metadata: run_metadata: 68 rows where experiment.library_layout = "PAIRED", technology = "celseq" and tissue

68 rows where experiment.library_layout = "PAIRED", technology = "celseq" and tissue_curation = "Whole Organism"

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
38078	38078	SRR1531477	SRX665258	SRS670072	SRP045064	PRJNA256975	Genome wide RNA tomography in the zebrafish embryo	GSE59873	Other	Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches using for example in situ hybridization can provide spatial information about gene expression but are limited to analyzing one or a few genes at a time. Here we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage 10 somites 15 somites 18 somites and mouse forelimbs E10.5 we cryosectioned samples extracted RNA from the individual sections and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al. Cell Reports 2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.		pubmed:25417113	15 somite stage secti1d from right to left	GSM1448815	tissue:whole embryo\|Stage:15 somites\|sectioning direction:right left\|section thickness:18 µm\|embedding strategy:intact embryo	15 somite stage secti1d from right to left	Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al. Cell Reports 2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections	whole embryo	Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned and individual slices were transferred to Eppendorf tubes on dry ice.	RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012		Stage:15 somites\|sectioning direction:right left\|section thickness:18 µm\|embedding strategy:intact embryo	GSM1448815	GSM1448815: 15 somite stage secti1d from right to left; Danio rerio; RNA Seq	GSM1448815		1	RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012	GEO Accession:GSM1448815	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP045064		dr_15ss_RL_R1.fastq.gz dr_15ss_RL_R2.fastq.gz	fastq fastq	3840123336.0	37648268.0	GSM1448815 r1	0:51 1:51	A:915153174;C:577478134;G:648196113;T:1695635476;N:3660439	51	51	915153174	577478134	648196113	1695635476	3660439	SRX665258	SRS670072	SRA177126	GEO	Hubrecht Institute	2	0.05313	0.71589	0.0419	0.15174	0.97717	0.77484	0.5218	0.45828	51	51	T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_plate	celseq	Netherlands	2014-07-29	Segmentation	Embryo	Whole Organism	All anatomical structures
38079	38079	SRR1531478	SRX665258	SRS670072	SRP045064	PRJNA256975	Genome wide RNA tomography in the zebrafish embryo	GSE59873	Other	Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches using for example in situ hybridization can provide spatial information about gene expression but are limited to analyzing one or a few genes at a time. Here we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage 10 somites 15 somites 18 somites and mouse forelimbs E10.5 we cryosectioned samples extracted RNA from the individual sections and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al. Cell Reports 2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.		pubmed:25417113	15 somite stage secti1d from right to left	GSM1448815	tissue:whole embryo\|Stage:15 somites\|sectioning direction:right left\|section thickness:18 µm\|embedding strategy:intact embryo	15 somite stage secti1d from right to left	Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al. Cell Reports 2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections	whole embryo	Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned and individual slices were transferred to Eppendorf tubes on dry ice.	RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012		Stage:15 somites\|sectioning direction:right left\|section thickness:18 µm\|embedding strategy:intact embryo	GSM1448815	GSM1448815: 15 somite stage secti1d from right to left; Danio rerio; RNA Seq	GSM1448815		1	RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012	GEO Accession:GSM1448815	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP045064	instrument model:Illumina MiSeq	miseq_dr_15ss_RL_R1.fastq.gz miseq_dr_15ss_RL_R2.fastq.gz	fastq fastq	619303490.0	1235999.0	GSM1448815 r2	0:251 1:250.06	A:196814024;C:126079066;G:111585151;T:184825248;N:1	251	250	196814024	126079066	111585151	184825248	1	SRX665258	SRS670072	SRA177126	GEO	Hubrecht Institute	2	0.37674	0.6743	0.06734	0.08523	0.92516	0.86196	0.56151	0.54745	251	251	B	B	mate1-mate2 similar by mapping diff	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_plate	celseq	Netherlands	2014-07-29	Segmentation	Embryo	Whole Organism	All anatomical structures
38080	38080	SRR1531475	SRX665257	SRS670070	SRP045064	PRJNA256975	Genome wide RNA tomography in the zebrafish embryo	GSE59873	Other	Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches using for example in situ hybridization can provide spatial information about gene expression but are limited to analyzing one or a few genes at a time. Here we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage 10 somites 15 somites 18 somites and mouse forelimbs E10.5 we cryosectioned samples extracted RNA from the individual sections and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al. Cell Reports 2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.		pubmed:25417113	15 somite stage secti1d from left to right	GSM1448814	tissue:whole embryo\|Stage:15 somites\|sectioning direction:left right\|section thickness:18 µm\|embedding strategy:intact embryo	15 somite stage secti1d from left to right	Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al. Cell Reports 2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections	whole embryo	Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned and individual slices were transferred to Eppendorf tubes on dry ice.	RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012		Stage:15 somites\|sectioning direction:left right\|section thickness:18 µm\|embedding strategy:intact embryo	GSM1448814	GSM1448814: 15 somite stage secti1d from left to right; Danio rerio; RNA Seq	GSM1448814		1	RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012	GEO Accession:GSM1448814	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP045064		dr_15ss_LR_R2.fastq.gz dr_15ss_LR_R1.fastq.gz	fastq fastq	2077803342.0	20370621.0	GSM1448814 r1	0:51 1:51	A:487276259;C:320933398;G:342175116;T:925418636;N:1999933	51	51	487276259	320933398	342175116	925418636	1999933	SRX665257	SRS670070	SRA177126	GEO	Hubrecht Institute	2	0.04544	0.77533	0.03741	0.15439	0.98435	0.77662	0.56397	0.57005	51	51	T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_plate	celseq	Netherlands	2014-07-29	Segmentation	Embryo	Whole Organism	All anatomical structures
38081	38081	SRR1531476	SRX665257	SRS670070	SRP045064	PRJNA256975	Genome wide RNA tomography in the zebrafish embryo	GSE59873	Other	Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches using for example in situ hybridization can provide spatial information about gene expression but are limited to analyzing one or a few genes at a time. Here we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage 10 somites 15 somites 18 somites and mouse forelimbs E10.5 we cryosectioned samples extracted RNA from the individual sections and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al. Cell Reports 2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.		pubmed:25417113	15 somite stage secti1d from left to right	GSM1448814	tissue:whole embryo\|Stage:15 somites\|sectioning direction:left right\|section thickness:18 µm\|embedding strategy:intact embryo	15 somite stage secti1d from left to right	Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al. Cell Reports 2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections	whole embryo	Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned and individual slices were transferred to Eppendorf tubes on dry ice.	RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012		Stage:15 somites\|sectioning direction:left right\|section thickness:18 µm\|embedding strategy:intact embryo	GSM1448814	GSM1448814: 15 somite stage secti1d from left to right; Danio rerio; RNA Seq	GSM1448814		1	RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012	GEO Accession:GSM1448814	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP045064	instrument model:Illumina MiSeq	miseq_dr_15ss_LR_R1.fastq.gz miseq_dr_15ss_LR_R2.fastq.gz	fastq fastq	648479770.0	1294232.0	GSM1448814 r2	0:251 1:250.05	A:208271519;C:133135452;G:114142609;T:192930139;N:51	251	250	208271519	133135452	114142609	192930139	51	SRX665257	SRS670070	SRA177126	GEO	Hubrecht Institute	2	0.34992	0.64011	0.08713	0.16967	0.92103	0.83853	0.54292	0.52547	251	250	B	B	mate1-mate2 similar by mapping diff	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_plate	celseq	Netherlands	2014-07-29	Segmentation	Embryo	Whole Organism	All anatomical structures
38082	38082	SRR1531473	SRX665256	SRS670071	SRP045064	PRJNA256975	Genome wide RNA tomography in the zebrafish embryo	GSE59873	Other	Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches using for example in situ hybridization can provide spatial information about gene expression but are limited to analyzing one or a few genes at a time. Here we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage 10 somites 15 somites 18 somites and mouse forelimbs E10.5 we cryosectioned samples extracted RNA from the individual sections and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al. Cell Reports 2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.		pubmed:25417113	15 somite stage secti1d from dorsal to ventral end	GSM1448813	tissue:whole embryo\|Stage:15 somites\|sectioning direction:dorsal ventral\|section thickness:18 µm\|embedding strategy:intact embryo	15 somite stage secti1d from dorsal to ventral end	Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al. Cell Reports 2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections	whole embryo	Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned and individual slices were transferred to Eppendorf tubes on dry ice.	RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012		Stage:15 somites\|sectioning direction:dorsal ventral\|section thickness:18 µm\|embedding strategy:intact embryo	GSM1448813	GSM1448813: 15 somite stage secti1d from dorsal to ventral end; Danio rerio; RNA Seq	GSM1448813		1	RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012	GEO Accession:GSM1448813	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP045064		dr_15ss_DV_R1.fastq.gz dr_15ss_DV_R2.fastq.gz	fastq fastq	2516804610.0	24674555.0	GSM1448813 r1	0:51 1:51	A:579818006;C:406550753;G:379205422;T:1129932140;N:21298289	51	51	579818006	406550753	379205422	1129932140	21298289	SRX665256	SRS670071	SRA177126	GEO	Hubrecht Institute	2	0.04189	0.74891	0.03368	0.12625	0.98695	0.78423	0.46823	0.53429	51	51	T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_plate	celseq	Netherlands	2014-07-29	Segmentation	Embryo	Whole Organism	All anatomical structures
