metadata: run_metadata: 20 rows where experiment.platform = "ILLUMINA", technology = "generic-scrnaseq-only" and tissue

20 rows where experiment.platform = "ILLUMINA", technology = "generic-scrnaseq-only" and tissue_curation = "Blood"

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.characteristics	GEOsample.accession	experiment.title	experiment.alias	experiment.library_name	experiment.design_description	experiment.library_construction_protocol	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.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.nofeature_rate.mate1	seqdetective.sparsity.mate1	seqdetective.pos_strand_rate.mate1	seqdetective.readlen.mate1	seqdetective.judgement.mate1	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
68081	68081	SRR17604932	SRX13773745	SRS11653746	SRP354901	PRJNA796794	Cell type specific transcriptome profiling reveals a role for thioredoxin in neutrophils and tumor initiation	GSE193591	Transcriptome Analysis	We report the application of Translating Ribosomal Affinity Purification TRAP seq for identifying cell type specific gene expression in the zebrafish larvae. Using cell specific promoters to drive an EGFP tagged ribosomal subunit we were able to identify translating mRNA transcripts in keratinocytes krt4 neutrophils lyz and macrophages mpeg during early cancer transformation. In our zebrafish model of HRasG12V transformed keratinocytes we identified 56 differentially expressed genes in keratinocytes 53 genes in neutrophils and no differentially expressed genes found in macrophages compared to control. These data indicate activation of gene expression pathways in distinct cell types following early keratinocyte transformation and validate the use of TRAPseq in the zebrafish model system. Overall design: Comparison of TRAP seq gene expression data in a HRasG12V transformed keratinocyte Zebrafish model in 3 different cells types	pubmed:35250998	Mpeg Ctrl rep3	GSM5814819	tissue:macrophage\|age:3dpf\|batch:3\|genotype:wild type\|cell type:macrophage\|cell type id:CL:0000235	Mpeg Ctrl rep3	Reads were aligned to the transcriptome using Bowtie v1.1.1 Gene abundances were estimated using RSEM v1.2.20 Genome build: GRCz10 Ensembl 83 annotation Supplementary files format and content: The processed data file for each sample is the gene level abundance output of RSEM and is a tab delimited text file	macrophage	Zebrafish larvae were microinjected into one cell stage embryos and screened 3 dpf for transgene expression. Microinjections for TRAP RNA sequencing included either control pTol2 krt4 RFP HRas or oncogenic pTol2 krt4 RFP HRasG12V constructs injected with pTol2 krt4 GFP L10a in wildtype larvae or into TgLyzC:EGFP L10a or Tgmpeg1:EGFP L10a larvae for keratinocyte neutrophil or macrophage specific expression profiling respectively.	Larvae were stored at 80°C in minimal residual media. QIAshredder Quiagen was used to homogenize the larvae prior to immunoprecipitation. mRNA was isolated from immunoprecipitated polysomes from 50 pooled oncogene expressing fish or controls using TRIzol reagent Invitrogen. RNA quality and concentration was assessed on Agilent RNA PicoChip and samples with a concentration < 200 pg/µl were concentrated in a SpeedVac. As RNA concentrations were low library prep was done with the NuGEN Ovation Single Cell RNA Seq System with 20 cycles of amplification. Libraries were then checked by QuBit and an AATI Fragment Analyzer for concentration and fragment size. Adaptors with barcodes were used and samples were sequenced on an Illumina HiSeq with an average of 8 samples per lane following manufacturer’s protocols.	age:3dpf\|batch:3\|genotype:wild type\|cell type:macrophage\|cell type id:CL:0000235	GSM5814819	GSM5814819: Mpeg Ctrl rep3; Danio rerio; RNA Seq	GSM5814819 r1	GSM5814819	1	Larvae were stored at 80°C in minimal residual media. QIAshredder Quiagen was used to homogenize the larvae prior to immunoprecipitation. mRNA was isolated from immunoprecipitated polysomes from 50 pooled oncogene expressing fish or controls using TRIzol reagent Invitrogen. RNA quality and concentration was assessed on Agilent RNA PicoChip and samples with a concentration < 200 pg/µl were concentrated in a SpeedVac. As RNA concentrations were low library prep was done with the NuGEN Ovation Single Cell RNA Seq System with 20 cycles of amplification. Libraries were then checked by QuBit and an AATI Fragment Analyzer for concentration and fragment size. Adaptors with barcodes were used and samples were sequenced on an Illumina HiSeq with an average of 8 samples per lane following manufacturer's protocols.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP354901	D8_GTCGTA_L007_R1_001.fastq.gz	fastq	2252199.0	22299.0	GSM5814819 r1	0:101 1:0	A:514455;C:544764;G:749718;T:443185;N:77	101	514455	544764	749718	443185	77	SRX13773745	SRS11653746	SRA1356563	University of Wisconsin-Madison	University of Wisconsin-Madison	1	0.85592	0.229	0.98664	0.73589	101	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc_generic	single_cell_generic	generic-scrnaseq-only	United States	2022-01-13	Larval	Larval	Blood	Hematopoietic System
68082	68082	SRR17604933	SRX13773745	SRS11653746	SRP354901	PRJNA796794	Cell type specific transcriptome profiling reveals a role for thioredoxin in neutrophils and tumor initiation	GSE193591	Transcriptome Analysis	We report the application of Translating Ribosomal Affinity Purification TRAP seq for identifying cell type specific gene expression in the zebrafish larvae. Using cell specific promoters to drive an EGFP tagged ribosomal subunit we were able to identify translating mRNA transcripts in keratinocytes krt4 neutrophils lyz and macrophages mpeg during early cancer transformation. In our zebrafish model of HRasG12V transformed keratinocytes we identified 56 differentially expressed genes in keratinocytes 53 genes in neutrophils and no differentially expressed genes found in macrophages compared to control. These data indicate activation of gene expression pathways in distinct cell types following early keratinocyte transformation and validate the use of TRAPseq in the zebrafish model system. Overall design: Comparison of TRAP seq gene expression data in a HRasG12V transformed keratinocyte Zebrafish model in 3 different cells types	pubmed:35250998	Mpeg Ctrl rep3	GSM5814819	tissue:macrophage\|age:3dpf\|batch:3\|genotype:wild type\|cell type:macrophage\|cell type id:CL:0000235	Mpeg Ctrl rep3	Reads were aligned to the transcriptome using Bowtie v1.1.1 Gene abundances were estimated using RSEM v1.2.20 Genome build: GRCz10 Ensembl 83 annotation Supplementary files format and content: The processed data file for each sample is the gene level abundance output of RSEM and is a tab delimited text file	macrophage	Zebrafish larvae were microinjected into one cell stage embryos and screened 3 dpf for transgene expression. Microinjections for TRAP RNA sequencing included either control pTol2 krt4 RFP HRas or oncogenic pTol2 krt4 RFP HRasG12V constructs injected with pTol2 krt4 GFP L10a in wildtype larvae or into TgLyzC:EGFP L10a or Tgmpeg1:EGFP L10a larvae for keratinocyte neutrophil or macrophage specific expression profiling respectively.	Larvae were stored at 80°C in minimal residual media. QIAshredder Quiagen was used to homogenize the larvae prior to immunoprecipitation. mRNA was isolated from immunoprecipitated polysomes from 50 pooled oncogene expressing fish or controls using TRIzol reagent Invitrogen. RNA quality and concentration was assessed on Agilent RNA PicoChip and samples with a concentration < 200 pg/µl were concentrated in a SpeedVac. As RNA concentrations were low library prep was done with the NuGEN Ovation Single Cell RNA Seq System with 20 cycles of amplification. Libraries were then checked by QuBit and an AATI Fragment Analyzer for concentration and fragment size. Adaptors with barcodes were used and samples were sequenced on an Illumina HiSeq with an average of 8 samples per lane following manufacturer’s protocols.	age:3dpf\|batch:3\|genotype:wild type\|cell type:macrophage\|cell type id:CL:0000235	GSM5814819	GSM5814819: Mpeg Ctrl rep3; Danio rerio; RNA Seq	GSM5814819 r1	GSM5814819	1	Larvae were stored at 80°C in minimal residual media. QIAshredder Quiagen was used to homogenize the larvae prior to immunoprecipitation. mRNA was isolated from immunoprecipitated polysomes from 50 pooled oncogene expressing fish or controls using TRIzol reagent Invitrogen. RNA quality and concentration was assessed on Agilent RNA PicoChip and samples with a concentration < 200 pg/µl were concentrated in a SpeedVac. As RNA concentrations were low library prep was done with the NuGEN Ovation Single Cell RNA Seq System with 20 cycles of amplification. Libraries were then checked by QuBit and an AATI Fragment Analyzer for concentration and fragment size. Adaptors with barcodes were used and samples were sequenced on an Illumina HiSeq with an average of 8 samples per lane following manufacturer's protocols.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP354901	D8_GTCGTA_L008_R1_001.fastq.gz	fastq	2296235.0	22735.0	GSM5814819 r2	0:101 1:0	A:522320;C:556731;G:765455;T:451622;N:107	101	522320	556731	765455	451622	107	SRX13773745	SRS11653746	SRA1356563	University of Wisconsin-Madison	University of Wisconsin-Madison	1	0.84559	0.22391	0.98646	0.69194	101	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc_generic	single_cell_generic	generic-scrnaseq-only	United States	2022-01-13	Larval	Larval	Blood	Hematopoietic System
