metadata: run_metadata: 97 rows where devstage_curation_coarse = "Multi-stage" and technology = "smartseq"

97 rows where devstage_curation_coarse = "Multi-stage" and technology = "smartseq"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.attributes	study.PMIDs	sample.title	sample.alias	sample.attributes	GEOsample.title	GEOsample.dataprocessing	GEOsample.source	GEOsample.treatmentprotocol	GEOsample.extractprotocol	GEOsample.growthprotocol	GEOsample.characteristics	GEOsample.accession	experiment.title	experiment.alias	experiment.library_name	experiment.design_description	experiment.library_construction_protocol	experiment.attributes	experiment.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	experiment.study_ref	run.attributes	run.filename	run.semantic_name	run.total_bases	run.total_spots	run.alias	run.read_lengths	run.base_counts	run.r1_length	run.r2_length	run.Acount	run.Ccount	run.Gcount	run.Tcount	run.Ncount	run.experiment	run.pool_member	submission.accession	submission.srasource	submission.bioprojectsource	seqdetective.n_mates	seqdetective.mapping_rate.mate1	seqdetective.mapping_rate.mate2	seqdetective.nofeature_rate.mate1	seqdetective.nofeature_rate.mate2	seqdetective.sparsity.mate1	seqdetective.sparsity.mate2	seqdetective.pos_strand_rate.mate1	seqdetective.pos_strand_rate.mate2	seqdetective.readlen.mate1	seqdetective.readlen.mate2	seqdetective.judgement.mate1	seqdetective.judgement.mate2	seqdetective.judgement.reason	platform_family	instrument_generation	read_bias	selection_class	prep_kit	sc_or_bulk	tech_class	technology	submission.bioprojectsource.country	earliest_date	devstage_curation	devstage_curation_coarse	tissue_curation	tissue_curation_coarse
41695	41695	SRR5125207	SRX2439963	SRS1874550	SRP095522	PRJNA358490	Transcriptomic analysis reveals inflammasome dependent mechanism for early neutrophil response to Mycobacterium Marinum	GSE92740	Transcriptome Analysis	The mechanisms that govern the neutrophil response to Mycobacterium tuberculosis remain poorly understood. In this study we utilize an innovative binary approach in zebrafish to perform in depth profiling of the initial response of neutrophils to Mycobacterium marinum by in vivo biotinylation of neutrophil nuclei and subsequent rapid isolation directly from the in vivo context. RNA seq and differential expression analysis of the neutrophil nuclear transcriptome reveals a significant upregulation in both damage sensing and effector components of the inflammasome including caspase b wu:fb15h11 NLRC3 ortholog and il1ß. Crispr/Cas9 mediated knockdown of caspase b which mediates its effects by the proteolytic processing of il1ß results in increased bacterial burden and less infiltration of macrophages to sites of mycobacterium infection thus impairing granuloma development. We also show that a number of immediate early response genes IEGs are responsible for orchestrating the initial response to mycobacterial infection in neutrophils. Further perturbation of the IEGs revealed egr3 as a key transcription factor regulating il1ß transcription. Overall design: We report the design of a binary approach in zebrafish that allows for profiling of the initial response of neutrophils to Mycobacterium Marinum by in vivo biotinylation of neutrophil nuclei and subsequent rapid isolation directly from the in vivo context allowing for RNA seq analysis of the active transcriptome.		pubmed:28747644	mpo RNAseqnuclear +Mm1 3	GSM2436723	tissue:mpo RNAseqnuclear +Mm1\|strain:Tgmpo:BirA 2A Citrine; bactin:Avi Cerulean Rangap128\|development:3 dpf method:InVivoBiotinylatedNuclei\|treatment:M. marinum 32 512 cell stage\|amplification:SMART seqTMv4\|strand:reverse	mpo RNAseqnuclear +Mm1 3	Reads were mapped using STAR v.2.4.2a to danRer10 and read counts were obtained using subreads FeatureCounts Genome build: danRer10 Supplementary files format and content: read counts	mpo RNAseqnuclear +Mm1	For M. marinum infection embryos were injected at the 32 512 cell stage with M. marinum	For nuclei isolation zebrafish embryos were anaesthetised with 0.01% Tricaine 0.01% and aggregates of mycobacterium dissected based on tdTomato fluorescence. Embryos were washed in hypotonic buffer H 20 mM HEPES pH 7.9 15 mM MgCl2 10 mM KCl 1 mM DTT and 1 X Complete protease inhibitor and subsequently resuspended in 500 μL of buffer H. Embryos were transferred to a Dounce homogenizer and dissociated by 10 strokes with the loose fitting pestal A and incubated on ice for 5 minutes. Further dissociation was carried out by 10 strokes with tight fitting pestal B every 5 minutes for 15 minutes. Nuclei were collected by centrifugation 2000 g 4 °C and resuspended in 1 mL buffer NDP 10 mM HEPES pH 7.9 40 mM NaCl 90 mM KCl 0.5 mM EDTA 0.5 mM spermidine 0.15 mM spermine 1 mM dithiothreitol and 1 X Complete protease inhibitor. For nuclei purification nuclei were incubated with 5 mg of M 280 streptavidin coated dynabeads with rotation for 30 minutes at 4 °C. A flow based system based on the previously published protocol by was used to capture the nuclei bound on the streptavidin beads. A 10 mL seriological pipette VWR cat # 8913 898 attached to a 1 mL micropipette tip Rainin reach pipet tip cat # RT L1000S both pre treated with NPB/BSA for 30 minutes and added to a MiniMACS separator magnet OctoMACS Separator Miltenyl Biotec cat # 130 042 109. A two way stopcock Biorad cat # 732 8102 was connected to the end of the 1mL micropipette tip via a piece of Tygon tubing Fisher Scientific cat # 8220 and the flow rate set to 0.75 mL/min. The nuclei beads suspension was diluted by addition of 9 mLs of nuclei pulldown buffer with 0.01 % Triton X 100 NPBt and added to the slow flow setup. The tip was subsequently removed from the stand and the nuclei beads released from the tip by slowly pipetting 1 mL of NPBt in and out of the tip. The solution was then diluted again to 10 mL with NPBt and added again to the slow flow setup. Nuclei beads were eluted in 1 mL of NPBt as described above and the NPBt removed using a ma…		strain:Tgmpo:BirA 2A Citrine;bactin:Avi Cerulean Rangap128\|development:3 dpf method:InVivoBiotinylatedNuclei\|treatment:M. marinum 32 512 cell stage\|amplification:SMART seqTMv4\|strand:reverse	GSM2436723	GSM2436723: mpo RNAseqnuclear +Mm1 3; Danio rerio; RNA Seq	GSM2436723		1	For nuclei isolation zebrafish embryos were anaesthetised with 0.01% Tricaine 0.01% and aggregates of mycobacterium dissected based on tdTomato fluorescence. Embryos were washed in hypotonic buffer H 20 mM HEPES pH 7.9 15 mM MgCl2 10 mM KCl 1 mM DTT and 1 X Complete protease inhibitor and subsequently resuspended in 500 μL of buffer H. Embryos were transferred to a Dounce homogenizer and dissociated by 10 strokes with the loose fitting pestal A and incubated on ice for 5 minutes. Further dissociation was carried out by 10 strokes with tight fitting pestal B every 5 minutes for 15 minutes. Nuclei were collected by centrifugation 2000 g 4 °C and resuspended in 1 mL buffer NDP 10 mM HEPES pH 7.9 40 mM NaCl 90 mM KCl 0.5 mM EDTA 0.5 mM spermidine 0.15 mM spermine 1 mM dithiothreitol and 1 X Complete protease inhibitor. For nuclei purification nuclei were incubated with 5 mg of M 280 streptavidin coated dynabeads with rotation for 30 minutes at 4 °C. A flow based system based on the previously published protocol by was used to capture the nuclei bound on the streptavidin beads. A 10 mL seriological pipette VWR cat # 8913 898 attached to a 1 mL micropipette tip Rainin reach pipet tip cat # RT L1000S both pre treated with NPB/BSA for 30 minutes and added to a MiniMACS separator magnet OctoMACS Separator Miltenyl Biotec cat # 130 042 109. A two way stopcock Biorad cat # 732 8102 was connected to the end of the 1mL micropipette tip via a piece of Tygon tubing Fisher Scientific cat # 8220 and the flow rate set to 0.75 mL/min. The nuclei beads suspension was diluted by addition of 9 mLs of nuclei pulldown buffer with 0.01 % Triton X 100 NPBt and added to the slow flow setup. The tip was subsequently removed from the stand and the nuclei beads released from the tip by slowly pipetting 1 mL of NPBt in and out of the tip. The solution was then diluted again to 10 mL with NPBt and added again to the slow flow setup. Nuclei beads were eluted in 1 mL of NPBt as described above and the NPBt removed using a ma…	GEO Accession:GSM2436723	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP095522		mpo_RNAseqnuclear_+Mm1_3_R1.fastq.gz mpo_RNAseqnuclear_+Mm1_3_R2.fastq.gz	fastq fastq	3577998648.0	22545816.0	GSM2436723 r1	0:79.35 1:79.35	A:1011625838;C:729918557;G:775924617;T:1059494973;N:1034663	79	79	1011625838	729918557	775924617	1059494973	1034663	SRX2439963	SRS1874550	SRA507700	GEO	Sauka-Spengler lab, University of Oxford, MRC Weatherall Institute of Molecular Medicine	2	0.87174	0.87231	0.17198	0.16358	0.83575	0.83816	0.39726	0.47698	80	80	B	B	biological fallback assumption	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United Kingdom	2016-12-22	Multi-stage	Multi-stage	Embryo Imprecise	All anatomical structures
41696	41696	SRR5125206	SRX2439962	SRS1874549	SRP095522	PRJNA358490	Transcriptomic analysis reveals inflammasome dependent mechanism for early neutrophil response to Mycobacterium Marinum	GSE92740	Transcriptome Analysis	The mechanisms that govern the neutrophil response to Mycobacterium tuberculosis remain poorly understood. In this study we utilize an innovative binary approach in zebrafish to perform in depth profiling of the initial response of neutrophils to Mycobacterium marinum by in vivo biotinylation of neutrophil nuclei and subsequent rapid isolation directly from the in vivo context. RNA seq and differential expression analysis of the neutrophil nuclear transcriptome reveals a significant upregulation in both damage sensing and effector components of the inflammasome including caspase b wu:fb15h11 NLRC3 ortholog and il1ß. Crispr/Cas9 mediated knockdown of caspase b which mediates its effects by the proteolytic processing of il1ß results in increased bacterial burden and less infiltration of macrophages to sites of mycobacterium infection thus impairing granuloma development. We also show that a number of immediate early response genes IEGs are responsible for orchestrating the initial response to mycobacterial infection in neutrophils. Further perturbation of the IEGs revealed egr3 as a key transcription factor regulating il1ß transcription. Overall design: We report the design of a binary approach in zebrafish that allows for profiling of the initial response of neutrophils to Mycobacterium Marinum by in vivo biotinylation of neutrophil nuclei and subsequent rapid isolation directly from the in vivo context allowing for RNA seq analysis of the active transcriptome.		pubmed:28747644	mpo RNAseqnuclear +Mm1 2	GSM2436722	tissue:mpo RNAseqnuclear +Mm1\|strain:Tgmpo:BirA 2A Citrine; bactin:Avi Cerulean Rangap128\|development:3 dpf method:InVivoBiotinylatedNuclei\|treatment:M. marinum 32 512 cell stage\|amplification:SMART seqTMv4\|strand:reverse	mpo RNAseqnuclear +Mm1 2	Reads were mapped using STAR v.2.4.2a to danRer10 and read counts were obtained using subreads FeatureCounts Genome build: danRer10 Supplementary files format and content: read counts	mpo RNAseqnuclear +Mm1	For M. marinum infection embryos were injected at the 32 512 cell stage with M. marinum	For nuclei isolation zebrafish embryos were anaesthetised with 0.01% Tricaine 0.01% and aggregates of mycobacterium dissected based on tdTomato fluorescence. Embryos were washed in hypotonic buffer H 20 mM HEPES pH 7.9 15 mM MgCl2 10 mM KCl 1 mM DTT and 1 X Complete protease inhibitor and subsequently resuspended in 500 μL of buffer H. Embryos were transferred to a Dounce homogenizer and dissociated by 10 strokes with the loose fitting pestal A and incubated on ice for 5 minutes. Further dissociation was carried out by 10 strokes with tight fitting pestal B every 5 minutes for 15 minutes. Nuclei were collected by centrifugation 2000 g 4 °C and resuspended in 1 mL buffer NDP 10 mM HEPES pH 7.9 40 mM NaCl 90 mM KCl 0.5 mM EDTA 0.5 mM spermidine 0.15 mM spermine 1 mM dithiothreitol and 1 X Complete protease inhibitor. For nuclei purification nuclei were incubated with 5 mg of M 280 streptavidin coated dynabeads with rotation for 30 minutes at 4 °C. A flow based system based on the previously published protocol by was used to capture the nuclei bound on the streptavidin beads. A 10 mL seriological pipette VWR cat # 8913 898 attached to a 1 mL micropipette tip Rainin reach pipet tip cat # RT L1000S both pre treated with NPB/BSA for 30 minutes and added to a MiniMACS separator magnet OctoMACS Separator Miltenyl Biotec cat # 130 042 109. A two way stopcock Biorad cat # 732 8102 was connected to the end of the 1mL micropipette tip via a piece of Tygon tubing Fisher Scientific cat # 8220 and the flow rate set to 0.75 mL/min. The nuclei beads suspension was diluted by addition of 9 mLs of nuclei pulldown buffer with 0.01 % Triton X 100 NPBt and added to the slow flow setup. The tip was subsequently removed from the stand and the nuclei beads released from the tip by slowly pipetting 1 mL of NPBt in and out of the tip. The solution was then diluted again to 10 mL with NPBt and added again to the slow flow setup. Nuclei beads were eluted in 1 mL of NPBt as described above and the NPBt removed using a ma…		strain:Tgmpo:BirA 2A Citrine;bactin:Avi Cerulean Rangap128\|development:3 dpf method:InVivoBiotinylatedNuclei\|treatment:M. marinum 32 512 cell stage\|amplification:SMART seqTMv4\|strand:reverse	GSM2436722	GSM2436722: mpo RNAseqnuclear +Mm1 2; Danio rerio; RNA Seq	GSM2436722		1	For nuclei isolation zebrafish embryos were anaesthetised with 0.01% Tricaine 0.01% and aggregates of mycobacterium dissected based on tdTomato fluorescence. Embryos were washed in hypotonic buffer H 20 mM HEPES pH 7.9 15 mM MgCl2 10 mM KCl 1 mM DTT and 1 X Complete protease inhibitor and subsequently resuspended in 500 μL of buffer H. Embryos were transferred to a Dounce homogenizer and dissociated by 10 strokes with the loose fitting pestal A and incubated on ice for 5 minutes. Further dissociation was carried out by 10 strokes with tight fitting pestal B every 5 minutes for 15 minutes. Nuclei were collected by centrifugation 2000 g 4 °C and resuspended in 1 mL buffer NDP 10 mM HEPES pH 7.9 40 mM NaCl 90 mM KCl 0.5 mM EDTA 0.5 mM spermidine 0.15 mM spermine 1 mM dithiothreitol and 1 X Complete protease inhibitor. For nuclei purification nuclei were incubated with 5 mg of M 280 streptavidin coated dynabeads with rotation for 30 minutes at 4 °C. A flow based system based on the previously published protocol by was used to capture the nuclei bound on the streptavidin beads. A 10 mL seriological pipette VWR cat # 8913 898 attached to a 1 mL micropipette tip Rainin reach pipet tip cat # RT L1000S both pre treated with NPB/BSA for 30 minutes and added to a MiniMACS separator magnet OctoMACS Separator Miltenyl Biotec cat # 130 042 109. A two way stopcock Biorad cat # 732 8102 was connected to the end of the 1mL micropipette tip via a piece of Tygon tubing Fisher Scientific cat # 8220 and the flow rate set to 0.75 mL/min. The nuclei beads suspension was diluted by addition of 9 mLs of nuclei pulldown buffer with 0.01 % Triton X 100 NPBt and added to the slow flow setup. The tip was subsequently removed from the stand and the nuclei beads released from the tip by slowly pipetting 1 mL of NPBt in and out of the tip. The solution was then diluted again to 10 mL with NPBt and added again to the slow flow setup. Nuclei beads were eluted in 1 mL of NPBt as described above and the NPBt removed using a ma…	GEO Accession:GSM2436722	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP095522		mpo_RNAseqnuclear_+Mm1_2_R1.fastq.gz mpo_RNAseqnuclear_+Mm1_2_R2.fastq.gz	fastq fastq	5570271667.0	35931731.0	GSM2436722 r1	0:77.49 1:77.53	A:1636374700;C:1118521700;G:1178516265;T:1627777920;N:9081082	77	77	1636374700	1118521700	1178516265	1627777920	9081082	SRX2439962	SRS1874549	SRA507700	GEO	Sauka-Spengler lab, University of Oxford, MRC Weatherall Institute of Molecular Medicine	2	0.87632	0.87894	0.25217	0.25103	0.77802	0.78236	0.45536	0.44351	80	79	B	B	biological fallback assumption	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United Kingdom	2016-12-22	Multi-stage	Multi-stage	Embryo Imprecise	All anatomical structures
41697	41697	SRR5125204	SRX2439961	SRS1874548	SRP095522	PRJNA358490	Transcriptomic analysis reveals inflammasome dependent mechanism for early neutrophil response to Mycobacterium Marinum	GSE92740	Transcriptome Analysis	The mechanisms that govern the neutrophil response to Mycobacterium tuberculosis remain poorly understood. In this study we utilize an innovative binary approach in zebrafish to perform in depth profiling of the initial response of neutrophils to Mycobacterium marinum by in vivo biotinylation of neutrophil nuclei and subsequent rapid isolation directly from the in vivo context. RNA seq and differential expression analysis of the neutrophil nuclear transcriptome reveals a significant upregulation in both damage sensing and effector components of the inflammasome including caspase b wu:fb15h11 NLRC3 ortholog and il1ß. Crispr/Cas9 mediated knockdown of caspase b which mediates its effects by the proteolytic processing of il1ß results in increased bacterial burden and less infiltration of macrophages to sites of mycobacterium infection thus impairing granuloma development. We also show that a number of immediate early response genes IEGs are responsible for orchestrating the initial response to mycobacterial infection in neutrophils. Further perturbation of the IEGs revealed egr3 as a key transcription factor regulating il1ß transcription. Overall design: We report the design of a binary approach in zebrafish that allows for profiling of the initial response of neutrophils to Mycobacterium Marinum by in vivo biotinylation of neutrophil nuclei and subsequent rapid isolation directly from the in vivo context allowing for RNA seq analysis of the active transcriptome.		pubmed:28747644	mpo RNAseqnuclear +Mm1 1	GSM2436721	tissue:mpo RNAseqnuclear +Mm1\|strain:Tgmpo:BirA 2A Citrine; bactin:Avi Cerulean Rangap128\|development:3 dpf method:InVivoBiotinylatedNuclei\|treatment:M. marinum 32 512 cell stage\|amplification:SMART seqTMv4\|strand:reverse	mpo RNAseqnuclear +Mm1 1	Reads were mapped using STAR v.2.4.2a to danRer10 and read counts were obtained using subreads FeatureCounts Genome build: danRer10 Supplementary files format and content: read counts	mpo RNAseqnuclear +Mm1	For M. marinum infection embryos were injected at the 32 512 cell stage with M. marinum	For nuclei isolation zebrafish embryos were anaesthetised with 0.01% Tricaine 0.01% and aggregates of mycobacterium dissected based on tdTomato fluorescence. Embryos were washed in hypotonic buffer H 20 mM HEPES pH 7.9 15 mM MgCl2 10 mM KCl 1 mM DTT and 1 X Complete protease inhibitor and subsequently resuspended in 500 μL of buffer H. Embryos were transferred to a Dounce homogenizer and dissociated by 10 strokes with the loose fitting pestal A and incubated on ice for 5 minutes. Further dissociation was carried out by 10 strokes with tight fitting pestal B every 5 minutes for 15 minutes. Nuclei were collected by centrifugation 2000 g 4 °C and resuspended in 1 mL buffer NDP 10 mM HEPES pH 7.9 40 mM NaCl 90 mM KCl 0.5 mM EDTA 0.5 mM spermidine 0.15 mM spermine 1 mM dithiothreitol and 1 X Complete protease inhibitor. For nuclei purification nuclei were incubated with 5 mg of M 280 streptavidin coated dynabeads with rotation for 30 minutes at 4 °C. A flow based system based on the previously published protocol by was used to capture the nuclei bound on the streptavidin beads. A 10 mL seriological pipette VWR cat # 8913 898 attached to a 1 mL micropipette tip Rainin reach pipet tip cat # RT L1000S both pre treated with NPB/BSA for 30 minutes and added to a MiniMACS separator magnet OctoMACS Separator Miltenyl Biotec cat # 130 042 109. A two way stopcock Biorad cat # 732 8102 was connected to the end of the 1mL micropipette tip via a piece of Tygon tubing Fisher Scientific cat # 8220 and the flow rate set to 0.75 mL/min. The nuclei beads suspension was diluted by addition of 9 mLs of nuclei pulldown buffer with 0.01 % Triton X 100 NPBt and added to the slow flow setup. The tip was subsequently removed from the stand and the nuclei beads released from the tip by slowly pipetting 1 mL of NPBt in and out of the tip. The solution was then diluted again to 10 mL with NPBt and added again to the slow flow setup. Nuclei beads were eluted in 1 mL of NPBt as described above and the NPBt removed using a ma…		strain:Tgmpo:BirA 2A Citrine;bactin:Avi Cerulean Rangap128\|development:3 dpf method:InVivoBiotinylatedNuclei\|treatment:M. marinum 32 512 cell stage\|amplification:SMART seqTMv4\|strand:reverse	GSM2436721	GSM2436721: mpo RNAseqnuclear +Mm1 1; Danio rerio; RNA Seq	GSM2436721		1	For nuclei isolation zebrafish embryos were anaesthetised with 0.01% Tricaine 0.01% and aggregates of mycobacterium dissected based on tdTomato fluorescence. Embryos were washed in hypotonic buffer H 20 mM HEPES pH 7.9 15 mM MgCl2 10 mM KCl 1 mM DTT and 1 X Complete protease inhibitor and subsequently resuspended in 500 μL of buffer H. Embryos were transferred to a Dounce homogenizer and dissociated by 10 strokes with the loose fitting pestal A and incubated on ice for 5 minutes. Further dissociation was carried out by 10 strokes with tight fitting pestal B every 5 minutes for 15 minutes. Nuclei were collected by centrifugation 2000 g 4 °C and resuspended in 1 mL buffer NDP 10 mM HEPES pH 7.9 40 mM NaCl 90 mM KCl 0.5 mM EDTA 0.5 mM spermidine 0.15 mM spermine 1 mM dithiothreitol and 1 X Complete protease inhibitor. For nuclei purification nuclei were incubated with 5 mg of M 280 streptavidin coated dynabeads with rotation for 30 minutes at 4 °C. A flow based system based on the previously published protocol by was used to capture the nuclei bound on the streptavidin beads. A 10 mL seriological pipette VWR cat # 8913 898 attached to a 1 mL micropipette tip Rainin reach pipet tip cat # RT L1000S both pre treated with NPB/BSA for 30 minutes and added to a MiniMACS separator magnet OctoMACS Separator Miltenyl Biotec cat # 130 042 109. A two way stopcock Biorad cat # 732 8102 was connected to the end of the 1mL micropipette tip via a piece of Tygon tubing Fisher Scientific cat # 8220 and the flow rate set to 0.75 mL/min. The nuclei beads suspension was diluted by addition of 9 mLs of nuclei pulldown buffer with 0.01 % Triton X 100 NPBt and added to the slow flow setup. The tip was subsequently removed from the stand and the nuclei beads released from the tip by slowly pipetting 1 mL of NPBt in and out of the tip. The solution was then diluted again to 10 mL with NPBt and added again to the slow flow setup. Nuclei beads were eluted in 1 mL of NPBt as described above and the NPBt removed using a ma…	GEO Accession:GSM2436721	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP095522		mpo_RNAseqnuclear_+Mm1_1_run1_R1.fastq.gz mpo_RNAseqnuclear_+Mm1_1_run1_R2.fastq.gz	fastq fastq	1726239158.0	10963548.0	GSM2436721 r1	0:78.71 1:78.74	A:513744700;C:341699560;G:360634107;T:508787617;N:1373174	78	78	513744700	341699560	360634107	508787617	1373174	SRX2439961	SRS1874548	SRA507700	GEO	Sauka-Spengler lab, University of Oxford, MRC Weatherall Institute of Molecular Medicine	2	0.84846	0.85305	0.24598	0.24259	0.79813	0.80316	0.41378	0.40578	80	80	B	B	biological fallback assumption	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United Kingdom	2016-12-22	Multi-stage	Multi-stage	Embryo Imprecise	All anatomical structures
41698	41698	SRR5125205	SRX2439961	SRS1874548	SRP095522	PRJNA358490	Transcriptomic analysis reveals inflammasome dependent mechanism for early neutrophil response to Mycobacterium Marinum	GSE92740	Transcriptome Analysis	The mechanisms that govern the neutrophil response to Mycobacterium tuberculosis remain poorly understood. In this study we utilize an innovative binary approach in zebrafish to perform in depth profiling of the initial response of neutrophils to Mycobacterium marinum by in vivo biotinylation of neutrophil nuclei and subsequent rapid isolation directly from the in vivo context. RNA seq and differential expression analysis of the neutrophil nuclear transcriptome reveals a significant upregulation in both damage sensing and effector components of the inflammasome including caspase b wu:fb15h11 NLRC3 ortholog and il1ß. Crispr/Cas9 mediated knockdown of caspase b which mediates its effects by the proteolytic processing of il1ß results in increased bacterial burden and less infiltration of macrophages to sites of mycobacterium infection thus impairing granuloma development. We also show that a number of immediate early response genes IEGs are responsible for orchestrating the initial response to mycobacterial infection in neutrophils. Further perturbation of the IEGs revealed egr3 as a key transcription factor regulating il1ß transcription. Overall design: We report the design of a binary approach in zebrafish that allows for profiling of the initial response of neutrophils to Mycobacterium Marinum by in vivo biotinylation of neutrophil nuclei and subsequent rapid isolation directly from the in vivo context allowing for RNA seq analysis of the active transcriptome.		pubmed:28747644	mpo RNAseqnuclear +Mm1 1	GSM2436721	tissue:mpo RNAseqnuclear +Mm1\|strain:Tgmpo:BirA 2A Citrine; bactin:Avi Cerulean Rangap128\|development:3 dpf method:InVivoBiotinylatedNuclei\|treatment:M. marinum 32 512 cell stage\|amplification:SMART seqTMv4\|strand:reverse	mpo RNAseqnuclear +Mm1 1	Reads were mapped using STAR v.2.4.2a to danRer10 and read counts were obtained using subreads FeatureCounts Genome build: danRer10 Supplementary files format and content: read counts	mpo RNAseqnuclear +Mm1	For M. marinum infection embryos were injected at the 32 512 cell stage with M. marinum	For nuclei isolation zebrafish embryos were anaesthetised with 0.01% Tricaine 0.01% and aggregates of mycobacterium dissected based on tdTomato fluorescence. Embryos were washed in hypotonic buffer H 20 mM HEPES pH 7.9 15 mM MgCl2 10 mM KCl 1 mM DTT and 1 X Complete protease inhibitor and subsequently resuspended in 500 μL of buffer H. Embryos were transferred to a Dounce homogenizer and dissociated by 10 strokes with the loose fitting pestal A and incubated on ice for 5 minutes. Further dissociation was carried out by 10 strokes with tight fitting pestal B every 5 minutes for 15 minutes. Nuclei were collected by centrifugation 2000 g 4 °C and resuspended in 1 mL buffer NDP 10 mM HEPES pH 7.9 40 mM NaCl 90 mM KCl 0.5 mM EDTA 0.5 mM spermidine 0.15 mM spermine 1 mM dithiothreitol and 1 X Complete protease inhibitor. For nuclei purification nuclei were incubated with 5 mg of M 280 streptavidin coated dynabeads with rotation for 30 minutes at 4 °C. A flow based system based on the previously published protocol by was used to capture the nuclei bound on the streptavidin beads. A 10 mL seriological pipette VWR cat # 8913 898 attached to a 1 mL micropipette tip Rainin reach pipet tip cat # RT L1000S both pre treated with NPB/BSA for 30 minutes and added to a MiniMACS separator magnet OctoMACS Separator Miltenyl Biotec cat # 130 042 109. A two way stopcock Biorad cat # 732 8102 was connected to the end of the 1mL micropipette tip via a piece of Tygon tubing Fisher Scientific cat # 8220 and the flow rate set to 0.75 mL/min. The nuclei beads suspension was diluted by addition of 9 mLs of nuclei pulldown buffer with 0.01 % Triton X 100 NPBt and added to the slow flow setup. The tip was subsequently removed from the stand and the nuclei beads released from the tip by slowly pipetting 1 mL of NPBt in and out of the tip. The solution was then diluted again to 10 mL with NPBt and added again to the slow flow setup. Nuclei beads were eluted in 1 mL of NPBt as described above and the NPBt removed using a ma…		strain:Tgmpo:BirA 2A Citrine;bactin:Avi Cerulean Rangap128\|development:3 dpf method:InVivoBiotinylatedNuclei\|treatment:M. marinum 32 512 cell stage\|amplification:SMART seqTMv4\|strand:reverse	GSM2436721	GSM2436721: mpo RNAseqnuclear +Mm1 1; Danio rerio; RNA Seq	GSM2436721		1	For nuclei isolation zebrafish embryos were anaesthetised with 0.01% Tricaine 0.01% and aggregates of mycobacterium dissected based on tdTomato fluorescence. Embryos were washed in hypotonic buffer H 20 mM HEPES pH 7.9 15 mM MgCl2 10 mM KCl 1 mM DTT and 1 X Complete protease inhibitor and subsequently resuspended in 500 μL of buffer H. Embryos were transferred to a Dounce homogenizer and dissociated by 10 strokes with the loose fitting pestal A and incubated on ice for 5 minutes. Further dissociation was carried out by 10 strokes with tight fitting pestal B every 5 minutes for 15 minutes. Nuclei were collected by centrifugation 2000 g 4 °C and resuspended in 1 mL buffer NDP 10 mM HEPES pH 7.9 40 mM NaCl 90 mM KCl 0.5 mM EDTA 0.5 mM spermidine 0.15 mM spermine 1 mM dithiothreitol and 1 X Complete protease inhibitor. For nuclei purification nuclei were incubated with 5 mg of M 280 streptavidin coated dynabeads with rotation for 30 minutes at 4 °C. A flow based system based on the previously published protocol by was used to capture the nuclei bound on the streptavidin beads. A 10 mL seriological pipette VWR cat # 8913 898 attached to a 1 mL micropipette tip Rainin reach pipet tip cat # RT L1000S both pre treated with NPB/BSA for 30 minutes and added to a MiniMACS separator magnet OctoMACS Separator Miltenyl Biotec cat # 130 042 109. A two way stopcock Biorad cat # 732 8102 was connected to the end of the 1mL micropipette tip via a piece of Tygon tubing Fisher Scientific cat # 8220 and the flow rate set to 0.75 mL/min. The nuclei beads suspension was diluted by addition of 9 mLs of nuclei pulldown buffer with 0.01 % Triton X 100 NPBt and added to the slow flow setup. The tip was subsequently removed from the stand and the nuclei beads released from the tip by slowly pipetting 1 mL of NPBt in and out of the tip. The solution was then diluted again to 10 mL with NPBt and added again to the slow flow setup. Nuclei beads were eluted in 1 mL of NPBt as described above and the NPBt removed using a ma…	GEO Accession:GSM2436721	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP095522		mpo_RNAseqnuclear_+Mm1_1_run2_R1.fastq.gz mpo_RNAseqnuclear_+Mm1_1_run2_R2.fastq.gz	fastq fastq	1545553215.0	9792222.0	GSM2436721 r2	0:78.91 1:78.93	A:443269412;C:311297118;G:328723159;T:461262986;N:1000540	78	78	443269412	311297118	328723159	461262986	1000540	SRX2439961	SRS1874548	SRA507700	GEO	Sauka-Spengler lab, University of Oxford, MRC Weatherall Institute of Molecular Medicine	2	0.85789	0.85447	0.23933	0.23401	0.79878	0.80355	0.40469	0.39742	80	35	B	B	biological fallback assumption	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United Kingdom	2016-12-22	Multi-stage	Multi-stage	Embryo Imprecise	All anatomical structures
41699	41699	SRR5125203	SRX2439960	SRS1874547	SRP095522	PRJNA358490	Transcriptomic analysis reveals inflammasome dependent mechanism for early neutrophil response to Mycobacterium Marinum	GSE92740	Transcriptome Analysis	The mechanisms that govern the neutrophil response to Mycobacterium tuberculosis remain poorly understood. In this study we utilize an innovative binary approach in zebrafish to perform in depth profiling of the initial response of neutrophils to Mycobacterium marinum by in vivo biotinylation of neutrophil nuclei and subsequent rapid isolation directly from the in vivo context. RNA seq and differential expression analysis of the neutrophil nuclear transcriptome reveals a significant upregulation in both damage sensing and effector components of the inflammasome including caspase b wu:fb15h11 NLRC3 ortholog and il1ß. Crispr/Cas9 mediated knockdown of caspase b which mediates its effects by the proteolytic processing of il1ß results in increased bacterial burden and less infiltration of macrophages to sites of mycobacterium infection thus impairing granuloma development. We also show that a number of immediate early response genes IEGs are responsible for orchestrating the initial response to mycobacterial infection in neutrophils. Further perturbation of the IEGs revealed egr3 as a key transcription factor regulating il1ß transcription. Overall design: We report the design of a binary approach in zebrafish that allows for profiling of the initial response of neutrophils to Mycobacterium Marinum by in vivo biotinylation of neutrophil nuclei and subsequent rapid isolation directly from the in vivo context allowing for RNA seq analysis of the active transcriptome.		pubmed:28747644	mpo RNAseqnuclear Mm1 3	GSM2436720	tissue:mpo RNAseqnuclear Mm1\|strain:Tgmpo:BirA 2A Citrine; bactin:Avi Cerulean Rangap128\|development:3 dpf method:InVivoBiotinylatedNuclei\|treatment:n1\|amplification:SMART seqTMv4\|strand:reverse	mpo RNAseqnuclear Mm1 3	Reads were mapped using STAR v.2.4.2a to danRer10 and read counts were obtained using subreads FeatureCounts Genome build: danRer10 Supplementary files format and content: read counts	mpo RNAseqnuclear Mm1	For M. marinum infection embryos were injected at the 32 512 cell stage with M. marinum	For nuclei isolation zebrafish embryos were anaesthetised with 0.01% Tricaine 0.01% and aggregates of mycobacterium dissected based on tdTomato fluorescence. Embryos were washed in hypotonic buffer H 20 mM HEPES pH 7.9 15 mM MgCl2 10 mM KCl 1 mM DTT and 1 X Complete protease inhibitor and subsequently resuspended in 500 μL of buffer H. Embryos were transferred to a Dounce homogenizer and dissociated by 10 strokes with the loose fitting pestal A and incubated on ice for 5 minutes. Further dissociation was carried out by 10 strokes with tight fitting pestal B every 5 minutes for 15 minutes. Nuclei were collected by centrifugation 2000 g 4 °C and resuspended in 1 mL buffer NDP 10 mM HEPES pH 7.9 40 mM NaCl 90 mM KCl 0.5 mM EDTA 0.5 mM spermidine 0.15 mM spermine 1 mM dithiothreitol and 1 X Complete protease inhibitor. For nuclei purification nuclei were incubated with 5 mg of M 280 streptavidin coated dynabeads with rotation for 30 minutes at 4 °C. A flow based system based on the previously published protocol by was used to capture the nuclei bound on the streptavidin beads. A 10 mL seriological pipette VWR cat # 8913 898 attached to a 1 mL micropipette tip Rainin reach pipet tip cat # RT L1000S both pre treated with NPB/BSA for 30 minutes and added to a MiniMACS separator magnet OctoMACS Separator Miltenyl Biotec cat # 130 042 109. A two way stopcock Biorad cat # 732 8102 was connected to the end of the 1mL micropipette tip via a piece of Tygon tubing Fisher Scientific cat # 8220 and the flow rate set to 0.75 mL/min. The nuclei beads suspension was diluted by addition of 9 mLs of nuclei pulldown buffer with 0.01 % Triton X 100 NPBt and added to the slow flow setup. The tip was subsequently removed from the stand and the nuclei beads released from the tip by slowly pipetting 1 mL of NPBt in and out of the tip. The solution was then diluted again to 10 mL with NPBt and added again to the slow flow setup. Nuclei beads were eluted in 1 mL of NPBt as described above and the NPBt removed using a ma…		strain:Tgmpo:BirA 2A Citrine;bactin:Avi Cerulean Rangap128\|development:3 dpf method:InVivoBiotinylatedNuclei\|treatment:n1\|amplification:SMART seqTMv4\|strand:reverse	GSM2436720	GSM2436720: mpo RNAseqnuclear Mm1 3; Danio rerio; RNA Seq	GSM2436720		1	For nuclei isolation zebrafish embryos were anaesthetised with 0.01% Tricaine 0.01% and aggregates of mycobacterium dissected based on tdTomato fluorescence. Embryos were washed in hypotonic buffer H 20 mM HEPES pH 7.9 15 mM MgCl2 10 mM KCl 1 mM DTT and 1 X Complete protease inhibitor and subsequently resuspended in 500 μL of buffer H. Embryos were transferred to a Dounce homogenizer and dissociated by 10 strokes with the loose fitting pestal A and incubated on ice for 5 minutes. Further dissociation was carried out by 10 strokes with tight fitting pestal B every 5 minutes for 15 minutes. Nuclei were collected by centrifugation 2000 g 4 °C and resuspended in 1 mL buffer NDP 10 mM HEPES pH 7.9 40 mM NaCl 90 mM KCl 0.5 mM EDTA 0.5 mM spermidine 0.15 mM spermine 1 mM dithiothreitol and 1 X Complete protease inhibitor. For nuclei purification nuclei were incubated with 5 mg of M 280 streptavidin coated dynabeads with rotation for 30 minutes at 4 °C. A flow based system based on the previously published protocol by was used to capture the nuclei bound on the streptavidin beads. A 10 mL seriological pipette VWR cat # 8913 898 attached to a 1 mL micropipette tip Rainin reach pipet tip cat # RT L1000S both pre treated with NPB/BSA for 30 minutes and added to a MiniMACS separator magnet OctoMACS Separator Miltenyl Biotec cat # 130 042 109. A two way stopcock Biorad cat # 732 8102 was connected to the end of the 1mL micropipette tip via a piece of Tygon tubing Fisher Scientific cat # 8220 and the flow rate set to 0.75 mL/min. The nuclei beads suspension was diluted by addition of 9 mLs of nuclei pulldown buffer with 0.01 % Triton X 100 NPBt and added to the slow flow setup. The tip was subsequently removed from the stand and the nuclei beads released from the tip by slowly pipetting 1 mL of NPBt in and out of the tip. The solution was then diluted again to 10 mL with NPBt and added again to the slow flow setup. Nuclei beads were eluted in 1 mL of NPBt as described above and the NPBt removed using a ma…	GEO Accession:GSM2436720	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP095522		mpo_RNAseqnuclear_-Mm1_3_R2.fastq.gz mpo_RNAseqnuclear_-Mm1_3_R1.fastq.gz	fastq fastq	5801339359.0	36782784.0	GSM2436720 r1	0:78.85 1:78.87	A:1571123404;C:1301496084;G:1367224653;T:1558195664;N:3299554	78	78	1571123404	1301496084	1367224653	1558195664	3299554	SRX2439960	SRS1874547	SRA507700	GEO	Sauka-Spengler lab, University of Oxford, MRC Weatherall Institute of Molecular Medicine	2	0.93187	0.9326	0.12448	0.12242	0.81702	0.8224	0.47606	0.47387	78	79	B	B	biological fallback assumption	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United Kingdom	2016-12-22	Multi-stage	Multi-stage	Embryo Imprecise	All anatomical structures
41700	41700	SRR5125201	SRX2439959	SRS1874546	SRP095522	PRJNA358490	Transcriptomic analysis reveals inflammasome dependent mechanism for early neutrophil response to Mycobacterium Marinum	GSE92740	Transcriptome Analysis	The mechanisms that govern the neutrophil response to Mycobacterium tuberculosis remain poorly understood. In this study we utilize an innovative binary approach in zebrafish to perform in depth profiling of the initial response of neutrophils to Mycobacterium marinum by in vivo biotinylation of neutrophil nuclei and subsequent rapid isolation directly from the in vivo context. RNA seq and differential expression analysis of the neutrophil nuclear transcriptome reveals a significant upregulation in both damage sensing and effector components of the inflammasome including caspase b wu:fb15h11 NLRC3 ortholog and il1ß. Crispr/Cas9 mediated knockdown of caspase b which mediates its effects by the proteolytic processing of il1ß results in increased bacterial burden and less infiltration of macrophages to sites of mycobacterium infection thus impairing granuloma development. We also show that a number of immediate early response genes IEGs are responsible for orchestrating the initial response to mycobacterial infection in neutrophils. Further perturbation of the IEGs revealed egr3 as a key transcription factor regulating il1ß transcription. Overall design: We report the design of a binary approach in zebrafish that allows for profiling of the initial response of neutrophils to Mycobacterium Marinum by in vivo biotinylation of neutrophil nuclei and subsequent rapid isolation directly from the in vivo context allowing for RNA seq analysis of the active transcriptome.		pubmed:28747644	mpo RNAseqnuclear Mm1 2	GSM2436719	tissue:mpo RNAseqnuclear Mm1\|strain:Tgmpo:BirA 2A Citrine; bactin:Avi Cerulean Rangap128\|development:3 dpf method:InVivoBiotinylatedNuclei\|treatment:n1\|amplification:SMART seqTMv4\|strand:reverse	mpo RNAseqnuclear Mm1 2	Reads were mapped using STAR v.2.4.2a to danRer10 and read counts were obtained using subreads FeatureCounts Genome build: danRer10 Supplementary files format and content: read counts	mpo RNAseqnuclear Mm1	For M. marinum infection embryos were injected at the 32 512 cell stage with M. marinum	For nuclei isolation zebrafish embryos were anaesthetised with 0.01% Tricaine 0.01% and aggregates of mycobacterium dissected based on tdTomato fluorescence. Embryos were washed in hypotonic buffer H 20 mM HEPES pH 7.9 15 mM MgCl2 10 mM KCl 1 mM DTT and 1 X Complete protease inhibitor and subsequently resuspended in 500 μL of buffer H. Embryos were transferred to a Dounce homogenizer and dissociated by 10 strokes with the loose fitting pestal A and incubated on ice for 5 minutes. Further dissociation was carried out by 10 strokes with tight fitting pestal B every 5 minutes for 15 minutes. Nuclei were collected by centrifugation 2000 g 4 °C and resuspended in 1 mL buffer NDP 10 mM HEPES pH 7.9 40 mM NaCl 90 mM KCl 0.5 mM EDTA 0.5 mM spermidine 0.15 mM spermine 1 mM dithiothreitol and 1 X Complete protease inhibitor. For nuclei purification nuclei were incubated with 5 mg of M 280 streptavidin coated dynabeads with rotation for 30 minutes at 4 °C. A flow based system based on the previously published protocol by was used to capture the nuclei bound on the streptavidin beads. A 10 mL seriological pipette VWR cat # 8913 898 attached to a 1 mL micropipette tip Rainin reach pipet tip cat # RT L1000S both pre treated with NPB/BSA for 30 minutes and added to a MiniMACS separator magnet OctoMACS Separator Miltenyl Biotec cat # 130 042 109. A two way stopcock Biorad cat # 732 8102 was connected to the end of the 1mL micropipette tip via a piece of Tygon tubing Fisher Scientific cat # 8220 and the flow rate set to 0.75 mL/min. The nuclei beads suspension was diluted by addition of 9 mLs of nuclei pulldown buffer with 0.01 % Triton X 100 NPBt and added to the slow flow setup. The tip was subsequently removed from the stand and the nuclei beads released from the tip by slowly pipetting 1 mL of NPBt in and out of the tip. The solution was then diluted again to 10 mL with NPBt and added again to the slow flow setup. Nuclei beads were eluted in 1 mL of NPBt as described above and the NPBt removed using a ma…		strain:Tgmpo:BirA 2A Citrine;bactin:Avi Cerulean Rangap128\|development:3 dpf method:InVivoBiotinylatedNuclei\|treatment:n1\|amplification:SMART seqTMv4\|strand:reverse	GSM2436719	GSM2436719: mpo RNAseqnuclear Mm1 2; Danio rerio; RNA Seq	GSM2436719		1	For nuclei isolation zebrafish embryos were anaesthetised with 0.01% Tricaine 0.01% and aggregates of mycobacterium dissected based on tdTomato fluorescence. Embryos were washed in hypotonic buffer H 20 mM HEPES pH 7.9 15 mM MgCl2 10 mM KCl 1 mM DTT and 1 X Complete protease inhibitor and subsequently resuspended in 500 μL of buffer H. Embryos were transferred to a Dounce homogenizer and dissociated by 10 strokes with the loose fitting pestal A and incubated on ice for 5 minutes. Further dissociation was carried out by 10 strokes with tight fitting pestal B every 5 minutes for 15 minutes. Nuclei were collected by centrifugation 2000 g 4 °C and resuspended in 1 mL buffer NDP 10 mM HEPES pH 7.9 40 mM NaCl 90 mM KCl 0.5 mM EDTA 0.5 mM spermidine 0.15 mM spermine 1 mM dithiothreitol and 1 X Complete protease inhibitor. For nuclei purification nuclei were incubated with 5 mg of M 280 streptavidin coated dynabeads with rotation for 30 minutes at 4 °C. A flow based system based on the previously published protocol by was used to capture the nuclei bound on the streptavidin beads. A 10 mL seriological pipette VWR cat # 8913 898 attached to a 1 mL micropipette tip Rainin reach pipet tip cat # RT L1000S both pre treated with NPB/BSA for 30 minutes and added to a MiniMACS separator magnet OctoMACS Separator Miltenyl Biotec cat # 130 042 109. A two way stopcock Biorad cat # 732 8102 was connected to the end of the 1mL micropipette tip via a piece of Tygon tubing Fisher Scientific cat # 8220 and the flow rate set to 0.75 mL/min. The nuclei beads suspension was diluted by addition of 9 mLs of nuclei pulldown buffer with 0.01 % Triton X 100 NPBt and added to the slow flow setup. The tip was subsequently removed from the stand and the nuclei beads released from the tip by slowly pipetting 1 mL of NPBt in and out of the tip. The solution was then diluted again to 10 mL with NPBt and added again to the slow flow setup. Nuclei beads were eluted in 1 mL of NPBt as described above and the NPBt removed using a ma…	GEO Accession:GSM2436719	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP095522		mpo_RNAseqnuclear_-Mm1_2_run1_R1.fastq.gz mpo_RNAseqnuclear_-Mm1_2_run1_R2.fastq.gz	fastq fastq	3344121365.0	21215427.0	GSM2436719 r1	0:78.80 1:78.82	A:956613483;C:709960019;G:740134318;T:935784812;N:1628733	78	78	956613483	709960019	740134318	935784812	1628733	SRX2439959	SRS1874546	SRA507700	GEO	Sauka-Spengler lab, University of Oxford, MRC Weatherall Institute of Molecular Medicine	2	0.91383	0.91404	0.21292	0.21338	0.76071	0.7666	0.42091	0.44217	80	80	B	B	biological fallback assumption	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United Kingdom	2016-12-22	Multi-stage	Multi-stage	Embryo Imprecise	All anatomical structures
41701	41701	SRR5125202	SRX2439959	SRS1874546	SRP095522	PRJNA358490	Transcriptomic analysis reveals inflammasome dependent mechanism for early neutrophil response to Mycobacterium Marinum	GSE92740	Transcriptome Analysis	The mechanisms that govern the neutrophil response to Mycobacterium tuberculosis remain poorly understood. In this study we utilize an innovative binary approach in zebrafish to perform in depth profiling of the initial response of neutrophils to Mycobacterium marinum by in vivo biotinylation of neutrophil nuclei and subsequent rapid isolation directly from the in vivo context. RNA seq and differential expression analysis of the neutrophil nuclear transcriptome reveals a significant upregulation in both damage sensing and effector components of the inflammasome including caspase b wu:fb15h11 NLRC3 ortholog and il1ß. Crispr/Cas9 mediated knockdown of caspase b which mediates its effects by the proteolytic processing of il1ß results in increased bacterial burden and less infiltration of macrophages to sites of mycobacterium infection thus impairing granuloma development. We also show that a number of immediate early response genes IEGs are responsible for orchestrating the initial response to mycobacterial infection in neutrophils. Further perturbation of the IEGs revealed egr3 as a key transcription factor regulating il1ß transcription. Overall design: We report the design of a binary approach in zebrafish that allows for profiling of the initial response of neutrophils to Mycobacterium Marinum by in vivo biotinylation of neutrophil nuclei and subsequent rapid isolation directly from the in vivo context allowing for RNA seq analysis of the active transcriptome.		pubmed:28747644	mpo RNAseqnuclear Mm1 2	GSM2436719	tissue:mpo RNAseqnuclear Mm1\|strain:Tgmpo:BirA 2A Citrine; bactin:Avi Cerulean Rangap128\|development:3 dpf method:InVivoBiotinylatedNuclei\|treatment:n1\|amplification:SMART seqTMv4\|strand:reverse	mpo RNAseqnuclear Mm1 2	Reads were mapped using STAR v.2.4.2a to danRer10 and read counts were obtained using subreads FeatureCounts Genome build: danRer10 Supplementary files format and content: read counts	mpo RNAseqnuclear Mm1	For M. marinum infection embryos were injected at the 32 512 cell stage with M. marinum	For nuclei isolation zebrafish embryos were anaesthetised with 0.01% Tricaine 0.01% and aggregates of mycobacterium dissected based on tdTomato fluorescence. Embryos were washed in hypotonic buffer H 20 mM HEPES pH 7.9 15 mM MgCl2 10 mM KCl 1 mM DTT and 1 X Complete protease inhibitor and subsequently resuspended in 500 μL of buffer H. Embryos were transferred to a Dounce homogenizer and dissociated by 10 strokes with the loose fitting pestal A and incubated on ice for 5 minutes. Further dissociation was carried out by 10 strokes with tight fitting pestal B every 5 minutes for 15 minutes. Nuclei were collected by centrifugation 2000 g 4 °C and resuspended in 1 mL buffer NDP 10 mM HEPES pH 7.9 40 mM NaCl 90 mM KCl 0.5 mM EDTA 0.5 mM spermidine 0.15 mM spermine 1 mM dithiothreitol and 1 X Complete protease inhibitor. For nuclei purification nuclei were incubated with 5 mg of M 280 streptavidin coated dynabeads with rotation for 30 minutes at 4 °C. A flow based system based on the previously published protocol by was used to capture the nuclei bound on the streptavidin beads. A 10 mL seriological pipette VWR cat # 8913 898 attached to a 1 mL micropipette tip Rainin reach pipet tip cat # RT L1000S both pre treated with NPB/BSA for 30 minutes and added to a MiniMACS separator magnet OctoMACS Separator Miltenyl Biotec cat # 130 042 109. A two way stopcock Biorad cat # 732 8102 was connected to the end of the 1mL micropipette tip via a piece of Tygon tubing Fisher Scientific cat # 8220 and the flow rate set to 0.75 mL/min. The nuclei beads suspension was diluted by addition of 9 mLs of nuclei pulldown buffer with 0.01 % Triton X 100 NPBt and added to the slow flow setup. The tip was subsequently removed from the stand and the nuclei beads released from the tip by slowly pipetting 1 mL of NPBt in and out of the tip. The solution was then diluted again to 10 mL with NPBt and added again to the slow flow setup. Nuclei beads were eluted in 1 mL of NPBt as described above and the NPBt removed using a ma…		strain:Tgmpo:BirA 2A Citrine;bactin:Avi Cerulean Rangap128\|development:3 dpf method:InVivoBiotinylatedNuclei\|treatment:n1\|amplification:SMART seqTMv4\|strand:reverse	GSM2436719	GSM2436719: mpo RNAseqnuclear Mm1 2; Danio rerio; RNA Seq	GSM2436719		1	For nuclei isolation zebrafish embryos were anaesthetised with 0.01% Tricaine 0.01% and aggregates of mycobacterium dissected based on tdTomato fluorescence. Embryos were washed in hypotonic buffer H 20 mM HEPES pH 7.9 15 mM MgCl2 10 mM KCl 1 mM DTT and 1 X Complete protease inhibitor and subsequently resuspended in 500 μL of buffer H. Embryos were transferred to a Dounce homogenizer and dissociated by 10 strokes with the loose fitting pestal A and incubated on ice for 5 minutes. Further dissociation was carried out by 10 strokes with tight fitting pestal B every 5 minutes for 15 minutes. Nuclei were collected by centrifugation 2000 g 4 °C and resuspended in 1 mL buffer NDP 10 mM HEPES pH 7.9 40 mM NaCl 90 mM KCl 0.5 mM EDTA 0.5 mM spermidine 0.15 mM spermine 1 mM dithiothreitol and 1 X Complete protease inhibitor. For nuclei purification nuclei were incubated with 5 mg of M 280 streptavidin coated dynabeads with rotation for 30 minutes at 4 °C. A flow based system based on the previously published protocol by was used to capture the nuclei bound on the streptavidin beads. A 10 mL seriological pipette VWR cat # 8913 898 attached to a 1 mL micropipette tip Rainin reach pipet tip cat # RT L1000S both pre treated with NPB/BSA for 30 minutes and added to a MiniMACS separator magnet OctoMACS Separator Miltenyl Biotec cat # 130 042 109. A two way stopcock Biorad cat # 732 8102 was connected to the end of the 1mL micropipette tip via a piece of Tygon tubing Fisher Scientific cat # 8220 and the flow rate set to 0.75 mL/min. The nuclei beads suspension was diluted by addition of 9 mLs of nuclei pulldown buffer with 0.01 % Triton X 100 NPBt and added to the slow flow setup. The tip was subsequently removed from the stand and the nuclei beads released from the tip by slowly pipetting 1 mL of NPBt in and out of the tip. The solution was then diluted again to 10 mL with NPBt and added again to the slow flow setup. Nuclei beads were eluted in 1 mL of NPBt as described above and the NPBt removed using a ma…	GEO Accession:GSM2436719	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP095522		mpo_RNAseqnuclear_-Mm1_2_run2_R1.fastq.gz mpo_RNAseqnuclear_-Mm1_2_run2_R2.fastq.gz	fastq fastq	668883064.0	4237340.0	GSM2436719 r2	0:78.92 1:78.93	A:188652230;C:142497958;G:148833418;T:188579601;N:319857	78	78	188652230	142497958	148833418	188579601	319857	SRX2439959	SRS1874546	SRA507700	GEO	Sauka-Spengler lab, University of Oxford, MRC Weatherall Institute of Molecular Medicine	2	0.91573	0.91451	0.21119	0.21078	0.76043	0.76731	0.434	0.40897	78	79	B	B	biological fallback assumption	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United Kingdom	2016-12-22	Multi-stage	Multi-stage	Embryo Imprecise	All anatomical structures