38083	38083	SRR1531474	SRX665256	SRS670071	SRP045064	PRJNA256975	Genome wide RNA tomography in the zebrafish embryo	GSE59873	Other	Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches using for example in situ hybridization can provide spatial information about gene expression but are limited to analyzing one or a few genes at a time. Here we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage 10 somites 15 somites 18 somites and mouse forelimbs E10.5 we cryosectioned samples extracted RNA from the individual sections and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al. Cell Reports 2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.		pubmed:25417113	15 somite stage secti1d from dorsal to ventral end	GSM1448813	tissue:whole embryo\|Stage:15 somites\|sectioning direction:dorsal ventral\|section thickness:18 µm\|embedding strategy:intact embryo	15 somite stage secti1d from dorsal to ventral end	Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al. Cell Reports 2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections	whole embryo	Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned and individual slices were transferred to Eppendorf tubes on dry ice.	RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012		Stage:15 somites\|sectioning direction:dorsal ventral\|section thickness:18 µm\|embedding strategy:intact embryo	GSM1448813	GSM1448813: 15 somite stage secti1d from dorsal to ventral end; Danio rerio; RNA Seq	GSM1448813		1	RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012	GEO Accession:GSM1448813	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP045064	instrument model:Illumina MiSeq	miseq_dr_15ss_DV_R1.fastq.gz miseq_dr_15ss_DV_R2.fastq.gz	fastq fastq	1831352383.0	3654695.0	GSM1448813 r2	0:251 1:250.10	A:593055798;C:392880040;G:312965357;T:532451118;N:70	251	250	593055798	392880040	312965357	532451118	70	SRX665256	SRS670071	SRA177126	GEO	Hubrecht Institute	2	0.27976	0.58087	0.05423	0.08127	0.93943	0.88868	0.51246	0.50653	251	251	B	B	mate1-mate2 similar by mapping diff	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_plate	celseq	Netherlands	2014-07-29	Segmentation	Embryo	Whole Organism	All anatomical structures
38084	38084	SRR1531471	SRX665255	SRS670069	SRP045064	PRJNA256975	Genome wide RNA tomography in the zebrafish embryo	GSE59873	Other	Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches using for example in situ hybridization can provide spatial information about gene expression but are limited to analyzing one or a few genes at a time. Here we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage 10 somites 15 somites 18 somites and mouse forelimbs E10.5 we cryosectioned samples extracted RNA from the individual sections and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al. Cell Reports 2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.		pubmed:25417113	15 somite stage secti1d from ventral to dorsal end	GSM1448812	tissue:whole embryo\|Stage:15 somites\|sectioning direction:ventral dorsal\|section thickness:18 µm\|embedding strategy:intact embryo	15 somite stage secti1d from ventral to dorsal end	Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al. Cell Reports 2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections	whole embryo	Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned and individual slices were transferred to Eppendorf tubes on dry ice.	RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012		Stage:15 somites\|sectioning direction:ventral dorsal\|section thickness:18 µm\|embedding strategy:intact embryo	GSM1448812	GSM1448812: 15 somite stage secti1d from ventral to dorsal end; Danio rerio; RNA Seq	GSM1448812		1	RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012	GEO Accession:GSM1448812	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP045064		dr_15ss_VD_R1.fastq.gz dr_15ss_VD_R2.fastq.gz	fastq fastq	1673808678.0	16409889.0	GSM1448812 r1	0:51 1:51	A:397744759;C:269067687;G:250815180;T:740808813;N:15372239	51	51	397744759	269067687	250815180	740808813	15372239	SRX665255	SRS670069	SRA177126	GEO	Hubrecht Institute	2	0.05917	0.69313	0.0499	0.19364	0.98364	0.78232	0.54626	0.5434	51	51	T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_plate	celseq	Netherlands	2014-07-29	Segmentation	Embryo	Whole Organism	All anatomical structures
38085	38085	SRR1531472	SRX665255	SRS670069	SRP045064	PRJNA256975	Genome wide RNA tomography in the zebrafish embryo	GSE59873	Other	Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches using for example in situ hybridization can provide spatial information about gene expression but are limited to analyzing one or a few genes at a time. Here we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage 10 somites 15 somites 18 somites and mouse forelimbs E10.5 we cryosectioned samples extracted RNA from the individual sections and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al. Cell Reports 2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.		pubmed:25417113	15 somite stage secti1d from ventral to dorsal end	GSM1448812	tissue:whole embryo\|Stage:15 somites\|sectioning direction:ventral dorsal\|section thickness:18 µm\|embedding strategy:intact embryo	15 somite stage secti1d from ventral to dorsal end	Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al. Cell Reports 2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections	whole embryo	Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned and individual slices were transferred to Eppendorf tubes on dry ice.	RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012		Stage:15 somites\|sectioning direction:ventral dorsal\|section thickness:18 µm\|embedding strategy:intact embryo	GSM1448812	GSM1448812: 15 somite stage secti1d from ventral to dorsal end; Danio rerio; RNA Seq	GSM1448812		1	RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012	GEO Accession:GSM1448812	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP045064	instrument model:Illumina MiSeq	miseq_dr_15ss_VD_R2.fastq.gz miseq_dr_15ss_VD_R1.fastq.gz	fastq fastq	587520609.0	1172567.0	GSM1448812 r2	0:251 1:250.06	A:194391951;C:123162952;G:98682047;T:171283648;N:11	251	250	194391951	123162952	98682047	171283648	11	SRX665255	SRS670069	SRA177126	GEO	Hubrecht Institute	2	0.25906	0.51091	0.10052	0.13544	0.94274	0.90015	0.54255	0.53365	251	251	B	B	mate1-mate2 similar by mapping diff	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_plate	celseq	Netherlands	2014-07-29	Segmentation	Embryo	Whole Organism	All anatomical structures
38086	38086	SRR1531470	SRX665254	SRS670068	SRP045064	PRJNA256975	Genome wide RNA tomography in the zebrafish embryo	GSE59873	Other	Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches using for example in situ hybridization can provide spatial information about gene expression but are limited to analyzing one or a few genes at a time. Here we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage 10 somites 15 somites 18 somites and mouse forelimbs E10.5 we cryosectioned samples extracted RNA from the individual sections and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al. Cell Reports 2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.		pubmed:25417113	15 somite stage secti1d from posterior to anterior end	GSM1448811	tissue:whole embryo\|Stage:15 somites\|sectioning direction:posterior anterior\|section thickness:18 µm\|embedding strategy:intact embryo	15 somite stage secti1d from posterior to anterior end	Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al. Cell Reports 2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections	whole embryo	Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned and individual slices were transferred to Eppendorf tubes on dry ice.	RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012		Stage:15 somites\|sectioning direction:posterior anterior\|section thickness:18 µm\|embedding strategy:intact embryo	GSM1448811	GSM1448811: 15 somite stage secti1d from posterior to anterior end; Danio rerio; RNA Seq	GSM1448811		1	RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012	GEO Accession:GSM1448811	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP045064		dr_15ss_PA_R2.fastq.gz dr_15ss_PA_R1.fastq.gz	fastq fastq	2483143794.0	24344547.0	GSM1448811 r1	0:51 1:51	A:563038776;C:400378151;G:372280878;T:1126633332;N:20812657	51	51	563038776	400378151	372280878	1126633332	20812657	SRX665254	SRS670068	SRA177126	GEO	Hubrecht Institute	2	0.04278	0.78001	0.03367	0.11539	0.98727	0.77865	0.49734	0.53041	51	51	T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_plate	celseq	Netherlands	2014-07-29	Segmentation	Embryo	Whole Organism	All anatomical structures
38087	38087	SRR1531469	SRX665253	SRS670067	SRP045064	PRJNA256975	Genome wide RNA tomography in the zebrafish embryo	GSE59873	Other	Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches using for example in situ hybridization can provide spatial information about gene expression but are limited to analyzing one or a few genes at a time. Here we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage 10 somites 15 somites 18 somites and mouse forelimbs E10.5 we cryosectioned samples extracted RNA from the individual sections and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al. Cell Reports 2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.		pubmed:25417113	15 somite stage secti1d from anterior to posterior end	GSM1448810	tissue:whole embryo\|Stage:15 somites\|sectioning direction:anterior posterior\|section thickness:18 µm\|embedding strategy:intact embryo	15 somite stage secti1d from anterior to posterior end	Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al. Cell Reports 2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections	whole embryo	Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned and individual slices were transferred to Eppendorf tubes on dry ice.	RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012		Stage:15 somites\|sectioning direction:anterior posterior\|section thickness:18 µm\|embedding strategy:intact embryo	GSM1448810	GSM1448810: 15 somite stage secti1d from anterior to posterior end; Danio rerio; RNA Seq	GSM1448810		1	RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012	GEO Accession:GSM1448810	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP045064		dr_15ss_AP_R2.fastq.gz dr_15ss_AP_R1.fastq.gz	fastq fastq	3436281570.0	33689035.0	GSM1448810 r1	0:51 1:51	A:794842891;C:552474558;G:514289189;T:1545720661;N:28954271	51	51	794842891	552474558	514289189	1545720661	28954271	SRX665253	SRS670067	SRA177126	GEO	Hubrecht Institute	2	0.04616	0.72787	0.03714	0.11902	0.98636	0.78372	0.50428	0.54252	51	51	T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_plate	celseq	Netherlands	2014-07-29	Segmentation	Embryo	Whole Organism	All anatomical structures
