\|line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	lckgfp s366	STAR 2.5 Htseq 0.8.0 htseq count m intersection nonempty nonunique all Genome build: GRCz10 Supplementary files format and content: Raw counts of numbers of reads aligned to each feature for each cell in tab separated format lckgfp counts.txt	Danio rerio tail	Liberase TL 100 ug/mL and manual trituration was used to dissociate tail tissue. Cells were FACS sorted FITC+	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018		line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	GSM4087487	GSM4087487: lckgfp s366; Danio rerio; RNA Seq	GSM4087487	1	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018	GEO Accession:GSM4087487	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP222763	lckgfp_s366_R1.fastq.gz lckgfp_s366_R2.fastq.gz	fastq fastq	286132600.0	1430663.0	GSM4087487 r1	0:100 1:100	A:86110388;C:58112895;G:57034401;T:84873652;N:1264	100	100	86110388	58112895	57034401	84873652	1264	SRX6877432	SRS5413214	SRA965286	GEO	Stanford University	2	0.7188	0.73304	0.23183	0.23804	0.97195	0.9724	0.60395	0.60083	100	100	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2019-09-20	Larval	Larval	Tail	Multi-system
54753	54753	SRR10151924	SRX6877431	SRS5413213	SRP222763	PRJNA572587	Characterization of T cells from the larval zebrafish tail via single cell RNAseq	GSE137770	Transcriptome Analysis	We report single cell RNA sequencing of cells from the Tglck:GFP larval zebrafish tail to identify cell types expressing the marker and to identify gene candidates related to T cell migration behaviors. We identified 330 putative T cells and 131 putative epithelial cells. Differential expression analysis between the two groups revealed genes related to actin cytoskeleton remodeling associated with the T cells in addition to canonical T and ubiquitous immune cell markers. Overall design: Single cells n=461 isolated from FACS of Tglck:GFP Danio rerio FITC+ were analyzed.	pubmed:32427565	lckgfp s365	GSM4087486	source name:Danio rerio tail\|line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	lckgfp s365	STAR 2.5 Htseq 0.8.0 htseq count m intersection nonempty nonunique all Genome build: GRCz10 Supplementary files format and content: Raw counts of numbers of reads aligned to each feature for each cell in tab separated format lckgfp counts.txt	Danio rerio tail	Liberase TL 100 ug/mL and manual trituration was used to dissociate tail tissue. Cells were FACS sorted FITC+	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018		line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	GSM4087486	GSM4087486: lckgfp s365; Danio rerio; RNA Seq	GSM4087486	1	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018	GEO Accession:GSM4087486	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP222763	lckgfp_s365_R1.fastq.gz lckgfp_s365_R2.fastq.gz	fastq fastq	129864000.0	649320.0	GSM4087486 r1	0:100 1:100	A:42306739;C:23190789;G:22929572;T:41436300;N:600	100	100	42306739	23190789	22929572	41436300	600	SRX6877431	SRS5413213	SRA965286	GEO	Stanford University	2	0.67875	0.694	0.29442	0.30278	0.98206	0.98212	0.60421	0.60135	100	100	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2019-09-20	Larval	Larval	Tail	Multi-system
54754	54754	SRR10151923	SRX6877430	SRS5413212	SRP222763	PRJNA572587	Characterization of T cells from the larval zebrafish tail via single cell RNAseq	GSE137770	Transcriptome Analysis	We report single cell RNA sequencing of cells from the Tglck:GFP larval zebrafish tail to identify cell types expressing the marker and to identify gene candidates related to T cell migration behaviors. We identified 330 putative T cells and 131 putative epithelial cells. Differential expression analysis between the two groups revealed genes related to actin cytoskeleton remodeling associated with the T cells in addition to canonical T and ubiquitous immune cell markers. Overall design: Single cells n=461 isolated from FACS of Tglck:GFP Danio rerio FITC+ were analyzed.	pubmed:32427565	lckgfp s364	GSM4087485	source name:Danio rerio tail\|line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	lckgfp s364	STAR 2.5 Htseq 0.8.0 htseq count m intersection nonempty nonunique all Genome build: GRCz10 Supplementary files format and content: Raw counts of numbers of reads aligned to each feature for each cell in tab separated format lckgfp counts.txt	Danio rerio tail	Liberase TL 100 ug/mL and manual trituration was used to dissociate tail tissue. Cells were FACS sorted FITC+	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018		line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	GSM4087485	GSM4087485: lckgfp s364; Danio rerio; RNA Seq	GSM4087485	1	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018	GEO Accession:GSM4087485	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP222763	lckgfp_s364_R1.fastq.gz lckgfp_s364_R2.fastq.gz	fastq fastq	552863400.0	2764317.0	GSM4087485 r1	0:100 1:100	A:156249646;C:120365964;G:119437753;T:156807349;N:2688	100	100	156249646	120365964	119437753	156807349	2688	SRX6877430	SRS5413212	SRA965286	GEO	Stanford University	2	0.89031	0.89577	0.17435	0.17553	0.96646	0.96688	0.55727	0.54994	100	100	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2019-09-20	Larval	Larval	Tail	Multi-system
54755	54755	SRR10151922	SRX6877429	SRS5413211	SRP222763	PRJNA572587	Characterization of T cells from the larval zebrafish tail via single cell RNAseq	GSE137770	Transcriptome Analysis	We report single cell RNA sequencing of cells from the Tglck:GFP larval zebrafish tail to identify cell types expressing the marker and to identify gene candidates related to T cell migration behaviors. We identified 330 putative T cells and 131 putative epithelial cells. Differential expression analysis between the two groups revealed genes related to actin cytoskeleton remodeling associated with the T cells in addition to canonical T and ubiquitous immune cell markers. Overall design: Single cells n=461 isolated from FACS of Tglck:GFP Danio rerio FITC+ were analyzed.	pubmed:32427565	lckgfp s363	GSM4087484	source name:Danio rerio tail\|line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	lckgfp s363	STAR 2.5 Htseq 0.8.0 htseq count m intersection nonempty nonunique all Genome build: GRCz10 Supplementary files format and content: Raw counts of numbers of reads aligned to each feature for each cell in tab separated format lckgfp counts.txt	Danio rerio tail	Liberase TL 100 ug/mL and manual trituration was used to dissociate tail tissue. Cells were FACS sorted FITC+	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018		line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	GSM4087484	GSM4087484: lckgfp s363; Danio rerio; RNA Seq	GSM4087484	1	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018	GEO Accession:GSM4087484	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP222763	lckgfp_s363_R1.fastq.gz lckgfp_s363_R2.fastq.gz	fastq fastq	627214400.0	3136072.0	GSM4087484 r1	0:100 1:100	A:181218539;C:131944904;G:131936387;T:182111593;N:2977	100	100	181218539	131944904	131936387	182111593	2977	SRX6877429	SRS5413211	SRA965286	GEO	Stanford University	2	0.8898	0.89468	0.25549	0.25745	0.96629	0.96682	0.5524	0.5679	100	100	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2019-09-20	Larval	Larval	Tail	Multi-system
54756	54756	SRR10151921	SRX6877428	SRS5413210	SRP222763	PRJNA572587	Characterization of T cells from the larval zebrafish tail via single cell RNAseq	GSE137770	Transcriptome Analysis	We report single cell RNA sequencing of cells from the Tglck:GFP larval zebrafish tail to identify cell types expressing the marker and to identify gene candidates related to T cell migration behaviors. We identified 330 putative T cells and 131 putative epithelial cells. Differential expression analysis between the two groups revealed genes related to actin cytoskeleton remodeling associated with the T cells in addition to canonical T and ubiquitous immune cell markers. Overall design: Single cells n=461 isolated from FACS of Tglck:GFP Danio rerio FITC+ were analyzed.	pubmed:32427565	lckgfp s362	GSM4087483	source name:Danio rerio tail\|line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	lckgfp s362	STAR 2.5 Htseq 0.8.0 htseq count m intersection nonempty nonunique all Genome build: GRCz10 Supplementary files format and content: Raw counts of numbers of reads aligned to each feature for each cell in tab separated format lckgfp counts.txt	Danio rerio tail	Liberase TL 100 ug/mL and manual trituration was used to dissociate tail tissue. Cells were FACS sorted FITC+	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018		line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	GSM4087483	GSM4087483: lckgfp s362; Danio rerio; RNA Seq	GSM4087483	1	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018	GEO Accession:GSM4087483	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP222763	lckgfp_s362_R1.fastq.gz lckgfp_s362_R2.fastq.gz	fastq fastq	85745400.0	428727.0	GSM4087483 r1	0:100 1:100	A:27389948;C:15262098;G:15349274;T:27743616;N:464	100	100	27389948	15262098	15349274	27743616	464	SRX6877428	SRS5413210	SRA965286	GEO	Stanford University	2	0.68527	0.70382	0.38779	0.40917	0.97954	0.97932	0.62335	0.62203	100	100	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2019-09-20	Larval	Larval	Tail	Multi-system
54757	54757	SRR10151920	SRX6877427	SRS5413209	SRP222763	PRJNA572587	Characterization of T cells from the larval zebrafish tail via single cell RNAseq	GSE137770	Transcriptome Analysis	We report single cell RNA sequencing of cells from the Tglck:GFP larval zebrafish tail to identify cell types expressing the marker and to identify gene candidates related to T cell migration behaviors. We identified 330 putative T cells and 131 putative epithelial cells. Differential expression analysis between the two groups revealed genes related to actin cytoskeleton remodeling associated with the T cells in addition to canonical T and ubiquitous immune cell markers. Overall design: Single cells n=461 isolated from FACS of Tglck:GFP Danio rerio FITC+ were analyzed.	pubmed:32427565	lckgfp s361	GSM4087482	source name:Danio rerio tail\|line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	lckgfp s361	STAR 2.5 Htseq 0.8.0 htseq count m intersection nonempty nonunique all Genome build: GRCz10 Supplementary files format and content: Raw counts of numbers of reads aligned to each feature for each cell in tab separated format lckgfp counts.txt	Danio rerio tail	Liberase TL 100 ug/mL and manual trituration was used to dissociate tail tissue. Cells were FACS sorted FITC+	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018		line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	GSM4087482	GSM4087482: lckgfp s361; Danio rerio; RNA Seq	GSM4087482	1	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018	GEO Accession:GSM4087482	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP222763	lckgfp_s361_R1.fastq.gz lckgfp_s361_R2.fastq.gz	fastq fastq	195593800.0	977969.0	GSM4087482 r1	0:100 1:100	A:56644246;C:40806137;G:40753130;T:57389382;N:905	100	100	56644246	40806137	40753130	57389382	905	SRX6877427	SRS5413209	SRA965286	GEO	Stanford University	2	0.83027	0.84227	0.11997	0.12315	0.94821	0.9483	0.62568	0.63216	100	100	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2019-09-20	Larval	Larval	Tail	Multi-system
54758	54758	SRR10151919	SRX6877426	SRS5413208	SRP222763	PRJNA572587	Characterization of T cells from the larval zebrafish tail via single cell RNAseq	GSE137770	Transcriptome Analysis	We report single cell RNA sequencing of cells from the Tglck:GFP larval zebrafish tail to identify cell types expressing the marker and to identify gene candidates related to T cell migration behaviors. We identified 330 putative T cells and 131 putative epithelial cells. Differential expression analysis between the two groups revealed genes related to actin cytoskeleton remodeling associated with the T cells in addition to canonical T and ubiquitous immune cell markers. Overall design: Single cells n=461 isolated from FACS of Tglck:GFP Danio rerio FITC+ were analyzed.	pubmed:32427565	lckgfp s360	GSM4087481	source name:Danio rerio tail\|line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	lckgfp s360	STAR 2.5 Htseq 0.8.0 htseq count m intersection nonempty nonunique all Genome build: GRCz10 Supplementary files format and content: Raw counts of numbers of reads aligned to each feature for each cell in tab separated format lckgfp counts.txt	Danio rerio tail	Liberase TL 100 ug/mL and manual trituration was used to dissociate tail tissue. Cells were FACS sorted FITC+	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018		line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	GSM4087481	GSM4087481: lckgfp s360; Danio rerio; RNA Seq	GSM4087481	1	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018	GEO Accession:GSM4087481	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP222763	lckgfp_s360_R1.fastq.gz lckgfp_s360_R2.fastq.gz	fastq fastq	67188800.0	335944.0	GSM4087481 r1	0:100 1:100	A:21206262;C:12841122;G:12703318;T:20437773;N:325	100	100	21206262	12841122	12703318	20437773	325	SRX6877426	SRS5413208	SRA965286	GEO	Stanford University	2	0.70901	0.72161	0.23299	0.23771	0.95694	0.95672	0.60159	0.58695	100	100	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2019-09-20	Larval	Larval	Tail	Multi-system
54759	54759	SRR10151726	SRX6877425	SRS5413207	SRP222763	PRJNA572587	Characterization of T cells from the larval zebrafish tail via single cell RNAseq	GSE137770	Transcriptome Analysis	We report single cell RNA sequencing of cells from the Tglck:GFP larval zebrafish tail to identify cell types expressing the marker and to identify gene candidates related to T cell migration behaviors. We identified 330 putative T cells and 131 putative epithelial cells. Differential expression analysis between the two groups revealed genes related to actin cytoskeleton remodeling associated with the T cells in addition to canonical T and ubiquitous immune cell markers. Overall design: Single cells n=461 isolated from FACS of Tglck:GFP Danio rerio FITC+ were analyzed.	pubmed:32427565	lckgfp s167	GSM4087288	source name:Danio rerio tail\|line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	lckgfp s167	STAR 2.5 Htseq 0.8.0 htseq count m intersection nonempty nonunique all Genome build: GRCz10 Supplementary files format and content: Raw counts of numbers of reads aligned to each feature for each cell in tab separated format lckgfp counts.txt	Danio rerio tail	Liberase TL 100 ug/mL and manual trituration was used to dissociate tail tissue. Cells were FACS sorted FITC+	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018		line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	GSM4087288	GSM4087288: lckgfp s167; Danio rerio; RNA Seq	GSM4087288	1	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018	GEO Accession:GSM4087288	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP222763	lckgfp_s167_R1.fastq.gz lckgfp_s167_R2.fastq.gz	fastq fastq	134099800.0	670499.0	GSM4087288 r1	0:100 1:100	A:38437552;C:29081890;G:28575183;T:38004579;N:596	100	100	38437552	29081890	28575183	38004579	596	SRX6877425	SRS5413207	SRA965286	GEO	Stanford University	2	0.88231	0.88686	0.18966	0.19146	0.96609	0.96575	0.59186	0.58694	100	100	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2019-09-20	Larval	Larval	Tail	Multi-system
54760	54760	SRR10151725	SRX6877424	SRS5413206	SRP222763	PRJNA572587	Characterization of T cells from the larval zebrafish tail via single cell RNAseq	GSE137770	Transcriptome Analysis	We report single cell RNA sequencing of cells from the Tglck:GFP larval zebrafish tail to identify cell types expressing the marker and to identify gene candidates related to T cell migration behaviors. We identified 330 putative T cells and 131 putative epithelial cells. Differential expression analysis between the two groups revealed genes related to actin cytoskeleton remodeling associated with the T cells in addition to canonical T and ubiquitous immune cell markers. Overall design: Single cells n=461 isolated from FACS of Tglck:GFP Danio rerio FITC+ were analyzed.	pubmed:32427565	lckgfp s166	GSM4087287	source name:Danio rerio tail\|line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	lckgfp s166	STAR 2.5 Htseq 0.8.0 htseq count m intersection nonempty nonunique all Genome build: GRCz10 Supplementary files format and content: Raw counts of numbers of reads aligned to each feature for each cell in tab separated format lckgfp counts.txt	Danio rerio tail	Liberase TL 100 ug/mL and manual trituration was used to dissociate tail tissue. Cells were FACS sorted FITC+	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018		line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	GSM4087287	GSM4087287: lckgfp s166; Danio rerio; RNA Seq	GSM4087287	1	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018	GEO Accession:GSM4087287	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP222763	lckgfp_s166_R1.fastq.gz lckgfp_s166_R2.fastq.gz	fastq fastq	318347200.0	1591736.0	GSM4087287 r1	0:100 1:100	A:94955561;C:67550017;G:65256279;T:90583701;N:1642	100	100	94955561	67550017	65256279	90583701	1642	SRX6877424	SRS5413206	SRA965286	GEO	Stanford University	2	0.79823	0.81128	0.10342	0.10628	0.9796	0.9796	0.67093	0.66512	100	100	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2019-09-20	Larval	Larval	Tail	Multi-system