41702	41702	SRR5125199	SRX2439958	SRS1874545	SRP095522	PRJNA358490	Transcriptomic analysis reveals inflammasome dependent mechanism for early neutrophil response to Mycobacterium Marinum	GSE92740	Transcriptome Analysis	The mechanisms that govern the neutrophil response to Mycobacterium tuberculosis remain poorly understood. In this study we utilize an innovative binary approach in zebrafish to perform in depth profiling of the initial response of neutrophils to Mycobacterium marinum by in vivo biotinylation of neutrophil nuclei and subsequent rapid isolation directly from the in vivo context. RNA seq and differential expression analysis of the neutrophil nuclear transcriptome reveals a significant upregulation in both damage sensing and effector components of the inflammasome including caspase b wu:fb15h11 NLRC3 ortholog and il1ß. Crispr/Cas9 mediated knockdown of caspase b which mediates its effects by the proteolytic processing of il1ß results in increased bacterial burden and less infiltration of macrophages to sites of mycobacterium infection thus impairing granuloma development. We also show that a number of immediate early response genes IEGs are responsible for orchestrating the initial response to mycobacterial infection in neutrophils. Further perturbation of the IEGs revealed egr3 as a key transcription factor regulating il1ß transcription. Overall design: We report the design of a binary approach in zebrafish that allows for profiling of the initial response of neutrophils to Mycobacterium Marinum by in vivo biotinylation of neutrophil nuclei and subsequent rapid isolation directly from the in vivo context allowing for RNA seq analysis of the active transcriptome.		pubmed:28747644	mpo RNAseqnuclear Mm1 1	GSM2436718	tissue:mpo RNAseqnuclear Mm1\|strain:Tgmpo:BirA 2A Citrine; bactin:Avi Cerulean Rangap128\|development:3 dpf method:InVivoBiotinylatedNuclei\|treatment:n1\|amplification:SMART seqTMv4\|strand:reverse	mpo RNAseqnuclear Mm1 1	Reads were mapped using STAR v.2.4.2a to danRer10 and read counts were obtained using subreads FeatureCounts Genome build: danRer10 Supplementary files format and content: read counts	mpo RNAseqnuclear Mm1	For M. marinum infection embryos were injected at the 32 512 cell stage with M. marinum	For nuclei isolation zebrafish embryos were anaesthetised with 0.01% Tricaine 0.01% and aggregates of mycobacterium dissected based on tdTomato fluorescence. Embryos were washed in hypotonic buffer H 20 mM HEPES pH 7.9 15 mM MgCl2 10 mM KCl 1 mM DTT and 1 X Complete protease inhibitor and subsequently resuspended in 500 μL of buffer H. Embryos were transferred to a Dounce homogenizer and dissociated by 10 strokes with the loose fitting pestal A and incubated on ice for 5 minutes. Further dissociation was carried out by 10 strokes with tight fitting pestal B every 5 minutes for 15 minutes. Nuclei were collected by centrifugation 2000 g 4 °C and resuspended in 1 mL buffer NDP 10 mM HEPES pH 7.9 40 mM NaCl 90 mM KCl 0.5 mM EDTA 0.5 mM spermidine 0.15 mM spermine 1 mM dithiothreitol and 1 X Complete protease inhibitor. For nuclei purification nuclei were incubated with 5 mg of M 280 streptavidin coated dynabeads with rotation for 30 minutes at 4 °C. A flow based system based on the previously published protocol by was used to capture the nuclei bound on the streptavidin beads. A 10 mL seriological pipette VWR cat # 8913 898 attached to a 1 mL micropipette tip Rainin reach pipet tip cat # RT L1000S both pre treated with NPB/BSA for 30 minutes and added to a MiniMACS separator magnet OctoMACS Separator Miltenyl Biotec cat # 130 042 109. A two way stopcock Biorad cat # 732 8102 was connected to the end of the 1mL micropipette tip via a piece of Tygon tubing Fisher Scientific cat # 8220 and the flow rate set to 0.75 mL/min. The nuclei beads suspension was diluted by addition of 9 mLs of nuclei pulldown buffer with 0.01 % Triton X 100 NPBt and added to the slow flow setup. The tip was subsequently removed from the stand and the nuclei beads released from the tip by slowly pipetting 1 mL of NPBt in and out of the tip. The solution was then diluted again to 10 mL with NPBt and added again to the slow flow setup. Nuclei beads were eluted in 1 mL of NPBt as described above and the NPBt removed using a ma…		strain:Tgmpo:BirA 2A Citrine;bactin:Avi Cerulean Rangap128\|development:3 dpf method:InVivoBiotinylatedNuclei\|treatment:n1\|amplification:SMART seqTMv4\|strand:reverse	GSM2436718	GSM2436718: mpo RNAseqnuclear Mm1 1; Danio rerio; RNA Seq	GSM2436718		1	For nuclei isolation zebrafish embryos were anaesthetised with 0.01% Tricaine 0.01% and aggregates of mycobacterium dissected based on tdTomato fluorescence. Embryos were washed in hypotonic buffer H 20 mM HEPES pH 7.9 15 mM MgCl2 10 mM KCl 1 mM DTT and 1 X Complete protease inhibitor and subsequently resuspended in 500 μL of buffer H. Embryos were transferred to a Dounce homogenizer and dissociated by 10 strokes with the loose fitting pestal A and incubated on ice for 5 minutes. Further dissociation was carried out by 10 strokes with tight fitting pestal B every 5 minutes for 15 minutes. Nuclei were collected by centrifugation 2000 g 4 °C and resuspended in 1 mL buffer NDP 10 mM HEPES pH 7.9 40 mM NaCl 90 mM KCl 0.5 mM EDTA 0.5 mM spermidine 0.15 mM spermine 1 mM dithiothreitol and 1 X Complete protease inhibitor. For nuclei purification nuclei were incubated with 5 mg of M 280 streptavidin coated dynabeads with rotation for 30 minutes at 4 °C. A flow based system based on the previously published protocol by was used to capture the nuclei bound on the streptavidin beads. A 10 mL seriological pipette VWR cat # 8913 898 attached to a 1 mL micropipette tip Rainin reach pipet tip cat # RT L1000S both pre treated with NPB/BSA for 30 minutes and added to a MiniMACS separator magnet OctoMACS Separator Miltenyl Biotec cat # 130 042 109. A two way stopcock Biorad cat # 732 8102 was connected to the end of the 1mL micropipette tip via a piece of Tygon tubing Fisher Scientific cat # 8220 and the flow rate set to 0.75 mL/min. The nuclei beads suspension was diluted by addition of 9 mLs of nuclei pulldown buffer with 0.01 % Triton X 100 NPBt and added to the slow flow setup. The tip was subsequently removed from the stand and the nuclei beads released from the tip by slowly pipetting 1 mL of NPBt in and out of the tip. The solution was then diluted again to 10 mL with NPBt and added again to the slow flow setup. Nuclei beads were eluted in 1 mL of NPBt as described above and the NPBt removed using a ma…	GEO Accession:GSM2436718	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP095522		mpo_RNAseqnuclear_-Mm1_1_run1_R1.fastq.gz mpo_RNAseqnuclear_-Mm1_1_run1_R2.fastq.gz	fastq fastq	2474265647.0	15682298.0	GSM2436718 r1	0:78.87 1:78.90	A:722401448;C:503136653;G:532320879;T:714968531;N:1438136	78	78	722401448	503136653	532320879	714968531	1438136	SRX2439958	SRS1874545	SRA507700	GEO	Sauka-Spengler lab, University of Oxford, MRC Weatherall Institute of Molecular Medicine	2	0.84335	0.84549	0.23871	0.23651	0.79882	0.80598	0.44178	0.41429	80	68	B	B	biological fallback assumption	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United Kingdom	2016-12-22	Multi-stage	Multi-stage	Embryo Imprecise	All anatomical structures
41703	41703	SRR5125200	SRX2439958	SRS1874545	SRP095522	PRJNA358490	Transcriptomic analysis reveals inflammasome dependent mechanism for early neutrophil response to Mycobacterium Marinum	GSE92740	Transcriptome Analysis	The mechanisms that govern the neutrophil response to Mycobacterium tuberculosis remain poorly understood. In this study we utilize an innovative binary approach in zebrafish to perform in depth profiling of the initial response of neutrophils to Mycobacterium marinum by in vivo biotinylation of neutrophil nuclei and subsequent rapid isolation directly from the in vivo context. RNA seq and differential expression analysis of the neutrophil nuclear transcriptome reveals a significant upregulation in both damage sensing and effector components of the inflammasome including caspase b wu:fb15h11 NLRC3 ortholog and il1ß. Crispr/Cas9 mediated knockdown of caspase b which mediates its effects by the proteolytic processing of il1ß results in increased bacterial burden and less infiltration of macrophages to sites of mycobacterium infection thus impairing granuloma development. We also show that a number of immediate early response genes IEGs are responsible for orchestrating the initial response to mycobacterial infection in neutrophils. Further perturbation of the IEGs revealed egr3 as a key transcription factor regulating il1ß transcription. Overall design: We report the design of a binary approach in zebrafish that allows for profiling of the initial response of neutrophils to Mycobacterium Marinum by in vivo biotinylation of neutrophil nuclei and subsequent rapid isolation directly from the in vivo context allowing for RNA seq analysis of the active transcriptome.		pubmed:28747644	mpo RNAseqnuclear Mm1 1	GSM2436718	tissue:mpo RNAseqnuclear Mm1\|strain:Tgmpo:BirA 2A Citrine; bactin:Avi Cerulean Rangap128\|development:3 dpf method:InVivoBiotinylatedNuclei\|treatment:n1\|amplification:SMART seqTMv4\|strand:reverse	mpo RNAseqnuclear Mm1 1	Reads were mapped using STAR v.2.4.2a to danRer10 and read counts were obtained using subreads FeatureCounts Genome build: danRer10 Supplementary files format and content: read counts	mpo RNAseqnuclear Mm1	For M. marinum infection embryos were injected at the 32 512 cell stage with M. marinum	For nuclei isolation zebrafish embryos were anaesthetised with 0.01% Tricaine 0.01% and aggregates of mycobacterium dissected based on tdTomato fluorescence. Embryos were washed in hypotonic buffer H 20 mM HEPES pH 7.9 15 mM MgCl2 10 mM KCl 1 mM DTT and 1 X Complete protease inhibitor and subsequently resuspended in 500 μL of buffer H. Embryos were transferred to a Dounce homogenizer and dissociated by 10 strokes with the loose fitting pestal A and incubated on ice for 5 minutes. Further dissociation was carried out by 10 strokes with tight fitting pestal B every 5 minutes for 15 minutes. Nuclei were collected by centrifugation 2000 g 4 °C and resuspended in 1 mL buffer NDP 10 mM HEPES pH 7.9 40 mM NaCl 90 mM KCl 0.5 mM EDTA 0.5 mM spermidine 0.15 mM spermine 1 mM dithiothreitol and 1 X Complete protease inhibitor. For nuclei purification nuclei were incubated with 5 mg of M 280 streptavidin coated dynabeads with rotation for 30 minutes at 4 °C. A flow based system based on the previously published protocol by was used to capture the nuclei bound on the streptavidin beads. A 10 mL seriological pipette VWR cat # 8913 898 attached to a 1 mL micropipette tip Rainin reach pipet tip cat # RT L1000S both pre treated with NPB/BSA for 30 minutes and added to a MiniMACS separator magnet OctoMACS Separator Miltenyl Biotec cat # 130 042 109. A two way stopcock Biorad cat # 732 8102 was connected to the end of the 1mL micropipette tip via a piece of Tygon tubing Fisher Scientific cat # 8220 and the flow rate set to 0.75 mL/min. The nuclei beads suspension was diluted by addition of 9 mLs of nuclei pulldown buffer with 0.01 % Triton X 100 NPBt and added to the slow flow setup. The tip was subsequently removed from the stand and the nuclei beads released from the tip by slowly pipetting 1 mL of NPBt in and out of the tip. The solution was then diluted again to 10 mL with NPBt and added again to the slow flow setup. Nuclei beads were eluted in 1 mL of NPBt as described above and the NPBt removed using a ma…		strain:Tgmpo:BirA 2A Citrine;bactin:Avi Cerulean Rangap128\|development:3 dpf method:InVivoBiotinylatedNuclei\|treatment:n1\|amplification:SMART seqTMv4\|strand:reverse	GSM2436718	GSM2436718: mpo RNAseqnuclear Mm1 1; Danio rerio; RNA Seq	GSM2436718		1	For nuclei isolation zebrafish embryos were anaesthetised with 0.01% Tricaine 0.01% and aggregates of mycobacterium dissected based on tdTomato fluorescence. Embryos were washed in hypotonic buffer H 20 mM HEPES pH 7.9 15 mM MgCl2 10 mM KCl 1 mM DTT and 1 X Complete protease inhibitor and subsequently resuspended in 500 μL of buffer H. Embryos were transferred to a Dounce homogenizer and dissociated by 10 strokes with the loose fitting pestal A and incubated on ice for 5 minutes. Further dissociation was carried out by 10 strokes with tight fitting pestal B every 5 minutes for 15 minutes. Nuclei were collected by centrifugation 2000 g 4 °C and resuspended in 1 mL buffer NDP 10 mM HEPES pH 7.9 40 mM NaCl 90 mM KCl 0.5 mM EDTA 0.5 mM spermidine 0.15 mM spermine 1 mM dithiothreitol and 1 X Complete protease inhibitor. For nuclei purification nuclei were incubated with 5 mg of M 280 streptavidin coated dynabeads with rotation for 30 minutes at 4 °C. A flow based system based on the previously published protocol by was used to capture the nuclei bound on the streptavidin beads. A 10 mL seriological pipette VWR cat # 8913 898 attached to a 1 mL micropipette tip Rainin reach pipet tip cat # RT L1000S both pre treated with NPB/BSA for 30 minutes and added to a MiniMACS separator magnet OctoMACS Separator Miltenyl Biotec cat # 130 042 109. A two way stopcock Biorad cat # 732 8102 was connected to the end of the 1mL micropipette tip via a piece of Tygon tubing Fisher Scientific cat # 8220 and the flow rate set to 0.75 mL/min. The nuclei beads suspension was diluted by addition of 9 mLs of nuclei pulldown buffer with 0.01 % Triton X 100 NPBt and added to the slow flow setup. The tip was subsequently removed from the stand and the nuclei beads released from the tip by slowly pipetting 1 mL of NPBt in and out of the tip. The solution was then diluted again to 10 mL with NPBt and added again to the slow flow setup. Nuclei beads were eluted in 1 mL of NPBt as described above and the NPBt removed using a ma…	GEO Accession:GSM2436718	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP095522		mpo_RNAseqnuclear_-Mm1_1_run2_R1.fastq.gz mpo_RNAseqnuclear_-Mm1_1_run2_R2.fastq.gz	fastq fastq	1177116054.0	7447879.0	GSM2436718 r2	0:79.01 1:79.03	A:331669376;C:242671148;G:257549828;T:344608431;N:617271	79	79	331669376	242671148	257549828	344608431	617271	SRX2439958	SRS1874545	SRA507700	GEO	Sauka-Spengler lab, University of Oxford, MRC Weatherall Institute of Molecular Medicine	2	0.8513	0.84944	0.23288	0.23032	0.79904	0.80643	0.44928	0.43423	65	65	B	B	biological fallback assumption	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United Kingdom	2016-12-22	Multi-stage	Multi-stage	Embryo Imprecise	All anatomical structures
41908	41908	SRR5338229	SRX2635543	SRS2044322	SRP101781	PRJNA378947	Generation of a binary transgenic zebrafish model to study myeloid gene regulation in response to pre neoplastic melanocytes	GSE96534	Transcriptome Analysis	A complex network of inflammation succeeds somatic cell transformation and malignant disease. Immune cells and their associated molecules are responsible for detecting and eliminating cancer cells as they establish themselves as the precursors of a tumour. By the time a patient has a detectable solid tumour cancer cells have escaped the initial immune response mechanisms. To date no model exists to allow us to study the underlying mechanisms that govern the initial phase of the immune response as cells are transformed to become the precursors of cancer. Here we describe the development of an innovative double binary animal model designed in zebrafish for exploring regulatory programming of the myeloid cells as they respond to oncogenic transformed melanocytes. This modular system harnesses the power of zebrafish genetics. For studies of melanocyte transformation we generated a hormone inducible binary system allowing for temporal control of different Ras oncogene NRasK61Q HRasG12V KRasG12V expression in melanocytes allowing us to truly study melanoma initiation. This binary model was then coupled to a model for regulatory profiling of the active transcriptome of macrophages and neutrophils which is based on the in vivo biotinylation of nuclei and their subsequent isolation by streptavidin affinity purification. For the first time regulatory profiling of neutrophils as they respond to the earliest precursors of melanoma revealed a number of factors upregulated in neutrophils that may promote progression to melanoma including fgf1 fgf6 cathepsin H cathepsin L galectin 1 and galectin 3. Overall design: We report the design of a double binary approach in zebrafish to study the neutrophil response to transformed melanocytes. By coupling a novel inducible model for melanocyte transformation to a model for the in vivo biotinylation of neutrophil nuclei we can isolate the neutrophil nuclei directly from the in vivo context allowing for RNA seq analysis of the active transcriptome.		pubmed:29666124	mpo RNAseqnuclear +mifNRas+ 2	GSM2535110	tissue:mpo RNAseqnuclear +mif head 2\|strain:Tgmpo:BirA Citrine; bactin:Avi Cerulean Rangapox128 X Tgkita:LexPR Cerulean; PcrysB:ECFP LexOP:mCherry NRasox130\|development:5 dpf method:In Vivo Biotinylated Nuclei\|treatment:1 μM mifeprist1 added to embryo water from 24 hpf\|amplification:SMART seqTMv4\|strand:reverse\|assay:RNA seq	mpo RNAseqnuclear +mifNRas+ 2	Reads were mapped using STAR v.2.4.2a to danRer10 and read counts were obtained using subreads FeatureCounts Genome build: danRer10 Supplementary files format and content: counts	mpo RNAseqnuclear +mif head 2	Incrossed larvae were treated with 1 μM from 24 hpf	For nuclei isolation zebrafish embryos were anaesthetised with 0.01% Tricaine and embryos dissected to separate the head from the trunk and tail. Heads were washed in hypotonic buffer H 20 mM HEPES pH 7.9 15 mM MgCl2 10 mM KCl 1 mM DTT and 1 X Complete protease inhibitor and subsequently resuspended in 500 μL of buffer H. Embryos were transferred to a Dounce homogenizer and dissociated by 10 strokes with the loose fitting pestal A and incubated on ice for 5 minutes. Further dissociation was carried out by 10 strokes with tight fitting pestal B every 5 minutes for 15 minutes. Nuclei were collected by centrifugation 2000 g 4 °C and resuspended in 1 mL buffer NDP 10 mM HEPES pH 7.9 40 mM NaCl 90 mM KCl 0.5 mM EDTA 0.5 mM spermidine 0.15 mM spermine 1 mM dithiothreitol and 1 X Complete protease inhibitor. For nuclei purification nuclei were incubated with 5 mg of M 280 streptavidin coated dynabeads with rotation for 30 minutes at 4 °C. A flow based system based on the previously published protocol by was used to capture the nuclei bound on the streptavidin beads. A 10 mL seriological pipette VWR cat # 8913 898 attached to a 1 mL micropipette tip Rainin reach pipet tip cat # RT L1000S both pre treated with NPB/BSA for 30 minutes and added to a MiniMACS separator magnet OctoMACS Separator Miltenyl Biotec cat # 130 042 109. A two way stopcock Biorad cat # 732 8102 was connected to the end of the 1mL micropipette tip via a piece of Tygon tubing Fisher Scientific cat # 8220 and the flow rate set to 0.75 mL/min. The nuclei beads suspension was diluted by addition of 9 mLs of nuclei pulldown buffer with 0.01 % Triton X 100 NPBt and added to the slow flow setup. The tip was subsequently removed from the stand and the nuclei beads released from the tip by slowly pipetting 1 mL of NPBt in and out of the tip. The solution was then diluted again to 10 mL with NPBt and added again to the slow flow setup. Nuclei beads were eluted in 1 mL of NPBt as described above and the NPBt removed using a magnetic stand D…		strain:Tgmpo:BirA Citrine;bactin:Avi Cerulean Rangapox128 X Tgkita:LexPR Cerulean;PcrysB:ECFP LexOP:mCherry NRasox130\|development:5 dpf method:In Vivo Biotinylated Nuclei\|treatment:1 μM mifeprist1 added to embryo water from 24 hpf\|amplification:SMART seqTMv4\|strand:reverse\|assay:RNA seq	GSM2535110	GSM2535110: mpo RNAseqnuclear +mifNRas+ 2; Danio rerio; RNA Seq	GSM2535110		1	For nuclei isolation zebrafish embryos were anaesthetised with 0.01% Tricaine and embryos dissected to separate the head from the trunk and tail. Heads were washed in hypotonic buffer H 20 mM HEPES pH 7.9 15 mM MgCl2 10 mM KCl 1 mM DTT and 1 X Complete protease inhibitor and subsequently resuspended in 500 μL of buffer H. Embryos were transferred to a Dounce homogenizer and dissociated by 10 strokes with the loose fitting pestal A and incubated on ice for 5 minutes. Further dissociation was carried out by 10 strokes with tight fitting pestal B every 5 minutes for 15 minutes. Nuclei were collected by centrifugation 2000 g 4 °C and resuspended in 1 mL buffer NDP 10 mM HEPES pH 7.9 40 mM NaCl 90 mM KCl 0.5 mM EDTA 0.5 mM spermidine 0.15 mM spermine 1 mM dithiothreitol and 1 X Complete protease inhibitor. For nuclei purification nuclei were incubated with 5 mg of M 280 streptavidin coated dynabeads with rotation for 30 minutes at 4 °C. A flow based system based on the previously published protocol by was used to capture the nuclei bound on the streptavidin beads. A 10 mL seriological pipette VWR cat # 8913 898 attached to a 1 mL micropipette tip Rainin reach pipet tip cat # RT L1000S both pre treated with NPB/BSA for 30 minutes and added to a MiniMACS separator magnet OctoMACS Separator Miltenyl Biotec cat # 130 042 109. A two way stopcock Biorad cat # 732 8102 was connected to the end of the 1mL micropipette tip via a piece of Tygon tubing Fisher Scientific cat # 8220 and the flow rate set to 0.75 mL/min. The nuclei beads suspension was diluted by addition of 9 mLs of nuclei pulldown buffer with 0.01 % Triton X 100 NPBt and added to the slow flow setup. The tip was subsequently removed from the stand and the nuclei beads released from the tip by slowly pipetting 1 mL of NPBt in and out of the tip. The solution was then diluted again to 10 mL with NPBt and added again to the slow flow setup. Nuclei beads were eluted in 1 mL of NPBt as described above and the NPBt removed using a magnetic stand D…	GEO Accession:GSM2535110	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP101781		shead_mif2Aligned.out.sort.bam	bam	7581928543.0	47699195.0	GSM2535110 r1	0:79.48 1:79.48	A:2083595704;C:1751859031;G:1833743542;T:1912626493;N:103773	79	79	2083595704	1751859031	1833743542	1912626493	103773	SRX2635543	SRS2044322	SRA544939	GEO	Sauka-Spengler lab, University of Oxford, MRC Weatherall Institute of Molecular Medicine	2	0.93437	0.93246	0.08098	0.08538	0.78589	0.79125	0.39046	0.38599	80	80	B	B	biological fallback assumption	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United Kingdom	2017-03-13	Multi-stage	Multi-stage	Head	Nervous System
41909	41909	SRR5338228	SRX2635542	SRS2044321	SRP101781	PRJNA378947	Generation of a binary transgenic zebrafish model to study myeloid gene regulation in response to pre neoplastic melanocytes	GSE96534	Transcriptome Analysis	A complex network of inflammation succeeds somatic cell transformation and malignant disease. Immune cells and their associated molecules are responsible for detecting and eliminating cancer cells as they establish themselves as the precursors of a tumour. By the time a patient has a detectable solid tumour cancer cells have escaped the initial immune response mechanisms. To date no model exists to allow us to study the underlying mechanisms that govern the initial phase of the immune response as cells are transformed to become the precursors of cancer. Here we describe the development of an innovative double binary animal model designed in zebrafish for exploring regulatory programming of the myeloid cells as they respond to oncogenic transformed melanocytes. This modular system harnesses the power of zebrafish genetics. For studies of melanocyte transformation we generated a hormone inducible binary system allowing for temporal control of different Ras oncogene NRasK61Q HRasG12V KRasG12V expression in melanocytes allowing us to truly study melanoma initiation. This binary model was then coupled to a model for regulatory profiling of the active transcriptome of macrophages and neutrophils which is based on the in vivo biotinylation of nuclei and their subsequent isolation by streptavidin affinity purification. For the first time regulatory profiling of neutrophils as they respond to the earliest precursors of melanoma revealed a number of factors upregulated in neutrophils that may promote progression to melanoma including fgf1 fgf6 cathepsin H cathepsin L galectin 1 and galectin 3. Overall design: We report the design of a double binary approach in zebrafish to study the neutrophil response to transformed melanocytes. By coupling a novel inducible model for melanocyte transformation to a model for the in vivo biotinylation of neutrophil nuclei we can isolate the neutrophil nuclei directly from the in vivo context allowing for RNA seq analysis of the active transcriptome.		pubmed:29666124	mpo RNAseqnuclear +mifNRas+ 1	GSM2535109	tissue:mpo RNAseqnuclear +mif head 1\|strain:Tgmpo:BirA Citrine; bactin:Avi Cerulean Rangapox128 X Tgkita:LexPR Cerulean; PcrysB:ECFP LexOP:mCherry NRasox130\|development:5 dpf method:In Vivo Biotinylated Nuclei\|treatment:1 μM mifeprist1 added to embryo water from 24 hpf\|amplification:SMART seqTMv4\|strand:reverse\|assay:RNA seq	mpo RNAseqnuclear +mifNRas+ 1	Reads were mapped using STAR v.2.4.2a to danRer10 and read counts were obtained using subreads FeatureCounts Genome build: danRer10 Supplementary files format and content: counts	mpo RNAseqnuclear +mif head 1	Incrossed larvae were treated with 1 μM from 24 hpf	For nuclei isolation zebrafish embryos were anaesthetised with 0.01% Tricaine and embryos dissected to separate the head from the trunk and tail. Heads were washed in hypotonic buffer H 20 mM HEPES pH 7.9 15 mM MgCl2 10 mM KCl 1 mM DTT and 1 X Complete protease inhibitor and subsequently resuspended in 500 μL of buffer H. Embryos were transferred to a Dounce homogenizer and dissociated by 10 strokes with the loose fitting pestal A and incubated on ice for 5 minutes. Further dissociation was carried out by 10 strokes with tight fitting pestal B every 5 minutes for 15 minutes. Nuclei were collected by centrifugation 2000 g 4 °C and resuspended in 1 mL buffer NDP 10 mM HEPES pH 7.9 40 mM NaCl 90 mM KCl 0.5 mM EDTA 0.5 mM spermidine 0.15 mM spermine 1 mM dithiothreitol and 1 X Complete protease inhibitor. For nuclei purification nuclei were incubated with 5 mg of M 280 streptavidin coated dynabeads with rotation for 30 minutes at 4 °C. A flow based system based on the previously published protocol by was used to capture the nuclei bound on the streptavidin beads. A 10 mL seriological pipette VWR cat # 8913 898 attached to a 1 mL micropipette tip Rainin reach pipet tip cat # RT L1000S both pre treated with NPB/BSA for 30 minutes and added to a MiniMACS separator magnet OctoMACS Separator Miltenyl Biotec cat # 130 042 109. A two way stopcock Biorad cat # 732 8102 was connected to the end of the 1mL micropipette tip via a piece of Tygon tubing Fisher Scientific cat # 8220 and the flow rate set to 0.75 mL/min. The nuclei beads suspension was diluted by addition of 9 mLs of nuclei pulldown buffer with 0.01 % Triton X 100 NPBt and added to the slow flow setup. The tip was subsequently removed from the stand and the nuclei beads released from the tip by slowly pipetting 1 mL of NPBt in and out of the tip. The solution was then diluted again to 10 mL with NPBt and added again to the slow flow setup. Nuclei beads were eluted in 1 mL of NPBt as described above and the NPBt removed using a magnetic stand D…		strain:Tgmpo:BirA Citrine;bactin:Avi Cerulean Rangapox128 X Tgkita:LexPR Cerulean;PcrysB:ECFP LexOP:mCherry NRasox130\|development:5 dpf method:In Vivo Biotinylated Nuclei\|treatment:1 μM mifeprist1 added to embryo water from 24 hpf\|amplification:SMART seqTMv4\|strand:reverse\|assay:RNA seq	GSM2535109	GSM2535109: mpo RNAseqnuclear +mifNRas+ 1; Danio rerio; RNA Seq	GSM2535109		1	For nuclei isolation zebrafish embryos were anaesthetised with 0.01% Tricaine and embryos dissected to separate the head from the trunk and tail. Heads were washed in hypotonic buffer H 20 mM HEPES pH 7.9 15 mM MgCl2 10 mM KCl 1 mM DTT and 1 X Complete protease inhibitor and subsequently resuspended in 500 μL of buffer H. Embryos were transferred to a Dounce homogenizer and dissociated by 10 strokes with the loose fitting pestal A and incubated on ice for 5 minutes. Further dissociation was carried out by 10 strokes with tight fitting pestal B every 5 minutes for 15 minutes. Nuclei were collected by centrifugation 2000 g 4 °C and resuspended in 1 mL buffer NDP 10 mM HEPES pH 7.9 40 mM NaCl 90 mM KCl 0.5 mM EDTA 0.5 mM spermidine 0.15 mM spermine 1 mM dithiothreitol and 1 X Complete protease inhibitor. For nuclei purification nuclei were incubated with 5 mg of M 280 streptavidin coated dynabeads with rotation for 30 minutes at 4 °C. A flow based system based on the previously published protocol by was used to capture the nuclei bound on the streptavidin beads. A 10 mL seriological pipette VWR cat # 8913 898 attached to a 1 mL micropipette tip Rainin reach pipet tip cat # RT L1000S both pre treated with NPB/BSA for 30 minutes and added to a MiniMACS separator magnet OctoMACS Separator Miltenyl Biotec cat # 130 042 109. A two way stopcock Biorad cat # 732 8102 was connected to the end of the 1mL micropipette tip via a piece of Tygon tubing Fisher Scientific cat # 8220 and the flow rate set to 0.75 mL/min. The nuclei beads suspension was diluted by addition of 9 mLs of nuclei pulldown buffer with 0.01 % Triton X 100 NPBt and added to the slow flow setup. The tip was subsequently removed from the stand and the nuclei beads released from the tip by slowly pipetting 1 mL of NPBt in and out of the tip. The solution was then diluted again to 10 mL with NPBt and added again to the slow flow setup. Nuclei beads were eluted in 1 mL of NPBt as described above and the NPBt removed using a magnetic stand D…	GEO Accession:GSM2535109	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP101781		shead_mif1Aligned.out.sort.bam	bam	7904423201.0	49746704.0	GSM2535109 r1	0:79.45 1:79.45	A:2153404550;C:1843316968;G:1926669197;T:1980935189;N:97297	79	79	2153404550	1843316968	1926669197	1980935189	97297	SRX2635542	SRS2044321	SRA544939	GEO	Sauka-Spengler lab, University of Oxford, MRC Weatherall Institute of Molecular Medicine	2	0.9341	0.931	0.07739	0.07981	0.79971	0.80568	0.38474	0.38892	80	80	B	B	biological fallback assumption	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United Kingdom	2017-03-13	Multi-stage	Multi-stage	Head	Nervous System
41910	41910	SRR5338227	SRX2635541	SRS2044320	SRP101781	PRJNA378947	Generation of a binary transgenic zebrafish model to study myeloid gene regulation in response to pre neoplastic melanocytes	GSE96534	Transcriptome Analysis	A complex network of inflammation succeeds somatic cell transformation and malignant disease. Immune cells and their associated molecules are responsible for detecting and eliminating cancer cells as they establish themselves as the precursors of a tumour. By the time a patient has a detectable solid tumour cancer cells have escaped the initial immune response mechanisms. To date no model exists to allow us to study the underlying mechanisms that govern the initial phase of the immune response as cells are transformed to become the precursors of cancer. Here we describe the development of an innovative double binary animal model designed in zebrafish for exploring regulatory programming of the myeloid cells as they respond to oncogenic transformed melanocytes. This modular system harnesses the power of zebrafish genetics. For studies of melanocyte transformation we generated a hormone inducible binary system allowing for temporal control of different Ras oncogene NRasK61Q HRasG12V KRasG12V expression in melanocytes allowing us to truly study melanoma initiation. This binary model was then coupled to a model for regulatory profiling of the active transcriptome of macrophages and neutrophils which is based on the in vivo biotinylation of nuclei and their subsequent isolation by streptavidin affinity purification. For the first time regulatory profiling of neutrophils as they respond to the earliest precursors of melanoma revealed a number of factors upregulated in neutrophils that may promote progression to melanoma including fgf1 fgf6 cathepsin H cathepsin L galectin 1 and galectin 3. Overall design: We report the design of a double binary approach in zebrafish to study the neutrophil response to transformed melanocytes. By coupling a novel inducible model for melanocyte transformation to a model for the in vivo biotinylation of neutrophil nuclei we can isolate the neutrophil nuclei directly from the in vivo context allowing for RNA seq analysis of the active transcriptome.		pubmed:29666124	mpo RNAseqnuclear mifcntrl 2	GSM2535108	tissue:mpo RNAseqnuclear mif head 2\|strain:Tgmpo:BirA Citrine; bactin:Avi Cerulean Rangapox128 X Tgkita:LexPR Cerulean; PcrysB:ECFP LexOP:mCherry NRasox130\|development:5 dpf method:In Vivo Biotinylated Nuclei\|treatment:n1\|amplification:SMART seqTMv4\|strand:reverse\|assay:RNA seq	mpo RNAseqnuclear mifcntrl 2	Reads were mapped using STAR v.2.4.2a to danRer10 and read counts were obtained using subreads FeatureCounts Genome build: danRer10 Supplementary files format and content: counts	mpo RNAseqnuclear mif head 2	Incrossed larvae were treated with 1 μM from 24 hpf	For nuclei isolation zebrafish embryos were anaesthetised with 0.01% Tricaine and embryos dissected to separate the head from the trunk and tail. Heads were washed in hypotonic buffer H 20 mM HEPES pH 7.9 15 mM MgCl2 10 mM KCl 1 mM DTT and 1 X Complete protease inhibitor and subsequently resuspended in 500 μL of buffer H. Embryos were transferred to a Dounce homogenizer and dissociated by 10 strokes with the loose fitting pestal A and incubated on ice for 5 minutes. Further dissociation was carried out by 10 strokes with tight fitting pestal B every 5 minutes for 15 minutes. Nuclei were collected by centrifugation 2000 g 4 °C and resuspended in 1 mL buffer NDP 10 mM HEPES pH 7.9 40 mM NaCl 90 mM KCl 0.5 mM EDTA 0.5 mM spermidine 0.15 mM spermine 1 mM dithiothreitol and 1 X Complete protease inhibitor. For nuclei purification nuclei were incubated with 5 mg of M 280 streptavidin coated dynabeads with rotation for 30 minutes at 4 °C. A flow based system based on the previously published protocol by was used to capture the nuclei bound on the streptavidin beads. A 10 mL seriological pipette VWR cat # 8913 898 attached to a 1 mL micropipette tip Rainin reach pipet tip cat # RT L1000S both pre treated with NPB/BSA for 30 minutes and added to a MiniMACS separator magnet OctoMACS Separator Miltenyl Biotec cat # 130 042 109. A two way stopcock Biorad cat # 732 8102 was connected to the end of the 1mL micropipette tip via a piece of Tygon tubing Fisher Scientific cat # 8220 and the flow rate set to 0.75 mL/min. The nuclei beads suspension was diluted by addition of 9 mLs of nuclei pulldown buffer with 0.01 % Triton X 100 NPBt and added to the slow flow setup. The tip was subsequently removed from the stand and the nuclei beads released from the tip by slowly pipetting 1 mL of NPBt in and out of the tip. The solution was then diluted again to 10 mL with NPBt and added again to the slow flow setup. Nuclei beads were eluted in 1 mL of NPBt as described above and the NPBt removed using a magnetic stand D…		strain:Tgmpo:BirA Citrine;bactin:Avi Cerulean Rangapox128 X Tgkita:LexPR Cerulean;PcrysB:ECFP LexOP:mCherry NRasox130\|development:5 dpf method:In Vivo Biotinylated Nuclei\|treatment:n1\|amplification:SMART seqTMv4\|strand:reverse\|assay:RNA seq	GSM2535108	GSM2535108: mpo RNAseqnuclear mifcntrl 2; Danio rerio; RNA Seq	GSM2535108		1	For nuclei isolation zebrafish embryos were anaesthetised with 0.01% Tricaine and embryos dissected to separate the head from the trunk and tail. Heads were washed in hypotonic buffer H 20 mM HEPES pH 7.9 15 mM MgCl2 10 mM KCl 1 mM DTT and 1 X Complete protease inhibitor and subsequently resuspended in 500 μL of buffer H. Embryos were transferred to a Dounce homogenizer and dissociated by 10 strokes with the loose fitting pestal A and incubated on ice for 5 minutes. Further dissociation was carried out by 10 strokes with tight fitting pestal B every 5 minutes for 15 minutes. Nuclei were collected by centrifugation 2000 g 4 °C and resuspended in 1 mL buffer NDP 10 mM HEPES pH 7.9 40 mM NaCl 90 mM KCl 0.5 mM EDTA 0.5 mM spermidine 0.15 mM spermine 1 mM dithiothreitol and 1 X Complete protease inhibitor. For nuclei purification nuclei were incubated with 5 mg of M 280 streptavidin coated dynabeads with rotation for 30 minutes at 4 °C. A flow based system based on the previously published protocol by was used to capture the nuclei bound on the streptavidin beads. A 10 mL seriological pipette VWR cat # 8913 898 attached to a 1 mL micropipette tip Rainin reach pipet tip cat # RT L1000S both pre treated with NPB/BSA for 30 minutes and added to a MiniMACS separator magnet OctoMACS Separator Miltenyl Biotec cat # 130 042 109. A two way stopcock Biorad cat # 732 8102 was connected to the end of the 1mL micropipette tip via a piece of Tygon tubing Fisher Scientific cat # 8220 and the flow rate set to 0.75 mL/min. The nuclei beads suspension was diluted by addition of 9 mLs of nuclei pulldown buffer with 0.01 % Triton X 100 NPBt and added to the slow flow setup. The tip was subsequently removed from the stand and the nuclei beads released from the tip by slowly pipetting 1 mL of NPBt in and out of the tip. The solution was then diluted again to 10 mL with NPBt and added again to the slow flow setup. Nuclei beads were eluted in 1 mL of NPBt as described above and the NPBt removed using a magnetic stand D…	GEO Accession:GSM2535108	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP101781		shead2Aligned.out.sort.bam	bam	8216508851.0	51890331.0	GSM2535108 r1	0:79.18 1:79.17	A:2297720467;C:1839611761;G:1894426911;T:2184654439;N:95273	79	79	2297720467	1839611761	1894426911	2184654439	95273	SRX2635541	SRS2044320	SRA544939	GEO	Sauka-Spengler lab, University of Oxford, MRC Weatherall Institute of Molecular Medicine	2	0.91404	0.91129	0.16863	0.17306	0.76108	0.76347	0.47228	0.47663	80	80	B	B	biological fallback assumption	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United Kingdom	2017-03-13	Multi-stage	Multi-stage	Head	Nervous System
41911	41911	SRR5338226	SRX2635540	SRS2044319	SRP101781	PRJNA378947	Generation of a binary transgenic zebrafish model to study myeloid gene regulation in response to pre neoplastic melanocytes	GSE96534	Transcriptome Analysis	A complex network of inflammation succeeds somatic cell transformation and malignant disease. Immune cells and their associated molecules are responsible for detecting and eliminating cancer cells as they establish themselves as the precursors of a tumour. By the time a patient has a detectable solid tumour cancer cells have escaped the initial immune response mechanisms. To date no model exists to allow us to study the underlying mechanisms that govern the initial phase of the immune response as cells are transformed to become the precursors of cancer. Here we describe the development of an innovative double binary animal model designed in zebrafish for exploring regulatory programming of the myeloid cells as they respond to oncogenic transformed melanocytes. This modular system harnesses the power of zebrafish genetics. For studies of melanocyte transformation we generated a hormone inducible binary system allowing for temporal control of different Ras oncogene NRasK61Q HRasG12V KRasG12V expression in melanocytes allowing us to truly study melanoma initiation. This binary model was then coupled to a model for regulatory profiling of the active transcriptome of macrophages and neutrophils which is based on the in vivo biotinylation of nuclei and their subsequent isolation by streptavidin affinity purification. For the first time regulatory profiling of neutrophils as they respond to the earliest precursors of melanoma revealed a number of factors upregulated in neutrophils that may promote progression to melanoma including fgf1 fgf6 cathepsin H cathepsin L galectin 1 and galectin 3. Overall design: We report the design of a double binary approach in zebrafish to study the neutrophil response to transformed melanocytes. By coupling a novel inducible model for melanocyte transformation to a model for the in vivo biotinylation of neutrophil nuclei we can isolate the neutrophil nuclei directly from the in vivo context allowing for RNA seq analysis of the active transcriptome.		pubmed:29666124	mpo RNAseqnuclear mifcntrl 1	GSM2535107	tissue:mpo RNAseqnuclear mif head 1\|strain:Tgmpo:BirA Citrine; bactin:Avi Cerulean Rangapox128 X Tgkita:LexPR Cerulean; PcrysB:ECFP LexOP:mCherry NRasox130\|development:5 dpf method:In Vivo Biotinylated Nuclei\|treatment:n1\|amplification:SMART seqTMv4\|strand:reverse\|assay:RNA seq	mpo RNAseqnuclear mifcntrl 1	Reads were mapped using STAR v.2.4.2a to danRer10 and read counts were obtained using subreads FeatureCounts Genome build: danRer10 Supplementary files format and content: counts	mpo RNAseqnuclear mif head 1	Incrossed larvae were treated with 1 μM from 24 hpf	For nuclei isolation zebrafish embryos were anaesthetised with 0.01% Tricaine and embryos dissected to separate the head from the trunk and tail. Heads were washed in hypotonic buffer H 20 mM HEPES pH 7.9 15 mM MgCl2 10 mM KCl 1 mM DTT and 1 X Complete protease inhibitor and subsequently resuspended in 500 μL of buffer H. Embryos were transferred to a Dounce homogenizer and dissociated by 10 strokes with the loose fitting pestal A and incubated on ice for 5 minutes. Further dissociation was carried out by 10 strokes with tight fitting pestal B every 5 minutes for 15 minutes. Nuclei were collected by centrifugation 2000 g 4 °C and resuspended in 1 mL buffer NDP 10 mM HEPES pH 7.9 40 mM NaCl 90 mM KCl 0.5 mM EDTA 0.5 mM spermidine 0.15 mM spermine 1 mM dithiothreitol and 1 X Complete protease inhibitor. For nuclei purification nuclei were incubated with 5 mg of M 280 streptavidin coated dynabeads with rotation for 30 minutes at 4 °C. A flow based system based on the previously published protocol by was used to capture the nuclei bound on the streptavidin beads. A 10 mL seriological pipette VWR cat # 8913 898 attached to a 1 mL micropipette tip Rainin reach pipet tip cat # RT L1000S both pre treated with NPB/BSA for 30 minutes and added to a MiniMACS separator magnet OctoMACS Separator Miltenyl Biotec cat # 130 042 109. A two way stopcock Biorad cat # 732 8102 was connected to the end of the 1mL micropipette tip via a piece of Tygon tubing Fisher Scientific cat # 8220 and the flow rate set to 0.75 mL/min. The nuclei beads suspension was diluted by addition of 9 mLs of nuclei pulldown buffer with 0.01 % Triton X 100 NPBt and added to the slow flow setup. The tip was subsequently removed from the stand and the nuclei beads released from the tip by slowly pipetting 1 mL of NPBt in and out of the tip. The solution was then diluted again to 10 mL with NPBt and added again to the slow flow setup. Nuclei beads were eluted in 1 mL of NPBt as described above and the NPBt removed using a magnetic stand D…		strain:Tgmpo:BirA Citrine;bactin:Avi Cerulean Rangapox128 X Tgkita:LexPR Cerulean;PcrysB:ECFP LexOP:mCherry NRasox130\|development:5 dpf method:In Vivo Biotinylated Nuclei\|treatment:n1\|amplification:SMART seqTMv4\|strand:reverse\|assay:RNA seq	GSM2535107	GSM2535107: mpo RNAseqnuclear mifcntrl 1; Danio rerio; RNA Seq	GSM2535107		1	For nuclei isolation zebrafish embryos were anaesthetised with 0.01% Tricaine and embryos dissected to separate the head from the trunk and tail. Heads were washed in hypotonic buffer H 20 mM HEPES pH 7.9 15 mM MgCl2 10 mM KCl 1 mM DTT and 1 X Complete protease inhibitor and subsequently resuspended in 500 μL of buffer H. Embryos were transferred to a Dounce homogenizer and dissociated by 10 strokes with the loose fitting pestal A and incubated on ice for 5 minutes. Further dissociation was carried out by 10 strokes with tight fitting pestal B every 5 minutes for 15 minutes. Nuclei were collected by centrifugation 2000 g 4 °C and resuspended in 1 mL buffer NDP 10 mM HEPES pH 7.9 40 mM NaCl 90 mM KCl 0.5 mM EDTA 0.5 mM spermidine 0.15 mM spermine 1 mM dithiothreitol and 1 X Complete protease inhibitor. For nuclei purification nuclei were incubated with 5 mg of M 280 streptavidin coated dynabeads with rotation for 30 minutes at 4 °C. A flow based system based on the previously published protocol by was used to capture the nuclei bound on the streptavidin beads. A 10 mL seriological pipette VWR cat # 8913 898 attached to a 1 mL micropipette tip Rainin reach pipet tip cat # RT L1000S both pre treated with NPB/BSA for 30 minutes and added to a MiniMACS separator magnet OctoMACS Separator Miltenyl Biotec cat # 130 042 109. A two way stopcock Biorad cat # 732 8102 was connected to the end of the 1mL micropipette tip via a piece of Tygon tubing Fisher Scientific cat # 8220 and the flow rate set to 0.75 mL/min. The nuclei beads suspension was diluted by addition of 9 mLs of nuclei pulldown buffer with 0.01 % Triton X 100 NPBt and added to the slow flow setup. The tip was subsequently removed from the stand and the nuclei beads released from the tip by slowly pipetting 1 mL of NPBt in and out of the tip. The solution was then diluted again to 10 mL with NPBt and added again to the slow flow setup. Nuclei beads were eluted in 1 mL of NPBt as described above and the NPBt removed using a magnetic stand D…	GEO Accession:GSM2535107	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP101781		shead1Aligned.out.sort.bam	bam	6223616133.0	39173742.0	GSM2535107 r1	0:79.44 1:79.43	A:1628842481;C:1512759691;G:1559820323;T:1522127590;N:66048	79	79	1628842481	1512759691	1559820323	1522127590	66048	SRX2635540	SRS2044319	SRA544939	GEO	Sauka-Spengler lab, University of Oxford, MRC Weatherall Institute of Molecular Medicine	2	0.91702	0.91416	0.08978	0.09081	0.80825	0.81225	0.47575	0.46407	78	80	B	B	biological fallback assumption	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United Kingdom	2017-03-13	Multi-stage	Multi-stage	Head	Nervous System
59131	59131	SRR11684032	SRX8244835	SRS6592471	SRP259989	PRJNA630163	Zebrafish juvenile mpeg+ macrophages	GSE149787	Transcriptome Analysis	We used zebrafish lacking functional csf1r or il34 to unravel how and when csf1r is necessary for macrophages. Transcriptomic analysis of mpeg+ macrophages isolated from juvenile fish revealed that csf1r deficient macrophages show a gross macrophage transcriptome but reduced expression of engulfment related genes and increased expression of genes typical for metaphocytes. Overall design: Bulk RNA sequencing of juvenile macrophages obtained from wildtype control il34 / and csf1rDM zebrafish triplicates	parent bioproject:PRJNA630158	pubmed:32367800	5mo il34 3	GSM4512724	tissue:whole fish\|developmental stage:1 mpf 5 mpf\|strain:il34re03/re03 tgmpeg GFP\|cell type:mpeg GFP+ cells	5mo il34 3	Sequencing and base calling was performed on the Illumina hiseq 2500. Resulting base calls were de multiplexed using the Illumina Casava 1.8 software. Subsequently SMARTer adapters were removed using cutadapt followed by the alignment step using STAR version 2.5.4b. Reference genome build GRCz10 danRer10 was used. Abundance estimation was performed using cufflinks v2.2.1 with both the frag bias correct and multi read correct flags set. The raw read counts were measured using HTSeq count version 0.11.0. using the union setting. The ensemble gene database was used. The aligned and filtered data was quantified with the Bioconductor package Genomic Ranges Lawrence et al. Plos Computational Biology 2013. Differential gene expression analysis was performed with Bioconductor package EdgeR Robinson et al. 2010. Genome build: GRCz10 Supplementary files format and content: CPM values [.csv] semicolon delimited files.	whole fish		Single juveniles were cut in small pieces using a razor blade and dissociated with trypsin on ice for 1 hour. mpeg GFP+ cells were FAC sorted directly into Trizol reagent. RNA was harvested using Trizol reagent. cDNA amplification: SMART seq V4 ultra low input RNA kit for sequencing Takara BIO USA Inc.. Illumina Truseq Sample Preparation V.2 guide was used and the samples were paired end sequenced 2x75 bp on the Illumina HiSeq 2500. RNA libraries were prepared for sequencing using standard Illumina protocols	HEPES buffered E3 medium 28 degrees celsius 14/10h light/dark cycle until 5 dpf from 5 dpf onwards in regular aquarium. Fed dry food + paramecia from 5 dpf 13 dpf. From 13 dpf onwards brine shrimps paramecia and dry food	developmental stage:1 mpf 5 mpf\|strain:il34re03/re03 tgmpeg GFP\|cell type:mpeg GFP+ cells	GSM4512724	GSM4512724: 5mo il34 3; Danio rerio; RNA Seq	GSM4512724		1	Single juveniles were cut in small pieces using a razor blade and dissociated with trypsin on ice for 1 hour. mpeg GFP+ cells were FAC sorted directly into Trizol reagent. RNA was harvested using Trizol reagent. cDNA amplification: SMART seq V4 ultra low input RNA kit for sequencing Takara BIO USA Inc.. Illumina Truseq Sample Preparation V.2 guide was used and the samples were paired end sequenced 2x75 bp on the Illumina HiSeq 2500. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM4512724	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP259989		5mo_il34_3_R2.fastq.gz 5mo_il34_3_R1.fastq.gz	fastq fastq	2866393332.0	14190066.0	GSM4512724 r1	0:101 1:101	A:820325277;C:598942699;G:621845494;T:825272271;N:7591	101	101	820325277	598942699	621845494	825272271	7591	SRX8244835	SRS6592471	SRA1072140	GEO	Erasmus MC	2	0.91456	0.88642	0.16807	0.16787	0.77717	0.78817	0.48538	0.47123	101	101	B	B	biological fallback assumption	illumina	hiseq_era	full_length	cdna_unspecified	trueseq	sc	single_cell_plate	smartseq	Netherlands	2020-05-04	Multi-stage	Multi-stage	Whole Organism	All anatomical structures