38088	38088	SRR1531468	SRX665252	SRS670066	SRP045064	PRJNA256975	Genome wide RNA tomography in the zebrafish embryo	GSE59873	Other	Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches using for example in situ hybridization can provide spatial information about gene expression but are limited to analyzing one or a few genes at a time. Here we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage 10 somites 15 somites 18 somites and mouse forelimbs E10.5 we cryosectioned samples extracted RNA from the individual sections and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al. Cell Reports 2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.		pubmed:25417113	10 somite stage secti1d from right to left	GSM1448809	tissue:whole embryo\|Stage:10 somites\|sectioning direction:right left\|section thickness:18 µm\|embedding strategy:intact embryo	10 somite stage secti1d from right to left	Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al. Cell Reports 2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections	whole embryo	Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned and individual slices were transferred to Eppendorf tubes on dry ice.	RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012		Stage:10 somites\|sectioning direction:right left\|section thickness:18 µm\|embedding strategy:intact embryo	GSM1448809	GSM1448809: 10 somite stage secti1d from right to left; Danio rerio; RNA Seq	GSM1448809		1	RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012	GEO Accession:GSM1448809	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP045064		dr_10ss_RL_R2.fastq.gz dr_10ss_RL_R1.fastq.gz	fastq fastq	2058025848.0	20176724.0	GSM1448809 r1	0:51 1:51	A:466388690;C:327195544;G:324646168;T:921984274;N:17811172	51	51	466388690	327195544	324646168	921984274	17811172	SRX665252	SRS670066	SRA177126	GEO	Hubrecht Institute	2	0.03352	0.82842	0.02775	0.10176	0.99019	0.7878	0.56827	0.53664	51	51	T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_plate	celseq	Netherlands	2014-07-29	Segmentation	Embryo	Whole Organism	All anatomical structures
38089	38089	SRR1531467	SRX665251	SRS670065	SRP045064	PRJNA256975	Genome wide RNA tomography in the zebrafish embryo	GSE59873	Other	Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches using for example in situ hybridization can provide spatial information about gene expression but are limited to analyzing one or a few genes at a time. Here we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage 10 somites 15 somites 18 somites and mouse forelimbs E10.5 we cryosectioned samples extracted RNA from the individual sections and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al. Cell Reports 2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.		pubmed:25417113	10 somite stage secti1d from left to right	GSM1448808	tissue:whole embryo\|Stage:10 somites\|sectioning direction:left right\|section thickness:18 µm\|embedding strategy:intact embryo	10 somite stage secti1d from left to right	Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al. Cell Reports 2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections	whole embryo	Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned and individual slices were transferred to Eppendorf tubes on dry ice.	RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012		Stage:10 somites\|sectioning direction:left right\|section thickness:18 µm\|embedding strategy:intact embryo	GSM1448808	GSM1448808: 10 somite stage secti1d from left to right; Danio rerio; RNA Seq	GSM1448808		1	RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012	GEO Accession:GSM1448808	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP045064		dr_10ss_LR_R1.fastq.gz dr_10ss_LR_R2.fastq.gz	fastq fastq	2372600886.0	23260793.0	GSM1448808 r1	0:51 1:51	A:539978604;C:369014393;G:373430985;T:1069557826;N:20619078	51	51	539978604	369014393	373430985	1069557826	20619078	SRX665251	SRS670065	SRA177126	GEO	Hubrecht Institute	2	0.04947	0.82594	0.04114	0.11817	0.98703	0.77727	0.5181	0.46105	51	51	T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_plate	celseq	Netherlands	2014-07-29	Segmentation	Embryo	Whole Organism	All anatomical structures
38090	38090	SRR1531465	SRX665250	SRS670064	SRP045064	PRJNA256975	Genome wide RNA tomography in the zebrafish embryo	GSE59873	Other	Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches using for example in situ hybridization can provide spatial information about gene expression but are limited to analyzing one or a few genes at a time. Here we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage 10 somites 15 somites 18 somites and mouse forelimbs E10.5 we cryosectioned samples extracted RNA from the individual sections and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al. Cell Reports 2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.		pubmed:25417113	10 somite stage secti1d from dorsal to ventral end	GSM1448807	tissue:whole embryo\|Stage:10 somites\|sectioning direction:dorsal ventral\|section thickness:18 µm\|embedding strategy:intact embryo	10 somite stage secti1d from dorsal to ventral end	Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al. Cell Reports 2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections	whole embryo	Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned and individual slices were transferred to Eppendorf tubes on dry ice.	RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012		Stage:10 somites\|sectioning direction:dorsal ventral\|section thickness:18 µm\|embedding strategy:intact embryo	GSM1448807	GSM1448807: 10 somite stage secti1d from dorsal to ventral end; Danio rerio; RNA Seq	GSM1448807		1	RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012	GEO Accession:GSM1448807	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP045064		dr_10ss_DV_R1.fastq.gz dr_10ss_DV_R2.fastq.gz	fastq fastq	4808137200.0	47138600.0	GSM1448807 r1	0:51 1:51	A:1069537756;C:773357615;G:788490520;T:2131916220;N:44835089	51	51	1069537756	773357615	788490520	2131916220	44835089	SRX665250	SRS670064	SRA177126	GEO	Hubrecht Institute	2	0.05336	0.7348	0.04376	0.11098	0.98311	0.78829	0.55869	0.5169	51	51	T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_plate	celseq	Netherlands	2014-07-29	Segmentation	Embryo	Whole Organism	All anatomical structures
38091	38091	SRR1531466	SRX665250	SRS670064	SRP045064	PRJNA256975	Genome wide RNA tomography in the zebrafish embryo	GSE59873	Other	Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches using for example in situ hybridization can provide spatial information about gene expression but are limited to analyzing one or a few genes at a time. Here we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage 10 somites 15 somites 18 somites and mouse forelimbs E10.5 we cryosectioned samples extracted RNA from the individual sections and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al. Cell Reports 2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.		pubmed:25417113	10 somite stage secti1d from dorsal to ventral end	GSM1448807	tissue:whole embryo\|Stage:10 somites\|sectioning direction:dorsal ventral\|section thickness:18 µm\|embedding strategy:intact embryo	10 somite stage secti1d from dorsal to ventral end	Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al. Cell Reports 2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections	whole embryo	Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned and individual slices were transferred to Eppendorf tubes on dry ice.	RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012		Stage:10 somites\|sectioning direction:dorsal ventral\|section thickness:18 µm\|embedding strategy:intact embryo	GSM1448807	GSM1448807: 10 somite stage secti1d from dorsal to ventral end; Danio rerio; RNA Seq	GSM1448807		1	RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012	GEO Accession:GSM1448807	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP045064	instrument model:Illumina MiSeq	miseq_dr_10ss_DV_R1.fastq.gz miseq_dr_10ss_DV_R2.fastq.gz	fastq fastq	981031778.0	1957880.0	GSM1448807 r2	0:251 1:250.07	A:318017696;C:204637111;G:170546834;T:287830124;N:13	251	250	318017696	204637111	170546834	287830124	13	SRX665250	SRS670064	SRA177126	GEO	Hubrecht Institute	2	0.28421	0.5957	0.04748	0.07361	0.93917	0.88298	0.53618	0.53493	251	251	B	B	mate1-mate2 similar by mapping diff	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_plate	celseq	Netherlands	2014-07-29	Segmentation	Embryo	Whole Organism	All anatomical structures
38092	38092	SRR1531463	SRX665249	SRS670063	SRP045064	PRJNA256975	Genome wide RNA tomography in the zebrafish embryo	GSE59873	Other	Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches using for example in situ hybridization can provide spatial information about gene expression but are limited to analyzing one or a few genes at a time. Here we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage 10 somites 15 somites 18 somites and mouse forelimbs E10.5 we cryosectioned samples extracted RNA from the individual sections and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al. Cell Reports 2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.		pubmed:25417113	10 somite stage secti1d from ventral to dorsal end	GSM1448806	tissue:whole embryo\|Stage:10 somites\|sectioning direction:ventral dorsal\|section thickness:18 µm\|embedding strategy:intact embryo	10 somite stage secti1d from ventral to dorsal end	Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al. Cell Reports 2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections	whole embryo	Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned and individual slices were transferred to Eppendorf tubes on dry ice.	RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012		Stage:10 somites\|sectioning direction:ventral dorsal\|section thickness:18 µm\|embedding strategy:intact embryo	GSM1448806	GSM1448806: 10 somite stage secti1d from ventral to dorsal end; Danio rerio; RNA Seq	GSM1448806		1	RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012	GEO Accession:GSM1448806	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP045064		dr_10ss_VD_R1.fastq.gz dr_10ss_VD_R2.fastq.gz	fastq fastq	4042242048.0	39629824.0	GSM1448806 r1	0:51 1:51	A:880941046;C:636899286;G:642176352;T:1845085169;N:37140195	51	51	880941046	636899286	642176352	1845085169	37140195	SRX665249	SRS670063	SRA177126	GEO	Hubrecht Institute	2	0.04898	0.80518	0.04234	0.10309	0.99044	0.78437	0.4974	0.53264	51	51	T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_plate	celseq	Netherlands	2014-07-29	Segmentation	Embryo	Whole Organism	All anatomical structures