68083	68083	SRR17604934	SRX13773744	SRS11653745	SRP354901	PRJNA796794	Cell type specific transcriptome profiling reveals a role for thioredoxin in neutrophils and tumor initiation	GSE193591	Transcriptome Analysis	We report the application of Translating Ribosomal Affinity Purification TRAP seq for identifying cell type specific gene expression in the zebrafish larvae. Using cell specific promoters to drive an EGFP tagged ribosomal subunit we were able to identify translating mRNA transcripts in keratinocytes krt4 neutrophils lyz and macrophages mpeg during early cancer transformation. In our zebrafish model of HRasG12V transformed keratinocytes we identified 56 differentially expressed genes in keratinocytes 53 genes in neutrophils and no differentially expressed genes found in macrophages compared to control. These data indicate activation of gene expression pathways in distinct cell types following early keratinocyte transformation and validate the use of TRAPseq in the zebrafish model system. Overall design: Comparison of TRAP seq gene expression data in a HRasG12V transformed keratinocyte Zebrafish model in 3 different cells types	pubmed:35250998	Lyz Ctrl rep3	GSM5814818	tissue:neutrophil\|age:3dpf\|batch:3\|genotype:wild type\|cell type:neutrophil\|cell type id:CL:0000775	Lyz Ctrl rep3	Reads were aligned to the transcriptome using Bowtie v1.1.1 Gene abundances were estimated using RSEM v1.2.20 Genome build: GRCz10 Ensembl 83 annotation Supplementary files format and content: The processed data file for each sample is the gene level abundance output of RSEM and is a tab delimited text file	neutrophil	Zebrafish larvae were microinjected into one cell stage embryos and screened 3 dpf for transgene expression. Microinjections for TRAP RNA sequencing included either control pTol2 krt4 RFP HRas or oncogenic pTol2 krt4 RFP HRasG12V constructs injected with pTol2 krt4 GFP L10a in wildtype larvae or into TgLyzC:EGFP L10a or Tgmpeg1:EGFP L10a larvae for keratinocyte neutrophil or macrophage specific expression profiling respectively.	Larvae were stored at 80°C in minimal residual media. QIAshredder Quiagen was used to homogenize the larvae prior to immunoprecipitation. mRNA was isolated from immunoprecipitated polysomes from 50 pooled oncogene expressing fish or controls using TRIzol reagent Invitrogen. RNA quality and concentration was assessed on Agilent RNA PicoChip and samples with a concentration < 200 pg/µl were concentrated in a SpeedVac. As RNA concentrations were low library prep was done with the NuGEN Ovation Single Cell RNA Seq System with 20 cycles of amplification. Libraries were then checked by QuBit and an AATI Fragment Analyzer for concentration and fragment size. Adaptors with barcodes were used and samples were sequenced on an Illumina HiSeq with an average of 8 samples per lane following manufacturer’s protocols.	age:3dpf\|batch:3\|genotype:wild type\|cell type:neutrophil\|cell type id:CL:0000775	GSM5814818	GSM5814818: Lyz Ctrl rep3; Danio rerio; RNA Seq	GSM5814818 r1	GSM5814818	1	Larvae were stored at 80°C in minimal residual media. QIAshredder Quiagen was used to homogenize the larvae prior to immunoprecipitation. mRNA was isolated from immunoprecipitated polysomes from 50 pooled oncogene expressing fish or controls using TRIzol reagent Invitrogen. RNA quality and concentration was assessed on Agilent RNA PicoChip and samples with a concentration < 200 pg/µl were concentrated in a SpeedVac. As RNA concentrations were low library prep was done with the NuGEN Ovation Single Cell RNA Seq System with 20 cycles of amplification. Libraries were then checked by QuBit and an AATI Fragment Analyzer for concentration and fragment size. Adaptors with barcodes were used and samples were sequenced on an Illumina HiSeq with an average of 8 samples per lane following manufacturer's protocols.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP354901	D7_AAGCCT_L007_R1_001.fastq.gz	fastq	1017922036.0	10078436.0	GSM5814818 r1	0:101 1:0	A:211263195;C:255471964;G:356158080;T:194948663;N:80134	101	211263195	255471964	356158080	194948663	80134	SRX13773744	SRS11653745	SRA1356563	University of Wisconsin-Madison	University of Wisconsin-Madison	1	0.9518	0.21615	0.94436	0.70474	101	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc_generic	single_cell_generic	generic-scrnaseq-only	United States	2022-01-13	Larval	Larval	Blood	Hematopoietic System
68084	68084	SRR17604935	SRX13773744	SRS11653745	SRP354901	PRJNA796794	Cell type specific transcriptome profiling reveals a role for thioredoxin in neutrophils and tumor initiation	GSE193591	Transcriptome Analysis	We report the application of Translating Ribosomal Affinity Purification TRAP seq for identifying cell type specific gene expression in the zebrafish larvae. Using cell specific promoters to drive an EGFP tagged ribosomal subunit we were able to identify translating mRNA transcripts in keratinocytes krt4 neutrophils lyz and macrophages mpeg during early cancer transformation. In our zebrafish model of HRasG12V transformed keratinocytes we identified 56 differentially expressed genes in keratinocytes 53 genes in neutrophils and no differentially expressed genes found in macrophages compared to control. These data indicate activation of gene expression pathways in distinct cell types following early keratinocyte transformation and validate the use of TRAPseq in the zebrafish model system. Overall design: Comparison of TRAP seq gene expression data in a HRasG12V transformed keratinocyte Zebrafish model in 3 different cells types	pubmed:35250998	Lyz Ctrl rep3	GSM5814818	tissue:neutrophil\|age:3dpf\|batch:3\|genotype:wild type\|cell type:neutrophil\|cell type id:CL:0000775	Lyz Ctrl rep3	Reads were aligned to the transcriptome using Bowtie v1.1.1 Gene abundances were estimated using RSEM v1.2.20 Genome build: GRCz10 Ensembl 83 annotation Supplementary files format and content: The processed data file for each sample is the gene level abundance output of RSEM and is a tab delimited text file	neutrophil	Zebrafish larvae were microinjected into one cell stage embryos and screened 3 dpf for transgene expression. Microinjections for TRAP RNA sequencing included either control pTol2 krt4 RFP HRas or oncogenic pTol2 krt4 RFP HRasG12V constructs injected with pTol2 krt4 GFP L10a in wildtype larvae or into TgLyzC:EGFP L10a or Tgmpeg1:EGFP L10a larvae for keratinocyte neutrophil or macrophage specific expression profiling respectively.	Larvae were stored at 80°C in minimal residual media. QIAshredder Quiagen was used to homogenize the larvae prior to immunoprecipitation. mRNA was isolated from immunoprecipitated polysomes from 50 pooled oncogene expressing fish or controls using TRIzol reagent Invitrogen. RNA quality and concentration was assessed on Agilent RNA PicoChip and samples with a concentration < 200 pg/µl were concentrated in a SpeedVac. As RNA concentrations were low library prep was done with the NuGEN Ovation Single Cell RNA Seq System with 20 cycles of amplification. Libraries were then checked by QuBit and an AATI Fragment Analyzer for concentration and fragment size. Adaptors with barcodes were used and samples were sequenced on an Illumina HiSeq with an average of 8 samples per lane following manufacturer’s protocols.	age:3dpf\|batch:3\|genotype:wild type\|cell type:neutrophil\|cell type id:CL:0000775	GSM5814818	GSM5814818: Lyz Ctrl rep3; Danio rerio; RNA Seq	GSM5814818 r1	GSM5814818	1	Larvae were stored at 80°C in minimal residual media. QIAshredder Quiagen was used to homogenize the larvae prior to immunoprecipitation. mRNA was isolated from immunoprecipitated polysomes from 50 pooled oncogene expressing fish or controls using TRIzol reagent Invitrogen. RNA quality and concentration was assessed on Agilent RNA PicoChip and samples with a concentration < 200 pg/µl were concentrated in a SpeedVac. As RNA concentrations were low library prep was done with the NuGEN Ovation Single Cell RNA Seq System with 20 cycles of amplification. Libraries were then checked by QuBit and an AATI Fragment Analyzer for concentration and fragment size. Adaptors with barcodes were used and samples were sequenced on an Illumina HiSeq with an average of 8 samples per lane following manufacturer's protocols.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP354901	D7_AAGCCT_L008_R1_001.fastq.gz	fastq	1003984137.0	9940437.0	GSM5814818 r2	0:101 1:0	A:208470451;C:251846847;G:350933835;T:192682137;N:50867	101	208470451	251846847	350933835	192682137	50867	SRX13773744	SRS11653745	SRA1356563	University of Wisconsin-Madison	University of Wisconsin-Madison	1	0.95157	0.21527	0.94397	0.67255	101	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc_generic	single_cell_generic	generic-scrnaseq-only	United States	2022-01-13	Larval	Larval	Blood	Hematopoietic System
68087	68087	SRR17604938	SRX13773742	SRS11653743	SRP354901	PRJNA796794	Cell type specific transcriptome profiling reveals a role for thioredoxin in neutrophils and tumor initiation	GSE193591	Transcriptome Analysis	We report the application of Translating Ribosomal Affinity Purification TRAP seq for identifying cell type specific gene expression in the zebrafish larvae. Using cell specific promoters to drive an EGFP tagged ribosomal subunit we were able to identify translating mRNA transcripts in keratinocytes krt4 neutrophils lyz and macrophages mpeg during early cancer transformation. In our zebrafish model of HRasG12V transformed keratinocytes we identified 56 differentially expressed genes in keratinocytes 53 genes in neutrophils and no differentially expressed genes found in macrophages compared to control. These data indicate activation of gene expression pathways in distinct cell types following early keratinocyte transformation and validate the use of TRAPseq in the zebrafish model system. Overall design: Comparison of TRAP seq gene expression data in a HRasG12V transformed keratinocyte Zebrafish model in 3 different cells types	pubmed:35250998	Mpeg V12 rep3	GSM5814816	tissue:macrophage\|age:3dpf\|batch:3\|genotype:mutant HRas G12V\|cell type:macrophage\|cell type id:CL:0000235	Mpeg V12 rep3	Reads were aligned to the transcriptome using Bowtie v1.1.1 Gene abundances were estimated using RSEM v1.2.20 Genome build: GRCz10 Ensembl 83 annotation Supplementary files format and content: The processed data file for each sample is the gene level abundance output of RSEM and is a tab delimited text file	macrophage	Zebrafish larvae were microinjected into one cell stage embryos and screened 3 dpf for transgene expression. Microinjections for TRAP RNA sequencing included either control pTol2 krt4 RFP HRas or oncogenic pTol2 krt4 RFP HRasG12V constructs injected with pTol2 krt4 GFP L10a in wildtype larvae or into TgLyzC:EGFP L10a or Tgmpeg1:EGFP L10a larvae for keratinocyte neutrophil or macrophage specific expression profiling respectively.	Larvae were stored at 80°C in minimal residual media. QIAshredder Quiagen was used to homogenize the larvae prior to immunoprecipitation. mRNA was isolated from immunoprecipitated polysomes from 50 pooled oncogene expressing fish or controls using TRIzol reagent Invitrogen. RNA quality and concentration was assessed on Agilent RNA PicoChip and samples with a concentration < 200 pg/µl were concentrated in a SpeedVac. As RNA concentrations were low library prep was done with the NuGEN Ovation Single Cell RNA Seq System with 20 cycles of amplification. Libraries were then checked by QuBit and an AATI Fragment Analyzer for concentration and fragment size. Adaptors with barcodes were used and samples were sequenced on an Illumina HiSeq with an average of 8 samples per lane following manufacturer’s protocols.	age:3dpf\|batch:3\|genotype:mutant HRas G12V\|cell type:macrophage\|cell type id:CL:0000235	GSM5814816	GSM5814816: Mpeg V12 rep3; Danio rerio; RNA Seq	GSM5814816 r1	GSM5814816	1	Larvae were stored at 80°C in minimal residual media. QIAshredder Quiagen was used to homogenize the larvae prior to immunoprecipitation. mRNA was isolated from immunoprecipitated polysomes from 50 pooled oncogene expressing fish or controls using TRIzol reagent Invitrogen. RNA quality and concentration was assessed on Agilent RNA PicoChip and samples with a concentration < 200 pg/µl were concentrated in a SpeedVac. As RNA concentrations were low library prep was done with the NuGEN Ovation Single Cell RNA Seq System with 20 cycles of amplification. Libraries were then checked by QuBit and an AATI Fragment Analyzer for concentration and fragment size. Adaptors with barcodes were used and samples were sequenced on an Illumina HiSeq with an average of 8 samples per lane following manufacturer's protocols.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP354901	d11_AGCATG_L007_R1_001.fastq.gz	fastq	1117487634.0	11064234.0	GSM5814816 r1	0:101 1:0	A:258329582;C:267694483;G:367895091;T:223479229;N:89249	101	258329582	267694483	367895091	223479229	89249	SRX13773742	SRS11653743	SRA1356563	University of Wisconsin-Madison	University of Wisconsin-Madison	1	0.84981	0.20008	0.89156	0.65923	101	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc_generic	single_cell_generic	generic-scrnaseq-only	United States	2022-01-13	Larval	Larval	Blood	Hematopoietic System