59132	59132	SRR11684031	SRX8244834	SRS6592470	SRP259989	PRJNA630163	Zebrafish juvenile mpeg+ macrophages	GSE149787	Transcriptome Analysis	We used zebrafish lacking functional csf1r or il34 to unravel how and when csf1r is necessary for macrophages. Transcriptomic analysis of mpeg+ macrophages isolated from juvenile fish revealed that csf1r deficient macrophages show a gross macrophage transcriptome but reduced expression of engulfment related genes and increased expression of genes typical for metaphocytes. Overall design: Bulk RNA sequencing of juvenile macrophages obtained from wildtype control il34 / and csf1rDM zebrafish triplicates	parent bioproject:PRJNA630158	pubmed:32367800	5mo il34 2	GSM4512723	tissue:whole fish\|developmental stage:1 mpf 5 mpf\|strain:il34re03/re03 tgmpeg GFP\|cell type:mpeg GFP+ cells	5mo il34 2	Sequencing and base calling was performed on the Illumina hiseq 2500. Resulting base calls were de multiplexed using the Illumina Casava 1.8 software. Subsequently SMARTer adapters were removed using cutadapt followed by the alignment step using STAR version 2.5.4b. Reference genome build GRCz10 danRer10 was used. Abundance estimation was performed using cufflinks v2.2.1 with both the frag bias correct and multi read correct flags set. The raw read counts were measured using HTSeq count version 0.11.0. using the union setting. The ensemble gene database was used. The aligned and filtered data was quantified with the Bioconductor package Genomic Ranges Lawrence et al. Plos Computational Biology 2013. Differential gene expression analysis was performed with Bioconductor package EdgeR Robinson et al. 2010. Genome build: GRCz10 Supplementary files format and content: CPM values [.csv] semicolon delimited files.	whole fish		Single juveniles were cut in small pieces using a razor blade and dissociated with trypsin on ice for 1 hour. mpeg GFP+ cells were FAC sorted directly into Trizol reagent. RNA was harvested using Trizol reagent. cDNA amplification: SMART seq V4 ultra low input RNA kit for sequencing Takara BIO USA Inc.. Illumina Truseq Sample Preparation V.2 guide was used and the samples were paired end sequenced 2x75 bp on the Illumina HiSeq 2500. RNA libraries were prepared for sequencing using standard Illumina protocols	HEPES buffered E3 medium 28 degrees celsius 14/10h light/dark cycle until 5 dpf from 5 dpf onwards in regular aquarium. Fed dry food + paramecia from 5 dpf 13 dpf. From 13 dpf onwards brine shrimps paramecia and dry food	developmental stage:1 mpf 5 mpf\|strain:il34re03/re03 tgmpeg GFP\|cell type:mpeg GFP+ cells	GSM4512723	GSM4512723: 5mo il34 2; Danio rerio; RNA Seq	GSM4512723		1	Single juveniles were cut in small pieces using a razor blade and dissociated with trypsin on ice for 1 hour. mpeg GFP+ cells were FAC sorted directly into Trizol reagent. RNA was harvested using Trizol reagent. cDNA amplification: SMART seq V4 ultra low input RNA kit for sequencing Takara BIO USA Inc.. Illumina Truseq Sample Preparation V.2 guide was used and the samples were paired end sequenced 2x75 bp on the Illumina HiSeq 2500. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM4512723	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP259989		5mo_il34_2_R2.fastq.gz 5mo_il34_2_R1.fastq.gz	fastq fastq	9358608692.0	46329746.0	GSM4512723 r1	0:101 1:101	A:2688145270;C:1936550600;G:2027452342;T:2706435131;N:25349	101	101	2688145270	1936550600	2027452342	2706435131	25349	SRX8244834	SRS6592470	SRA1072140	GEO	Erasmus MC	2	0.90713	0.87837	0.17353	0.17278	0.77413	0.78494	0.47813	0.45746	101	101	B	B	biological fallback assumption	illumina	hiseq_era	full_length	cdna_unspecified	trueseq	sc	single_cell_plate	smartseq	Netherlands	2020-05-04	Multi-stage	Multi-stage	Whole Organism	All anatomical structures
59133	59133	SRR11684030	SRX8244833	SRS6592469	SRP259989	PRJNA630163	Zebrafish juvenile mpeg+ macrophages	GSE149787	Transcriptome Analysis	We used zebrafish lacking functional csf1r or il34 to unravel how and when csf1r is necessary for macrophages. Transcriptomic analysis of mpeg+ macrophages isolated from juvenile fish revealed that csf1r deficient macrophages show a gross macrophage transcriptome but reduced expression of engulfment related genes and increased expression of genes typical for metaphocytes. Overall design: Bulk RNA sequencing of juvenile macrophages obtained from wildtype control il34 / and csf1rDM zebrafish triplicates	parent bioproject:PRJNA630158	pubmed:32367800	5mo il34 1	GSM4512722	tissue:whole fish\|developmental stage:1 mpf 5 mpf\|strain:il34re03/re03 tgmpeg GFP\|cell type:mpeg GFP+ cells	5mo il34 1	Sequencing and base calling was performed on the Illumina hiseq 2500. Resulting base calls were de multiplexed using the Illumina Casava 1.8 software. Subsequently SMARTer adapters were removed using cutadapt followed by the alignment step using STAR version 2.5.4b. Reference genome build GRCz10 danRer10 was used. Abundance estimation was performed using cufflinks v2.2.1 with both the frag bias correct and multi read correct flags set. The raw read counts were measured using HTSeq count version 0.11.0. using the union setting. The ensemble gene database was used. The aligned and filtered data was quantified with the Bioconductor package Genomic Ranges Lawrence et al. Plos Computational Biology 2013. Differential gene expression analysis was performed with Bioconductor package EdgeR Robinson et al. 2010. Genome build: GRCz10 Supplementary files format and content: CPM values [.csv] semicolon delimited files.	whole fish		Single juveniles were cut in small pieces using a razor blade and dissociated with trypsin on ice for 1 hour. mpeg GFP+ cells were FAC sorted directly into Trizol reagent. RNA was harvested using Trizol reagent. cDNA amplification: SMART seq V4 ultra low input RNA kit for sequencing Takara BIO USA Inc.. Illumina Truseq Sample Preparation V.2 guide was used and the samples were paired end sequenced 2x75 bp on the Illumina HiSeq 2500. RNA libraries were prepared for sequencing using standard Illumina protocols	HEPES buffered E3 medium 28 degrees celsius 14/10h light/dark cycle until 5 dpf from 5 dpf onwards in regular aquarium. Fed dry food + paramecia from 5 dpf 13 dpf. From 13 dpf onwards brine shrimps paramecia and dry food	developmental stage:1 mpf 5 mpf\|strain:il34re03/re03 tgmpeg GFP\|cell type:mpeg GFP+ cells	GSM4512722	GSM4512722: 5mo il34 1; Danio rerio; RNA Seq	GSM4512722		1	Single juveniles were cut in small pieces using a razor blade and dissociated with trypsin on ice for 1 hour. mpeg GFP+ cells were FAC sorted directly into Trizol reagent. RNA was harvested using Trizol reagent. cDNA amplification: SMART seq V4 ultra low input RNA kit for sequencing Takara BIO USA Inc.. Illumina Truseq Sample Preparation V.2 guide was used and the samples were paired end sequenced 2x75 bp on the Illumina HiSeq 2500. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM4512722	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP259989		5mo_il34_1_R2.fastq.gz 5mo_il34_1_R1.fastq.gz	fastq fastq	2301153296.0	11391848.0	GSM4512722 r1	0:101 1:101	A:654795654;C:483118243;G:496611634;T:666621412;N:6353	101	101	654795654	483118243	496611634	666621412	6353	SRX8244833	SRS6592469	SRA1072140	GEO	Erasmus MC	2	0.91036	0.88104	0.15732	0.15536	0.7543	0.76355	0.47519	0.47489	101	101	B	B	biological fallback assumption	illumina	hiseq_era	full_length	cdna_unspecified	trueseq	sc	single_cell_plate	smartseq	Netherlands	2020-05-04	Multi-stage	Multi-stage	Whole Organism	All anatomical structures
59134	59134	SRR11684029	SRX8244832	SRS6592467	SRP259989	PRJNA630163	Zebrafish juvenile mpeg+ macrophages	GSE149787	Transcriptome Analysis	We used zebrafish lacking functional csf1r or il34 to unravel how and when csf1r is necessary for macrophages. Transcriptomic analysis of mpeg+ macrophages isolated from juvenile fish revealed that csf1r deficient macrophages show a gross macrophage transcriptome but reduced expression of engulfment related genes and increased expression of genes typical for metaphocytes. Overall design: Bulk RNA sequencing of juvenile macrophages obtained from wildtype control il34 / and csf1rDM zebrafish triplicates	parent bioproject:PRJNA630158	pubmed:32367800	5mo csf1rdm 3	GSM4512721	tissue:whole fish\|developmental stage:1 mpf 5 mpf\|strain:csf1raj4e1/j4e1; csf1rbre01/re01 tgmpeg GFP\|cell type:mpeg GFP+ cells	5mo csf1rdm 3	Sequencing and base calling was performed on the Illumina hiseq 2500. Resulting base calls were de multiplexed using the Illumina Casava 1.8 software. Subsequently SMARTer adapters were removed using cutadapt followed by the alignment step using STAR version 2.5.4b. Reference genome build GRCz10 danRer10 was used. Abundance estimation was performed using cufflinks v2.2.1 with both the frag bias correct and multi read correct flags set. The raw read counts were measured using HTSeq count version 0.11.0. using the union setting. The ensemble gene database was used. The aligned and filtered data was quantified with the Bioconductor package Genomic Ranges Lawrence et al. Plos Computational Biology 2013. Differential gene expression analysis was performed with Bioconductor package EdgeR Robinson et al. 2010. Genome build: GRCz10 Supplementary files format and content: CPM values [.csv] semicolon delimited files.	whole fish		Single juveniles were cut in small pieces using a razor blade and dissociated with trypsin on ice for 1 hour. mpeg GFP+ cells were FAC sorted directly into Trizol reagent. RNA was harvested using Trizol reagent. cDNA amplification: SMART seq V4 ultra low input RNA kit for sequencing Takara BIO USA Inc.. Illumina Truseq Sample Preparation V.2 guide was used and the samples were paired end sequenced 2x75 bp on the Illumina HiSeq 2500. RNA libraries were prepared for sequencing using standard Illumina protocols	HEPES buffered E3 medium 28 degrees celsius 14/10h light/dark cycle until 5 dpf from 5 dpf onwards in regular aquarium. Fed dry food + paramecia from 5 dpf 13 dpf. From 13 dpf onwards brine shrimps paramecia and dry food	developmental stage:1 mpf 5 mpf\|strain:csf1raj4e1/j4e1;csf1rbre01/re01 tgmpeg GFP\|cell type:mpeg GFP+ cells	GSM4512721	GSM4512721: 5mo csf1rdm 3; Danio rerio; RNA Seq	GSM4512721		1	Single juveniles were cut in small pieces using a razor blade and dissociated with trypsin on ice for 1 hour. mpeg GFP+ cells were FAC sorted directly into Trizol reagent. RNA was harvested using Trizol reagent. cDNA amplification: SMART seq V4 ultra low input RNA kit for sequencing Takara BIO USA Inc.. Illumina Truseq Sample Preparation V.2 guide was used and the samples were paired end sequenced 2x75 bp on the Illumina HiSeq 2500. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM4512721	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP259989		5mo_csf1rdm_3_R2.fastq.gz 5mo_csf1rdm_3_R1.fastq.gz	fastq fastq	3452649448.0	17092324.0	GSM4512721 r1	0:101 1:101	A:999459335;C:713557103;G:730450368;T:1009173875;N:8767	101	101	999459335	713557103	730450368	1009173875	8767	SRX8244832	SRS6592467	SRA1072140	GEO	Erasmus MC	2	0.89236	0.86757	0.18589	0.18351	0.76745	0.77717	0.47984	0.48136	101	101	B	B	biological fallback assumption	illumina	hiseq_era	full_length	cdna_unspecified	trueseq	sc	single_cell_plate	smartseq	Netherlands	2020-05-04	Multi-stage	Multi-stage	Whole Organism	All anatomical structures
59135	59135	SRR11684028	SRX8244831	SRS6592466	SRP259989	PRJNA630163	Zebrafish juvenile mpeg+ macrophages	GSE149787	Transcriptome Analysis	We used zebrafish lacking functional csf1r or il34 to unravel how and when csf1r is necessary for macrophages. Transcriptomic analysis of mpeg+ macrophages isolated from juvenile fish revealed that csf1r deficient macrophages show a gross macrophage transcriptome but reduced expression of engulfment related genes and increased expression of genes typical for metaphocytes. Overall design: Bulk RNA sequencing of juvenile macrophages obtained from wildtype control il34 / and csf1rDM zebrafish triplicates	parent bioproject:PRJNA630158	pubmed:32367800	5mo csf1rdm 2	GSM4512720	tissue:whole fish\|developmental stage:1 mpf 5 mpf\|strain:csf1raj4e1/j4e1; csf1rbre01/re01 tgmpeg GFP\|cell type:mpeg GFP+ cells	5mo csf1rdm 2	Sequencing and base calling was performed on the Illumina hiseq 2500. Resulting base calls were de multiplexed using the Illumina Casava 1.8 software. Subsequently SMARTer adapters were removed using cutadapt followed by the alignment step using STAR version 2.5.4b. Reference genome build GRCz10 danRer10 was used. Abundance estimation was performed using cufflinks v2.2.1 with both the frag bias correct and multi read correct flags set. The raw read counts were measured using HTSeq count version 0.11.0. using the union setting. The ensemble gene database was used. The aligned and filtered data was quantified with the Bioconductor package Genomic Ranges Lawrence et al. Plos Computational Biology 2013. Differential gene expression analysis was performed with Bioconductor package EdgeR Robinson et al. 2010. Genome build: GRCz10 Supplementary files format and content: CPM values [.csv] semicolon delimited files.	whole fish		Single juveniles were cut in small pieces using a razor blade and dissociated with trypsin on ice for 1 hour. mpeg GFP+ cells were FAC sorted directly into Trizol reagent. RNA was harvested using Trizol reagent. cDNA amplification: SMART seq V4 ultra low input RNA kit for sequencing Takara BIO USA Inc.. Illumina Truseq Sample Preparation V.2 guide was used and the samples were paired end sequenced 2x75 bp on the Illumina HiSeq 2500. RNA libraries were prepared for sequencing using standard Illumina protocols	HEPES buffered E3 medium 28 degrees celsius 14/10h light/dark cycle until 5 dpf from 5 dpf onwards in regular aquarium. Fed dry food + paramecia from 5 dpf 13 dpf. From 13 dpf onwards brine shrimps paramecia and dry food	developmental stage:1 mpf 5 mpf\|strain:csf1raj4e1/j4e1;csf1rbre01/re01 tgmpeg GFP\|cell type:mpeg GFP+ cells	GSM4512720	GSM4512720: 5mo csf1rdm 2; Danio rerio; RNA Seq	GSM4512720		1	Single juveniles were cut in small pieces using a razor blade and dissociated with trypsin on ice for 1 hour. mpeg GFP+ cells were FAC sorted directly into Trizol reagent. RNA was harvested using Trizol reagent. cDNA amplification: SMART seq V4 ultra low input RNA kit for sequencing Takara BIO USA Inc.. Illumina Truseq Sample Preparation V.2 guide was used and the samples were paired end sequenced 2x75 bp on the Illumina HiSeq 2500. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM4512720	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP259989		5mo_csf1rdm_2_R2.fastq.gz 5mo_csf1rdm_2_R1.fastq.gz	fastq fastq	9868898870.0	48855935.0	GSM4512720 r1	0:101 1:101	A:2841225530;C:2066572676;G:2116298647;T:2844775713;N:26304	101	101	2841225530	2066572676	2116298647	2844775713	26304	SRX8244831	SRS6592466	SRA1072140	GEO	Erasmus MC	2	0.89516	0.87542	0.18501	0.18252	0.764	0.77293	0.47581	0.47272	101	101	B	B	biological fallback assumption	illumina	hiseq_era	full_length	cdna_unspecified	trueseq	sc	single_cell_plate	smartseq	Netherlands	2020-05-04	Multi-stage	Multi-stage	Whole Organism	All anatomical structures
59136	59136	SRR11684027	SRX8244830	SRS6592472	SRP259989	PRJNA630163	Zebrafish juvenile mpeg+ macrophages	GSE149787	Transcriptome Analysis	We used zebrafish lacking functional csf1r or il34 to unravel how and when csf1r is necessary for macrophages. Transcriptomic analysis of mpeg+ macrophages isolated from juvenile fish revealed that csf1r deficient macrophages show a gross macrophage transcriptome but reduced expression of engulfment related genes and increased expression of genes typical for metaphocytes. Overall design: Bulk RNA sequencing of juvenile macrophages obtained from wildtype control il34 / and csf1rDM zebrafish triplicates	parent bioproject:PRJNA630158	pubmed:32367800	5mo csf1rdm 1	GSM4512719	tissue:whole fish\|developmental stage:1 mpf 5 mpf\|strain:csf1raj4e1/j4e1; csf1rbre01/re01 tgmpeg GFP\|cell type:mpeg GFP+ cells	5mo csf1rdm 1	Sequencing and base calling was performed on the Illumina hiseq 2500. Resulting base calls were de multiplexed using the Illumina Casava 1.8 software. Subsequently SMARTer adapters were removed using cutadapt followed by the alignment step using STAR version 2.5.4b. Reference genome build GRCz10 danRer10 was used. Abundance estimation was performed using cufflinks v2.2.1 with both the frag bias correct and multi read correct flags set. The raw read counts were measured using HTSeq count version 0.11.0. using the union setting. The ensemble gene database was used. The aligned and filtered data was quantified with the Bioconductor package Genomic Ranges Lawrence et al. Plos Computational Biology 2013. Differential gene expression analysis was performed with Bioconductor package EdgeR Robinson et al. 2010. Genome build: GRCz10 Supplementary files format and content: CPM values [.csv] semicolon delimited files.	whole fish		Single juveniles were cut in small pieces using a razor blade and dissociated with trypsin on ice for 1 hour. mpeg GFP+ cells were FAC sorted directly into Trizol reagent. RNA was harvested using Trizol reagent. cDNA amplification: SMART seq V4 ultra low input RNA kit for sequencing Takara BIO USA Inc.. Illumina Truseq Sample Preparation V.2 guide was used and the samples were paired end sequenced 2x75 bp on the Illumina HiSeq 2500. RNA libraries were prepared for sequencing using standard Illumina protocols	HEPES buffered E3 medium 28 degrees celsius 14/10h light/dark cycle until 5 dpf from 5 dpf onwards in regular aquarium. Fed dry food + paramecia from 5 dpf 13 dpf. From 13 dpf onwards brine shrimps paramecia and dry food	developmental stage:1 mpf 5 mpf\|strain:csf1raj4e1/j4e1;csf1rbre01/re01 tgmpeg GFP\|cell type:mpeg GFP+ cells	GSM4512719	GSM4512719: 5mo csf1rdm 1; Danio rerio; RNA Seq	GSM4512719		1	Single juveniles were cut in small pieces using a razor blade and dissociated with trypsin on ice for 1 hour. mpeg GFP+ cells were FAC sorted directly into Trizol reagent. RNA was harvested using Trizol reagent. cDNA amplification: SMART seq V4 ultra low input RNA kit for sequencing Takara BIO USA Inc.. Illumina Truseq Sample Preparation V.2 guide was used and the samples were paired end sequenced 2x75 bp on the Illumina HiSeq 2500. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM4512719	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP259989		5mo_csf1rdm_1_R2.fastq.gz 5mo_csf1rdm_1_R1.fastq.gz	fastq fastq	2592133084.0	12832342.0	GSM4512719 r1	0:101 1:101	A:752421497;C:536462229;G:554014038;T:749228471;N:6849	101	101	752421497	536462229	554014038	749228471	6849	SRX8244830	SRS6592472	SRA1072140	GEO	Erasmus MC	2	0.89674	0.87504	0.19407	0.19286	0.76266	0.77128	0.47136	0.47621	101	101	B	B	biological fallback assumption	illumina	hiseq_era	full_length	cdna_unspecified	trueseq	sc	single_cell_plate	smartseq	Netherlands	2020-05-04	Multi-stage	Multi-stage	Whole Organism	All anatomical structures
59137	59137	SRR11684026	SRX8244829	SRS6592468	SRP259989	PRJNA630163	Zebrafish juvenile mpeg+ macrophages	GSE149787	Transcriptome Analysis	We used zebrafish lacking functional csf1r or il34 to unravel how and when csf1r is necessary for macrophages. Transcriptomic analysis of mpeg+ macrophages isolated from juvenile fish revealed that csf1r deficient macrophages show a gross macrophage transcriptome but reduced expression of engulfment related genes and increased expression of genes typical for metaphocytes. Overall design: Bulk RNA sequencing of juvenile macrophages obtained from wildtype control il34 / and csf1rDM zebrafish triplicates	parent bioproject:PRJNA630158	pubmed:32367800	5mo control 3	GSM4512718	tissue:whole fish\|developmental stage:1 mpf 5 mpf\|strain:wildtype tgmpeg GFP\|cell type:mpeg GFP+ cells	5mo control 3	Sequencing and base calling was performed on the Illumina hiseq 2500. Resulting base calls were de multiplexed using the Illumina Casava 1.8 software. Subsequently SMARTer adapters were removed using cutadapt followed by the alignment step using STAR version 2.5.4b. Reference genome build GRCz10 danRer10 was used. Abundance estimation was performed using cufflinks v2.2.1 with both the frag bias correct and multi read correct flags set. The raw read counts were measured using HTSeq count version 0.11.0. using the union setting. The ensemble gene database was used. The aligned and filtered data was quantified with the Bioconductor package Genomic Ranges Lawrence et al. Plos Computational Biology 2013. Differential gene expression analysis was performed with Bioconductor package EdgeR Robinson et al. 2010. Genome build: GRCz10 Supplementary files format and content: CPM values [.csv] semicolon delimited files.	whole fish		Single juveniles were cut in small pieces using a razor blade and dissociated with trypsin on ice for 1 hour. mpeg GFP+ cells were FAC sorted directly into Trizol reagent. RNA was harvested using Trizol reagent. cDNA amplification: SMART seq V4 ultra low input RNA kit for sequencing Takara BIO USA Inc.. Illumina Truseq Sample Preparation V.2 guide was used and the samples were paired end sequenced 2x75 bp on the Illumina HiSeq 2500. RNA libraries were prepared for sequencing using standard Illumina protocols	HEPES buffered E3 medium 28 degrees celsius 14/10h light/dark cycle until 5 dpf from 5 dpf onwards in regular aquarium. Fed dry food + paramecia from 5 dpf 13 dpf. From 13 dpf onwards brine shrimps paramecia and dry food	developmental stage:1 mpf 5 mpf\|strain:wildtype tgmpeg GFP\|cell type:mpeg GFP+ cells	GSM4512718	GSM4512718: 5mo control 3; Danio rerio; RNA Seq	GSM4512718		1	Single juveniles were cut in small pieces using a razor blade and dissociated with trypsin on ice for 1 hour. mpeg GFP+ cells were FAC sorted directly into Trizol reagent. RNA was harvested using Trizol reagent. cDNA amplification: SMART seq V4 ultra low input RNA kit for sequencing Takara BIO USA Inc.. Illumina Truseq Sample Preparation V.2 guide was used and the samples were paired end sequenced 2x75 bp on the Illumina HiSeq 2500. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM4512718	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP259989		5mo_control_3_R1.fastq.gz 5mo_control_3_R2.fastq.gz	fastq fastq	2900146724.0	14357162.0	GSM4512718 r1	0:101 1:101	A:836328631;C:590839440;G:610358908;T:862611563;N:8182	101	101	836328631	590839440	610358908	862611563	8182	SRX8244829	SRS6592468	SRA1072140	GEO	Erasmus MC	2	0.92029	0.88055	0.20101	0.19762	0.77575	0.78843	0.47683	0.46576	101	101	B	B	biological fallback assumption	illumina	hiseq_era	full_length	cdna_unspecified	trueseq	sc	single_cell_plate	smartseq	Netherlands	2020-05-04	Multi-stage	Multi-stage	Whole Organism	All anatomical structures
59138	59138	SRR11684025	SRX8244828	SRS6592465	SRP259989	PRJNA630163	Zebrafish juvenile mpeg+ macrophages	GSE149787	Transcriptome Analysis	We used zebrafish lacking functional csf1r or il34 to unravel how and when csf1r is necessary for macrophages. Transcriptomic analysis of mpeg+ macrophages isolated from juvenile fish revealed that csf1r deficient macrophages show a gross macrophage transcriptome but reduced expression of engulfment related genes and increased expression of genes typical for metaphocytes. Overall design: Bulk RNA sequencing of juvenile macrophages obtained from wildtype control il34 / and csf1rDM zebrafish triplicates	parent bioproject:PRJNA630158	pubmed:32367800	5mo control 2	GSM4512717	tissue:whole fish\|developmental stage:1 mpf 5 mpf\|strain:wildtype tgmpeg GFP\|cell type:mpeg GFP+ cells	5mo control 2	Sequencing and base calling was performed on the Illumina hiseq 2500. Resulting base calls were de multiplexed using the Illumina Casava 1.8 software. Subsequently SMARTer adapters were removed using cutadapt followed by the alignment step using STAR version 2.5.4b. Reference genome build GRCz10 danRer10 was used. Abundance estimation was performed using cufflinks v2.2.1 with both the frag bias correct and multi read correct flags set. The raw read counts were measured using HTSeq count version 0.11.0. using the union setting. The ensemble gene database was used. The aligned and filtered data was quantified with the Bioconductor package Genomic Ranges Lawrence et al. Plos Computational Biology 2013. Differential gene expression analysis was performed with Bioconductor package EdgeR Robinson et al. 2010. Genome build: GRCz10 Supplementary files format and content: CPM values [.csv] semicolon delimited files.	whole fish		Single juveniles were cut in small pieces using a razor blade and dissociated with trypsin on ice for 1 hour. mpeg GFP+ cells were FAC sorted directly into Trizol reagent. RNA was harvested using Trizol reagent. cDNA amplification: SMART seq V4 ultra low input RNA kit for sequencing Takara BIO USA Inc.. Illumina Truseq Sample Preparation V.2 guide was used and the samples were paired end sequenced 2x75 bp on the Illumina HiSeq 2500. RNA libraries were prepared for sequencing using standard Illumina protocols	HEPES buffered E3 medium 28 degrees celsius 14/10h light/dark cycle until 5 dpf from 5 dpf onwards in regular aquarium. Fed dry food + paramecia from 5 dpf 13 dpf. From 13 dpf onwards brine shrimps paramecia and dry food	developmental stage:1 mpf 5 mpf\|strain:wildtype tgmpeg GFP\|cell type:mpeg GFP+ cells	GSM4512717	GSM4512717: 5mo control 2; Danio rerio; RNA Seq	GSM4512717		1	Single juveniles were cut in small pieces using a razor blade and dissociated with trypsin on ice for 1 hour. mpeg GFP+ cells were FAC sorted directly into Trizol reagent. RNA was harvested using Trizol reagent. cDNA amplification: SMART seq V4 ultra low input RNA kit for sequencing Takara BIO USA Inc.. Illumina Truseq Sample Preparation V.2 guide was used and the samples were paired end sequenced 2x75 bp on the Illumina HiSeq 2500. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM4512717	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP259989		5mo_control_2_R2.fastq.gz 5mo_control_2_R1.fastq.gz	fastq fastq	3569121840.0	17668920.0	GSM4512717 r1	0:101 1:101	A:1029586591;C:742959141;G:766068597;T:1030497700;N:9811	101	101	1029586591	742959141	766068597	1030497700	9811	SRX8244828	SRS6592465	SRA1072140	GEO	Erasmus MC	2	0.92823	0.90526	0.19813	0.19655	0.77386	0.78153	0.47798	0.45944	101	101	B	B	biological fallback assumption	illumina	hiseq_era	full_length	cdna_unspecified	trueseq	sc	single_cell_plate	smartseq	Netherlands	2020-05-04	Multi-stage	Multi-stage	Whole Organism	All anatomical structures
59139	59139	SRR11684024	SRX8244827	SRS6592464	SRP259989	PRJNA630163	Zebrafish juvenile mpeg+ macrophages	GSE149787	Transcriptome Analysis	We used zebrafish lacking functional csf1r or il34 to unravel how and when csf1r is necessary for macrophages. Transcriptomic analysis of mpeg+ macrophages isolated from juvenile fish revealed that csf1r deficient macrophages show a gross macrophage transcriptome but reduced expression of engulfment related genes and increased expression of genes typical for metaphocytes. Overall design: Bulk RNA sequencing of juvenile macrophages obtained from wildtype control il34 / and csf1rDM zebrafish triplicates	parent bioproject:PRJNA630158	pubmed:32367800	5mo control 1	GSM4512716	tissue:whole fish\|developmental stage:1 mpf 5 mpf\|strain:wildtype tgmpeg GFP\|cell type:mpeg GFP+ cells	5mo control 1	Sequencing and base calling was performed on the Illumina hiseq 2500. Resulting base calls were de multiplexed using the Illumina Casava 1.8 software. Subsequently SMARTer adapters were removed using cutadapt followed by the alignment step using STAR version 2.5.4b. Reference genome build GRCz10 danRer10 was used. Abundance estimation was performed using cufflinks v2.2.1 with both the frag bias correct and multi read correct flags set. The raw read counts were measured using HTSeq count version 0.11.0. using the union setting. The ensemble gene database was used. The aligned and filtered data was quantified with the Bioconductor package Genomic Ranges Lawrence et al. Plos Computational Biology 2013. Differential gene expression analysis was performed with Bioconductor package EdgeR Robinson et al. 2010. Genome build: GRCz10 Supplementary files format and content: CPM values [.csv] semicolon delimited files.	whole fish		Single juveniles were cut in small pieces using a razor blade and dissociated with trypsin on ice for 1 hour. mpeg GFP+ cells were FAC sorted directly into Trizol reagent. RNA was harvested using Trizol reagent. cDNA amplification: SMART seq V4 ultra low input RNA kit for sequencing Takara BIO USA Inc.. Illumina Truseq Sample Preparation V.2 guide was used and the samples were paired end sequenced 2x75 bp on the Illumina HiSeq 2500. RNA libraries were prepared for sequencing using standard Illumina protocols	HEPES buffered E3 medium 28 degrees celsius 14/10h light/dark cycle until 5 dpf from 5 dpf onwards in regular aquarium. Fed dry food + paramecia from 5 dpf 13 dpf. From 13 dpf onwards brine shrimps paramecia and dry food	developmental stage:1 mpf 5 mpf\|strain:wildtype tgmpeg GFP\|cell type:mpeg GFP+ cells	GSM4512716	GSM4512716: 5mo control 1; Danio rerio; RNA Seq	GSM4512716		1	Single juveniles were cut in small pieces using a razor blade and dissociated with trypsin on ice for 1 hour. mpeg GFP+ cells were FAC sorted directly into Trizol reagent. RNA was harvested using Trizol reagent. cDNA amplification: SMART seq V4 ultra low input RNA kit for sequencing Takara BIO USA Inc.. Illumina Truseq Sample Preparation V.2 guide was used and the samples were paired end sequenced 2x75 bp on the Illumina HiSeq 2500. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM4512716	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP259989		5mo_control_1_R1.fastq.gz 5mo_control_1_R2.fastq.gz	fastq fastq	2998749792.0	14845296.0	GSM4512716 r1	0:101 1:101	A:865245738;C:611065712;G:637501234;T:884928997;N:8111	101	101	865245738	611065712	637501234	884928997	8111	SRX8244827	SRS6592464	SRA1072140	GEO	Erasmus MC	2	0.9234	0.8848	0.19688	0.19386	0.73285	0.7469	0.48735	0.46533	101	101	B	B	biological fallback assumption	illumina	hiseq_era	full_length	cdna_unspecified	trueseq	sc	single_cell_plate	smartseq	Netherlands	2020-05-04	Multi-stage	Multi-stage	Whole Organism	All anatomical structures
63526	63526	SRR13938396	SRX10317718	SRS8438155	SRP310259	PRJNA713782	TLR7 ligation augments hematopoiesis in Rps14 deficiency via paradoxical inflammatory signalling	GSE168727	Transcriptome Analysis	Myelodysplastic syndrome MDS is a haematological malignancy characterised by blood cytopenias and predisposition to acute myeloid leukaemia. We developed a model of MDS using zebrafish using knockout of Rps14 the primary mediator of the anaemia associated with del 5q MDS. These mutant animals develop bone marrow failure with dysplastic features. We conducted an in vivo small molecule screen to identify compounds that ameliorate the MDS phenotype identifying imiquimod an agonist of TLR7. We conducted RNA seq analysis of both treated and untreated animals to define the mechanism of imiquimod in alleviating anaemia. We find imiquimod alleviates anaemia by promoting haematopoietic stem and progenitor cell expansion and erythroid differentiation the mechanism of which is dependent on TLR7 ligation. TLR7 activation in this setting paradoxically promoted an anti inflammatory gene signature suggesting crosstalk between pro inflammatory pathways endogenous to Rps14 loss and TLR7 pathway activation. Overall design: RNA seq analysis of HSPCs TgItga2b:GFPlo cells from pooled rps14+/ or wildtype zebrafish embryos which were phenylhydrazine Phz stressed or unstressed and then treated with imiquimod or vehicle control. A minimum of three replicates per condition were analysed.			Het Phz DMSO 5	GSM5160076	tissue:TgItga2b:GFPlo cells\|genotype:Rps14+/ \|stress:Phz\|treatment:DMSO	Het Phz DMSO 5	Data QC was conducted using FastQC 0.11.9 and reads trimmed using Trimmomatic 0.39 Reads were aligned to the zebrafish genome GRCz11 using HISAT2 2.1.0 Alignments were sorted and indexed with samtools 1.9 Reads were counted using featureCounts from subread 2.0.0 and GTF Danio Rerio GRCz11.97 Counts were normalised and differential gene expression was analysed using DESeq2 Genome build: GRCz11 Supplementary files format and content: Matrix of normalised raw counts for every gene and every sample	TgItga2b:GFPlo cells	Haemolytic stress was induced by exposure of embryos to phenylhydrazine. Embryos were incubated in 1 µg/mL PHZ from 24 hpf to 48 hpf and then washed. Embryos were then incubated 20 µM Imiquimod or DMSO control for 4 days from 48hpf to 6dpf. Rps14 genotypes were determined with tailclips and embryos pooled before sorting.	Embryos were pooled by rps14 genotype stress and treatment and TgItga2b:GFPlo cells were sorted directly into Trizol for RNA extraction Libraries were prepared using the Smart seq2 protocol	Tgitga2b:GFP zebrafish were maintained according to standard procedures and UK Home Office guidelines	genotype:Rps14+/ \|stress:Phz\|treatment:DMSO	GSM5160076	GSM5160076: Het Phz DMSO 5; Danio rerio; RNA Seq	GSM5160076		1	Embryos were pooled by rps14 genotype stress and treatment and TgItga2b:GFPlo cells were sorted directly into Trizol for RNA extraction Libraries were prepared using the Smart seq2 protocol	GEO Accession:GSM5160076	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP310259	loader:fastq load.py	33_S33_L001_R1_001.fastq 33_S33_L001_R2_001.fastq	fastq fastq	572962494.0	4732369.0	GSM5160076 r1	0:60.54 1:60.53	A:157363606;C:127380989;G:132333639;T:155856278;N:27982	60	60	157363606	127380989	132333639	155856278	27982	SRX10317718	SRS8438155	SRA1205468	GEO	Department of Haematology, UCL Cancer Institute	2	0.91322	0.91809	0.1772	0.17812	0.76919	0.76956	0.52874	0.52027	61	61	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	United Kingdom	2021-03-11	Multi-stage	Multi-stage	Embryo Imprecise	All anatomical structures
63527	63527	SRR13938397	SRX10317718	SRS8438155	SRP310259	PRJNA713782	TLR7 ligation augments hematopoiesis in Rps14 deficiency via paradoxical inflammatory signalling	GSE168727	Transcriptome Analysis	Myelodysplastic syndrome MDS is a haematological malignancy characterised by blood cytopenias and predisposition to acute myeloid leukaemia. We developed a model of MDS using zebrafish using knockout of Rps14 the primary mediator of the anaemia associated with del 5q MDS. These mutant animals develop bone marrow failure with dysplastic features. We conducted an in vivo small molecule screen to identify compounds that ameliorate the MDS phenotype identifying imiquimod an agonist of TLR7. We conducted RNA seq analysis of both treated and untreated animals to define the mechanism of imiquimod in alleviating anaemia. We find imiquimod alleviates anaemia by promoting haematopoietic stem and progenitor cell expansion and erythroid differentiation the mechanism of which is dependent on TLR7 ligation. TLR7 activation in this setting paradoxically promoted an anti inflammatory gene signature suggesting crosstalk between pro inflammatory pathways endogenous to Rps14 loss and TLR7 pathway activation. Overall design: RNA seq analysis of HSPCs TgItga2b:GFPlo cells from pooled rps14+/ or wildtype zebrafish embryos which were phenylhydrazine Phz stressed or unstressed and then treated with imiquimod or vehicle control. A minimum of three replicates per condition were analysed.			Het Phz DMSO 5	GSM5160076	tissue:TgItga2b:GFPlo cells\|genotype:Rps14+/ \|stress:Phz\|treatment:DMSO	Het Phz DMSO 5	Data QC was conducted using FastQC 0.11.9 and reads trimmed using Trimmomatic 0.39 Reads were aligned to the zebrafish genome GRCz11 using HISAT2 2.1.0 Alignments were sorted and indexed with samtools 1.9 Reads were counted using featureCounts from subread 2.0.0 and GTF Danio Rerio GRCz11.97 Counts were normalised and differential gene expression was analysed using DESeq2 Genome build: GRCz11 Supplementary files format and content: Matrix of normalised raw counts for every gene and every sample	TgItga2b:GFPlo cells	Haemolytic stress was induced by exposure of embryos to phenylhydrazine. Embryos were incubated in 1 µg/mL PHZ from 24 hpf to 48 hpf and then washed. Embryos were then incubated 20 µM Imiquimod or DMSO control for 4 days from 48hpf to 6dpf. Rps14 genotypes were determined with tailclips and embryos pooled before sorting.	Embryos were pooled by rps14 genotype stress and treatment and TgItga2b:GFPlo cells were sorted directly into Trizol for RNA extraction Libraries were prepared using the Smart seq2 protocol	Tgitga2b:GFP zebrafish were maintained according to standard procedures and UK Home Office guidelines	genotype:Rps14+/ \|stress:Phz\|treatment:DMSO	GSM5160076	GSM5160076: Het Phz DMSO 5; Danio rerio; RNA Seq	GSM5160076		1	Embryos were pooled by rps14 genotype stress and treatment and TgItga2b:GFPlo cells were sorted directly into Trizol for RNA extraction Libraries were prepared using the Smart seq2 protocol	GEO Accession:GSM5160076	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP310259	loader:fastq load.py	33_S33_L002_R1_001.fastq 33_S33_L002_R2_001.fastq	fastq fastq	584634733.0	4828714.0	GSM5160076 r2	0:60.54 1:60.54	A:160580309;C:130003371;G:135039808;T:158988474;N:22771	60	60	160580309	130003371	135039808	158988474	22771	SRX10317718	SRS8438155	SRA1205468	GEO	Department of Haematology, UCL Cancer Institute	2	0.91102	0.91668	0.1757	0.17816	0.76664	0.76822	0.52521	0.51996	61	61	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	United Kingdom	2021-03-11	Multi-stage	Multi-stage	Embryo Imprecise	All anatomical structures
63528	63528	SRR13938394	SRX10317717	SRS8438154	SRP310259	PRJNA713782	TLR7 ligation augments hematopoiesis in Rps14 deficiency via paradoxical inflammatory signalling	GSE168727	Transcriptome Analysis	Myelodysplastic syndrome MDS is a haematological malignancy characterised by blood cytopenias and predisposition to acute myeloid leukaemia. We developed a model of MDS using zebrafish using knockout of Rps14 the primary mediator of the anaemia associated with del 5q MDS. These mutant animals develop bone marrow failure with dysplastic features. We conducted an in vivo small molecule screen to identify compounds that ameliorate the MDS phenotype identifying imiquimod an agonist of TLR7. We conducted RNA seq analysis of both treated and untreated animals to define the mechanism of imiquimod in alleviating anaemia. We find imiquimod alleviates anaemia by promoting haematopoietic stem and progenitor cell expansion and erythroid differentiation the mechanism of which is dependent on TLR7 ligation. TLR7 activation in this setting paradoxically promoted an anti inflammatory gene signature suggesting crosstalk between pro inflammatory pathways endogenous to Rps14 loss and TLR7 pathway activation. Overall design: RNA seq analysis of HSPCs TgItga2b:GFPlo cells from pooled rps14+/ or wildtype zebrafish embryos which were phenylhydrazine Phz stressed or unstressed and then treated with imiquimod or vehicle control. A minimum of three replicates per condition were analysed.			Het Phz DMSO 4	GSM5160075	tissue:TgItga2b:GFPlo cells\|genotype:Rps14+/ \|stress:Phz\|treatment:DMSO	Het Phz DMSO 4	Data QC was conducted using FastQC 0.11.9 and reads trimmed using Trimmomatic 0.39 Reads were aligned to the zebrafish genome GRCz11 using HISAT2 2.1.0 Alignments were sorted and indexed with samtools 1.9 Reads were counted using featureCounts from subread 2.0.0 and GTF Danio Rerio GRCz11.97 Counts were normalised and differential gene expression was analysed using DESeq2 Genome build: GRCz11 Supplementary files format and content: Matrix of normalised raw counts for every gene and every sample	TgItga2b:GFPlo cells	Haemolytic stress was induced by exposure of embryos to phenylhydrazine. Embryos were incubated in 1 µg/mL PHZ from 24 hpf to 48 hpf and then washed. Embryos were then incubated 20 µM Imiquimod or DMSO control for 4 days from 48hpf to 6dpf. Rps14 genotypes were determined with tailclips and embryos pooled before sorting.	Embryos were pooled by rps14 genotype stress and treatment and TgItga2b:GFPlo cells were sorted directly into Trizol for RNA extraction Libraries were prepared using the Smart seq2 protocol	Tgitga2b:GFP zebrafish were maintained according to standard procedures and UK Home Office guidelines	genotype:Rps14+/ \|stress:Phz\|treatment:DMSO	GSM5160075	GSM5160075: Het Phz DMSO 4; Danio rerio; RNA Seq	GSM5160075		1	Embryos were pooled by rps14 genotype stress and treatment and TgItga2b:GFPlo cells were sorted directly into Trizol for RNA extraction Libraries were prepared using the Smart seq2 protocol	GEO Accession:GSM5160075	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP310259	loader:fastq load.py	32_S32_L001_R1_001.fastq 32_S32_L001_R2_001.fastq	fastq fastq	694242632.0	5733799.0	GSM5160075 r1	0:60.54 1:60.54	A:190452479;C:154431412;G:160338326;T:188980753;N:39662	60	60	190452479	154431412	160338326	188980753	39662	SRX10317717	SRS8438154	SRA1205468	GEO	Department of Haematology, UCL Cancer Institute	2	0.91001	0.91437	0.19563	0.19708	0.75749	0.76051	0.53118	0.52052	61	61	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	United Kingdom	2021-03-11	Multi-stage	Multi-stage	Embryo Imprecise	All anatomical structures
63529	63529	SRR13938395	SRX10317717	SRS8438154	SRP310259	PRJNA713782	TLR7 ligation augments hematopoiesis in Rps14 deficiency via paradoxical inflammatory signalling	GSE168727	Transcriptome Analysis	Myelodysplastic syndrome MDS is a haematological malignancy characterised by blood cytopenias and predisposition to acute myeloid leukaemia. We developed a model of MDS using zebrafish using knockout of Rps14 the primary mediator of the anaemia associated with del 5q MDS. These mutant animals develop bone marrow failure with dysplastic features. We conducted an in vivo small molecule screen to identify compounds that ameliorate the MDS phenotype identifying imiquimod an agonist of TLR7. We conducted RNA seq analysis of both treated and untreated animals to define the mechanism of imiquimod in alleviating anaemia. We find imiquimod alleviates anaemia by promoting haematopoietic stem and progenitor cell expansion and erythroid differentiation the mechanism of which is dependent on TLR7 ligation. TLR7 activation in this setting paradoxically promoted an anti inflammatory gene signature suggesting crosstalk between pro inflammatory pathways endogenous to Rps14 loss and TLR7 pathway activation. Overall design: RNA seq analysis of HSPCs TgItga2b:GFPlo cells from pooled rps14+/ or wildtype zebrafish embryos which were phenylhydrazine Phz stressed or unstressed and then treated with imiquimod or vehicle control. A minimum of three replicates per condition were analysed.			Het Phz DMSO 4	GSM5160075	tissue:TgItga2b:GFPlo cells\|genotype:Rps14+/ \|stress:Phz\|treatment:DMSO	Het Phz DMSO 4	Data QC was conducted using FastQC 0.11.9 and reads trimmed using Trimmomatic 0.39 Reads were aligned to the zebrafish genome GRCz11 using HISAT2 2.1.0 Alignments were sorted and indexed with samtools 1.9 Reads were counted using featureCounts from subread 2.0.0 and GTF Danio Rerio GRCz11.97 Counts were normalised and differential gene expression was analysed using DESeq2 Genome build: GRCz11 Supplementary files format and content: Matrix of normalised raw counts for every gene and every sample	TgItga2b:GFPlo cells	Haemolytic stress was induced by exposure of embryos to phenylhydrazine. Embryos were incubated in 1 µg/mL PHZ from 24 hpf to 48 hpf and then washed. Embryos were then incubated 20 µM Imiquimod or DMSO control for 4 days from 48hpf to 6dpf. Rps14 genotypes were determined with tailclips and embryos pooled before sorting.	Embryos were pooled by rps14 genotype stress and treatment and TgItga2b:GFPlo cells were sorted directly into Trizol for RNA extraction Libraries were prepared using the Smart seq2 protocol	Tgitga2b:GFP zebrafish were maintained according to standard procedures and UK Home Office guidelines	genotype:Rps14+/ \|stress:Phz\|treatment:DMSO	GSM5160075	GSM5160075: Het Phz DMSO 4; Danio rerio; RNA Seq	GSM5160075		1	Embryos were pooled by rps14 genotype stress and treatment and TgItga2b:GFPlo cells were sorted directly into Trizol for RNA extraction Libraries were prepared using the Smart seq2 protocol	GEO Accession:GSM5160075	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP310259	loader:fastq load.py	32_S32_L002_R1_001.fastq 32_S32_L002_R2_001.fastq	fastq fastq	709456844.0	5859428.0	GSM5160075 r2	0:60.54 1:60.54	A:194621122;C:157855223;G:163911399;T:193036573;N:32527	60	60	194621122	157855223	163911399	193036573	32527	SRX10317717	SRS8438154	SRA1205468	GEO	Department of Haematology, UCL Cancer Institute	2	0.90998	0.91438	0.19539	0.19709	0.75801	0.7598	0.52537	0.52661	60	61	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	United Kingdom	2021-03-11	Multi-stage	Multi-stage	Embryo Imprecise	All anatomical structures
63530	63530	SRR13938392	SRX10317716	SRS8438153	SRP310259	PRJNA713782	TLR7 ligation augments hematopoiesis in Rps14 deficiency via paradoxical inflammatory signalling	GSE168727	Transcriptome Analysis	Myelodysplastic syndrome MDS is a haematological malignancy characterised by blood cytopenias and predisposition to acute myeloid leukaemia. We developed a model of MDS using zebrafish using knockout of Rps14 the primary mediator of the anaemia associated with del 5q MDS. These mutant animals develop bone marrow failure with dysplastic features. We conducted an in vivo small molecule screen to identify compounds that ameliorate the MDS phenotype identifying imiquimod an agonist of TLR7. We conducted RNA seq analysis of both treated and untreated animals to define the mechanism of imiquimod in alleviating anaemia. We find imiquimod alleviates anaemia by promoting haematopoietic stem and progenitor cell expansion and erythroid differentiation the mechanism of which is dependent on TLR7 ligation. TLR7 activation in this setting paradoxically promoted an anti inflammatory gene signature suggesting crosstalk between pro inflammatory pathways endogenous to Rps14 loss and TLR7 pathway activation. Overall design: RNA seq analysis of HSPCs TgItga2b:GFPlo cells from pooled rps14+/ or wildtype zebrafish embryos which were phenylhydrazine Phz stressed or unstressed and then treated with imiquimod or vehicle control. A minimum of three replicates per condition were analysed.			WT Phz DMSO 3	GSM5160074	tissue:TgItga2b:GFPlo cells\|genotype:Rps14+/+\|stress:Phz\|treatment:DMSO	WT Phz DMSO 3	Data QC was conducted using FastQC 0.11.9 and reads trimmed using Trimmomatic 0.39 Reads were aligned to the zebrafish genome GRCz11 using HISAT2 2.1.0 Alignments were sorted and indexed with samtools 1.9 Reads were counted using featureCounts from subread 2.0.0 and GTF Danio Rerio GRCz11.97 Counts were normalised and differential gene expression was analysed using DESeq2 Genome build: GRCz11 Supplementary files format and content: Matrix of normalised raw counts for every gene and every sample	TgItga2b:GFPlo cells	Haemolytic stress was induced by exposure of embryos to phenylhydrazine. Embryos were incubated in 1 µg/mL PHZ from 24 hpf to 48 hpf and then washed. Embryos were then incubated 20 µM Imiquimod or DMSO control for 4 days from 48hpf to 6dpf. Rps14 genotypes were determined with tailclips and embryos pooled before sorting.	Embryos were pooled by rps14 genotype stress and treatment and TgItga2b:GFPlo cells were sorted directly into Trizol for RNA extraction Libraries were prepared using the Smart seq2 protocol	Tgitga2b:GFP zebrafish were maintained according to standard procedures and UK Home Office guidelines	genotype:Rps14+/+\|stress:Phz\|treatment:DMSO	GSM5160074	GSM5160074: WT Phz DMSO 3; Danio rerio; RNA Seq	GSM5160074		1	Embryos were pooled by rps14 genotype stress and treatment and TgItga2b:GFPlo cells were sorted directly into Trizol for RNA extraction Libraries were prepared using the Smart seq2 protocol	GEO Accession:GSM5160074	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP310259	loader:fastq load.py	31_S31_L001_R1_001.fastq 31_S31_L001_R2_001.fastq	fastq fastq	679694270.0	5613240.0	GSM5160074 r1	0:60.55 1:60.54	A:187380299;C:149957372;G:155769992;T:186550292;N:36315	60	60	187380299	149957372	155769992	186550292	36315	SRX10317716	SRS8438153	SRA1205468	GEO	Department of Haematology, UCL Cancer Institute	2	0.89276	0.89879	0.19926	0.20232	0.76644	0.77005	0.53541	0.53556	61	61	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	United Kingdom	2021-03-11	Multi-stage	Multi-stage	Embryo Imprecise	All anatomical structures