38093	38093	SRR1531464	SRX665249	SRS670063	SRP045064	PRJNA256975	Genome wide RNA tomography in the zebrafish embryo	GSE59873	Other	Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches using for example in situ hybridization can provide spatial information about gene expression but are limited to analyzing one or a few genes at a time. Here we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage 10 somites 15 somites 18 somites and mouse forelimbs E10.5 we cryosectioned samples extracted RNA from the individual sections and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al. Cell Reports 2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.		pubmed:25417113	10 somite stage secti1d from ventral to dorsal end	GSM1448806	tissue:whole embryo\|Stage:10 somites\|sectioning direction:ventral dorsal\|section thickness:18 µm\|embedding strategy:intact embryo	10 somite stage secti1d from ventral to dorsal end	Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al. Cell Reports 2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections	whole embryo	Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned and individual slices were transferred to Eppendorf tubes on dry ice.	RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012		Stage:10 somites\|sectioning direction:ventral dorsal\|section thickness:18 µm\|embedding strategy:intact embryo	GSM1448806	GSM1448806: 10 somite stage secti1d from ventral to dorsal end; Danio rerio; RNA Seq	GSM1448806		1	RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012	GEO Accession:GSM1448806	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP045064	instrument model:Illumina MiSeq	miseq_dr_10ss_VD_R1.fastq.gz miseq_dr_10ss_VD_R2.fastq.gz	fastq fastq	738071470.0	1473056.0	GSM1448806 r2	0:251 1:250.05	A:241662059;C:148514183;G:127467910;T:220427298;N:20	251	250	241662059	148514183	127467910	220427298	20	SRX665249	SRS670063	SRA177126	GEO	Hubrecht Institute	2	0.33554	0.65168	0.04798	0.07375	0.93334	0.87121	0.53425	0.51721	251	251	B	B	mate1-mate2 similar by mapping diff	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_plate	celseq	Netherlands	2014-07-29	Segmentation	Embryo	Whole Organism	All anatomical structures
38094	38094	SRR1531461	SRX665248	SRS670062	SRP045064	PRJNA256975	Genome wide RNA tomography in the zebrafish embryo	GSE59873	Other	Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches using for example in situ hybridization can provide spatial information about gene expression but are limited to analyzing one or a few genes at a time. Here we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage 10 somites 15 somites 18 somites and mouse forelimbs E10.5 we cryosectioned samples extracted RNA from the individual sections and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al. Cell Reports 2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.		pubmed:25417113	10 somite stage secti1d from posterior to anterior end	GSM1448805	tissue:whole embryo\|Stage:10 somites\|sectioning direction:anterior posterior\|section thickness:18 µm\|embedding strategy:intact embryo	10 somite stage secti1d from posterior to anterior end	Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al. Cell Reports 2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections	whole embryo	Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned and individual slices were transferred to Eppendorf tubes on dry ice.	RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012		Stage:10 somites\|sectioning direction:anterior posterior\|section thickness:18 µm\|embedding strategy:intact embryo	GSM1448805	GSM1448805: 10 somite stage secti1d from posterior to anterior end; Danio rerio; RNA Seq	GSM1448805		1	RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012	GEO Accession:GSM1448805	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP045064		dr_10ss_PA_R1.fastq.gz dr_10ss_PA_R2.fastq.gz	fastq fastq	4759203720.0	46658860.0	GSM1448805 r1	0:51 1:51	A:1044025561;C:745846492;G:761494052;T:2164007108;N:43830507	51	51	1044025561	745846492	761494052	2164007108	43830507	SRX665248	SRS670062	SRA177126	GEO	Hubrecht Institute	2	0.04594	0.81204	0.0388	0.10992	0.98938	0.78244	0.51272	0.52639	51	51	T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_plate	celseq	Netherlands	2014-07-29	Segmentation	Embryo	Whole Organism	All anatomical structures
38095	38095	SRR1531462	SRX665248	SRS670062	SRP045064	PRJNA256975	Genome wide RNA tomography in the zebrafish embryo	GSE59873	Other	Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches using for example in situ hybridization can provide spatial information about gene expression but are limited to analyzing one or a few genes at a time. Here we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage 10 somites 15 somites 18 somites and mouse forelimbs E10.5 we cryosectioned samples extracted RNA from the individual sections and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al. Cell Reports 2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.		pubmed:25417113	10 somite stage secti1d from posterior to anterior end	GSM1448805	tissue:whole embryo\|Stage:10 somites\|sectioning direction:anterior posterior\|section thickness:18 µm\|embedding strategy:intact embryo	10 somite stage secti1d from posterior to anterior end	Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al. Cell Reports 2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections	whole embryo	Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned and individual slices were transferred to Eppendorf tubes on dry ice.	RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012		Stage:10 somites\|sectioning direction:anterior posterior\|section thickness:18 µm\|embedding strategy:intact embryo	GSM1448805	GSM1448805: 10 somite stage secti1d from posterior to anterior end; Danio rerio; RNA Seq	GSM1448805		1	RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012	GEO Accession:GSM1448805	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP045064	instrument model:Illumina MiSeq	miseq_dr_10ss_PA_R2.fastq.gz miseq_dr_10ss_PA_R1.fastq.gz	fastq fastq	923948352.0	1843960.0	GSM1448805 r2	0:251 1:250.07	A:301981474;C:189568545;G:157916393;T:274481921;N:19	251	250	301981474	189568545	157916393	274481921	19	SRX665248	SRS670062	SRA177126	GEO	Hubrecht Institute	2	0.33803	0.65569	0.05131	0.07917	0.93419	0.87355	0.4399	0.52526	251	251	B	B	mate1-mate2 similar by mapping diff	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_plate	celseq	Netherlands	2014-07-29	Segmentation	Embryo	Whole Organism	All anatomical structures
38096	38096	SRR1531460	SRX665247	SRS670061	SRP045064	PRJNA256975	Genome wide RNA tomography in the zebrafish embryo	GSE59873	Other	Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches using for example in situ hybridization can provide spatial information about gene expression but are limited to analyzing one or a few genes at a time. Here we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage 10 somites 15 somites 18 somites and mouse forelimbs E10.5 we cryosectioned samples extracted RNA from the individual sections and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al. Cell Reports 2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.		pubmed:25417113	10 somite stage secti1d from anterior to posterior end replicate	GSM1448804	tissue:whole embryo\|Stage:10 somites\|sectioning direction:anterior posterior\|section thickness:18 µm\|embedding strategy:intact embryo	10 somite stage secti1d from anterior to posterior end replicate	Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al. Cell Reports 2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections	whole embryo	Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned and individual slices were transferred to Eppendorf tubes on dry ice.	RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012		Stage:10 somites\|sectioning direction:anterior posterior\|section thickness:18 µm\|embedding strategy:intact embryo	GSM1448804	GSM1448804: 10 somite stage secti1d from anterior to posterior end replicate; Danio rerio; RNA Seq	GSM1448804		1	RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012	GEO Accession:GSM1448804	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP045064		dr_10ss_AP2_R1.fastq.gz dr_10ss_AP2_R2.fastq.gz	fastq fastq	2096761878.0	20556489.0	GSM1448804 r1	0:51 1:51	A:486131317;C:330426143;G:323887100;T:938024368;N:18292950	51	51	486131317	330426143	323887100	938024368	18292950	SRX665247	SRS670061	SRA177126	GEO	Hubrecht Institute	2	0.0484	0.78914	0.0396	0.12303	0.9866	0.78234	0.53395	0.53422	51	51	T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_plate	celseq	Netherlands	2014-07-29	Segmentation	Embryo	Whole Organism	All anatomical structures
38097	38097	SRR1531458	SRX665246	SRS670060	SRP045064	PRJNA256975	Genome wide RNA tomography in the zebrafish embryo	GSE59873	Other	Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches using for example in situ hybridization can provide spatial information about gene expression but are limited to analyzing one or a few genes at a time. Here we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage 10 somites 15 somites 18 somites and mouse forelimbs E10.5 we cryosectioned samples extracted RNA from the individual sections and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al. Cell Reports 2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.		pubmed:25417113	10 somite stage secti1d from anterior to posterior end	GSM1448803	tissue:whole embryo\|Stage:10 somites\|sectioning direction:anterior posterior\|section thickness:18 µm\|embedding strategy:intact embryo	10 somite stage secti1d from anterior to posterior end	Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al. Cell Reports 2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections	whole embryo	Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned and individual slices were transferred to Eppendorf tubes on dry ice.	RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012		Stage:10 somites\|sectioning direction:anterior posterior\|section thickness:18 µm\|embedding strategy:intact embryo	GSM1448803	GSM1448803: 10 somite stage secti1d from anterior to posterior end; Danio rerio; RNA Seq	GSM1448803		1	RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012	GEO Accession:GSM1448803	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP045064		dr_10ss_AP_R2.fastq.gz dr_10ss_AP_R1.fastq.gz	fastq fastq	3873169500.0	37972250.0	GSM1448803 r1	0:51 1:51	A:844434990;C:614503150;G:615061181;T:1763736099;N:35434080	51	51	844434990	614503150	615061181	1763736099	35434080	SRX665246	SRS670060	SRA177126	GEO	Hubrecht Institute	2	0.0354	0.81065	0.02893	0.12263	0.98944	0.77386	0.52631	0.52007	51	51	T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_plate	celseq	Netherlands	2014-07-29	Segmentation	Embryo	Whole Organism	All anatomical structures