68088	68088	SRR17604939	SRX13773742	SRS11653743	SRP354901	PRJNA796794	Cell type specific transcriptome profiling reveals a role for thioredoxin in neutrophils and tumor initiation	GSE193591	Transcriptome Analysis	We report the application of Translating Ribosomal Affinity Purification TRAP seq for identifying cell type specific gene expression in the zebrafish larvae. Using cell specific promoters to drive an EGFP tagged ribosomal subunit we were able to identify translating mRNA transcripts in keratinocytes krt4 neutrophils lyz and macrophages mpeg during early cancer transformation. In our zebrafish model of HRasG12V transformed keratinocytes we identified 56 differentially expressed genes in keratinocytes 53 genes in neutrophils and no differentially expressed genes found in macrophages compared to control. These data indicate activation of gene expression pathways in distinct cell types following early keratinocyte transformation and validate the use of TRAPseq in the zebrafish model system. Overall design: Comparison of TRAP seq gene expression data in a HRasG12V transformed keratinocyte Zebrafish model in 3 different cells types	pubmed:35250998	Mpeg V12 rep3	GSM5814816	tissue:macrophage\|age:3dpf\|batch:3\|genotype:mutant HRas G12V\|cell type:macrophage\|cell type id:CL:0000235	Mpeg V12 rep3	Reads were aligned to the transcriptome using Bowtie v1.1.1 Gene abundances were estimated using RSEM v1.2.20 Genome build: GRCz10 Ensembl 83 annotation Supplementary files format and content: The processed data file for each sample is the gene level abundance output of RSEM and is a tab delimited text file	macrophage	Zebrafish larvae were microinjected into one cell stage embryos and screened 3 dpf for transgene expression. Microinjections for TRAP RNA sequencing included either control pTol2 krt4 RFP HRas or oncogenic pTol2 krt4 RFP HRasG12V constructs injected with pTol2 krt4 GFP L10a in wildtype larvae or into TgLyzC:EGFP L10a or Tgmpeg1:EGFP L10a larvae for keratinocyte neutrophil or macrophage specific expression profiling respectively.	Larvae were stored at 80°C in minimal residual media. QIAshredder Quiagen was used to homogenize the larvae prior to immunoprecipitation. mRNA was isolated from immunoprecipitated polysomes from 50 pooled oncogene expressing fish or controls using TRIzol reagent Invitrogen. RNA quality and concentration was assessed on Agilent RNA PicoChip and samples with a concentration < 200 pg/µl were concentrated in a SpeedVac. As RNA concentrations were low library prep was done with the NuGEN Ovation Single Cell RNA Seq System with 20 cycles of amplification. Libraries were then checked by QuBit and an AATI Fragment Analyzer for concentration and fragment size. Adaptors with barcodes were used and samples were sequenced on an Illumina HiSeq with an average of 8 samples per lane following manufacturer’s protocols.	age:3dpf\|batch:3\|genotype:mutant HRas G12V\|cell type:macrophage\|cell type id:CL:0000235	GSM5814816	GSM5814816: Mpeg V12 rep3; Danio rerio; RNA Seq	GSM5814816 r1	GSM5814816	1	Larvae were stored at 80°C in minimal residual media. QIAshredder Quiagen was used to homogenize the larvae prior to immunoprecipitation. mRNA was isolated from immunoprecipitated polysomes from 50 pooled oncogene expressing fish or controls using TRIzol reagent Invitrogen. RNA quality and concentration was assessed on Agilent RNA PicoChip and samples with a concentration < 200 pg/µl were concentrated in a SpeedVac. As RNA concentrations were low library prep was done with the NuGEN Ovation Single Cell RNA Seq System with 20 cycles of amplification. Libraries were then checked by QuBit and an AATI Fragment Analyzer for concentration and fragment size. Adaptors with barcodes were used and samples were sequenced on an Illumina HiSeq with an average of 8 samples per lane following manufacturer's protocols.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP354901	d11_AGCATG_L008_R1_001.fastq.gz	fastq	1103643867.0	10927167.0	GSM5814816 r2	0:101 1:0	A:255221519;C:264284982;G:363032184;T:221051396;N:53786	101	255221519	264284982	363032184	221051396	53786	SRX13773742	SRS11653743	SRA1356563	University of Wisconsin-Madison	University of Wisconsin-Madison	1	0.85088	0.19956	0.89108	0.67953	101	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc_generic	single_cell_generic	generic-scrnaseq-only	United States	2022-01-13	Larval	Larval	Blood	Hematopoietic System
68089	68089	SRR17604940	SRX13773741	SRS11653742	SRP354901	PRJNA796794	Cell type specific transcriptome profiling reveals a role for thioredoxin in neutrophils and tumor initiation	GSE193591	Transcriptome Analysis	We report the application of Translating Ribosomal Affinity Purification TRAP seq for identifying cell type specific gene expression in the zebrafish larvae. Using cell specific promoters to drive an EGFP tagged ribosomal subunit we were able to identify translating mRNA transcripts in keratinocytes krt4 neutrophils lyz and macrophages mpeg during early cancer transformation. In our zebrafish model of HRasG12V transformed keratinocytes we identified 56 differentially expressed genes in keratinocytes 53 genes in neutrophils and no differentially expressed genes found in macrophages compared to control. These data indicate activation of gene expression pathways in distinct cell types following early keratinocyte transformation and validate the use of TRAPseq in the zebrafish model system. Overall design: Comparison of TRAP seq gene expression data in a HRasG12V transformed keratinocyte Zebrafish model in 3 different cells types	pubmed:35250998	Lyz V12 rep3	GSM5814815	tissue:neutrophil\|age:3dpf\|batch:3\|genotype:mutant HRas G12V\|cell type:neutrophil\|cell type id:CL:0000775	Lyz V12 rep3	Reads were aligned to the transcriptome using Bowtie v1.1.1 Gene abundances were estimated using RSEM v1.2.20 Genome build: GRCz10 Ensembl 83 annotation Supplementary files format and content: The processed data file for each sample is the gene level abundance output of RSEM and is a tab delimited text file	neutrophil	Zebrafish larvae were microinjected into one cell stage embryos and screened 3 dpf for transgene expression. Microinjections for TRAP RNA sequencing included either control pTol2 krt4 RFP HRas or oncogenic pTol2 krt4 RFP HRasG12V constructs injected with pTol2 krt4 GFP L10a in wildtype larvae or into TgLyzC:EGFP L10a or Tgmpeg1:EGFP L10a larvae for keratinocyte neutrophil or macrophage specific expression profiling respectively.	Larvae were stored at 80°C in minimal residual media. QIAshredder Quiagen was used to homogenize the larvae prior to immunoprecipitation. mRNA was isolated from immunoprecipitated polysomes from 50 pooled oncogene expressing fish or controls using TRIzol reagent Invitrogen. RNA quality and concentration was assessed on Agilent RNA PicoChip and samples with a concentration < 200 pg/µl were concentrated in a SpeedVac. As RNA concentrations were low library prep was done with the NuGEN Ovation Single Cell RNA Seq System with 20 cycles of amplification. Libraries were then checked by QuBit and an AATI Fragment Analyzer for concentration and fragment size. Adaptors with barcodes were used and samples were sequenced on an Illumina HiSeq with an average of 8 samples per lane following manufacturer’s protocols.	age:3dpf\|batch:3\|genotype:mutant HRas G12V\|cell type:neutrophil\|cell type id:CL:0000775	GSM5814815	GSM5814815: Lyz V12 rep3; Danio rerio; RNA Seq	GSM5814815 r1	GSM5814815	1	Larvae were stored at 80°C in minimal residual media. QIAshredder Quiagen was used to homogenize the larvae prior to immunoprecipitation. mRNA was isolated from immunoprecipitated polysomes from 50 pooled oncogene expressing fish or controls using TRIzol reagent Invitrogen. RNA quality and concentration was assessed on Agilent RNA PicoChip and samples with a concentration < 200 pg/µl were concentrated in a SpeedVac. As RNA concentrations were low library prep was done with the NuGEN Ovation Single Cell RNA Seq System with 20 cycles of amplification. Libraries were then checked by QuBit and an AATI Fragment Analyzer for concentration and fragment size. Adaptors with barcodes were used and samples were sequenced on an Illumina HiSeq with an average of 8 samples per lane following manufacturer's protocols.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP354901	d10_GGAGAA_L007_R1_001.fastq.gz	fastq	960647865.0	9511365.0	GSM5814815 r1	0:101 1:0	A:212806547;C:232511926;G:325161334;T:190091050;N:77008	101	212806547	232511926	325161334	190091050	77008	SRX13773741	SRS11653742	SRA1356563	University of Wisconsin-Madison	University of Wisconsin-Madison	1	0.87006	0.21965	0.90788	0.64906	101	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc_generic	single_cell_generic	generic-scrnaseq-only	United States	2022-01-13	Larval	Larval	Blood	Hematopoietic System
68090	68090	SRR17604941	SRX13773741	SRS11653742	SRP354901	PRJNA796794	Cell type specific transcriptome profiling reveals a role for thioredoxin in neutrophils and tumor initiation	GSE193591	Transcriptome Analysis	We report the application of Translating Ribosomal Affinity Purification TRAP seq for identifying cell type specific gene expression in the zebrafish larvae. Using cell specific promoters to drive an EGFP tagged ribosomal subunit we were able to identify translating mRNA transcripts in keratinocytes krt4 neutrophils lyz and macrophages mpeg during early cancer transformation. In our zebrafish model of HRasG12V transformed keratinocytes we identified 56 differentially expressed genes in keratinocytes 53 genes in neutrophils and no differentially expressed genes found in macrophages compared to control. These data indicate activation of gene expression pathways in distinct cell types following early keratinocyte transformation and validate the use of TRAPseq in the zebrafish model system. Overall design: Comparison of TRAP seq gene expression data in a HRasG12V transformed keratinocyte Zebrafish model in 3 different cells types	pubmed:35250998	Lyz V12 rep3	GSM5814815	tissue:neutrophil\|age:3dpf\|batch:3\|genotype:mutant HRas G12V\|cell type:neutrophil\|cell type id:CL:0000775	Lyz V12 rep3	Reads were aligned to the transcriptome using Bowtie v1.1.1 Gene abundances were estimated using RSEM v1.2.20 Genome build: GRCz10 Ensembl 83 annotation Supplementary files format and content: The processed data file for each sample is the gene level abundance output of RSEM and is a tab delimited text file	neutrophil	Zebrafish larvae were microinjected into one cell stage embryos and screened 3 dpf for transgene expression. Microinjections for TRAP RNA sequencing included either control pTol2 krt4 RFP HRas or oncogenic pTol2 krt4 RFP HRasG12V constructs injected with pTol2 krt4 GFP L10a in wildtype larvae or into TgLyzC:EGFP L10a or Tgmpeg1:EGFP L10a larvae for keratinocyte neutrophil or macrophage specific expression profiling respectively.	