63531	63531	SRR13938393	SRX10317716	SRS8438153	SRP310259	PRJNA713782	TLR7 ligation augments hematopoiesis in Rps14 deficiency via paradoxical inflammatory signalling	GSE168727	Transcriptome Analysis	Myelodysplastic syndrome MDS is a haematological malignancy characterised by blood cytopenias and predisposition to acute myeloid leukaemia. We developed a model of MDS using zebrafish using knockout of Rps14 the primary mediator of the anaemia associated with del 5q MDS. These mutant animals develop bone marrow failure with dysplastic features. We conducted an in vivo small molecule screen to identify compounds that ameliorate the MDS phenotype identifying imiquimod an agonist of TLR7. We conducted RNA seq analysis of both treated and untreated animals to define the mechanism of imiquimod in alleviating anaemia. We find imiquimod alleviates anaemia by promoting haematopoietic stem and progenitor cell expansion and erythroid differentiation the mechanism of which is dependent on TLR7 ligation. TLR7 activation in this setting paradoxically promoted an anti inflammatory gene signature suggesting crosstalk between pro inflammatory pathways endogenous to Rps14 loss and TLR7 pathway activation. Overall design: RNA seq analysis of HSPCs TgItga2b:GFPlo cells from pooled rps14+/ or wildtype zebrafish embryos which were phenylhydrazine Phz stressed or unstressed and then treated with imiquimod or vehicle control. A minimum of three replicates per condition were analysed.			WT Phz DMSO 3	GSM5160074	tissue:TgItga2b:GFPlo cells\|genotype:Rps14+/+\|stress:Phz\|treatment:DMSO	WT Phz DMSO 3	Data QC was conducted using FastQC 0.11.9 and reads trimmed using Trimmomatic 0.39 Reads were aligned to the zebrafish genome GRCz11 using HISAT2 2.1.0 Alignments were sorted and indexed with samtools 1.9 Reads were counted using featureCounts from subread 2.0.0 and GTF Danio Rerio GRCz11.97 Counts were normalised and differential gene expression was analysed using DESeq2 Genome build: GRCz11 Supplementary files format and content: Matrix of normalised raw counts for every gene and every sample	TgItga2b:GFPlo cells	Haemolytic stress was induced by exposure of embryos to phenylhydrazine. Embryos were incubated in 1 µg/mL PHZ from 24 hpf to 48 hpf and then washed. Embryos were then incubated 20 µM Imiquimod or DMSO control for 4 days from 48hpf to 6dpf. Rps14 genotypes were determined with tailclips and embryos pooled before sorting.	Embryos were pooled by rps14 genotype stress and treatment and TgItga2b:GFPlo cells were sorted directly into Trizol for RNA extraction Libraries were prepared using the Smart seq2 protocol	Tgitga2b:GFP zebrafish were maintained according to standard procedures and UK Home Office guidelines	genotype:Rps14+/+\|stress:Phz\|treatment:DMSO	GSM5160074	GSM5160074: WT Phz DMSO 3; Danio rerio; RNA Seq	GSM5160074		1	Embryos were pooled by rps14 genotype stress and treatment and TgItga2b:GFPlo cells were sorted directly into Trizol for RNA extraction Libraries were prepared using the Smart seq2 protocol	GEO Accession:GSM5160074	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP310259	loader:fastq load.py	31_S31_L002_R1_001.fastq 31_S31_L002_R2_001.fastq	fastq fastq	693749434.0	5729329.0	GSM5160074 r2	0:60.55 1:60.54	A:191308582;C:153055956;G:159055142;T:190302086;N:27668	60	60	191308582	153055956	159055142	190302086	27668	SRX10317716	SRS8438153	SRA1205468	GEO	Department of Haematology, UCL Cancer Institute	2	0.89222	0.89824	0.19886	0.2002	0.76577	0.7679	0.53388	0.5378	61	61	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	United Kingdom	2021-03-11	Multi-stage	Multi-stage	Embryo Imprecise	All anatomical structures
63532	63532	SRR13938390	SRX10317715	SRS8438152	SRP310259	PRJNA713782	TLR7 ligation augments hematopoiesis in Rps14 deficiency via paradoxical inflammatory signalling	GSE168727	Transcriptome Analysis	Myelodysplastic syndrome MDS is a haematological malignancy characterised by blood cytopenias and predisposition to acute myeloid leukaemia. We developed a model of MDS using zebrafish using knockout of Rps14 the primary mediator of the anaemia associated with del 5q MDS. These mutant animals develop bone marrow failure with dysplastic features. We conducted an in vivo small molecule screen to identify compounds that ameliorate the MDS phenotype identifying imiquimod an agonist of TLR7. We conducted RNA seq analysis of both treated and untreated animals to define the mechanism of imiquimod in alleviating anaemia. We find imiquimod alleviates anaemia by promoting haematopoietic stem and progenitor cell expansion and erythroid differentiation the mechanism of which is dependent on TLR7 ligation. TLR7 activation in this setting paradoxically promoted an anti inflammatory gene signature suggesting crosstalk between pro inflammatory pathways endogenous to Rps14 loss and TLR7 pathway activation. Overall design: RNA seq analysis of HSPCs TgItga2b:GFPlo cells from pooled rps14+/ or wildtype zebrafish embryos which were phenylhydrazine Phz stressed or unstressed and then treated with imiquimod or vehicle control. A minimum of three replicates per condition were analysed.			WT Phz DMSO 2	GSM5160073	tissue:TgItga2b:GFPlo cells\|genotype:Rps14+/+\|stress:Phz\|treatment:DMSO	WT Phz DMSO 2	Data QC was conducted using FastQC 0.11.9 and reads trimmed using Trimmomatic 0.39 Reads were aligned to the zebrafish genome GRCz11 using HISAT2 2.1.0 Alignments were sorted and indexed with samtools 1.9 Reads were counted using featureCounts from subread 2.0.0 and GTF Danio Rerio GRCz11.97 Counts were normalised and differential gene expression was analysed using DESeq2 Genome build: GRCz11 Supplementary files format and content: Matrix of normalised raw counts for every gene and every sample	TgItga2b:GFPlo cells	Haemolytic stress was induced by exposure of embryos to phenylhydrazine. Embryos were incubated in 1 µg/mL PHZ from 24 hpf to 48 hpf and then washed. Embryos were then incubated 20 µM Imiquimod or DMSO control for 4 days from 48hpf to 6dpf. Rps14 genotypes were determined with tailclips and embryos pooled before sorting.	Embryos were pooled by rps14 genotype stress and treatment and TgItga2b:GFPlo cells were sorted directly into Trizol for RNA extraction Libraries were prepared using the Smart seq2 protocol	Tgitga2b:GFP zebrafish were maintained according to standard procedures and UK Home Office guidelines	genotype:Rps14+/+\|stress:Phz\|treatment:DMSO	GSM5160073	GSM5160073: WT Phz DMSO 2; Danio rerio; RNA Seq	GSM5160073		1	Embryos were pooled by rps14 genotype stress and treatment and TgItga2b:GFPlo cells were sorted directly into Trizol for RNA extraction Libraries were prepared using the Smart seq2 protocol	GEO Accession:GSM5160073	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP310259	loader:fastq load.py	30_S30_L001_R1_001.fastq 30_S30_L001_R2_001.fastq	fastq fastq	623343542.0	5148419.0	GSM5160073 r1	0:60.54 1:60.54	A:170020144;C:139678655;G:145043883;T:168569461;N:31399	60	60	170020144	139678655	145043883	168569461	31399	SRX10317715	SRS8438152	SRA1205468	GEO	Department of Haematology, UCL Cancer Institute	2	0.91638	0.92098	0.17895	0.18108	0.75875	0.76317	0.53112	0.5373	61	61	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	United Kingdom	2021-03-11	Multi-stage	Multi-stage	Embryo Imprecise	All anatomical structures
63533	63533	SRR13938391	SRX10317715	SRS8438152	SRP310259	PRJNA713782	TLR7 ligation augments hematopoiesis in Rps14 deficiency via paradoxical inflammatory signalling	GSE168727	Transcriptome Analysis	Myelodysplastic syndrome MDS is a haematological malignancy characterised by blood cytopenias and predisposition to acute myeloid leukaemia. We developed a model of MDS using zebrafish using knockout of Rps14 the primary mediator of the anaemia associated with del 5q MDS. These mutant animals develop bone marrow failure with dysplastic features. We conducted an in vivo small molecule screen to identify compounds that ameliorate the MDS phenotype identifying imiquimod an agonist of TLR7. We conducted RNA seq analysis of both treated and untreated animals to define the mechanism of imiquimod in alleviating anaemia. We find imiquimod alleviates anaemia by promoting haematopoietic stem and progenitor cell expansion and erythroid differentiation the mechanism of which is dependent on TLR7 ligation. TLR7 activation in this setting paradoxically promoted an anti inflammatory gene signature suggesting crosstalk between pro inflammatory pathways endogenous to Rps14 loss and TLR7 pathway activation. Overall design: RNA seq analysis of HSPCs TgItga2b:GFPlo cells from pooled rps14+/ or wildtype zebrafish embryos which were phenylhydrazine Phz stressed or unstressed and then treated with imiquimod or vehicle control. A minimum of three replicates per condition were analysed.			WT Phz DMSO 2	GSM5160073	tissue:TgItga2b:GFPlo cells\|genotype:Rps14+/+\|stress:Phz\|treatment:DMSO	WT Phz DMSO 2	Data QC was conducted using FastQC 0.11.9 and reads trimmed using Trimmomatic 0.39 Reads were aligned to the zebrafish genome GRCz11 using HISAT2 2.1.0 Alignments were sorted and indexed with samtools 1.9 Reads were counted using featureCounts from subread 2.0.0 and GTF Danio Rerio GRCz11.97 Counts were normalised and differential gene expression was analysed using DESeq2 Genome build: GRCz11 Supplementary files format and content: Matrix of normalised raw counts for every gene and every sample	TgItga2b:GFPlo cells	Haemolytic stress was induced by exposure of embryos to phenylhydrazine. Embryos were incubated in 1 µg/mL PHZ from 24 hpf to 48 hpf and then washed. Embryos were then incubated 20 µM Imiquimod or DMSO control for 4 days from 48hpf to 6dpf. Rps14 genotypes were determined with tailclips and embryos pooled before sorting.	Embryos were pooled by rps14 genotype stress and treatment and TgItga2b:GFPlo cells were sorted directly into Trizol for RNA extraction Libraries were prepared using the Smart seq2 protocol	Tgitga2b:GFP zebrafish were maintained according to standard procedures and UK Home Office guidelines	genotype:Rps14+/+\|stress:Phz\|treatment:DMSO	GSM5160073	GSM5160073: WT Phz DMSO 2; Danio rerio; RNA Seq	GSM5160073		1	Embryos were pooled by rps14 genotype stress and treatment and TgItga2b:GFPlo cells were sorted directly into Trizol for RNA extraction Libraries were prepared using the Smart seq2 protocol	GEO Accession:GSM5160073	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP310259	loader:fastq load.py	30_S30_L002_R1_001.fastq 30_S30_L002_R2_001.fastq	fastq fastq	633338417.0	5230945.0	GSM5160073 r2	0:60.54 1:60.54	A:172735379;C:141923833;G:147363448;T:171289741;N:26016	60	60	172735379	141923833	147363448	171289741	26016	SRX10317715	SRS8438152	SRA1205468	GEO	Department of Haematology, UCL Cancer Institute	2	0.91597	0.92125	0.17871	0.18016	0.75913	0.7625	0.54109	0.54348	61	60	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	United Kingdom	2021-03-11	Multi-stage	Multi-stage	Embryo Imprecise	All anatomical structures
63534	63534	SRR13938388	SRX10317714	SRS8438151	SRP310259	PRJNA713782	TLR7 ligation augments hematopoiesis in Rps14 deficiency via paradoxical inflammatory signalling	GSE168727	Transcriptome Analysis	Myelodysplastic syndrome MDS is a haematological malignancy characterised by blood cytopenias and predisposition to acute myeloid leukaemia. We developed a model of MDS using zebrafish using knockout of Rps14 the primary mediator of the anaemia associated with del 5q MDS. These mutant animals develop bone marrow failure with dysplastic features. We conducted an in vivo small molecule screen to identify compounds that ameliorate the MDS phenotype identifying imiquimod an agonist of TLR7. We conducted RNA seq analysis of both treated and untreated animals to define the mechanism of imiquimod in alleviating anaemia. We find imiquimod alleviates anaemia by promoting haematopoietic stem and progenitor cell expansion and erythroid differentiation the mechanism of which is dependent on TLR7 ligation. TLR7 activation in this setting paradoxically promoted an anti inflammatory gene signature suggesting crosstalk between pro inflammatory pathways endogenous to Rps14 loss and TLR7 pathway activation. Overall design: RNA seq analysis of HSPCs TgItga2b:GFPlo cells from pooled rps14+/ or wildtype zebrafish embryos which were phenylhydrazine Phz stressed or unstressed and then treated with imiquimod or vehicle control. A minimum of three replicates per condition were analysed.			Het Phz DMSO 3	GSM5160072	tissue:TgItga2b:GFPlo cells\|genotype:Rps14+/ \|stress:Phz\|treatment:DMSO	Het Phz DMSO 3	Data QC was conducted using FastQC 0.11.9 and reads trimmed using Trimmomatic 0.39 Reads were aligned to the zebrafish genome GRCz11 using HISAT2 2.1.0 Alignments were sorted and indexed with samtools 1.9 Reads were counted using featureCounts from subread 2.0.0 and GTF Danio Rerio GRCz11.97 Counts were normalised and differential gene expression was analysed using DESeq2 Genome build: GRCz11 Supplementary files format and content: Matrix of normalised raw counts for every gene and every sample	TgItga2b:GFPlo cells	Haemolytic stress was induced by exposure of embryos to phenylhydrazine. Embryos were incubated in 1 µg/mL PHZ from 24 hpf to 48 hpf and then washed. Embryos were then incubated 20 µM Imiquimod or DMSO control for 4 days from 48hpf to 6dpf. Rps14 genotypes were determined with tailclips and embryos pooled before sorting.	Embryos were pooled by rps14 genotype stress and treatment and TgItga2b:GFPlo cells were sorted directly into Trizol for RNA extraction Libraries were prepared using the Smart seq2 protocol	Tgitga2b:GFP zebrafish were maintained according to standard procedures and UK Home Office guidelines	genotype:Rps14+/ \|stress:Phz\|treatment:DMSO	GSM5160072	GSM5160072: Het Phz DMSO 3; Danio rerio; RNA Seq	GSM5160072		1	Embryos were pooled by rps14 genotype stress and treatment and TgItga2b:GFPlo cells were sorted directly into Trizol for RNA extraction Libraries were prepared using the Smart seq2 protocol	GEO Accession:GSM5160072	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP310259	loader:fastq load.py	29_S29_L001_R1_001.fastq 29_S29_L001_R2_001.fastq	fastq fastq	692675616.0	5721690.0	GSM5160072 r1	0:60.53 1:60.53	A:187793287;C:156519060;G:162212288;T:186108340;N:42641	60	60	187793287	156519060	162212288	186108340	42641	SRX10317714	SRS8438151	SRA1205468	GEO	Department of Haematology, UCL Cancer Institute	2	0.92345	0.92842	0.14198	0.14364	0.75605	0.75639	0.50419	0.50901	60	61	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	United Kingdom	2021-03-11	Multi-stage	Multi-stage	Embryo Imprecise	All anatomical structures
63535	63535	SRR13938389	SRX10317714	SRS8438151	SRP310259	PRJNA713782	TLR7 ligation augments hematopoiesis in Rps14 deficiency via paradoxical inflammatory signalling	GSE168727	Transcriptome Analysis	Myelodysplastic syndrome MDS is a haematological malignancy characterised by blood cytopenias and predisposition to acute myeloid leukaemia. We developed a model of MDS using zebrafish using knockout of Rps14 the primary mediator of the anaemia associated with del 5q MDS. These mutant animals develop bone marrow failure with dysplastic features. We conducted an in vivo small molecule screen to identify compounds that ameliorate the MDS phenotype identifying imiquimod an agonist of TLR7. We conducted RNA seq analysis of both treated and untreated animals to define the mechanism of imiquimod in alleviating anaemia. We find imiquimod alleviates anaemia by promoting haematopoietic stem and progenitor cell expansion and erythroid differentiation the mechanism of which is dependent on TLR7 ligation. TLR7 activation in this setting paradoxically promoted an anti inflammatory gene signature suggesting crosstalk between pro inflammatory pathways endogenous to Rps14 loss and TLR7 pathway activation. Overall design: RNA seq analysis of HSPCs TgItga2b:GFPlo cells from pooled rps14+/ or wildtype zebrafish embryos which were phenylhydrazine Phz stressed or unstressed and then treated with imiquimod or vehicle control. A minimum of three replicates per condition were analysed.			Het Phz DMSO 3	GSM5160072	tissue:TgItga2b:GFPlo cells\|genotype:Rps14+/ \|stress:Phz\|treatment:DMSO	Het Phz DMSO 3	Data QC was conducted using FastQC 0.11.9 and reads trimmed using Trimmomatic 0.39 Reads were aligned to the zebrafish genome GRCz11 using HISAT2 2.1.0 Alignments were sorted and indexed with samtools 1.9 Reads were counted using featureCounts from subread 2.0.0 and GTF Danio Rerio GRCz11.97 Counts were normalised and differential gene expression was analysed using DESeq2 Genome build: GRCz11 Supplementary files format and content: Matrix of normalised raw counts for every gene and every sample	TgItga2b:GFPlo cells	Haemolytic stress was induced by exposure of embryos to phenylhydrazine. Embryos were incubated in 1 µg/mL PHZ from 24 hpf to 48 hpf and then washed. Embryos were then incubated 20 µM Imiquimod or DMSO control for 4 days from 48hpf to 6dpf. Rps14 genotypes were determined with tailclips and embryos pooled before sorting.	Embryos were pooled by rps14 genotype stress and treatment and TgItga2b:GFPlo cells were sorted directly into Trizol for RNA extraction Libraries were prepared using the Smart seq2 protocol	Tgitga2b:GFP zebrafish were maintained according to standard procedures and UK Home Office guidelines	genotype:Rps14+/ \|stress:Phz\|treatment:DMSO	GSM5160072	GSM5160072: Het Phz DMSO 3; Danio rerio; RNA Seq	GSM5160072		1	Embryos were pooled by rps14 genotype stress and treatment and TgItga2b:GFPlo cells were sorted directly into Trizol for RNA extraction Libraries were prepared using the Smart seq2 protocol	GEO Accession:GSM5160072	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP310259	loader:fastq load.py	29_S29_L002_R1_001.fastq 29_S29_L002_R2_001.fastq	fastq fastq	706127028.0	5832741.0	GSM5160072 r2	0:60.53 1:60.53	A:191426608;C:159582684;G:165388236;T:189696436;N:33064	60	60	191426608	159582684	165388236	189696436	33064	SRX10317714	SRS8438151	SRA1205468	GEO	Department of Haematology, UCL Cancer Institute	2	0.92271	0.92784	0.14263	0.14424	0.75544	0.75576	0.512	0.50926	59	59	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	United Kingdom	2021-03-11	Multi-stage	Multi-stage	Embryo Imprecise	All anatomical structures
63536	63536	SRR13938386	SRX10317713	SRS8438150	SRP310259	PRJNA713782	TLR7 ligation augments hematopoiesis in Rps14 deficiency via paradoxical inflammatory signalling	GSE168727	Transcriptome Analysis	Myelodysplastic syndrome MDS is a haematological malignancy characterised by blood cytopenias and predisposition to acute myeloid leukaemia. We developed a model of MDS using zebrafish using knockout of Rps14 the primary mediator of the anaemia associated with del 5q MDS. These mutant animals develop bone marrow failure with dysplastic features. We conducted an in vivo small molecule screen to identify compounds that ameliorate the MDS phenotype identifying imiquimod an agonist of TLR7. We conducted RNA seq analysis of both treated and untreated animals to define the mechanism of imiquimod in alleviating anaemia. We find imiquimod alleviates anaemia by promoting haematopoietic stem and progenitor cell expansion and erythroid differentiation the mechanism of which is dependent on TLR7 ligation. TLR7 activation in this setting paradoxically promoted an anti inflammatory gene signature suggesting crosstalk between pro inflammatory pathways endogenous to Rps14 loss and TLR7 pathway activation. Overall design: RNA seq analysis of HSPCs TgItga2b:GFPlo cells from pooled rps14+/ or wildtype zebrafish embryos which were phenylhydrazine Phz stressed or unstressed and then treated with imiquimod or vehicle control. A minimum of three replicates per condition were analysed.			Het Phz DMSO 2	GSM5160071	tissue:TgItga2b:GFPlo cells\|genotype:Rps14+/ \|stress:Phz\|treatment:DMSO	Het Phz DMSO 2	Data QC was conducted using FastQC 0.11.9 and reads trimmed using Trimmomatic 0.39 Reads were aligned to the zebrafish genome GRCz11 using HISAT2 2.1.0 Alignments were sorted and indexed with samtools 1.9 Reads were counted using featureCounts from subread 2.0.0 and GTF Danio Rerio GRCz11.97 Counts were normalised and differential gene expression was analysed using DESeq2 Genome build: GRCz11 Supplementary files format and content: Matrix of normalised raw counts for every gene and every sample	TgItga2b:GFPlo cells	Haemolytic stress was induced by exposure of embryos to phenylhydrazine. Embryos were incubated in 1 µg/mL PHZ from 24 hpf to 48 hpf and then washed. Embryos were then incubated 20 µM Imiquimod or DMSO control for 4 days from 48hpf to 6dpf. Rps14 genotypes were determined with tailclips and embryos pooled before sorting.	Embryos were pooled by rps14 genotype stress and treatment and TgItga2b:GFPlo cells were sorted directly into Trizol for RNA extraction Libraries were prepared using the Smart seq2 protocol	Tgitga2b:GFP zebrafish were maintained according to standard procedures and UK Home Office guidelines	genotype:Rps14+/ \|stress:Phz\|treatment:DMSO	GSM5160071	GSM5160071: Het Phz DMSO 2; Danio rerio; RNA Seq	GSM5160071		1	Embryos were pooled by rps14 genotype stress and treatment and TgItga2b:GFPlo cells were sorted directly into Trizol for RNA extraction Libraries were prepared using the Smart seq2 protocol	GEO Accession:GSM5160071	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP310259	loader:fastq load.py	28_S28_L001_R1_001.fastq 28_S28_L001_R2_001.fastq	fastq fastq	527618428.0	4357669.0	GSM5160071 r1	0:60.54 1:60.54	A:144574218;C:117637182;G:121882071;T:143494029;N:30928	60	60	144574218	117637182	121882071	143494029	30928	SRX10317713	SRS8438150	SRA1205468	GEO	Department of Haematology, UCL Cancer Institute	2	0.90716	0.91069	0.17663	0.17808	0.75097	0.75361	0.51554	0.51893	61	61	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	United Kingdom	2021-03-11	Multi-stage	Multi-stage	Embryo Imprecise	All anatomical structures
63537	63537	SRR13938387	SRX10317713	SRS8438150	SRP310259	PRJNA713782	TLR7 ligation augments hematopoiesis in Rps14 deficiency via paradoxical inflammatory signalling	GSE168727	Transcriptome Analysis	Myelodysplastic syndrome MDS is a haematological malignancy characterised by blood cytopenias and predisposition to acute myeloid leukaemia. We developed a model of MDS using zebrafish using knockout of Rps14 the primary mediator of the anaemia associated with del 5q MDS. These mutant animals develop bone marrow failure with dysplastic features. We conducted an in vivo small molecule screen to identify compounds that ameliorate the MDS phenotype identifying imiquimod an agonist of TLR7. We conducted RNA seq analysis of both treated and untreated animals to define the mechanism of imiquimod in alleviating anaemia. We find imiquimod alleviates anaemia by promoting haematopoietic stem and progenitor cell expansion and erythroid differentiation the mechanism of which is dependent on TLR7 ligation. TLR7 activation in this setting paradoxically promoted an anti inflammatory gene signature suggesting crosstalk between pro inflammatory pathways endogenous to Rps14 loss and TLR7 pathway activation. Overall design: RNA seq analysis of HSPCs TgItga2b:GFPlo cells from pooled rps14+/ or wildtype zebrafish embryos which were phenylhydrazine Phz stressed or unstressed and then treated with imiquimod or vehicle control. A minimum of three replicates per condition were analysed.			Het Phz DMSO 2	GSM5160071	tissue:TgItga2b:GFPlo cells\|genotype:Rps14+/ \|stress:Phz\|treatment:DMSO	Het Phz DMSO 2	Data QC was conducted using FastQC 0.11.9 and reads trimmed using Trimmomatic 0.39 Reads were aligned to the zebrafish genome GRCz11 using HISAT2 2.1.0 Alignments were sorted and indexed with samtools 1.9 Reads were counted using featureCounts from subread 2.0.0 and GTF Danio Rerio GRCz11.97 Counts were normalised and differential gene expression was analysed using DESeq2 Genome build: GRCz11 Supplementary files format and content: Matrix of normalised raw counts for every gene and every sample	TgItga2b:GFPlo cells	Haemolytic stress was induced by exposure of embryos to phenylhydrazine. Embryos were incubated in 1 µg/mL PHZ from 24 hpf to 48 hpf and then washed. Embryos were then incubated 20 µM Imiquimod or DMSO control for 4 days from 48hpf to 6dpf. Rps14 genotypes were determined with tailclips and embryos pooled before sorting.	Embryos were pooled by rps14 genotype stress and treatment and TgItga2b:GFPlo cells were sorted directly into Trizol for RNA extraction Libraries were prepared using the Smart seq2 protocol	Tgitga2b:GFP zebrafish were maintained according to standard procedures and UK Home Office guidelines	genotype:Rps14+/ \|stress:Phz\|treatment:DMSO	GSM5160071	GSM5160071: Het Phz DMSO 2; Danio rerio; RNA Seq	GSM5160071		1	Embryos were pooled by rps14 genotype stress and treatment and TgItga2b:GFPlo cells were sorted directly into Trizol for RNA extraction Libraries were prepared using the Smart seq2 protocol	GEO Accession:GSM5160071	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP310259	loader:fastq load.py	28_S28_L002_R1_001.fastq 28_S28_L002_R2_001.fastq	fastq fastq	539070462.0	4452231.0	GSM5160071 r2	0:60.54 1:60.54	A:147757622;C:120179248;G:124553791;T:146555205;N:24596	60	60	147757622	120179248	124553791	146555205	24596	SRX10317713	SRS8438150	SRA1205468	GEO	Department of Haematology, UCL Cancer Institute	2	0.9042	0.91046	0.17744	0.17877	0.7527	0.75595	0.51424	0.51773	60	61	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	United Kingdom	2021-03-11	Multi-stage	Multi-stage	Embryo Imprecise	All anatomical structures
63538	63538	SRR13938384	SRX10317712	SRS8438149	SRP310259	PRJNA713782	TLR7 ligation augments hematopoiesis in Rps14 deficiency via paradoxical inflammatory signalling	GSE168727	Transcriptome Analysis	Myelodysplastic syndrome MDS is a haematological malignancy characterised by blood cytopenias and predisposition to acute myeloid leukaemia. We developed a model of MDS using zebrafish using knockout of Rps14 the primary mediator of the anaemia associated with del 5q MDS. These mutant animals develop bone marrow failure with dysplastic features. We conducted an in vivo small molecule screen to identify compounds that ameliorate the MDS phenotype identifying imiquimod an agonist of TLR7. We conducted RNA seq analysis of both treated and untreated animals to define the mechanism of imiquimod in alleviating anaemia. We find imiquimod alleviates anaemia by promoting haematopoietic stem and progenitor cell expansion and erythroid differentiation the mechanism of which is dependent on TLR7 ligation. TLR7 activation in this setting paradoxically promoted an anti inflammatory gene signature suggesting crosstalk between pro inflammatory pathways endogenous to Rps14 loss and TLR7 pathway activation. Overall design: RNA seq analysis of HSPCs TgItga2b:GFPlo cells from pooled rps14+/ or wildtype zebrafish embryos which were phenylhydrazine Phz stressed or unstressed and then treated with imiquimod or vehicle control. A minimum of three replicates per condition were analysed.			Het Phz DMSO 1	GSM5160070	tissue:TgItga2b:GFPlo cells\|genotype:Rps14+/ \|stress:Phz\|treatment:DMSO	Het Phz DMSO 1	Data QC was conducted using FastQC 0.11.9 and reads trimmed using Trimmomatic 0.39 Reads were aligned to the zebrafish genome GRCz11 using HISAT2 2.1.0 Alignments were sorted and indexed with samtools 1.9 Reads were counted using featureCounts from subread 2.0.0 and GTF Danio Rerio GRCz11.97 Counts were normalised and differential gene expression was analysed using DESeq2 Genome build: GRCz11 Supplementary files format and content: Matrix of normalised raw counts for every gene and every sample	TgItga2b:GFPlo cells	Haemolytic stress was induced by exposure of embryos to phenylhydrazine. Embryos were incubated in 1 µg/mL PHZ from 24 hpf to 48 hpf and then washed. Embryos were then incubated 20 µM Imiquimod or DMSO control for 4 days from 48hpf to 6dpf. Rps14 genotypes were determined with tailclips and embryos pooled before sorting.	Embryos were pooled by rps14 genotype stress and treatment and TgItga2b:GFPlo cells were sorted directly into Trizol for RNA extraction Libraries were prepared using the Smart seq2 protocol	Tgitga2b:GFP zebrafish were maintained according to standard procedures and UK Home Office guidelines	genotype:Rps14+/ \|stress:Phz\|treatment:DMSO	GSM5160070	GSM5160070: Het Phz DMSO 1; Danio rerio; RNA Seq	GSM5160070		1	Embryos were pooled by rps14 genotype stress and treatment and TgItga2b:GFPlo cells were sorted directly into Trizol for RNA extraction Libraries were prepared using the Smart seq2 protocol	GEO Accession:GSM5160070	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP310259	loader:fastq load.py	27_S27_L001_R1_001.fastq 27_S27_L001_R2_001.fastq	fastq fastq	571076947.0	4716553.0	GSM5160070 r1	0:60.54 1:60.54	A:156802796;C:127151870;G:131628960;T:155463210;N:30111	60	60	156802796	127151870	131628960	155463210	30111	SRX10317712	SRS8438149	SRA1205468	GEO	Department of Haematology, UCL Cancer Institute	2	0.91634	0.92214	0.16788	0.16917	0.75566	0.75771	0.44594	0.45532	61	61	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	United Kingdom	2021-03-11	Multi-stage	Multi-stage	Embryo Imprecise	All anatomical structures
63539	63539	SRR13938385	SRX10317712	SRS8438149	SRP310259	PRJNA713782	TLR7 ligation augments hematopoiesis in Rps14 deficiency via paradoxical inflammatory signalling	GSE168727	Transcriptome Analysis	Myelodysplastic syndrome MDS is a haematological malignancy characterised by blood cytopenias and predisposition to acute myeloid leukaemia. We developed a model of MDS using zebrafish using knockout of Rps14 the primary mediator of the anaemia associated with del 5q MDS. These mutant animals develop bone marrow failure with dysplastic features. We conducted an in vivo small molecule screen to identify compounds that ameliorate the MDS phenotype identifying imiquimod an agonist of TLR7. We conducted RNA seq analysis of both treated and untreated animals to define the mechanism of imiquimod in alleviating anaemia. We find imiquimod alleviates anaemia by promoting haematopoietic stem and progenitor cell expansion and erythroid differentiation the mechanism of which is dependent on TLR7 ligation. TLR7 activation in this setting paradoxically promoted an anti inflammatory gene signature suggesting crosstalk between pro inflammatory pathways endogenous to Rps14 loss and TLR7 pathway activation. Overall design: RNA seq analysis of HSPCs TgItga2b:GFPlo cells from pooled rps14+/ or wildtype zebrafish embryos which were phenylhydrazine Phz stressed or unstressed and then treated with imiquimod or vehicle control. A minimum of three replicates per condition were analysed.			Het Phz DMSO 1	GSM5160070	tissue:TgItga2b:GFPlo cells\|genotype:Rps14+/ \|stress:Phz\|treatment:DMSO	Het Phz DMSO 1	Data QC was conducted using FastQC 0.11.9 and reads trimmed using Trimmomatic 0.39 Reads were aligned to the zebrafish genome GRCz11 using HISAT2 2.1.0 Alignments were sorted and indexed with samtools 1.9 Reads were counted using featureCounts from subread 2.0.0 and GTF Danio Rerio GRCz11.97 Counts were normalised and differential gene expression was analysed using DESeq2 Genome build: GRCz11 Supplementary files format and content: Matrix of normalised raw counts for every gene and every sample	TgItga2b:GFPlo cells	Haemolytic stress was induced by exposure of embryos to phenylhydrazine. Embryos were incubated in 1 µg/mL PHZ from 24 hpf to 48 hpf and then washed. Embryos were then incubated 20 µM Imiquimod or DMSO control for 4 days from 48hpf to 6dpf. Rps14 genotypes were determined with tailclips and embryos pooled before sorting.	Embryos were pooled by rps14 genotype stress and treatment and TgItga2b:GFPlo cells were sorted directly into Trizol for RNA extraction Libraries were prepared using the Smart seq2 protocol	Tgitga2b:GFP zebrafish were maintained according to standard procedures and UK Home Office guidelines	genotype:Rps14+/ \|stress:Phz\|treatment:DMSO	GSM5160070	GSM5160070: Het Phz DMSO 1; Danio rerio; RNA Seq	GSM5160070		1	Embryos were pooled by rps14 genotype stress and treatment and TgItga2b:GFPlo cells were sorted directly into Trizol for RNA extraction Libraries were prepared using the Smart seq2 protocol	GEO Accession:GSM5160070	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP310259	loader:fastq load.py	27_S27_L002_R1_001.fastq 27_S27_L002_R2_001.fastq	fastq fastq	581937512.0	4806238.0	GSM5160070 r2	0:60.54 1:60.54	A:159798991;C:129572296;G:134158366;T:158384394;N:23465	60	60	159798991	129572296	134158366	158384394	23465	SRX10317712	SRS8438149	SRA1205468	GEO	Department of Haematology, UCL Cancer Institute	2	0.91388	0.92	0.16798	0.16971	0.75615	0.75757	0.44912	0.45923	61	61	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	United Kingdom	2021-03-11	Multi-stage	Multi-stage	Embryo Imprecise	All anatomical structures
63540	63540	SRR13938382	SRX10317711	SRS8438148	SRP310259	PRJNA713782	TLR7 ligation augments hematopoiesis in Rps14 deficiency via paradoxical inflammatory signalling	GSE168727	Transcriptome Analysis	Myelodysplastic syndrome MDS is a haematological malignancy characterised by blood cytopenias and predisposition to acute myeloid leukaemia. We developed a model of MDS using zebrafish using knockout of Rps14 the primary mediator of the anaemia associated with del 5q MDS. These mutant animals develop bone marrow failure with dysplastic features. We conducted an in vivo small molecule screen to identify compounds that ameliorate the MDS phenotype identifying imiquimod an agonist of TLR7. We conducted RNA seq analysis of both treated and untreated animals to define the mechanism of imiquimod in alleviating anaemia. We find imiquimod alleviates anaemia by promoting haematopoietic stem and progenitor cell expansion and erythroid differentiation the mechanism of which is dependent on TLR7 ligation. TLR7 activation in this setting paradoxically promoted an anti inflammatory gene signature suggesting crosstalk between pro inflammatory pathways endogenous to Rps14 loss and TLR7 pathway activation. Overall design: RNA seq analysis of HSPCs TgItga2b:GFPlo cells from pooled rps14+/ or wildtype zebrafish embryos which were phenylhydrazine Phz stressed or unstressed and then treated with imiquimod or vehicle control. A minimum of three replicates per condition were analysed.			WT Phz DMSO 1	GSM5160069	tissue:TgItga2b:GFPlo cells\|genotype:Rps14+/+\|stress:Phz\|treatment:DMSO	WT Phz DMSO 1	Data QC was conducted using FastQC 0.11.9 and reads trimmed using Trimmomatic 0.39 Reads were aligned to the zebrafish genome GRCz11 using HISAT2 2.1.0 Alignments were sorted and indexed with samtools 1.9 Reads were counted using featureCounts from subread 2.0.0 and GTF Danio Rerio GRCz11.97 Counts were normalised and differential gene expression was analysed using DESeq2 Genome build: GRCz11 Supplementary files format and content: Matrix of normalised raw counts for every gene and every sample	TgItga2b:GFPlo cells	Haemolytic stress was induced by exposure of embryos to phenylhydrazine. Embryos were incubated in 1 µg/mL PHZ from 24 hpf to 48 hpf and then washed. Embryos were then incubated 20 µM Imiquimod or DMSO control for 4 days from 48hpf to 6dpf. Rps14 genotypes were determined with tailclips and embryos pooled before sorting.	Embryos were pooled by rps14 genotype stress and treatment and TgItga2b:GFPlo cells were sorted directly into Trizol for RNA extraction Libraries were prepared using the Smart seq2 protocol	Tgitga2b:GFP zebrafish were maintained according to standard procedures and UK Home Office guidelines	genotype:Rps14+/+\|stress:Phz\|treatment:DMSO	GSM5160069	GSM5160069: WT Phz DMSO 1; Danio rerio; RNA Seq	GSM5160069		1	Embryos were pooled by rps14 genotype stress and treatment and TgItga2b:GFPlo cells were sorted directly into Trizol for RNA extraction Libraries were prepared using the Smart seq2 protocol	GEO Accession:GSM5160069	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP310259	loader:fastq load.py	26_S26_L001_R1_001.fastq 26_S26_L001_R2_001.fastq	fastq fastq	670659811.0	5538755.0	GSM5160069 r1	0:60.54 1:60.54	A:184976929;C:148828676;G:153813841;T:182999862;N:40503	60	60	184976929	148828676	153813841	182999862	40503	SRX10317711	SRS8438148	SRA1205468	GEO	Department of Haematology, UCL Cancer Institute	2	0.91056	0.92036	0.18897	0.19198	0.76958	0.77697	0.50818	0.52633	61	61	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	United Kingdom	2021-03-11	Multi-stage	Multi-stage	Embryo Imprecise	All anatomical structures
63541	63541	SRR13938383	SRX10317711	SRS8438148	SRP310259	PRJNA713782	TLR7 ligation augments hematopoiesis in Rps14 deficiency via paradoxical inflammatory signalling	GSE168727	Transcriptome Analysis	Myelodysplastic syndrome MDS is a haematological malignancy characterised by blood cytopenias and predisposition to acute myeloid leukaemia. We developed a model of MDS using zebrafish using knockout of Rps14 the primary mediator of the anaemia associated with del 5q MDS. These mutant animals develop bone marrow failure with dysplastic features. We conducted an in vivo small molecule screen to identify compounds that ameliorate the MDS phenotype identifying imiquimod an agonist of TLR7. We conducted RNA seq analysis of both treated and untreated animals to define the mechanism of imiquimod in alleviating anaemia. We find imiquimod alleviates anaemia by promoting haematopoietic stem and progenitor cell expansion and erythroid differentiation the mechanism of which is dependent on TLR7 ligation. TLR7 activation in this setting paradoxically promoted an anti inflammatory gene signature suggesting crosstalk between pro inflammatory pathways endogenous to Rps14 loss and TLR7 pathway activation. Overall design: RNA seq analysis of HSPCs TgItga2b:GFPlo cells from pooled rps14+/ or wildtype zebrafish embryos which were phenylhydrazine Phz stressed or unstressed and then treated with imiquimod or vehicle control. A minimum of three replicates per condition were analysed.			WT Phz DMSO 1	GSM5160069	tissue:TgItga2b:GFPlo cells\|genotype:Rps14+/+\|stress:Phz\|treatment:DMSO	WT Phz DMSO 1	Data QC was conducted using FastQC 0.11.9 and reads trimmed using Trimmomatic 0.39 Reads were aligned to the zebrafish genome GRCz11 using HISAT2 2.1.0 Alignments were sorted and indexed with samtools 1.9 Reads were counted using featureCounts from subread 2.0.0 and GTF Danio Rerio GRCz11.97 Counts were normalised and differential gene expression was analysed using DESeq2 Genome build: GRCz11 Supplementary files format and content: Matrix of normalised raw counts for every gene and every sample	TgItga2b:GFPlo cells	Haemolytic stress was induced by exposure of embryos to phenylhydrazine. Embryos were incubated in 1 µg/mL PHZ from 24 hpf to 48 hpf and then washed. Embryos were then incubated 20 µM Imiquimod or DMSO control for 4 days from 48hpf to 6dpf. Rps14 genotypes were determined with tailclips and embryos pooled before sorting.	Embryos were pooled by rps14 genotype stress and treatment and TgItga2b:GFPlo cells were sorted directly into Trizol for RNA extraction Libraries were prepared using the Smart seq2 protocol	Tgitga2b:GFP zebrafish were maintained according to standard procedures and UK Home Office guidelines	genotype:Rps14+/+\|stress:Phz\|treatment:DMSO	GSM5160069	GSM5160069: WT Phz DMSO 1; Danio rerio; RNA Seq	GSM5160069		1	Embryos were pooled by rps14 genotype stress and treatment and TgItga2b:GFPlo cells were sorted directly into Trizol for RNA extraction Libraries were prepared using the Smart seq2 protocol	GEO Accession:GSM5160069	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP310259	loader:fastq load.py	26_S26_L002_R1_001.fastq 26_S26_L002_R2_001.fastq	fastq fastq	684448698.0	5652626.0	GSM5160069 r2	0:60.54 1:60.54	A:188863087;C:151911583;G:156986319;T:186656978;N:30731	60	60	188863087	151911583	156986319	186656978	30731	SRX10317711	SRS8438148	SRA1205468	GEO	Department of Haematology, UCL Cancer Institute	2	0.90865	0.91859	0.18854	0.19147	0.77055	0.77753	0.5118	0.51779	61	61	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	United Kingdom	2021-03-11	Multi-stage	Multi-stage	Embryo Imprecise	All anatomical structures
63542	63542	SRR13938380	SRX10317710	SRS8438147	SRP310259	PRJNA713782	TLR7 ligation augments hematopoiesis in Rps14 deficiency via paradoxical inflammatory signalling	GSE168727	Transcriptome Analysis	Myelodysplastic syndrome MDS is a haematological malignancy characterised by blood cytopenias and predisposition to acute myeloid leukaemia. We developed a model of MDS using zebrafish using knockout of Rps14 the primary mediator of the anaemia associated with del 5q MDS. These mutant animals develop bone marrow failure with dysplastic features. We conducted an in vivo small molecule screen to identify compounds that ameliorate the MDS phenotype identifying imiquimod an agonist of TLR7. We conducted RNA seq analysis of both treated and untreated animals to define the mechanism of imiquimod in alleviating anaemia. We find imiquimod alleviates anaemia by promoting haematopoietic stem and progenitor cell expansion and erythroid differentiation the mechanism of which is dependent on TLR7 ligation. TLR7 activation in this setting paradoxically promoted an anti inflammatory gene signature suggesting crosstalk between pro inflammatory pathways endogenous to Rps14 loss and TLR7 pathway activation. Overall design: RNA seq analysis of HSPCs TgItga2b:GFPlo cells from pooled rps14+/ or wildtype zebrafish embryos which were phenylhydrazine Phz stressed or unstressed and then treated with imiquimod or vehicle control. A minimum of three replicates per condition were analysed.			Het Phz Imi 4	GSM5160068	tissue:TgItga2b:GFPlo cells\|genotype:Rps14+/ \|stress:Phz\|treatment:Imiquimod	Het Phz Imi 4	Data QC was conducted using FastQC 0.11.9 and reads trimmed using Trimmomatic 0.39 Reads were aligned to the zebrafish genome GRCz11 using HISAT2 2.1.0 Alignments were sorted and indexed with samtools 1.9 Reads were counted using featureCounts from subread 2.0.0 and GTF Danio Rerio GRCz11.97 Counts were normalised and differential gene expression was analysed using DESeq2 Genome build: GRCz11 Supplementary files format and content: Matrix of normalised raw counts for every gene and every sample	TgItga2b:GFPlo cells	Haemolytic stress was induced by exposure of embryos to phenylhydrazine. Embryos were incubated in 1 µg/mL PHZ from 24 hpf to 48 hpf and then washed. Embryos were then incubated 20 µM Imiquimod or DMSO control for 4 days from 48hpf to 6dpf. Rps14 genotypes were determined with tailclips and embryos pooled before sorting.	Embryos were pooled by rps14 genotype stress and treatment and TgItga2b:GFPlo cells were sorted directly into Trizol for RNA extraction Libraries were prepared using the Smart seq2 protocol	Tgitga2b:GFP zebrafish were maintained according to standard procedures and UK Home Office guidelines	genotype:Rps14+/ \|stress:Phz\|treatment:Imiquimod	GSM5160068	GSM5160068: Het Phz Imi 4; Danio rerio; RNA Seq	GSM5160068		1	Embryos were pooled by rps14 genotype stress and treatment and TgItga2b:GFPlo cells were sorted directly into Trizol for RNA extraction Libraries were prepared using the Smart seq2 protocol	GEO Accession:GSM5160068	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP310259	loader:fastq load.py	24_S24_L001_R1_001.fastq 24_S24_L001_R2_001.fastq	fastq fastq	1196442152.0	9882921.0	GSM5160068 r1	0:60.53 1:60.53	A:327143401;C:268190604;G:277733656;T:323307007;N:67484	60	60	327143401	268190604	277733656	323307007	67484	SRX10317710	SRS8438147	SRA1205468	GEO	Department of Haematology, UCL Cancer Institute	2	0.92219	0.92938	0.1424	0.14523	0.7414	0.75022	0.5129	0.51195	60	61	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	United Kingdom	2021-03-11	Multi-stage	Multi-stage	Embryo Imprecise	All anatomical structures
63543	63543	SRR13938381	SRX10317710	SRS8438147	SRP310259	PRJNA713782	TLR7 ligation augments hematopoiesis in Rps14 deficiency via paradoxical inflammatory signalling	GSE168727	Transcriptome Analysis	Myelodysplastic syndrome MDS is a haematological malignancy characterised by blood cytopenias and predisposition to acute myeloid leukaemia. We developed a model of MDS using zebrafish using knockout of Rps14 the primary mediator of the anaemia associated with del 5q MDS. These mutant animals develop bone marrow failure with dysplastic features. We conducted an in vivo small molecule screen to identify compounds that ameliorate the MDS phenotype identifying imiquimod an agonist of TLR7. We conducted RNA seq analysis of both treated and untreated animals to define the mechanism of imiquimod in alleviating anaemia. We find imiquimod alleviates anaemia by promoting haematopoietic stem and progenitor cell expansion and erythroid differentiation the mechanism of which is dependent on TLR7 ligation. TLR7 activation in this setting paradoxically promoted an anti inflammatory gene signature suggesting crosstalk between pro inflammatory pathways endogenous to Rps14 loss and TLR7 pathway activation. Overall design: RNA seq analysis of HSPCs TgItga2b:GFPlo cells from pooled rps14+/ or wildtype zebrafish embryos which were phenylhydrazine Phz stressed or unstressed and then treated with imiquimod or vehicle control. A minimum of three replicates per condition were analysed.			Het Phz Imi 4	GSM5160068	tissue:TgItga2b:GFPlo cells\|genotype:Rps14+/ \|stress:Phz\|treatment:Imiquimod	Het Phz Imi 4	Data QC was conducted using FastQC 0.11.9 and reads trimmed using Trimmomatic 0.39 Reads were aligned to the zebrafish genome GRCz11 using HISAT2 2.1.0 Alignments were sorted and indexed with samtools 1.9 Reads were counted using featureCounts from subread 2.0.0 and GTF Danio Rerio GRCz11.97 Counts were normalised and differential gene expression was analysed using DESeq2 Genome build: GRCz11 Supplementary files format and content: Matrix of normalised raw counts for every gene and every sample	TgItga2b:GFPlo cells	Haemolytic stress was induced by exposure of embryos to phenylhydrazine. Embryos were incubated in 1 µg/mL PHZ from 24 hpf to 48 hpf and then washed. Embryos were then incubated 20 µM Imiquimod or DMSO control for 4 days from 48hpf to 6dpf. Rps14 genotypes were determined with tailclips and embryos pooled before sorting.	Embryos were pooled by rps14 genotype stress and treatment and TgItga2b:GFPlo cells were sorted directly into Trizol for RNA extraction Libraries were prepared using the Smart seq2 protocol	Tgitga2b:GFP zebrafish were maintained according to standard procedures and UK Home Office guidelines	genotype:Rps14+/ \|stress:Phz\|treatment:Imiquimod	GSM5160068	GSM5160068: Het Phz Imi 4; Danio rerio; RNA Seq	GSM5160068		1	Embryos were pooled by rps14 genotype stress and treatment and TgItga2b:GFPlo cells were sorted directly into Trizol for RNA extraction Libraries were prepared using the Smart seq2 protocol	GEO Accession:GSM5160068	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP310259	loader:fastq load.py	24_S24_L002_R1_001.fastq 24_S24_L002_R2_001.fastq	fastq fastq	1221383547.0	10088872.0	GSM5160068 r2	0:60.53 1:60.53	A:334066083;C:273814105;G:283547780;T:329901661;N:53918	60	60	334066083	273814105	283547780	329901661	53918	SRX10317710	SRS8438147	SRA1205468	GEO	Department of Haematology, UCL Cancer Institute	2	0.92059	0.92851	0.1427	0.14587	0.74574	0.75357	0.51671	0.51697	61	61	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	United Kingdom	2021-03-11	Multi-stage	Multi-stage	Embryo Imprecise	All anatomical structures
63544	63544	SRR13938378	SRX10317709	SRS8438146	SRP310259	PRJNA713782	TLR7 ligation augments hematopoiesis in Rps14 deficiency via paradoxical inflammatory signalling	GSE168727	Transcriptome Analysis	Myelodysplastic syndrome MDS is a haematological malignancy characterised by blood cytopenias and predisposition to acute myeloid leukaemia. We developed a model of MDS using zebrafish using knockout of Rps14 the primary mediator of the anaemia associated with del 5q MDS. These mutant animals develop bone marrow failure with dysplastic features. We conducted an in vivo small molecule screen to identify compounds that ameliorate the MDS phenotype identifying imiquimod an agonist of TLR7. We conducted RNA seq analysis of both treated and untreated animals to define the mechanism of imiquimod in alleviating anaemia. We find imiquimod alleviates anaemia by promoting haematopoietic stem and progenitor cell expansion and erythroid differentiation the mechanism of which is dependent on TLR7 ligation. TLR7 activation in this setting paradoxically promoted an anti inflammatory gene signature suggesting crosstalk between pro inflammatory pathways endogenous to Rps14 loss and TLR7 pathway activation. Overall design: RNA seq analysis of HSPCs TgItga2b:GFPlo cells from pooled rps14+/ or wildtype zebrafish embryos which were phenylhydrazine Phz stressed or unstressed and then treated with imiquimod or vehicle control. A minimum of three replicates per condition were analysed.			Het Phz Imi 3	GSM5160067	tissue:TgItga2b:GFPlo cells\|genotype:Rps14+/ \|stress:Phz\|treatment:Imiquimod	Het Phz Imi 3	Data QC was conducted using FastQC 0.11.9 and reads trimmed using Trimmomatic 0.39 Reads were aligned to the zebrafish genome GRCz11 using HISAT2 2.1.0 Alignments were sorted and indexed with samtools 1.9 Reads were counted using featureCounts from subread 2.0.0 and GTF Danio Rerio GRCz11.97 Counts were normalised and differential gene expression was analysed using DESeq2 Genome build: GRCz11 Supplementary files format and content: Matrix of normalised raw counts for every gene and every sample	TgItga2b:GFPlo cells	Haemolytic stress was induced by exposure of embryos to phenylhydrazine. Embryos were incubated in 1 µg/mL PHZ from 24 hpf to 48 hpf and then washed. Embryos were then incubated 20 µM Imiquimod or DMSO control for 4 days from 48hpf to 6dpf. Rps14 genotypes were determined with tailclips and embryos pooled before sorting.	Embryos were pooled by rps14 genotype stress and treatment and TgItga2b:GFPlo cells were sorted directly into Trizol for RNA extraction Libraries were prepared using the Smart seq2 protocol	Tgitga2b:GFP zebrafish were maintained according to standard procedures and UK Home Office guidelines	genotype:Rps14+/ \|stress:Phz\|treatment:Imiquimod	GSM5160067	GSM5160067: Het Phz Imi 3; Danio rerio; RNA Seq	GSM5160067		1	Embryos were pooled by rps14 genotype stress and treatment and TgItga2b:GFPlo cells were sorted directly into Trizol for RNA extraction Libraries were prepared using the Smart seq2 protocol	GEO Accession:GSM5160067	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP310259	loader:fastq load.py	23_S23_L001_R1_001.fastq 23_S23_L001_R2_001.fastq	fastq fastq	708558393.0	5852466.0	GSM5160067 r1	0:60.54 1:60.53	A:195852920;C:156595065;G:162211978;T:193856476;N:41954	60	60	195852920	156595065	162211978	193856476	41954	SRX10317709	SRS8438146	SRA1205468	GEO	Department of Haematology, UCL Cancer Institute	2	0.90964	0.91777	0.18355	0.18774	0.73977	0.74698	0.51494	0.52177	61	59	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	United Kingdom	2021-03-11	Multi-stage	Multi-stage	Embryo Imprecise	All anatomical structures