38098	38098	SRR1531459	SRX665246	SRS670060	SRP045064	PRJNA256975	Genome wide RNA tomography in the zebrafish embryo	GSE59873	Other	Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches using for example in situ hybridization can provide spatial information about gene expression but are limited to analyzing one or a few genes at a time. Here we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage 10 somites 15 somites 18 somites and mouse forelimbs E10.5 we cryosectioned samples extracted RNA from the individual sections and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al. Cell Reports 2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.		pubmed:25417113	10 somite stage secti1d from anterior to posterior end	GSM1448803	tissue:whole embryo\|Stage:10 somites\|sectioning direction:anterior posterior\|section thickness:18 µm\|embedding strategy:intact embryo	10 somite stage secti1d from anterior to posterior end	Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al. Cell Reports 2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections	whole embryo	Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned and individual slices were transferred to Eppendorf tubes on dry ice.	RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012		Stage:10 somites\|sectioning direction:anterior posterior\|section thickness:18 µm\|embedding strategy:intact embryo	GSM1448803	GSM1448803: 10 somite stage secti1d from anterior to posterior end; Danio rerio; RNA Seq	GSM1448803		1	RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012	GEO Accession:GSM1448803	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP045064	instrument model:Illumina MiSeq	miseq_dr_10ss_AP_R1.fastq.gz miseq_dr_10ss_AP_R2.fastq.gz	fastq fastq	496084013.0	990096.0	GSM1448803 r2	0:251 1:250.05	A:161790706;C:99237964;G:85634725;T:149420610;N:8	251	250	161790706	99237964	85634725	149420610	8	SRX665246	SRS670060	SRA177126	GEO	Hubrecht Institute	2	0.35483	0.66804	0.06659	0.09269	0.92699	0.86113	0.53381	0.51797	251	251	B	B	mate1-mate2 similar by mapping diff	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_plate	celseq	Netherlands	2014-07-29	Segmentation	Embryo	Whole Organism	All anatomical structures
38099	38099	SRR1531457	SRX665245	SRS670059	SRP045064	PRJNA256975	Genome wide RNA tomography in the zebrafish embryo	GSE59873	Other	Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches using for example in situ hybridization can provide spatial information about gene expression but are limited to analyzing one or a few genes at a time. Here we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage 10 somites 15 somites 18 somites and mouse forelimbs E10.5 we cryosectioned samples extracted RNA from the individual sections and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al. Cell Reports 2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.		pubmed:25417113	shield stage secti1d from dorsal to ventral end replicate	GSM1448802	tissue:whole embryo\|Stage:shield stage\|sectioning direction:dorsal ventral\|section thickness:18 µm\|embedding strategy:intact embryo	shield stage secti1d from dorsal to ventral end replicate	Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al. Cell Reports 2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections	whole embryo	Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned and individual slices were transferred to Eppendorf tubes on dry ice.	RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012		Stage:shield stage\|sectioning direction:dorsal ventral\|section thickness:18 µm\|embedding strategy:intact embryo	GSM1448802	GSM1448802: shield stage secti1d from dorsal to ventral end replicate; Danio rerio; RNA Seq	GSM1448802		1	RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012	GEO Accession:GSM1448802	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP045064		dr_shield_DV2_R2.fastq.gz dr_shield_DV2_R1.fastq.gz	fastq fastq	2735350014.0	26817157.0	GSM1448802 r1	0:51 1:51	A:650077339;C:412458828;G:411687121;T:1237686190;N:23440536	51	51	650077339	412458828	411687121	1237686190	23440536	SRX665245	SRS670059	SRA177126	GEO	Hubrecht Institute	2	0.02556	0.75175	0.01912	0.10697	0.99076	0.79819	0.54093	0.55229	51	51	T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_plate	celseq	Netherlands	2014-07-29	Gastrula	Embryo	Whole Organism	All anatomical structures
38100	38100	SRR1531455	SRX665244	SRS670058	SRP045064	PRJNA256975	Genome wide RNA tomography in the zebrafish embryo	GSE59873	Other	Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches using for example in situ hybridization can provide spatial information about gene expression but are limited to analyzing one or a few genes at a time. Here we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage 10 somites 15 somites 18 somites and mouse forelimbs E10.5 we cryosectioned samples extracted RNA from the individual sections and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al. Cell Reports 2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.		pubmed:25417113	shield stage secti1d from dorsal to ventral end	GSM1448801	tissue:whole embryo\|Stage:shield stage\|sectioning direction:dorsal ventral\|section thickness:18 µm\|embedding strategy:intact embryo	shield stage secti1d from dorsal to ventral end	Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al. Cell Reports 2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections	whole embryo	Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned and individual slices were transferred to Eppendorf tubes on dry ice.	RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012		Stage:shield stage\|sectioning direction:dorsal ventral\|section thickness:18 µm\|embedding strategy:intact embryo	GSM1448801	GSM1448801: shield stage secti1d from dorsal to ventral end; Danio rerio; RNA Seq	GSM1448801		1	RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012	GEO Accession:GSM1448801	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP045064		dr_shield_DV_R1.fastq.gz dr_shield_DV_R2.fastq.gz	fastq fastq	1605318738.0	15738419.0	GSM1448801 r1	0:51 1:51	A:361176217;C:248822696;G:253372108;T:726629351;N:15318366	51	51	361176217	248822696	253372108	726629351	15318366	SRX665244	SRS670058	SRA177126	GEO	Hubrecht Institute	2	0.02633	0.68496	0.02344	0.10104	0.99638	0.80006	0.46031	0.57655	51	51	T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_plate	celseq	Netherlands	2014-07-29	Gastrula	Embryo	Whole Organism	All anatomical structures
38101	38101	SRR1531456	SRX665244	SRS670058	SRP045064	PRJNA256975	Genome wide RNA tomography in the zebrafish embryo	GSE59873	Other	Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches using for example in situ hybridization can provide spatial information about gene expression but are limited to analyzing one or a few genes at a time. Here we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage 10 somites 15 somites 18 somites and mouse forelimbs E10.5 we cryosectioned samples extracted RNA from the individual sections and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al. Cell Reports 2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.		pubmed:25417113	shield stage secti1d from dorsal to ventral end	GSM1448801	tissue:whole embryo\|Stage:shield stage\|sectioning direction:dorsal ventral\|section thickness:18 µm\|embedding strategy:intact embryo	shield stage secti1d from dorsal to ventral end	Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al. Cell Reports 2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections	whole embryo	Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned and individual slices were transferred to Eppendorf tubes on dry ice.	RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012		Stage:shield stage\|sectioning direction:dorsal ventral\|section thickness:18 µm\|embedding strategy:intact embryo	GSM1448801	GSM1448801: shield stage secti1d from dorsal to ventral end; Danio rerio; RNA Seq	GSM1448801		1	RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012	GEO Accession:GSM1448801	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP045064	instrument model:Illumina MiSeq	miseq_dr_shield_DV_R1.fastq.gz miseq_dr_shield_DV_R2.fastq.gz	fastq fastq	114907294.0	229320.0	GSM1448801 r2	0:251 1:250.08	A:37813553;C:24168661;G:19441624;T:33483456;N:0	251	250	37813553	24168661	19441624	33483456	0	SRX665244	SRS670058	SRA177126	GEO	Hubrecht Institute	2	0.26022	0.46204	0.03083	0.05933	0.94627	0.89301	0.56728	0.55478	251	250	B	B	mate1-mate2 similar by mapping diff	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_plate	celseq	Netherlands	2014-07-29	Gastrula	Embryo	Whole Organism	All anatomical structures
38102	38102	SRR1531453	SRX665243	SRS670056	SRP045064	PRJNA256975	Genome wide RNA tomography in the zebrafish embryo	GSE59873	Other	Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches using for example in situ hybridization can provide spatial information about gene expression but are limited to analyzing one or a few genes at a time. Here we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage 10 somites 15 somites 18 somites and mouse forelimbs E10.5 we cryosectioned samples extracted RNA from the individual sections and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al. Cell Reports 2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.		pubmed:25417113	shield stage secti1d from ventral to dorsal end	GSM1448800	tissue:whole embryo\|Stage:shield stage\|sectioning direction:ventral dorsal\|section thickness:18 µm\|embedding strategy:intact embryo	shield stage secti1d from ventral to dorsal end	Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al. Cell Reports 2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections	whole embryo	Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned and individual slices were transferred to Eppendorf tubes on dry ice.	RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012		Stage:shield stage\|sectioning direction:ventral dorsal\|section thickness:18 µm\|embedding strategy:intact embryo	GSM1448800	GSM1448800: shield stage secti1d from ventral to dorsal end; Danio rerio; RNA Seq	GSM1448800		1	RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012	GEO Accession:GSM1448800	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP045064		dr_shield_VD_R1.fastq.gz dr_shield_VD_R2.fastq.gz	fastq fastq	1840839492.0	18047446.0	GSM1448800 r1	0:51 1:51	A:421253850;C:292045914;G:295175858;T:814744774;N:17619096	51	51	421253850	292045914	295175858	814744774	17619096	SRX665243	SRS670056	SRA177126	GEO	Hubrecht Institute	2	0.01815	0.6287	0.01468	0.09567	0.99452	0.80975	0.5259	0.58926	51	51	T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_plate	celseq	Netherlands	2014-07-29	Gastrula	Embryo	Whole Organism	All anatomical structures