Larvae were stored at 80°C in minimal residual media. QIAshredder Quiagen was used to homogenize the larvae prior to immunoprecipitation. mRNA was isolated from immunoprecipitated polysomes from 50 pooled oncogene expressing fish or controls using TRIzol reagent Invitrogen. RNA quality and concentration was assessed on Agilent RNA PicoChip and samples with a concentration < 200 pg/µl were concentrated in a SpeedVac. As RNA concentrations were low library prep was done with the NuGEN Ovation Single Cell RNA Seq System with 20 cycles of amplification. Libraries were then checked by QuBit and an AATI Fragment Analyzer for concentration and fragment size. Adaptors with barcodes were used and samples were sequenced on an Illumina HiSeq with an average of 8 samples per lane following manufacturer’s protocols.	age:3dpf\|batch:3\|genotype:mutant HRas G12V\|cell type:neutrophil\|cell type id:CL:0000775	GSM5814815	GSM5814815: Lyz V12 rep3; Danio rerio; RNA Seq	GSM5814815 r1	GSM5814815	1	Larvae were stored at 80°C in minimal residual media. QIAshredder Quiagen was used to homogenize the larvae prior to immunoprecipitation. mRNA was isolated from immunoprecipitated polysomes from 50 pooled oncogene expressing fish or controls using TRIzol reagent Invitrogen. RNA quality and concentration was assessed on Agilent RNA PicoChip and samples with a concentration < 200 pg/µl were concentrated in a SpeedVac. As RNA concentrations were low library prep was done with the NuGEN Ovation Single Cell RNA Seq System with 20 cycles of amplification. Libraries were then checked by QuBit and an AATI Fragment Analyzer for concentration and fragment size. Adaptors with barcodes were used and samples were sequenced on an Illumina HiSeq with an average of 8 samples per lane following manufacturer's protocols.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP354901	d10_GGAGAA_L008_R1_001.fastq.gz	fastq	948355357.0	9389657.0	GSM5814815 r2	0:101 1:0	A:210159593;C:229409756;G:320709432;T:188030646;N:45930	101	210159593	229409756	320709432	188030646	45930	SRX13773741	SRS11653742	SRA1356563	University of Wisconsin-Madison	University of Wisconsin-Madison	1	0.87179	0.22092	0.91029	0.65705	101	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc_generic	single_cell_generic	generic-scrnaseq-only	United States	2022-01-13	Larval	Larval	Blood	Hematopoietic System
68092	68092	SRR17604943	SRX13773739	SRS11653740	SRP354901	PRJNA796794	Cell type specific transcriptome profiling reveals a role for thioredoxin in neutrophils and tumor initiation	GSE193591	Transcriptome Analysis	We report the application of Translating Ribosomal Affinity Purification TRAP seq for identifying cell type specific gene expression in the zebrafish larvae. Using cell specific promoters to drive an EGFP tagged ribosomal subunit we were able to identify translating mRNA transcripts in keratinocytes krt4 neutrophils lyz and macrophages mpeg during early cancer transformation. In our zebrafish model of HRasG12V transformed keratinocytes we identified 56 differentially expressed genes in keratinocytes 53 genes in neutrophils and no differentially expressed genes found in macrophages compared to control. These data indicate activation of gene expression pathways in distinct cell types following early keratinocyte transformation and validate the use of TRAPseq in the zebrafish model system. Overall design: Comparison of TRAP seq gene expression data in a HRasG12V transformed keratinocyte Zebrafish model in 3 different cells types	pubmed:35250998	Mpeg Ctrl rep2	GSM5814813	tissue:macrophage\|age:3dpf\|batch:2\|genotype:wild type\|cell type:macrophage\|cell type id:CL:0000235	Mpeg Ctrl rep2	Reads were aligned to the transcriptome using Bowtie v1.1.1 Gene abundances were estimated using RSEM v1.2.20 Genome build: GRCz10 Ensembl 83 annotation Supplementary files format and content: The processed data file for each sample is the gene level abundance output of RSEM and is a tab delimited text file	macrophage	Zebrafish larvae were microinjected into one cell stage embryos and screened 3 dpf for transgene expression. Microinjections for TRAP RNA sequencing included either control pTol2 krt4 RFP HRas or oncogenic pTol2 krt4 RFP HRasG12V constructs injected with pTol2 krt4 GFP L10a in wildtype larvae or into TgLyzC:EGFP L10a or Tgmpeg1:EGFP L10a larvae for keratinocyte neutrophil or macrophage specific expression profiling respectively.	Larvae were stored at 80°C in minimal residual media. QIAshredder Quiagen was used to homogenize the larvae prior to immunoprecipitation. mRNA was isolated from immunoprecipitated polysomes from 50 pooled oncogene expressing fish or controls using TRIzol reagent Invitrogen. RNA quality and concentration was assessed on Agilent RNA PicoChip and samples with a concentration < 200 pg/µl were concentrated in a SpeedVac. As RNA concentrations were low library prep was done with the NuGEN Ovation Single Cell RNA Seq System with 20 cycles of amplification. Libraries were then checked by QuBit and an AATI Fragment Analyzer for concentration and fragment size. Adaptors with barcodes were used and samples were sequenced on an Illumina HiSeq with an average of 8 samples per lane following manufacturer’s protocols.	age:3dpf\|batch:2\|genotype:wild type\|cell type:macrophage\|cell type id:CL:0000235	GSM5814813	GSM5814813: Mpeg Ctrl rep2; Danio rerio; RNA Seq	GSM5814813 r1	GSM5814813	1	Larvae were stored at 80°C in minimal residual media. QIAshredder Quiagen was used to homogenize the larvae prior to immunoprecipitation. mRNA was isolated from immunoprecipitated polysomes from 50 pooled oncogene expressing fish or controls using TRIzol reagent Invitrogen. RNA quality and concentration was assessed on Agilent RNA PicoChip and samples with a concentration < 200 pg/µl were concentrated in a SpeedVac. As RNA concentrations were low library prep was done with the NuGEN Ovation Single Cell RNA Seq System with 20 cycles of amplification. Libraries were then checked by QuBit and an AATI Fragment Analyzer for concentration and fragment size. Adaptors with barcodes were used and samples were sequenced on an Illumina HiSeq with an average of 8 samples per lane following manufacturer's protocols.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP354901	C8_GTGCTT_L007_R1_001.fastq.gz	fastq	3633285625.0	35973125.0	GSM5814813 r1	0:101 1:0	A:857463844;C:881761168;G:1168499917;T:725509500;N:51196	101	857463844	881761168	1168499917	725509500	51196	SRX13773739	SRS11653740	SRA1356563	University of Wisconsin-Madison	University of Wisconsin-Madison	1	0.81381	0.188	0.91827	0.76814	101	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc_generic	single_cell_generic	generic-scrnaseq-only	United States	2022-01-13	Larval	Larval	Blood	Hematopoietic System
68093	68093	SRR17604944	SRX13773738	SRS11653739	SRP354901	PRJNA796794	Cell type specific transcriptome profiling reveals a role for thioredoxin in neutrophils and tumor initiation	GSE193591	Transcriptome Analysis	We report the application of Translating Ribosomal Affinity Purification TRAP seq for identifying cell type specific gene expression in the zebrafish larvae. Using cell specific promoters to drive an EGFP tagged ribosomal subunit we were able to identify translating mRNA transcripts in keratinocytes krt4 neutrophils lyz and macrophages mpeg during early cancer transformation. In our zebrafish model of HRasG12V transformed keratinocytes we identified 56 differentially expressed genes in keratinocytes 53 genes in neutrophils and no differentially expressed genes found in macrophages compared to control. These data indicate activation of gene expression pathways in distinct cell types following early keratinocyte transformation and validate the use of TRAPseq in the zebrafish model system. Overall design: Comparison of TRAP seq gene expression data in a HRasG12V transformed keratinocyte Zebrafish model in 3 different cells types	pubmed:35250998	Lyz Ctrl rep2	GSM5814812	tissue:neutrophil\|age:3dpf\|batch:2\|genotype:wild type\|cell type:neutrophil\|cell type id:CL:0000775	Lyz Ctrl rep2	Reads were aligned to the transcriptome using Bowtie v1.1.1 Gene abundances were estimated using RSEM v1.2.20 Genome build: GRCz10 Ensembl 83 annotation Supplementary files format and content: The processed data file for each sample is the gene level abundance output of RSEM and is a tab delimited text file	neutrophil	Zebrafish larvae were microinjected into one cell stage embryos and screened 3 dpf for transgene expression. Microinjections for TRAP RNA sequencing included either control pTol2 krt4 RFP HRas or oncogenic pTol2 krt4 RFP HRasG12V constructs injected with pTol2 krt4 GFP L10a in wildtype larvae or into TgLyzC:EGFP L10a or Tgmpeg1:EGFP L10a larvae for keratinocyte neutrophil or macrophage specific expression profiling respectively.	Larvae were stored at 80°C in minimal residual media. QIAshredder Quiagen was used to homogenize the larvae prior to immunoprecipitation. mRNA was isolated from immunoprecipitated polysomes from 50 pooled oncogene expressing fish or controls using TRIzol reagent Invitrogen. RNA quality and concentration was assessed on Agilent RNA PicoChip and samples with a concentration < 200 pg/µl were concentrated in a SpeedVac. As RNA concentrations were low library prep was done with the NuGEN Ovation Single Cell RNA Seq System with 20 cycles of amplification. Libraries were then checked by QuBit and an AATI Fragment Analyzer for concentration and fragment size. Adaptors with barcodes were used and samples were sequenced on an Illumina HiSeq with an average of 8 samples per lane following manufacturer’s protocols.	age:3dpf\|batch:2\|genotype:wild type\|cell type:neutrophil\|cell type id:CL:0000775	GSM5814812	GSM5814812: Lyz Ctrl rep2; Danio rerio; RNA Seq	GSM5814812 r1	GSM5814812	1	Larvae were stored at 80°C in minimal residual media. QIAshredder Quiagen was used to homogenize the larvae prior to immunoprecipitation. mRNA was isolated from immunoprecipitated polysomes from 50 pooled oncogene expressing fish or controls using TRIzol reagent Invitrogen. RNA quality and concentration was assessed on Agilent RNA PicoChip and samples with a concentration < 200 pg/µl were concentrated in a SpeedVac. As RNA concentrations were low library prep was done with the NuGEN Ovation Single Cell RNA Seq System with 20 cycles of amplification. Libraries were then checked by QuBit and an AATI Fragment Analyzer for concentration and fragment size. Adaptors with barcodes were used and samples were sequenced on an Illumina HiSeq with an average of 8 samples per lane following manufacturer's protocols.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP354901	C7_ACCTCA_L007_R1_001.fastq.gz	fastq	6653789605.0	65879105.0	GSM5814812 r1	0:101 1:0	A:1612535065;C:1544008675;G:1997585571;T:1499564492;N:95802	101	1612535065	1544008675	1997585571	1499564492	95802	SRX13773738	SRS11653739	SRA1356563	University of Wisconsin-Madison	University of Wisconsin-Madison	1	0.47383	0.11874	0.94612	0.76142	101	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc_generic	single_cell_generic	generic-scrnaseq-only	United States	2022-01-13	Larval	Larval	Blood	Hematopoietic System