63545	63545	SRR13938379	SRX10317709	SRS8438146	SRP310259	PRJNA713782	TLR7 ligation augments hematopoiesis in Rps14 deficiency via paradoxical inflammatory signalling	GSE168727	Transcriptome Analysis	Myelodysplastic syndrome MDS is a haematological malignancy characterised by blood cytopenias and predisposition to acute myeloid leukaemia. We developed a model of MDS using zebrafish using knockout of Rps14 the primary mediator of the anaemia associated with del 5q MDS. These mutant animals develop bone marrow failure with dysplastic features. We conducted an in vivo small molecule screen to identify compounds that ameliorate the MDS phenotype identifying imiquimod an agonist of TLR7. We conducted RNA seq analysis of both treated and untreated animals to define the mechanism of imiquimod in alleviating anaemia. We find imiquimod alleviates anaemia by promoting haematopoietic stem and progenitor cell expansion and erythroid differentiation the mechanism of which is dependent on TLR7 ligation. TLR7 activation in this setting paradoxically promoted an anti inflammatory gene signature suggesting crosstalk between pro inflammatory pathways endogenous to Rps14 loss and TLR7 pathway activation. Overall design: RNA seq analysis of HSPCs TgItga2b:GFPlo cells from pooled rps14+/ or wildtype zebrafish embryos which were phenylhydrazine Phz stressed or unstressed and then treated with imiquimod or vehicle control. A minimum of three replicates per condition were analysed.			Het Phz Imi 3	GSM5160067	tissue:TgItga2b:GFPlo cells\|genotype:Rps14+/ \|stress:Phz\|treatment:Imiquimod	Het Phz Imi 3	Data QC was conducted using FastQC 0.11.9 and reads trimmed using Trimmomatic 0.39 Reads were aligned to the zebrafish genome GRCz11 using HISAT2 2.1.0 Alignments were sorted and indexed with samtools 1.9 Reads were counted using featureCounts from subread 2.0.0 and GTF Danio Rerio GRCz11.97 Counts were normalised and differential gene expression was analysed using DESeq2 Genome build: GRCz11 Supplementary files format and content: Matrix of normalised raw counts for every gene and every sample	TgItga2b:GFPlo cells	Haemolytic stress was induced by exposure of embryos to phenylhydrazine. Embryos were incubated in 1 µg/mL PHZ from 24 hpf to 48 hpf and then washed. Embryos were then incubated 20 µM Imiquimod or DMSO control for 4 days from 48hpf to 6dpf. Rps14 genotypes were determined with tailclips and embryos pooled before sorting.	Embryos were pooled by rps14 genotype stress and treatment and TgItga2b:GFPlo cells were sorted directly into Trizol for RNA extraction Libraries were prepared using the Smart seq2 protocol	Tgitga2b:GFP zebrafish were maintained according to standard procedures and UK Home Office guidelines	genotype:Rps14+/ \|stress:Phz\|treatment:Imiquimod	GSM5160067	GSM5160067: Het Phz Imi 3; Danio rerio; RNA Seq	GSM5160067		1	Embryos were pooled by rps14 genotype stress and treatment and TgItga2b:GFPlo cells were sorted directly into Trizol for RNA extraction Libraries were prepared using the Smart seq2 protocol	GEO Accession:GSM5160067	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP310259	loader:fastq load.py	23_S23_L002_R1_001.fastq 23_S23_L002_R2_001.fastq	fastq fastq	726712214.0	6002382.0	GSM5160067 r2	0:60.54 1:60.53	A:200958535;C:160583124;G:166389339;T:198745192;N:36024	60	60	200958535	160583124	166389339	198745192	36024	SRX10317709	SRS8438146	SRA1205468	GEO	Department of Haematology, UCL Cancer Institute	2	0.90881	0.91762	0.18283	0.18727	0.73845	0.74525	0.51725	0.5211	60	61	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	United Kingdom	2021-03-11	Multi-stage	Multi-stage	Embryo Imprecise	All anatomical structures
63546	63546	SRR13938376	SRX10317708	SRS8438145	SRP310259	PRJNA713782	TLR7 ligation augments hematopoiesis in Rps14 deficiency via paradoxical inflammatory signalling	GSE168727	Transcriptome Analysis	Myelodysplastic syndrome MDS is a haematological malignancy characterised by blood cytopenias and predisposition to acute myeloid leukaemia. We developed a model of MDS using zebrafish using knockout of Rps14 the primary mediator of the anaemia associated with del 5q MDS. These mutant animals develop bone marrow failure with dysplastic features. We conducted an in vivo small molecule screen to identify compounds that ameliorate the MDS phenotype identifying imiquimod an agonist of TLR7. We conducted RNA seq analysis of both treated and untreated animals to define the mechanism of imiquimod in alleviating anaemia. We find imiquimod alleviates anaemia by promoting haematopoietic stem and progenitor cell expansion and erythroid differentiation the mechanism of which is dependent on TLR7 ligation. TLR7 activation in this setting paradoxically promoted an anti inflammatory gene signature suggesting crosstalk between pro inflammatory pathways endogenous to Rps14 loss and TLR7 pathway activation. Overall design: RNA seq analysis of HSPCs TgItga2b:GFPlo cells from pooled rps14+/ or wildtype zebrafish embryos which were phenylhydrazine Phz stressed or unstressed and then treated with imiquimod or vehicle control. A minimum of three replicates per condition were analysed.			Het Phz Imi 2	GSM5160066	tissue:TgItga2b:GFPlo cells\|genotype:Rps14+/ \|stress:Phz\|treatment:Imiquimod	Het Phz Imi 2	Data QC was conducted using FastQC 0.11.9 and reads trimmed using Trimmomatic 0.39 Reads were aligned to the zebrafish genome GRCz11 using HISAT2 2.1.0 Alignments were sorted and indexed with samtools 1.9 Reads were counted using featureCounts from subread 2.0.0 and GTF Danio Rerio GRCz11.97 Counts were normalised and differential gene expression was analysed using DESeq2 Genome build: GRCz11 Supplementary files format and content: Matrix of normalised raw counts for every gene and every sample	TgItga2b:GFPlo cells	Haemolytic stress was induced by exposure of embryos to phenylhydrazine. Embryos were incubated in 1 µg/mL PHZ from 24 hpf to 48 hpf and then washed. Embryos were then incubated 20 µM Imiquimod or DMSO control for 4 days from 48hpf to 6dpf. Rps14 genotypes were determined with tailclips and embryos pooled before sorting.	Embryos were pooled by rps14 genotype stress and treatment and TgItga2b:GFPlo cells were sorted directly into Trizol for RNA extraction Libraries were prepared using the Smart seq2 protocol	Tgitga2b:GFP zebrafish were maintained according to standard procedures and UK Home Office guidelines	genotype:Rps14+/ \|stress:Phz\|treatment:Imiquimod	GSM5160066	GSM5160066: Het Phz Imi 2; Danio rerio; RNA Seq	GSM5160066		1	Embryos were pooled by rps14 genotype stress and treatment and TgItga2b:GFPlo cells were sorted directly into Trizol for RNA extraction Libraries were prepared using the Smart seq2 protocol	GEO Accession:GSM5160066	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP310259	loader:fastq load.py	22_S22_L001_R1_001.fastq 22_S22_L001_R2_001.fastq	fastq fastq	566668475.0	4680486.0	GSM5160066 r1	0:60.54 1:60.53	A:155882104;C:126067182;G:130534716;T:154153311;N:31162	60	60	155882104	126067182	130534716	154153311	31162	SRX10317708	SRS8438145	SRA1205468	GEO	Department of Haematology, UCL Cancer Institute	2	0.92359	0.93113	0.16126	0.16629	0.74972	0.75875	0.52217	0.5248	61	61	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	United Kingdom	2021-03-11	Multi-stage	Multi-stage	Embryo Imprecise	All anatomical structures
63547	63547	SRR13938377	SRX10317708	SRS8438145	SRP310259	PRJNA713782	TLR7 ligation augments hematopoiesis in Rps14 deficiency via paradoxical inflammatory signalling	GSE168727	Transcriptome Analysis	Myelodysplastic syndrome MDS is a haematological malignancy characterised by blood cytopenias and predisposition to acute myeloid leukaemia. We developed a model of MDS using zebrafish using knockout of Rps14 the primary mediator of the anaemia associated with del 5q MDS. These mutant animals develop bone marrow failure with dysplastic features. We conducted an in vivo small molecule screen to identify compounds that ameliorate the MDS phenotype identifying imiquimod an agonist of TLR7. We conducted RNA seq analysis of both treated and untreated animals to define the mechanism of imiquimod in alleviating anaemia. We find imiquimod alleviates anaemia by promoting haematopoietic stem and progenitor cell expansion and erythroid differentiation the mechanism of which is dependent on TLR7 ligation. TLR7 activation in this setting paradoxically promoted an anti inflammatory gene signature suggesting crosstalk between pro inflammatory pathways endogenous to Rps14 loss and TLR7 pathway activation. Overall design: RNA seq analysis of HSPCs TgItga2b:GFPlo cells from pooled rps14+/ or wildtype zebrafish embryos which were phenylhydrazine Phz stressed or unstressed and then treated with imiquimod or vehicle control. A minimum of three replicates per condition were analysed.			Het Phz Imi 2	GSM5160066	tissue:TgItga2b:GFPlo cells\|genotype:Rps14+/ \|stress:Phz\|treatment:Imiquimod	Het Phz Imi 2	Data QC was conducted using FastQC 0.11.9 and reads trimmed using Trimmomatic 0.39 Reads were aligned to the zebrafish genome GRCz11 using HISAT2 2.1.0 Alignments were sorted and indexed with samtools 1.9 Reads were counted using featureCounts from subread 2.0.0 and GTF Danio Rerio GRCz11.97 Counts were normalised and differential gene expression was analysed using DESeq2 Genome build: GRCz11 Supplementary files format and content: Matrix of normalised raw counts for every gene and every sample	TgItga2b:GFPlo cells	Haemolytic stress was induced by exposure of embryos to phenylhydrazine. Embryos were incubated in 1 µg/mL PHZ from 24 hpf to 48 hpf and then washed. Embryos were then incubated 20 µM Imiquimod or DMSO control for 4 days from 48hpf to 6dpf. Rps14 genotypes were determined with tailclips and embryos pooled before sorting.	Embryos were pooled by rps14 genotype stress and treatment and TgItga2b:GFPlo cells were sorted directly into Trizol for RNA extraction Libraries were prepared using the Smart seq2 protocol	Tgitga2b:GFP zebrafish were maintained according to standard procedures and UK Home Office guidelines	genotype:Rps14+/ \|stress:Phz\|treatment:Imiquimod	GSM5160066	GSM5160066: Het Phz Imi 2; Danio rerio; RNA Seq	GSM5160066		1	Embryos were pooled by rps14 genotype stress and treatment and TgItga2b:GFPlo cells were sorted directly into Trizol for RNA extraction Libraries were prepared using the Smart seq2 protocol	GEO Accession:GSM5160066	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP310259	loader:fastq load.py	22_S22_L002_R1_001.fastq 22_S22_L002_R2_001.fastq	fastq fastq	576287663.0	4759868.0	GSM5160066 r2	0:60.54 1:60.53	A:158599301;C:128218236;G:132752367;T:156691301;N:26458	60	60	158599301	128218236	132752367	156691301	26458	SRX10317708	SRS8438145	SRA1205468	GEO	Department of Haematology, UCL Cancer Institute	2	0.92203	0.92998	0.16233	0.16747	0.75057	0.76079	0.52644	0.505	61	61	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	United Kingdom	2021-03-11	Multi-stage	Multi-stage	Embryo Imprecise	All anatomical structures
63548	63548	SRR13938374	SRX10317707	SRS8438144	SRP310259	PRJNA713782	TLR7 ligation augments hematopoiesis in Rps14 deficiency via paradoxical inflammatory signalling	GSE168727	Transcriptome Analysis	Myelodysplastic syndrome MDS is a haematological malignancy characterised by blood cytopenias and predisposition to acute myeloid leukaemia. We developed a model of MDS using zebrafish using knockout of Rps14 the primary mediator of the anaemia associated with del 5q MDS. These mutant animals develop bone marrow failure with dysplastic features. We conducted an in vivo small molecule screen to identify compounds that ameliorate the MDS phenotype identifying imiquimod an agonist of TLR7. We conducted RNA seq analysis of both treated and untreated animals to define the mechanism of imiquimod in alleviating anaemia. We find imiquimod alleviates anaemia by promoting haematopoietic stem and progenitor cell expansion and erythroid differentiation the mechanism of which is dependent on TLR7 ligation. TLR7 activation in this setting paradoxically promoted an anti inflammatory gene signature suggesting crosstalk between pro inflammatory pathways endogenous to Rps14 loss and TLR7 pathway activation. Overall design: RNA seq analysis of HSPCs TgItga2b:GFPlo cells from pooled rps14+/ or wildtype zebrafish embryos which were phenylhydrazine Phz stressed or unstressed and then treated with imiquimod or vehicle control. A minimum of three replicates per condition were analysed.			WT Phz Imi 4	GSM5160065	tissue:TgItga2b:GFPlo cells\|genotype:Rps14+/+\|stress:Phz\|treatment:Imiquimod	WT Phz Imi 4	Data QC was conducted using FastQC 0.11.9 and reads trimmed using Trimmomatic 0.39 Reads were aligned to the zebrafish genome GRCz11 using HISAT2 2.1.0 Alignments were sorted and indexed with samtools 1.9 Reads were counted using featureCounts from subread 2.0.0 and GTF Danio Rerio GRCz11.97 Counts were normalised and differential gene expression was analysed using DESeq2 Genome build: GRCz11 Supplementary files format and content: Matrix of normalised raw counts for every gene and every sample	TgItga2b:GFPlo cells	Haemolytic stress was induced by exposure of embryos to phenylhydrazine. Embryos were incubated in 1 µg/mL PHZ from 24 hpf to 48 hpf and then washed. Embryos were then incubated 20 µM Imiquimod or DMSO control for 4 days from 48hpf to 6dpf. Rps14 genotypes were determined with tailclips and embryos pooled before sorting.	Embryos were pooled by rps14 genotype stress and treatment and TgItga2b:GFPlo cells were sorted directly into Trizol for RNA extraction Libraries were prepared using the Smart seq2 protocol	Tgitga2b:GFP zebrafish were maintained according to standard procedures and UK Home Office guidelines	genotype:Rps14+/+\|stress:Phz\|treatment:Imiquimod	GSM5160065	GSM5160065: WT Phz Imi 4; Danio rerio; RNA Seq	GSM5160065		1	Embryos were pooled by rps14 genotype stress and treatment and TgItga2b:GFPlo cells were sorted directly into Trizol for RNA extraction Libraries were prepared using the Smart seq2 protocol	GEO Accession:GSM5160065	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP310259	loader:fastq load.py	21_S21_L001_R1_001.fastq 21_S21_L001_R2_001.fastq	fastq fastq	677510002.0	5596362.0	GSM5160065 r1	0:60.53 1:60.53	A:185165437;C:151360693;G:156840899;T:184100589;N:42384	60	60	185165437	151360693	156840899	184100589	42384	SRX10317707	SRS8438144	SRA1205468	GEO	Department of Haematology, UCL Cancer Institute	2	0.91523	0.92425	0.17642	0.18156	0.75207	0.75739	0.51319	0.51635	59	58	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	United Kingdom	2021-03-11	Multi-stage	Multi-stage	Embryo Imprecise	All anatomical structures
63549	63549	SRR13938375	SRX10317707	SRS8438144	SRP310259	PRJNA713782	TLR7 ligation augments hematopoiesis in Rps14 deficiency via paradoxical inflammatory signalling	GSE168727	Transcriptome Analysis	Myelodysplastic syndrome MDS is a haematological malignancy characterised by blood cytopenias and predisposition to acute myeloid leukaemia. We developed a model of MDS using zebrafish using knockout of Rps14 the primary mediator of the anaemia associated with del 5q MDS. These mutant animals develop bone marrow failure with dysplastic features. We conducted an in vivo small molecule screen to identify compounds that ameliorate the MDS phenotype identifying imiquimod an agonist of TLR7. We conducted RNA seq analysis of both treated and untreated animals to define the mechanism of imiquimod in alleviating anaemia. We find imiquimod alleviates anaemia by promoting haematopoietic stem and progenitor cell expansion and erythroid differentiation the mechanism of which is dependent on TLR7 ligation. TLR7 activation in this setting paradoxically promoted an anti inflammatory gene signature suggesting crosstalk between pro inflammatory pathways endogenous to Rps14 loss and TLR7 pathway activation. Overall design: RNA seq analysis of HSPCs TgItga2b:GFPlo cells from pooled rps14+/ or wildtype zebrafish embryos which were phenylhydrazine Phz stressed or unstressed and then treated with imiquimod or vehicle control. A minimum of three replicates per condition were analysed.			WT Phz Imi 4	GSM5160065	tissue:TgItga2b:GFPlo cells\|genotype:Rps14+/+\|stress:Phz\|treatment:Imiquimod	WT Phz Imi 4	Data QC was conducted using FastQC 0.11.9 and reads trimmed using Trimmomatic 0.39 Reads were aligned to the zebrafish genome GRCz11 using HISAT2 2.1.0 Alignments were sorted and indexed with samtools 1.9 Reads were counted using featureCounts from subread 2.0.0 and GTF Danio Rerio GRCz11.97 Counts were normalised and differential gene expression was analysed using DESeq2 Genome build: GRCz11 Supplementary files format and content: Matrix of normalised raw counts for every gene and every sample	TgItga2b:GFPlo cells	Haemolytic stress was induced by exposure of embryos to phenylhydrazine. Embryos were incubated in 1 µg/mL PHZ from 24 hpf to 48 hpf and then washed. Embryos were then incubated 20 µM Imiquimod or DMSO control for 4 days from 48hpf to 6dpf. Rps14 genotypes were determined with tailclips and embryos pooled before sorting.	Embryos were pooled by rps14 genotype stress and treatment and TgItga2b:GFPlo cells were sorted directly into Trizol for RNA extraction Libraries were prepared using the Smart seq2 protocol	Tgitga2b:GFP zebrafish were maintained according to standard procedures and UK Home Office guidelines	genotype:Rps14+/+\|stress:Phz\|treatment:Imiquimod	GSM5160065	GSM5160065: WT Phz Imi 4; Danio rerio; RNA Seq	GSM5160065		1	Embryos were pooled by rps14 genotype stress and treatment and TgItga2b:GFPlo cells were sorted directly into Trizol for RNA extraction Libraries were prepared using the Smart seq2 protocol	GEO Accession:GSM5160065	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP310259	loader:fastq load.py	21_S21_L002_R1_001.fastq 21_S21_L002_R2_001.fastq	fastq fastq	690271271.0	5701738.0	GSM5160065 r2	0:60.53 1:60.53	A:188745622;C:154207068;G:159822727;T:187461936;N:33918	60	60	188745622	154207068	159822727	187461936	33918	SRX10317707	SRS8438144	SRA1205468	GEO	Department of Haematology, UCL Cancer Institute	2	0.91484	0.92404	0.17553	0.18025	0.75235	0.75692	0.51102	0.51035	61	57	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	United Kingdom	2021-03-11	Multi-stage	Multi-stage	Embryo Imprecise	All anatomical structures
63550	63550	SRR13938372	SRX10317706	SRS8438143	SRP310259	PRJNA713782	TLR7 ligation augments hematopoiesis in Rps14 deficiency via paradoxical inflammatory signalling	GSE168727	Transcriptome Analysis	Myelodysplastic syndrome MDS is a haematological malignancy characterised by blood cytopenias and predisposition to acute myeloid leukaemia. We developed a model of MDS using zebrafish using knockout of Rps14 the primary mediator of the anaemia associated with del 5q MDS. These mutant animals develop bone marrow failure with dysplastic features. We conducted an in vivo small molecule screen to identify compounds that ameliorate the MDS phenotype identifying imiquimod an agonist of TLR7. We conducted RNA seq analysis of both treated and untreated animals to define the mechanism of imiquimod in alleviating anaemia. We find imiquimod alleviates anaemia by promoting haematopoietic stem and progenitor cell expansion and erythroid differentiation the mechanism of which is dependent on TLR7 ligation. TLR7 activation in this setting paradoxically promoted an anti inflammatory gene signature suggesting crosstalk between pro inflammatory pathways endogenous to Rps14 loss and TLR7 pathway activation. Overall design: RNA seq analysis of HSPCs TgItga2b:GFPlo cells from pooled rps14+/ or wildtype zebrafish embryos which were phenylhydrazine Phz stressed or unstressed and then treated with imiquimod or vehicle control. A minimum of three replicates per condition were analysed.			WT Phz Imi 3	GSM5160064	tissue:TgItga2b:GFPlo cells\|genotype:Rps14+/+\|stress:Phz\|treatment:Imiquimod	WT Phz Imi 3	Data QC was conducted using FastQC 0.11.9 and reads trimmed using Trimmomatic 0.39 Reads were aligned to the zebrafish genome GRCz11 using HISAT2 2.1.0 Alignments were sorted and indexed with samtools 1.9 Reads were counted using featureCounts from subread 2.0.0 and GTF Danio Rerio GRCz11.97 Counts were normalised and differential gene expression was analysed using DESeq2 Genome build: GRCz11 Supplementary files format and content: Matrix of normalised raw counts for every gene and every sample	TgItga2b:GFPlo cells	Haemolytic stress was induced by exposure of embryos to phenylhydrazine. Embryos were incubated in 1 µg/mL PHZ from 24 hpf to 48 hpf and then washed. Embryos were then incubated 20 µM Imiquimod or DMSO control for 4 days from 48hpf to 6dpf. Rps14 genotypes were determined with tailclips and embryos pooled before sorting.	Embryos were pooled by rps14 genotype stress and treatment and TgItga2b:GFPlo cells were sorted directly into Trizol for RNA extraction Libraries were prepared using the Smart seq2 protocol	Tgitga2b:GFP zebrafish were maintained according to standard procedures and UK Home Office guidelines	genotype:Rps14+/+\|stress:Phz\|treatment:Imiquimod	GSM5160064	GSM5160064: WT Phz Imi 3; Danio rerio; RNA Seq	GSM5160064		1	Embryos were pooled by rps14 genotype stress and treatment and TgItga2b:GFPlo cells were sorted directly into Trizol for RNA extraction Libraries were prepared using the Smart seq2 protocol	GEO Accession:GSM5160064	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP310259	loader:fastq load.py	20_S20_L001_R1_001.fastq 20_S20_L001_R2_001.fastq	fastq fastq	681626341.0	5629674.0	GSM5160064 r1	0:60.54 1:60.54	A:187062721;C:151509885;G:156438404;T:186572229;N:43102	60	60	187062721	151509885	156438404	186572229	43102	SRX10317706	SRS8438143	SRA1205468	GEO	Department of Haematology, UCL Cancer Institute	2	0.90937	0.92012	0.22079	0.22472	0.75485	0.76106	0.5303	0.51887	61	61	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	United Kingdom	2021-03-11	Multi-stage	Multi-stage	Embryo Imprecise	All anatomical structures
63551	63551	SRR13938373	SRX10317706	SRS8438143	SRP310259	PRJNA713782	TLR7 ligation augments hematopoiesis in Rps14 deficiency via paradoxical inflammatory signalling	GSE168727	Transcriptome Analysis	Myelodysplastic syndrome MDS is a haematological malignancy characterised by blood cytopenias and predisposition to acute myeloid leukaemia. We developed a model of MDS using zebrafish using knockout of Rps14 the primary mediator of the anaemia associated with del 5q MDS. These mutant animals develop bone marrow failure with dysplastic features. We conducted an in vivo small molecule screen to identify compounds that ameliorate the MDS phenotype identifying imiquimod an agonist of TLR7. We conducted RNA seq analysis of both treated and untreated animals to define the mechanism of imiquimod in alleviating anaemia. We find imiquimod alleviates anaemia by promoting haematopoietic stem and progenitor cell expansion and erythroid differentiation the mechanism of which is dependent on TLR7 ligation. TLR7 activation in this setting paradoxically promoted an anti inflammatory gene signature suggesting crosstalk between pro inflammatory pathways endogenous to Rps14 loss and TLR7 pathway activation. Overall design: RNA seq analysis of HSPCs TgItga2b:GFPlo cells from pooled rps14+/ or wildtype zebrafish embryos which were phenylhydrazine Phz stressed or unstressed and then treated with imiquimod or vehicle control. A minimum of three replicates per condition were analysed.			WT Phz Imi 3	GSM5160064	tissue:TgItga2b:GFPlo cells\|genotype:Rps14+/+\|stress:Phz\|treatment:Imiquimod	WT Phz Imi 3	Data QC was conducted using FastQC 0.11.9 and reads trimmed using Trimmomatic 0.39 Reads were aligned to the zebrafish genome GRCz11 using HISAT2 2.1.0 Alignments were sorted and indexed with samtools 1.9 Reads were counted using featureCounts from subread 2.0.0 and GTF Danio Rerio GRCz11.97 Counts were normalised and differential gene expression was analysed using DESeq2 Genome build: GRCz11 Supplementary files format and content: Matrix of normalised raw counts for every gene and every sample	TgItga2b:GFPlo cells	Haemolytic stress was induced by exposure of embryos to phenylhydrazine. Embryos were incubated in 1 µg/mL PHZ from 24 hpf to 48 hpf and then washed. Embryos were then incubated 20 µM Imiquimod or DMSO control for 4 days from 48hpf to 6dpf. Rps14 genotypes were determined with tailclips and embryos pooled before sorting.	Embryos were pooled by rps14 genotype stress and treatment and TgItga2b:GFPlo cells were sorted directly into Trizol for RNA extraction Libraries were prepared using the Smart seq2 protocol	Tgitga2b:GFP zebrafish were maintained according to standard procedures and UK Home Office guidelines	genotype:Rps14+/+\|stress:Phz\|treatment:Imiquimod	GSM5160064	GSM5160064: WT Phz Imi 3; Danio rerio; RNA Seq	GSM5160064		1	Embryos were pooled by rps14 genotype stress and treatment and TgItga2b:GFPlo cells were sorted directly into Trizol for RNA extraction Libraries were prepared using the Smart seq2 protocol	GEO Accession:GSM5160064	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP310259	loader:fastq load.py	20_S20_L002_R1_001.fastq 20_S20_L002_R2_001.fastq	fastq fastq	694085920.0	5732581.0	GSM5160064 r2	0:60.54 1:60.54	A:190553551;C:154271025;G:159354530;T:189870306;N:36508	60	60	190553551	154271025	159354530	189870306	36508	SRX10317706	SRS8438143	SRA1205468	GEO	Department of Haematology, UCL Cancer Institute	2	0.90896	0.91808	0.21993	0.22324	0.75442	0.76136	0.52372	0.53132	60	61	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	United Kingdom	2021-03-11	Multi-stage	Multi-stage	Embryo Imprecise	All anatomical structures
63552	63552	SRR13938370	SRX10317705	SRS8438142	SRP310259	PRJNA713782	TLR7 ligation augments hematopoiesis in Rps14 deficiency via paradoxical inflammatory signalling	GSE168727	Transcriptome Analysis	Myelodysplastic syndrome MDS is a haematological malignancy characterised by blood cytopenias and predisposition to acute myeloid leukaemia. We developed a model of MDS using zebrafish using knockout of Rps14 the primary mediator of the anaemia associated with del 5q MDS. These mutant animals develop bone marrow failure with dysplastic features. We conducted an in vivo small molecule screen to identify compounds that ameliorate the MDS phenotype identifying imiquimod an agonist of TLR7. We conducted RNA seq analysis of both treated and untreated animals to define the mechanism of imiquimod in alleviating anaemia. We find imiquimod alleviates anaemia by promoting haematopoietic stem and progenitor cell expansion and erythroid differentiation the mechanism of which is dependent on TLR7 ligation. TLR7 activation in this setting paradoxically promoted an anti inflammatory gene signature suggesting crosstalk between pro inflammatory pathways endogenous to Rps14 loss and TLR7 pathway activation. Overall design: RNA seq analysis of HSPCs TgItga2b:GFPlo cells from pooled rps14+/ or wildtype zebrafish embryos which were phenylhydrazine Phz stressed or unstressed and then treated with imiquimod or vehicle control. A minimum of three replicates per condition were analysed.			WT Phz Imi 2	GSM5160063	tissue:TgItga2b:GFPlo cells\|genotype:Rps14+/+\|stress:Phz\|treatment:Imiquimod	WT Phz Imi 2	Data QC was conducted using FastQC 0.11.9 and reads trimmed using Trimmomatic 0.39 Reads were aligned to the zebrafish genome GRCz11 using HISAT2 2.1.0 Alignments were sorted and indexed with samtools 1.9 Reads were counted using featureCounts from subread 2.0.0 and GTF Danio Rerio GRCz11.97 Counts were normalised and differential gene expression was analysed using DESeq2 Genome build: GRCz11 Supplementary files format and content: Matrix of normalised raw counts for every gene and every sample	TgItga2b:GFPlo cells	Haemolytic stress was induced by exposure of embryos to phenylhydrazine. Embryos were incubated in 1 µg/mL PHZ from 24 hpf to 48 hpf and then washed. Embryos were then incubated 20 µM Imiquimod or DMSO control for 4 days from 48hpf to 6dpf. Rps14 genotypes were determined with tailclips and embryos pooled before sorting.	Embryos were pooled by rps14 genotype stress and treatment and TgItga2b:GFPlo cells were sorted directly into Trizol for RNA extraction Libraries were prepared using the Smart seq2 protocol	Tgitga2b:GFP zebrafish were maintained according to standard procedures and UK Home Office guidelines	genotype:Rps14+/+\|stress:Phz\|treatment:Imiquimod	GSM5160063	GSM5160063: WT Phz Imi 2; Danio rerio; RNA Seq	GSM5160063		1	Embryos were pooled by rps14 genotype stress and treatment and TgItga2b:GFPlo cells were sorted directly into Trizol for RNA extraction Libraries were prepared using the Smart seq2 protocol	GEO Accession:GSM5160063	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP310259	loader:fastq load.py	19_S19_L001_R1_001.fastq 19_S19_L001_R2_001.fastq	fastq fastq	587942887.0	4856054.0	GSM5160063 r1	0:60.54 1:60.54	A:161711029;C:130381290;G:135477437;T:160341958;N:31173	60	60	161711029	130381290	135477437	160341958	31173	SRX10317705	SRS8438142	SRA1205468	GEO	Department of Haematology, UCL Cancer Institute	2	0.90649	0.90938	0.1635	0.16416	0.76406	0.76447	0.44315	0.50128	61	61	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	United Kingdom	2021-03-11	Multi-stage	Multi-stage	Embryo Imprecise	All anatomical structures
63553	63553	SRR13938371	SRX10317705	SRS8438142	SRP310259	PRJNA713782	TLR7 ligation augments hematopoiesis in Rps14 deficiency via paradoxical inflammatory signalling	GSE168727	Transcriptome Analysis	Myelodysplastic syndrome MDS is a haematological malignancy characterised by blood cytopenias and predisposition to acute myeloid leukaemia. We developed a model of MDS using zebrafish using knockout of Rps14 the primary mediator of the anaemia associated with del 5q MDS. These mutant animals develop bone marrow failure with dysplastic features. We conducted an in vivo small molecule screen to identify compounds that ameliorate the MDS phenotype identifying imiquimod an agonist of TLR7. We conducted RNA seq analysis of both treated and untreated animals to define the mechanism of imiquimod in alleviating anaemia. We find imiquimod alleviates anaemia by promoting haematopoietic stem and progenitor cell expansion and erythroid differentiation the mechanism of which is dependent on TLR7 ligation. TLR7 activation in this setting paradoxically promoted an anti inflammatory gene signature suggesting crosstalk between pro inflammatory pathways endogenous to Rps14 loss and TLR7 pathway activation. Overall design: RNA seq analysis of HSPCs TgItga2b:GFPlo cells from pooled rps14+/ or wildtype zebrafish embryos which were phenylhydrazine Phz stressed or unstressed and then treated with imiquimod or vehicle control. A minimum of three replicates per condition were analysed.			WT Phz Imi 2	GSM5160063	tissue:TgItga2b:GFPlo cells\|genotype:Rps14+/+\|stress:Phz\|treatment:Imiquimod	WT Phz Imi 2	Data QC was conducted using FastQC 0.11.9 and reads trimmed using Trimmomatic 0.39 Reads were aligned to the zebrafish genome GRCz11 using HISAT2 2.1.0 Alignments were sorted and indexed with samtools 1.9 Reads were counted using featureCounts from subread 2.0.0 and GTF Danio Rerio GRCz11.97 Counts were normalised and differential gene expression was analysed using DESeq2 Genome build: GRCz11 Supplementary files format and content: Matrix of normalised raw counts for every gene and every sample	TgItga2b:GFPlo cells	Haemolytic stress was induced by exposure of embryos to phenylhydrazine. Embryos were incubated in 1 µg/mL PHZ from 24 hpf to 48 hpf and then washed. Embryos were then incubated 20 µM Imiquimod or DMSO control for 4 days from 48hpf to 6dpf. Rps14 genotypes were determined with tailclips and embryos pooled before sorting.	Embryos were pooled by rps14 genotype stress and treatment and TgItga2b:GFPlo cells were sorted directly into Trizol for RNA extraction Libraries were prepared using the Smart seq2 protocol	Tgitga2b:GFP zebrafish were maintained according to standard procedures and UK Home Office guidelines	genotype:Rps14+/+\|stress:Phz\|treatment:Imiquimod	GSM5160063	GSM5160063: WT Phz Imi 2; Danio rerio; RNA Seq	GSM5160063		1	Embryos were pooled by rps14 genotype stress and treatment and TgItga2b:GFPlo cells were sorted directly into Trizol for RNA extraction Libraries were prepared using the Smart seq2 protocol	GEO Accession:GSM5160063	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP310259	loader:fastq load.py	19_S19_L002_R1_001.fastq 19_S19_L002_R2_001.fastq	fastq fastq	601165141.0	4965229.0	GSM5160063 r2	0:60.54 1:60.54	A:165335450;C:133364178;G:138554754;T:163886161;N:24598	60	60	165335450	133364178	138554754	163886161	24598	SRX10317705	SRS8438142	SRA1205468	GEO	Department of Haematology, UCL Cancer Institute	2	0.90509	0.90708	0.16436	0.16546	0.7651	0.76625	0.49978	0.50378	61	61	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	United Kingdom	2021-03-11	Multi-stage	Multi-stage	Embryo Imprecise	All anatomical structures
63554	63554	SRR13938368	SRX10317704	SRS8438141	SRP310259	PRJNA713782	TLR7 ligation augments hematopoiesis in Rps14 deficiency via paradoxical inflammatory signalling	GSE168727	Transcriptome Analysis	Myelodysplastic syndrome MDS is a haematological malignancy characterised by blood cytopenias and predisposition to acute myeloid leukaemia. We developed a model of MDS using zebrafish using knockout of Rps14 the primary mediator of the anaemia associated with del 5q MDS. These mutant animals develop bone marrow failure with dysplastic features. We conducted an in vivo small molecule screen to identify compounds that ameliorate the MDS phenotype identifying imiquimod an agonist of TLR7. We conducted RNA seq analysis of both treated and untreated animals to define the mechanism of imiquimod in alleviating anaemia. We find imiquimod alleviates anaemia by promoting haematopoietic stem and progenitor cell expansion and erythroid differentiation the mechanism of which is dependent on TLR7 ligation. TLR7 activation in this setting paradoxically promoted an anti inflammatory gene signature suggesting crosstalk between pro inflammatory pathways endogenous to Rps14 loss and TLR7 pathway activation. Overall design: RNA seq analysis of HSPCs TgItga2b:GFPlo cells from pooled rps14+/ or wildtype zebrafish embryos which were phenylhydrazine Phz stressed or unstressed and then treated with imiquimod or vehicle control. A minimum of three replicates per condition were analysed.			Het N1 DMSO 4	GSM5160062	tissue:TgItga2b:GFPlo cells\|genotype:Rps14+/ \|stress:N1\|treatment:DMSO	Het N1 DMSO 4	Data QC was conducted using FastQC 0.11.9 and reads trimmed using Trimmomatic 0.39 Reads were aligned to the zebrafish genome GRCz11 using HISAT2 2.1.0 Alignments were sorted and indexed with samtools 1.9 Reads were counted using featureCounts from subread 2.0.0 and GTF Danio Rerio GRCz11.97 Counts were normalised and differential gene expression was analysed using DESeq2 Genome build: GRCz11 Supplementary files format and content: Matrix of normalised raw counts for every gene and every sample	TgItga2b:GFPlo cells	Haemolytic stress was induced by exposure of embryos to phenylhydrazine. Embryos were incubated in 1 µg/mL PHZ from 24 hpf to 48 hpf and then washed. Embryos were then incubated 20 µM Imiquimod or DMSO control for 4 days from 48hpf to 6dpf. Rps14 genotypes were determined with tailclips and embryos pooled before sorting.	Embryos were pooled by rps14 genotype stress and treatment and TgItga2b:GFPlo cells were sorted directly into Trizol for RNA extraction Libraries were prepared using the Smart seq2 protocol	Tgitga2b:GFP zebrafish were maintained according to standard procedures and UK Home Office guidelines	genotype:Rps14+/ \|stress:N1\|treatment:DMSO	GSM5160062	GSM5160062: Het N1 DMSO 4; Danio rerio; RNA Seq	GSM5160062		1	Embryos were pooled by rps14 genotype stress and treatment and TgItga2b:GFPlo cells were sorted directly into Trizol for RNA extraction Libraries were prepared using the Smart seq2 protocol	GEO Accession:GSM5160062	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP310259	loader:fastq load.py	18_S18_L001_R1_001.fastq 18_S18_L001_R2_001.fastq	fastq fastq	542137246.0	4477584.0	GSM5160062 r1	0:60.54 1:60.54	A:150151627;C:119415405;G:123560860;T:148977485;N:31869	60	60	150151627	119415405	123560860	148977485	31869	SRX10317704	SRS8438141	SRA1205468	GEO	Department of Haematology, UCL Cancer Institute	2	0.90826	0.9156	0.19851	0.20236	0.75061	0.75755	0.51512	0.51786	61	60	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	United Kingdom	2021-03-11	Multi-stage	Multi-stage	Embryo Imprecise	All anatomical structures
63555	63555	SRR13938369	SRX10317704	SRS8438141	SRP310259	PRJNA713782	TLR7 ligation augments hematopoiesis in Rps14 deficiency via paradoxical inflammatory signalling	GSE168727	Transcriptome Analysis	Myelodysplastic syndrome MDS is a haematological malignancy characterised by blood cytopenias and predisposition to acute myeloid leukaemia. We developed a model of MDS using zebrafish using knockout of Rps14 the primary mediator of the anaemia associated with del 5q MDS. These mutant animals develop bone marrow failure with dysplastic features. We conducted an in vivo small molecule screen to identify compounds that ameliorate the MDS phenotype identifying imiquimod an agonist of TLR7. We conducted RNA seq analysis of both treated and untreated animals to define the mechanism of imiquimod in alleviating anaemia. We find imiquimod alleviates anaemia by promoting haematopoietic stem and progenitor cell expansion and erythroid differentiation the mechanism of which is dependent on TLR7 ligation. TLR7 activation in this setting paradoxically promoted an anti inflammatory gene signature suggesting crosstalk between pro inflammatory pathways endogenous to Rps14 loss and TLR7 pathway activation. Overall design: RNA seq analysis of HSPCs TgItga2b:GFPlo cells from pooled rps14+/ or wildtype zebrafish embryos which were phenylhydrazine Phz stressed or unstressed and then treated with imiquimod or vehicle control. A minimum of three replicates per condition were analysed.			Het N1 DMSO 4	GSM5160062	tissue:TgItga2b:GFPlo cells\|genotype:Rps14+/ \|stress:N1\|treatment:DMSO	Het N1 DMSO 4	Data QC was conducted using FastQC 0.11.9 and reads trimmed using Trimmomatic 0.39 Reads were aligned to the zebrafish genome GRCz11 using HISAT2 2.1.0 Alignments were sorted and indexed with samtools 1.9 Reads were counted using featureCounts from subread 2.0.0 and GTF Danio Rerio GRCz11.97 Counts were normalised and differential gene expression was analysed using DESeq2 Genome build: GRCz11 Supplementary files format and content: Matrix of normalised raw counts for every gene and every sample	TgItga2b:GFPlo cells	Haemolytic stress was induced by exposure of embryos to phenylhydrazine. Embryos were incubated in 1 µg/mL PHZ from 24 hpf to 48 hpf and then washed. Embryos were then incubated 20 µM Imiquimod or DMSO control for 4 days from 48hpf to 6dpf. Rps14 genotypes were determined with tailclips and embryos pooled before sorting.	Embryos were pooled by rps14 genotype stress and treatment and TgItga2b:GFPlo cells were sorted directly into Trizol for RNA extraction Libraries were prepared using the Smart seq2 protocol	Tgitga2b:GFP zebrafish were maintained according to standard procedures and UK Home Office guidelines	genotype:Rps14+/ \|stress:N1\|treatment:DMSO	GSM5160062	GSM5160062: Het N1 DMSO 4; Danio rerio; RNA Seq	GSM5160062		1	Embryos were pooled by rps14 genotype stress and treatment and TgItga2b:GFPlo cells were sorted directly into Trizol for RNA extraction Libraries were prepared using the Smart seq2 protocol	GEO Accession:GSM5160062	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP310259	loader:fastq load.py	18_S18_L002_R1_001.fastq 18_S18_L002_R2_001.fastq	fastq fastq	553566309.0	4571913.0	GSM5160062 r2	0:60.54 1:60.54	A:153392476;C:121939262;G:126160061;T:152050698;N:23812	60	60	153392476	121939262	126160061	152050698	23812	SRX10317704	SRS8438141	SRA1205468	GEO	Department of Haematology, UCL Cancer Institute	2	0.90855	0.91514	0.19909	0.20127	0.75181	0.75885	0.51227	0.51648	61	61	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	United Kingdom	2021-03-11	Multi-stage	Multi-stage	Embryo Imprecise	All anatomical structures
63556	63556	SRR13938366	SRX10317703	SRS8438140	SRP310259	PRJNA713782	TLR7 ligation augments hematopoiesis in Rps14 deficiency via paradoxical inflammatory signalling	GSE168727	Transcriptome Analysis	Myelodysplastic syndrome MDS is a haematological malignancy characterised by blood cytopenias and predisposition to acute myeloid leukaemia. We developed a model of MDS using zebrafish using knockout of Rps14 the primary mediator of the anaemia associated with del 5q MDS. These mutant animals develop bone marrow failure with dysplastic features. We conducted an in vivo small molecule screen to identify compounds that ameliorate the MDS phenotype identifying imiquimod an agonist of TLR7. We conducted RNA seq analysis of both treated and untreated animals to define the mechanism of imiquimod in alleviating anaemia. We find imiquimod alleviates anaemia by promoting haematopoietic stem and progenitor cell expansion and erythroid differentiation the mechanism of which is dependent on TLR7 ligation. TLR7 activation in this setting paradoxically promoted an anti inflammatory gene signature suggesting crosstalk between pro inflammatory pathways endogenous to Rps14 loss and TLR7 pathway activation. Overall design: RNA seq analysis of HSPCs TgItga2b:GFPlo cells from pooled rps14+/ or wildtype zebrafish embryos which were phenylhydrazine Phz stressed or unstressed and then treated with imiquimod or vehicle control. A minimum of three replicates per condition were analysed.			Het N1 DMSO 3	GSM5160061	tissue:TgItga2b:GFPlo cells\|genotype:Rps14+/ \|stress:N1\|treatment:DMSO	Het N1 DMSO 3	Data QC was conducted using FastQC 0.11.9 and reads trimmed using Trimmomatic 0.39 Reads were aligned to the zebrafish genome GRCz11 using HISAT2 2.1.0 Alignments were sorted and indexed with samtools 1.9 Reads were counted using featureCounts from subread 2.0.0 and GTF Danio Rerio GRCz11.97 Counts were normalised and differential gene expression was analysed using DESeq2 Genome build: GRCz11 Supplementary files format and content: Matrix of normalised raw counts for every gene and every sample	TgItga2b:GFPlo cells	Haemolytic stress was induced by exposure of embryos to phenylhydrazine. Embryos were incubated in 1 µg/mL PHZ from 24 hpf to 48 hpf and then washed. Embryos were then incubated 20 µM Imiquimod or DMSO control for 4 days from 48hpf to 6dpf. Rps14 genotypes were determined with tailclips and embryos pooled before sorting.	Embryos were pooled by rps14 genotype stress and treatment and TgItga2b:GFPlo cells were sorted directly into Trizol for RNA extraction Libraries were prepared using the Smart seq2 protocol	Tgitga2b:GFP zebrafish were maintained according to standard procedures and UK Home Office guidelines	genotype:Rps14+/ \|stress:N1\|treatment:DMSO	GSM5160061	GSM5160061: Het N1 DMSO 3; Danio rerio; RNA Seq	GSM5160061		1	Embryos were pooled by rps14 genotype stress and treatment and TgItga2b:GFPlo cells were sorted directly into Trizol for RNA extraction Libraries were prepared using the Smart seq2 protocol	GEO Accession:GSM5160061	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP310259	loader:fastq load.py	17_S17_L001_R1_001.fastq 17_S17_L001_R2_001.fastq	fastq fastq	594544345.0	4909791.0	GSM5160061 r1	0:60.55 1:60.55	A:166699831;C:128603532;G:133164799;T:166037362;N:38821	60	60	166699831	128603532	133164799	166037362	38821	SRX10317703	SRS8438140	SRA1205468	GEO	Department of Haematology, UCL Cancer Institute	2	0.90169	0.90632	0.28039	0.28448	0.73369	0.73996	0.52321	0.52493	61	61	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	United Kingdom	2021-03-11	Multi-stage	Multi-stage	Embryo Imprecise	All anatomical structures
63557	63557	SRR13938367	SRX10317703	SRS8438140	SRP310259	PRJNA713782	TLR7 ligation augments hematopoiesis in Rps14 deficiency via paradoxical inflammatory signalling	GSE168727	Transcriptome Analysis	Myelodysplastic syndrome MDS is a haematological malignancy characterised by blood cytopenias and predisposition to acute myeloid leukaemia. We developed a model of MDS using zebrafish using knockout of Rps14 the primary mediator of the anaemia associated with del 5q MDS. These mutant animals develop bone marrow failure with dysplastic features. We conducted an in vivo small molecule screen to identify compounds that ameliorate the MDS phenotype identifying imiquimod an agonist of TLR7. We conducted RNA seq analysis of both treated and untreated animals to define the mechanism of imiquimod in alleviating anaemia. We find imiquimod alleviates anaemia by promoting haematopoietic stem and progenitor cell expansion and erythroid differentiation the mechanism of which is dependent on TLR7 ligation. TLR7 activation in this setting paradoxically promoted an anti inflammatory gene signature suggesting crosstalk between pro inflammatory pathways endogenous to Rps14 loss and TLR7 pathway activation. Overall design: RNA seq analysis of HSPCs TgItga2b:GFPlo cells from pooled rps14+/ or wildtype zebrafish embryos which were phenylhydrazine Phz stressed or unstressed and then treated with imiquimod or vehicle control. A minimum of three replicates per condition were analysed.			Het N1 DMSO 3	GSM5160061	tissue:TgItga2b:GFPlo cells\|genotype:Rps14+/ \|stress:N1\|treatment:DMSO	Het N1 DMSO 3	Data QC was conducted using FastQC 0.11.9 and reads trimmed using Trimmomatic 0.39 Reads were aligned to the zebrafish genome GRCz11 using HISAT2 2.1.0 Alignments were sorted and indexed with samtools 1.9 Reads were counted using featureCounts from subread 2.0.0 and GTF Danio Rerio GRCz11.97 Counts were normalised and differential gene expression was analysed using DESeq2 Genome build: GRCz11 Supplementary files format and content: Matrix of normalised raw counts for every gene and every sample	TgItga2b:GFPlo cells	Haemolytic stress was induced by exposure of embryos to phenylhydrazine. Embryos were incubated in 1 µg/mL PHZ from 24 hpf to 48 hpf and then washed. Embryos were then incubated 20 µM Imiquimod or DMSO control for 4 days from 48hpf to 6dpf. Rps14 genotypes were determined with tailclips and embryos pooled before sorting.	Embryos were pooled by rps14 genotype stress and treatment and TgItga2b:GFPlo cells were sorted directly into Trizol for RNA extraction Libraries were prepared using the Smart seq2 protocol	Tgitga2b:GFP zebrafish were maintained according to standard procedures and UK Home Office guidelines	genotype:Rps14+/ \|stress:N1\|treatment:DMSO	GSM5160061	GSM5160061: Het N1 DMSO 3; Danio rerio; RNA Seq	GSM5160061		1	Embryos were pooled by rps14 genotype stress and treatment and TgItga2b:GFPlo cells were sorted directly into Trizol for RNA extraction Libraries were prepared using the Smart seq2 protocol	GEO Accession:GSM5160061	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP310259	loader:fastq load.py	17_S17_L002_R1_001.fastq 17_S17_L002_R2_001.fastq	fastq fastq	604200451.0	4989465.0	GSM5160061 r2	0:60.55 1:60.55	A:169470064;C:130687108;G:135325833;T:168686709;N:30737	60	60	169470064	130687108	135325833	168686709	30737	SRX10317703	SRS8438140	SRA1205468	GEO	Department of Haematology, UCL Cancer Institute	2	0.89987	0.9058	0.27992	0.28527	0.73365	0.73807	0.45117	0.52585	61	61	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	United Kingdom	2021-03-11	Multi-stage	Multi-stage	Embryo Imprecise	All anatomical structures
63558	63558	SRR13938364	SRX10317702	SRS8438139	SRP310259	PRJNA713782	TLR7 ligation augments hematopoiesis in Rps14 deficiency via paradoxical inflammatory signalling	GSE168727	Transcriptome Analysis	Myelodysplastic syndrome MDS is a haematological malignancy characterised by blood cytopenias and predisposition to acute myeloid leukaemia. We developed a model of MDS using zebrafish using knockout of Rps14 the primary mediator of the anaemia associated with del 5q MDS. These mutant animals develop bone marrow failure with dysplastic features. We conducted an in vivo small molecule screen to identify compounds that ameliorate the MDS phenotype identifying imiquimod an agonist of TLR7. We conducted RNA seq analysis of both treated and untreated animals to define the mechanism of imiquimod in alleviating anaemia. We find imiquimod alleviates anaemia by promoting haematopoietic stem and progenitor cell expansion and erythroid differentiation the mechanism of which is dependent on TLR7 ligation. TLR7 activation in this setting paradoxically promoted an anti inflammatory gene signature suggesting crosstalk between pro inflammatory pathways endogenous to Rps14 loss and TLR7 pathway activation. Overall design: RNA seq analysis of HSPCs TgItga2b:GFPlo cells from pooled rps14+/ or wildtype zebrafish embryos which were phenylhydrazine Phz stressed or unstressed and then treated with imiquimod or vehicle control. A minimum of three replicates per condition were analysed.			Het N1 DMSO 2	GSM5160060	tissue:TgItga2b:GFPlo cells\|genotype:Rps14+/ \|stress:N1\|treatment:DMSO	Het N1 DMSO 2	Data QC was conducted using FastQC 0.11.9 and reads trimmed using Trimmomatic 0.39 Reads were aligned to the zebrafish genome GRCz11 using HISAT2 2.1.0 Alignments were sorted and indexed with samtools 1.9 Reads were counted using featureCounts from subread 2.0.0 and GTF Danio Rerio GRCz11.97 Counts were normalised and differential gene expression was analysed using DESeq2 Genome build: GRCz11 Supplementary files format and content: Matrix of normalised raw counts for every gene and every sample	TgItga2b:GFPlo cells	Haemolytic stress was induced by exposure of embryos to phenylhydrazine. Embryos were incubated in 1 µg/mL PHZ from 24 hpf to 48 hpf and then washed. Embryos were then incubated 20 µM Imiquimod or DMSO control for 4 days from 48hpf to 6dpf. Rps14 genotypes were determined with tailclips and embryos pooled before sorting.	Embryos were pooled by rps14 genotype stress and treatment and TgItga2b:GFPlo cells were sorted directly into Trizol for RNA extraction Libraries were prepared using the Smart seq2 protocol	Tgitga2b:GFP zebrafish were maintained according to standard procedures and UK Home Office guidelines	genotype:Rps14+/ \|stress:N1\|treatment:DMSO	GSM5160060	GSM5160060: Het N1 DMSO 2; Danio rerio; RNA Seq	GSM5160060		1	Embryos were pooled by rps14 genotype stress and treatment and TgItga2b:GFPlo cells were sorted directly into Trizol for RNA extraction Libraries were prepared using the Smart seq2 protocol	GEO Accession:GSM5160060	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP310259	loader:fastq load.py	16_S16_L001_R1_001.fastq 16_S16_L001_R2_001.fastq	fastq fastq	620617665.0	5125923.0	GSM5160060 r1	0:60.54 1:60.54	A:170672670;C:137718744;G:142673958;T:169515073;N:37220	60	60	170672670	137718744	142673958	169515073	37220	SRX10317702	SRS8438139	SRA1205468	GEO	Department of Haematology, UCL Cancer Institute	2	0.91021	0.91587	0.20592	0.20961	0.74761	0.75341	0.50633	0.51053	59	61	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	United Kingdom	2021-03-11	Multi-stage	Multi-stage	Embryo Imprecise	All anatomical structures