54761	54761	SRR10151724	SRX6877423	SRS5413205	SRP222763	PRJNA572587	Characterization of T cells from the larval zebrafish tail via single cell RNAseq	GSE137770	Transcriptome Analysis	We report single cell RNA sequencing of cells from the Tglck:GFP larval zebrafish tail to identify cell types expressing the marker and to identify gene candidates related to T cell migration behaviors. We identified 330 putative T cells and 131 putative epithelial cells. Differential expression analysis between the two groups revealed genes related to actin cytoskeleton remodeling associated with the T cells in addition to canonical T and ubiquitous immune cell markers. Overall design: Single cells n=461 isolated from FACS of Tglck:GFP Danio rerio FITC+ were analyzed.	pubmed:32427565	lckgfp s165	GSM4087286	source name:Danio rerio tail\|line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	lckgfp s165	STAR 2.5 Htseq 0.8.0 htseq count m intersection nonempty nonunique all Genome build: GRCz10 Supplementary files format and content: Raw counts of numbers of reads aligned to each feature for each cell in tab separated format lckgfp counts.txt	Danio rerio tail	Liberase TL 100 ug/mL and manual trituration was used to dissociate tail tissue. Cells were FACS sorted FITC+	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018		line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	GSM4087286	GSM4087286: lckgfp s165; Danio rerio; RNA Seq	GSM4087286	1	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018	GEO Accession:GSM4087286	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP222763	lckgfp_s165_R1.fastq.gz lckgfp_s165_R2.fastq.gz	fastq fastq	191716400.0	958582.0	GSM4087286 r1	0:100 1:100	A:59383270;C:36673248;G:35909976;T:59748924;N:982	100	100	59383270	36673248	35909976	59748924	982	SRX6877423	SRS5413205	SRA965286	GEO	Stanford University	2	0.78441	0.79326	0.33307	0.33886	0.97281	0.97285	0.56961	0.56435	100	100	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2019-09-20	Larval	Larval	Tail	Multi-system
54762	54762	SRR10151723	SRX6877422	SRS5413204	SRP222763	PRJNA572587	Characterization of T cells from the larval zebrafish tail via single cell RNAseq	GSE137770	Transcriptome Analysis	We report single cell RNA sequencing of cells from the Tglck:GFP larval zebrafish tail to identify cell types expressing the marker and to identify gene candidates related to T cell migration behaviors. We identified 330 putative T cells and 131 putative epithelial cells. Differential expression analysis between the two groups revealed genes related to actin cytoskeleton remodeling associated with the T cells in addition to canonical T and ubiquitous immune cell markers. Overall design: Single cells n=461 isolated from FACS of Tglck:GFP Danio rerio FITC+ were analyzed.	pubmed:32427565	lckgfp s164	GSM4087285	source name:Danio rerio tail\|line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	lckgfp s164	STAR 2.5 Htseq 0.8.0 htseq count m intersection nonempty nonunique all Genome build: GRCz10 Supplementary files format and content: Raw counts of numbers of reads aligned to each feature for each cell in tab separated format lckgfp counts.txt	Danio rerio tail	Liberase TL 100 ug/mL and manual trituration was used to dissociate tail tissue. Cells were FACS sorted FITC+	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018		line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	GSM4087285	GSM4087285: lckgfp s164; Danio rerio; RNA Seq	GSM4087285	1	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018	GEO Accession:GSM4087285	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP222763	lckgfp_s164_R1.fastq.gz lckgfp_s164_R2.fastq.gz	fastq fastq	149204800.0	746024.0	GSM4087285 r1	0:100 1:100	A:42851684;C:31730281;G:31227028;T:43395062;N:745	100	100	42851684	31730281	31227028	43395062	745	SRX6877422	SRS5413204	SRA965286	GEO	Stanford University	2	0.8756	0.88232	0.21262	0.21546	0.97212	0.97169	0.53497	0.54245	100	100	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2019-09-20	Larval	Larval	Tail	Multi-system
54763	54763	SRR10151722	SRX6877421	SRS5413203	SRP222763	PRJNA572587	Characterization of T cells from the larval zebrafish tail via single cell RNAseq	GSE137770	Transcriptome Analysis	We report single cell RNA sequencing of cells from the Tglck:GFP larval zebrafish tail to identify cell types expressing the marker and to identify gene candidates related to T cell migration behaviors. We identified 330 putative T cells and 131 putative epithelial cells. Differential expression analysis between the two groups revealed genes related to actin cytoskeleton remodeling associated with the T cells in addition to canonical T and ubiquitous immune cell markers. Overall design: Single cells n=461 isolated from FACS of Tglck:GFP Danio rerio FITC+ were analyzed.	pubmed:32427565	lckgfp s163	GSM4087284	source name:Danio rerio tail\|line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	lckgfp s163	STAR 2.5 Htseq 0.8.0 htseq count m intersection nonempty nonunique all Genome build: GRCz10 Supplementary files format and content: Raw counts of numbers of reads aligned to each feature for each cell in tab separated format lckgfp counts.txt	Danio rerio tail	Liberase TL 100 ug/mL and manual trituration was used to dissociate tail tissue. Cells were FACS sorted FITC+	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018		line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	GSM4087284	GSM4087284: lckgfp s163; Danio rerio; RNA Seq	GSM4087284	1	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018	GEO Accession:GSM4087284	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP222763	lckgfp_s163_R1.fastq.gz lckgfp_s163_R2.fastq.gz	fastq fastq	277914000.0	1389570.0	GSM4087284 r1	0:100 1:100	A:82409899;C:58251309;G:57339795;T:79911604;N:1393	100	100	82409899	58251309	57339795	79911604	1393	SRX6877421	SRS5413203	SRA965286	GEO	Stanford University	2	0.76932	0.77938	0.13303	0.13733	0.9707	0.97092	0.62097	0.53929	100	100	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2019-09-20	Larval	Larval	Tail	Multi-system
54764	54764	SRR10151721	SRX6877420	SRS5413202	SRP222763	PRJNA572587	Characterization of T cells from the larval zebrafish tail via single cell RNAseq	GSE137770	Transcriptome Analysis	We report single cell RNA sequencing of cells from the Tglck:GFP larval zebrafish tail to identify cell types expressing the marker and to identify gene candidates related to T cell migration behaviors. We identified 330 putative T cells and 131 putative epithelial cells. Differential expression analysis between the two groups revealed genes related to actin cytoskeleton remodeling associated with the T cells in addition to canonical T and ubiquitous immune cell markers. Overall design: Single cells n=461 isolated from FACS of Tglck:GFP Danio rerio FITC+ were analyzed.	pubmed:32427565	lckgfp s162	GSM4087283	source name:Danio rerio tail\|line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	lckgfp s162	STAR 2.5 Htseq 0.8.0 htseq count m intersection nonempty nonunique all Genome build: GRCz10 Supplementary files format and content: Raw counts of numbers of reads aligned to each feature for each cell in tab separated format lckgfp counts.txt	Danio rerio tail	Liberase TL 100 ug/mL and manual trituration was used to dissociate tail tissue. Cells were FACS sorted FITC+	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018		line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	GSM4087283	GSM4087283: lckgfp s162; Danio rerio; RNA Seq	GSM4087283	1	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018	GEO Accession:GSM4087283	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP222763	lckgfp_s162_R1.fastq.gz lckgfp_s162_R2.fastq.gz	fastq fastq	341944200.0	1709721.0	GSM4087283 r1	0:100 1:100	A:100250968;C:69296796;G:69902077;T:102492670;N:1689	100	100	100250968	69296796	69902077	102492670	1689	SRX6877420	SRS5413202	SRA965286	GEO	Stanford University	2	0.86953	0.87259	0.21619	0.21725	0.95954	0.95915	0.62694	0.6345	100	100	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2019-09-20	Larval	Larval	Tail	Multi-system
54765	54765	SRR10151720	SRX6877419	SRS5413201	SRP222763	PRJNA572587	Characterization of T cells from the larval zebrafish tail via single cell RNAseq	GSE137770	Transcriptome Analysis	We report single cell RNA sequencing of cells from the Tglck:GFP larval zebrafish tail to identify cell types expressing the marker and to identify gene candidates related to T cell migration behaviors. We identified 330 putative T cells and 131 putative epithelial cells. Differential expression analysis between the two groups revealed genes related to actin cytoskeleton remodeling associated with the T cells in addition to canonical T and ubiquitous immune cell markers. Overall design: Single cells n=461 isolated from FACS of Tglck:GFP Danio rerio FITC+ were analyzed.	pubmed:32427565	lckgfp s161	GSM4087282	source name:Danio rerio tail\|line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	lckgfp s161	STAR 2.5 Htseq 0.8.0 htseq count m intersection nonempty nonunique all Genome build: GRCz10 Supplementary files format and content: Raw counts of numbers of reads aligned to each feature for each cell in tab separated format lckgfp counts.txt	Danio rerio tail	Liberase TL 100 ug/mL and manual trituration was used to dissociate tail tissue. Cells were FACS sorted FITC+	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018		line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	GSM4087282	GSM4087282: lckgfp s161; Danio rerio; RNA Seq	GSM4087282	1	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018	GEO Accession:GSM4087282	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP222763	lckgfp_s161_R1.fastq.gz lckgfp_s161_R2.fastq.gz	fastq fastq	264906400.0	1324532.0	GSM4087282 r1	0:100 1:100	A:80311157;C:49607384;G:50146596;T:84840148;N:1115	100	100	80311157	49607384	50146596	84840148	1115	SRX6877419	SRS5413201	SRA965286	GEO	Stanford University	2	0.76275	0.76861	0.28929	0.29961	0.97199	0.97165	0.57284	0.56866	100	100	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2019-09-20	Larval	Larval	Tail	Multi-system
54766	54766	SRR10151719	SRX6877418	SRS5413200	SRP222763	PRJNA572587	Characterization of T cells from the larval zebrafish tail via single cell RNAseq	GSE137770	Transcriptome Analysis	We report single cell RNA sequencing of cells from the Tglck:GFP larval zebrafish tail to identify cell types expressing the marker and to identify gene candidates related to T cell migration behaviors. We identified 330 putative T cells and 131 putative epithelial cells. Differential expression analysis between the two groups revealed genes related to actin cytoskeleton remodeling associated with the T cells in addition to canonical T and ubiquitous immune cell markers. Overall design: Single cells n=461 isolated from FACS of Tglck:GFP Danio rerio FITC+ were analyzed.	pubmed:32427565	lckgfp s160	GSM4087281	source name:Danio rerio tail\|line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	lckgfp s160	STAR 2.5 Htseq 0.8.0 htseq count m intersection nonempty nonunique all Genome build: GRCz10 Supplementary files format and content: Raw counts of numbers of reads aligned to each feature for each cell in tab separated format lckgfp counts.txt	Danio rerio tail	Liberase TL 100 ug/mL and manual trituration was used to dissociate tail tissue. Cells were FACS sorted FITC+	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018		line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	GSM4087281	GSM4087281: lckgfp s160; Danio rerio; RNA Seq	GSM4087281	1	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018	GEO Accession:GSM4087281	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP222763	lckgfp_s160_R1.fastq.gz lckgfp_s160_R2.fastq.gz	fastq fastq	283260200.0	1416301.0	GSM4087281 r1	0:100 1:100	A:82604853;C:58139032;G:58184686;T:84330181;N:1448	100	100	82604853	58139032	58184686	84330181	1448	SRX6877418	SRS5413200	SRA965286	GEO	Stanford University	2	0.86656	0.87093	0.23748	0.23909	0.95933	0.95923	0.52555	0.52709	100	100	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2019-09-20	Larval	Larval	Tail	Multi-system
54767	54767	SRR10151718	SRX6877417	SRS5413199	SRP222763	PRJNA572587	Characterization of T cells from the larval zebrafish tail via single cell RNAseq	GSE137770	Transcriptome Analysis	We report single cell RNA sequencing of cells from the Tglck:GFP larval zebrafish tail to identify cell types expressing the marker and to identify gene candidates related to T cell migration behaviors. We identified 330 putative T cells and 131 putative epithelial cells. Differential expression analysis between the two groups revealed genes related to actin cytoskeleton remodeling associated with the T cells in addition to canonical T and ubiquitous immune cell markers. Overall design: Single cells n=461 isolated from FACS of Tglck:GFP Danio rerio FITC+ were analyzed.	pubmed:32427565	lckgfp s159	GSM4087280	source name:Danio rerio tail\|line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	lckgfp s159	STAR 2.5 Htseq 0.8.0 htseq count m intersection nonempty nonunique all Genome build: GRCz10 Supplementary files format and content: Raw counts of numbers of reads aligned to each feature for each cell in tab separated format lckgfp counts.txt	Danio rerio tail	Liberase TL 100 ug/mL and manual trituration was used to dissociate tail tissue. Cells were FACS sorted FITC+	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018		line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	GSM4087280	GSM4087280: lckgfp s159; Danio rerio; RNA Seq	GSM4087280	1	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018	GEO Accession:GSM4087280	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP222763	lckgfp_s159_R1.fastq.gz lckgfp_s159_R2.fastq.gz	fastq fastq	113585400.0	567927.0	GSM4087280 r1	0:100 1:100	A:33517264;C:24562626;G:23339275;T:32165724;N:511	100	100	33517264	24562626	23339275	32165724	511	SRX6877417	SRS5413199	SRA965286	GEO	Stanford University	2	0.76624	0.77949	0.1336	0.13755	0.97571	0.97605	0.68103	0.67648	100	100	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2019-09-20	Larval	Larval	Tail	Multi-system
54768	54768	SRR10151717	SRX6877416	SRS5413198	SRP222763	PRJNA572587	Characterization of T cells from the larval zebrafish tail via single cell RNAseq	GSE137770	Transcriptome Analysis	We report single cell RNA sequencing of cells from the Tglck:GFP larval zebrafish tail to identify cell types expressing the marker and to identify gene candidates related to T cell migration behaviors. We identified 330 putative T cells and 131 putative epithelial cells. Differential expression analysis between the two groups revealed genes related to actin cytoskeleton remodeling associated with the T cells in addition to canonical T and ubiquitous immune cell markers. Overall design: Single cells n=461 isolated from FACS of Tglck:GFP Danio rerio FITC+ were analyzed.	pubmed:32427565	lckgfp s158	GSM4087279	source name:Danio rerio tail\|line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	lckgfp s158	STAR 2.5 Htseq 0.8.0 htseq count m intersection nonempty nonunique all Genome build: GRCz10 Supplementary files format and content: Raw counts of numbers of reads aligned to each feature for each cell in tab separated format lckgfp counts.txt	Danio rerio tail	Liberase TL 100 ug/mL and manual trituration was used to dissociate tail tissue. Cells were FACS sorted FITC+	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018		line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	GSM4087279	GSM4087279: lckgfp s158; Danio rerio; RNA Seq	GSM4087279	1	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018	GEO Accession:GSM4087279	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP222763	lckgfp_s158_R1.fastq.gz lckgfp_s158_R2.fastq.gz	fastq fastq	399993200.0	1999966.0	GSM4087279 r1	0:100 1:100	A:117130575;C:84505609;G:85131263;T:113223731;N:2022	100	100	117130575	84505609	85131263	113223731	2022	SRX6877416	SRS5413198	SRA965286	GEO	Stanford University	2	0.82036	0.83218	0.14448	0.14619	0.9796	0.97956	0.62613	0.62015	100	100	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2019-09-20	Larval	Larval	Tail	Multi-system
54769	54769	SRR10151716	SRX6877415	SRS5413197	SRP222763	PRJNA572587	Characterization of T cells from the larval zebrafish tail via single cell RNAseq	GSE137770	Transcriptome Analysis	We report single cell RNA sequencing of cells from the Tglck:GFP larval zebrafish tail to identify cell types expressing the marker and to identify gene candidates related to T cell migration behaviors. We identified 330 putative T cells and 131 putative epithelial cells. Differential expression analysis between the two groups revealed genes related to actin cytoskeleton remodeling associated with the T cells in addition to canonical T and ubiquitous immune cell markers. Overall design: Single cells n=461 isolated from FACS of Tglck:GFP Danio rerio FITC+ were analyzed.	pubmed:32427565	lckgfp s157	GSM4087278	source name:Danio rerio tail\|line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	lckgfp s157	STAR 2.5 Htseq 0.8.0 htseq count m intersection nonempty nonunique all Genome build: GRCz10 Supplementary files format and content: Raw counts of numbers of reads aligned to each feature for each cell in tab separated format lckgfp counts.txt	Danio rerio tail	Liberase TL 100 ug/mL and manual trituration was used to dissociate tail tissue. Cells were FACS sorted FITC+	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018		line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	GSM4087278	GSM4087278: lckgfp s157; Danio rerio; RNA Seq	GSM4087278	1	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018	GEO Accession:GSM4087278	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP222763	lckgfp_s157_R1.fastq.gz lckgfp_s157_R2.fastq.gz	fastq fastq	398558200.0	1992791.0	GSM4087278 r1	0:100 1:100	A:111681868;C:86694123;G:85997723;T:114182532;N:1954	100	100	111681868	86694123	85997723	114182532	1954	SRX6877415	SRS5413197	SRA965286	GEO	Stanford University	2	0.90085	0.90428	0.14906	0.1514	0.96104	0.9611	0.53613	0.53319	100	100	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2019-09-20	Larval	Larval	Tail	Multi-system