68095	68095	SRR17604946	SRX13773736	SRS11653737	SRP354901	PRJNA796794	Cell type specific transcriptome profiling reveals a role for thioredoxin in neutrophils and tumor initiation	GSE193591	Transcriptome Analysis	We report the application of Translating Ribosomal Affinity Purification TRAP seq for identifying cell type specific gene expression in the zebrafish larvae. Using cell specific promoters to drive an EGFP tagged ribosomal subunit we were able to identify translating mRNA transcripts in keratinocytes krt4 neutrophils lyz and macrophages mpeg during early cancer transformation. In our zebrafish model of HRasG12V transformed keratinocytes we identified 56 differentially expressed genes in keratinocytes 53 genes in neutrophils and no differentially expressed genes found in macrophages compared to control. These data indicate activation of gene expression pathways in distinct cell types following early keratinocyte transformation and validate the use of TRAPseq in the zebrafish model system. Overall design: Comparison of TRAP seq gene expression data in a HRasG12V transformed keratinocyte Zebrafish model in 3 different cells types	pubmed:35250998	Mpeg V12 rep2	GSM5814810	tissue:macrophage\|age:3dpf\|batch:2\|genotype:mutant HRas G12V\|cell type:macrophage\|cell type id:CL:0000235	Mpeg V12 rep2	Reads were aligned to the transcriptome using Bowtie v1.1.1 Gene abundances were estimated using RSEM v1.2.20 Genome build: GRCz10 Ensembl 83 annotation Supplementary files format and content: The processed data file for each sample is the gene level abundance output of RSEM and is a tab delimited text file	macrophage	Zebrafish larvae were microinjected into one cell stage embryos and screened 3 dpf for transgene expression. Microinjections for TRAP RNA sequencing included either control pTol2 krt4 RFP HRas or oncogenic pTol2 krt4 RFP HRasG12V constructs injected with pTol2 krt4 GFP L10a in wildtype larvae or into TgLyzC:EGFP L10a or Tgmpeg1:EGFP L10a larvae for keratinocyte neutrophil or macrophage specific expression profiling respectively.	Larvae were stored at 80°C in minimal residual media. QIAshredder Quiagen was used to homogenize the larvae prior to immunoprecipitation. mRNA was isolated from immunoprecipitated polysomes from 50 pooled oncogene expressing fish or controls using TRIzol reagent Invitrogen. RNA quality and concentration was assessed on Agilent RNA PicoChip and samples with a concentration < 200 pg/µl were concentrated in a SpeedVac. As RNA concentrations were low library prep was done with the NuGEN Ovation Single Cell RNA Seq System with 20 cycles of amplification. Libraries were then checked by QuBit and an AATI Fragment Analyzer for concentration and fragment size. Adaptors with barcodes were used and samples were sequenced on an Illumina HiSeq with an average of 8 samples per lane following manufacturer’s protocols.	age:3dpf\|batch:2\|genotype:mutant HRas G12V\|cell type:macrophage\|cell type id:CL:0000235	GSM5814810	GSM5814810: Mpeg V12 rep2; Danio rerio; RNA Seq	GSM5814810 r1	GSM5814810	1	Larvae were stored at 80°C in minimal residual media. QIAshredder Quiagen was used to homogenize the larvae prior to immunoprecipitation. mRNA was isolated from immunoprecipitated polysomes from 50 pooled oncogene expressing fish or controls using TRIzol reagent Invitrogen. RNA quality and concentration was assessed on Agilent RNA PicoChip and samples with a concentration < 200 pg/µl were concentrated in a SpeedVac. As RNA concentrations were low library prep was done with the NuGEN Ovation Single Cell RNA Seq System with 20 cycles of amplification. Libraries were then checked by QuBit and an AATI Fragment Analyzer for concentration and fragment size. Adaptors with barcodes were used and samples were sequenced on an Illumina HiSeq with an average of 8 samples per lane following manufacturer's protocols.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP354901	C11_AAGAGG_L007_R1_001.fastq.gz	fastq	2065771281.0	20453181.0	GSM5814810 r1	0:101 1:0	A:507674562;C:495211667;G:618229279;T:444625380;N:30393	101	507674562	495211667	618229279	444625380	30393	SRX13773736	SRS11653737	SRA1356563	University of Wisconsin-Madison	University of Wisconsin-Madison	1	0.9099	0.2577	0.83524	0.69559	101	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc_generic	single_cell_generic	generic-scrnaseq-only	United States	2022-01-13	Larval	Larval	Blood	Hematopoietic System
68096	68096	SRR17604947	SRX13773735	SRS11653736	SRP354901	PRJNA796794	Cell type specific transcriptome profiling reveals a role for thioredoxin in neutrophils and tumor initiation	GSE193591	Transcriptome Analysis	We report the application of Translating Ribosomal Affinity Purification TRAP seq for identifying cell type specific gene expression in the zebrafish larvae. Using cell specific promoters to drive an EGFP tagged ribosomal subunit we were able to identify translating mRNA transcripts in keratinocytes krt4 neutrophils lyz and macrophages mpeg during early cancer transformation. In our zebrafish model of HRasG12V transformed keratinocytes we identified 56 differentially expressed genes in keratinocytes 53 genes in neutrophils and no differentially expressed genes found in macrophages compared to control. These data indicate activation of gene expression pathways in distinct cell types following early keratinocyte transformation and validate the use of TRAPseq in the zebrafish model system. Overall design: Comparison of TRAP seq gene expression data in a HRasG12V transformed keratinocyte Zebrafish model in 3 different cells types	pubmed:35250998	Lyz V12 rep2	GSM5814809	tissue:neutrophil\|age:3dpf\|batch:2\|genotype:mutant HRas G12V\|cell type:neutrophil\|cell type id:CL:0000775	Lyz V12 rep2	Reads were aligned to the transcriptome using Bowtie v1.1.1 Gene abundances were estimated using RSEM v1.2.20 Genome build: GRCz10 Ensembl 83 annotation Supplementary files format and content: The processed data file for each sample is the gene level abundance output of RSEM and is a tab delimited text file	neutrophil	Zebrafish larvae were microinjected into one cell stage embryos and screened 3 dpf for transgene expression. Microinjections for TRAP RNA sequencing included either control pTol2 krt4 RFP HRas or oncogenic pTol2 krt4 RFP HRasG12V constructs injected with pTol2 krt4 GFP L10a in wildtype larvae or into TgLyzC:EGFP L10a or Tgmpeg1:EGFP L10a larvae for keratinocyte neutrophil or macrophage specific expression profiling respectively.	Larvae were stored at 80°C in minimal residual media. QIAshredder Quiagen was used to homogenize the larvae prior to immunoprecipitation. mRNA was isolated from immunoprecipitated polysomes from 50 pooled oncogene expressing fish or controls using TRIzol reagent Invitrogen. RNA quality and concentration was assessed on Agilent RNA PicoChip and samples with a concentration < 200 pg/µl were concentrated in a SpeedVac. As RNA concentrations were low library prep was done with the NuGEN Ovation Single Cell RNA Seq System with 20 cycles of amplification. Libraries were then checked by QuBit and an AATI Fragment Analyzer for concentration and fragment size. Adaptors with barcodes were used and samples were sequenced on an Illumina HiSeq with an average of 8 samples per lane following manufacturer’s protocols.	age:3dpf\|batch:2\|genotype:mutant HRas G12V\|cell type:neutrophil\|cell type id:CL:0000775	GSM5814809	GSM5814809: Lyz V12 rep2; Danio rerio; RNA Seq	GSM5814809 r1	GSM5814809	1	Larvae were stored at 80°C in minimal residual media. QIAshredder Quiagen was used to homogenize the larvae prior to immunoprecipitation. mRNA was isolated from immunoprecipitated polysomes from 50 pooled oncogene expressing fish or controls using TRIzol reagent Invitrogen. RNA quality and concentration was assessed on Agilent RNA PicoChip and samples with a concentration < 200 pg/µl were concentrated in a SpeedVac. As RNA concentrations were low library prep was done with the NuGEN Ovation Single Cell RNA Seq System with 20 cycles of amplification. Libraries were then checked by QuBit and an AATI Fragment Analyzer for concentration and fragment size. Adaptors with barcodes were used and samples were sequenced on an Illumina HiSeq with an average of 8 samples per lane following manufacturer's protocols.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP354901	C10_GTCGTA_L007_R1_001.fastq.gz	fastq	2765825107.0	27384407.0	GSM5814809 r1	0:101 1:0	A:626093577;C:667011715;G:906574905;T:566105177;N:39733	101	626093577	667011715	906574905	566105177	39733	SRX13773735	SRS11653736	SRA1356563	University of Wisconsin-Madison	University of Wisconsin-Madison	1	0.90358	0.23005	0.87448	0.74321	101	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc_generic	single_cell_generic	generic-scrnaseq-only	United States	2022-01-13	Larval	Larval	Blood	Hematopoietic System
68099	68099	SRR17604950	SRX13773733	SRS11653734	SRP354901	PRJNA796794	Cell type specific transcriptome profiling reveals a role for thioredoxin in neutrophils and tumor initiation	GSE193591	Transcriptome Analysis	We report the application of Translating Ribosomal Affinity Purification TRAP seq for identifying cell type specific gene expression in the zebrafish larvae. Using cell specific promoters to drive an EGFP tagged ribosomal subunit we were able to identify translating mRNA transcripts in keratinocytes krt4 neutrophils lyz and macrophages mpeg during early cancer transformation. In our zebrafish model of HRasG12V transformed keratinocytes we identified 56 differentially expressed genes in keratinocytes 53 genes in neutrophils and no differentially expressed genes found in macrophages compared to control. These data indicate activation of gene expression pathways in distinct cell types following early keratinocyte transformation and validate the use of TRAPseq in the zebrafish model system. Overall design: Comparison of TRAP seq gene expression data in a HRasG12V transformed keratinocyte Zebrafish model in 3 different cells types	pubmed:35250998	Mpeg Ctrl rep1	GSM5814807	tissue:macrophage\|age:3dpf\|batch:1\|genotype:wild type\|cell type:macrophage\|cell type id:CL:0000235	Mpeg Ctrl rep1	Reads were aligned to the transcriptome using Bowtie v1.1.1 Gene abundances were estimated using RSEM v1.2.20 Genome build: GRCz10 Ensembl 83 annotation Supplementary files format and content: The processed data file for each sample is the gene level abundance output of RSEM and is a tab delimited text file	macrophage	Zebrafish larvae were microinjected into one cell stage embryos and screened 3 dpf for transgene expression. Microinjections for TRAP RNA sequencing included either control pTol2 krt4 RFP HRas or oncogenic pTol2 krt4 RFP HRasG12V constructs injected with pTol2 krt4 GFP L10a in wildtype larvae or into TgLyzC:EGFP L10a or Tgmpeg1:EGFP L10a larvae for keratinocyte neutrophil or macrophage specific expression profiling respectively.	