63559	63559	SRR13938365	SRX10317702	SRS8438139	SRP310259	PRJNA713782	TLR7 ligation augments hematopoiesis in Rps14 deficiency via paradoxical inflammatory signalling	GSE168727	Transcriptome Analysis	Myelodysplastic syndrome MDS is a haematological malignancy characterised by blood cytopenias and predisposition to acute myeloid leukaemia. We developed a model of MDS using zebrafish using knockout of Rps14 the primary mediator of the anaemia associated with del 5q MDS. These mutant animals develop bone marrow failure with dysplastic features. We conducted an in vivo small molecule screen to identify compounds that ameliorate the MDS phenotype identifying imiquimod an agonist of TLR7. We conducted RNA seq analysis of both treated and untreated animals to define the mechanism of imiquimod in alleviating anaemia. We find imiquimod alleviates anaemia by promoting haematopoietic stem and progenitor cell expansion and erythroid differentiation the mechanism of which is dependent on TLR7 ligation. TLR7 activation in this setting paradoxically promoted an anti inflammatory gene signature suggesting crosstalk between pro inflammatory pathways endogenous to Rps14 loss and TLR7 pathway activation. Overall design: RNA seq analysis of HSPCs TgItga2b:GFPlo cells from pooled rps14+/ or wildtype zebrafish embryos which were phenylhydrazine Phz stressed or unstressed and then treated with imiquimod or vehicle control. A minimum of three replicates per condition were analysed.			Het N1 DMSO 2	GSM5160060	tissue:TgItga2b:GFPlo cells\|genotype:Rps14+/ \|stress:N1\|treatment:DMSO	Het N1 DMSO 2	Data QC was conducted using FastQC 0.11.9 and reads trimmed using Trimmomatic 0.39 Reads were aligned to the zebrafish genome GRCz11 using HISAT2 2.1.0 Alignments were sorted and indexed with samtools 1.9 Reads were counted using featureCounts from subread 2.0.0 and GTF Danio Rerio GRCz11.97 Counts were normalised and differential gene expression was analysed using DESeq2 Genome build: GRCz11 Supplementary files format and content: Matrix of normalised raw counts for every gene and every sample	TgItga2b:GFPlo cells	Haemolytic stress was induced by exposure of embryos to phenylhydrazine. Embryos were incubated in 1 µg/mL PHZ from 24 hpf to 48 hpf and then washed. Embryos were then incubated 20 µM Imiquimod or DMSO control for 4 days from 48hpf to 6dpf. Rps14 genotypes were determined with tailclips and embryos pooled before sorting.	Embryos were pooled by rps14 genotype stress and treatment and TgItga2b:GFPlo cells were sorted directly into Trizol for RNA extraction Libraries were prepared using the Smart seq2 protocol	Tgitga2b:GFP zebrafish were maintained according to standard procedures and UK Home Office guidelines	genotype:Rps14+/ \|stress:N1\|treatment:DMSO	GSM5160060	GSM5160060: Het N1 DMSO 2; Danio rerio; RNA Seq	GSM5160060		1	Embryos were pooled by rps14 genotype stress and treatment and TgItga2b:GFPlo cells were sorted directly into Trizol for RNA extraction Libraries were prepared using the Smart seq2 protocol	GEO Accession:GSM5160060	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP310259	loader:fastq load.py	16_S16_L002_R1_001.fastq 16_S16_L002_R2_001.fastq	fastq fastq	632001304.0	5219941.0	GSM5160060 r2	0:60.54 1:60.54	A:173842840;C:140252731;G:145279364;T:172596846;N:29523	60	60	173842840	140252731	145279364	172596846	29523	SRX10317702	SRS8438139	SRA1205468	GEO	Department of Haematology, UCL Cancer Institute	2	0.90946	0.91607	0.20556	0.20872	0.75114	0.75499	0.50022	0.5179	60	61	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	United Kingdom	2021-03-11	Multi-stage	Multi-stage	Embryo Imprecise	All anatomical structures
63560	63560	SRR13938362	SRX10317701	SRS8438137	SRP310259	PRJNA713782	TLR7 ligation augments hematopoiesis in Rps14 deficiency via paradoxical inflammatory signalling	GSE168727	Transcriptome Analysis	Myelodysplastic syndrome MDS is a haematological malignancy characterised by blood cytopenias and predisposition to acute myeloid leukaemia. We developed a model of MDS using zebrafish using knockout of Rps14 the primary mediator of the anaemia associated with del 5q MDS. These mutant animals develop bone marrow failure with dysplastic features. We conducted an in vivo small molecule screen to identify compounds that ameliorate the MDS phenotype identifying imiquimod an agonist of TLR7. We conducted RNA seq analysis of both treated and untreated animals to define the mechanism of imiquimod in alleviating anaemia. We find imiquimod alleviates anaemia by promoting haematopoietic stem and progenitor cell expansion and erythroid differentiation the mechanism of which is dependent on TLR7 ligation. TLR7 activation in this setting paradoxically promoted an anti inflammatory gene signature suggesting crosstalk between pro inflammatory pathways endogenous to Rps14 loss and TLR7 pathway activation. Overall design: RNA seq analysis of HSPCs TgItga2b:GFPlo cells from pooled rps14+/ or wildtype zebrafish embryos which were phenylhydrazine Phz stressed or unstressed and then treated with imiquimod or vehicle control. A minimum of three replicates per condition were analysed.			WT N1 DMSO 3	GSM5160059	tissue:TgItga2b:GFPlo cells\|genotype:Rps14+/+\|stress:N1\|treatment:DMSO	WT N1 DMSO 3	Data QC was conducted using FastQC 0.11.9 and reads trimmed using Trimmomatic 0.39 Reads were aligned to the zebrafish genome GRCz11 using HISAT2 2.1.0 Alignments were sorted and indexed with samtools 1.9 Reads were counted using featureCounts from subread 2.0.0 and GTF Danio Rerio GRCz11.97 Counts were normalised and differential gene expression was analysed using DESeq2 Genome build: GRCz11 Supplementary files format and content: Matrix of normalised raw counts for every gene and every sample	TgItga2b:GFPlo cells	Haemolytic stress was induced by exposure of embryos to phenylhydrazine. Embryos were incubated in 1 µg/mL PHZ from 24 hpf to 48 hpf and then washed. Embryos were then incubated 20 µM Imiquimod or DMSO control for 4 days from 48hpf to 6dpf. Rps14 genotypes were determined with tailclips and embryos pooled before sorting.	Embryos were pooled by rps14 genotype stress and treatment and TgItga2b:GFPlo cells were sorted directly into Trizol for RNA extraction Libraries were prepared using the Smart seq2 protocol	Tgitga2b:GFP zebrafish were maintained according to standard procedures and UK Home Office guidelines	genotype:Rps14+/+\|stress:N1\|treatment:DMSO	GSM5160059	GSM5160059: WT N1 DMSO 3; Danio rerio; RNA Seq	GSM5160059		1	Embryos were pooled by rps14 genotype stress and treatment and TgItga2b:GFPlo cells were sorted directly into Trizol for RNA extraction Libraries were prepared using the Smart seq2 protocol	GEO Accession:GSM5160059	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP310259	loader:fastq load.py	14_S14_L001_R1_001.fastq 14_S14_L001_R2_001.fastq	fastq fastq	607958307.0	5021714.0	GSM5160059 r1	0:60.54 1:60.53	A:165795459;C:135597638;G:140571775;T:165949091;N:44344	60	60	165795459	135597638	140571775	165949091	44344	SRX10317701	SRS8438137	SRA1205468	GEO	Department of Haematology, UCL Cancer Institute	2	0.89791	0.90831	0.18387	0.18624	0.77843	0.78108	0.51066	0.52088	61	61	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	United Kingdom	2021-03-11	Multi-stage	Multi-stage	Embryo Imprecise	All anatomical structures
63561	63561	SRR13938363	SRX10317701	SRS8438137	SRP310259	PRJNA713782	TLR7 ligation augments hematopoiesis in Rps14 deficiency via paradoxical inflammatory signalling	GSE168727	Transcriptome Analysis	Myelodysplastic syndrome MDS is a haematological malignancy characterised by blood cytopenias and predisposition to acute myeloid leukaemia. We developed a model of MDS using zebrafish using knockout of Rps14 the primary mediator of the anaemia associated with del 5q MDS. These mutant animals develop bone marrow failure with dysplastic features. We conducted an in vivo small molecule screen to identify compounds that ameliorate the MDS phenotype identifying imiquimod an agonist of TLR7. We conducted RNA seq analysis of both treated and untreated animals to define the mechanism of imiquimod in alleviating anaemia. We find imiquimod alleviates anaemia by promoting haematopoietic stem and progenitor cell expansion and erythroid differentiation the mechanism of which is dependent on TLR7 ligation. TLR7 activation in this setting paradoxically promoted an anti inflammatory gene signature suggesting crosstalk between pro inflammatory pathways endogenous to Rps14 loss and TLR7 pathway activation. Overall design: RNA seq analysis of HSPCs TgItga2b:GFPlo cells from pooled rps14+/ or wildtype zebrafish embryos which were phenylhydrazine Phz stressed or unstressed and then treated with imiquimod or vehicle control. A minimum of three replicates per condition were analysed.			WT N1 DMSO 3	GSM5160059	tissue:TgItga2b:GFPlo cells\|genotype:Rps14+/+\|stress:N1\|treatment:DMSO	WT N1 DMSO 3	Data QC was conducted using FastQC 0.11.9 and reads trimmed using Trimmomatic 0.39 Reads were aligned to the zebrafish genome GRCz11 using HISAT2 2.1.0 Alignments were sorted and indexed with samtools 1.9 Reads were counted using featureCounts from subread 2.0.0 and GTF Danio Rerio GRCz11.97 Counts were normalised and differential gene expression was analysed using DESeq2 Genome build: GRCz11 Supplementary files format and content: Matrix of normalised raw counts for every gene and every sample	TgItga2b:GFPlo cells	Haemolytic stress was induced by exposure of embryos to phenylhydrazine. Embryos were incubated in 1 µg/mL PHZ from 24 hpf to 48 hpf and then washed. Embryos were then incubated 20 µM Imiquimod or DMSO control for 4 days from 48hpf to 6dpf. Rps14 genotypes were determined with tailclips and embryos pooled before sorting.	Embryos were pooled by rps14 genotype stress and treatment and TgItga2b:GFPlo cells were sorted directly into Trizol for RNA extraction Libraries were prepared using the Smart seq2 protocol	Tgitga2b:GFP zebrafish were maintained according to standard procedures and UK Home Office guidelines	genotype:Rps14+/+\|stress:N1\|treatment:DMSO	GSM5160059	GSM5160059: WT N1 DMSO 3; Danio rerio; RNA Seq	GSM5160059		1	Embryos were pooled by rps14 genotype stress and treatment and TgItga2b:GFPlo cells were sorted directly into Trizol for RNA extraction Libraries were prepared using the Smart seq2 protocol	GEO Accession:GSM5160059	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP310259	loader:fastq load.py	14_S14_L002_R1_001.fastq 14_S14_L002_R2_001.fastq	fastq fastq	619438248.0	5116484.0	GSM5160059 r2	0:60.54 1:60.53	A:169049008;C:138136378;G:143191764;T:169024290;N:36808	60	60	169049008	138136378	143191764	169024290	36808	SRX10317701	SRS8438137	SRA1205468	GEO	Department of Haematology, UCL Cancer Institute	2	0.89804	0.90797	0.18244	0.1863	0.77784	0.78106	0.50438	0.50775	61	60	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	United Kingdom	2021-03-11	Multi-stage	Multi-stage	Embryo Imprecise	All anatomical structures
63562	63562	SRR13938360	SRX10317700	SRS8438138	SRP310259	PRJNA713782	TLR7 ligation augments hematopoiesis in Rps14 deficiency via paradoxical inflammatory signalling	GSE168727	Transcriptome Analysis	Myelodysplastic syndrome MDS is a haematological malignancy characterised by blood cytopenias and predisposition to acute myeloid leukaemia. We developed a model of MDS using zebrafish using knockout of Rps14 the primary mediator of the anaemia associated with del 5q MDS. These mutant animals develop bone marrow failure with dysplastic features. We conducted an in vivo small molecule screen to identify compounds that ameliorate the MDS phenotype identifying imiquimod an agonist of TLR7. We conducted RNA seq analysis of both treated and untreated animals to define the mechanism of imiquimod in alleviating anaemia. We find imiquimod alleviates anaemia by promoting haematopoietic stem and progenitor cell expansion and erythroid differentiation the mechanism of which is dependent on TLR7 ligation. TLR7 activation in this setting paradoxically promoted an anti inflammatory gene signature suggesting crosstalk between pro inflammatory pathways endogenous to Rps14 loss and TLR7 pathway activation. Overall design: RNA seq analysis of HSPCs TgItga2b:GFPlo cells from pooled rps14+/ or wildtype zebrafish embryos which were phenylhydrazine Phz stressed or unstressed and then treated with imiquimod or vehicle control. A minimum of three replicates per condition were analysed.			WT N1 DMSO 2	GSM5160058	tissue:TgItga2b:GFPlo cells\|genotype:Rps14+/+\|stress:N1\|treatment:DMSO	WT N1 DMSO 2	Data QC was conducted using FastQC 0.11.9 and reads trimmed using Trimmomatic 0.39 Reads were aligned to the zebrafish genome GRCz11 using HISAT2 2.1.0 Alignments were sorted and indexed with samtools 1.9 Reads were counted using featureCounts from subread 2.0.0 and GTF Danio Rerio GRCz11.97 Counts were normalised and differential gene expression was analysed using DESeq2 Genome build: GRCz11 Supplementary files format and content: Matrix of normalised raw counts for every gene and every sample	TgItga2b:GFPlo cells	Haemolytic stress was induced by exposure of embryos to phenylhydrazine. Embryos were incubated in 1 µg/mL PHZ from 24 hpf to 48 hpf and then washed. Embryos were then incubated 20 µM Imiquimod or DMSO control for 4 days from 48hpf to 6dpf. Rps14 genotypes were determined with tailclips and embryos pooled before sorting.	Embryos were pooled by rps14 genotype stress and treatment and TgItga2b:GFPlo cells were sorted directly into Trizol for RNA extraction Libraries were prepared using the Smart seq2 protocol	Tgitga2b:GFP zebrafish were maintained according to standard procedures and UK Home Office guidelines	genotype:Rps14+/+\|stress:N1\|treatment:DMSO	GSM5160058	GSM5160058: WT N1 DMSO 2; Danio rerio; RNA Seq	GSM5160058		1	Embryos were pooled by rps14 genotype stress and treatment and TgItga2b:GFPlo cells were sorted directly into Trizol for RNA extraction Libraries were prepared using the Smart seq2 protocol	GEO Accession:GSM5160058	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP310259	loader:fastq load.py	13_S13_L001_R1_001.fastq 13_S13_L001_R2_001.fastq	fastq fastq	684107206.0	5649938.0	GSM5160058 r1	0:60.54 1:60.54	A:187806824;C:151992329;G:157294465;T:186976808;N:36780	60	60	187806824	151992329	157294465	186976808	36780	SRX10317700	SRS8438138	SRA1205468	GEO	Department of Haematology, UCL Cancer Institute	2	0.91484	0.92195	0.21428	0.21879	0.75132	0.75793	0.53173	0.53235	60	61	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	United Kingdom	2021-03-11	Multi-stage	Multi-stage	Embryo Imprecise	All anatomical structures
63563	63563	SRR13938361	SRX10317700	SRS8438138	SRP310259	PRJNA713782	TLR7 ligation augments hematopoiesis in Rps14 deficiency via paradoxical inflammatory signalling	GSE168727	Transcriptome Analysis	Myelodysplastic syndrome MDS is a haematological malignancy characterised by blood cytopenias and predisposition to acute myeloid leukaemia. We developed a model of MDS using zebrafish using knockout of Rps14 the primary mediator of the anaemia associated with del 5q MDS. These mutant animals develop bone marrow failure with dysplastic features. We conducted an in vivo small molecule screen to identify compounds that ameliorate the MDS phenotype identifying imiquimod an agonist of TLR7. We conducted RNA seq analysis of both treated and untreated animals to define the mechanism of imiquimod in alleviating anaemia. We find imiquimod alleviates anaemia by promoting haematopoietic stem and progenitor cell expansion and erythroid differentiation the mechanism of which is dependent on TLR7 ligation. TLR7 activation in this setting paradoxically promoted an anti inflammatory gene signature suggesting crosstalk between pro inflammatory pathways endogenous to Rps14 loss and TLR7 pathway activation. Overall design: RNA seq analysis of HSPCs TgItga2b:GFPlo cells from pooled rps14+/ or wildtype zebrafish embryos which were phenylhydrazine Phz stressed or unstressed and then treated with imiquimod or vehicle control. A minimum of three replicates per condition were analysed.			WT N1 DMSO 2	GSM5160058	tissue:TgItga2b:GFPlo cells\|genotype:Rps14+/+\|stress:N1\|treatment:DMSO	WT N1 DMSO 2	Data QC was conducted using FastQC 0.11.9 and reads trimmed using Trimmomatic 0.39 Reads were aligned to the zebrafish genome GRCz11 using HISAT2 2.1.0 Alignments were sorted and indexed with samtools 1.9 Reads were counted using featureCounts from subread 2.0.0 and GTF Danio Rerio GRCz11.97 Counts were normalised and differential gene expression was analysed using DESeq2 Genome build: GRCz11 Supplementary files format and content: Matrix of normalised raw counts for every gene and every sample	TgItga2b:GFPlo cells	Haemolytic stress was induced by exposure of embryos to phenylhydrazine. Embryos were incubated in 1 µg/mL PHZ from 24 hpf to 48 hpf and then washed. Embryos were then incubated 20 µM Imiquimod or DMSO control for 4 days from 48hpf to 6dpf. Rps14 genotypes were determined with tailclips and embryos pooled before sorting.	Embryos were pooled by rps14 genotype stress and treatment and TgItga2b:GFPlo cells were sorted directly into Trizol for RNA extraction Libraries were prepared using the Smart seq2 protocol	Tgitga2b:GFP zebrafish were maintained according to standard procedures and UK Home Office guidelines	genotype:Rps14+/+\|stress:N1\|treatment:DMSO	GSM5160058	GSM5160058: WT N1 DMSO 2; Danio rerio; RNA Seq	GSM5160058		1	Embryos were pooled by rps14 genotype stress and treatment and TgItga2b:GFPlo cells were sorted directly into Trizol for RNA extraction Libraries were prepared using the Smart seq2 protocol	GEO Accession:GSM5160058	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP310259	loader:fastq load.py	13_S13_L002_R1_001.fastq 13_S13_L002_R2_001.fastq	fastq fastq	695021441.0	5740078.0	GSM5160058 r2	0:60.54 1:60.54	A:190922068;C:154425004;G:159781642;T:189861763;N:30964	60	60	190922068	154425004	159781642	189861763	30964	SRX10317700	SRS8438138	SRA1205468	GEO	Department of Haematology, UCL Cancer Institute	2	0.91142	0.91912	0.21332	0.21806	0.75191	0.75808	0.45233	0.52993	61	61	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	United Kingdom	2021-03-11	Multi-stage	Multi-stage	Embryo Imprecise	All anatomical structures
63564	63564	SRR13938358	SRX10317699	SRS8438136	SRP310259	PRJNA713782	TLR7 ligation augments hematopoiesis in Rps14 deficiency via paradoxical inflammatory signalling	GSE168727	Transcriptome Analysis	Myelodysplastic syndrome MDS is a haematological malignancy characterised by blood cytopenias and predisposition to acute myeloid leukaemia. We developed a model of MDS using zebrafish using knockout of Rps14 the primary mediator of the anaemia associated with del 5q MDS. These mutant animals develop bone marrow failure with dysplastic features. We conducted an in vivo small molecule screen to identify compounds that ameliorate the MDS phenotype identifying imiquimod an agonist of TLR7. We conducted RNA seq analysis of both treated and untreated animals to define the mechanism of imiquimod in alleviating anaemia. We find imiquimod alleviates anaemia by promoting haematopoietic stem and progenitor cell expansion and erythroid differentiation the mechanism of which is dependent on TLR7 ligation. TLR7 activation in this setting paradoxically promoted an anti inflammatory gene signature suggesting crosstalk between pro inflammatory pathways endogenous to Rps14 loss and TLR7 pathway activation. Overall design: RNA seq analysis of HSPCs TgItga2b:GFPlo cells from pooled rps14+/ or wildtype zebrafish embryos which were phenylhydrazine Phz stressed or unstressed and then treated with imiquimod or vehicle control. A minimum of three replicates per condition were analysed.			Het N1 Imi 3	GSM5160057	tissue:TgItga2b:GFPlo cells\|genotype:Rps14+/ \|stress:N1\|treatment:Imiquimod	Het N1 Imi 3	Data QC was conducted using FastQC 0.11.9 and reads trimmed using Trimmomatic 0.39 Reads were aligned to the zebrafish genome GRCz11 using HISAT2 2.1.0 Alignments were sorted and indexed with samtools 1.9 Reads were counted using featureCounts from subread 2.0.0 and GTF Danio Rerio GRCz11.97 Counts were normalised and differential gene expression was analysed using DESeq2 Genome build: GRCz11 Supplementary files format and content: Matrix of normalised raw counts for every gene and every sample	TgItga2b:GFPlo cells	Haemolytic stress was induced by exposure of embryos to phenylhydrazine. Embryos were incubated in 1 µg/mL PHZ from 24 hpf to 48 hpf and then washed. Embryos were then incubated 20 µM Imiquimod or DMSO control for 4 days from 48hpf to 6dpf. Rps14 genotypes were determined with tailclips and embryos pooled before sorting.	Embryos were pooled by rps14 genotype stress and treatment and TgItga2b:GFPlo cells were sorted directly into Trizol for RNA extraction Libraries were prepared using the Smart seq2 protocol	Tgitga2b:GFP zebrafish were maintained according to standard procedures and UK Home Office guidelines	genotype:Rps14+/ \|stress:N1\|treatment:Imiquimod	GSM5160057	GSM5160057: Het N1 Imi 3; Danio rerio; RNA Seq	GSM5160057		1	Embryos were pooled by rps14 genotype stress and treatment and TgItga2b:GFPlo cells were sorted directly into Trizol for RNA extraction Libraries were prepared using the Smart seq2 protocol	GEO Accession:GSM5160057	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP310259	loader:fastq load.py	12_S12_L001_R1_001.fastq 12_S12_L001_R2_001.fastq	fastq fastq	579197486.0	4782857.0	GSM5160057 r1	0:60.55 1:60.55	A:163283553;C:124810345;G:129489772;T:161582756;N:31060	60	60	163283553	124810345	129489772	161582756	31060	SRX10317699	SRS8438136	SRA1205468	GEO	Department of Haematology, UCL Cancer Institute	2	0.89831	0.90167	0.27167	0.27381	0.73298	0.73687	0.51828	0.52918	60	61	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	United Kingdom	2021-03-11	Multi-stage	Multi-stage	Embryo Imprecise	All anatomical structures
63565	63565	SRR13938359	SRX10317699	SRS8438136	SRP310259	PRJNA713782	TLR7 ligation augments hematopoiesis in Rps14 deficiency via paradoxical inflammatory signalling	GSE168727	Transcriptome Analysis	Myelodysplastic syndrome MDS is a haematological malignancy characterised by blood cytopenias and predisposition to acute myeloid leukaemia. We developed a model of MDS using zebrafish using knockout of Rps14 the primary mediator of the anaemia associated with del 5q MDS. These mutant animals develop bone marrow failure with dysplastic features. We conducted an in vivo small molecule screen to identify compounds that ameliorate the MDS phenotype identifying imiquimod an agonist of TLR7. We conducted RNA seq analysis of both treated and untreated animals to define the mechanism of imiquimod in alleviating anaemia. We find imiquimod alleviates anaemia by promoting haematopoietic stem and progenitor cell expansion and erythroid differentiation the mechanism of which is dependent on TLR7 ligation. TLR7 activation in this setting paradoxically promoted an anti inflammatory gene signature suggesting crosstalk between pro inflammatory pathways endogenous to Rps14 loss and TLR7 pathway activation. Overall design: RNA seq analysis of HSPCs TgItga2b:GFPlo cells from pooled rps14+/ or wildtype zebrafish embryos which were phenylhydrazine Phz stressed or unstressed and then treated with imiquimod or vehicle control. A minimum of three replicates per condition were analysed.			Het N1 Imi 3	GSM5160057	tissue:TgItga2b:GFPlo cells\|genotype:Rps14+/ \|stress:N1\|treatment:Imiquimod	Het N1 Imi 3	Data QC was conducted using FastQC 0.11.9 and reads trimmed using Trimmomatic 0.39 Reads were aligned to the zebrafish genome GRCz11 using HISAT2 2.1.0 Alignments were sorted and indexed with samtools 1.9 Reads were counted using featureCounts from subread 2.0.0 and GTF Danio Rerio GRCz11.97 Counts were normalised and differential gene expression was analysed using DESeq2 Genome build: GRCz11 Supplementary files format and content: Matrix of normalised raw counts for every gene and every sample	TgItga2b:GFPlo cells	Haemolytic stress was induced by exposure of embryos to phenylhydrazine. Embryos were incubated in 1 µg/mL PHZ from 24 hpf to 48 hpf and then washed. Embryos were then incubated 20 µM Imiquimod or DMSO control for 4 days from 48hpf to 6dpf. Rps14 genotypes were determined with tailclips and embryos pooled before sorting.	Embryos were pooled by rps14 genotype stress and treatment and TgItga2b:GFPlo cells were sorted directly into Trizol for RNA extraction Libraries were prepared using the Smart seq2 protocol	Tgitga2b:GFP zebrafish were maintained according to standard procedures and UK Home Office guidelines	genotype:Rps14+/ \|stress:N1\|treatment:Imiquimod	GSM5160057	GSM5160057: Het N1 Imi 3; Danio rerio; RNA Seq	GSM5160057		1	Embryos were pooled by rps14 genotype stress and treatment and TgItga2b:GFPlo cells were sorted directly into Trizol for RNA extraction Libraries were prepared using the Smart seq2 protocol	GEO Accession:GSM5160057	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP310259	loader:fastq load.py	12_S12_L002_R1_001.fastq 12_S12_L002_R2_001.fastq	fastq fastq	591515239.0	4884561.0	GSM5160057 r2	0:60.55 1:60.55	A:166761512;C:127490435;G:132295789;T:164941768;N:25735	60	60	166761512	127490435	132295789	164941768	25735	SRX10317699	SRS8438136	SRA1205468	GEO	Department of Haematology, UCL Cancer Institute	2	0.89627	0.89969	0.27051	0.27275	0.7346	0.73953	0.5222	0.52352	58	61	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	United Kingdom	2021-03-11	Multi-stage	Multi-stage	Embryo Imprecise	All anatomical structures
63566	63566	SRR13938356	SRX10317698	SRS8438135	SRP310259	PRJNA713782	TLR7 ligation augments hematopoiesis in Rps14 deficiency via paradoxical inflammatory signalling	GSE168727	Transcriptome Analysis	Myelodysplastic syndrome MDS is a haematological malignancy characterised by blood cytopenias and predisposition to acute myeloid leukaemia. We developed a model of MDS using zebrafish using knockout of Rps14 the primary mediator of the anaemia associated with del 5q MDS. These mutant animals develop bone marrow failure with dysplastic features. We conducted an in vivo small molecule screen to identify compounds that ameliorate the MDS phenotype identifying imiquimod an agonist of TLR7. We conducted RNA seq analysis of both treated and untreated animals to define the mechanism of imiquimod in alleviating anaemia. We find imiquimod alleviates anaemia by promoting haematopoietic stem and progenitor cell expansion and erythroid differentiation the mechanism of which is dependent on TLR7 ligation. TLR7 activation in this setting paradoxically promoted an anti inflammatory gene signature suggesting crosstalk between pro inflammatory pathways endogenous to Rps14 loss and TLR7 pathway activation. Overall design: RNA seq analysis of HSPCs TgItga2b:GFPlo cells from pooled rps14+/ or wildtype zebrafish embryos which were phenylhydrazine Phz stressed or unstressed and then treated with imiquimod or vehicle control. A minimum of three replicates per condition were analysed.			Het N1 Imi 2	GSM5160056	tissue:TgItga2b:GFPlo cells\|genotype:Rps14+/ \|stress:N1\|treatment:Imiquimod	Het N1 Imi 2	Data QC was conducted using FastQC 0.11.9 and reads trimmed using Trimmomatic 0.39 Reads were aligned to the zebrafish genome GRCz11 using HISAT2 2.1.0 Alignments were sorted and indexed with samtools 1.9 Reads were counted using featureCounts from subread 2.0.0 and GTF Danio Rerio GRCz11.97 Counts were normalised and differential gene expression was analysed using DESeq2 Genome build: GRCz11 Supplementary files format and content: Matrix of normalised raw counts for every gene and every sample	TgItga2b:GFPlo cells	Haemolytic stress was induced by exposure of embryos to phenylhydrazine. Embryos were incubated in 1 µg/mL PHZ from 24 hpf to 48 hpf and then washed. Embryos were then incubated 20 µM Imiquimod or DMSO control for 4 days from 48hpf to 6dpf. Rps14 genotypes were determined with tailclips and embryos pooled before sorting.	Embryos were pooled by rps14 genotype stress and treatment and TgItga2b:GFPlo cells were sorted directly into Trizol for RNA extraction Libraries were prepared using the Smart seq2 protocol	Tgitga2b:GFP zebrafish were maintained according to standard procedures and UK Home Office guidelines	genotype:Rps14+/ \|stress:N1\|treatment:Imiquimod	GSM5160056	GSM5160056: Het N1 Imi 2; Danio rerio; RNA Seq	GSM5160056		1	Embryos were pooled by rps14 genotype stress and treatment and TgItga2b:GFPlo cells were sorted directly into Trizol for RNA extraction Libraries were prepared using the Smart seq2 protocol	GEO Accession:GSM5160056	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP310259	loader:fastq load.py	10_S10_L001_R1_001.fastq 10_S10_L001_R2_001.fastq	fastq fastq	602739422.0	4978156.0	GSM5160056 r1	0:60.54 1:60.54	A:166530078;C:133193420;G:137720590;T:165250752;N:44582	60	60	166530078	133193420	137720590	165250752	44582	SRX10317698	SRS8438135	SRA1205468	GEO	Department of Haematology, UCL Cancer Institute	2	0.89266	0.90198	0.22551	0.22841	0.75615	0.76075	0.5432	0.54109	61	61	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	United Kingdom	2021-03-11	Multi-stage	Multi-stage	Embryo Imprecise	All anatomical structures
63567	63567	SRR13938357	SRX10317698	SRS8438135	SRP310259	PRJNA713782	TLR7 ligation augments hematopoiesis in Rps14 deficiency via paradoxical inflammatory signalling	GSE168727	Transcriptome Analysis	Myelodysplastic syndrome MDS is a haematological malignancy characterised by blood cytopenias and predisposition to acute myeloid leukaemia. We developed a model of MDS using zebrafish using knockout of Rps14 the primary mediator of the anaemia associated with del 5q MDS. These mutant animals develop bone marrow failure with dysplastic features. We conducted an in vivo small molecule screen to identify compounds that ameliorate the MDS phenotype identifying imiquimod an agonist of TLR7. We conducted RNA seq analysis of both treated and untreated animals to define the mechanism of imiquimod in alleviating anaemia. We find imiquimod alleviates anaemia by promoting haematopoietic stem and progenitor cell expansion and erythroid differentiation the mechanism of which is dependent on TLR7 ligation. TLR7 activation in this setting paradoxically promoted an anti inflammatory gene signature suggesting crosstalk between pro inflammatory pathways endogenous to Rps14 loss and TLR7 pathway activation. Overall design: RNA seq analysis of HSPCs TgItga2b:GFPlo cells from pooled rps14+/ or wildtype zebrafish embryos which were phenylhydrazine Phz stressed or unstressed and then treated with imiquimod or vehicle control. A minimum of three replicates per condition were analysed.			Het N1 Imi 2	GSM5160056	tissue:TgItga2b:GFPlo cells\|genotype:Rps14+/ \|stress:N1\|treatment:Imiquimod	Het N1 Imi 2	Data QC was conducted using FastQC 0.11.9 and reads trimmed using Trimmomatic 0.39 Reads were aligned to the zebrafish genome GRCz11 using HISAT2 2.1.0 Alignments were sorted and indexed with samtools 1.9 Reads were counted using featureCounts from subread 2.0.0 and GTF Danio Rerio GRCz11.97 Counts were normalised and differential gene expression was analysed using DESeq2 Genome build: GRCz11 Supplementary files format and content: Matrix of normalised raw counts for every gene and every sample	TgItga2b:GFPlo cells	Haemolytic stress was induced by exposure of embryos to phenylhydrazine. Embryos were incubated in 1 µg/mL PHZ from 24 hpf to 48 hpf and then washed. Embryos were then incubated 20 µM Imiquimod or DMSO control for 4 days from 48hpf to 6dpf. Rps14 genotypes were determined with tailclips and embryos pooled before sorting.	Embryos were pooled by rps14 genotype stress and treatment and TgItga2b:GFPlo cells were sorted directly into Trizol for RNA extraction Libraries were prepared using the Smart seq2 protocol	Tgitga2b:GFP zebrafish were maintained according to standard procedures and UK Home Office guidelines	genotype:Rps14+/ \|stress:N1\|treatment:Imiquimod	GSM5160056	GSM5160056: Het N1 Imi 2; Danio rerio; RNA Seq	GSM5160056		1	Embryos were pooled by rps14 genotype stress and treatment and TgItga2b:GFPlo cells were sorted directly into Trizol for RNA extraction Libraries were prepared using the Smart seq2 protocol	GEO Accession:GSM5160056	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP310259	loader:fastq load.py	10_S10_L002_R1_001.fastq 10_S10_L002_R2_001.fastq	fastq fastq	613935506.0	5070552.0	GSM5160056 r2	0:60.54 1:60.54	A:169705354;C:135657399;G:140280484;T:168253039;N:39230	60	60	169705354	135657399	140280484	168253039	39230	SRX10317698	SRS8438135	SRA1205468	GEO	Department of Haematology, UCL Cancer Institute	2	0.89181	0.90103	0.22524	0.22951	0.75726	0.76197	0.53973	0.54068	61	61	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	United Kingdom	2021-03-11	Multi-stage	Multi-stage	Embryo Imprecise	All anatomical structures
63568	63568	SRR13938354	SRX10317697	SRS8438134	SRP310259	PRJNA713782	TLR7 ligation augments hematopoiesis in Rps14 deficiency via paradoxical inflammatory signalling	GSE168727	Transcriptome Analysis	Myelodysplastic syndrome MDS is a haematological malignancy characterised by blood cytopenias and predisposition to acute myeloid leukaemia. We developed a model of MDS using zebrafish using knockout of Rps14 the primary mediator of the anaemia associated with del 5q MDS. These mutant animals develop bone marrow failure with dysplastic features. We conducted an in vivo small molecule screen to identify compounds that ameliorate the MDS phenotype identifying imiquimod an agonist of TLR7. We conducted RNA seq analysis of both treated and untreated animals to define the mechanism of imiquimod in alleviating anaemia. We find imiquimod alleviates anaemia by promoting haematopoietic stem and progenitor cell expansion and erythroid differentiation the mechanism of which is dependent on TLR7 ligation. TLR7 activation in this setting paradoxically promoted an anti inflammatory gene signature suggesting crosstalk between pro inflammatory pathways endogenous to Rps14 loss and TLR7 pathway activation. Overall design: RNA seq analysis of HSPCs TgItga2b:GFPlo cells from pooled rps14+/ or wildtype zebrafish embryos which were phenylhydrazine Phz stressed or unstressed and then treated with imiquimod or vehicle control. A minimum of three replicates per condition were analysed.			WT N1 Imi 4	GSM5160055	tissue:TgItga2b:GFPlo cells\|genotype:Rps14+/+\|stress:N1\|treatment:Imiquimod	WT N1 Imi 4	Data QC was conducted using FastQC 0.11.9 and reads trimmed using Trimmomatic 0.39 Reads were aligned to the zebrafish genome GRCz11 using HISAT2 2.1.0 Alignments were sorted and indexed with samtools 1.9 Reads were counted using featureCounts from subread 2.0.0 and GTF Danio Rerio GRCz11.97 Counts were normalised and differential gene expression was analysed using DESeq2 Genome build: GRCz11 Supplementary files format and content: Matrix of normalised raw counts for every gene and every sample	TgItga2b:GFPlo cells	Haemolytic stress was induced by exposure of embryos to phenylhydrazine. Embryos were incubated in 1 µg/mL PHZ from 24 hpf to 48 hpf and then washed. Embryos were then incubated 20 µM Imiquimod or DMSO control for 4 days from 48hpf to 6dpf. Rps14 genotypes were determined with tailclips and embryos pooled before sorting.	Embryos were pooled by rps14 genotype stress and treatment and TgItga2b:GFPlo cells were sorted directly into Trizol for RNA extraction Libraries were prepared using the Smart seq2 protocol	Tgitga2b:GFP zebrafish were maintained according to standard procedures and UK Home Office guidelines	genotype:Rps14+/+\|stress:N1\|treatment:Imiquimod	GSM5160055	GSM5160055: WT N1 Imi 4; Danio rerio; RNA Seq	GSM5160055		1	Embryos were pooled by rps14 genotype stress and treatment and TgItga2b:GFPlo cells were sorted directly into Trizol for RNA extraction Libraries were prepared using the Smart seq2 protocol	GEO Accession:GSM5160055	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP310259	loader:fastq load.py	9_S9_L001_R1_001.fastq 9_S9_L001_R2_001.fastq	fastq fastq	568610530.0	4695975.0	GSM5160055 r1	0:60.54 1:60.54	A:156002679;C:126121073;G:130241913;T:156213974;N:30891	60	60	156002679	126121073	130241913	156213974	30891	SRX10317697	SRS8438134	SRA1205468	GEO	Department of Haematology, UCL Cancer Institute	2	0.9049	0.91221	0.26088	0.26482	0.74894	0.75424	0.5191	0.51925	60	61	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	United Kingdom	2021-03-11	Multi-stage	Multi-stage	Embryo Imprecise	All anatomical structures
63569	63569	SRR13938355	SRX10317697	SRS8438134	SRP310259	PRJNA713782	TLR7 ligation augments hematopoiesis in Rps14 deficiency via paradoxical inflammatory signalling	GSE168727	Transcriptome Analysis	Myelodysplastic syndrome MDS is a haematological malignancy characterised by blood cytopenias and predisposition to acute myeloid leukaemia. We developed a model of MDS using zebrafish using knockout of Rps14 the primary mediator of the anaemia associated with del 5q MDS. These mutant animals develop bone marrow failure with dysplastic features. We conducted an in vivo small molecule screen to identify compounds that ameliorate the MDS phenotype identifying imiquimod an agonist of TLR7. We conducted RNA seq analysis of both treated and untreated animals to define the mechanism of imiquimod in alleviating anaemia. We find imiquimod alleviates anaemia by promoting haematopoietic stem and progenitor cell expansion and erythroid differentiation the mechanism of which is dependent on TLR7 ligation. TLR7 activation in this setting paradoxically promoted an anti inflammatory gene signature suggesting crosstalk between pro inflammatory pathways endogenous to Rps14 loss and TLR7 pathway activation. Overall design: RNA seq analysis of HSPCs TgItga2b:GFPlo cells from pooled rps14+/ or wildtype zebrafish embryos which were phenylhydrazine Phz stressed or unstressed and then treated with imiquimod or vehicle control. A minimum of three replicates per condition were analysed.			WT N1 Imi 4	GSM5160055	tissue:TgItga2b:GFPlo cells\|genotype:Rps14+/+\|stress:N1\|treatment:Imiquimod	WT N1 Imi 4	Data QC was conducted using FastQC 0.11.9 and reads trimmed using Trimmomatic 0.39 Reads were aligned to the zebrafish genome GRCz11 using HISAT2 2.1.0 Alignments were sorted and indexed with samtools 1.9 Reads were counted using featureCounts from subread 2.0.0 and GTF Danio Rerio GRCz11.97 Counts were normalised and differential gene expression was analysed using DESeq2 Genome build: GRCz11 Supplementary files format and content: Matrix of normalised raw counts for every gene and every sample	TgItga2b:GFPlo cells	Haemolytic stress was induced by exposure of embryos to phenylhydrazine. Embryos were incubated in 1 µg/mL PHZ from 24 hpf to 48 hpf and then washed. Embryos were then incubated 20 µM Imiquimod or DMSO control for 4 days from 48hpf to 6dpf. Rps14 genotypes were determined with tailclips and embryos pooled before sorting.	Embryos were pooled by rps14 genotype stress and treatment and TgItga2b:GFPlo cells were sorted directly into Trizol for RNA extraction Libraries were prepared using the Smart seq2 protocol	Tgitga2b:GFP zebrafish were maintained according to standard procedures and UK Home Office guidelines	genotype:Rps14+/+\|stress:N1\|treatment:Imiquimod	GSM5160055	GSM5160055: WT N1 Imi 4; Danio rerio; RNA Seq	GSM5160055		1	Embryos were pooled by rps14 genotype stress and treatment and TgItga2b:GFPlo cells were sorted directly into Trizol for RNA extraction Libraries were prepared using the Smart seq2 protocol	GEO Accession:GSM5160055	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP310259	loader:fastq load.py	9_S9_L002_R1_001.fastq 9_S9_L002_R2_001.fastq	fastq fastq	579548648.0	4786265.0	GSM5160055 r2	0:60.54 1:60.54	A:159056955;C:128543011;G:132762647;T:159159846;N:26189	60	60	159056955	128543011	132762647	159159846	26189	SRX10317697	SRS8438134	SRA1205468	GEO	Department of Haematology, UCL Cancer Institute	2	0.90505	0.91104	0.26453	0.2669	0.75028	0.75369	0.51314	0.51863	60	59	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	United Kingdom	2021-03-11	Multi-stage	Multi-stage	Embryo Imprecise	All anatomical structures
63570	63570	SRR13938352	SRX10317696	SRS8438133	SRP310259	PRJNA713782	TLR7 ligation augments hematopoiesis in Rps14 deficiency via paradoxical inflammatory signalling	GSE168727	Transcriptome Analysis	Myelodysplastic syndrome MDS is a haematological malignancy characterised by blood cytopenias and predisposition to acute myeloid leukaemia. We developed a model of MDS using zebrafish using knockout of Rps14 the primary mediator of the anaemia associated with del 5q MDS. These mutant animals develop bone marrow failure with dysplastic features. We conducted an in vivo small molecule screen to identify compounds that ameliorate the MDS phenotype identifying imiquimod an agonist of TLR7. We conducted RNA seq analysis of both treated and untreated animals to define the mechanism of imiquimod in alleviating anaemia. We find imiquimod alleviates anaemia by promoting haematopoietic stem and progenitor cell expansion and erythroid differentiation the mechanism of which is dependent on TLR7 ligation. TLR7 activation in this setting paradoxically promoted an anti inflammatory gene signature suggesting crosstalk between pro inflammatory pathways endogenous to Rps14 loss and TLR7 pathway activation. Overall design: RNA seq analysis of HSPCs TgItga2b:GFPlo cells from pooled rps14+/ or wildtype zebrafish embryos which were phenylhydrazine Phz stressed or unstressed and then treated with imiquimod or vehicle control. A minimum of three replicates per condition were analysed.			WT N1 Imi 3	GSM5160054	tissue:TgItga2b:GFPlo cells\|genotype:Rps14+/+\|stress:N1\|treatment:Imiquimod	WT N1 Imi 3	Data QC was conducted using FastQC 0.11.9 and reads trimmed using Trimmomatic 0.39 Reads were aligned to the zebrafish genome GRCz11 using HISAT2 2.1.0 Alignments were sorted and indexed with samtools 1.9 Reads were counted using featureCounts from subread 2.0.0 and GTF Danio Rerio GRCz11.97 Counts were normalised and differential gene expression was analysed using DESeq2 Genome build: GRCz11 Supplementary files format and content: Matrix of normalised raw counts for every gene and every sample	TgItga2b:GFPlo cells	Haemolytic stress was induced by exposure of embryos to phenylhydrazine. Embryos were incubated in 1 µg/mL PHZ from 24 hpf to 48 hpf and then washed. Embryos were then incubated 20 µM Imiquimod or DMSO control for 4 days from 48hpf to 6dpf. Rps14 genotypes were determined with tailclips and embryos pooled before sorting.	Embryos were pooled by rps14 genotype stress and treatment and TgItga2b:GFPlo cells were sorted directly into Trizol for RNA extraction Libraries were prepared using the Smart seq2 protocol	Tgitga2b:GFP zebrafish were maintained according to standard procedures and UK Home Office guidelines	genotype:Rps14+/+\|stress:N1\|treatment:Imiquimod	GSM5160054	GSM5160054: WT N1 Imi 3; Danio rerio; RNA Seq	GSM5160054		1	Embryos were pooled by rps14 genotype stress and treatment and TgItga2b:GFPlo cells were sorted directly into Trizol for RNA extraction Libraries were prepared using the Smart seq2 protocol	GEO Accession:GSM5160054	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP310259	loader:fastq load.py	8_S8_L001_R1_001.fastq 8_S8_L001_R2_001.fastq	fastq fastq	596584025.0	4927099.0	GSM5160054 r1	0:60.54 1:60.54	A:164628001;C:131860234;G:136342700;T:163719461;N:33629	60	60	164628001	131860234	136342700	163719461	33629	SRX10317696	SRS8438133	SRA1205468	GEO	Department of Haematology, UCL Cancer Institute	2	0.90939	0.91526	0.22124	0.22436	0.75103	0.75759	0.50628	0.51206	61	61	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	United Kingdom	2021-03-11	Multi-stage	Multi-stage	Embryo Imprecise	All anatomical structures
63571	63571	SRR13938353	SRX10317696	SRS8438133	SRP310259	PRJNA713782	TLR7 ligation augments hematopoiesis in Rps14 deficiency via paradoxical inflammatory signalling	GSE168727	Transcriptome Analysis	Myelodysplastic syndrome MDS is a haematological malignancy characterised by blood cytopenias and predisposition to acute myeloid leukaemia. We developed a model of MDS using zebrafish using knockout of Rps14 the primary mediator of the anaemia associated with del 5q MDS. These mutant animals develop bone marrow failure with dysplastic features. We conducted an in vivo small molecule screen to identify compounds that ameliorate the MDS phenotype identifying imiquimod an agonist of TLR7. We conducted RNA seq analysis of both treated and untreated animals to define the mechanism of imiquimod in alleviating anaemia. We find imiquimod alleviates anaemia by promoting haematopoietic stem and progenitor cell expansion and erythroid differentiation the mechanism of which is dependent on TLR7 ligation. TLR7 activation in this setting paradoxically promoted an anti inflammatory gene signature suggesting crosstalk between pro inflammatory pathways endogenous to Rps14 loss and TLR7 pathway activation. Overall design: RNA seq analysis of HSPCs TgItga2b:GFPlo cells from pooled rps14+/ or wildtype zebrafish embryos which were phenylhydrazine Phz stressed or unstressed and then treated with imiquimod or vehicle control. A minimum of three replicates per condition were analysed.			WT N1 Imi 3	GSM5160054	tissue:TgItga2b:GFPlo cells\|genotype:Rps14+/+\|stress:N1\|treatment:Imiquimod	WT N1 Imi 3	Data QC was conducted using FastQC 0.11.9 and reads trimmed using Trimmomatic 0.39 Reads were aligned to the zebrafish genome GRCz11 using HISAT2 2.1.0 Alignments were sorted and indexed with samtools 1.9 Reads were counted using featureCounts from subread 2.0.0 and GTF Danio Rerio GRCz11.97 Counts were normalised and differential gene expression was analysed using DESeq2 Genome build: GRCz11 Supplementary files format and content: Matrix of normalised raw counts for every gene and every sample	TgItga2b:GFPlo cells	Haemolytic stress was induced by exposure of embryos to phenylhydrazine. Embryos were incubated in 1 µg/mL PHZ from 24 hpf to 48 hpf and then washed. Embryos were then incubated 20 µM Imiquimod or DMSO control for 4 days from 48hpf to 6dpf. Rps14 genotypes were determined with tailclips and embryos pooled before sorting.	Embryos were pooled by rps14 genotype stress and treatment and TgItga2b:GFPlo cells were sorted directly into Trizol for RNA extraction Libraries were prepared using the Smart seq2 protocol	Tgitga2b:GFP zebrafish were maintained according to standard procedures and UK Home Office guidelines	genotype:Rps14+/+\|stress:N1\|treatment:Imiquimod	GSM5160054	GSM5160054: WT N1 Imi 3; Danio rerio; RNA Seq	GSM5160054		1	Embryos were pooled by rps14 genotype stress and treatment and TgItga2b:GFPlo cells were sorted directly into Trizol for RNA extraction Libraries were prepared using the Smart seq2 protocol	GEO Accession:GSM5160054	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP310259	loader:fastq load.py	8_S8_L002_R1_001.fastq 8_S8_L002_R2_001.fastq	fastq fastq	609557528.0	5034210.0	GSM5160054 r2	0:60.54 1:60.54	A:168284242;C:134697245;G:139282959;T:167266046;N:27036	60	60	168284242	134697245	139282959	167266046	27036	SRX10317696	SRS8438133	SRA1205468	GEO	Department of Haematology, UCL Cancer Institute	2	0.90743	0.91496	0.21887	0.2245	0.75227	0.75834	0.50942	0.50602	61	60	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	United Kingdom	2021-03-11	Multi-stage	Multi-stage	Embryo Imprecise	All anatomical structures
63572	63572	SRR13938350	SRX10317695	SRS8438131	SRP310259	PRJNA713782	TLR7 ligation augments hematopoiesis in Rps14 deficiency via paradoxical inflammatory signalling	GSE168727	Transcriptome Analysis	Myelodysplastic syndrome MDS is a haematological malignancy characterised by blood cytopenias and predisposition to acute myeloid leukaemia. We developed a model of MDS using zebrafish using knockout of Rps14 the primary mediator of the anaemia associated with del 5q MDS. These mutant animals develop bone marrow failure with dysplastic features. We conducted an in vivo small molecule screen to identify compounds that ameliorate the MDS phenotype identifying imiquimod an agonist of TLR7. We conducted RNA seq analysis of both treated and untreated animals to define the mechanism of imiquimod in alleviating anaemia. We find imiquimod alleviates anaemia by promoting haematopoietic stem and progenitor cell expansion and erythroid differentiation the mechanism of which is dependent on TLR7 ligation. TLR7 activation in this setting paradoxically promoted an anti inflammatory gene signature suggesting crosstalk between pro inflammatory pathways endogenous to Rps14 loss and TLR7 pathway activation. Overall design: RNA seq analysis of HSPCs TgItga2b:GFPlo cells from pooled rps14+/ or wildtype zebrafish embryos which were phenylhydrazine Phz stressed or unstressed and then treated with imiquimod or vehicle control. A minimum of three replicates per condition were analysed.			WT N1 Imi 2	GSM5160053	tissue:TgItga2b:GFPlo cells\|genotype:Rps14+/+\|stress:N1\|treatment:Imiquimod	WT N1 Imi 2	Data QC was conducted using FastQC 0.11.9 and reads trimmed using Trimmomatic 0.39 Reads were aligned to the zebrafish genome GRCz11 using HISAT2 2.1.0 Alignments were sorted and indexed with samtools 1.9 Reads were counted using featureCounts from subread 2.0.0 and GTF Danio Rerio GRCz11.97 Counts were normalised and differential gene expression was analysed using DESeq2 Genome build: GRCz11 Supplementary files format and content: Matrix of normalised raw counts for every gene and every sample	TgItga2b:GFPlo cells	Haemolytic stress was induced by exposure of embryos to phenylhydrazine. Embryos were incubated in 1 µg/mL PHZ from 24 hpf to 48 hpf and then washed. Embryos were then incubated 20 µM Imiquimod or DMSO control for 4 days from 48hpf to 6dpf. Rps14 genotypes were determined with tailclips and embryos pooled before sorting.	Embryos were pooled by rps14 genotype stress and treatment and TgItga2b:GFPlo cells were sorted directly into Trizol for RNA extraction Libraries were prepared using the Smart seq2 protocol	Tgitga2b:GFP zebrafish were maintained according to standard procedures and UK Home Office guidelines	genotype:Rps14+/+\|stress:N1\|treatment:Imiquimod	GSM5160053	GSM5160053: WT N1 Imi 2; Danio rerio; RNA Seq	GSM5160053		1	Embryos were pooled by rps14 genotype stress and treatment and TgItga2b:GFPlo cells were sorted directly into Trizol for RNA extraction Libraries were prepared using the Smart seq2 protocol	GEO Accession:GSM5160053	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP310259	loader:fastq load.py	7_S7_L001_R1_001.fastq 7_S7_L001_R2_001.fastq	fastq fastq	578161587.0	4775009.0	GSM5160053 r1	0:60.54 1:60.54	A:158931735;C:128157428;G:132507114;T:158533107;N:32203	60	60	158931735	128157428	132507114	158533107	32203	SRX10317695	SRS8438131	SRA1205468	GEO	Department of Haematology, UCL Cancer Institute	2	0.90887	0.91481	0.26002	0.2656	0.7363	0.74594	0.50617	0.50864	61	61	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	United Kingdom	2021-03-11	Multi-stage	Multi-stage	Embryo Imprecise	All anatomical structures