54770	54770	SRR10151715	SRX6877414	SRS5413196	SRP222763	PRJNA572587	Characterization of T cells from the larval zebrafish tail via single cell RNAseq	GSE137770	Transcriptome Analysis	We report single cell RNA sequencing of cells from the Tglck:GFP larval zebrafish tail to identify cell types expressing the marker and to identify gene candidates related to T cell migration behaviors. We identified 330 putative T cells and 131 putative epithelial cells. Differential expression analysis between the two groups revealed genes related to actin cytoskeleton remodeling associated with the T cells in addition to canonical T and ubiquitous immune cell markers. Overall design: Single cells n=461 isolated from FACS of Tglck:GFP Danio rerio FITC+ were analyzed.	pubmed:32427565	lckgfp s156	GSM4087277	source name:Danio rerio tail\|line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	lckgfp s156	STAR 2.5 Htseq 0.8.0 htseq count m intersection nonempty nonunique all Genome build: GRCz10 Supplementary files format and content: Raw counts of numbers of reads aligned to each feature for each cell in tab separated format lckgfp counts.txt	Danio rerio tail	Liberase TL 100 ug/mL and manual trituration was used to dissociate tail tissue. Cells were FACS sorted FITC+	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018		line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	GSM4087277	GSM4087277: lckgfp s156; Danio rerio; RNA Seq	GSM4087277	1	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018	GEO Accession:GSM4087277	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP222763	lckgfp_s156_R1.fastq.gz lckgfp_s156_R2.fastq.gz	fastq fastq	328941200.0	1644706.0	GSM4087277 r1	0:100 1:100	A:92399112;C:71662966;G:71210741;T:93666738;N:1643	100	100	92399112	71662966	71210741	93666738	1643	SRX6877414	SRS5413196	SRA965286	GEO	Stanford University	2	0.89771	0.90148	0.1272	0.12826	0.96355	0.96351	0.56142	0.55489	100	100	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2019-09-20	Larval	Larval	Tail	Multi-system
54771	54771	SRR10151714	SRX6877413	SRS5413195	SRP222763	PRJNA572587	Characterization of T cells from the larval zebrafish tail via single cell RNAseq	GSE137770	Transcriptome Analysis	We report single cell RNA sequencing of cells from the Tglck:GFP larval zebrafish tail to identify cell types expressing the marker and to identify gene candidates related to T cell migration behaviors. We identified 330 putative T cells and 131 putative epithelial cells. Differential expression analysis between the two groups revealed genes related to actin cytoskeleton remodeling associated with the T cells in addition to canonical T and ubiquitous immune cell markers. Overall design: Single cells n=461 isolated from FACS of Tglck:GFP Danio rerio FITC+ were analyzed.	pubmed:32427565	lckgfp s155	GSM4087276	source name:Danio rerio tail\|line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	lckgfp s155	STAR 2.5 Htseq 0.8.0 htseq count m intersection nonempty nonunique all Genome build: GRCz10 Supplementary files format and content: Raw counts of numbers of reads aligned to each feature for each cell in tab separated format lckgfp counts.txt	Danio rerio tail	Liberase TL 100 ug/mL and manual trituration was used to dissociate tail tissue. Cells were FACS sorted FITC+	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018		line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	GSM4087276	GSM4087276: lckgfp s155; Danio rerio; RNA Seq	GSM4087276	1	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018	GEO Accession:GSM4087276	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP222763	lckgfp_s155_R1.fastq.gz lckgfp_s155_R2.fastq.gz	fastq fastq	94356200.0	471781.0	GSM4087276 r1	0:100 1:100	A:28836770;C:20019385;G:19335070;T:26164477;N:498	100	100	28836770	20019385	19335070	26164477	498	SRX6877413	SRS5413195	SRA965286	GEO	Stanford University	2	0.66835	0.68158	0.18101	0.18641	0.97906	0.97837	0.71244	0.7043	100	100	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2019-09-20	Larval	Larval	Tail	Multi-system
54772	54772	SRR10151713	SRX6877412	SRS5413194	SRP222763	PRJNA572587	Characterization of T cells from the larval zebrafish tail via single cell RNAseq	GSE137770	Transcriptome Analysis	We report single cell RNA sequencing of cells from the Tglck:GFP larval zebrafish tail to identify cell types expressing the marker and to identify gene candidates related to T cell migration behaviors. We identified 330 putative T cells and 131 putative epithelial cells. Differential expression analysis between the two groups revealed genes related to actin cytoskeleton remodeling associated with the T cells in addition to canonical T and ubiquitous immune cell markers. Overall design: Single cells n=461 isolated from FACS of Tglck:GFP Danio rerio FITC+ were analyzed.	pubmed:32427565	lckgfp s154	GSM4087275	source name:Danio rerio tail\|line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	lckgfp s154	STAR 2.5 Htseq 0.8.0 htseq count m intersection nonempty nonunique all Genome build: GRCz10 Supplementary files format and content: Raw counts of numbers of reads aligned to each feature for each cell in tab separated format lckgfp counts.txt	Danio rerio tail	Liberase TL 100 ug/mL and manual trituration was used to dissociate tail tissue. Cells were FACS sorted FITC+	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018		line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	GSM4087275	GSM4087275: lckgfp s154; Danio rerio; RNA Seq	GSM4087275	1	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018	GEO Accession:GSM4087275	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP222763	lckgfp_s154_R1.fastq.gz lckgfp_s154_R2.fastq.gz	fastq fastq	347199000.0	1735995.0	GSM4087275 r1	0:100 1:100	A:100034656;C:73316254;G:72860794;T:100985563;N:1733	100	100	100034656	73316254	72860794	100985563	1733	SRX6877412	SRS5413194	SRA965286	GEO	Stanford University	2	0.88154	0.88494	0.21058	0.21197	0.97307	0.97307	0.54664	0.54437	100	100	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2019-09-20	Larval	Larval	Tail	Multi-system
54773	54773	SRR10151712	SRX6877411	SRS5413193	SRP222763	PRJNA572587	Characterization of T cells from the larval zebrafish tail via single cell RNAseq	GSE137770	Transcriptome Analysis	We report single cell RNA sequencing of cells from the Tglck:GFP larval zebrafish tail to identify cell types expressing the marker and to identify gene candidates related to T cell migration behaviors. We identified 330 putative T cells and 131 putative epithelial cells. Differential expression analysis between the two groups revealed genes related to actin cytoskeleton remodeling associated with the T cells in addition to canonical T and ubiquitous immune cell markers. Overall design: Single cells n=461 isolated from FACS of Tglck:GFP Danio rerio FITC+ were analyzed.	pubmed:32427565	lckgfp s153	GSM4087274	source name:Danio rerio tail\|line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	lckgfp s153	STAR 2.5 Htseq 0.8.0 htseq count m intersection nonempty nonunique all Genome build: GRCz10 Supplementary files format and content: Raw counts of numbers of reads aligned to each feature for each cell in tab separated format lckgfp counts.txt	Danio rerio tail	Liberase TL 100 ug/mL and manual trituration was used to dissociate tail tissue. Cells were FACS sorted FITC+	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018		line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	GSM4087274	GSM4087274: lckgfp s153; Danio rerio; RNA Seq	GSM4087274	1	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018	GEO Accession:GSM4087274	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP222763	lckgfp_s153_R1.fastq.gz lckgfp_s153_R2.fastq.gz	fastq fastq	62311800.0	311559.0	GSM4087274 r1	0:100 1:100	A:18913849;C:11367655;G:11408908;T:20621068;N:320	100	100	18913849	11367655	11408908	20621068	320	SRX6877411	SRS5413193	SRA965286	GEO	Stanford University	2	0.71644	0.7248	0.26054	0.2637	0.92533	0.92462	0.51549	0.51743	100	100	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2019-09-20	Larval	Larval	Tail	Multi-system
54774	54774	SRR10151711	SRX6877410	SRS5413192	SRP222763	PRJNA572587	Characterization of T cells from the larval zebrafish tail via single cell RNAseq	GSE137770	Transcriptome Analysis	We report single cell RNA sequencing of cells from the Tglck:GFP larval zebrafish tail to identify cell types expressing the marker and to identify gene candidates related to T cell migration behaviors. We identified 330 putative T cells and 131 putative epithelial cells. Differential expression analysis between the two groups revealed genes related to actin cytoskeleton remodeling associated with the T cells in addition to canonical T and ubiquitous immune cell markers. Overall design: Single cells n=461 isolated from FACS of Tglck:GFP Danio rerio FITC+ were analyzed.	pubmed:32427565	lckgfp s152	GSM4087273	source name:Danio rerio tail\|line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	lckgfp s152	STAR 2.5 Htseq 0.8.0 htseq count m intersection nonempty nonunique all Genome build: GRCz10 Supplementary files format and content: Raw counts of numbers of reads aligned to each feature for each cell in tab separated format lckgfp counts.txt	Danio rerio tail	Liberase TL 100 ug/mL and manual trituration was used to dissociate tail tissue. Cells were FACS sorted FITC+	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018		line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	GSM4087273	GSM4087273: lckgfp s152; Danio rerio; RNA Seq	GSM4087273	1	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018	GEO Accession:GSM4087273	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP222763	lckgfp_s152_R1.fastq.gz lckgfp_s152_R2.fastq.gz	fastq fastq	144238600.0	721193.0	GSM4087273 r1	0:100 1:100	A:45120486;C:26673395;G:26068858;T:46375099;N:762	100	100	45120486	26673395	26068858	46375099	762	SRX6877410	SRS5413192	SRA965286	GEO	Stanford University	2	0.71878	0.73535	0.28355	0.29314	0.97341	0.97356	0.57729	0.50541	100	100	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2019-09-20	Larval	Larval	Tail	Multi-system
54775	54775	SRR10151710	SRX6877409	SRS5413191	SRP222763	PRJNA572587	Characterization of T cells from the larval zebrafish tail via single cell RNAseq	GSE137770	Transcriptome Analysis	We report single cell RNA sequencing of cells from the Tglck:GFP larval zebrafish tail to identify cell types expressing the marker and to identify gene candidates related to T cell migration behaviors. We identified 330 putative T cells and 131 putative epithelial cells. Differential expression analysis between the two groups revealed genes related to actin cytoskeleton remodeling associated with the T cells in addition to canonical T and ubiquitous immune cell markers. Overall design: Single cells n=461 isolated from FACS of Tglck:GFP Danio rerio FITC+ were analyzed.	pubmed:32427565	lckgfp s151	GSM4087272	source name:Danio rerio tail\|line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	lckgfp s151	STAR 2.5 Htseq 0.8.0 htseq count m intersection nonempty nonunique all Genome build: GRCz10 Supplementary files format and content: Raw counts of numbers of reads aligned to each feature for each cell in tab separated format lckgfp counts.txt	Danio rerio tail	Liberase TL 100 ug/mL and manual trituration was used to dissociate tail tissue. Cells were FACS sorted FITC+	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018		line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	GSM4087272	GSM4087272: lckgfp s151; Danio rerio; RNA Seq	GSM4087272	1	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018	GEO Accession:GSM4087272	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP222763	lckgfp_s151_R1.fastq.gz lckgfp_s151_R2.fastq.gz	fastq fastq	146641800.0	733209.0	GSM4087272 r1	0:100 1:100	A:45410213;C:27128910;G:26872793;T:47229161;N:723	100	100	45410213	27128910	26872793	47229161	723	SRX6877409	SRS5413191	SRA965286	GEO	Stanford University	2	0.73931	0.75266	0.32123	0.3278	0.97177	0.97181	0.57725	0.56644	100	100	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2019-09-20	Larval	Larval	Tail	Multi-system
54776	54776	SRR10151709	SRX6877408	SRS5413190	SRP222763	PRJNA572587	Characterization of T cells from the larval zebrafish tail via single cell RNAseq	GSE137770	Transcriptome Analysis	We report single cell RNA sequencing of cells from the Tglck:GFP larval zebrafish tail to identify cell types expressing the marker and to identify gene candidates related to T cell migration behaviors. We identified 330 putative T cells and 131 putative epithelial cells. Differential expression analysis between the two groups revealed genes related to actin cytoskeleton remodeling associated with the T cells in addition to canonical T and ubiquitous immune cell markers. Overall design: Single cells n=461 isolated from FACS of Tglck:GFP Danio rerio FITC+ were analyzed.	pubmed:32427565	lckgfp s150	GSM4087271	source name:Danio rerio tail\|line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	lckgfp s150	STAR 2.5 Htseq 0.8.0 htseq count m intersection nonempty nonunique all Genome build: GRCz10 Supplementary files format and content: Raw counts of numbers of reads aligned to each feature for each cell in tab separated format lckgfp counts.txt	Danio rerio tail	Liberase TL 100 ug/mL and manual trituration was used to dissociate tail tissue. Cells were FACS sorted FITC+	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018		line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	GSM4087271	GSM4087271: lckgfp s150; Danio rerio; RNA Seq	GSM4087271	1	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018	GEO Accession:GSM4087271	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP222763	lckgfp_s150_R1.fastq.gz lckgfp_s150_R2.fastq.gz	fastq fastq	255337000.0	1276685.0	GSM4087271 r1	0:100 1:100	A:75226278;C:50196924;G:50996568;T:78916258;N:972	100	100	75226278	50196924	50996568	78916258	972	SRX6877408	SRS5413190	SRA965286	GEO	Stanford University	2	0.86043	0.8626	0.15419	0.16488	0.97928	0.97962	0.51211	0.51506	100	100	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2019-09-20	Larval	Larval	Tail	Multi-system
54777	54777	SRR10151708	SRX6877407	SRS5413189	SRP222763	PRJNA572587	Characterization of T cells from the larval zebrafish tail via single cell RNAseq	GSE137770	Transcriptome Analysis	We report single cell RNA sequencing of cells from the Tglck:GFP larval zebrafish tail to identify cell types expressing the marker and to identify gene candidates related to T cell migration behaviors. We identified 330 putative T cells and 131 putative epithelial cells. Differential expression analysis between the two groups revealed genes related to actin cytoskeleton remodeling associated with the T cells in addition to canonical T and ubiquitous immune cell markers. Overall design: Single cells n=461 isolated from FACS of Tglck:GFP Danio rerio FITC+ were analyzed.	pubmed:32427565	lckgfp s149	GSM4087270	source name:Danio rerio tail\|line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	lckgfp s149	STAR 2.5 Htseq 0.8.0 htseq count m intersection nonempty nonunique all Genome build: GRCz10 Supplementary files format and content: Raw counts of numbers of reads aligned to each feature for each cell in tab separated format lckgfp counts.txt	Danio rerio tail	Liberase TL 100 ug/mL and manual trituration was used to dissociate tail tissue. Cells were FACS sorted FITC+	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018		line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	GSM4087270	GSM4087270: lckgfp s149; Danio rerio; RNA Seq	GSM4087270	1	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018	GEO Accession:GSM4087270	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP222763	lckgfp_s149_R1.fastq.gz lckgfp_s149_R2.fastq.gz	fastq fastq	194156400.0	970782.0	GSM4087270 r1	0:100 1:100	A:59897924;C:39615168;G:39190310;T:55452086;N:912	100	100	59897924	39615168	39190310	55452086	912	SRX6877407	SRS5413189	SRA965286	GEO	Stanford University	2	0.73197	0.7347	0.21099	0.21268	0.97973	0.97987	0.63199	0.6265	100	100	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2019-09-20	Larval	Larval	Tail	Multi-system
54778	54778	SRR10151707	SRX6877406	SRS5413188	SRP222763	PRJNA572587	Characterization of T cells from the larval zebrafish tail via single cell RNAseq	GSE137770	Transcriptome Analysis	We report single cell RNA sequencing of cells from the Tglck:GFP larval zebrafish tail to identify cell types expressing the marker and to identify gene candidates related to T cell migration behaviors. We identified 330 putative T cells and 131 putative epithelial cells. Differential expression analysis between the two groups revealed genes related to actin cytoskeleton remodeling associated with the T cells in addition to canonical T and ubiquitous immune cell markers. Overall design: Single cells n=461 isolated from FACS of Tglck:GFP Danio rerio FITC+ were analyzed.	pubmed:32427565	lckgfp s148	GSM4087269	source name:Danio rerio tail\|line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	lckgfp s148	STAR 2.5 Htseq 0.8.0 htseq count m intersection nonempty nonunique all Genome build: GRCz10 Supplementary files format and content: Raw counts of numbers of reads aligned to each feature for each cell in tab separated format lckgfp counts.txt	Danio rerio tail	Liberase TL 100 ug/mL and manual trituration was used to dissociate tail tissue. Cells were FACS sorted FITC+	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018		line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	GSM4087269	GSM4087269: lckgfp s148; Danio rerio; RNA Seq	GSM4087269	1	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018	GEO Accession:GSM4087269	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP222763	lckgfp_s148_R1.fastq.gz lckgfp_s148_R2.fastq.gz	fastq fastq	414642800.0	2073214.0	GSM4087269 r1	0:100 1:100	A:119142848;C:88002543;G:88261993;T:119233331;N:2085	100	100	119142848	88002543	88261993	119233331	2085	SRX6877406	SRS5413188	SRA965286	GEO	Stanford University	2	0.8558	0.86372	0.2333	0.23687	0.97656	0.97709	0.48822	0.48602	100	100	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2019-09-20	Larval	Larval	Tail	Multi-system