38103	38103	SRR1531454	SRX665243	SRS670056	SRP045064	PRJNA256975	Genome wide RNA tomography in the zebrafish embryo	GSE59873	Other	Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches using for example in situ hybridization can provide spatial information about gene expression but are limited to analyzing one or a few genes at a time. Here we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage 10 somites 15 somites 18 somites and mouse forelimbs E10.5 we cryosectioned samples extracted RNA from the individual sections and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al. Cell Reports 2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.		pubmed:25417113	shield stage secti1d from ventral to dorsal end	GSM1448800	tissue:whole embryo\|Stage:shield stage\|sectioning direction:ventral dorsal\|section thickness:18 µm\|embedding strategy:intact embryo	shield stage secti1d from ventral to dorsal end	Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al. Cell Reports 2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections	whole embryo	Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned and individual slices were transferred to Eppendorf tubes on dry ice.	RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012		Stage:shield stage\|sectioning direction:ventral dorsal\|section thickness:18 µm\|embedding strategy:intact embryo	GSM1448800	GSM1448800: shield stage secti1d from ventral to dorsal end; Danio rerio; RNA Seq	GSM1448800		1	RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012	GEO Accession:GSM1448800	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP045064	instrument model:Illumina MiSeq	miseq_dr_shield_VD_R2.fastq.gz miseq_dr_shield_VD_R1.fastq.gz	fastq fastq	158531701.0	316379.0	GSM1448800 r2										SRX665243	SRS670056	SRA177126	GEO	Hubrecht Institute	2	0.06803	0.1733	0.00916	0.026	0.94085	0.88899	0.58254	0.5723	251	251	B	B	mate1-mate2 similar by mapping diff	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_plate	celseq	Netherlands	2014-07-29	Gastrula	Embryo	Whole Organism	All anatomical structures
38104	38104	SRR1531451	SRX665242	SRS670055	SRP045064	PRJNA256975	Genome wide RNA tomography in the zebrafish embryo	GSE59873	Other	Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches using for example in situ hybridization can provide spatial information about gene expression but are limited to analyzing one or a few genes at a time. Here we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage 10 somites 15 somites 18 somites and mouse forelimbs E10.5 we cryosectioned samples extracted RNA from the individual sections and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al. Cell Reports 2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.		pubmed:25417113	shield stage secti1d from right to left	GSM1448799	tissue:whole embryo\|Stage:shield stage\|sectioning direction:right left\|section thickness:18 µm\|embedding strategy:intact embryo	shield stage secti1d from right to left	Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al. Cell Reports 2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections	whole embryo	Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned and individual slices were transferred to Eppendorf tubes on dry ice.	RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012		Stage:shield stage\|sectioning direction:right left\|section thickness:18 µm\|embedding strategy:intact embryo	GSM1448799	GSM1448799: shield stage secti1d from right to left; Danio rerio; RNA Seq	GSM1448799		1	RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012	GEO Accession:GSM1448799	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP045064		dr_shield_RL_R1.fastq.gz dr_shield_RL_R2.fastq.gz	fastq fastq	2003076918.0	19638009.0	GSM1448799 r1	0:51 1:51	A:457537608;C:308292947;G:312973612;T:905317961;N:18954790	51	51	457537608	308292947	312973612	905317961	18954790	SRX665242	SRS670055	SRA177126	GEO	Hubrecht Institute	2	0.02111	0.7573	0.01656	0.11316	0.99364	0.8005	0.4501	0.59142	51	51	T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_plate	celseq	Netherlands	2014-07-29	Gastrula	Embryo	Whole Organism	All anatomical structures
38105	38105	SRR1531452	SRX665242	SRS670055	SRP045064	PRJNA256975	Genome wide RNA tomography in the zebrafish embryo	GSE59873	Other	Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches using for example in situ hybridization can provide spatial information about gene expression but are limited to analyzing one or a few genes at a time. Here we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage 10 somites 15 somites 18 somites and mouse forelimbs E10.5 we cryosectioned samples extracted RNA from the individual sections and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al. Cell Reports 2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.		pubmed:25417113	shield stage secti1d from right to left	GSM1448799	tissue:whole embryo\|Stage:shield stage\|sectioning direction:right left\|section thickness:18 µm\|embedding strategy:intact embryo	shield stage secti1d from right to left	Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al. Cell Reports 2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections	whole embryo	Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned and individual slices were transferred to Eppendorf tubes on dry ice.	RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012		Stage:shield stage\|sectioning direction:right left\|section thickness:18 µm\|embedding strategy:intact embryo	GSM1448799	GSM1448799: shield stage secti1d from right to left; Danio rerio; RNA Seq	GSM1448799		1	RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012	GEO Accession:GSM1448799	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP045064	instrument model:Illumina MiSeq	miseq_dr_shield_RL_R1.fastq.gz miseq_dr_shield_RL_R2.fastq.gz	fastq fastq	154180181.0	307695.0	GSM1448799 r2	0:251 1:250.08	A:50801230;C:32293099;G:25917988;T:45167860;N:4	251	250	50801230	32293099	25917988	45167860	4	SRX665242	SRS670055	SRA177126	GEO	Hubrecht Institute	2	0.31553	0.64085	0.03613	0.06829	0.94101	0.8938	0.60272	0.58117	251	251	B	B	mate1-mate2 similar by mapping diff	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_plate	celseq	Netherlands	2014-07-29	Gastrula	Embryo	Whole Organism	All anatomical structures
38106	38106	SRR1531449	SRX665241	SRS670053	SRP045064	PRJNA256975	Genome wide RNA tomography in the zebrafish embryo	GSE59873	Other	Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches using for example in situ hybridization can provide spatial information about gene expression but are limited to analyzing one or a few genes at a time. Here we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage 10 somites 15 somites 18 somites and mouse forelimbs E10.5 we cryosectioned samples extracted RNA from the individual sections and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al. Cell Reports 2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.		pubmed:25417113	shield stage secti1d from left to right	GSM1448798	tissue:whole embryo\|Stage:shield stage\|sectioning direction:left right\|section thickness:18 µm\|embedding strategy:intact embryo	shield stage secti1d from left to right	Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al. Cell Reports 2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections	whole embryo	Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned and individual slices were transferred to Eppendorf tubes on dry ice.	RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012		Stage:shield stage\|sectioning direction:left right\|section thickness:18 µm\|embedding strategy:intact embryo	GSM1448798	GSM1448798: shield stage secti1d from left to right; Danio rerio; RNA Seq	GSM1448798		1	RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012	GEO Accession:GSM1448798	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP045064		dr_shield_LR_R1.fastq.gz dr_shield_LR_R2.fastq.gz	fastq fastq	1755442542.0	17210221.0	GSM1448798 r1	0:51 1:51	A:401133098;C:265688355;G:264899378;T:807011867;N:16709844	51	51	401133098	265688355	264899378	807011867	16709844	SRX665241	SRS670053	SRA177126	GEO	Hubrecht Institute	2	0.02829	0.71918	0.02455	0.14486	0.99484	0.79866	0.50383	0.57925	51	51	T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_plate	celseq	Netherlands	2014-07-29	Gastrula	Embryo	Whole Organism	All anatomical structures
38107	38107	SRR1531450	SRX665241	SRS670053	SRP045064	PRJNA256975	Genome wide RNA tomography in the zebrafish embryo	GSE59873	Other	Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches using for example in situ hybridization can provide spatial information about gene expression but are limited to analyzing one or a few genes at a time. Here we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage 10 somites 15 somites 18 somites and mouse forelimbs E10.5 we cryosectioned samples extracted RNA from the individual sections and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al. Cell Reports 2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.		pubmed:25417113	shield stage secti1d from left to right	GSM1448798	tissue:whole embryo\|Stage:shield stage\|sectioning direction:left right\|section thickness:18 µm\|embedding strategy:intact embryo	shield stage secti1d from left to right	Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al. Cell Reports 2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections	whole embryo	Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned and individual slices were transferred to Eppendorf tubes on dry ice.	RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012		Stage:shield stage\|sectioning direction:left right\|section thickness:18 µm\|embedding strategy:intact embryo	GSM1448798	GSM1448798: shield stage secti1d from left to right; Danio rerio; RNA Seq	GSM1448798		1	RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012	GEO Accession:GSM1448798	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP045064	instrument model:Illumina MiSeq	miseq_dr_shield_LR_R1.fastq.gz miseq_dr_shield_LR_R2.fastq.gz	fastq fastq	139755993.0	278913.0	GSM1448798 r2	0:251 1:250.07	A:46536591;C:28346077;G:23036783;T:41836538;N:4	251	250	46536591	28346077	23036783	41836538	4	SRX665241	SRS670053	SRA177126	GEO	Hubrecht Institute	2	0.27443	0.57858	0.06346	0.09954	0.94194	0.89522	0.55896	0.56169	251	251	B	B	mate1-mate2 similar by mapping diff	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_plate	celseq	Netherlands	2014-07-29	Gastrula	Embryo	Whole Organism	All anatomical structures