63573	63573	SRR13938351	SRX10317695	SRS8438131	SRP310259	PRJNA713782	TLR7 ligation augments hematopoiesis in Rps14 deficiency via paradoxical inflammatory signalling	GSE168727	Transcriptome Analysis	Myelodysplastic syndrome MDS is a haematological malignancy characterised by blood cytopenias and predisposition to acute myeloid leukaemia. We developed a model of MDS using zebrafish using knockout of Rps14 the primary mediator of the anaemia associated with del 5q MDS. These mutant animals develop bone marrow failure with dysplastic features. We conducted an in vivo small molecule screen to identify compounds that ameliorate the MDS phenotype identifying imiquimod an agonist of TLR7. We conducted RNA seq analysis of both treated and untreated animals to define the mechanism of imiquimod in alleviating anaemia. We find imiquimod alleviates anaemia by promoting haematopoietic stem and progenitor cell expansion and erythroid differentiation the mechanism of which is dependent on TLR7 ligation. TLR7 activation in this setting paradoxically promoted an anti inflammatory gene signature suggesting crosstalk between pro inflammatory pathways endogenous to Rps14 loss and TLR7 pathway activation. Overall design: RNA seq analysis of HSPCs TgItga2b:GFPlo cells from pooled rps14+/ or wildtype zebrafish embryos which were phenylhydrazine Phz stressed or unstressed and then treated with imiquimod or vehicle control. A minimum of three replicates per condition were analysed.			WT N1 Imi 2	GSM5160053	tissue:TgItga2b:GFPlo cells\|genotype:Rps14+/+\|stress:N1\|treatment:Imiquimod	WT N1 Imi 2	Data QC was conducted using FastQC 0.11.9 and reads trimmed using Trimmomatic 0.39 Reads were aligned to the zebrafish genome GRCz11 using HISAT2 2.1.0 Alignments were sorted and indexed with samtools 1.9 Reads were counted using featureCounts from subread 2.0.0 and GTF Danio Rerio GRCz11.97 Counts were normalised and differential gene expression was analysed using DESeq2 Genome build: GRCz11 Supplementary files format and content: Matrix of normalised raw counts for every gene and every sample	TgItga2b:GFPlo cells	Haemolytic stress was induced by exposure of embryos to phenylhydrazine. Embryos were incubated in 1 µg/mL PHZ from 24 hpf to 48 hpf and then washed. Embryos were then incubated 20 µM Imiquimod or DMSO control for 4 days from 48hpf to 6dpf. Rps14 genotypes were determined with tailclips and embryos pooled before sorting.	Embryos were pooled by rps14 genotype stress and treatment and TgItga2b:GFPlo cells were sorted directly into Trizol for RNA extraction Libraries were prepared using the Smart seq2 protocol	Tgitga2b:GFP zebrafish were maintained according to standard procedures and UK Home Office guidelines	genotype:Rps14+/+\|stress:N1\|treatment:Imiquimod	GSM5160053	GSM5160053: WT N1 Imi 2; Danio rerio; RNA Seq	GSM5160053		1	Embryos were pooled by rps14 genotype stress and treatment and TgItga2b:GFPlo cells were sorted directly into Trizol for RNA extraction Libraries were prepared using the Smart seq2 protocol	GEO Accession:GSM5160053	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP310259	loader:fastq load.py	7_S7_L002_R1_001.fastq 7_S7_L002_R2_001.fastq	fastq fastq	590300896.0	4875221.0	GSM5160053 r2	0:60.54 1:60.54	A:162351548;C:130837473;G:135245093;T:161840784;N:25998	60	60	162351548	130837473	135245093	161840784	25998	SRX10317695	SRS8438131	SRA1205468	GEO	Department of Haematology, UCL Cancer Institute	2	0.90589	0.91257	0.25941	0.26507	0.73801	0.74716	0.51075	0.50742	61	61	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	United Kingdom	2021-03-11	Multi-stage	Multi-stage	Embryo Imprecise	All anatomical structures
63574	63574	SRR13938348	SRX10317694	SRS8438132	SRP310259	PRJNA713782	TLR7 ligation augments hematopoiesis in Rps14 deficiency via paradoxical inflammatory signalling	GSE168727	Transcriptome Analysis	Myelodysplastic syndrome MDS is a haematological malignancy characterised by blood cytopenias and predisposition to acute myeloid leukaemia. We developed a model of MDS using zebrafish using knockout of Rps14 the primary mediator of the anaemia associated with del 5q MDS. These mutant animals develop bone marrow failure with dysplastic features. We conducted an in vivo small molecule screen to identify compounds that ameliorate the MDS phenotype identifying imiquimod an agonist of TLR7. We conducted RNA seq analysis of both treated and untreated animals to define the mechanism of imiquimod in alleviating anaemia. We find imiquimod alleviates anaemia by promoting haematopoietic stem and progenitor cell expansion and erythroid differentiation the mechanism of which is dependent on TLR7 ligation. TLR7 activation in this setting paradoxically promoted an anti inflammatory gene signature suggesting crosstalk between pro inflammatory pathways endogenous to Rps14 loss and TLR7 pathway activation. Overall design: RNA seq analysis of HSPCs TgItga2b:GFPlo cells from pooled rps14+/ or wildtype zebrafish embryos which were phenylhydrazine Phz stressed or unstressed and then treated with imiquimod or vehicle control. A minimum of three replicates per condition were analysed.			Het Phz Imi 1	GSM5160052	tissue:TgItga2b:GFPlo cells\|genotype:Rps14+/ \|stress:Phz\|treatment:Imiquimod	Het Phz Imi 1	Data QC was conducted using FastQC 0.11.9 and reads trimmed using Trimmomatic 0.39 Reads were aligned to the zebrafish genome GRCz11 using HISAT2 2.1.0 Alignments were sorted and indexed with samtools 1.9 Reads were counted using featureCounts from subread 2.0.0 and GTF Danio Rerio GRCz11.97 Counts were normalised and differential gene expression was analysed using DESeq2 Genome build: GRCz11 Supplementary files format and content: Matrix of normalised raw counts for every gene and every sample	TgItga2b:GFPlo cells	Haemolytic stress was induced by exposure of embryos to phenylhydrazine. Embryos were incubated in 1 µg/mL PHZ from 24 hpf to 48 hpf and then washed. Embryos were then incubated 20 µM Imiquimod or DMSO control for 4 days from 48hpf to 6dpf. Rps14 genotypes were determined with tailclips and embryos pooled before sorting.	Embryos were pooled by rps14 genotype stress and treatment and TgItga2b:GFPlo cells were sorted directly into Trizol for RNA extraction Libraries were prepared using the Smart seq2 protocol	Tgitga2b:GFP zebrafish were maintained according to standard procedures and UK Home Office guidelines	genotype:Rps14+/ \|stress:Phz\|treatment:Imiquimod	GSM5160052	GSM5160052: Het Phz Imi 1; Danio rerio; RNA Seq	GSM5160052		1	Embryos were pooled by rps14 genotype stress and treatment and TgItga2b:GFPlo cells were sorted directly into Trizol for RNA extraction Libraries were prepared using the Smart seq2 protocol	GEO Accession:GSM5160052	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP310259	loader:fastq load.py	6_S6_L001_R1_001.fastq 6_S6_L001_R2_001.fastq	fastq fastq	655511448.0	5414794.0	GSM5160052 r1	0:60.53 1:60.53	A:179162588;C:146851420;G:152053624;T:177399495;N:44321	60	60	179162588	146851420	152053624	177399495	44321	SRX10317694	SRS8438132	SRA1205468	GEO	Department of Haematology, UCL Cancer Institute	2	0.91643	0.92232	0.16695	0.16819	0.75256	0.75572	0.51935	0.52005	61	61	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	United Kingdom	2021-03-11	Multi-stage	Multi-stage	Embryo Imprecise	All anatomical structures
63575	63575	SRR13938349	SRX10317694	SRS8438132	SRP310259	PRJNA713782	TLR7 ligation augments hematopoiesis in Rps14 deficiency via paradoxical inflammatory signalling	GSE168727	Transcriptome Analysis	Myelodysplastic syndrome MDS is a haematological malignancy characterised by blood cytopenias and predisposition to acute myeloid leukaemia. We developed a model of MDS using zebrafish using knockout of Rps14 the primary mediator of the anaemia associated with del 5q MDS. These mutant animals develop bone marrow failure with dysplastic features. We conducted an in vivo small molecule screen to identify compounds that ameliorate the MDS phenotype identifying imiquimod an agonist of TLR7. We conducted RNA seq analysis of both treated and untreated animals to define the mechanism of imiquimod in alleviating anaemia. We find imiquimod alleviates anaemia by promoting haematopoietic stem and progenitor cell expansion and erythroid differentiation the mechanism of which is dependent on TLR7 ligation. TLR7 activation in this setting paradoxically promoted an anti inflammatory gene signature suggesting crosstalk between pro inflammatory pathways endogenous to Rps14 loss and TLR7 pathway activation. Overall design: RNA seq analysis of HSPCs TgItga2b:GFPlo cells from pooled rps14+/ or wildtype zebrafish embryos which were phenylhydrazine Phz stressed or unstressed and then treated with imiquimod or vehicle control. A minimum of three replicates per condition were analysed.			Het Phz Imi 1	GSM5160052	tissue:TgItga2b:GFPlo cells\|genotype:Rps14+/ \|stress:Phz\|treatment:Imiquimod	Het Phz Imi 1	Data QC was conducted using FastQC 0.11.9 and reads trimmed using Trimmomatic 0.39 Reads were aligned to the zebrafish genome GRCz11 using HISAT2 2.1.0 Alignments were sorted and indexed with samtools 1.9 Reads were counted using featureCounts from subread 2.0.0 and GTF Danio Rerio GRCz11.97 Counts were normalised and differential gene expression was analysed using DESeq2 Genome build: GRCz11 Supplementary files format and content: Matrix of normalised raw counts for every gene and every sample	TgItga2b:GFPlo cells	Haemolytic stress was induced by exposure of embryos to phenylhydrazine. Embryos were incubated in 1 µg/mL PHZ from 24 hpf to 48 hpf and then washed. Embryos were then incubated 20 µM Imiquimod or DMSO control for 4 days from 48hpf to 6dpf. Rps14 genotypes were determined with tailclips and embryos pooled before sorting.	Embryos were pooled by rps14 genotype stress and treatment and TgItga2b:GFPlo cells were sorted directly into Trizol for RNA extraction Libraries were prepared using the Smart seq2 protocol	Tgitga2b:GFP zebrafish were maintained according to standard procedures and UK Home Office guidelines	genotype:Rps14+/ \|stress:Phz\|treatment:Imiquimod	GSM5160052	GSM5160052: Het Phz Imi 1; Danio rerio; RNA Seq	GSM5160052		1	Embryos were pooled by rps14 genotype stress and treatment and TgItga2b:GFPlo cells were sorted directly into Trizol for RNA extraction Libraries were prepared using the Smart seq2 protocol	GEO Accession:GSM5160052	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP310259	loader:fastq load.py	6_S6_L002_R1_001.fastq 6_S6_L002_R2_001.fastq	fastq fastq	669798098.0	5532748.0	GSM5160052 r2	0:60.53 1:60.53	A:183108728;C:150042746;G:155399345;T:181210862;N:36417	60	60	183108728	150042746	155399345	181210862	36417	SRX10317694	SRS8438132	SRA1205468	GEO	Department of Haematology, UCL Cancer Institute	2	0.91459	0.9212	0.16546	0.16731	0.7525	0.75611	0.51671	0.52186	61	61	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	United Kingdom	2021-03-11	Multi-stage	Multi-stage	Embryo Imprecise	All anatomical structures
63576	63576	SRR13938346	SRX10317693	SRS8438129	SRP310259	PRJNA713782	TLR7 ligation augments hematopoiesis in Rps14 deficiency via paradoxical inflammatory signalling	GSE168727	Transcriptome Analysis	Myelodysplastic syndrome MDS is a haematological malignancy characterised by blood cytopenias and predisposition to acute myeloid leukaemia. We developed a model of MDS using zebrafish using knockout of Rps14 the primary mediator of the anaemia associated with del 5q MDS. These mutant animals develop bone marrow failure with dysplastic features. We conducted an in vivo small molecule screen to identify compounds that ameliorate the MDS phenotype identifying imiquimod an agonist of TLR7. We conducted RNA seq analysis of both treated and untreated animals to define the mechanism of imiquimod in alleviating anaemia. We find imiquimod alleviates anaemia by promoting haematopoietic stem and progenitor cell expansion and erythroid differentiation the mechanism of which is dependent on TLR7 ligation. TLR7 activation in this setting paradoxically promoted an anti inflammatory gene signature suggesting crosstalk between pro inflammatory pathways endogenous to Rps14 loss and TLR7 pathway activation. Overall design: RNA seq analysis of HSPCs TgItga2b:GFPlo cells from pooled rps14+/ or wildtype zebrafish embryos which were phenylhydrazine Phz stressed or unstressed and then treated with imiquimod or vehicle control. A minimum of three replicates per condition were analysed.			WT Phz Imi 1	GSM5160051	tissue:TgItga2b:GFPlo cells\|genotype:Rps14+/+\|stress:Phz\|treatment:Imiquimod	WT Phz Imi 1	Data QC was conducted using FastQC 0.11.9 and reads trimmed using Trimmomatic 0.39 Reads were aligned to the zebrafish genome GRCz11 using HISAT2 2.1.0 Alignments were sorted and indexed with samtools 1.9 Reads were counted using featureCounts from subread 2.0.0 and GTF Danio Rerio GRCz11.97 Counts were normalised and differential gene expression was analysed using DESeq2 Genome build: GRCz11 Supplementary files format and content: Matrix of normalised raw counts for every gene and every sample	TgItga2b:GFPlo cells	Haemolytic stress was induced by exposure of embryos to phenylhydrazine. Embryos were incubated in 1 µg/mL PHZ from 24 hpf to 48 hpf and then washed. Embryos were then incubated 20 µM Imiquimod or DMSO control for 4 days from 48hpf to 6dpf. Rps14 genotypes were determined with tailclips and embryos pooled before sorting.	Embryos were pooled by rps14 genotype stress and treatment and TgItga2b:GFPlo cells were sorted directly into Trizol for RNA extraction Libraries were prepared using the Smart seq2 protocol	Tgitga2b:GFP zebrafish were maintained according to standard procedures and UK Home Office guidelines	genotype:Rps14+/+\|stress:Phz\|treatment:Imiquimod	GSM5160051	GSM5160051: WT Phz Imi 1; Danio rerio; RNA Seq	GSM5160051		1	Embryos were pooled by rps14 genotype stress and treatment and TgItga2b:GFPlo cells were sorted directly into Trizol for RNA extraction Libraries were prepared using the Smart seq2 protocol	GEO Accession:GSM5160051	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP310259	loader:fastq load.py	5_S5_L001_R1_001.fastq 5_S5_L001_R2_001.fastq	fastq fastq	691109710.0	5708354.0	GSM5160051 r1	0:60.54 1:60.53	A:188961645;C:154424862;G:159793282;T:187890995;N:38926	60	60	188961645	154424862	159793282	187890995	38926	SRX10317693	SRS8438129	SRA1205468	GEO	Department of Haematology, UCL Cancer Institute	2	0.9143	0.91997	0.19503	0.19718	0.74389	0.75041	0.51731	0.51682	60	61	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	United Kingdom	2021-03-11	Multi-stage	Multi-stage	Embryo Imprecise	All anatomical structures
63577	63577	SRR13938347	SRX10317693	SRS8438129	SRP310259	PRJNA713782	TLR7 ligation augments hematopoiesis in Rps14 deficiency via paradoxical inflammatory signalling	GSE168727	Transcriptome Analysis	Myelodysplastic syndrome MDS is a haematological malignancy characterised by blood cytopenias and predisposition to acute myeloid leukaemia. We developed a model of MDS using zebrafish using knockout of Rps14 the primary mediator of the anaemia associated with del 5q MDS. These mutant animals develop bone marrow failure with dysplastic features. We conducted an in vivo small molecule screen to identify compounds that ameliorate the MDS phenotype identifying imiquimod an agonist of TLR7. We conducted RNA seq analysis of both treated and untreated animals to define the mechanism of imiquimod in alleviating anaemia. We find imiquimod alleviates anaemia by promoting haematopoietic stem and progenitor cell expansion and erythroid differentiation the mechanism of which is dependent on TLR7 ligation. TLR7 activation in this setting paradoxically promoted an anti inflammatory gene signature suggesting crosstalk between pro inflammatory pathways endogenous to Rps14 loss and TLR7 pathway activation. Overall design: RNA seq analysis of HSPCs TgItga2b:GFPlo cells from pooled rps14+/ or wildtype zebrafish embryos which were phenylhydrazine Phz stressed or unstressed and then treated with imiquimod or vehicle control. A minimum of three replicates per condition were analysed.			WT Phz Imi 1	GSM5160051	tissue:TgItga2b:GFPlo cells\|genotype:Rps14+/+\|stress:Phz\|treatment:Imiquimod	WT Phz Imi 1	Data QC was conducted using FastQC 0.11.9 and reads trimmed using Trimmomatic 0.39 Reads were aligned to the zebrafish genome GRCz11 using HISAT2 2.1.0 Alignments were sorted and indexed with samtools 1.9 Reads were counted using featureCounts from subread 2.0.0 and GTF Danio Rerio GRCz11.97 Counts were normalised and differential gene expression was analysed using DESeq2 Genome build: GRCz11 Supplementary files format and content: Matrix of normalised raw counts for every gene and every sample	TgItga2b:GFPlo cells	Haemolytic stress was induced by exposure of embryos to phenylhydrazine. Embryos were incubated in 1 µg/mL PHZ from 24 hpf to 48 hpf and then washed. Embryos were then incubated 20 µM Imiquimod or DMSO control for 4 days from 48hpf to 6dpf. Rps14 genotypes were determined with tailclips and embryos pooled before sorting.	Embryos were pooled by rps14 genotype stress and treatment and TgItga2b:GFPlo cells were sorted directly into Trizol for RNA extraction Libraries were prepared using the Smart seq2 protocol	Tgitga2b:GFP zebrafish were maintained according to standard procedures and UK Home Office guidelines	genotype:Rps14+/+\|stress:Phz\|treatment:Imiquimod	GSM5160051	GSM5160051: WT Phz Imi 1; Danio rerio; RNA Seq	GSM5160051		1	Embryos were pooled by rps14 genotype stress and treatment and TgItga2b:GFPlo cells were sorted directly into Trizol for RNA extraction Libraries were prepared using the Smart seq2 protocol	GEO Accession:GSM5160051	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP310259	loader:fastq load.py	5_S5_L002_R1_001.fastq 5_S5_L002_R2_001.fastq	fastq fastq	706338331.0	5834182.0	GSM5160051 r2	0:60.54 1:60.53	A:193170362;C:157809865;G:163323854;T:192001976;N:32274	60	60	193170362	157809865	163323854	192001976	32274	SRX10317693	SRS8438129	SRA1205468	GEO	Department of Haematology, UCL Cancer Institute	2	0.91346	0.91919	0.19671	0.19885	0.7456	0.75103	0.53048	0.52163	61	61	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	United Kingdom	2021-03-11	Multi-stage	Multi-stage	Embryo Imprecise	All anatomical structures
63578	63578	SRR13938344	SRX10317692	SRS8438130	SRP310259	PRJNA713782	TLR7 ligation augments hematopoiesis in Rps14 deficiency via paradoxical inflammatory signalling	GSE168727	Transcriptome Analysis	Myelodysplastic syndrome MDS is a haematological malignancy characterised by blood cytopenias and predisposition to acute myeloid leukaemia. We developed a model of MDS using zebrafish using knockout of Rps14 the primary mediator of the anaemia associated with del 5q MDS. These mutant animals develop bone marrow failure with dysplastic features. We conducted an in vivo small molecule screen to identify compounds that ameliorate the MDS phenotype identifying imiquimod an agonist of TLR7. We conducted RNA seq analysis of both treated and untreated animals to define the mechanism of imiquimod in alleviating anaemia. We find imiquimod alleviates anaemia by promoting haematopoietic stem and progenitor cell expansion and erythroid differentiation the mechanism of which is dependent on TLR7 ligation. TLR7 activation in this setting paradoxically promoted an anti inflammatory gene signature suggesting crosstalk between pro inflammatory pathways endogenous to Rps14 loss and TLR7 pathway activation. Overall design: RNA seq analysis of HSPCs TgItga2b:GFPlo cells from pooled rps14+/ or wildtype zebrafish embryos which were phenylhydrazine Phz stressed or unstressed and then treated with imiquimod or vehicle control. A minimum of three replicates per condition were analysed.			Het N1 DMSO 1	GSM5160050	tissue:TgItga2b:GFPlo cells\|genotype:Rps14+/ \|stress:N1\|treatment:DMSO	Het N1 DMSO 1	Data QC was conducted using FastQC 0.11.9 and reads trimmed using Trimmomatic 0.39 Reads were aligned to the zebrafish genome GRCz11 using HISAT2 2.1.0 Alignments were sorted and indexed with samtools 1.9 Reads were counted using featureCounts from subread 2.0.0 and GTF Danio Rerio GRCz11.97 Counts were normalised and differential gene expression was analysed using DESeq2 Genome build: GRCz11 Supplementary files format and content: Matrix of normalised raw counts for every gene and every sample	TgItga2b:GFPlo cells	Haemolytic stress was induced by exposure of embryos to phenylhydrazine. Embryos were incubated in 1 µg/mL PHZ from 24 hpf to 48 hpf and then washed. Embryos were then incubated 20 µM Imiquimod or DMSO control for 4 days from 48hpf to 6dpf. Rps14 genotypes were determined with tailclips and embryos pooled before sorting.	Embryos were pooled by rps14 genotype stress and treatment and TgItga2b:GFPlo cells were sorted directly into Trizol for RNA extraction Libraries were prepared using the Smart seq2 protocol	Tgitga2b:GFP zebrafish were maintained according to standard procedures and UK Home Office guidelines	genotype:Rps14+/ \|stress:N1\|treatment:DMSO	GSM5160050	GSM5160050: Het N1 DMSO 1; Danio rerio; RNA Seq	GSM5160050		1	Embryos were pooled by rps14 genotype stress and treatment and TgItga2b:GFPlo cells were sorted directly into Trizol for RNA extraction Libraries were prepared using the Smart seq2 protocol	GEO Accession:GSM5160050	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP310259	loader:fastq load.py	4_S4_L001_R1_001.fastq 4_S4_L001_R2_001.fastq	fastq fastq	642110489.0	5303572.0	GSM5160050 r1	0:60.54 1:60.53	A:176616331;C:142892220;G:148094380;T:174474628;N:32930	60	60	176616331	142892220	148094380	174474628	32930	SRX10317692	SRS8438130	SRA1205468	GEO	Department of Haematology, UCL Cancer Institute	2	0.90928	0.91775	0.1343	0.13681	0.76002	0.76579	0.5185	0.52192	61	61	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	United Kingdom	2021-03-11	Multi-stage	Multi-stage	Embryo Imprecise	All anatomical structures
63579	63579	SRR13938345	SRX10317692	SRS8438130	SRP310259	PRJNA713782	TLR7 ligation augments hematopoiesis in Rps14 deficiency via paradoxical inflammatory signalling	GSE168727	Transcriptome Analysis	Myelodysplastic syndrome MDS is a haematological malignancy characterised by blood cytopenias and predisposition to acute myeloid leukaemia. We developed a model of MDS using zebrafish using knockout of Rps14 the primary mediator of the anaemia associated with del 5q MDS. These mutant animals develop bone marrow failure with dysplastic features. We conducted an in vivo small molecule screen to identify compounds that ameliorate the MDS phenotype identifying imiquimod an agonist of TLR7. We conducted RNA seq analysis of both treated and untreated animals to define the mechanism of imiquimod in alleviating anaemia. We find imiquimod alleviates anaemia by promoting haematopoietic stem and progenitor cell expansion and erythroid differentiation the mechanism of which is dependent on TLR7 ligation. TLR7 activation in this setting paradoxically promoted an anti inflammatory gene signature suggesting crosstalk between pro inflammatory pathways endogenous to Rps14 loss and TLR7 pathway activation. Overall design: RNA seq analysis of HSPCs TgItga2b:GFPlo cells from pooled rps14+/ or wildtype zebrafish embryos which were phenylhydrazine Phz stressed or unstressed and then treated with imiquimod or vehicle control. A minimum of three replicates per condition were analysed.			Het N1 DMSO 1	GSM5160050	tissue:TgItga2b:GFPlo cells\|genotype:Rps14+/ \|stress:N1\|treatment:DMSO	Het N1 DMSO 1	Data QC was conducted using FastQC 0.11.9 and reads trimmed using Trimmomatic 0.39 Reads were aligned to the zebrafish genome GRCz11 using HISAT2 2.1.0 Alignments were sorted and indexed with samtools 1.9 Reads were counted using featureCounts from subread 2.0.0 and GTF Danio Rerio GRCz11.97 Counts were normalised and differential gene expression was analysed using DESeq2 Genome build: GRCz11 Supplementary files format and content: Matrix of normalised raw counts for every gene and every sample	TgItga2b:GFPlo cells	Haemolytic stress was induced by exposure of embryos to phenylhydrazine. Embryos were incubated in 1 µg/mL PHZ from 24 hpf to 48 hpf and then washed. Embryos were then incubated 20 µM Imiquimod or DMSO control for 4 days from 48hpf to 6dpf. Rps14 genotypes were determined with tailclips and embryos pooled before sorting.	Embryos were pooled by rps14 genotype stress and treatment and TgItga2b:GFPlo cells were sorted directly into Trizol for RNA extraction Libraries were prepared using the Smart seq2 protocol	Tgitga2b:GFP zebrafish were maintained according to standard procedures and UK Home Office guidelines	genotype:Rps14+/ \|stress:N1\|treatment:DMSO	GSM5160050	GSM5160050: Het N1 DMSO 1; Danio rerio; RNA Seq	GSM5160050		1	Embryos were pooled by rps14 genotype stress and treatment and TgItga2b:GFPlo cells were sorted directly into Trizol for RNA extraction Libraries were prepared using the Smart seq2 protocol	GEO Accession:GSM5160050	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP310259	loader:fastq load.py	4_S4_L002_R1_001.fastq 4_S4_L002_R2_001.fastq	fastq fastq	652214010.0	5386985.0	GSM5160050 r2	0:60.54 1:60.53	A:179443228;C:145149485;G:150440696;T:177155650;N:24951	60	60	179443228	145149485	150440696	177155650	24951	SRX10317692	SRS8438130	SRA1205468	GEO	Department of Haematology, UCL Cancer Institute	2	0.90865	0.917	0.13327	0.13633	0.75941	0.76593	0.52279	0.52315	61	61	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	United Kingdom	2021-03-11	Multi-stage	Multi-stage	Embryo Imprecise	All anatomical structures
63580	63580	SRR13938342	SRX10317691	SRS8438128	SRP310259	PRJNA713782	TLR7 ligation augments hematopoiesis in Rps14 deficiency via paradoxical inflammatory signalling	GSE168727	Transcriptome Analysis	Myelodysplastic syndrome MDS is a haematological malignancy characterised by blood cytopenias and predisposition to acute myeloid leukaemia. We developed a model of MDS using zebrafish using knockout of Rps14 the primary mediator of the anaemia associated with del 5q MDS. These mutant animals develop bone marrow failure with dysplastic features. We conducted an in vivo small molecule screen to identify compounds that ameliorate the MDS phenotype identifying imiquimod an agonist of TLR7. We conducted RNA seq analysis of both treated and untreated animals to define the mechanism of imiquimod in alleviating anaemia. We find imiquimod alleviates anaemia by promoting haematopoietic stem and progenitor cell expansion and erythroid differentiation the mechanism of which is dependent on TLR7 ligation. TLR7 activation in this setting paradoxically promoted an anti inflammatory gene signature suggesting crosstalk between pro inflammatory pathways endogenous to Rps14 loss and TLR7 pathway activation. Overall design: RNA seq analysis of HSPCs TgItga2b:GFPlo cells from pooled rps14+/ or wildtype zebrafish embryos which were phenylhydrazine Phz stressed or unstressed and then treated with imiquimod or vehicle control. A minimum of three replicates per condition were analysed.			WT N1 DMSO 1	GSM5160049	tissue:TgItga2b:GFPlo cells\|genotype:Rps14+/+\|stress:N1\|treatment:DMSO	WT N1 DMSO 1	Data QC was conducted using FastQC 0.11.9 and reads trimmed using Trimmomatic 0.39 Reads were aligned to the zebrafish genome GRCz11 using HISAT2 2.1.0 Alignments were sorted and indexed with samtools 1.9 Reads were counted using featureCounts from subread 2.0.0 and GTF Danio Rerio GRCz11.97 Counts were normalised and differential gene expression was analysed using DESeq2 Genome build: GRCz11 Supplementary files format and content: Matrix of normalised raw counts for every gene and every sample	TgItga2b:GFPlo cells	Haemolytic stress was induced by exposure of embryos to phenylhydrazine. Embryos were incubated in 1 µg/mL PHZ from 24 hpf to 48 hpf and then washed. Embryos were then incubated 20 µM Imiquimod or DMSO control for 4 days from 48hpf to 6dpf. Rps14 genotypes were determined with tailclips and embryos pooled before sorting.	Embryos were pooled by rps14 genotype stress and treatment and TgItga2b:GFPlo cells were sorted directly into Trizol for RNA extraction Libraries were prepared using the Smart seq2 protocol	Tgitga2b:GFP zebrafish were maintained according to standard procedures and UK Home Office guidelines	genotype:Rps14+/+\|stress:N1\|treatment:DMSO	GSM5160049	GSM5160049: WT N1 DMSO 1; Danio rerio; RNA Seq	GSM5160049		1	Embryos were pooled by rps14 genotype stress and treatment and TgItga2b:GFPlo cells were sorted directly into Trizol for RNA extraction Libraries were prepared using the Smart seq2 protocol	GEO Accession:GSM5160049	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP310259	loader:fastq load.py	3_S3_L001_R1_001.fastq 3_S3_L001_R2_001.fastq	fastq fastq	623797940.0	5151640.0	GSM5160049 r1	0:60.55 1:60.54	A:173161787;C:136534464;G:141195459;T:172865158;N:41072	60	60	173161787	136534464	141195459	172865158	41072	SRX10317691	SRS8438128	SRA1205468	GEO	Department of Haematology, UCL Cancer Institute	2	0.90132	0.90854	0.24701	0.24995	0.74629	0.75148	0.51118	0.5229	61	61	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	United Kingdom	2021-03-11	Multi-stage	Multi-stage	Embryo Imprecise	All anatomical structures
63581	63581	SRR13938343	SRX10317691	SRS8438128	SRP310259	PRJNA713782	TLR7 ligation augments hematopoiesis in Rps14 deficiency via paradoxical inflammatory signalling	GSE168727	Transcriptome Analysis	Myelodysplastic syndrome MDS is a haematological malignancy characterised by blood cytopenias and predisposition to acute myeloid leukaemia. We developed a model of MDS using zebrafish using knockout of Rps14 the primary mediator of the anaemia associated with del 5q MDS. These mutant animals develop bone marrow failure with dysplastic features. We conducted an in vivo small molecule screen to identify compounds that ameliorate the MDS phenotype identifying imiquimod an agonist of TLR7. We conducted RNA seq analysis of both treated and untreated animals to define the mechanism of imiquimod in alleviating anaemia. We find imiquimod alleviates anaemia by promoting haematopoietic stem and progenitor cell expansion and erythroid differentiation the mechanism of which is dependent on TLR7 ligation. TLR7 activation in this setting paradoxically promoted an anti inflammatory gene signature suggesting crosstalk between pro inflammatory pathways endogenous to Rps14 loss and TLR7 pathway activation. Overall design: RNA seq analysis of HSPCs TgItga2b:GFPlo cells from pooled rps14+/ or wildtype zebrafish embryos which were phenylhydrazine Phz stressed or unstressed and then treated with imiquimod or vehicle control. A minimum of three replicates per condition were analysed.			WT N1 DMSO 1	GSM5160049	tissue:TgItga2b:GFPlo cells\|genotype:Rps14+/+\|stress:N1\|treatment:DMSO	WT N1 DMSO 1	Data QC was conducted using FastQC 0.11.9 and reads trimmed using Trimmomatic 0.39 Reads were aligned to the zebrafish genome GRCz11 using HISAT2 2.1.0 Alignments were sorted and indexed with samtools 1.9 Reads were counted using featureCounts from subread 2.0.0 and GTF Danio Rerio GRCz11.97 Counts were normalised and differential gene expression was analysed using DESeq2 Genome build: GRCz11 Supplementary files format and content: Matrix of normalised raw counts for every gene and every sample	TgItga2b:GFPlo cells	Haemolytic stress was induced by exposure of embryos to phenylhydrazine. Embryos were incubated in 1 µg/mL PHZ from 24 hpf to 48 hpf and then washed. Embryos were then incubated 20 µM Imiquimod or DMSO control for 4 days from 48hpf to 6dpf. Rps14 genotypes were determined with tailclips and embryos pooled before sorting.	Embryos were pooled by rps14 genotype stress and treatment and TgItga2b:GFPlo cells were sorted directly into Trizol for RNA extraction Libraries were prepared using the Smart seq2 protocol	Tgitga2b:GFP zebrafish were maintained according to standard procedures and UK Home Office guidelines	genotype:Rps14+/+\|stress:N1\|treatment:DMSO	GSM5160049	GSM5160049: WT N1 DMSO 1; Danio rerio; RNA Seq	GSM5160049		1	Embryos were pooled by rps14 genotype stress and treatment and TgItga2b:GFPlo cells were sorted directly into Trizol for RNA extraction Libraries were prepared using the Smart seq2 protocol	GEO Accession:GSM5160049	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP310259	loader:fastq load.py	3_S3_L002_R1_001.fastq 3_S3_L002_R2_001.fastq	fastq fastq	636152833.0	5253623.0	GSM5160049 r2	0:60.55 1:60.54	A:176704298;C:139222679;G:143963973;T:176227505;N:34378	60	60	176704298	139222679	143963973	176227505	34378	SRX10317691	SRS8438128	SRA1205468	GEO	Department of Haematology, UCL Cancer Institute	2	0.90003	0.90639	0.24653	0.24871	0.74509	0.75	0.5209	0.51705	57	61	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	United Kingdom	2021-03-11	Multi-stage	Multi-stage	Embryo Imprecise	All anatomical structures
63582	63582	SRR13938340	SRX10317690	SRS8438127	SRP310259	PRJNA713782	TLR7 ligation augments hematopoiesis in Rps14 deficiency via paradoxical inflammatory signalling	GSE168727	Transcriptome Analysis	Myelodysplastic syndrome MDS is a haematological malignancy characterised by blood cytopenias and predisposition to acute myeloid leukaemia. We developed a model of MDS using zebrafish using knockout of Rps14 the primary mediator of the anaemia associated with del 5q MDS. These mutant animals develop bone marrow failure with dysplastic features. We conducted an in vivo small molecule screen to identify compounds that ameliorate the MDS phenotype identifying imiquimod an agonist of TLR7. We conducted RNA seq analysis of both treated and untreated animals to define the mechanism of imiquimod in alleviating anaemia. We find imiquimod alleviates anaemia by promoting haematopoietic stem and progenitor cell expansion and erythroid differentiation the mechanism of which is dependent on TLR7 ligation. TLR7 activation in this setting paradoxically promoted an anti inflammatory gene signature suggesting crosstalk between pro inflammatory pathways endogenous to Rps14 loss and TLR7 pathway activation. Overall design: RNA seq analysis of HSPCs TgItga2b:GFPlo cells from pooled rps14+/ or wildtype zebrafish embryos which were phenylhydrazine Phz stressed or unstressed and then treated with imiquimod or vehicle control. A minimum of three replicates per condition were analysed.			Het N1 Imi 1	GSM5160048	tissue:TgItga2b:GFPlo cells\|genotype:Rps14+/ \|stress:N1\|treatment:Imiquimod	Het N1 Imi 1	Data QC was conducted using FastQC 0.11.9 and reads trimmed using Trimmomatic 0.39 Reads were aligned to the zebrafish genome GRCz11 using HISAT2 2.1.0 Alignments were sorted and indexed with samtools 1.9 Reads were counted using featureCounts from subread 2.0.0 and GTF Danio Rerio GRCz11.97 Counts were normalised and differential gene expression was analysed using DESeq2 Genome build: GRCz11 Supplementary files format and content: Matrix of normalised raw counts for every gene and every sample	TgItga2b:GFPlo cells	Haemolytic stress was induced by exposure of embryos to phenylhydrazine. Embryos were incubated in 1 µg/mL PHZ from 24 hpf to 48 hpf and then washed. Embryos were then incubated 20 µM Imiquimod or DMSO control for 4 days from 48hpf to 6dpf. Rps14 genotypes were determined with tailclips and embryos pooled before sorting.	Embryos were pooled by rps14 genotype stress and treatment and TgItga2b:GFPlo cells were sorted directly into Trizol for RNA extraction Libraries were prepared using the Smart seq2 protocol	Tgitga2b:GFP zebrafish were maintained according to standard procedures and UK Home Office guidelines	genotype:Rps14+/ \|stress:N1\|treatment:Imiquimod	GSM5160048	GSM5160048: Het N1 Imi 1; Danio rerio; RNA Seq	GSM5160048		1	Embryos were pooled by rps14 genotype stress and treatment and TgItga2b:GFPlo cells were sorted directly into Trizol for RNA extraction Libraries were prepared using the Smart seq2 protocol	GEO Accession:GSM5160048	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP310259	loader:fastq load.py	2_S2_L001_R1_001.fastq 2_S2_L001_R2_001.fastq	fastq fastq	524038601.0	4327704.0	GSM5160048 r1	0:60.55 1:60.54	A:144809582;C:115393351;G:119547224;T:144259903;N:28541	60	60	144809582	115393351	119547224	144259903	28541	SRX10317690	SRS8438127	SRA1205468	GEO	Department of Haematology, UCL Cancer Institute	2	0.90626	0.91425	0.19739	0.20143	0.74978	0.75743	0.51591	0.50861	61	61	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	United Kingdom	2021-03-11	Multi-stage	Multi-stage	Embryo Imprecise	All anatomical structures
63583	63583	SRR13938341	SRX10317690	SRS8438127	SRP310259	PRJNA713782	TLR7 ligation augments hematopoiesis in Rps14 deficiency via paradoxical inflammatory signalling	GSE168727	Transcriptome Analysis	Myelodysplastic syndrome MDS is a haematological malignancy characterised by blood cytopenias and predisposition to acute myeloid leukaemia. We developed a model of MDS using zebrafish using knockout of Rps14 the primary mediator of the anaemia associated with del 5q MDS. These mutant animals develop bone marrow failure with dysplastic features. We conducted an in vivo small molecule screen to identify compounds that ameliorate the MDS phenotype identifying imiquimod an agonist of TLR7. We conducted RNA seq analysis of both treated and untreated animals to define the mechanism of imiquimod in alleviating anaemia. We find imiquimod alleviates anaemia by promoting haematopoietic stem and progenitor cell expansion and erythroid differentiation the mechanism of which is dependent on TLR7 ligation. TLR7 activation in this setting paradoxically promoted an anti inflammatory gene signature suggesting crosstalk between pro inflammatory pathways endogenous to Rps14 loss and TLR7 pathway activation. Overall design: RNA seq analysis of HSPCs TgItga2b:GFPlo cells from pooled rps14+/ or wildtype zebrafish embryos which were phenylhydrazine Phz stressed or unstressed and then treated with imiquimod or vehicle control. A minimum of three replicates per condition were analysed.			Het N1 Imi 1	GSM5160048	tissue:TgItga2b:GFPlo cells\|genotype:Rps14+/ \|stress:N1\|treatment:Imiquimod	Het N1 Imi 1	Data QC was conducted using FastQC 0.11.9 and reads trimmed using Trimmomatic 0.39 Reads were aligned to the zebrafish genome GRCz11 using HISAT2 2.1.0 Alignments were sorted and indexed with samtools 1.9 Reads were counted using featureCounts from subread 2.0.0 and GTF Danio Rerio GRCz11.97 Counts were normalised and differential gene expression was analysed using DESeq2 Genome build: GRCz11 Supplementary files format and content: Matrix of normalised raw counts for every gene and every sample	TgItga2b:GFPlo cells	Haemolytic stress was induced by exposure of embryos to phenylhydrazine. Embryos were incubated in 1 µg/mL PHZ from 24 hpf to 48 hpf and then washed. Embryos were then incubated 20 µM Imiquimod or DMSO control for 4 days from 48hpf to 6dpf. Rps14 genotypes were determined with tailclips and embryos pooled before sorting.	Embryos were pooled by rps14 genotype stress and treatment and TgItga2b:GFPlo cells were sorted directly into Trizol for RNA extraction Libraries were prepared using the Smart seq2 protocol	Tgitga2b:GFP zebrafish were maintained according to standard procedures and UK Home Office guidelines	genotype:Rps14+/ \|stress:N1\|treatment:Imiquimod	GSM5160048	GSM5160048: Het N1 Imi 1; Danio rerio; RNA Seq	GSM5160048		1	Embryos were pooled by rps14 genotype stress and treatment and TgItga2b:GFPlo cells were sorted directly into Trizol for RNA extraction Libraries were prepared using the Smart seq2 protocol	GEO Accession:GSM5160048	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP310259	loader:fastq load.py	2_S2_L002_R1_001.fastq 2_S2_L002_R2_001.fastq	fastq fastq	533892164.0	4409048.0	GSM5160048 r2	0:60.55 1:60.54	A:147623859;C:117540979;G:121817468;T:146886621;N:23237	60	60	147623859	117540979	121817468	146886621	23237	SRX10317690	SRS8438127	SRA1205468	GEO	Department of Haematology, UCL Cancer Institute	2	0.90639	0.91393	0.19863	0.2037	0.7503	0.75749	0.51572	0.51067	61	60	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	United Kingdom	2021-03-11	Multi-stage	Multi-stage	Embryo Imprecise	All anatomical structures
63584	63584	SRR13938338	SRX10317689	SRS8438126	SRP310259	PRJNA713782	TLR7 ligation augments hematopoiesis in Rps14 deficiency via paradoxical inflammatory signalling	GSE168727	Transcriptome Analysis	Myelodysplastic syndrome MDS is a haematological malignancy characterised by blood cytopenias and predisposition to acute myeloid leukaemia. We developed a model of MDS using zebrafish using knockout of Rps14 the primary mediator of the anaemia associated with del 5q MDS. These mutant animals develop bone marrow failure with dysplastic features. We conducted an in vivo small molecule screen to identify compounds that ameliorate the MDS phenotype identifying imiquimod an agonist of TLR7. We conducted RNA seq analysis of both treated and untreated animals to define the mechanism of imiquimod in alleviating anaemia. We find imiquimod alleviates anaemia by promoting haematopoietic stem and progenitor cell expansion and erythroid differentiation the mechanism of which is dependent on TLR7 ligation. TLR7 activation in this setting paradoxically promoted an anti inflammatory gene signature suggesting crosstalk between pro inflammatory pathways endogenous to Rps14 loss and TLR7 pathway activation. Overall design: RNA seq analysis of HSPCs TgItga2b:GFPlo cells from pooled rps14+/ or wildtype zebrafish embryos which were phenylhydrazine Phz stressed or unstressed and then treated with imiquimod or vehicle control. A minimum of three replicates per condition were analysed.			WT N1 Imi 1	GSM5160047	tissue:TgItga2b:GFPlo cells\|genotype:Rps14+/+\|stress:N1\|treatment:Imiquimod	WT N1 Imi 1	Data QC was conducted using FastQC 0.11.9 and reads trimmed using Trimmomatic 0.39 Reads were aligned to the zebrafish genome GRCz11 using HISAT2 2.1.0 Alignments were sorted and indexed with samtools 1.9 Reads were counted using featureCounts from subread 2.0.0 and GTF Danio Rerio GRCz11.97 Counts were normalised and differential gene expression was analysed using DESeq2 Genome build: GRCz11 Supplementary files format and content: Matrix of normalised raw counts for every gene and every sample	TgItga2b:GFPlo cells	Haemolytic stress was induced by exposure of embryos to phenylhydrazine. Embryos were incubated in 1 µg/mL PHZ from 24 hpf to 48 hpf and then washed. Embryos were then incubated 20 µM Imiquimod or DMSO control for 4 days from 48hpf to 6dpf. Rps14 genotypes were determined with tailclips and embryos pooled before sorting.	Embryos were pooled by rps14 genotype stress and treatment and TgItga2b:GFPlo cells were sorted directly into Trizol for RNA extraction Libraries were prepared using the Smart seq2 protocol	Tgitga2b:GFP zebrafish were maintained according to standard procedures and UK Home Office guidelines	genotype:Rps14+/+\|stress:N1\|treatment:Imiquimod	GSM5160047	GSM5160047: WT N1 Imi 1; Danio rerio; RNA Seq	GSM5160047		1	Embryos were pooled by rps14 genotype stress and treatment and TgItga2b:GFPlo cells were sorted directly into Trizol for RNA extraction Libraries were prepared using the Smart seq2 protocol	GEO Accession:GSM5160047	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP310259	loader:fastq load.py	1_S1_L001_R1_001.fastq 1_S1_L001_R2_001.fastq	fastq fastq	539190712.0	4453488.0	GSM5160047 r1	0:60.54 1:60.53	A:147404929;C:120185071;G:124497544;T:147072317;N:30851	60	60	147404929	120185071	124497544	147072317	30851	SRX10317689	SRS8438126	SRA1205468	GEO	Department of Haematology, UCL Cancer Institute	2	0.90535	0.91158	0.22484	0.23116	0.74119	0.74935	0.51549	0.51518	60	60	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	United Kingdom	2021-03-11	Multi-stage	Multi-stage	Embryo Imprecise	All anatomical structures
63585	63585	SRR13938339	SRX10317689	SRS8438126	SRP310259	PRJNA713782	TLR7 ligation augments hematopoiesis in Rps14 deficiency via paradoxical inflammatory signalling	GSE168727	Transcriptome Analysis	Myelodysplastic syndrome MDS is a haematological malignancy characterised by blood cytopenias and predisposition to acute myeloid leukaemia. We developed a model of MDS using zebrafish using knockout of Rps14 the primary mediator of the anaemia associated with del 5q MDS. These mutant animals develop bone marrow failure with dysplastic features. We conducted an in vivo small molecule screen to identify compounds that ameliorate the MDS phenotype identifying imiquimod an agonist of TLR7. We conducted RNA seq analysis of both treated and untreated animals to define the mechanism of imiquimod in alleviating anaemia. We find imiquimod alleviates anaemia by promoting haematopoietic stem and progenitor cell expansion and erythroid differentiation the mechanism of which is dependent on TLR7 ligation. TLR7 activation in this setting paradoxically promoted an anti inflammatory gene signature suggesting crosstalk between pro inflammatory pathways endogenous to Rps14 loss and TLR7 pathway activation. Overall design: RNA seq analysis of HSPCs TgItga2b:GFPlo cells from pooled rps14+/ or wildtype zebrafish embryos which were phenylhydrazine Phz stressed or unstressed and then treated with imiquimod or vehicle control. A minimum of three replicates per condition were analysed.			WT N1 Imi 1	GSM5160047	tissue:TgItga2b:GFPlo cells\|genotype:Rps14+/+\|stress:N1\|treatment:Imiquimod	WT N1 Imi 1	Data QC was conducted using FastQC 0.11.9 and reads trimmed using Trimmomatic 0.39 Reads were aligned to the zebrafish genome GRCz11 using HISAT2 2.1.0 Alignments were sorted and indexed with samtools 1.9 Reads were counted using featureCounts from subread 2.0.0 and GTF Danio Rerio GRCz11.97 Counts were normalised and differential gene expression was analysed using DESeq2 Genome build: GRCz11 Supplementary files format and content: Matrix of normalised raw counts for every gene and every sample	TgItga2b:GFPlo cells	Haemolytic stress was induced by exposure of embryos to phenylhydrazine. Embryos were incubated in 1 µg/mL PHZ from 24 hpf to 48 hpf and then washed. Embryos were then incubated 20 µM Imiquimod or DMSO control for 4 days from 48hpf to 6dpf. Rps14 genotypes were determined with tailclips and embryos pooled before sorting.	Embryos were pooled by rps14 genotype stress and treatment and TgItga2b:GFPlo cells were sorted directly into Trizol for RNA extraction Libraries were prepared using the Smart seq2 protocol	Tgitga2b:GFP zebrafish were maintained according to standard procedures and UK Home Office guidelines	genotype:Rps14+/+\|stress:N1\|treatment:Imiquimod	GSM5160047	GSM5160047: WT N1 Imi 1; Danio rerio; RNA Seq	GSM5160047		1	Embryos were pooled by rps14 genotype stress and treatment and TgItga2b:GFPlo cells were sorted directly into Trizol for RNA extraction Libraries were prepared using the Smart seq2 protocol	GEO Accession:GSM5160047	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP310259	loader:fastq load.py	1_S1_L002_R1_001.fastq 1_S1_L002_R2_001.fastq	fastq fastq	550944123.0	4550474.0	GSM5160047 r2	0:60.54 1:60.54	A:150661567;C:122831668;G:127199870;T:150226692;N:24326	60	60	150661567	122831668	127199870	150226692	24326	SRX10317689	SRS8438126	SRA1205468	GEO	Department of Haematology, UCL Cancer Institute	2	0.90318	0.91071	0.22491	0.23165	0.74359	0.75097	0.50529	0.51514	61	61	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	United Kingdom	2021-03-11	Multi-stage	Multi-stage	Embryo Imprecise	All anatomical structures
71957	71957	SRR22143711	SRX18123007	SRS15624881	SRP405931	PRJNA896973	Vitamin D Receptor regulation of hepatic energy metabolism in zebrafish	GSE217120	Transcriptome Analysis	Vitamin D deficiency and mutations in Vitamin D Receptor VDR are associated with liver disease and obesity but the functions of vitamin D signaling in metabolism are poorly understood. Though vitamin D signaling is best known for its functions in mineral homeostasis and skeleton calcification in terrestrial vertebrates this is unlikely to be the evolutionary function of vitamin D signaling. We utilize tissue specific genetic modulation of Vdr signaling to investigate the function of the vitamin D endocrine system in zebrafish. We find that hepatocyte Vdr regulates organismal response to nutritional cues and coordinates hepatic and organismal energy metabolism by balancing energy storage and tissue growth. Overall design: Comparative gene expression profiling analysis of RNA seq data following hepatocyte specific Vdr modulation in larval and adult zebrafish. fabp10a:dn vdra and fabp10a:ca vdra transgenes were used to achieve hepatocyte Vdr impairment or hyperactivation respectively. Larval experiments were performed on sorted hepatocytes at 96 hpf and reflect approximately 35 pooled fish per sample. Adult experiments were performed on dissected male liver collected at 4.5 mpf mpf and are composed of 3 livers per sample. wild type controls are included for each experiment. For larval fabp10a:dn vdra N = 4 wt 4 dn vdra. For fabp10a:ca vdra N = 4 wt 3 ca vdra. For adult fabp10a:dn vdra N = 4 wt 4 dn vdra.		pubmed:38944835	hepatocytes 96hpf cavdra expt2 rep3	GSM6705365	tissue:hepatocytes sorted\|cell type:hepatocytes sorted\|genotype:fabp10a:ca vdra\|time:96 hpf	hepatocytes 96hpf cavdra expt2 rep3	FASTQ files were mapped to GRCz11 using STAR v2.5.3 and read counting was performed using HTSeq v0.11.1. Read count normalization was performed using the R package DEseq2. Assembly: GRCz11 Supplementary files format and content: .csv files containing ensembl ids gene names and raw read counts or normalized read counts for each experiment	hepatocytes sorted		Hepatocytes were sorted into 75 uL Buffer RLT containing b mercaptoethanol. Total RNA was extracted using the Qiagen RNA Micro Kit with on column DNase treatment. cDNA synthesis and amplification were performed according to the Smart seq2 protocol https://doi.org/10.1038/nprot.2014.006. Library prep was performed with the Nextera XT DNA Library Preparation Kit Illumina.	Larval zebrafish were reared at 28.5 C in E3 salt solution. Adult fish were reared in density matched tanks and fed artemia twice daily.	cell type:hepatocytes sorted\|genotype:fabp10a:ca vdra\|time:96 hpf	GSM6705365	GSM6705365: hepatocytes 96hpf cavdra expt2 rep3; Danio rerio; RNA Seq	GSM6705365 r1	GSM6705365	1	Hepatocytes were sorted into 75 uL Buffer RLT containing b mercaptoethanol. Total RNA was extracted using the Qiagen RNA Micro Kit with on column DNase treatment. cDNA synthesis and amplification were performed according to the Smart seq2 protocol https://doi.org/10.1038/nprot.2014.006. Library prep was performed with the Nextera XT DNA Library Preparation Kit Illumina.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP405931		cavdra_expt2_rep3_R1.fastq.gz	fastq	6706002750.0	44706685.0	GSM6705365 r1	0:150 1:0	A:1750156238;C:1597023915;G:1614921548;T:1743765130;N:135919	150	0	1750156238	1597023915	1614921548	1743765130	135919	SRX18123007	SRS15624881			Goessling Lab, Brigham and Women's Hospital	1	0.88313		0.04409		0.87661		0.55505		150		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2022-11-02	Multi-stage	Multi-stage	Liver	Liver and Biliary System