Larvae were stored at 80°C in minimal residual media. QIAshredder Quiagen was used to homogenize the larvae prior to immunoprecipitation. mRNA was isolated from immunoprecipitated polysomes from 50 pooled oncogene expressing fish or controls using TRIzol reagent Invitrogen. RNA quality and concentration was assessed on Agilent RNA PicoChip and samples with a concentration < 200 pg/µl were concentrated in a SpeedVac. As RNA concentrations were low library prep was done with the NuGEN Ovation Single Cell RNA Seq System with 20 cycles of amplification. Libraries were then checked by QuBit and an AATI Fragment Analyzer for concentration and fragment size. Adaptors with barcodes were used and samples were sequenced on an Illumina HiSeq with an average of 8 samples per lane following manufacturer’s protocols.	age:3dpf\|batch:1\|genotype:wild type\|cell type:macrophage\|cell type id:CL:0000235	GSM5814807	GSM5814807: Mpeg Ctrl rep1; Danio rerio; RNA Seq	GSM5814807 r1	GSM5814807	1	Larvae were stored at 80°C in minimal residual media. QIAshredder Quiagen was used to homogenize the larvae prior to immunoprecipitation. mRNA was isolated from immunoprecipitated polysomes from 50 pooled oncogene expressing fish or controls using TRIzol reagent Invitrogen. RNA quality and concentration was assessed on Agilent RNA PicoChip and samples with a concentration < 200 pg/µl were concentrated in a SpeedVac. As RNA concentrations were low library prep was done with the NuGEN Ovation Single Cell RNA Seq System with 20 cycles of amplification. Libraries were then checked by QuBit and an AATI Fragment Analyzer for concentration and fragment size. Adaptors with barcodes were used and samples were sequenced on an Illumina HiSeq with an average of 8 samples per lane following manufacturer's protocols.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP354901	B8_GCACTA_L003_R1_001.fastq.gz	fastq	1089956852.0	10791652.0	GSM5814807 r1	0:101 1:0	A:233616569;C:269164072;G:375032160;T:212097812;N:46239	101	233616569	269164072	375032160	212097812	46239	SRX13773733	SRS11653734	SRA1356563	University of Wisconsin-Madison	University of Wisconsin-Madison	1	0.92414	0.20628	0.92267	0.64101	101	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc_generic	single_cell_generic	generic-scrnaseq-only	United States	2022-01-13	Larval	Larval	Blood	Hematopoietic System
68100	68100	SRR17604951	SRX13773733	SRS11653734	SRP354901	PRJNA796794	Cell type specific transcriptome profiling reveals a role for thioredoxin in neutrophils and tumor initiation	GSE193591	Transcriptome Analysis	We report the application of Translating Ribosomal Affinity Purification TRAP seq for identifying cell type specific gene expression in the zebrafish larvae. Using cell specific promoters to drive an EGFP tagged ribosomal subunit we were able to identify translating mRNA transcripts in keratinocytes krt4 neutrophils lyz and macrophages mpeg during early cancer transformation. In our zebrafish model of HRasG12V transformed keratinocytes we identified 56 differentially expressed genes in keratinocytes 53 genes in neutrophils and no differentially expressed genes found in macrophages compared to control. These data indicate activation of gene expression pathways in distinct cell types following early keratinocyte transformation and validate the use of TRAPseq in the zebrafish model system. Overall design: Comparison of TRAP seq gene expression data in a HRasG12V transformed keratinocyte Zebrafish model in 3 different cells types	pubmed:35250998	Mpeg Ctrl rep1	GSM5814807	tissue:macrophage\|age:3dpf\|batch:1\|genotype:wild type\|cell type:macrophage\|cell type id:CL:0000235	Mpeg Ctrl rep1	Reads were aligned to the transcriptome using Bowtie v1.1.1 Gene abundances were estimated using RSEM v1.2.20 Genome build: GRCz10 Ensembl 83 annotation Supplementary files format and content: The processed data file for each sample is the gene level abundance output of RSEM and is a tab delimited text file	macrophage	Zebrafish larvae were microinjected into one cell stage embryos and screened 3 dpf for transgene expression. Microinjections for TRAP RNA sequencing included either control pTol2 krt4 RFP HRas or oncogenic pTol2 krt4 RFP HRasG12V constructs injected with pTol2 krt4 GFP L10a in wildtype larvae or into TgLyzC:EGFP L10a or Tgmpeg1:EGFP L10a larvae for keratinocyte neutrophil or macrophage specific expression profiling respectively.	Larvae were stored at 80°C in minimal residual media. QIAshredder Quiagen was used to homogenize the larvae prior to immunoprecipitation. mRNA was isolated from immunoprecipitated polysomes from 50 pooled oncogene expressing fish or controls using TRIzol reagent Invitrogen. RNA quality and concentration was assessed on Agilent RNA PicoChip and samples with a concentration < 200 pg/µl were concentrated in a SpeedVac. As RNA concentrations were low library prep was done with the NuGEN Ovation Single Cell RNA Seq System with 20 cycles of amplification. Libraries were then checked by QuBit and an AATI Fragment Analyzer for concentration and fragment size. Adaptors with barcodes were used and samples were sequenced on an Illumina HiSeq with an average of 8 samples per lane following manufacturer’s protocols.	age:3dpf\|batch:1\|genotype:wild type\|cell type:macrophage\|cell type id:CL:0000235	GSM5814807	GSM5814807: Mpeg Ctrl rep1; Danio rerio; RNA Seq	GSM5814807 r1	GSM5814807	1	Larvae were stored at 80°C in minimal residual media. QIAshredder Quiagen was used to homogenize the larvae prior to immunoprecipitation. mRNA was isolated from immunoprecipitated polysomes from 50 pooled oncogene expressing fish or controls using TRIzol reagent Invitrogen. RNA quality and concentration was assessed on Agilent RNA PicoChip and samples with a concentration < 200 pg/µl were concentrated in a SpeedVac. As RNA concentrations were low library prep was done with the NuGEN Ovation Single Cell RNA Seq System with 20 cycles of amplification. Libraries were then checked by QuBit and an AATI Fragment Analyzer for concentration and fragment size. Adaptors with barcodes were used and samples were sequenced on an Illumina HiSeq with an average of 8 samples per lane following manufacturer's protocols.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP354901	B8_GCACTA_L004_R1_001.fastq.gz	fastq	1099178758.0	10882958.0	GSM5814807 r2	0:101 1:0	A:235518746;C:271396002;G:378096056;T:214063897;N:104057	101	235518746	271396002	378096056	214063897	104057	SRX13773733	SRS11653734	SRA1356563	University of Wisconsin-Madison	University of Wisconsin-Madison	1	0.92394	0.20528	0.92241	0.69966	101	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc_generic	single_cell_generic	generic-scrnaseq-only	United States	2022-01-13	Larval	Larval	Blood	Hematopoietic System
68101	68101	SRR17604952	SRX13773732	SRS11653733	SRP354901	PRJNA796794	Cell type specific transcriptome profiling reveals a role for thioredoxin in neutrophils and tumor initiation	GSE193591	Transcriptome Analysis	We report the application of Translating Ribosomal Affinity Purification TRAP seq for identifying cell type specific gene expression in the zebrafish larvae. Using cell specific promoters to drive an EGFP tagged ribosomal subunit we were able to identify translating mRNA transcripts in keratinocytes krt4 neutrophils lyz and macrophages mpeg during early cancer transformation. In our zebrafish model of HRasG12V transformed keratinocytes we identified 56 differentially expressed genes in keratinocytes 53 genes in neutrophils and no differentially expressed genes found in macrophages compared to control. These data indicate activation of gene expression pathways in distinct cell types following early keratinocyte transformation and validate the use of TRAPseq in the zebrafish model system. Overall design: Comparison of TRAP seq gene expression data in a HRasG12V transformed keratinocyte Zebrafish model in 3 different cells types	pubmed:35250998	Lyz Ctrl rep1	GSM5814806	tissue:neutrophil\|age:3dpf\|batch:1\|genotype:wild type\|cell type:neutrophil\|cell type id:CL:0000775	Lyz Ctrl rep1	Reads were aligned to the transcriptome using Bowtie v1.1.1 Gene abundances were estimated using RSEM v1.2.20 Genome build: GRCz10 Ensembl 83 annotation Supplementary files format and content: The processed data file for each sample is the gene level abundance output of RSEM and is a tab delimited text file	neutrophil	Zebrafish larvae were microinjected into one cell stage embryos and screened 3 dpf for transgene expression. Microinjections for TRAP RNA sequencing included either control pTol2 krt4 RFP HRas or oncogenic pTol2 krt4 RFP HRasG12V constructs injected with pTol2 krt4 GFP L10a in wildtype larvae or into TgLyzC:EGFP L10a or Tgmpeg1:EGFP L10a larvae for keratinocyte neutrophil or macrophage specific expression profiling respectively.	Larvae were stored at 80°C in minimal residual media. QIAshredder Quiagen was used to homogenize the larvae prior to immunoprecipitation. mRNA was isolated from immunoprecipitated polysomes from 50 pooled oncogene expressing fish or controls using TRIzol reagent Invitrogen. RNA quality and concentration was assessed on Agilent RNA PicoChip and samples with a concentration < 200 pg/µl were concentrated in a SpeedVac. As RNA concentrations were low library prep was done with the NuGEN Ovation Single Cell RNA Seq System with 20 cycles of amplification. Libraries were then checked by QuBit and an AATI Fragment Analyzer for concentration and fragment size. Adaptors with barcodes were used and samples were sequenced on an Illumina HiSeq with an average of 8 samples per lane following manufacturer’s protocols.	age:3dpf\|batch:1\|genotype:wild type\|cell type:neutrophil\|cell type id:CL:0000775	GSM5814806	GSM5814806: Lyz Ctrl rep1; Danio rerio; RNA Seq	GSM5814806 r1	GSM5814806	1	Larvae were stored at 80°C in minimal residual media. QIAshredder Quiagen was used to homogenize the larvae prior to immunoprecipitation. mRNA was isolated from immunoprecipitated polysomes from 50 pooled oncogene expressing fish or controls using TRIzol reagent Invitrogen. RNA quality and concentration was assessed on Agilent RNA PicoChip and samples with a concentration < 200 pg/µl were concentrated in a SpeedVac. As RNA concentrations were low library prep was done with the NuGEN Ovation Single Cell RNA Seq System with 20 cycles of amplification. Libraries were then checked by QuBit and an AATI Fragment Analyzer for concentration and fragment size. Adaptors with barcodes were used and samples were sequenced on an Illumina HiSeq with an average of 8 samples per lane following manufacturer's protocols.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP354901	B7_AGTGAG_L003_R1_001.fastq.gz	fastq	1083973309.0	10732409.0	GSM5814806 r1	0:101 1:0	A:237166302;C:265178193;G:365235419;T:216346907;N:46488	101	237166302	265178193	365235419	216346907	46488	SRX13773732	SRS11653733	SRA1356563	University of Wisconsin-Madison	University of Wisconsin-Madison	1	0.92626	0.22913	0.90059	0.76051	101	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc_generic	single_cell_generic	generic-scrnaseq-only	United States	2022-01-13	Larval	Larval	Blood	Hematopoietic System