38108	38108	SRR1531448	SRX665240	SRS670054	SRP045064	PRJNA256975	Genome wide RNA tomography in the zebrafish embryo	GSE59873	Other	Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches using for example in situ hybridization can provide spatial information about gene expression but are limited to analyzing one or a few genes at a time. Here we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage 10 somites 15 somites 18 somites and mouse forelimbs E10.5 we cryosectioned samples extracted RNA from the individual sections and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al. Cell Reports 2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.		pubmed:25417113	shield stage secti1d from vegetal to animal pole replicate	GSM1448797	tissue:whole embryo\|Stage:shield stage\|sectioning direction:vegetal animal\|section thickness:18 µm\|embedding strategy:intact embryo	shield stage secti1d from vegetal to animal pole replicate	Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al. Cell Reports 2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections	whole embryo	Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned and individual slices were transferred to Eppendorf tubes on dry ice.	RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012		Stage:shield stage\|sectioning direction:vegetal animal\|section thickness:18 µm\|embedding strategy:intact embryo	GSM1448797	GSM1448797: shield stage secti1d from vegetal to animal pole replicate; Danio rerio; RNA Seq	GSM1448797		1	RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012	GEO Accession:GSM1448797	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP045064		dr_shield_VA2_R1.fastq.gz dr_shield_VA2_R2.fastq.gz	fastq fastq	1962884532.0	19243966.0	GSM1448797 r1	0:51 1:51	A:449529690;C:292065368;G:287973067;T:916330652;N:16985755	51	51	449529690	292065368	287973067	916330652	16985755	SRX665240	SRS670054	SRA177126	GEO	Hubrecht Institute	2	0.04512	0.77455	0.03997	0.11233	0.99293	0.78488	0.50931	0.5171	51	51	T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_plate	celseq	Netherlands	2014-07-29	Gastrula	Embryo	Whole Organism	All anatomical structures
38109	38109	SRR1531446	SRX665239	SRS670057	SRP045064	PRJNA256975	Genome wide RNA tomography in the zebrafish embryo	GSE59873	Other	Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches using for example in situ hybridization can provide spatial information about gene expression but are limited to analyzing one or a few genes at a time. Here we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage 10 somites 15 somites 18 somites and mouse forelimbs E10.5 we cryosectioned samples extracted RNA from the individual sections and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al. Cell Reports 2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.		pubmed:25417113	shield stage secti1d from vegetal to animal pole	GSM1448796	tissue:whole embryo\|Stage:shield stage\|sectioning direction:vegetal animal\|section thickness:18 µm\|embedding strategy:intact embryo	shield stage secti1d from vegetal to animal pole	Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al. Cell Reports 2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections	whole embryo	Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned and individual slices were transferred to Eppendorf tubes on dry ice.	RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012		Stage:shield stage\|sectioning direction:vegetal animal\|section thickness:18 µm\|embedding strategy:intact embryo	GSM1448796	GSM1448796: shield stage secti1d from vegetal to animal pole; Danio rerio; RNA Seq	GSM1448796		1	RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012	GEO Accession:GSM1448796	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP045064		dr_shield_VA_R2.fastq.gz dr_shield_VA_R1.fastq.gz	fastq fastq	2367839934.0	23214117.0	GSM1448796 r1	0:51 1:51	A:544061124;C:369321045;G:383489434;T:1047897582;N:23070749	51	51	544061124	369321045	383489434	1047897582	23070749	SRX665239	SRS670057	SRA177126	GEO	Hubrecht Institute	2	0.02284	0.57831	0.0199	0.08251	0.99579	0.81653	0.4451	0.5792	51	51	T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_plate	celseq	Netherlands	2014-07-29	Gastrula	Embryo	Whole Organism	All anatomical structures
38110	38110	SRR1531447	SRX665239	SRS670057	SRP045064	PRJNA256975	Genome wide RNA tomography in the zebrafish embryo	GSE59873	Other	Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches using for example in situ hybridization can provide spatial information about gene expression but are limited to analyzing one or a few genes at a time. Here we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage 10 somites 15 somites 18 somites and mouse forelimbs E10.5 we cryosectioned samples extracted RNA from the individual sections and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al. Cell Reports 2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.		pubmed:25417113	shield stage secti1d from vegetal to animal pole	GSM1448796	tissue:whole embryo\|Stage:shield stage\|sectioning direction:vegetal animal\|section thickness:18 µm\|embedding strategy:intact embryo	shield stage secti1d from vegetal to animal pole	Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al. Cell Reports 2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections	whole embryo	Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned and individual slices were transferred to Eppendorf tubes on dry ice.	RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012		Stage:shield stage\|sectioning direction:vegetal animal\|section thickness:18 µm\|embedding strategy:intact embryo	GSM1448796	GSM1448796: shield stage secti1d from vegetal to animal pole; Danio rerio; RNA Seq	GSM1448796		1	RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012	GEO Accession:GSM1448796	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP045064	instrument model:Illumina MiSeq	miseq_dr_shield_VA_R1.fastq.gz miseq_dr_shield_VA_R2.fastq.gz	fastq fastq	139677889.0	278764.0	GSM1448796 r2	0:251 1:250.06	A:45877333;C:29821713;G:24032460;T:39946380;N:3	251	250	45877333	29821713	24032460	39946380	3	SRX665239	SRS670057	SRA177126	GEO	Hubrecht Institute	2	0.21444	0.33364	0.02489	0.04529	0.95156	0.901	0.56549	0.55749	251	251	B	B	mate1-mate2 similar by mapping diff	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_plate	celseq	Netherlands	2014-07-29	Gastrula	Embryo	Whole Organism	All anatomical structures
38111	38111	SRR1531444	SRX665238	SRS670052	SRP045064	PRJNA256975	Genome wide RNA tomography in the zebrafish embryo	GSE59873	Other	Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches using for example in situ hybridization can provide spatial information about gene expression but are limited to analyzing one or a few genes at a time. Here we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage 10 somites 15 somites 18 somites and mouse forelimbs E10.5 we cryosectioned samples extracted RNA from the individual sections and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al. Cell Reports 2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.		pubmed:25417113	shield stage secti1d from animal to vegetal pole	GSM1448795	tissue:whole embryo\|Stage:shield stage\|sectioning direction:animal vegetal\|section thickness:18 µm\|embedding strategy:intact embryo	shield stage secti1d from animal to vegetal pole	Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al. Cell Reports 2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections	whole embryo	Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned and individual slices were transferred to Eppendorf tubes on dry ice.	RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012		Stage:shield stage\|sectioning direction:animal vegetal\|section thickness:18 µm\|embedding strategy:intact embryo	GSM1448795	GSM1448795: shield stage secti1d from animal to vegetal pole; Danio rerio; RNA Seq	GSM1448795		1	RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012	GEO Accession:GSM1448795	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP045064		dr_shield_AV_R1.fastq.gz dr_shield_AV_R2.fastq.gz	fastq fastq	2059615110.0	20192305.0	GSM1448795 r1	0:51 1:51	A:487942041;C:328047311;G:336282927;T:886836259;N:20506572	51	51	487942041	328047311	336282927	886836259	20506572	SRX665238	SRS670052	SRA177126	GEO	Hubrecht Institute	2	0.01633	0.50842	0.0136	0.07269	0.99541	0.82183	0.51242	0.59281	51	51	T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_plate	celseq	Netherlands	2014-07-29	Gastrula	Embryo	Whole Organism	All anatomical structures
38112	38112	SRR1531445	SRX665238	SRS670052	SRP045064	PRJNA256975	Genome wide RNA tomography in the zebrafish embryo	GSE59873	Other	Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches using for example in situ hybridization can provide spatial information about gene expression but are limited to analyzing one or a few genes at a time. Here we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage 10 somites 15 somites 18 somites and mouse forelimbs E10.5 we cryosectioned samples extracted RNA from the individual sections and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al. Cell Reports 2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.		pubmed:25417113	shield stage secti1d from animal to vegetal pole	GSM1448795	tissue:whole embryo\|Stage:shield stage\|sectioning direction:animal vegetal\|section thickness:18 µm\|embedding strategy:intact embryo	shield stage secti1d from animal to vegetal pole	Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al. Cell Reports 2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections	whole embryo	Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned and individual slices were transferred to Eppendorf tubes on dry ice.	RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012		Stage:shield stage\|sectioning direction:animal vegetal\|section thickness:18 µm\|embedding strategy:intact embryo	GSM1448795	GSM1448795: shield stage secti1d from animal to vegetal pole; Danio rerio; RNA Seq	GSM1448795		1	RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012	GEO Accession:GSM1448795	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP045064	instrument model:Illumina MiSeq	miseq_dr_shield_AV_R1.fastq.gz miseq_dr_shield_AV_R2.fastq.gz	fastq fastq	176530873.0	352271.0	GSM1448795 r2	0:251 1:250.12	A:57029265;C:38838035;G:30065677;T:50597891;N:5	251	250	57029265	38838035	30065677	50597891	5	SRX665238	SRS670052	SRA177126	GEO	Hubrecht Institute	2	0.20318	0.26844	0.02342	0.03751	0.95499	0.9069	0.4325	0.57102	251	251	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_plate	celseq	Netherlands	2014-07-29	Gastrula	Embryo	Whole Organism	All anatomical structures