71958	71958	SRR22143712	SRX18123006	SRS15624880	SRP405931	PRJNA896973	Vitamin D Receptor regulation of hepatic energy metabolism in zebrafish	GSE217120	Transcriptome Analysis	Vitamin D deficiency and mutations in Vitamin D Receptor VDR are associated with liver disease and obesity but the functions of vitamin D signaling in metabolism are poorly understood. Though vitamin D signaling is best known for its functions in mineral homeostasis and skeleton calcification in terrestrial vertebrates this is unlikely to be the evolutionary function of vitamin D signaling. We utilize tissue specific genetic modulation of Vdr signaling to investigate the function of the vitamin D endocrine system in zebrafish. We find that hepatocyte Vdr regulates organismal response to nutritional cues and coordinates hepatic and organismal energy metabolism by balancing energy storage and tissue growth. Overall design: Comparative gene expression profiling analysis of RNA seq data following hepatocyte specific Vdr modulation in larval and adult zebrafish. fabp10a:dn vdra and fabp10a:ca vdra transgenes were used to achieve hepatocyte Vdr impairment or hyperactivation respectively. Larval experiments were performed on sorted hepatocytes at 96 hpf and reflect approximately 35 pooled fish per sample. Adult experiments were performed on dissected male liver collected at 4.5 mpf mpf and are composed of 3 livers per sample. wild type controls are included for each experiment. For larval fabp10a:dn vdra N = 4 wt 4 dn vdra. For fabp10a:ca vdra N = 4 wt 3 ca vdra. For adult fabp10a:dn vdra N = 4 wt 4 dn vdra.		pubmed:38944835	hepatocytes 96hpf cavdra expt2 rep2	GSM6705364	tissue:hepatocytes sorted\|cell type:hepatocytes sorted\|genotype:fabp10a:ca vdra\|time:96 hpf	hepatocytes 96hpf cavdra expt2 rep2	FASTQ files were mapped to GRCz11 using STAR v2.5.3 and read counting was performed using HTSeq v0.11.1. Read count normalization was performed using the R package DEseq2. Assembly: GRCz11 Supplementary files format and content: .csv files containing ensembl ids gene names and raw read counts or normalized read counts for each experiment	hepatocytes sorted		Hepatocytes were sorted into 75 uL Buffer RLT containing b mercaptoethanol. Total RNA was extracted using the Qiagen RNA Micro Kit with on column DNase treatment. cDNA synthesis and amplification were performed according to the Smart seq2 protocol https://doi.org/10.1038/nprot.2014.006. Library prep was performed with the Nextera XT DNA Library Preparation Kit Illumina.	Larval zebrafish were reared at 28.5 C in E3 salt solution. Adult fish were reared in density matched tanks and fed artemia twice daily.	cell type:hepatocytes sorted\|genotype:fabp10a:ca vdra\|time:96 hpf	GSM6705364	GSM6705364: hepatocytes 96hpf cavdra expt2 rep2; Danio rerio; RNA Seq	GSM6705364 r1	GSM6705364	1	Hepatocytes were sorted into 75 uL Buffer RLT containing b mercaptoethanol. Total RNA was extracted using the Qiagen RNA Micro Kit with on column DNase treatment. cDNA synthesis and amplification were performed according to the Smart seq2 protocol https://doi.org/10.1038/nprot.2014.006. Library prep was performed with the Nextera XT DNA Library Preparation Kit Illumina.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP405931		cavdra_expt2_rep2_R1.fastq.gz	fastq	7680154500.0	51201030.0	GSM6705364 r1	0:150 1:0	A:1982779701;C:1851808902;G:1881749764;T:1963662978;N:153155	150	0	1982779701	1851808902	1881749764	1963662978	153155	SRX18123006	SRS15624880			Goessling Lab, Brigham and Women's Hospital	1	0.8513		0.05087		0.8756		0.58342		150		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2022-11-02	Multi-stage	Multi-stage	Liver	Liver and Biliary System
71959	71959	SRR22143713	SRX18123005	SRS15624879	SRP405931	PRJNA896973	Vitamin D Receptor regulation of hepatic energy metabolism in zebrafish	GSE217120	Transcriptome Analysis	Vitamin D deficiency and mutations in Vitamin D Receptor VDR are associated with liver disease and obesity but the functions of vitamin D signaling in metabolism are poorly understood. Though vitamin D signaling is best known for its functions in mineral homeostasis and skeleton calcification in terrestrial vertebrates this is unlikely to be the evolutionary function of vitamin D signaling. We utilize tissue specific genetic modulation of Vdr signaling to investigate the function of the vitamin D endocrine system in zebrafish. We find that hepatocyte Vdr regulates organismal response to nutritional cues and coordinates hepatic and organismal energy metabolism by balancing energy storage and tissue growth. Overall design: Comparative gene expression profiling analysis of RNA seq data following hepatocyte specific Vdr modulation in larval and adult zebrafish. fabp10a:dn vdra and fabp10a:ca vdra transgenes were used to achieve hepatocyte Vdr impairment or hyperactivation respectively. Larval experiments were performed on sorted hepatocytes at 96 hpf and reflect approximately 35 pooled fish per sample. Adult experiments were performed on dissected male liver collected at 4.5 mpf mpf and are composed of 3 livers per sample. wild type controls are included for each experiment. For larval fabp10a:dn vdra N = 4 wt 4 dn vdra. For fabp10a:ca vdra N = 4 wt 3 ca vdra. For adult fabp10a:dn vdra N = 4 wt 4 dn vdra.		pubmed:38944835	hepatocytes 96hpf cavdra expt2 rep1	GSM6705363	tissue:hepatocytes sorted\|cell type:hepatocytes sorted\|genotype:fabp10a:ca vdra\|time:96 hpf	hepatocytes 96hpf cavdra expt2 rep1	FASTQ files were mapped to GRCz11 using STAR v2.5.3 and read counting was performed using HTSeq v0.11.1. Read count normalization was performed using the R package DEseq2. Assembly: GRCz11 Supplementary files format and content: .csv files containing ensembl ids gene names and raw read counts or normalized read counts for each experiment	hepatocytes sorted		Hepatocytes were sorted into 75 uL Buffer RLT containing b mercaptoethanol. Total RNA was extracted using the Qiagen RNA Micro Kit with on column DNase treatment. cDNA synthesis and amplification were performed according to the Smart seq2 protocol https://doi.org/10.1038/nprot.2014.006. Library prep was performed with the Nextera XT DNA Library Preparation Kit Illumina.	Larval zebrafish were reared at 28.5 C in E3 salt solution. Adult fish were reared in density matched tanks and fed artemia twice daily.	cell type:hepatocytes sorted\|genotype:fabp10a:ca vdra\|time:96 hpf	GSM6705363	GSM6705363: hepatocytes 96hpf cavdra expt2 rep1; Danio rerio; RNA Seq	GSM6705363 r1	GSM6705363	1	Hepatocytes were sorted into 75 uL Buffer RLT containing b mercaptoethanol. Total RNA was extracted using the Qiagen RNA Micro Kit with on column DNase treatment. cDNA synthesis and amplification were performed according to the Smart seq2 protocol https://doi.org/10.1038/nprot.2014.006. Library prep was performed with the Nextera XT DNA Library Preparation Kit Illumina.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP405931		cavdra_expt2_rep1_R1.fastq.gz	fastq	8901213300.0	59341422.0	GSM6705363 r1	0:150 1:0	A:2306334188;C:2127419797;G:2168880418;T:2298400416;N:178481	150	0	2306334188	2127419797	2168880418	2298400416	178481	SRX18123005	SRS15624879			Goessling Lab, Brigham and Women's Hospital	1	0.90473		0.05586		0.88347		0.56493		150		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2022-11-02	Multi-stage	Multi-stage	Liver	Liver and Biliary System
71960	71960	SRR22143714	SRX18123004	SRS15624878	SRP405931	PRJNA896973	Vitamin D Receptor regulation of hepatic energy metabolism in zebrafish	GSE217120	Transcriptome Analysis	Vitamin D deficiency and mutations in Vitamin D Receptor VDR are associated with liver disease and obesity but the functions of vitamin D signaling in metabolism are poorly understood. Though vitamin D signaling is best known for its functions in mineral homeostasis and skeleton calcification in terrestrial vertebrates this is unlikely to be the evolutionary function of vitamin D signaling. We utilize tissue specific genetic modulation of Vdr signaling to investigate the function of the vitamin D endocrine system in zebrafish. We find that hepatocyte Vdr regulates organismal response to nutritional cues and coordinates hepatic and organismal energy metabolism by balancing energy storage and tissue growth. Overall design: Comparative gene expression profiling analysis of RNA seq data following hepatocyte specific Vdr modulation in larval and adult zebrafish. fabp10a:dn vdra and fabp10a:ca vdra transgenes were used to achieve hepatocyte Vdr impairment or hyperactivation respectively. Larval experiments were performed on sorted hepatocytes at 96 hpf and reflect approximately 35 pooled fish per sample. Adult experiments were performed on dissected male liver collected at 4.5 mpf mpf and are composed of 3 livers per sample. wild type controls are included for each experiment. For larval fabp10a:dn vdra N = 4 wt 4 dn vdra. For fabp10a:ca vdra N = 4 wt 3 ca vdra. For adult fabp10a:dn vdra N = 4 wt 4 dn vdra.		pubmed:38944835	hepatocytes 96hpf wt expt2 rep4	GSM6705362	tissue:hepatocytes sorted\|cell type:hepatocytes sorted\|genotype:wt\|time:96 hpf	hepatocytes 96hpf wt expt2 rep4	FASTQ files were mapped to GRCz11 using STAR v2.5.3 and read counting was performed using HTSeq v0.11.1. Read count normalization was performed using the R package DEseq2. Assembly: GRCz11 Supplementary files format and content: .csv files containing ensembl ids gene names and raw read counts or normalized read counts for each experiment	hepatocytes sorted		Hepatocytes were sorted into 75 uL Buffer RLT containing b mercaptoethanol. Total RNA was extracted using the Qiagen RNA Micro Kit with on column DNase treatment. cDNA synthesis and amplification were performed according to the Smart seq2 protocol https://doi.org/10.1038/nprot.2014.006. Library prep was performed with the Nextera XT DNA Library Preparation Kit Illumina.	Larval zebrafish were reared at 28.5 C in E3 salt solution. Adult fish were reared in density matched tanks and fed artemia twice daily.	cell type:hepatocytes sorted\|genotype:wt\|time:96 hpf	GSM6705362	GSM6705362: hepatocytes 96hpf wt expt2 rep4; Danio rerio; RNA Seq	GSM6705362 r1	GSM6705362	1	Hepatocytes were sorted into 75 uL Buffer RLT containing b mercaptoethanol. Total RNA was extracted using the Qiagen RNA Micro Kit with on column DNase treatment. cDNA synthesis and amplification were performed according to the Smart seq2 protocol https://doi.org/10.1038/nprot.2014.006. Library prep was performed with the Nextera XT DNA Library Preparation Kit Illumina.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP405931		wt_expt2_rep4_R1.fastq.gz	fastq	11932077600.0	79547184.0	GSM6705362 r1	0:150 1:0	A:3141493904;C:2835740238;G:2863257406;T:3091339595;N:246457	150	0	3141493904	2835740238	2863257406	3091339595	246457	SRX18123004	SRS15624878			Goessling Lab, Brigham and Women's Hospital	1	0.88366		0.04537		0.88185		0.58207		150		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2022-11-02	Multi-stage	Multi-stage	Liver	Liver and Biliary System
71961	71961	SRR22143715	SRX18123003	SRS15624877	SRP405931	PRJNA896973	Vitamin D Receptor regulation of hepatic energy metabolism in zebrafish	GSE217120	Transcriptome Analysis	Vitamin D deficiency and mutations in Vitamin D Receptor VDR are associated with liver disease and obesity but the functions of vitamin D signaling in metabolism are poorly understood. Though vitamin D signaling is best known for its functions in mineral homeostasis and skeleton calcification in terrestrial vertebrates this is unlikely to be the evolutionary function of vitamin D signaling. We utilize tissue specific genetic modulation of Vdr signaling to investigate the function of the vitamin D endocrine system in zebrafish. We find that hepatocyte Vdr regulates organismal response to nutritional cues and coordinates hepatic and organismal energy metabolism by balancing energy storage and tissue growth. Overall design: Comparative gene expression profiling analysis of RNA seq data following hepatocyte specific Vdr modulation in larval and adult zebrafish. fabp10a:dn vdra and fabp10a:ca vdra transgenes were used to achieve hepatocyte Vdr impairment or hyperactivation respectively. Larval experiments were performed on sorted hepatocytes at 96 hpf and reflect approximately 35 pooled fish per sample. Adult experiments were performed on dissected male liver collected at 4.5 mpf mpf and are composed of 3 livers per sample. wild type controls are included for each experiment. For larval fabp10a:dn vdra N = 4 wt 4 dn vdra. For fabp10a:ca vdra N = 4 wt 3 ca vdra. For adult fabp10a:dn vdra N = 4 wt 4 dn vdra.		pubmed:38944835	hepatocytes 96hpf wt expt2 rep3	GSM6705361	tissue:hepatocytes sorted\|cell type:hepatocytes sorted\|genotype:wt\|time:96 hpf	hepatocytes 96hpf wt expt2 rep3	FASTQ files were mapped to GRCz11 using STAR v2.5.3 and read counting was performed using HTSeq v0.11.1. Read count normalization was performed using the R package DEseq2. Assembly: GRCz11 Supplementary files format and content: .csv files containing ensembl ids gene names and raw read counts or normalized read counts for each experiment	hepatocytes sorted		Hepatocytes were sorted into 75 uL Buffer RLT containing b mercaptoethanol. Total RNA was extracted using the Qiagen RNA Micro Kit with on column DNase treatment. cDNA synthesis and amplification were performed according to the Smart seq2 protocol https://doi.org/10.1038/nprot.2014.006. Library prep was performed with the Nextera XT DNA Library Preparation Kit Illumina.	Larval zebrafish were reared at 28.5 C in E3 salt solution. Adult fish were reared in density matched tanks and fed artemia twice daily.	cell type:hepatocytes sorted\|genotype:wt\|time:96 hpf	GSM6705361	GSM6705361: hepatocytes 96hpf wt expt2 rep3; Danio rerio; RNA Seq	GSM6705361 r1	GSM6705361	1	Hepatocytes were sorted into 75 uL Buffer RLT containing b mercaptoethanol. Total RNA was extracted using the Qiagen RNA Micro Kit with on column DNase treatment. cDNA synthesis and amplification were performed according to the Smart seq2 protocol https://doi.org/10.1038/nprot.2014.006. Library prep was performed with the Nextera XT DNA Library Preparation Kit Illumina.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP405931		wt_expt2_rep3_R1.fastq.gz	fastq	9232946100.0	61552974.0	GSM6705361 r1	0:150 1:0	A:2407612258;C:2198887087;G:2229947120;T:2396306352;N:193283	150	0	2407612258	2198887087	2229947120	2396306352	193283	SRX18123003	SRS15624877			Goessling Lab, Brigham and Women's Hospital	1	0.87181		0.05876		0.87864		0.58855		150		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2022-11-02	Multi-stage	Multi-stage	Liver	Liver and Biliary System
71962	71962	SRR22143716	SRX18123002	SRS15624876	SRP405931	PRJNA896973	Vitamin D Receptor regulation of hepatic energy metabolism in zebrafish	GSE217120	Transcriptome Analysis	Vitamin D deficiency and mutations in Vitamin D Receptor VDR are associated with liver disease and obesity but the functions of vitamin D signaling in metabolism are poorly understood. Though vitamin D signaling is best known for its functions in mineral homeostasis and skeleton calcification in terrestrial vertebrates this is unlikely to be the evolutionary function of vitamin D signaling. We utilize tissue specific genetic modulation of Vdr signaling to investigate the function of the vitamin D endocrine system in zebrafish. We find that hepatocyte Vdr regulates organismal response to nutritional cues and coordinates hepatic and organismal energy metabolism by balancing energy storage and tissue growth. Overall design: Comparative gene expression profiling analysis of RNA seq data following hepatocyte specific Vdr modulation in larval and adult zebrafish. fabp10a:dn vdra and fabp10a:ca vdra transgenes were used to achieve hepatocyte Vdr impairment or hyperactivation respectively. Larval experiments were performed on sorted hepatocytes at 96 hpf and reflect approximately 35 pooled fish per sample. Adult experiments were performed on dissected male liver collected at 4.5 mpf mpf and are composed of 3 livers per sample. wild type controls are included for each experiment. For larval fabp10a:dn vdra N = 4 wt 4 dn vdra. For fabp10a:ca vdra N = 4 wt 3 ca vdra. For adult fabp10a:dn vdra N = 4 wt 4 dn vdra.		pubmed:38944835	hepatocytes 96hpf wt expt2 rep2	GSM6705360	tissue:hepatocytes sorted\|cell type:hepatocytes sorted\|genotype:wt\|time:96 hpf	hepatocytes 96hpf wt expt2 rep2	FASTQ files were mapped to GRCz11 using STAR v2.5.3 and read counting was performed using HTSeq v0.11.1. Read count normalization was performed using the R package DEseq2. Assembly: GRCz11 Supplementary files format and content: .csv files containing ensembl ids gene names and raw read counts or normalized read counts for each experiment	hepatocytes sorted		Hepatocytes were sorted into 75 uL Buffer RLT containing b mercaptoethanol. Total RNA was extracted using the Qiagen RNA Micro Kit with on column DNase treatment. cDNA synthesis and amplification were performed according to the Smart seq2 protocol https://doi.org/10.1038/nprot.2014.006. Library prep was performed with the Nextera XT DNA Library Preparation Kit Illumina.	Larval zebrafish were reared at 28.5 C in E3 salt solution. Adult fish were reared in density matched tanks and fed artemia twice daily.	cell type:hepatocytes sorted\|genotype:wt\|time:96 hpf	GSM6705360	GSM6705360: hepatocytes 96hpf wt expt2 rep2; Danio rerio; RNA Seq	GSM6705360 r1	GSM6705360	1	Hepatocytes were sorted into 75 uL Buffer RLT containing b mercaptoethanol. Total RNA was extracted using the Qiagen RNA Micro Kit with on column DNase treatment. cDNA synthesis and amplification were performed according to the Smart seq2 protocol https://doi.org/10.1038/nprot.2014.006. Library prep was performed with the Nextera XT DNA Library Preparation Kit Illumina.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP405931		wt_expt2_rep2_R1.fastq.gz	fastq	6185704050.0	41238027.0	GSM6705360 r1	0:150 1:0	A:1603435702;C:1515988796;G:1488677966;T:1577474793;N:126793	150	0	1603435702	1515988796	1488677966	1577474793	126793	SRX18123002	SRS15624876			Goessling Lab, Brigham and Women's Hospital	1	0.78101		0.04338		0.88266		0.5608		150		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2022-11-02	Multi-stage	Multi-stage	Liver	Liver and Biliary System
71963	71963	SRR22143717	SRX18123001	SRS15624875	SRP405931	PRJNA896973	Vitamin D Receptor regulation of hepatic energy metabolism in zebrafish	GSE217120	Transcriptome Analysis	Vitamin D deficiency and mutations in Vitamin D Receptor VDR are associated with liver disease and obesity but the functions of vitamin D signaling in metabolism are poorly understood. Though vitamin D signaling is best known for its functions in mineral homeostasis and skeleton calcification in terrestrial vertebrates this is unlikely to be the evolutionary function of vitamin D signaling. We utilize tissue specific genetic modulation of Vdr signaling to investigate the function of the vitamin D endocrine system in zebrafish. We find that hepatocyte Vdr regulates organismal response to nutritional cues and coordinates hepatic and organismal energy metabolism by balancing energy storage and tissue growth. Overall design: Comparative gene expression profiling analysis of RNA seq data following hepatocyte specific Vdr modulation in larval and adult zebrafish. fabp10a:dn vdra and fabp10a:ca vdra transgenes were used to achieve hepatocyte Vdr impairment or hyperactivation respectively. Larval experiments were performed on sorted hepatocytes at 96 hpf and reflect approximately 35 pooled fish per sample. Adult experiments were performed on dissected male liver collected at 4.5 mpf mpf and are composed of 3 livers per sample. wild type controls are included for each experiment. For larval fabp10a:dn vdra N = 4 wt 4 dn vdra. For fabp10a:ca vdra N = 4 wt 3 ca vdra. For adult fabp10a:dn vdra N = 4 wt 4 dn vdra.		pubmed:38944835	hepatocytes 96hpf wt expt2 rep1	GSM6705359	tissue:hepatocytes sorted\|cell type:hepatocytes sorted\|genotype:wt\|time:96 hpf	hepatocytes 96hpf wt expt2 rep1	FASTQ files were mapped to GRCz11 using STAR v2.5.3 and read counting was performed using HTSeq v0.11.1. Read count normalization was performed using the R package DEseq2. Assembly: GRCz11 Supplementary files format and content: .csv files containing ensembl ids gene names and raw read counts or normalized read counts for each experiment	hepatocytes sorted		Hepatocytes were sorted into 75 uL Buffer RLT containing b mercaptoethanol. Total RNA was extracted using the Qiagen RNA Micro Kit with on column DNase treatment. cDNA synthesis and amplification were performed according to the Smart seq2 protocol https://doi.org/10.1038/nprot.2014.006. Library prep was performed with the Nextera XT DNA Library Preparation Kit Illumina.	Larval zebrafish were reared at 28.5 C in E3 salt solution. Adult fish were reared in density matched tanks and fed artemia twice daily.	cell type:hepatocytes sorted\|genotype:wt\|time:96 hpf	GSM6705359	GSM6705359: hepatocytes 96hpf wt expt2 rep1; Danio rerio; RNA Seq	GSM6705359 r1	GSM6705359	1	Hepatocytes were sorted into 75 uL Buffer RLT containing b mercaptoethanol. Total RNA was extracted using the Qiagen RNA Micro Kit with on column DNase treatment. cDNA synthesis and amplification were performed according to the Smart seq2 protocol https://doi.org/10.1038/nprot.2014.006. Library prep was performed with the Nextera XT DNA Library Preparation Kit Illumina.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP405931		wt_expt2_rep1_R1.fastq.gz	fastq	6197680950.0	41317873.0	GSM6705359 r1	0:150 1:0	A:1603637872;C:1495661601;G:1502876654;T:1595377016;N:127807	150	0	1603637872	1495661601	1502876654	1595377016	127807	SRX18123001	SRS15624875			Goessling Lab, Brigham and Women's Hospital	1	0.86333		0.05099		0.88919		0.56132		150		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2022-11-02	Multi-stage	Multi-stage	Liver	Liver and Biliary System
71964	71964	SRR22143718	SRX18123000	SRS15624874	SRP405931	PRJNA896973	Vitamin D Receptor regulation of hepatic energy metabolism in zebrafish	GSE217120	Transcriptome Analysis	Vitamin D deficiency and mutations in Vitamin D Receptor VDR are associated with liver disease and obesity but the functions of vitamin D signaling in metabolism are poorly understood. Though vitamin D signaling is best known for its functions in mineral homeostasis and skeleton calcification in terrestrial vertebrates this is unlikely to be the evolutionary function of vitamin D signaling. We utilize tissue specific genetic modulation of Vdr signaling to investigate the function of the vitamin D endocrine system in zebrafish. We find that hepatocyte Vdr regulates organismal response to nutritional cues and coordinates hepatic and organismal energy metabolism by balancing energy storage and tissue growth. Overall design: Comparative gene expression profiling analysis of RNA seq data following hepatocyte specific Vdr modulation in larval and adult zebrafish. fabp10a:dn vdra and fabp10a:ca vdra transgenes were used to achieve hepatocyte Vdr impairment or hyperactivation respectively. Larval experiments were performed on sorted hepatocytes at 96 hpf and reflect approximately 35 pooled fish per sample. Adult experiments were performed on dissected male liver collected at 4.5 mpf mpf and are composed of 3 livers per sample. wild type controls are included for each experiment. For larval fabp10a:dn vdra N = 4 wt 4 dn vdra. For fabp10a:ca vdra N = 4 wt 3 ca vdra. For adult fabp10a:dn vdra N = 4 wt 4 dn vdra.		pubmed:38944835	hepatocytes 96hpf dnvdra expt1 rep4	GSM6705358	tissue:hepatocytes sorted\|cell type:hepatocytes sorted\|genotype:fabp10a:dn vdra\|time:96 hpf	hepatocytes 96hpf dnvdra expt1 rep4	FASTQ files were mapped to GRCz11 using STAR v2.5.3 and read counting was performed using HTSeq v0.11.1. Read count normalization was performed using the R package DEseq2. Assembly: GRCz11 Supplementary files format and content: .csv files containing ensembl ids gene names and raw read counts or normalized read counts for each experiment	hepatocytes sorted		Hepatocytes were sorted into 75 uL Buffer RLT containing b mercaptoethanol. Total RNA was extracted using the Qiagen RNA Micro Kit with on column DNase treatment. The SMART Seq v4 Ultra Low Input Kit for Sequencing Clontech kit was used for cDNA synthesis and amplification. Library prep was performed with the Nextera XT DNA Library Preparation Kit.	Larval zebrafish were reared at 28.5 C in E3 salt solution. Adult fish were reared in density matched tanks and fed artemia twice daily.	cell type:hepatocytes sorted\|genotype:fabp10a:dn vdra\|time:96 hpf	GSM6705358	GSM6705358: hepatocytes 96hpf dnvdra expt1 rep4; Danio rerio; RNA Seq	GSM6705358 r1	GSM6705358	1	Hepatocytes were sorted into 75 uL Buffer RLT containing b mercaptoethanol. Total RNA was extracted using the Qiagen RNA Micro Kit with on column DNase treatment. The SMART Seq v4 Ultra Low Input Kit for Sequencing Clontech kit was used for cDNA synthesis and amplification. Library prep was performed with the Nextera XT DNA Library Preparation Kit.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP405931	loader:fastq load.py	dnvdra_expt1_rep4_R1.fastq.gz dnvdra_expt1_rep4_R2.fastq.gz	fastq fastq	18831415800.0	62771386.0	GSM6705358 r1	0:150 1:150	A:4640361931;C:4661552439;G:4707320281;T:4820985318;N:1195831	150	150	4640361931	4661552439	4707320281	4820985318	1195831	SRX18123000	SRS15624874			Goessling Lab, Brigham and Women's Hospital	2	0.94748	0.94729	0.03313	0.03287	0.79719	0.79945	0.47574	0.47792	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2022-11-02	Multi-stage	Multi-stage	Liver	Liver and Biliary System
71965	71965	SRR22143719	SRX18122999	SRS15624873	SRP405931	PRJNA896973	Vitamin D Receptor regulation of hepatic energy metabolism in zebrafish	GSE217120	Transcriptome Analysis	Vitamin D deficiency and mutations in Vitamin D Receptor VDR are associated with liver disease and obesity but the functions of vitamin D signaling in metabolism are poorly understood. Though vitamin D signaling is best known for its functions in mineral homeostasis and skeleton calcification in terrestrial vertebrates this is unlikely to be the evolutionary function of vitamin D signaling. We utilize tissue specific genetic modulation of Vdr signaling to investigate the function of the vitamin D endocrine system in zebrafish. We find that hepatocyte Vdr regulates organismal response to nutritional cues and coordinates hepatic and organismal energy metabolism by balancing energy storage and tissue growth. Overall design: Comparative gene expression profiling analysis of RNA seq data following hepatocyte specific Vdr modulation in larval and adult zebrafish. fabp10a:dn vdra and fabp10a:ca vdra transgenes were used to achieve hepatocyte Vdr impairment or hyperactivation respectively. Larval experiments were performed on sorted hepatocytes at 96 hpf and reflect approximately 35 pooled fish per sample. Adult experiments were performed on dissected male liver collected at 4.5 mpf mpf and are composed of 3 livers per sample. wild type controls are included for each experiment. For larval fabp10a:dn vdra N = 4 wt 4 dn vdra. For fabp10a:ca vdra N = 4 wt 3 ca vdra. For adult fabp10a:dn vdra N = 4 wt 4 dn vdra.		pubmed:38944835	hepatocytes 96hpf dnvdra expt1 rep3	GSM6705357	tissue:hepatocytes sorted\|cell type:hepatocytes sorted\|genotype:fabp10a:dn vdra\|time:96 hpf	hepatocytes 96hpf dnvdra expt1 rep3	FASTQ files were mapped to GRCz11 using STAR v2.5.3 and read counting was performed using HTSeq v0.11.1. Read count normalization was performed using the R package DEseq2. Assembly: GRCz11 Supplementary files format and content: .csv files containing ensembl ids gene names and raw read counts or normalized read counts for each experiment	hepatocytes sorted		Hepatocytes were sorted into 75 uL Buffer RLT containing b mercaptoethanol. Total RNA was extracted using the Qiagen RNA Micro Kit with on column DNase treatment. The SMART Seq v4 Ultra Low Input Kit for Sequencing Clontech kit was used for cDNA synthesis and amplification. Library prep was performed with the Nextera XT DNA Library Preparation Kit.	Larval zebrafish were reared at 28.5 C in E3 salt solution. Adult fish were reared in density matched tanks and fed artemia twice daily.	cell type:hepatocytes sorted\|genotype:fabp10a:dn vdra\|time:96 hpf	GSM6705357	GSM6705357: hepatocytes 96hpf dnvdra expt1 rep3; Danio rerio; RNA Seq	GSM6705357 r1	GSM6705357	1	Hepatocytes were sorted into 75 uL Buffer RLT containing b mercaptoethanol. Total RNA was extracted using the Qiagen RNA Micro Kit with on column DNase treatment. The SMART Seq v4 Ultra Low Input Kit for Sequencing Clontech kit was used for cDNA synthesis and amplification. Library prep was performed with the Nextera XT DNA Library Preparation Kit.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP405931	loader:fastq load.py	dnvdra_expt1_rep3_R1.fastq.gz dnvdra_expt1_rep3_R2.fastq.gz	fastq fastq	16955597400.0	56518658.0	GSM6705357 r1	0:150 1:150	A:4191429329;C:4181155612;G:4191314524;T:4390631329;N:1066606	150	150	4191429329	4181155612	4191314524	4390631329	1066606	SRX18122999	SRS15624873			Goessling Lab, Brigham and Women's Hospital	2	0.94938	0.94935	0.0338	0.03364	0.79545	0.79695	0.48365	0.48166	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2022-11-02	Multi-stage	Multi-stage	Liver	Liver and Biliary System
71966	71966	SRR22143720	SRX18122998	SRS15624872	SRP405931	PRJNA896973	Vitamin D Receptor regulation of hepatic energy metabolism in zebrafish	GSE217120	Transcriptome Analysis	Vitamin D deficiency and mutations in Vitamin D Receptor VDR are associated with liver disease and obesity but the functions of vitamin D signaling in metabolism are poorly understood. Though vitamin D signaling is best known for its functions in mineral homeostasis and skeleton calcification in terrestrial vertebrates this is unlikely to be the evolutionary function of vitamin D signaling. We utilize tissue specific genetic modulation of Vdr signaling to investigate the function of the vitamin D endocrine system in zebrafish. We find that hepatocyte Vdr regulates organismal response to nutritional cues and coordinates hepatic and organismal energy metabolism by balancing energy storage and tissue growth. Overall design: Comparative gene expression profiling analysis of RNA seq data following hepatocyte specific Vdr modulation in larval and adult zebrafish. fabp10a:dn vdra and fabp10a:ca vdra transgenes were used to achieve hepatocyte Vdr impairment or hyperactivation respectively. Larval experiments were performed on sorted hepatocytes at 96 hpf and reflect approximately 35 pooled fish per sample. Adult experiments were performed on dissected male liver collected at 4.5 mpf mpf and are composed of 3 livers per sample. wild type controls are included for each experiment. For larval fabp10a:dn vdra N = 4 wt 4 dn vdra. For fabp10a:ca vdra N = 4 wt 3 ca vdra. For adult fabp10a:dn vdra N = 4 wt 4 dn vdra.		pubmed:38944835	hepatocytes 96hpf dnvdra expt1 rep2	GSM6705356	tissue:hepatocytes sorted\|cell type:hepatocytes sorted\|genotype:fabp10a:dn vdra\|time:96 hpf	hepatocytes 96hpf dnvdra expt1 rep2	FASTQ files were mapped to GRCz11 using STAR v2.5.3 and read counting was performed using HTSeq v0.11.1. Read count normalization was performed using the R package DEseq2. Assembly: GRCz11 Supplementary files format and content: .csv files containing ensembl ids gene names and raw read counts or normalized read counts for each experiment	hepatocytes sorted		Hepatocytes were sorted into 75 uL Buffer RLT containing b mercaptoethanol. Total RNA was extracted using the Qiagen RNA Micro Kit with on column DNase treatment. The SMART Seq v4 Ultra Low Input Kit for Sequencing Clontech kit was used for cDNA synthesis and amplification. Library prep was performed with the Nextera XT DNA Library Preparation Kit.	Larval zebrafish were reared at 28.5 C in E3 salt solution. Adult fish were reared in density matched tanks and fed artemia twice daily.	cell type:hepatocytes sorted\|genotype:fabp10a:dn vdra\|time:96 hpf	GSM6705356	GSM6705356: hepatocytes 96hpf dnvdra expt1 rep2; Danio rerio; RNA Seq	GSM6705356 r1	GSM6705356	1	Hepatocytes were sorted into 75 uL Buffer RLT containing b mercaptoethanol. Total RNA was extracted using the Qiagen RNA Micro Kit with on column DNase treatment. The SMART Seq v4 Ultra Low Input Kit for Sequencing Clontech kit was used for cDNA synthesis and amplification. Library prep was performed with the Nextera XT DNA Library Preparation Kit.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP405931	loader:fastq load.py	dnvdra_expt1_rep2_R1.fastq.gz dnvdra_expt1_rep2_R2.fastq.gz	fastq fastq	17388104700.0	57960349.0	GSM6705356 r1	0:150 1:150	A:4247868125;C:4323132556;G:4325289881;T:4490744969;N:1069169	150	150	4247868125	4323132556	4325289881	4490744969	1069169	SRX18122998	SRS15624872			Goessling Lab, Brigham and Women's Hospital	2	0.94837	0.94745	0.03174	0.03157	0.79184	0.79381	0.47513	0.47039	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2022-11-02	Multi-stage	Multi-stage	Liver	Liver and Biliary System
71967	71967	SRR22143721	SRX18122997	SRS15624871	SRP405931	PRJNA896973	Vitamin D Receptor regulation of hepatic energy metabolism in zebrafish	GSE217120	Transcriptome Analysis	Vitamin D deficiency and mutations in Vitamin D Receptor VDR are associated with liver disease and obesity but the functions of vitamin D signaling in metabolism are poorly understood. Though vitamin D signaling is best known for its functions in mineral homeostasis and skeleton calcification in terrestrial vertebrates this is unlikely to be the evolutionary function of vitamin D signaling. We utilize tissue specific genetic modulation of Vdr signaling to investigate the function of the vitamin D endocrine system in zebrafish. We find that hepatocyte Vdr regulates organismal response to nutritional cues and coordinates hepatic and organismal energy metabolism by balancing energy storage and tissue growth. Overall design: Comparative gene expression profiling analysis of RNA seq data following hepatocyte specific Vdr modulation in larval and adult zebrafish. fabp10a:dn vdra and fabp10a:ca vdra transgenes were used to achieve hepatocyte Vdr impairment or hyperactivation respectively. Larval experiments were performed on sorted hepatocytes at 96 hpf and reflect approximately 35 pooled fish per sample. Adult experiments were performed on dissected male liver collected at 4.5 mpf mpf and are composed of 3 livers per sample. wild type controls are included for each experiment. For larval fabp10a:dn vdra N = 4 wt 4 dn vdra. For fabp10a:ca vdra N = 4 wt 3 ca vdra. For adult fabp10a:dn vdra N = 4 wt 4 dn vdra.		pubmed:38944835	hepatocytes 96hpf dnvdra expt1 rep1	GSM6705355	tissue:hepatocytes sorted\|cell type:hepatocytes sorted\|genotype:fabp10a:dn vdra\|time:96 hpf	hepatocytes 96hpf dnvdra expt1 rep1	FASTQ files were mapped to GRCz11 using STAR v2.5.3 and read counting was performed using HTSeq v0.11.1. Read count normalization was performed using the R package DEseq2. Assembly: GRCz11 Supplementary files format and content: .csv files containing ensembl ids gene names and raw read counts or normalized read counts for each experiment	hepatocytes sorted		Hepatocytes were sorted into 75 uL Buffer RLT containing b mercaptoethanol. Total RNA was extracted using the Qiagen RNA Micro Kit with on column DNase treatment. The SMART Seq v4 Ultra Low Input Kit for Sequencing Clontech kit was used for cDNA synthesis and amplification. Library prep was performed with the Nextera XT DNA Library Preparation Kit.	Larval zebrafish were reared at 28.5 C in E3 salt solution. Adult fish were reared in density matched tanks and fed artemia twice daily.	cell type:hepatocytes sorted\|genotype:fabp10a:dn vdra\|time:96 hpf	GSM6705355	GSM6705355: hepatocytes 96hpf dnvdra expt1 rep1; Danio rerio; RNA Seq	GSM6705355 r1	GSM6705355	1	Hepatocytes were sorted into 75 uL Buffer RLT containing b mercaptoethanol. Total RNA was extracted using the Qiagen RNA Micro Kit with on column DNase treatment. The SMART Seq v4 Ultra Low Input Kit for Sequencing Clontech kit was used for cDNA synthesis and amplification. Library prep was performed with the Nextera XT DNA Library Preparation Kit.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP405931	loader:fastq load.py	dnvdra_expt1_rep1_R1.fastq.gz dnvdra_expt1_rep1_R2.fastq.gz	fastq fastq	18386589600.0	61288632.0	GSM6705355 r1	0:150 1:150	A:4509534555;C:4473109680;G:4706080457;T:4696713250;N:1151658	150	150	4509534555	4473109680	4706080457	4696713250	1151658	SRX18122997	SRS15624871			Goessling Lab, Brigham and Women's Hospital	2	0.94402	0.94369	0.03471	0.03448	0.79478	0.7964	0.43544	0.43575	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2022-11-02	Multi-stage	Multi-stage	Liver	Liver and Biliary System
71968	71968	SRR22143722	SRX18122996	SRS15624870	SRP405931	PRJNA896973	Vitamin D Receptor regulation of hepatic energy metabolism in zebrafish	GSE217120	Transcriptome Analysis	Vitamin D deficiency and mutations in Vitamin D Receptor VDR are associated with liver disease and obesity but the functions of vitamin D signaling in metabolism are poorly understood. Though vitamin D signaling is best known for its functions in mineral homeostasis and skeleton calcification in terrestrial vertebrates this is unlikely to be the evolutionary function of vitamin D signaling. We utilize tissue specific genetic modulation of Vdr signaling to investigate the function of the vitamin D endocrine system in zebrafish. We find that hepatocyte Vdr regulates organismal response to nutritional cues and coordinates hepatic and organismal energy metabolism by balancing energy storage and tissue growth. Overall design: Comparative gene expression profiling analysis of RNA seq data following hepatocyte specific Vdr modulation in larval and adult zebrafish. fabp10a:dn vdra and fabp10a:ca vdra transgenes were used to achieve hepatocyte Vdr impairment or hyperactivation respectively. Larval experiments were performed on sorted hepatocytes at 96 hpf and reflect approximately 35 pooled fish per sample. Adult experiments were performed on dissected male liver collected at 4.5 mpf mpf and are composed of 3 livers per sample. wild type controls are included for each experiment. For larval fabp10a:dn vdra N = 4 wt 4 dn vdra. For fabp10a:ca vdra N = 4 wt 3 ca vdra. For adult fabp10a:dn vdra N = 4 wt 4 dn vdra.		pubmed:38944835	hepatocytes 96hpf wt expt1 rep4	GSM6705354	tissue:hepatocytes sorted\|cell type:hepatocytes sorted\|genotype:wt\|time:96 hpf	hepatocytes 96hpf wt expt1 rep4	FASTQ files were mapped to GRCz11 using STAR v2.5.3 and read counting was performed using HTSeq v0.11.1. Read count normalization was performed using the R package DEseq2. Assembly: GRCz11 Supplementary files format and content: .csv files containing ensembl ids gene names and raw read counts or normalized read counts for each experiment	hepatocytes sorted		Hepatocytes were sorted into 75 uL Buffer RLT containing b mercaptoethanol. Total RNA was extracted using the Qiagen RNA Micro Kit with on column DNase treatment. The SMART Seq v4 Ultra Low Input Kit for Sequencing Clontech kit was used for cDNA synthesis and amplification. Library prep was performed with the Nextera XT DNA Library Preparation Kit.	Larval zebrafish were reared at 28.5 C in E3 salt solution. Adult fish were reared in density matched tanks and fed artemia twice daily.	cell type:hepatocytes sorted\|genotype:wt\|time:96 hpf	GSM6705354	GSM6705354: hepatocytes 96hpf wt expt1 rep4; Danio rerio; RNA Seq	GSM6705354 r1	GSM6705354	1	Hepatocytes were sorted into 75 uL Buffer RLT containing b mercaptoethanol. Total RNA was extracted using the Qiagen RNA Micro Kit with on column DNase treatment. The SMART Seq v4 Ultra Low Input Kit for Sequencing Clontech kit was used for cDNA synthesis and amplification. Library prep was performed with the Nextera XT DNA Library Preparation Kit.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP405931	loader:fastq load.py	wt_expt1_rep4_R1.fastq.gz wt_expt1_rep4_R2.fastq.gz	fastq fastq	14844320700.0	49481069.0	GSM6705354 r1	0:150 1:150	A:3676168506;C:3664928523;G:3671171564;T:3831144092;N:908015	150	150	3676168506	3664928523	3671171564	3831144092	908015	SRX18122996	SRS15624870			Goessling Lab, Brigham and Women's Hospital	2	0.94938	0.94888	0.02974	0.02976	0.80444	0.80614	0.47385	0.42037	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2022-11-02	Multi-stage	Multi-stage	Liver	Liver and Biliary System
71969	71969	SRR22143723	SRX18122995	SRS15624869	SRP405931	PRJNA896973	Vitamin D Receptor regulation of hepatic energy metabolism in zebrafish	GSE217120	Transcriptome Analysis	Vitamin D deficiency and mutations in Vitamin D Receptor VDR are associated with liver disease and obesity but the functions of vitamin D signaling in metabolism are poorly understood. Though vitamin D signaling is best known for its functions in mineral homeostasis and skeleton calcification in terrestrial vertebrates this is unlikely to be the evolutionary function of vitamin D signaling. We utilize tissue specific genetic modulation of Vdr signaling to investigate the function of the vitamin D endocrine system in zebrafish. We find that hepatocyte Vdr regulates organismal response to nutritional cues and coordinates hepatic and organismal energy metabolism by balancing energy storage and tissue growth. Overall design: Comparative gene expression profiling analysis of RNA seq data following hepatocyte specific Vdr modulation in larval and adult zebrafish. fabp10a:dn vdra and fabp10a:ca vdra transgenes were used to achieve hepatocyte Vdr impairment or hyperactivation respectively. Larval experiments were performed on sorted hepatocytes at 96 hpf and reflect approximately 35 pooled fish per sample. Adult experiments were performed on dissected male liver collected at 4.5 mpf mpf and are composed of 3 livers per sample. wild type controls are included for each experiment. For larval fabp10a:dn vdra N = 4 wt 4 dn vdra. For fabp10a:ca vdra N = 4 wt 3 ca vdra. For adult fabp10a:dn vdra N = 4 wt 4 dn vdra.		pubmed:38944835	hepatocytes 96hpf wt expt1 rep3	GSM6705353	tissue:hepatocytes sorted\|cell type:hepatocytes sorted\|genotype:wt\|time:96 hpf	hepatocytes 96hpf wt expt1 rep3	FASTQ files were mapped to GRCz11 using STAR v2.5.3 and read counting was performed using HTSeq v0.11.1. Read count normalization was performed using the R package DEseq2. Assembly: GRCz11 Supplementary files format and content: .csv files containing ensembl ids gene names and raw read counts or normalized read counts for each experiment	hepatocytes sorted		Hepatocytes were sorted into 75 uL Buffer RLT containing b mercaptoethanol. Total RNA was extracted using the Qiagen RNA Micro Kit with on column DNase treatment. The SMART Seq v4 Ultra Low Input Kit for Sequencing Clontech kit was used for cDNA synthesis and amplification. Library prep was performed with the Nextera XT DNA Library Preparation Kit.	Larval zebrafish were reared at 28.5 C in E3 salt solution. Adult fish were reared in density matched tanks and fed artemia twice daily.	cell type:hepatocytes sorted\|genotype:wt\|time:96 hpf	GSM6705353	GSM6705353: hepatocytes 96hpf wt expt1 rep3; Danio rerio; RNA Seq	GSM6705353 r1	GSM6705353	1	Hepatocytes were sorted into 75 uL Buffer RLT containing b mercaptoethanol. Total RNA was extracted using the Qiagen RNA Micro Kit with on column DNase treatment. The SMART Seq v4 Ultra Low Input Kit for Sequencing Clontech kit was used for cDNA synthesis and amplification. Library prep was performed with the Nextera XT DNA Library Preparation Kit.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP405931	loader:fastq load.py	wt_expt1_rep3_R1.fastq.gz wt_expt1_rep3_R2.fastq.gz	fastq fastq	16613218800.0	55377396.0	GSM6705353 r1	0:150 1:150	A:4069624360;C:4165320060;G:4040198029;T:4337025346;N:1051005	150	150	4069624360	4165320060	4040198029	4337025346	1051005	SRX18122995	SRS15624869			Goessling Lab, Brigham and Women's Hospital	2	0.94839	0.94783	0.03158	0.03154	0.79703	0.79859	0.41789	0.4109	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2022-11-02	Multi-stage	Multi-stage	Liver	Liver and Biliary System
71970	71970	SRR22143724	SRX18122994	SRS15624868	SRP405931	PRJNA896973	Vitamin D Receptor regulation of hepatic energy metabolism in zebrafish	GSE217120	Transcriptome Analysis	Vitamin D deficiency and mutations in Vitamin D Receptor VDR are associated with liver disease and obesity but the functions of vitamin D signaling in metabolism are poorly understood. Though vitamin D signaling is best known for its functions in mineral homeostasis and skeleton calcification in terrestrial vertebrates this is unlikely to be the evolutionary function of vitamin D signaling. We utilize tissue specific genetic modulation of Vdr signaling to investigate the function of the vitamin D endocrine system in zebrafish. We find that hepatocyte Vdr regulates organismal response to nutritional cues and coordinates hepatic and organismal energy metabolism by balancing energy storage and tissue growth. Overall design: Comparative gene expression profiling analysis of RNA seq data following hepatocyte specific Vdr modulation in larval and adult zebrafish. fabp10a:dn vdra and fabp10a:ca vdra transgenes were used to achieve hepatocyte Vdr impairment or hyperactivation respectively. Larval experiments were performed on sorted hepatocytes at 96 hpf and reflect approximately 35 pooled fish per sample. Adult experiments were performed on dissected male liver collected at 4.5 mpf mpf and are composed of 3 livers per sample. wild type controls are included for each experiment. For larval fabp10a:dn vdra N = 4 wt 4 dn vdra. For fabp10a:ca vdra N = 4 wt 3 ca vdra. For adult fabp10a:dn vdra N = 4 wt 4 dn vdra.		pubmed:38944835	hepatocytes 96hpf wt expt1 rep2	GSM6705352	tissue:hepatocytes sorted\|cell type:hepatocytes sorted\|genotype:wt\|time:96 hpf	hepatocytes 96hpf wt expt1 rep2	FASTQ files were mapped to GRCz11 using STAR v2.5.3 and read counting was performed using HTSeq v0.11.1. Read count normalization was performed using the R package DEseq2. Assembly: GRCz11 Supplementary files format and content: .csv files containing ensembl ids gene names and raw read counts or normalized read counts for each experiment	hepatocytes sorted		Hepatocytes were sorted into 75 uL Buffer RLT containing b mercaptoethanol. Total RNA was extracted using the Qiagen RNA Micro Kit with on column DNase treatment. The SMART Seq v4 Ultra Low Input Kit for Sequencing Clontech kit was used for cDNA synthesis and amplification. Library prep was performed with the Nextera XT DNA Library Preparation Kit.	Larval zebrafish were reared at 28.5 C in E3 salt solution. Adult fish were reared in density matched tanks and fed artemia twice daily.	cell type:hepatocytes sorted\|genotype:wt\|time:96 hpf	GSM6705352	GSM6705352: hepatocytes 96hpf wt expt1 rep2; Danio rerio; RNA Seq	GSM6705352 r1	GSM6705352	1	Hepatocytes were sorted into 75 uL Buffer RLT containing b mercaptoethanol. Total RNA was extracted using the Qiagen RNA Micro Kit with on column DNase treatment. The SMART Seq v4 Ultra Low Input Kit for Sequencing Clontech kit was used for cDNA synthesis and amplification. Library prep was performed with the Nextera XT DNA Library Preparation Kit.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP405931	loader:fastq load.py	wt_expt1_rep2_R1.fastq.gz wt_expt1_rep2_R2.fastq.gz	fastq fastq	15406857900.0	51356193.0	GSM6705352 r1	0:150 1:150	A:3790021506;C:3872684076;G:3750856541;T:3992308410;N:987367	150	150	3790021506	3872684076	3750856541	3992308410	987367	SRX18122994	SRS15624868			Goessling Lab, Brigham and Women's Hospital	2	0.94749	0.94642	0.02824	0.02814	0.80044	0.80275	0.41703	0.46905	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2022-11-02	Multi-stage	Multi-stage	Liver	Liver and Biliary System
71971	71971	SRR22143725	SRX18122993	SRS15624867	SRP405931	PRJNA896973	Vitamin D Receptor regulation of hepatic energy metabolism in zebrafish	GSE217120	Transcriptome Analysis	Vitamin D deficiency and mutations in Vitamin D Receptor VDR are associated with liver disease and obesity but the functions of vitamin D signaling in metabolism are poorly understood. Though vitamin D signaling is best known for its functions in mineral homeostasis and skeleton calcification in terrestrial vertebrates this is unlikely to be the evolutionary function of vitamin D signaling. We utilize tissue specific genetic modulation of Vdr signaling to investigate the function of the vitamin D endocrine system in zebrafish. We find that hepatocyte Vdr regulates organismal response to nutritional cues and coordinates hepatic and organismal energy metabolism by balancing energy storage and tissue growth. Overall design: Comparative gene expression profiling analysis of RNA seq data following hepatocyte specific Vdr modulation in larval and adult zebrafish. fabp10a:dn vdra and fabp10a:ca vdra transgenes were used to achieve hepatocyte Vdr impairment or hyperactivation respectively. Larval experiments were performed on sorted hepatocytes at 96 hpf and reflect approximately 35 pooled fish per sample. Adult experiments were performed on dissected male liver collected at 4.5 mpf mpf and are composed of 3 livers per sample. wild type controls are included for each experiment. For larval fabp10a:dn vdra N = 4 wt 4 dn vdra. For fabp10a:ca vdra N = 4 wt 3 ca vdra. For adult fabp10a:dn vdra N = 4 wt 4 dn vdra.		pubmed:38944835	hepatocytes 96hpf wt expt1 rep1	GSM6705351	tissue:hepatocytes sorted\|cell type:hepatocytes sorted\|genotype:wt\|time:96 hpf	hepatocytes 96hpf wt expt1 rep1	FASTQ files were mapped to GRCz11 using STAR v2.5.3 and read counting was performed using HTSeq v0.11.1. Read count normalization was performed using the R package DEseq2. Assembly: GRCz11 Supplementary files format and content: .csv files containing ensembl ids gene names and raw read counts or normalized read counts for each experiment	hepatocytes sorted		Hepatocytes were sorted into 75 uL Buffer RLT containing b mercaptoethanol. Total RNA was extracted using the Qiagen RNA Micro Kit with on column DNase treatment. The SMART Seq v4 Ultra Low Input Kit for Sequencing Clontech kit was used for cDNA synthesis and amplification. Library prep was performed with the Nextera XT DNA Library Preparation Kit.	Larval zebrafish were reared at 28.5 C in E3 salt solution. Adult fish were reared in density matched tanks and fed artemia twice daily.	cell type:hepatocytes sorted\|genotype:wt\|time:96 hpf	GSM6705351	GSM6705351: hepatocytes 96hpf wt expt1 rep1; Danio rerio; RNA Seq	GSM6705351 r1	GSM6705351	1	Hepatocytes were sorted into 75 uL Buffer RLT containing b mercaptoethanol. Total RNA was extracted using the Qiagen RNA Micro Kit with on column DNase treatment. The SMART Seq v4 Ultra Low Input Kit for Sequencing Clontech kit was used for cDNA synthesis and amplification. Library prep was performed with the Nextera XT DNA Library Preparation Kit.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP405931	loader:fastq load.py	wt_expt1_rep1_R1.fastq.gz wt_expt1_rep1_R2.fastq.gz	fastq fastq	17241539100.0	57471797.0	GSM6705351 r1	0:150 1:150	A:4266092960;C:4150739925;G:4403086295;T:4420536893;N:1083027	150	150	4266092960	4150739925	4403086295	4420536893	1083027	SRX18122993	SRS15624867			Goessling Lab, Brigham and Women's Hospital	2	0.9395	0.93854	0.03615	0.03586	0.79715	0.79906	0.48099	0.46325	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United States	2022-11-02	Multi-stage	Multi-stage	Liver	Liver and Biliary 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");;