54779	54779	SRR10151706	SRX6877405	SRS5413187	SRP222763	PRJNA572587	Characterization of T cells from the larval zebrafish tail via single cell RNAseq	GSE137770	Transcriptome Analysis	We report single cell RNA sequencing of cells from the Tglck:GFP larval zebrafish tail to identify cell types expressing the marker and to identify gene candidates related to T cell migration behaviors. We identified 330 putative T cells and 131 putative epithelial cells. Differential expression analysis between the two groups revealed genes related to actin cytoskeleton remodeling associated with the T cells in addition to canonical T and ubiquitous immune cell markers. Overall design: Single cells n=461 isolated from FACS of Tglck:GFP Danio rerio FITC+ were analyzed.	pubmed:32427565	lckgfp s147	GSM4087268	source name:Danio rerio tail\|line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	lckgfp s147	STAR 2.5 Htseq 0.8.0 htseq count m intersection nonempty nonunique all Genome build: GRCz10 Supplementary files format and content: Raw counts of numbers of reads aligned to each feature for each cell in tab separated format lckgfp counts.txt	Danio rerio tail	Liberase TL 100 ug/mL and manual trituration was used to dissociate tail tissue. Cells were FACS sorted FITC+	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018		line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	GSM4087268	GSM4087268: lckgfp s147; Danio rerio; RNA Seq	GSM4087268	1	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018	GEO Accession:GSM4087268	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP222763	lckgfp_s147_R1.fastq.gz lckgfp_s147_R2.fastq.gz	fastq fastq	43288800.0	216444.0	GSM4087268 r1	0:100 1:100	A:13740048;C:8211542;G:7907067;T:13429939;N:204	100	100	13740048	8211542	7907067	13429939	204	SRX6877405	SRS5413187	SRA965286	GEO	Stanford University	2	0.74681	0.76138	0.2961	0.30306	0.97912	0.97908	0.57322	0.56744	100	100	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2019-09-20	Larval	Larval	Tail	Multi-system
54780	54780	SRR10151705	SRX6877404	SRS5413186	SRP222763	PRJNA572587	Characterization of T cells from the larval zebrafish tail via single cell RNAseq	GSE137770	Transcriptome Analysis	We report single cell RNA sequencing of cells from the Tglck:GFP larval zebrafish tail to identify cell types expressing the marker and to identify gene candidates related to T cell migration behaviors. We identified 330 putative T cells and 131 putative epithelial cells. Differential expression analysis between the two groups revealed genes related to actin cytoskeleton remodeling associated with the T cells in addition to canonical T and ubiquitous immune cell markers. Overall design: Single cells n=461 isolated from FACS of Tglck:GFP Danio rerio FITC+ were analyzed.	pubmed:32427565	lckgfp s146	GSM4087267	source name:Danio rerio tail\|line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	lckgfp s146	STAR 2.5 Htseq 0.8.0 htseq count m intersection nonempty nonunique all Genome build: GRCz10 Supplementary files format and content: Raw counts of numbers of reads aligned to each feature for each cell in tab separated format lckgfp counts.txt	Danio rerio tail	Liberase TL 100 ug/mL and manual trituration was used to dissociate tail tissue. Cells were FACS sorted FITC+	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018		line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	GSM4087267	GSM4087267: lckgfp s146; Danio rerio; RNA Seq	GSM4087267	1	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018	GEO Accession:GSM4087267	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP222763	lckgfp_s146_R1.fastq.gz lckgfp_s146_R2.fastq.gz	fastq fastq	97216400.0	486082.0	GSM4087267 r1	0:100 1:100	A:29646425;C:19960075;G:19334976;T:28274446;N:478	100	100	29646425	19960075	19334976	28274446	478	SRX6877404	SRS5413186	SRA965286	GEO	Stanford University	2	0.71587	0.72921	0.34087	0.34957	0.97926	0.97936	0.76031	0.76324	100	100	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2019-09-20	Larval	Larval	Tail	Multi-system
54781	54781	SRR10151704	SRX6877403	SRS5413185	SRP222763	PRJNA572587	Characterization of T cells from the larval zebrafish tail via single cell RNAseq	GSE137770	Transcriptome Analysis	We report single cell RNA sequencing of cells from the Tglck:GFP larval zebrafish tail to identify cell types expressing the marker and to identify gene candidates related to T cell migration behaviors. We identified 330 putative T cells and 131 putative epithelial cells. Differential expression analysis between the two groups revealed genes related to actin cytoskeleton remodeling associated with the T cells in addition to canonical T and ubiquitous immune cell markers. Overall design: Single cells n=461 isolated from FACS of Tglck:GFP Danio rerio FITC+ were analyzed.	pubmed:32427565	lckgfp s145	GSM4087266	source name:Danio rerio tail\|line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	lckgfp s145	STAR 2.5 Htseq 0.8.0 htseq count m intersection nonempty nonunique all Genome build: GRCz10 Supplementary files format and content: Raw counts of numbers of reads aligned to each feature for each cell in tab separated format lckgfp counts.txt	Danio rerio tail	Liberase TL 100 ug/mL and manual trituration was used to dissociate tail tissue. Cells were FACS sorted FITC+	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018		line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	GSM4087266	GSM4087266: lckgfp s145; Danio rerio; RNA Seq	GSM4087266	1	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018	GEO Accession:GSM4087266	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP222763	lckgfp_s145_R1.fastq.gz lckgfp_s145_R2.fastq.gz	fastq fastq	379322000.0	1896610.0	GSM4087266 r1	0:100 1:100	A:109353830;C:80413955;G:79872676;T:109679806;N:1733	100	100	109353830	80413955	79872676	109679806	1733	SRX6877403	SRS5413185	SRA965286	GEO	Stanford University	2	0.87709	0.87951	0.19705	0.199	0.97362	0.97382	0.5766	0.56878	100	100	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2019-09-20	Larval	Larval	Tail	Multi-system
54782	54782	SRR10151703	SRX6877402	SRS5413184	SRP222763	PRJNA572587	Characterization of T cells from the larval zebrafish tail via single cell RNAseq	GSE137770	Transcriptome Analysis	We report single cell RNA sequencing of cells from the Tglck:GFP larval zebrafish tail to identify cell types expressing the marker and to identify gene candidates related to T cell migration behaviors. We identified 330 putative T cells and 131 putative epithelial cells. Differential expression analysis between the two groups revealed genes related to actin cytoskeleton remodeling associated with the T cells in addition to canonical T and ubiquitous immune cell markers. Overall design: Single cells n=461 isolated from FACS of Tglck:GFP Danio rerio FITC+ were analyzed.	pubmed:32427565	lckgfp s144	GSM4087265	source name:Danio rerio tail\|line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	lckgfp s144	STAR 2.5 Htseq 0.8.0 htseq count m intersection nonempty nonunique all Genome build: GRCz10 Supplementary files format and content: Raw counts of numbers of reads aligned to each feature for each cell in tab separated format lckgfp counts.txt	Danio rerio tail	Liberase TL 100 ug/mL and manual trituration was used to dissociate tail tissue. Cells were FACS sorted FITC+	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018		line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	GSM4087265	GSM4087265: lckgfp s144; Danio rerio; RNA Seq	GSM4087265	1	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018	GEO Accession:GSM4087265	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP222763	lckgfp_s144_R1.fastq.gz lckgfp_s144_R2.fastq.gz	fastq fastq	231020000.0	1155100.0	GSM4087265 r1	0:100 1:100	A:77379294;C:43768856;G:42326505;T:67544213;N:1132	100	100	77379294	43768856	42326505	67544213	1132	SRX6877402	SRS5413184	SRA965286	GEO	Stanford University	2	0.49506	0.51863	0.10183	0.10619	0.97839	0.97873	0.58601	0.57166	100	100	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2019-09-20	Larval	Larval	Tail	Multi-system
54783	54783	SRR10151822	SRX6877401	SRS5413183	SRP222763	PRJNA572587	Characterization of T cells from the larval zebrafish tail via single cell RNAseq	GSE137770	Transcriptome Analysis	We report single cell RNA sequencing of cells from the Tglck:GFP larval zebrafish tail to identify cell types expressing the marker and to identify gene candidates related to T cell migration behaviors. We identified 330 putative T cells and 131 putative epithelial cells. Differential expression analysis between the two groups revealed genes related to actin cytoskeleton remodeling associated with the T cells in addition to canonical T and ubiquitous immune cell markers. Overall design: Single cells n=461 isolated from FACS of Tglck:GFP Danio rerio FITC+ were analyzed.	pubmed:32427565	lckgfp s263	GSM4087384	source name:Danio rerio tail\|line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	lckgfp s263	STAR 2.5 Htseq 0.8.0 htseq count m intersection nonempty nonunique all Genome build: GRCz10 Supplementary files format and content: Raw counts of numbers of reads aligned to each feature for each cell in tab separated format lckgfp counts.txt	Danio rerio tail	Liberase TL 100 ug/mL and manual trituration was used to dissociate tail tissue. Cells were FACS sorted FITC+	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018		line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	GSM4087384	GSM4087384: lckgfp s263; Danio rerio; RNA Seq	GSM4087384	1	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018	GEO Accession:GSM4087384	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP222763	lckgfp_s263_R1.fastq.gz lckgfp_s263_R2.fastq.gz	fastq fastq	712463800.0	3562319.0	GSM4087384 r1	0:100 1:100	A:205721507;C:152468113;G:151554984;T:202715680;N:3516	100	100	205721507	152468113	151554984	202715680	3516	SRX6877401	SRS5413183	SRA965286	GEO	Stanford University	2	0.88497	0.88733	0.22509	0.22728	0.97743	0.97808	0.50855	0.50538	100	100	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2019-09-20	Larval	Larval	Tail	Multi-system
54784	54784	SRR10151821	SRX6877400	SRS5413182	SRP222763	PRJNA572587	Characterization of T cells from the larval zebrafish tail via single cell RNAseq	GSE137770	Transcriptome Analysis	We report single cell RNA sequencing of cells from the Tglck:GFP larval zebrafish tail to identify cell types expressing the marker and to identify gene candidates related to T cell migration behaviors. We identified 330 putative T cells and 131 putative epithelial cells. Differential expression analysis between the two groups revealed genes related to actin cytoskeleton remodeling associated with the T cells in addition to canonical T and ubiquitous immune cell markers. Overall design: Single cells n=461 isolated from FACS of Tglck:GFP Danio rerio FITC+ were analyzed.	pubmed:32427565	lckgfp s262	GSM4087383	source name:Danio rerio tail\|line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	lckgfp s262	STAR 2.5 Htseq 0.8.0 htseq count m intersection nonempty nonunique all Genome build: GRCz10 Supplementary files format and content: Raw counts of numbers of reads aligned to each feature for each cell in tab separated format lckgfp counts.txt	Danio rerio tail	Liberase TL 100 ug/mL and manual trituration was used to dissociate tail tissue. Cells were FACS sorted FITC+	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018		line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	GSM4087383	GSM4087383: lckgfp s262; Danio rerio; RNA Seq	GSM4087383	1	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018	GEO Accession:GSM4087383	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP222763	lckgfp_s262_R1.fastq.gz lckgfp_s262_R2.fastq.gz	fastq fastq	178675400.0	893377.0	GSM4087383 r1	0:100 1:100	A:53088541;C:37211458;G:36084309;T:52290116;N:976	100	100	53088541	37211458	36084309	52290116	976	SRX6877400	SRS5413182	SRA965286	GEO	Stanford University	2	0.79432	0.80429	0.12839	0.13011	0.95239	0.95164	0.61717	0.61618	100	100	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2019-09-20	Larval	Larval	Tail	Multi-system
54785	54785	SRR10151820	SRX6877399	SRS5413181	SRP222763	PRJNA572587	Characterization of T cells from the larval zebrafish tail via single cell RNAseq	GSE137770	Transcriptome Analysis	We report single cell RNA sequencing of cells from the Tglck:GFP larval zebrafish tail to identify cell types expressing the marker and to identify gene candidates related to T cell migration behaviors. We identified 330 putative T cells and 131 putative epithelial cells. Differential expression analysis between the two groups revealed genes related to actin cytoskeleton remodeling associated with the T cells in addition to canonical T and ubiquitous immune cell markers. Overall design: Single cells n=461 isolated from FACS of Tglck:GFP Danio rerio FITC+ were analyzed.	pubmed:32427565	lckgfp s261	GSM4087382	source name:Danio rerio tail\|line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	lckgfp s261	STAR 2.5 Htseq 0.8.0 htseq count m intersection nonempty nonunique all Genome build: GRCz10 Supplementary files format and content: Raw counts of numbers of reads aligned to each feature for each cell in tab separated format lckgfp counts.txt	Danio rerio tail	Liberase TL 100 ug/mL and manual trituration was used to dissociate tail tissue. Cells were FACS sorted FITC+	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018		line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	GSM4087382	GSM4087382: lckgfp s261; Danio rerio; RNA Seq	GSM4087382	1	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018	GEO Accession:GSM4087382	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP222763	lckgfp_s261_R1.fastq.gz lckgfp_s261_R2.fastq.gz	fastq fastq	252768600.0	1263843.0	GSM4087382 r1	0:100 1:100	A:75518513;C:48713471;G:48832901;T:79702638;N:1077	100	100	75518513	48713471	48832901	79702638	1077	SRX6877399	SRS5413181	SRA965286	GEO	Stanford University	2	0.77679	0.78282	0.25516	0.25959	0.95732	0.95755	0.58772	0.5841	100	100	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2019-09-20	Larval	Larval	Tail	Multi-system
54786	54786	SRR10151819	SRX6877398	SRS5413180	SRP222763	PRJNA572587	Characterization of T cells from the larval zebrafish tail via single cell RNAseq	GSE137770	Transcriptome Analysis	We report single cell RNA sequencing of cells from the Tglck:GFP larval zebrafish tail to identify cell types expressing the marker and to identify gene candidates related to T cell migration behaviors. We identified 330 putative T cells and 131 putative epithelial cells. Differential expression analysis between the two groups revealed genes related to actin cytoskeleton remodeling associated with the T cells in addition to canonical T and ubiquitous immune cell markers. Overall design: Single cells n=461 isolated from FACS of Tglck:GFP Danio rerio FITC+ were analyzed.	pubmed:32427565	lckgfp s260	GSM4087381	source name:Danio rerio tail\|line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	lckgfp s260	STAR 2.5 Htseq 0.8.0 htseq count m intersection nonempty nonunique all Genome build: GRCz10 Supplementary files format and content: Raw counts of numbers of reads aligned to each feature for each cell in tab separated format lckgfp counts.txt	Danio rerio tail	Liberase TL 100 ug/mL and manual trituration was used to dissociate tail tissue. Cells were FACS sorted FITC+	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018		line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	GSM4087381	GSM4087381: lckgfp s260; Danio rerio; RNA Seq	GSM4087381	1	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018	GEO Accession:GSM4087381	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP222763	lckgfp_s260_R1.fastq.gz lckgfp_s260_R2.fastq.gz	fastq fastq	640574600.0	3202873.0	GSM4087381 r1	0:100 1:100	A:193610199;C:125516191;G:124583853;T:196860953;N:3404	100	100	193610199	125516191	124583853	196860953	3404	SRX6877398	SRS5413180	SRA965286	GEO	Stanford University	2	0.83935	0.84602	0.40709	0.41161	0.97516	0.97475	0.57799	0.56883	100	100	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2019-09-20	Larval	Larval	Tail	Multi-system
54787	54787	SRR10151818	SRX6877397	SRS5413179	SRP222763	PRJNA572587	Characterization of T cells from the larval zebrafish tail via single cell RNAseq	GSE137770	Transcriptome Analysis	We report single cell RNA sequencing of cells from the Tglck:GFP larval zebrafish tail to identify cell types expressing the marker and to identify gene candidates related to T cell migration behaviors. We identified 330 putative T cells and 131 putative epithelial cells. Differential expression analysis between the two groups revealed genes related to actin cytoskeleton remodeling associated with the T cells in addition to canonical T and ubiquitous immune cell markers. Overall design: Single cells n=461 isolated from FACS of Tglck:GFP Danio rerio FITC+ were analyzed.	pubmed:32427565	lckgfp s259	GSM4087380	source name:Danio rerio tail\|line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	lckgfp s259	STAR 2.5 Htseq 0.8.0 htseq count m intersection nonempty nonunique all Genome build: GRCz10 Supplementary files format and content: Raw counts of numbers of reads aligned to each feature for each cell in tab separated format lckgfp counts.txt	Danio rerio tail	Liberase TL 100 ug/mL and manual trituration was used to dissociate tail tissue. Cells were FACS sorted FITC+	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018		line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	GSM4087380	GSM4087380: lckgfp s259; Danio rerio; RNA Seq	GSM4087380	1	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018	GEO Accession:GSM4087380	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP222763	lckgfp_s259_R1.fastq.gz lckgfp_s259_R2.fastq.gz	fastq fastq	442001600.0	2210008.0	GSM4087380 r1	0:100 1:100	A:132718375;C:93145071;G:89720970;T:126414987;N:2197	100	100	132718375	93145071	89720970	126414987	2197	SRX6877397	SRS5413179	SRA965286	GEO	Stanford University	2	0.7658	0.77463	0.22923	0.23214	0.97741	0.97804	0.53957	0.533	100	100	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2019-09-20	Larval	Larval	Tail	Multi-system