68102	68102	SRR17604953	SRX13773732	SRS11653733	SRP354901	PRJNA796794	Cell type specific transcriptome profiling reveals a role for thioredoxin in neutrophils and tumor initiation	GSE193591	Transcriptome Analysis	We report the application of Translating Ribosomal Affinity Purification TRAP seq for identifying cell type specific gene expression in the zebrafish larvae. Using cell specific promoters to drive an EGFP tagged ribosomal subunit we were able to identify translating mRNA transcripts in keratinocytes krt4 neutrophils lyz and macrophages mpeg during early cancer transformation. In our zebrafish model of HRasG12V transformed keratinocytes we identified 56 differentially expressed genes in keratinocytes 53 genes in neutrophils and no differentially expressed genes found in macrophages compared to control. These data indicate activation of gene expression pathways in distinct cell types following early keratinocyte transformation and validate the use of TRAPseq in the zebrafish model system. Overall design: Comparison of TRAP seq gene expression data in a HRasG12V transformed keratinocyte Zebrafish model in 3 different cells types	pubmed:35250998	Lyz Ctrl rep1	GSM5814806	tissue:neutrophil\|age:3dpf\|batch:1\|genotype:wild type\|cell type:neutrophil\|cell type id:CL:0000775	Lyz Ctrl rep1	Reads were aligned to the transcriptome using Bowtie v1.1.1 Gene abundances were estimated using RSEM v1.2.20 Genome build: GRCz10 Ensembl 83 annotation Supplementary files format and content: The processed data file for each sample is the gene level abundance output of RSEM and is a tab delimited text file	neutrophil	Zebrafish larvae were microinjected into one cell stage embryos and screened 3 dpf for transgene expression. Microinjections for TRAP RNA sequencing included either control pTol2 krt4 RFP HRas or oncogenic pTol2 krt4 RFP HRasG12V constructs injected with pTol2 krt4 GFP L10a in wildtype larvae or into TgLyzC:EGFP L10a or Tgmpeg1:EGFP L10a larvae for keratinocyte neutrophil or macrophage specific expression profiling respectively.	Larvae were stored at 80°C in minimal residual media. QIAshredder Quiagen was used to homogenize the larvae prior to immunoprecipitation. mRNA was isolated from immunoprecipitated polysomes from 50 pooled oncogene expressing fish or controls using TRIzol reagent Invitrogen. RNA quality and concentration was assessed on Agilent RNA PicoChip and samples with a concentration < 200 pg/µl were concentrated in a SpeedVac. As RNA concentrations were low library prep was done with the NuGEN Ovation Single Cell RNA Seq System with 20 cycles of amplification. Libraries were then checked by QuBit and an AATI Fragment Analyzer for concentration and fragment size. Adaptors with barcodes were used and samples were sequenced on an Illumina HiSeq with an average of 8 samples per lane following manufacturer’s protocols.	age:3dpf\|batch:1\|genotype:wild type\|cell type:neutrophil\|cell type id:CL:0000775	GSM5814806	GSM5814806: Lyz Ctrl rep1; Danio rerio; RNA Seq	GSM5814806 r1	GSM5814806	1	Larvae were stored at 80°C in minimal residual media. QIAshredder Quiagen was used to homogenize the larvae prior to immunoprecipitation. mRNA was isolated from immunoprecipitated polysomes from 50 pooled oncogene expressing fish or controls using TRIzol reagent Invitrogen. RNA quality and concentration was assessed on Agilent RNA PicoChip and samples with a concentration < 200 pg/µl were concentrated in a SpeedVac. As RNA concentrations were low library prep was done with the NuGEN Ovation Single Cell RNA Seq System with 20 cycles of amplification. Libraries were then checked by QuBit and an AATI Fragment Analyzer for concentration and fragment size. Adaptors with barcodes were used and samples were sequenced on an Illumina HiSeq with an average of 8 samples per lane following manufacturer's protocols.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP354901	B7_AGTGAG_L004_R1_001.fastq.gz	fastq	1086542345.0	10757845.0	GSM5814806 r2	0:101 1:0	A:237663470;C:265705217;G:365976757;T:217092022;N:104879	101	237663470	265705217	365976757	217092022	104879	SRX13773732	SRS11653733	SRA1356563	University of Wisconsin-Madison	University of Wisconsin-Madison	1	0.92592	0.23202	0.9022	0.76245	101	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc_generic	single_cell_generic	generic-scrnaseq-only	United States	2022-01-13	Larval	Larval	Blood	Hematopoietic System
68105	68105	SRR17604956	SRX13773730	SRS11653731	SRP354901	PRJNA796794	Cell type specific transcriptome profiling reveals a role for thioredoxin in neutrophils and tumor initiation	GSE193591	Transcriptome Analysis	We report the application of Translating Ribosomal Affinity Purification TRAP seq for identifying cell type specific gene expression in the zebrafish larvae. Using cell specific promoters to drive an EGFP tagged ribosomal subunit we were able to identify translating mRNA transcripts in keratinocytes krt4 neutrophils lyz and macrophages mpeg during early cancer transformation. In our zebrafish model of HRasG12V transformed keratinocytes we identified 56 differentially expressed genes in keratinocytes 53 genes in neutrophils and no differentially expressed genes found in macrophages compared to control. These data indicate activation of gene expression pathways in distinct cell types following early keratinocyte transformation and validate the use of TRAPseq in the zebrafish model system. Overall design: Comparison of TRAP seq gene expression data in a HRasG12V transformed keratinocyte Zebrafish model in 3 different cells types	pubmed:35250998	Mpeg V12 rep1	GSM5814804	tissue:macrophage\|age:3dpf\|batch:1\|genotype:mutant HRas G12V\|cell type:macrophage\|cell type id:CL:0000235	Mpeg V12 rep1	Reads were aligned to the transcriptome using Bowtie v1.1.1 Gene abundances were estimated using RSEM v1.2.20 Genome build: GRCz10 Ensembl 83 annotation Supplementary files format and content: The processed data file for each sample is the gene level abundance output of RSEM and is a tab delimited text file	macrophage	Zebrafish larvae were microinjected into one cell stage embryos and screened 3 dpf for transgene expression. Microinjections for TRAP RNA sequencing included either control pTol2 krt4 RFP HRas or oncogenic pTol2 krt4 RFP HRasG12V constructs injected with pTol2 krt4 GFP L10a in wildtype larvae or into TgLyzC:EGFP L10a or Tgmpeg1:EGFP L10a larvae for keratinocyte neutrophil or macrophage specific expression profiling respectively.	Larvae were stored at 80°C in minimal residual media. QIAshredder Quiagen was used to homogenize the larvae prior to immunoprecipitation. mRNA was isolated from immunoprecipitated polysomes from 50 pooled oncogene expressing fish or controls using TRIzol reagent Invitrogen. RNA quality and concentration was assessed on Agilent RNA PicoChip and samples with a concentration < 200 pg/µl were concentrated in a SpeedVac. As RNA concentrations were low library prep was done with the NuGEN Ovation Single Cell RNA Seq System with 20 cycles of amplification. Libraries were then checked by QuBit and an AATI Fragment Analyzer for concentration and fragment size. Adaptors with barcodes were used and samples were sequenced on an Illumina HiSeq with an average of 8 samples per lane following manufacturer’s protocols.	age:3dpf\|batch:1\|genotype:mutant HRas G12V\|cell type:macrophage\|cell type id:CL:0000235	GSM5814804	GSM5814804: Mpeg V12 rep1; Danio rerio; RNA Seq	GSM5814804 r1	GSM5814804	1	Larvae were stored at 80°C in minimal residual media. QIAshredder Quiagen was used to homogenize the larvae prior to immunoprecipitation. mRNA was isolated from immunoprecipitated polysomes from 50 pooled oncogene expressing fish or controls using TRIzol reagent Invitrogen. RNA quality and concentration was assessed on Agilent RNA PicoChip and samples with a concentration < 200 pg/µl were concentrated in a SpeedVac. As RNA concentrations were low library prep was done with the NuGEN Ovation Single Cell RNA Seq System with 20 cycles of amplification. Libraries were then checked by QuBit and an AATI Fragment Analyzer for concentration and fragment size. Adaptors with barcodes were used and samples were sequenced on an Illumina HiSeq with an average of 8 samples per lane following manufacturer's protocols.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP354901	B11_AAGCCT_L003_R1_001.fastq.gz	fastq	1142947411.0	11316311.0	GSM5814804 r1	0:101 1:0	A:252533017;C:279992483;G:380449659;T:229923397;N:48855	101	252533017	279992483	380449659	229923397	48855	SRX13773730	SRS11653731	SRA1356563	University of Wisconsin-Madison	University of Wisconsin-Madison	1	0.92125	0.22724	0.89869	0.75703	101	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc_generic	single_cell_generic	generic-scrnaseq-only	United States	2022-01-13	Larval	Larval	Blood	Hematopoietic System
68106	68106	SRR17604957	SRX13773730	SRS11653731	SRP354901	PRJNA796794	Cell type specific transcriptome profiling reveals a role for thioredoxin in neutrophils and tumor initiation	GSE193591	Transcriptome Analysis	We report the application of Translating Ribosomal Affinity Purification TRAP seq for identifying cell type specific gene expression in the zebrafish larvae. Using cell specific promoters to drive an EGFP tagged ribosomal subunit we were able to identify translating mRNA transcripts in keratinocytes krt4 neutrophils lyz and macrophages mpeg during early cancer transformation. In our zebrafish model of HRasG12V transformed keratinocytes we identified 56 differentially expressed genes in keratinocytes 53 genes in neutrophils and no differentially expressed genes found in macrophages compared to control. These data indicate activation of gene expression pathways in distinct cell types following early keratinocyte transformation and validate the use of TRAPseq in the zebrafish model system. Overall design: Comparison of TRAP seq gene expression data in a HRasG12V transformed keratinocyte Zebrafish model in 3 different cells types	pubmed:35250998	Mpeg V12 rep1	GSM5814804	tissue:macrophage\|age:3dpf\|batch:1\|genotype:mutant HRas G12V\|cell type:macrophage\|cell type id:CL:0000235	Mpeg V12 rep1	Reads were aligned to the transcriptome using Bowtie v1.1.1 Gene abundances were estimated using RSEM v1.2.20 Genome build: GRCz10 Ensembl 83 annotation Supplementary files format and content: The processed data file for each sample is the gene level abundance output of RSEM and is a tab delimited text file	macrophage	Zebrafish larvae were microinjected into one cell stage embryos and screened 3 dpf for transgene expression. Microinjections for TRAP RNA sequencing included either control pTol2 krt4 RFP HRas or oncogenic pTol2 krt4 RFP HRasG12V constructs injected with pTol2 krt4 GFP L10a in wildtype larvae or into TgLyzC:EGFP L10a or Tgmpeg1:EGFP L10a larvae for keratinocyte neutrophil or macrophage specific expression profiling respectively.	