54788	54788	SRR10151817	SRX6877396	SRS5413178	SRP222763	PRJNA572587	Characterization of T cells from the larval zebrafish tail via single cell RNAseq	GSE137770	Transcriptome Analysis	We report single cell RNA sequencing of cells from the Tglck:GFP larval zebrafish tail to identify cell types expressing the marker and to identify gene candidates related to T cell migration behaviors. We identified 330 putative T cells and 131 putative epithelial cells. Differential expression analysis between the two groups revealed genes related to actin cytoskeleton remodeling associated with the T cells in addition to canonical T and ubiquitous immune cell markers. Overall design: Single cells n=461 isolated from FACS of Tglck:GFP Danio rerio FITC+ were analyzed.	pubmed:32427565	lckgfp s258	GSM4087379	source name:Danio rerio tail\|line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	lckgfp s258	STAR 2.5 Htseq 0.8.0 htseq count m intersection nonempty nonunique all Genome build: GRCz10 Supplementary files format and content: Raw counts of numbers of reads aligned to each feature for each cell in tab separated format lckgfp counts.txt	Danio rerio tail	Liberase TL 100 ug/mL and manual trituration was used to dissociate tail tissue. Cells were FACS sorted FITC+	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018		line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	GSM4087379	GSM4087379: lckgfp s258; Danio rerio; RNA Seq	GSM4087379	1	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018	GEO Accession:GSM4087379	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP222763	lckgfp_s258_R1.fastq.gz lckgfp_s258_R2.fastq.gz	fastq fastq	768891200.0	3844456.0	GSM4087379 r1	0:100 1:100	A:221919805;C:160432858;G:160462157;T:226073019;N:3361	100	100	221919805	160432858	160462157	226073019	3361	SRX6877396	SRS5413178	SRA965286	GEO	Stanford University	2	0.87353	0.87502	0.19594	0.203	0.98344	0.98309	0.59672	0.60437	100	100	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2019-09-20	Larval	Larval	Tail	Multi-system
54789	54789	SRR10151816	SRX6877395	SRS5413177	SRP222763	PRJNA572587	Characterization of T cells from the larval zebrafish tail via single cell RNAseq	GSE137770	Transcriptome Analysis	We report single cell RNA sequencing of cells from the Tglck:GFP larval zebrafish tail to identify cell types expressing the marker and to identify gene candidates related to T cell migration behaviors. We identified 330 putative T cells and 131 putative epithelial cells. Differential expression analysis between the two groups revealed genes related to actin cytoskeleton remodeling associated with the T cells in addition to canonical T and ubiquitous immune cell markers. Overall design: Single cells n=461 isolated from FACS of Tglck:GFP Danio rerio FITC+ were analyzed.	pubmed:32427565	lckgfp s257	GSM4087378	source name:Danio rerio tail\|line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	lckgfp s257	STAR 2.5 Htseq 0.8.0 htseq count m intersection nonempty nonunique all Genome build: GRCz10 Supplementary files format and content: Raw counts of numbers of reads aligned to each feature for each cell in tab separated format lckgfp counts.txt	Danio rerio tail	Liberase TL 100 ug/mL and manual trituration was used to dissociate tail tissue. Cells were FACS sorted FITC+	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018		line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	GSM4087378	GSM4087378: lckgfp s257; Danio rerio; RNA Seq	GSM4087378	1	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018	GEO Accession:GSM4087378	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP222763	lckgfp_s257_R1.fastq.gz lckgfp_s257_R2.fastq.gz	fastq fastq	111123800.0	555619.0	GSM4087378 r1	0:100 1:100	A:33584827;C:23346349;G:22705440;T:31486575;N:609	100	100	33584827	23346349	22705440	31486575	609	SRX6877395	SRS5413177	SRA965286	GEO	Stanford University	2	0.77078	0.78615	0.12471	0.12764	0.9825	0.9822	0.64769	0.64665	100	100	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2019-09-20	Larval	Larval	Tail	Multi-system
54790	54790	SRR10151815	SRX6877394	SRS5413176	SRP222763	PRJNA572587	Characterization of T cells from the larval zebrafish tail via single cell RNAseq	GSE137770	Transcriptome Analysis	We report single cell RNA sequencing of cells from the Tglck:GFP larval zebrafish tail to identify cell types expressing the marker and to identify gene candidates related to T cell migration behaviors. We identified 330 putative T cells and 131 putative epithelial cells. Differential expression analysis between the two groups revealed genes related to actin cytoskeleton remodeling associated with the T cells in addition to canonical T and ubiquitous immune cell markers. Overall design: Single cells n=461 isolated from FACS of Tglck:GFP Danio rerio FITC+ were analyzed.	pubmed:32427565	lckgfp s256	GSM4087377	source name:Danio rerio tail\|line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	lckgfp s256	STAR 2.5 Htseq 0.8.0 htseq count m intersection nonempty nonunique all Genome build: GRCz10 Supplementary files format and content: Raw counts of numbers of reads aligned to each feature for each cell in tab separated format lckgfp counts.txt	Danio rerio tail	Liberase TL 100 ug/mL and manual trituration was used to dissociate tail tissue. Cells were FACS sorted FITC+	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018		line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	GSM4087377	GSM4087377: lckgfp s256; Danio rerio; RNA Seq	GSM4087377	1	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018	GEO Accession:GSM4087377	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP222763	lckgfp_s256_R1.fastq.gz lckgfp_s256_R2.fastq.gz	fastq fastq	224647200.0	1123236.0	GSM4087377 r1	0:100 1:100	A:64126817;C:48580286;G:48138688;T:63800313;N:1096	100	100	64126817	48580286	48138688	63800313	1096	SRX6877394	SRS5413176	SRA965286	GEO	Stanford University	2	0.88362	0.88769	0.14051	0.14263	0.96262	0.9629	0.56492	0.5715	100	100	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2019-09-20	Larval	Larval	Tail	Multi-system
54791	54791	SRR10151814	SRX6877393	SRS5413175	SRP222763	PRJNA572587	Characterization of T cells from the larval zebrafish tail via single cell RNAseq	GSE137770	Transcriptome Analysis	We report single cell RNA sequencing of cells from the Tglck:GFP larval zebrafish tail to identify cell types expressing the marker and to identify gene candidates related to T cell migration behaviors. We identified 330 putative T cells and 131 putative epithelial cells. Differential expression analysis between the two groups revealed genes related to actin cytoskeleton remodeling associated with the T cells in addition to canonical T and ubiquitous immune cell markers. Overall design: Single cells n=461 isolated from FACS of Tglck:GFP Danio rerio FITC+ were analyzed.	pubmed:32427565	lckgfp s255	GSM4087376	source name:Danio rerio tail\|line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	lckgfp s255	STAR 2.5 Htseq 0.8.0 htseq count m intersection nonempty nonunique all Genome build: GRCz10 Supplementary files format and content: Raw counts of numbers of reads aligned to each feature for each cell in tab separated format lckgfp counts.txt	Danio rerio tail	Liberase TL 100 ug/mL and manual trituration was used to dissociate tail tissue. Cells were FACS sorted FITC+	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018		line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	GSM4087376	GSM4087376: lckgfp s255; Danio rerio; RNA Seq	GSM4087376	1	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018	GEO Accession:GSM4087376	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP222763	lckgfp_s255_R1.fastq.gz lckgfp_s255_R2.fastq.gz	fastq fastq	638629200.0	3193146.0	GSM4087376 r1	0:100 1:100	A:180213037;C:137091196;G:136887885;T:184433891;N:3191	100	100	180213037	137091196	136887885	184433891	3191	SRX6877393	SRS5413175	SRA965286	GEO	Stanford University	2	0.89004	0.89579	0.16231	0.16498	0.95645	0.95639	0.4788	0.55779	100	100	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2019-09-20	Larval	Larval	Tail	Multi-system
54792	54792	SRR10151813	SRX6877392	SRS5413174	SRP222763	PRJNA572587	Characterization of T cells from the larval zebrafish tail via single cell RNAseq	GSE137770	Transcriptome Analysis	We report single cell RNA sequencing of cells from the Tglck:GFP larval zebrafish tail to identify cell types expressing the marker and to identify gene candidates related to T cell migration behaviors. We identified 330 putative T cells and 131 putative epithelial cells. Differential expression analysis between the two groups revealed genes related to actin cytoskeleton remodeling associated with the T cells in addition to canonical T and ubiquitous immune cell markers. Overall design: Single cells n=461 isolated from FACS of Tglck:GFP Danio rerio FITC+ were analyzed.	pubmed:32427565	lckgfp s254	GSM4087375	source name:Danio rerio tail\|line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	lckgfp s254	STAR 2.5 Htseq 0.8.0 htseq count m intersection nonempty nonunique all Genome build: GRCz10 Supplementary files format and content: Raw counts of numbers of reads aligned to each feature for each cell in tab separated format lckgfp counts.txt	Danio rerio tail	Liberase TL 100 ug/mL and manual trituration was used to dissociate tail tissue. Cells were FACS sorted FITC+	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018		line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	GSM4087375	GSM4087375: lckgfp s254; Danio rerio; RNA Seq	GSM4087375	1	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018	GEO Accession:GSM4087375	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP222763	lckgfp_s254_R1.fastq.gz lckgfp_s254_R2.fastq.gz	fastq fastq	31360400.0	156802.0	GSM4087375 r1	0:100 1:100	A:8827768;C:7340349;G:6501576;T:8690590;N:117	100	100	8827768	7340349	6501576	8690590	117	SRX6877392	SRS5413174	SRA965286	GEO	Stanford University	2	0.83031	0.82256	0.25236	0.25193	0.9609	0.96051	0.61835	0.62023	100	100	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2019-09-20	Larval	Larval	Tail	Multi-system
54793	54793	SRR10151812	SRX6877391	SRS5413173	SRP222763	PRJNA572587	Characterization of T cells from the larval zebrafish tail via single cell RNAseq	GSE137770	Transcriptome Analysis	We report single cell RNA sequencing of cells from the Tglck:GFP larval zebrafish tail to identify cell types expressing the marker and to identify gene candidates related to T cell migration behaviors. We identified 330 putative T cells and 131 putative epithelial cells. Differential expression analysis between the two groups revealed genes related to actin cytoskeleton remodeling associated with the T cells in addition to canonical T and ubiquitous immune cell markers. Overall design: Single cells n=461 isolated from FACS of Tglck:GFP Danio rerio FITC+ were analyzed.	pubmed:32427565	lckgfp s253	GSM4087374	source name:Danio rerio tail\|line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	lckgfp s253	STAR 2.5 Htseq 0.8.0 htseq count m intersection nonempty nonunique all Genome build: GRCz10 Supplementary files format and content: Raw counts of numbers of reads aligned to each feature for each cell in tab separated format lckgfp counts.txt	Danio rerio tail	Liberase TL 100 ug/mL and manual trituration was used to dissociate tail tissue. Cells were FACS sorted FITC+	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018		line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	GSM4087374	GSM4087374: lckgfp s253; Danio rerio; RNA Seq	GSM4087374	1	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018	GEO Accession:GSM4087374	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP222763	lckgfp_s253_R1.fastq.gz lckgfp_s253_R2.fastq.gz	fastq fastq	278116800.0	1390584.0	GSM4087374 r1	0:100 1:100	A:81621196;C:58531356;G:57679579;T:80283279;N:1390	100	100	81621196	58531356	57679579	80283279	1390	SRX6877391	SRS5413173	SRA965286	GEO	Stanford University	2	0.82554	0.83184	0.18026	0.18251	0.97313	0.97374	0.62647	0.62099	100	100	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2019-09-20	Larval	Larval	Tail	Multi-system
54794	54794	SRR10151811	SRX6877390	SRS5413172	SRP222763	PRJNA572587	Characterization of T cells from the larval zebrafish tail via single cell RNAseq	GSE137770	Transcriptome Analysis	We report single cell RNA sequencing of cells from the Tglck:GFP larval zebrafish tail to identify cell types expressing the marker and to identify gene candidates related to T cell migration behaviors. We identified 330 putative T cells and 131 putative epithelial cells. Differential expression analysis between the two groups revealed genes related to actin cytoskeleton remodeling associated with the T cells in addition to canonical T and ubiquitous immune cell markers. Overall design: Single cells n=461 isolated from FACS of Tglck:GFP Danio rerio FITC+ were analyzed.	pubmed:32427565	lckgfp s252	GSM4087373	source name:Danio rerio tail\|line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	lckgfp s252	STAR 2.5 Htseq 0.8.0 htseq count m intersection nonempty nonunique all Genome build: GRCz10 Supplementary files format and content: Raw counts of numbers of reads aligned to each feature for each cell in tab separated format lckgfp counts.txt	Danio rerio tail	Liberase TL 100 ug/mL and manual trituration was used to dissociate tail tissue. Cells were FACS sorted FITC+	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018		line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	GSM4087373	GSM4087373: lckgfp s252; Danio rerio; RNA Seq	GSM4087373	1	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018	GEO Accession:GSM4087373	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP222763	lckgfp_s252_R1.fastq.gz lckgfp_s252_R2.fastq.gz	fastq fastq	357782000.0	1788910.0	GSM4087373 r1	0:100 1:100	A:100211591;C:79953356;G:78673775;T:98941609;N:1669	100	100	100211591	79953356	78673775	98941609	1669	SRX6877390	SRS5413172	SRA965286	GEO	Stanford University	2	0.90178	0.90652	0.19325	0.19452	0.97281	0.9727	0.46592	0.55759	100	100	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2019-09-20	Larval	Larval	Tail	Multi-system
54795	54795	SRR10151810	SRX6877389	SRS5413171	SRP222763	PRJNA572587	Characterization of T cells from the larval zebrafish tail via single cell RNAseq	GSE137770	Transcriptome Analysis	We report single cell RNA sequencing of cells from the Tglck:GFP larval zebrafish tail to identify cell types expressing the marker and to identify gene candidates related to T cell migration behaviors. We identified 330 putative T cells and 131 putative epithelial cells. Differential expression analysis between the two groups revealed genes related to actin cytoskeleton remodeling associated with the T cells in addition to canonical T and ubiquitous immune cell markers. Overall design: Single cells n=461 isolated from FACS of Tglck:GFP Danio rerio FITC+ were analyzed.	pubmed:32427565	lckgfp s251	GSM4087372	source name:Danio rerio tail\|line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	lckgfp s251	STAR 2.5 Htseq 0.8.0 htseq count m intersection nonempty nonunique all Genome build: GRCz10 Supplementary files format and content: Raw counts of numbers of reads aligned to each feature for each cell in tab separated format lckgfp counts.txt	Danio rerio tail	Liberase TL 100 ug/mL and manual trituration was used to dissociate tail tissue. Cells were FACS sorted FITC+	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018		line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	GSM4087372	GSM4087372: lckgfp s251; Danio rerio; RNA Seq	GSM4087372	1	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018	GEO Accession:GSM4087372	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP222763	lckgfp_s251_R1.fastq.gz lckgfp_s251_R2.fastq.gz	fastq fastq	154662200.0	773311.0	GSM4087372 r1	0:100 1:100	A:46195763;C:30904197;G:30540939;T:47020511;N:790	100	100	46195763	30904197	30540939	47020511	790	SRX6877389	SRS5413171	SRA965286	GEO	Stanford University	2	0.77199	0.78625	0.15104	0.15562	0.94251	0.94312	0.64877	0.65251	100	100	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2019-09-20	Larval	Larval	Tail	Multi-system
54796	54796	SRR10151809	SRX6877388	SRS5413170	SRP222763	PRJNA572587	Characterization of T cells from the larval zebrafish tail via single cell RNAseq	GSE137770	Transcriptome Analysis	We report single cell RNA sequencing of cells from the Tglck:GFP larval zebrafish tail to identify cell types expressing the marker and to identify gene candidates related to T cell migration behaviors. We identified 330 putative T cells and 131 putative epithelial cells. Differential expression analysis between the two groups revealed genes related to actin cytoskeleton remodeling associated with the T cells in addition to canonical T and ubiquitous immune cell markers. Overall design: Single cells n=461 isolated from FACS of Tglck:GFP Danio rerio FITC+ were analyzed.	pubmed:32427565	lckgfp s250	GSM4087371	source name:Danio rerio tail\|line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	lckgfp s250	STAR 2.5 Htseq 0.8.0 htseq count m intersection nonempty nonunique all Genome build: GRCz10 Supplementary files format and content: Raw counts of numbers of reads aligned to each feature for each cell in tab separated format lckgfp counts.txt	Danio rerio tail	Liberase TL 100 ug/mL and manual trituration was used to dissociate tail tissue. Cells were FACS sorted FITC+	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018		line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	GSM4087371	GSM4087371: lckgfp s250; Danio rerio; RNA Seq	GSM4087371	1	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018	GEO Accession:GSM4087371	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP222763	lckgfp_s250_R1.fastq.gz lckgfp_s250_R2.fastq.gz	fastq fastq	209954800.0	1049774.0	GSM4087371 r1	0:100 1:100	A:64870402;C:41383363;G:40467851;T:63232087;N:1097	100	100	64870402	41383363	40467851	63232087	1097	SRX6877388	SRS5413170	SRA965286	GEO	Stanford University	2	0.70643	0.71876	0.36885	0.37692	0.97751	0.97757	0.66872	0.6539	100	100	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2019-09-20	Larval	Larval	Tail	Multi-system
54797	54797	SRR10151808	SRX6877387	SRS5413169	SRP222763	PRJNA572587	Characterization of T cells from the larval zebrafish tail via single cell RNAseq	GSE137770	Transcriptome Analysis	We report single cell RNA sequencing of cells from the Tglck:GFP larval zebrafish tail to identify cell types expressing the marker and to identify gene candidates related to T cell migration behaviors. We identified 330 putative T cells and 131 putative epithelial cells. Differential expression analysis between the two groups revealed genes related to actin cytoskeleton remodeling associated with the T cells in addition to canonical T and ubiquitous immune cell markers. Overall design: Single cells n=461 isolated from FACS of Tglck:GFP Danio rerio FITC+ were analyzed.	pubmed:32427565	lckgfp s249	GSM4087370	source name:Danio rerio tail\|line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	lckgfp s249	STAR 2.5 Htseq 0.8.0 htseq count m intersection nonempty nonunique all Genome build: GRCz10 Supplementary files format and content: Raw counts of numbers of reads aligned to each feature for each cell in tab separated format lckgfp counts.txt	Danio rerio tail	Liberase TL 100 ug/mL and manual trituration was used to dissociate tail tissue. Cells were FACS sorted FITC+	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018		line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	GSM4087370	GSM4087370: lckgfp s249; Danio rerio; RNA Seq	GSM4087370	1	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018	GEO Accession:GSM4087370	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP222763	lckgfp_s249_R1.fastq.gz lckgfp_s249_R2.fastq.gz	fastq fastq	300503400.0	1502517.0	GSM4087370 r1	0:100 1:100	A:87918930;C:64039264;G:62110563;T:86433086;N:1557	100	100	87918930	64039264	62110563	86433086	1557	SRX6877387	SRS5413169	SRA965286	GEO	Stanford University	2	0.80576	0.81508	0.13364	0.13617	0.98001	0.98023	0.5399	0.53423	100	100	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2019-09-20	Larval	Larval	Tail	Multi-system
54798	54798	SRR10151807	SRX6877386	SRS5413168	SRP222763	PRJNA572587	Characterization of T cells from the larval zebrafish tail via single cell RNAseq	GSE137770	Transcriptome Analysis	We report single cell RNA sequencing of cells from the Tglck:GFP larval zebrafish tail to identify cell types expressing the marker and to identify gene candidates related to T cell migration behaviors. We identified 330 putative T cells and 131 putative epithelial cells. Differential expression analysis between the two groups revealed genes related to actin cytoskeleton remodeling associated with the T cells in addition to canonical T and ubiquitous immune cell markers. Overall design: Single cells n=461 isolated from FACS of Tglck:GFP Danio rerio FITC+ were analyzed.	pubmed:32427565	lckgfp s248	GSM4087369	source name:Danio rerio tail\|line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	lckgfp s248	STAR 2.5 Htseq 0.8.0 htseq count m intersection nonempty nonunique all Genome build: GRCz10 Supplementary files format and content: Raw counts of numbers of reads aligned to each feature for each cell in tab separated format lckgfp counts.txt	Danio rerio tail	Liberase TL 100 ug/mL and manual trituration was used to dissociate tail tissue. Cells were FACS sorted FITC+	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018		line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	GSM4087369	GSM4087369: lckgfp s248; Danio rerio; RNA Seq	GSM4087369	1	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018	GEO Accession:GSM4087369	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP222763	lckgfp_s248_R1.fastq.gz lckgfp_s248_R2.fastq.gz	fastq fastq	508455000.0	2542275.0	GSM4087369 r1	0:100 1:100	A:145063832;C:108777134;G:107969639;T:146641852;N:2543	100	100	145063832	108777134	107969639	146641852	2543	SRX6877386	SRS5413168	SRA965286	GEO	Stanford University	2	0.87661	0.87906	0.17214	0.17469	0.97007	0.97021	0.54058	0.54793	100	100	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2019-09-20	Larval	Larval	Tail	Multi-system
54799	54799	SRR10151806	SRX6877385	SRS5413167	SRP222763	PRJNA572587	Characterization of T cells from the larval zebrafish tail via single cell RNAseq	GSE137770	Transcriptome Analysis	We report single cell RNA sequencing of cells from the Tglck:GFP larval zebrafish tail to identify cell types expressing the marker and to identify gene candidates related to T cell migration behaviors. We identified 330 putative T cells and 131 putative epithelial cells. Differential expression analysis between the two groups revealed genes related to actin cytoskeleton remodeling associated with the T cells in addition to canonical T and ubiquitous immune cell markers. Overall design: Single cells n=461 isolated from FACS of Tglck:GFP Danio rerio FITC+ were analyzed.	pubmed:32427565	lckgfp s247	GSM4087368	source name:Danio rerio tail\|line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	lckgfp s247	STAR 2.5 Htseq 0.8.0 htseq count m intersection nonempty nonunique all Genome build: GRCz10 Supplementary files format and content: Raw counts of numbers of reads aligned to each feature for each cell in tab separated format lckgfp counts.txt	Danio rerio tail	Liberase TL 100 ug/mL and manual trituration was used to dissociate tail tissue. Cells were FACS sorted FITC+	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018		line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	GSM4087368	GSM4087368: lckgfp s247; Danio rerio; RNA Seq	GSM4087368	1	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018	GEO Accession:GSM4087368	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP222763	lckgfp_s247_R1.fastq.gz lckgfp_s247_R2.fastq.gz	fastq fastq	503439800.0	2517199.0	GSM4087368 r1	0:100 1:100	A:144603360;C:106681907;G:107064271;T:145087767;N:2495	100	100	144603360	106681907	107064271	145087767	2495	SRX6877385	SRS5413167	SRA965286	GEO	Stanford University	2	0.90271	0.90502	0.16525	0.16592	0.96958	0.96988	0.53789	0.55192	100	100	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2019-09-20	Larval	Larval	Tail	Multi-system
54800	54800	SRR10151805	SRX6877384	SRS5413166	SRP222763	PRJNA572587	Characterization of T cells from the larval zebrafish tail via single cell RNAseq	GSE137770	Transcriptome Analysis	We report single cell RNA sequencing of cells from the Tglck:GFP larval zebrafish tail to identify cell types expressing the marker and to identify gene candidates related to T cell migration behaviors. We identified 330 putative T cells and 131 putative epithelial cells. Differential expression analysis between the two groups revealed genes related to actin cytoskeleton remodeling associated with the T cells in addition to canonical T and ubiquitous immune cell markers. Overall design: Single cells n=461 isolated from FACS of Tglck:GFP Danio rerio FITC+ were analyzed.	pubmed:32427565	lckgfp s246	GSM4087367	source name:Danio rerio tail\|line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	lckgfp s246	STAR 2.5 Htseq 0.8.0 htseq count m intersection nonempty nonunique all Genome build: GRCz10 Supplementary files format and content: Raw counts of numbers of reads aligned to each feature for each cell in tab separated format lckgfp counts.txt	Danio rerio tail	Liberase TL 100 ug/mL and manual trituration was used to dissociate tail tissue. Cells were FACS sorted FITC+	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018		line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	GSM4087367	GSM4087367: lckgfp s246; Danio rerio; RNA Seq	GSM4087367	1	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018	GEO Accession:GSM4087367	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP222763	lckgfp_s246_R1.fastq.gz lckgfp_s246_R2.fastq.gz	fastq fastq	56423000.0	282115.0	GSM4087367 r1	0:100 1:100	A:16703198;C:11821345;G:11582009;T:16316138;N:310	100	100	16703198	11821345	11582009	16316138	310	SRX6877384	SRS5413166	SRA965286	GEO	Stanford University	2	0.86004	0.86722	0.20783	0.2103	0.97437	0.97413	0.52979	0.52929	100	100	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2019-09-20	Larval	Larval	Tail	Multi-system
54801	54801	SRR10151804	SRX6877383	SRS5413165	SRP222763	PRJNA572587	Characterization of T cells from the larval zebrafish tail via single cell RNAseq	GSE137770	Transcriptome Analysis	We report single cell RNA sequencing of cells from the Tglck:GFP larval zebrafish tail to identify cell types expressing the marker and to identify gene candidates related to T cell migration behaviors. We identified 330 putative T cells and 131 putative epithelial cells. Differential expression analysis between the two groups revealed genes related to actin cytoskeleton remodeling associated with the T cells in addition to canonical T and ubiquitous immune cell markers. Overall design: Single cells n=461 isolated from FACS of Tglck:GFP Danio rerio FITC+ were analyzed.	pubmed:32427565	lckgfp s245	GSM4087366	source name:Danio rerio tail\|line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	lckgfp s245	STAR 2.5 Htseq 0.8.0 htseq count m intersection nonempty nonunique all Genome build: GRCz10 Supplementary files format and content: Raw counts of numbers of reads aligned to each feature for each cell in tab separated format lckgfp counts.txt	Danio rerio tail	Liberase TL 100 ug/mL and manual trituration was used to dissociate tail tissue. Cells were FACS sorted FITC+	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018		line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	GSM4087366	GSM4087366: lckgfp s245; Danio rerio; RNA Seq	GSM4087366	1	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018	GEO Accession:GSM4087366	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP222763	lckgfp_s245_R1.fastq.gz lckgfp_s245_R2.fastq.gz	fastq fastq	199249200.0	996246.0	GSM4087366 r1	0:100 1:100	A:63853905;C:39801278;G:38619900;T:56973038;N:1079	100	100	63853905	39801278	38619900	56973038	1079	SRX6877383	SRS5413165	SRA965286	GEO	Stanford University	2	0.69175	0.70899	0.18871	0.19499	0.98248	0.98265	0.69347	0.69228	100	100	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2019-09-20	Larval	Larval	Tail	Multi-system
54802	54802	SRR10151803	SRX6877382	SRS5413164	SRP222763	PRJNA572587	Characterization of T cells from the larval zebrafish tail via single cell RNAseq	GSE137770	Transcriptome Analysis	We report single cell RNA sequencing of cells from the Tglck:GFP larval zebrafish tail to identify cell types expressing the marker and to identify gene candidates related to T cell migration behaviors. We identified 330 putative T cells and 131 putative epithelial cells. Differential expression analysis between the two groups revealed genes related to actin cytoskeleton remodeling associated with the T cells in addition to canonical T and ubiquitous immune cell markers. Overall design: Single cells n=461 isolated from FACS of Tglck:GFP Danio rerio FITC+ were analyzed.	pubmed:32427565	lckgfp s244	GSM4087365	source name:Danio rerio tail\|line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	lckgfp s244	STAR 2.5 Htseq 0.8.0 htseq count m intersection nonempty nonunique all Genome build: GRCz10 Supplementary files format and content: Raw counts of numbers of reads aligned to each feature for each cell in tab separated format lckgfp counts.txt	Danio rerio tail	Liberase TL 100 ug/mL and manual trituration was used to dissociate tail tissue. Cells were FACS sorted FITC+	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018		line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	GSM4087365	GSM4087365: lckgfp s244; Danio rerio; RNA Seq	GSM4087365	1	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018	GEO Accession:GSM4087365	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP222763	lckgfp_s244_R1.fastq.gz lckgfp_s244_R2.fastq.gz	fastq fastq	59458000.0	297290.0	GSM4087365 r1	0:100 1:100	A:19368446;C:11883955;G:11060031;T:17145254;N:314	100	100	19368446	11883955	11060031	17145254	314	SRX6877382	SRS5413164	SRA965286	GEO	Stanford University	2	0.64861	0.67048	0.17158	0.17966	0.98013	0.98098	0.67747	0.67468	100	100	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2019-09-20	Larval	Larval	Tail	Multi-system
54803	54803	SRR10151802	SRX6877381	SRS5413163	SRP222763	PRJNA572587	Characterization of T cells from the larval zebrafish tail via single cell RNAseq	GSE137770	Transcriptome Analysis	We report single cell RNA sequencing of cells from the Tglck:GFP larval zebrafish tail to identify cell types expressing the marker and to identify gene candidates related to T cell migration behaviors. We identified 330 putative T cells and 131 putative epithelial cells. Differential expression analysis between the two groups revealed genes related to actin cytoskeleton remodeling associated with the T cells in addition to canonical T and ubiquitous immune cell markers. Overall design: Single cells n=461 isolated from FACS of Tglck:GFP Danio rerio FITC+ were analyzed.	pubmed:32427565	lckgfp s243	GSM4087364	source name:Danio rerio tail\|line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	lckgfp s243	STAR 2.5 Htseq 0.8.0 htseq count m intersection nonempty nonunique all Genome build: GRCz10 Supplementary files format and content: Raw counts of numbers of reads aligned to each feature for each cell in tab separated format lckgfp counts.txt	Danio rerio tail	Liberase TL 100 ug/mL and manual trituration was used to dissociate tail tissue. Cells were FACS sorted FITC+	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018		line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	GSM4087364	GSM4087364: lckgfp s243; Danio rerio; RNA Seq	GSM4087364	1	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018	GEO Accession:GSM4087364	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP222763	lckgfp_s243_R1.fastq.gz lckgfp_s243_R2.fastq.gz	fastq fastq	912862800.0	4564314.0	GSM4087364 r1	0:100 1:100	A:256150630;C:198146668;G:198794207;T:259767092;N:4203	100	100	256150630	198146668	198794207	259767092	4203	SRX6877381	SRS5413163	SRA965286	GEO	Stanford University	2	0.90111	0.9029	0.16436	0.16741	0.95321	0.95229	0.54584	0.54742	100	100	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2019-09-20	Larval	Larval	Tail	Multi-system
54804	54804	SRR10151801	SRX6877380	SRS5413162	SRP222763	PRJNA572587	Characterization of T cells from the larval zebrafish tail via single cell RNAseq	GSE137770	Transcriptome Analysis	We report single cell RNA sequencing of cells from the Tglck:GFP larval zebrafish tail to identify cell types expressing the marker and to identify gene candidates related to T cell migration behaviors. We identified 330 putative T cells and 131 putative epithelial cells. Differential expression analysis between the two groups revealed genes related to actin cytoskeleton remodeling associated with the T cells in addition to canonical T and ubiquitous immune cell markers. Overall design: Single cells n=461 isolated from FACS of Tglck:GFP Danio rerio FITC+ were analyzed.	pubmed:32427565	lckgfp s242	GSM4087363	source name:Danio rerio tail\|line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	lckgfp s242	STAR 2.5 Htseq 0.8.0 htseq count m intersection nonempty nonunique all Genome build: GRCz10 Supplementary files format and content: Raw counts of numbers of reads aligned to each feature for each cell in tab separated format lckgfp counts.txt	Danio rerio tail	Liberase TL 100 ug/mL and manual trituration was used to dissociate tail tissue. Cells were FACS sorted FITC+	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018		line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	GSM4087363	GSM4087363: lckgfp s242; Danio rerio; RNA Seq	GSM4087363	1	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018	GEO Accession:GSM4087363	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP222763	lckgfp_s242_R1.fastq.gz lckgfp_s242_R2.fastq.gz	fastq fastq	212411000.0	1062055.0	GSM4087363 r1	0:100 1:100	A:64672691;C:44589172;G:41615063;T:61532914;N:1160	100	100	64672691	44589172	41615063	61532914	1160	SRX6877380	SRS5413162	SRA965286	GEO	Stanford University	2	0.62044	0.63602	0.48721	0.49958	0.96404	0.96404	0.56834	0.53787	100	100	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2019-09-20	Larval	Larval	Tail	Multi-system