Larvae were stored at 80°C in minimal residual media. QIAshredder Quiagen was used to homogenize the larvae prior to immunoprecipitation. mRNA was isolated from immunoprecipitated polysomes from 50 pooled oncogene expressing fish or controls using TRIzol reagent Invitrogen. RNA quality and concentration was assessed on Agilent RNA PicoChip and samples with a concentration < 200 pg/µl were concentrated in a SpeedVac. As RNA concentrations were low library prep was done with the NuGEN Ovation Single Cell RNA Seq System with 20 cycles of amplification. Libraries were then checked by QuBit and an AATI Fragment Analyzer for concentration and fragment size. Adaptors with barcodes were used and samples were sequenced on an Illumina HiSeq with an average of 8 samples per lane following manufacturer’s protocols.	age:3dpf\|batch:1\|genotype:mutant HRas G12V\|cell type:macrophage\|cell type id:CL:0000235	GSM5814804	GSM5814804: Mpeg V12 rep1; Danio rerio; RNA Seq	GSM5814804 r1	GSM5814804	1	Larvae were stored at 80°C in minimal residual media. QIAshredder Quiagen was used to homogenize the larvae prior to immunoprecipitation. mRNA was isolated from immunoprecipitated polysomes from 50 pooled oncogene expressing fish or controls using TRIzol reagent Invitrogen. RNA quality and concentration was assessed on Agilent RNA PicoChip and samples with a concentration < 200 pg/µl were concentrated in a SpeedVac. As RNA concentrations were low library prep was done with the NuGEN Ovation Single Cell RNA Seq System with 20 cycles of amplification. Libraries were then checked by QuBit and an AATI Fragment Analyzer for concentration and fragment size. Adaptors with barcodes were used and samples were sequenced on an Illumina HiSeq with an average of 8 samples per lane following manufacturer's protocols.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP354901	B11_AAGCCT_L004_R1_001.fastq.gz	fastq	1152276276.0	11408676.0	GSM5814804 r2	0:101 1:0	A:254537018;C:282186822;G:383383776;T:232059187;N:109473	101	254537018	282186822	383383776	232059187	109473	SRX13773730	SRS11653731	SRA1356563	University of Wisconsin-Madison	University of Wisconsin-Madison	1	0.91995	0.22757	0.89846	0.71014	101	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc_generic	single_cell_generic	generic-scrnaseq-only	United States	2022-01-13	Larval	Larval	Blood	Hematopoietic System
68107	68107	SRR17604958	SRX13773729	SRS11653730	SRP354901	PRJNA796794	Cell type specific transcriptome profiling reveals a role for thioredoxin in neutrophils and tumor initiation	GSE193591	Transcriptome Analysis	We report the application of Translating Ribosomal Affinity Purification TRAP seq for identifying cell type specific gene expression in the zebrafish larvae. Using cell specific promoters to drive an EGFP tagged ribosomal subunit we were able to identify translating mRNA transcripts in keratinocytes krt4 neutrophils lyz and macrophages mpeg during early cancer transformation. In our zebrafish model of HRasG12V transformed keratinocytes we identified 56 differentially expressed genes in keratinocytes 53 genes in neutrophils and no differentially expressed genes found in macrophages compared to control. These data indicate activation of gene expression pathways in distinct cell types following early keratinocyte transformation and validate the use of TRAPseq in the zebrafish model system. Overall design: Comparison of TRAP seq gene expression data in a HRasG12V transformed keratinocyte Zebrafish model in 3 different cells types	pubmed:35250998	Lyz V12 rep1	GSM5814803	tissue:neutrophil\|age:3dpf\|batch:1\|genotype:mutant HRas G12V\|cell type:neutrophil\|cell type id:CL:0000775	Lyz V12 rep1	Reads were aligned to the transcriptome using Bowtie v1.1.1 Gene abundances were estimated using RSEM v1.2.20 Genome build: GRCz10 Ensembl 83 annotation Supplementary files format and content: The processed data file for each sample is the gene level abundance output of RSEM and is a tab delimited text file	neutrophil	Zebrafish larvae were microinjected into one cell stage embryos and screened 3 dpf for transgene expression. Microinjections for TRAP RNA sequencing included either control pTol2 krt4 RFP HRas or oncogenic pTol2 krt4 RFP HRasG12V constructs injected with pTol2 krt4 GFP L10a in wildtype larvae or into TgLyzC:EGFP L10a or Tgmpeg1:EGFP L10a larvae for keratinocyte neutrophil or macrophage specific expression profiling respectively.	Larvae were stored at 80°C in minimal residual media. QIAshredder Quiagen was used to homogenize the larvae prior to immunoprecipitation. mRNA was isolated from immunoprecipitated polysomes from 50 pooled oncogene expressing fish or controls using TRIzol reagent Invitrogen. RNA quality and concentration was assessed on Agilent RNA PicoChip and samples with a concentration < 200 pg/µl were concentrated in a SpeedVac. As RNA concentrations were low library prep was done with the NuGEN Ovation Single Cell RNA Seq System with 20 cycles of amplification. Libraries were then checked by QuBit and an AATI Fragment Analyzer for concentration and fragment size. Adaptors with barcodes were used and samples were sequenced on an Illumina HiSeq with an average of 8 samples per lane following manufacturer’s protocols.	age:3dpf\|batch:1\|genotype:mutant HRas G12V\|cell type:neutrophil\|cell type id:CL:0000775	GSM5814803	GSM5814803: Lyz V12 rep1; Danio rerio; RNA Seq	GSM5814803 r1	GSM5814803	1	Larvae were stored at 80°C in minimal residual media. QIAshredder Quiagen was used to homogenize the larvae prior to immunoprecipitation. mRNA was isolated from immunoprecipitated polysomes from 50 pooled oncogene expressing fish or controls using TRIzol reagent Invitrogen. RNA quality and concentration was assessed on Agilent RNA PicoChip and samples with a concentration < 200 pg/µl were concentrated in a SpeedVac. As RNA concentrations were low library prep was done with the NuGEN Ovation Single Cell RNA Seq System with 20 cycles of amplification. Libraries were then checked by QuBit and an AATI Fragment Analyzer for concentration and fragment size. Adaptors with barcodes were used and samples were sequenced on an Illumina HiSeq with an average of 8 samples per lane following manufacturer's protocols.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP354901	B10_GTGCTT_L003_R1_001.fastq.gz	fastq	1824098784.0	18060384.0	GSM5814803 r1	0:101 1:0	A:442201601;C:436189969;G:576670991;T:368963729;N:72494	101	442201601	436189969	576670991	368963729	72494	SRX13773729	SRS11653730	SRA1356563	University of Wisconsin-Madison	University of Wisconsin-Madison	1	0.68478	0.17153	0.93194	0.71383	101	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc_generic	single_cell_generic	generic-scrnaseq-only	United States	2022-01-13	Larval	Larval	Blood	Hematopoietic System
68108	68108	SRR17604959	SRX13773729	SRS11653730	SRP354901	PRJNA796794	Cell type specific transcriptome profiling reveals a role for thioredoxin in neutrophils and tumor initiation	GSE193591	Transcriptome Analysis	We report the application of Translating Ribosomal Affinity Purification TRAP seq for identifying cell type specific gene expression in the zebrafish larvae. Using cell specific promoters to drive an EGFP tagged ribosomal subunit we were able to identify translating mRNA transcripts in keratinocytes krt4 neutrophils lyz and macrophages mpeg during early cancer transformation. In our zebrafish model of HRasG12V transformed keratinocytes we identified 56 differentially expressed genes in keratinocytes 53 genes in neutrophils and no differentially expressed genes found in macrophages compared to control. These data indicate activation of gene expression pathways in distinct cell types following early keratinocyte transformation and validate the use of TRAPseq in the zebrafish model system. Overall design: Comparison of TRAP seq gene expression data in a HRasG12V transformed keratinocyte Zebrafish model in 3 different cells types	pubmed:35250998	Lyz V12 rep1	GSM5814803	tissue:neutrophil\|age:3dpf\|batch:1\|genotype:mutant HRas G12V\|cell type:neutrophil\|cell type id:CL:0000775	Lyz V12 rep1	Reads were aligned to the transcriptome using Bowtie v1.1.1 Gene abundances were estimated using RSEM v1.2.20 Genome build: GRCz10 Ensembl 83 annotation Supplementary files format and content: The processed data file for each sample is the gene level abundance output of RSEM and is a tab delimited text file	neutrophil	Zebrafish larvae were microinjected into one cell stage embryos and screened 3 dpf for transgene expression. Microinjections for TRAP RNA sequencing included either control pTol2 krt4 RFP HRas or oncogenic pTol2 krt4 RFP HRasG12V constructs injected with pTol2 krt4 GFP L10a in wildtype larvae or into TgLyzC:EGFP L10a or Tgmpeg1:EGFP L10a larvae for keratinocyte neutrophil or macrophage specific expression profiling respectively.	Larvae were stored at 80°C in minimal residual media. QIAshredder Quiagen was used to homogenize the larvae prior to immunoprecipitation. mRNA was isolated from immunoprecipitated polysomes from 50 pooled oncogene expressing fish or controls using TRIzol reagent Invitrogen. RNA quality and concentration was assessed on Agilent RNA PicoChip and samples with a concentration < 200 pg/µl were concentrated in a SpeedVac. As RNA concentrations were low library prep was done with the NuGEN Ovation Single Cell RNA Seq System with 20 cycles of amplification. Libraries were then checked by QuBit and an AATI Fragment Analyzer for concentration and fragment size. Adaptors with barcodes were used and samples were sequenced on an Illumina HiSeq with an average of 8 samples per lane following manufacturer’s protocols.	age:3dpf\|batch:1\|genotype:mutant HRas G12V\|cell type:neutrophil\|cell type id:CL:0000775	GSM5814803	GSM5814803: Lyz V12 rep1; Danio rerio; RNA Seq	GSM5814803 r1	GSM5814803	1	Larvae were stored at 80°C in minimal residual media. QIAshredder Quiagen was used to homogenize the larvae prior to immunoprecipitation. mRNA was isolated from immunoprecipitated polysomes from 50 pooled oncogene expressing fish or controls using TRIzol reagent Invitrogen. RNA quality and concentration was assessed on Agilent RNA PicoChip and samples with a concentration < 200 pg/µl were concentrated in a SpeedVac. As RNA concentrations were low library prep was done with the NuGEN Ovation Single Cell RNA Seq System with 20 cycles of amplification. Libraries were then checked by QuBit and an AATI Fragment Analyzer for concentration and fragment size. Adaptors with barcodes were used and samples were sequenced on an Illumina HiSeq with an average of 8 samples per lane following manufacturer's protocols.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP354901	B10_GTGCTT_L004_R1_001.fastq.gz	fastq	1859395456.0	18409856.0	GSM5814803 r2	0:101 1:0	A:450263765;C:444632870;G:587867138;T:376465490;N:166193	101	450263765	444632870	587867138	376465490	166193	SRX13773729	SRS11653730	SRA1356563	University of Wisconsin-Madison	University of Wisconsin-Madison	1	0.68295	0.17068	0.93026	0.76288	101	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc_generic	single_cell_generic	generic-scrnaseq-only	United States	2022-01-13	Larval	Larval	Blood	Hematopoietic 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");;