54805	54805	SRR10151800	SRX6877379	SRS5413161	SRP222763	PRJNA572587	Characterization of T cells from the larval zebrafish tail via single cell RNAseq	GSE137770	Transcriptome Analysis	We report single cell RNA sequencing of cells from the Tglck:GFP larval zebrafish tail to identify cell types expressing the marker and to identify gene candidates related to T cell migration behaviors. We identified 330 putative T cells and 131 putative epithelial cells. Differential expression analysis between the two groups revealed genes related to actin cytoskeleton remodeling associated with the T cells in addition to canonical T and ubiquitous immune cell markers. Overall design: Single cells n=461 isolated from FACS of Tglck:GFP Danio rerio FITC+ were analyzed.	pubmed:32427565	lckgfp s241	GSM4087362	source name:Danio rerio tail\|line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	lckgfp s241	STAR 2.5 Htseq 0.8.0 htseq count m intersection nonempty nonunique all Genome build: GRCz10 Supplementary files format and content: Raw counts of numbers of reads aligned to each feature for each cell in tab separated format lckgfp counts.txt	Danio rerio tail	Liberase TL 100 ug/mL and manual trituration was used to dissociate tail tissue. Cells were FACS sorted FITC+	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018		line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	GSM4087362	GSM4087362: lckgfp s241; Danio rerio; RNA Seq	GSM4087362	1	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018	GEO Accession:GSM4087362	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP222763	lckgfp_s241_R1.fastq.gz lckgfp_s241_R2.fastq.gz	fastq fastq	222790000.0	1113950.0	GSM4087362 r1	0:100 1:100	A:67590311;C:41984958;G:41881875;T:71331643;N:1213	100	100	67590311	41984958	41881875	71331643	1213	SRX6877379	SRS5413161	SRA965286	GEO	Stanford University	2	0.77605	0.78297	0.28043	0.28651	0.97538	0.97557	0.53532	0.57878	100	100	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2019-09-20	Larval	Larval	Tail	Multi-system
54806	54806	SRR10151799	SRX6877378	SRS5413160	SRP222763	PRJNA572587	Characterization of T cells from the larval zebrafish tail via single cell RNAseq	GSE137770	Transcriptome Analysis	We report single cell RNA sequencing of cells from the Tglck:GFP larval zebrafish tail to identify cell types expressing the marker and to identify gene candidates related to T cell migration behaviors. We identified 330 putative T cells and 131 putative epithelial cells. Differential expression analysis between the two groups revealed genes related to actin cytoskeleton remodeling associated with the T cells in addition to canonical T and ubiquitous immune cell markers. Overall design: Single cells n=461 isolated from FACS of Tglck:GFP Danio rerio FITC+ were analyzed.	pubmed:32427565	lckgfp s240	GSM4087361	source name:Danio rerio tail\|line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	lckgfp s240	STAR 2.5 Htseq 0.8.0 htseq count m intersection nonempty nonunique all Genome build: GRCz10 Supplementary files format and content: Raw counts of numbers of reads aligned to each feature for each cell in tab separated format lckgfp counts.txt	Danio rerio tail	Liberase TL 100 ug/mL and manual trituration was used to dissociate tail tissue. Cells were FACS sorted FITC+	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018		line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	GSM4087361	GSM4087361: lckgfp s240; Danio rerio; RNA Seq	GSM4087361	1	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018	GEO Accession:GSM4087361	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP222763	lckgfp_s240_R1.fastq.gz lckgfp_s240_R2.fastq.gz	fastq fastq	153466400.0	767332.0	GSM4087361 r1	0:100 1:100	A:50048852;C:28704914;G:28416813;T:46295033;N:788	100	100	50048852	28704914	28416813	46295033	788	SRX6877378	SRS5413160	SRA965286	GEO	Stanford University	2	0.71293	0.72959	0.31443	0.32369	0.97966	0.98015	0.71821	0.7056	100	100	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2019-09-20	Larval	Larval	Tail	Multi-system
54807	54807	SRR10151918	SRX6877377	SRS5413159	SRP222763	PRJNA572587	Characterization of T cells from the larval zebrafish tail via single cell RNAseq	GSE137770	Transcriptome Analysis	We report single cell RNA sequencing of cells from the Tglck:GFP larval zebrafish tail to identify cell types expressing the marker and to identify gene candidates related to T cell migration behaviors. We identified 330 putative T cells and 131 putative epithelial cells. Differential expression analysis between the two groups revealed genes related to actin cytoskeleton remodeling associated with the T cells in addition to canonical T and ubiquitous immune cell markers. Overall design: Single cells n=461 isolated from FACS of Tglck:GFP Danio rerio FITC+ were analyzed.	pubmed:32427565	lckgfp s359	GSM4087480	source name:Danio rerio tail\|line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	lckgfp s359	STAR 2.5 Htseq 0.8.0 htseq count m intersection nonempty nonunique all Genome build: GRCz10 Supplementary files format and content: Raw counts of numbers of reads aligned to each feature for each cell in tab separated format lckgfp counts.txt	Danio rerio tail	Liberase TL 100 ug/mL and manual trituration was used to dissociate tail tissue. Cells were FACS sorted FITC+	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018		line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	GSM4087480	GSM4087480: lckgfp s359; Danio rerio; RNA Seq	GSM4087480	1	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018	GEO Accession:GSM4087480	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP222763	lckgfp_s359_R1.fastq.gz lckgfp_s359_R2.fastq.gz	fastq fastq	180259400.0	901297.0	GSM4087480 r1	0:100 1:100	A:51414242;C:38692238;G:38347124;T:51804826;N:970	100	100	51414242	38692238	38347124	51804826	970	SRX6877377	SRS5413159	SRA965286	GEO	Stanford University	2	0.88833	0.89291	0.23149	0.23212	0.97047	0.97088	0.49045	0.55701	100	100	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2019-09-20	Larval	Larval	Tail	Multi-system
54808	54808	SRR10151917	SRX6877376	SRS5413158	SRP222763	PRJNA572587	Characterization of T cells from the larval zebrafish tail via single cell RNAseq	GSE137770	Transcriptome Analysis	We report single cell RNA sequencing of cells from the Tglck:GFP larval zebrafish tail to identify cell types expressing the marker and to identify gene candidates related to T cell migration behaviors. We identified 330 putative T cells and 131 putative epithelial cells. Differential expression analysis between the two groups revealed genes related to actin cytoskeleton remodeling associated with the T cells in addition to canonical T and ubiquitous immune cell markers. Overall design: Single cells n=461 isolated from FACS of Tglck:GFP Danio rerio FITC+ were analyzed.	pubmed:32427565	lckgfp s358	GSM4087479	source name:Danio rerio tail\|line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	lckgfp s358	STAR 2.5 Htseq 0.8.0 htseq count m intersection nonempty nonunique all Genome build: GRCz10 Supplementary files format and content: Raw counts of numbers of reads aligned to each feature for each cell in tab separated format lckgfp counts.txt	Danio rerio tail	Liberase TL 100 ug/mL and manual trituration was used to dissociate tail tissue. Cells were FACS sorted FITC+	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018		line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	GSM4087479	GSM4087479: lckgfp s358; Danio rerio; RNA Seq	GSM4087479	1	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018	GEO Accession:GSM4087479	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP222763	lckgfp_s358_R1.fastq.gz lckgfp_s358_R2.fastq.gz	fastq fastq	375455400.0	1877277.0	GSM4087479 r1	0:100 1:100	A:109265882;C:78761598;G:77114775;T:110311304;N:1841	100	100	109265882	78761598	77114775	110311304	1841	SRX6877376	SRS5413158	SRA965286	GEO	Stanford University	2	0.86409	0.86748	0.23888	0.24065	0.96897	0.96919	0.57659	0.56636	100	100	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2019-09-20	Larval	Larval	Tail	Multi-system
54809	54809	SRR10151916	SRX6877375	SRS5413157	SRP222763	PRJNA572587	Characterization of T cells from the larval zebrafish tail via single cell RNAseq	GSE137770	Transcriptome Analysis	We report single cell RNA sequencing of cells from the Tglck:GFP larval zebrafish tail to identify cell types expressing the marker and to identify gene candidates related to T cell migration behaviors. We identified 330 putative T cells and 131 putative epithelial cells. Differential expression analysis between the two groups revealed genes related to actin cytoskeleton remodeling associated with the T cells in addition to canonical T and ubiquitous immune cell markers. Overall design: Single cells n=461 isolated from FACS of Tglck:GFP Danio rerio FITC+ were analyzed.	pubmed:32427565	lckgfp s357	GSM4087478	source name:Danio rerio tail\|line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	lckgfp s357	STAR 2.5 Htseq 0.8.0 htseq count m intersection nonempty nonunique all Genome build: GRCz10 Supplementary files format and content: Raw counts of numbers of reads aligned to each feature for each cell in tab separated format lckgfp counts.txt	Danio rerio tail	Liberase TL 100 ug/mL and manual trituration was used to dissociate tail tissue. Cells were FACS sorted FITC+	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018		line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	GSM4087478	GSM4087478: lckgfp s357; Danio rerio; RNA Seq	GSM4087478	1	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018	GEO Accession:GSM4087478	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP222763	lckgfp_s357_R1.fastq.gz lckgfp_s357_R2.fastq.gz	fastq fastq	1031071600.0	5155358.0	GSM4087478 r1	0:100 1:100	A:290286165;C:220464752;G:221676322;T:298639325;N:5036	100	100	290286165	220464752	221676322	298639325	5036	SRX6877375	SRS5413157	SRA965286	GEO	Stanford University	2	0.89351	0.8959	0.15814	0.15969	0.95483	0.95501	0.5582	0.55541	100	100	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2019-09-20	Larval	Larval	Tail	Multi-system
54810	54810	SRR10151915	SRX6877374	SRS5413156	SRP222763	PRJNA572587	Characterization of T cells from the larval zebrafish tail via single cell RNAseq	GSE137770	Transcriptome Analysis	We report single cell RNA sequencing of cells from the Tglck:GFP larval zebrafish tail to identify cell types expressing the marker and to identify gene candidates related to T cell migration behaviors. We identified 330 putative T cells and 131 putative epithelial cells. Differential expression analysis between the two groups revealed genes related to actin cytoskeleton remodeling associated with the T cells in addition to canonical T and ubiquitous immune cell markers. Overall design: Single cells n=461 isolated from FACS of Tglck:GFP Danio rerio FITC+ were analyzed.	pubmed:32427565	lckgfp s356	GSM4087477	source name:Danio rerio tail\|line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	lckgfp s356	STAR 2.5 Htseq 0.8.0 htseq count m intersection nonempty nonunique all Genome build: GRCz10 Supplementary files format and content: Raw counts of numbers of reads aligned to each feature for each cell in tab separated format lckgfp counts.txt	Danio rerio tail	Liberase TL 100 ug/mL and manual trituration was used to dissociate tail tissue. Cells were FACS sorted FITC+	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018		line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	GSM4087477	GSM4087477: lckgfp s356; Danio rerio; RNA Seq	GSM4087477	1	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018	GEO Accession:GSM4087477	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP222763	lckgfp_s356_R1.fastq.gz lckgfp_s356_R2.fastq.gz	fastq fastq	631604600.0	3158023.0	GSM4087477 r1	0:100 1:100	A:179705284;C:135901184;G:136090966;T:179904181;N:2985	100	100	179705284	135901184	136090966	179904181	2985	SRX6877374	SRS5413156	SRA965286	GEO	Stanford University	2	0.89013	0.89373	0.16216	0.16397	0.97159	0.97153	0.52157	0.52159	100	100	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2019-09-20	Larval	Larval	Tail	Multi-system
54811	54811	SRR10151914	SRX6877373	SRS5413155	SRP222763	PRJNA572587	Characterization of T cells from the larval zebrafish tail via single cell RNAseq	GSE137770	Transcriptome Analysis	We report single cell RNA sequencing of cells from the Tglck:GFP larval zebrafish tail to identify cell types expressing the marker and to identify gene candidates related to T cell migration behaviors. We identified 330 putative T cells and 131 putative epithelial cells. Differential expression analysis between the two groups revealed genes related to actin cytoskeleton remodeling associated with the T cells in addition to canonical T and ubiquitous immune cell markers. Overall design: Single cells n=461 isolated from FACS of Tglck:GFP Danio rerio FITC+ were analyzed.	pubmed:32427565	lckgfp s355	GSM4087476	source name:Danio rerio tail\|line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	lckgfp s355	STAR 2.5 Htseq 0.8.0 htseq count m intersection nonempty nonunique all Genome build: GRCz10 Supplementary files format and content: Raw counts of numbers of reads aligned to each feature for each cell in tab separated format lckgfp counts.txt	Danio rerio tail	Liberase TL 100 ug/mL and manual trituration was used to dissociate tail tissue. Cells were FACS sorted FITC+	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018		line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	GSM4087476	GSM4087476: lckgfp s355; Danio rerio; RNA Seq	GSM4087476	1	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018	GEO Accession:GSM4087476	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP222763	lckgfp_s355_R1.fastq.gz lckgfp_s355_R2.fastq.gz	fastq fastq	437755400.0	2188777.0	GSM4087476 r1	0:100 1:100	A:125630217;C:93000635;G:93133725;T:125988715;N:2108	100	100	125630217	93000635	93133725	125988715	2108	SRX6877373	SRS5413155	SRA965286	GEO	Stanford University	2	0.8771	0.88183	0.22446	0.22704	0.97682	0.97715	0.51148	0.51062	100	100	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2019-09-20	Larval	Larval	Tail	Multi-system
54812	54812	SRR10151913	SRX6877372	SRS5413154	SRP222763	PRJNA572587	Characterization of T cells from the larval zebrafish tail via single cell RNAseq	GSE137770	Transcriptome Analysis	We report single cell RNA sequencing of cells from the Tglck:GFP larval zebrafish tail to identify cell types expressing the marker and to identify gene candidates related to T cell migration behaviors. We identified 330 putative T cells and 131 putative epithelial cells. Differential expression analysis between the two groups revealed genes related to actin cytoskeleton remodeling associated with the T cells in addition to canonical T and ubiquitous immune cell markers. Overall design: Single cells n=461 isolated from FACS of Tglck:GFP Danio rerio FITC+ were analyzed.	pubmed:32427565	lckgfp s354	GSM4087475	source name:Danio rerio tail\|line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	lckgfp s354	STAR 2.5 Htseq 0.8.0 htseq count m intersection nonempty nonunique all Genome build: GRCz10 Supplementary files format and content: Raw counts of numbers of reads aligned to each feature for each cell in tab separated format lckgfp counts.txt	Danio rerio tail	Liberase TL 100 ug/mL and manual trituration was used to dissociate tail tissue. Cells were FACS sorted FITC+	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018		line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	GSM4087475	GSM4087475: lckgfp s354; Danio rerio; RNA Seq	GSM4087475	1	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018	GEO Accession:GSM4087475	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP222763	lckgfp_s354_R1.fastq.gz lckgfp_s354_R2.fastq.gz	fastq fastq	187430200.0	937151.0	GSM4087475 r1	0:100 1:100	A:56210423;C:40204731;G:37870530;T:53143658;N:858	100	100	56210423	40204731	37870530	53143658	858	SRX6877372	SRS5413154	SRA965286	GEO	Stanford University	2	0.79366	0.81071	0.12291	0.12589	0.98033	0.98031	0.6249	0.63056	100	100	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2019-09-20	Larval	Larval	Tail	Multi-system
54813	54813	SRR10151912	SRX6877371	SRS5413153	SRP222763	PRJNA572587	Characterization of T cells from the larval zebrafish tail via single cell RNAseq	GSE137770	Transcriptome Analysis	We report single cell RNA sequencing of cells from the Tglck:GFP larval zebrafish tail to identify cell types expressing the marker and to identify gene candidates related to T cell migration behaviors. We identified 330 putative T cells and 131 putative epithelial cells. Differential expression analysis between the two groups revealed genes related to actin cytoskeleton remodeling associated with the T cells in addition to canonical T and ubiquitous immune cell markers. Overall design: Single cells n=461 isolated from FACS of Tglck:GFP Danio rerio FITC+ were analyzed.	pubmed:32427565	lckgfp s353	GSM4087474	source name:Danio rerio tail\|line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	lckgfp s353	STAR 2.5 Htseq 0.8.0 htseq count m intersection nonempty nonunique all Genome build: GRCz10 Supplementary files format and content: Raw counts of numbers of reads aligned to each feature for each cell in tab separated format lckgfp counts.txt	Danio rerio tail	Liberase TL 100 ug/mL and manual trituration was used to dissociate tail tissue. Cells were FACS sorted FITC+	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018		line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	GSM4087474	GSM4087474: lckgfp s353; Danio rerio; RNA Seq	GSM4087474	1	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018	GEO Accession:GSM4087474	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP222763	lckgfp_s353_R1.fastq.gz lckgfp_s353_R2.fastq.gz	fastq fastq	288086200.0	1440431.0	GSM4087474 r1	0:100 1:100	A:82382315;C:61117555;G:61270028;T:83314923;N:1379	100	100	82382315	61117555	61270028	83314923	1379	SRX6877371	SRS5413153	SRA965286	GEO	Stanford University	2	0.87548	0.87893	0.21375	0.21654	0.96678	0.96633	0.49046	0.4943	100	100	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2019-09-20	Larval	Larval	Tail	Multi-system
54814	54814	SRR10151911	SRX6877370	SRS5413152	SRP222763	PRJNA572587	Characterization of T cells from the larval zebrafish tail via single cell RNAseq	GSE137770	Transcriptome Analysis	We report single cell RNA sequencing of cells from the Tglck:GFP larval zebrafish tail to identify cell types expressing the marker and to identify gene candidates related to T cell migration behaviors. We identified 330 putative T cells and 131 putative epithelial cells. Differential expression analysis between the two groups revealed genes related to actin cytoskeleton remodeling associated with the T cells in addition to canonical T and ubiquitous immune cell markers. Overall design: Single cells n=461 isolated from FACS of Tglck:GFP Danio rerio FITC+ were analyzed.	pubmed:32427565	lckgfp s352	GSM4087473	source name:Danio rerio tail\|line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	lckgfp s352	STAR 2.5 Htseq 0.8.0 htseq count m intersection nonempty nonunique all Genome build: GRCz10 Supplementary files format and content: Raw counts of numbers of reads aligned to each feature for each cell in tab separated format lckgfp counts.txt	Danio rerio tail	Liberase TL 100 ug/mL and manual trituration was used to dissociate tail tissue. Cells were FACS sorted FITC+	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018		line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	GSM4087473	GSM4087473: lckgfp s352; Danio rerio; RNA Seq	GSM4087473	1	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018	GEO Accession:GSM4087473	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP222763	lckgfp_s352_R1.fastq.gz lckgfp_s352_R2.fastq.gz	fastq fastq	234676200.0	1173381.0	GSM4087473 r1	0:100 1:100	A:71012748;C:48194679;G:47384221;T:68083483;N:1069	100	100	71012748	48194679	47384221	68083483	1069	SRX6877370	SRS5413152	SRA965286	GEO	Stanford University	2	0.78896	0.80572	0.16654	0.17056	0.97761	0.97753	0.58617	0.5841	100	100	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2019-09-20	Larval	Larval	Tail	Multi-system
54815	54815	SRR10151910	SRX6877369	SRS5413151	SRP222763	PRJNA572587	Characterization of T cells from the larval zebrafish tail via single cell RNAseq	GSE137770	Transcriptome Analysis	We report single cell RNA sequencing of cells from the Tglck:GFP larval zebrafish tail to identify cell types expressing the marker and to identify gene candidates related to T cell migration behaviors. We identified 330 putative T cells and 131 putative epithelial cells. Differential expression analysis between the two groups revealed genes related to actin cytoskeleton remodeling associated with the T cells in addition to canonical T and ubiquitous immune cell markers. Overall design: Single cells n=461 isolated from FACS of Tglck:GFP Danio rerio FITC+ were analyzed.	pubmed:32427565	lckgfp s351	GSM4087472	source name:Danio rerio tail\|line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	lckgfp s351	STAR 2.5 Htseq 0.8.0 htseq count m intersection nonempty nonunique all Genome build: GRCz10 Supplementary files format and content: Raw counts of numbers of reads aligned to each feature for each cell in tab separated format lckgfp counts.txt	Danio rerio tail	Liberase TL 100 ug/mL and manual trituration was used to dissociate tail tissue. Cells were FACS sorted FITC+	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018		line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	GSM4087472	GSM4087472: lckgfp s351; Danio rerio; RNA Seq	GSM4087472	1	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018	GEO Accession:GSM4087472	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP222763	lckgfp_s351_R1.fastq.gz lckgfp_s351_R2.fastq.gz	fastq fastq	142332600.0	711663.0	GSM4087472 r1	0:100 1:100	A:46730887;C:27992765;G:26483796;T:41124486;N:666	100	100	46730887	27992765	26483796	41124486	666	SRX6877369	SRS5413151	SRA965286	GEO	Stanford University	2	0.63313	0.65934	0.17905	0.18805	0.98397	0.98429	0.68129	0.67934	100	100	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2019-09-20	Larval	Larval	Tail	Multi-system
54816	54816	SRR10151909	SRX6877368	SRS5413150	SRP222763	PRJNA572587	Characterization of T cells from the larval zebrafish tail via single cell RNAseq	GSE137770	Transcriptome Analysis	We report single cell RNA sequencing of cells from the Tglck:GFP larval zebrafish tail to identify cell types expressing the marker and to identify gene candidates related to T cell migration behaviors. We identified 330 putative T cells and 131 putative epithelial cells. Differential expression analysis between the two groups revealed genes related to actin cytoskeleton remodeling associated with the T cells in addition to canonical T and ubiquitous immune cell markers. Overall design: Single cells n=461 isolated from FACS of Tglck:GFP Danio rerio FITC+ were analyzed.	pubmed:32427565	lckgfp s350	GSM4087471	source name:Danio rerio tail\|line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	lckgfp s350	STAR 2.5 Htseq 0.8.0 htseq count m intersection nonempty nonunique all Genome build: GRCz10 Supplementary files format and content: Raw counts of numbers of reads aligned to each feature for each cell in tab separated format lckgfp counts.txt	Danio rerio tail	Liberase TL 100 ug/mL and manual trituration was used to dissociate tail tissue. Cells were FACS sorted FITC+	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018		line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	GSM4087471	GSM4087471: lckgfp s350; Danio rerio; RNA Seq	GSM4087471	1	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018	GEO Accession:GSM4087471	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP222763	lckgfp_s350_R1.fastq.gz lckgfp_s350_R2.fastq.gz	fastq fastq	256653200.0	1283266.0	GSM4087471 r1	0:100 1:100	A:79486976;C:53119381;G:50178393;T:73867234;N:1216	100	100	79486976	53119381	50178393	73867234	1216	SRX6877368	SRS5413150	SRA965286	GEO	Stanford University	2	0.74257	0.75866	0.1224	0.12466	0.97693	0.97688	0.64957	0.65551	100	100	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2019-09-20	Larval	Larval	Tail	Multi-system
54817	54817	SRR10151908	SRX6877367	SRS5413149	SRP222763	PRJNA572587	Characterization of T cells from the larval zebrafish tail via single cell RNAseq	GSE137770	Transcriptome Analysis	We report single cell RNA sequencing of cells from the Tglck:GFP larval zebrafish tail to identify cell types expressing the marker and to identify gene candidates related to T cell migration behaviors. We identified 330 putative T cells and 131 putative epithelial cells. Differential expression analysis between the two groups revealed genes related to actin cytoskeleton remodeling associated with the T cells in addition to canonical T and ubiquitous immune cell markers. Overall design: Single cells n=461 isolated from FACS of Tglck:GFP Danio rerio FITC+ were analyzed.	pubmed:32427565	lckgfp s349	GSM4087470	source name:Danio rerio tail\|line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	lckgfp s349	STAR 2.5 Htseq 0.8.0 htseq count m intersection nonempty nonunique all Genome build: GRCz10 Supplementary files format and content: Raw counts of numbers of reads aligned to each feature for each cell in tab separated format lckgfp counts.txt	Danio rerio tail	Liberase TL 100 ug/mL and manual trituration was used to dissociate tail tissue. Cells were FACS sorted FITC+	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018		line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	GSM4087470	GSM4087470: lckgfp s349; Danio rerio; RNA Seq	GSM4087470	1	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018	GEO Accession:GSM4087470	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP222763	lckgfp_s349_R1.fastq.gz lckgfp_s349_R2.fastq.gz	fastq fastq	266517000.0	1332585.0	GSM4087470 r1	0:100 1:100	A:78245242;C:50857180;G:52125469;T:85287928;N:1181	100	100	78245242	50857180	52125469	85287928	1181	SRX6877367	SRS5413149	SRA965286	GEO	Stanford University	2	0.8172	0.81942	0.22884	0.23527	0.95069	0.95043	0.53777	0.53346	100	100	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2019-09-20	Larval	Larval	Tail	Multi-system
54818	54818	SRR10151907	SRX6877366	SRS5413148	SRP222763	PRJNA572587	Characterization of T cells from the larval zebrafish tail via single cell RNAseq	GSE137770	Transcriptome Analysis	We report single cell RNA sequencing of cells from the Tglck:GFP larval zebrafish tail to identify cell types expressing the marker and to identify gene candidates related to T cell migration behaviors. We identified 330 putative T cells and 131 putative epithelial cells. Differential expression analysis between the two groups revealed genes related to actin cytoskeleton remodeling associated with the T cells in addition to canonical T and ubiquitous immune cell markers. Overall design: Single cells n=461 isolated from FACS of Tglck:GFP Danio rerio FITC+ were analyzed.	pubmed:32427565	lckgfp s348	GSM4087469	source name:Danio rerio tail\|line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	lckgfp s348	STAR 2.5 Htseq 0.8.0 htseq count m intersection nonempty nonunique all Genome build: GRCz10 Supplementary files format and content: Raw counts of numbers of reads aligned to each feature for each cell in tab separated format lckgfp counts.txt	Danio rerio tail	Liberase TL 100 ug/mL and manual trituration was used to dissociate tail tissue. Cells were FACS sorted FITC+	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018		line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	GSM4087469	GSM4087469: lckgfp s348; Danio rerio; RNA Seq	GSM4087469	1	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018	GEO Accession:GSM4087469	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP222763	lckgfp_s348_R1.fastq.gz lckgfp_s348_R2.fastq.gz	fastq fastq	218351400.0	1091757.0	GSM4087469 r1	0:100 1:100	A:64900003;C:46681580;G:45663559;T:61105186;N:1072	100	100	64900003	46681580	45663559	61105186	1072	SRX6877366	SRS5413148	SRA965286	GEO	Stanford University	2	0.80696	0.81832	0.12677	0.12868	0.97798	0.97768	0.47529	0.47334	100	100	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2019-09-20	Larval	Larval	Tail	Multi-system
54819	54819	SRR10151906	SRX6877365	SRS5413147	SRP222763	PRJNA572587	Characterization of T cells from the larval zebrafish tail via single cell RNAseq	GSE137770	Transcriptome Analysis	We report single cell RNA sequencing of cells from the Tglck:GFP larval zebrafish tail to identify cell types expressing the marker and to identify gene candidates related to T cell migration behaviors. We identified 330 putative T cells and 131 putative epithelial cells. Differential expression analysis between the two groups revealed genes related to actin cytoskeleton remodeling associated with the T cells in addition to canonical T and ubiquitous immune cell markers. Overall design: Single cells n=461 isolated from FACS of Tglck:GFP Danio rerio FITC+ were analyzed.	pubmed:32427565	lckgfp s347	GSM4087468	source name:Danio rerio tail\|line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	lckgfp s347	STAR 2.5 Htseq 0.8.0 htseq count m intersection nonempty nonunique all Genome build: GRCz10 Supplementary files format and content: Raw counts of numbers of reads aligned to each feature for each cell in tab separated format lckgfp counts.txt	Danio rerio tail	Liberase TL 100 ug/mL and manual trituration was used to dissociate tail tissue. Cells were FACS sorted FITC+	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018		line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	GSM4087468	GSM4087468: lckgfp s347; Danio rerio; RNA Seq	GSM4087468	1	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018	GEO Accession:GSM4087468	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP222763	lckgfp_s347_R1.fastq.gz lckgfp_s347_R2.fastq.gz	fastq fastq	1283436400.0	6417182.0	GSM4087468 r1	0:100 1:100	A:360512221;C:280178229;G:280104753;T:362636146;N:5051	100	100	360512221	280178229	280104753	362636146	5051	SRX6877365	SRS5413147	SRA965286	GEO	Stanford University	2	0.90384	0.90101	0.23515	0.23455	0.98307	0.9835	0.53235	0.60485	100	100	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2019-09-20	Larval	Larval	Tail	Multi-system
54820	54820	SRR10151905	SRX6877364	SRS5413146	SRP222763	PRJNA572587	Characterization of T cells from the larval zebrafish tail via single cell RNAseq	GSE137770	Transcriptome Analysis	We report single cell RNA sequencing of cells from the Tglck:GFP larval zebrafish tail to identify cell types expressing the marker and to identify gene candidates related to T cell migration behaviors. We identified 330 putative T cells and 131 putative epithelial cells. Differential expression analysis between the two groups revealed genes related to actin cytoskeleton remodeling associated with the T cells in addition to canonical T and ubiquitous immune cell markers. Overall design: Single cells n=461 isolated from FACS of Tglck:GFP Danio rerio FITC+ were analyzed.	pubmed:32427565	lckgfp s346	GSM4087467	source name:Danio rerio tail\|line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	lckgfp s346	STAR 2.5 Htseq 0.8.0 htseq count m intersection nonempty nonunique all Genome build: GRCz10 Supplementary files format and content: Raw counts of numbers of reads aligned to each feature for each cell in tab separated format lckgfp counts.txt	Danio rerio tail	Liberase TL 100 ug/mL and manual trituration was used to dissociate tail tissue. Cells were FACS sorted FITC+	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018		line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	GSM4087467	GSM4087467: lckgfp s346; Danio rerio; RNA Seq	GSM4087467	1	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018	GEO Accession:GSM4087467	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP222763	lckgfp_s346_R1.fastq.gz lckgfp_s346_R2.fastq.gz	fastq fastq	265081400.0	1325407.0	GSM4087467 r1	0:100 1:100	A:77020683;C:56160067;G:55647714;T:76251684;N:1252	100	100	77020683	56160067	55647714	76251684	1252	SRX6877364	SRS5413146	SRA965286	GEO	Stanford University	2	0.88027	0.88557	0.22235	0.22374	0.9736	0.97337	0.53556	0.53951	100	100	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2019-09-20	Larval	Larval	Tail	Multi-system
54821	54821	SRR10151904	SRX6877363	SRS5413145	SRP222763	PRJNA572587	Characterization of T cells from the larval zebrafish tail via single cell RNAseq	GSE137770	Transcriptome Analysis	We report single cell RNA sequencing of cells from the Tglck:GFP larval zebrafish tail to identify cell types expressing the marker and to identify gene candidates related to T cell migration behaviors. We identified 330 putative T cells and 131 putative epithelial cells. Differential expression analysis between the two groups revealed genes related to actin cytoskeleton remodeling associated with the T cells in addition to canonical T and ubiquitous immune cell markers. Overall design: Single cells n=461 isolated from FACS of Tglck:GFP Danio rerio FITC+ were analyzed.	pubmed:32427565	lckgfp s345	GSM4087466	source name:Danio rerio tail\|line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	lckgfp s345	STAR 2.5 Htseq 0.8.0 htseq count m intersection nonempty nonunique all Genome build: GRCz10 Supplementary files format and content: Raw counts of numbers of reads aligned to each feature for each cell in tab separated format lckgfp counts.txt	Danio rerio tail	Liberase TL 100 ug/mL and manual trituration was used to dissociate tail tissue. Cells were FACS sorted FITC+	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018		line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	GSM4087466	GSM4087466: lckgfp s345; Danio rerio; RNA Seq	GSM4087466	1	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018	GEO Accession:GSM4087466	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP222763	lckgfp_s345_R1.fastq.gz lckgfp_s345_R2.fastq.gz	fastq fastq	920847800.0	4604239.0	GSM4087466 r1	0:100 1:100	A:262122009;C:197882908;G:197475240;T:263362852;N:4791	100	100	262122009	197882908	197475240	263362852	4791	SRX6877363	SRS5413145	SRA965286	GEO	Stanford University	2	0.90511	0.90613	0.20408	0.20473	0.97388	0.97372	0.54732	0.53091	100	100	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2019-09-20	Larval	Larval	Tail	Multi-system
54822	54822	SRR10151903	SRX6877362	SRS5413144	SRP222763	PRJNA572587	Characterization of T cells from the larval zebrafish tail via single cell RNAseq	GSE137770	Transcriptome Analysis	We report single cell RNA sequencing of cells from the Tglck:GFP larval zebrafish tail to identify cell types expressing the marker and to identify gene candidates related to T cell migration behaviors. We identified 330 putative T cells and 131 putative epithelial cells. Differential expression analysis between the two groups revealed genes related to actin cytoskeleton remodeling associated with the T cells in addition to canonical T and ubiquitous immune cell markers. Overall design: Single cells n=461 isolated from FACS of Tglck:GFP Danio rerio FITC+ were analyzed.	pubmed:32427565	lckgfp s344	GSM4087465	source name:Danio rerio tail\|line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	lckgfp s344	STAR 2.5 Htseq 0.8.0 htseq count m intersection nonempty nonunique all Genome build: GRCz10 Supplementary files format and content: Raw counts of numbers of reads aligned to each feature for each cell in tab separated format lckgfp counts.txt	Danio rerio tail	Liberase TL 100 ug/mL and manual trituration was used to dissociate tail tissue. Cells were FACS sorted FITC+	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018		line:Tglck:GFP\|tissue:tail\|devlopmental stage:15 dpf	GSM4087465	GSM4087465: lckgfp s344; Danio rerio; RNA Seq	GSM4087465	1	Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018	GEO Accession:GSM4087465	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP222763	lckgfp_s344_R1.fastq.gz lckgfp_s344_R2.fastq.gz	fastq fastq	397396000.0	1986980.0	GSM4087465 r1	0:100 1:100	A:114048468;C:83076003;G:83782458;T:116487410;N:1661	100	100	114048468	83076003	83782458	116487410	1661	SRX6877362	SRS5413144	SRA965286	GEO	Stanford University	2	0.87017	0.87046	0.17392	0.17754	0.96613	0.96658	0.52672	0.53224	100	100	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2019-09-20	Larval	Larval	Tail	Multi-system

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