48248	48248	SRR7119805	SRX4041448	SRS3258926	SRP144601	PRJNA459724	The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis	GSE114038	Other	Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1 2 3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos wild types and rnf2 mutants 8 and 7 replicates respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1 2 dpf and 3 dpf Danio rerio dissected hearts wild types 9 13 and 10 replicates respectively and rnf2 mutants 8 9 and 9 replicates respectively		pubmed:30867528	Danio rerio RNAseq 3dpf mut8	GSM3131196	tissue:whole embryo\|strain:TU/TLF mixed background\|cell type:whole embryo\|age:3 dpf\|genotype:rnf2 /	Danio rerio RNAseq 3dpf mut8	RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format	whole embryo		RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	Zebrafish Danio rerio were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al. 1995.	strain:TU/TLF mixed background\|cell type:whole embryo\|age:3 dpf\|genotype:rnf2 /	GSM3131196	GSM3131196: Danio rerio RNAseq 3dpf mut8; Danio rerio; RNA Seq	GSM3131196		1	RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	GEO Accession:GSM3131196	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2000	SRP144601		NDC-ring1b-3dpf-repl8-13282_R1.fastq.gz NDC-ring1b-3dpf-repl8-13282_R2.fastq.gz	fastq fastq	2586301116.0	30789299.0	GSM3131196 r1	0:42 1:42	A:689082798;C:590336938;G:600860389;T:705094245;N:926746	42	42	689082798	590336938	600860389	705094245	926746	SRX4041448	SRS3258926	SRA699717	GEO	Molecular Biology, Radboud University	2	0.87813	0.89136	0.27656	0.27012	0.67351	0.6745	0.44828	0.44382	42	42	B	B	biological fallback assumption	illumina	hiseq_era	unknown	rrna_depletion	ribozero	sc	single_cell_plate	celseq	Netherlands	2018-05-04	Larval	Larval	Whole Organism	All anatomical structures
48249	48249	SRR7119804	SRX4041447	SRS3258925	SRP144601	PRJNA459724	The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis	GSE114038	Other	Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1 2 3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos wild types and rnf2 mutants 8 and 7 replicates respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1 2 dpf and 3 dpf Danio rerio dissected hearts wild types 9 13 and 10 replicates respectively and rnf2 mutants 8 9 and 9 replicates respectively		pubmed:30867528	Danio rerio RNAseq 3dpf mut7	GSM3131195	tissue:whole embryo\|strain:TU/TLF mixed background\|cell type:whole embryo\|age:3 dpf\|genotype:rnf2 /	Danio rerio RNAseq 3dpf mut7	RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format	whole embryo		RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	Zebrafish Danio rerio were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al. 1995.	strain:TU/TLF mixed background\|cell type:whole embryo\|age:3 dpf\|genotype:rnf2 /	GSM3131195	GSM3131195: Danio rerio RNAseq 3dpf mut7; Danio rerio; RNA Seq	GSM3131195		1	RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	GEO Accession:GSM3131195	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2000	SRP144601		NDC-ring1b-3dpf-repl7-13281_R2.fastq.gz NDC-ring1b-3dpf-repl7-13281_R1.fastq.gz	fastq fastq	1514220876.0	18026439.0	GSM3131195 r1	0:42 1:42	A:409686548;C:340910820;G:347249065;T:415826325;N:548118	42	42	409686548	340910820	347249065	415826325	548118	SRX4041447	SRS3258925	SRA699717	GEO	Molecular Biology, Radboud University	2	0.88991	0.90191	0.30704	0.30119	0.66695	0.66922	0.45618	0.46008	42	42	B	B	biological fallback assumption	illumina	hiseq_era	unknown	rrna_depletion	ribozero	sc	single_cell_plate	celseq	Netherlands	2018-05-04	Larval	Larval	Whole Organism	All anatomical structures
48250	48250	SRR7119802	SRX4041446	SRS3258924	SRP144601	PRJNA459724	The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis	GSE114038	Other	Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1 2 3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos wild types and rnf2 mutants 8 and 7 replicates respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1 2 dpf and 3 dpf Danio rerio dissected hearts wild types 9 13 and 10 replicates respectively and rnf2 mutants 8 9 and 9 replicates respectively		pubmed:30867528	Danio rerio RNAseq 3dpf mut6	GSM3131194	tissue:whole embryo\|strain:TU/TLF mixed background\|cell type:whole embryo\|age:3 dpf\|genotype:rnf2 /	Danio rerio RNAseq 3dpf mut6	RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format	whole embryo		RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	Zebrafish Danio rerio were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al. 1995.	strain:TU/TLF mixed background\|cell type:whole embryo\|age:3 dpf\|genotype:rnf2 /	GSM3131194	GSM3131194: Danio rerio RNAseq 3dpf mut6; Danio rerio; RNA Seq	GSM3131194		1	RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	GEO Accession:GSM3131194	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2000	SRP144601		NDC-ring1b-3dpf-repl6-13280_R1.fastq.gz NDC-ring1b-3dpf-repl6-13280_R2.fastq.gz	fastq fastq	2265837168.0	26974252.0	GSM3131194 r1	0:42 1:42	A:528919905;C:579225021;G:616897328;T:539985252;N:809662	42	42	528919905	579225021	616897328	539985252	809662	SRX4041446	SRS3258924	SRA699717	GEO	Molecular Biology, Radboud University	2	0.73468	0.76482	0.24568	0.25398	0.70516	0.70414	0.44042	0.43826	42	42	B	B	biological fallback assumption	illumina	hiseq_era	unknown	rrna_depletion	ribozero	sc	single_cell_plate	celseq	Netherlands	2018-05-04	Larval	Larval	Whole Organism	All anatomical structures
48251	48251	SRR7119801	SRX4041445	SRS3258923	SRP144601	PRJNA459724	The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis	GSE114038	Other	Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1 2 3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos wild types and rnf2 mutants 8 and 7 replicates respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1 2 dpf and 3 dpf Danio rerio dissected hearts wild types 9 13 and 10 replicates respectively and rnf2 mutants 8 9 and 9 replicates respectively		pubmed:30867528	Danio rerio RNAseq 3dpf mut5	GSM3131193	tissue:whole embryo\|strain:TU/TLF mixed background\|cell type:whole embryo\|age:3 dpf\|genotype:rnf2 /	Danio rerio RNAseq 3dpf mut5	RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format	whole embryo		RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	Zebrafish Danio rerio were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al. 1995.	strain:TU/TLF mixed background\|cell type:whole embryo\|age:3 dpf\|genotype:rnf2 /	GSM3131193	GSM3131193: Danio rerio RNAseq 3dpf mut5; Danio rerio; RNA Seq	GSM3131193		1	RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	GEO Accession:GSM3131193	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2000	SRP144601		NDC-ring1b-3dpf-repl5-13279_R1.fastq.gz NDC-ring1b-3dpf-repl5-13279_R2.fastq.gz	fastq fastq	2434539072.0	28982608.0	GSM3131193 r1	0:42 1:42	A:657750716;C:546331298;G:559727917;T:669858999;N:870142	42	42	657750716	546331298	559727917	669858999	870142	SRX4041445	SRS3258923	SRA699717	GEO	Molecular Biology, Radboud University	2	0.88994	0.9052	0.31921	0.31753	0.67105	0.67245	0.43524	0.44685	42	42	B	B	biological fallback assumption	illumina	hiseq_era	unknown	rrna_depletion	ribozero	sc	single_cell_plate	celseq	Netherlands	2018-05-04	Larval	Larval	Whole Organism	All anatomical structures
48252	48252	SRR7119800	SRX4041444	SRS3258922	SRP144601	PRJNA459724	The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis	GSE114038	Other	Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1 2 3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos wild types and rnf2 mutants 8 and 7 replicates respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1 2 dpf and 3 dpf Danio rerio dissected hearts wild types 9 13 and 10 replicates respectively and rnf2 mutants 8 9 and 9 replicates respectively		pubmed:30867528	Danio rerio RNAseq 3dpf mut3	GSM3131192	tissue:whole embryo\|strain:TU/TLF mixed background\|cell type:whole embryo\|age:3 dpf\|genotype:rnf2 /	Danio rerio RNAseq 3dpf mut3	RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format	whole embryo		RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	Zebrafish Danio rerio were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al. 1995.	strain:TU/TLF mixed background\|cell type:whole embryo\|age:3 dpf\|genotype:rnf2 /	GSM3131192	GSM3131192: Danio rerio RNAseq 3dpf mut3; Danio rerio; RNA Seq	GSM3131192		1	RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	GEO Accession:GSM3131192	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2000	SRP144601		Ring1b-3dpf-replicate3-12247_R1.fastq.gz Ring1b-3dpf-replicate3-12247_R2.fastq.gz	fastq fastq	932865948.0	11105547.0	GSM3131192 r1	0:42 1:42	A:254207252;C:191875016;G:235114678;T:251619175;N:49827	42	42	254207252	191875016	235114678	251619175	49827	SRX4041444	SRS3258922	SRA699717	GEO	Molecular Biology, Radboud University	2	0.83623	0.84228	0.56402	0.55503	0.69193	0.69045	0.46635	0.47045	42	42	B	B	biological fallback assumption	illumina	hiseq_era	unknown	rrna_depletion	ribozero	sc	single_cell_plate	celseq	Netherlands	2018-05-04	Larval	Larval	Whole Organism	All anatomical structures
48253	48253	SRR7119799	SRX4041443	SRS3258933	SRP144601	PRJNA459724	The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis	GSE114038	Other	Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1 2 3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos wild types and rnf2 mutants 8 and 7 replicates respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1 2 dpf and 3 dpf Danio rerio dissected hearts wild types 9 13 and 10 replicates respectively and rnf2 mutants 8 9 and 9 replicates respectively		pubmed:30867528	Danio rerio RNAseq 3dpf mut2	GSM3131191	tissue:whole embryo\|strain:TU/TLF mixed background\|cell type:whole embryo\|age:3 dpf\|genotype:rnf2 /	Danio rerio RNAseq 3dpf mut2	RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format	whole embryo		RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	Zebrafish Danio rerio were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al. 1995.	strain:TU/TLF mixed background\|cell type:whole embryo\|age:3 dpf\|genotype:rnf2 /	GSM3131191	GSM3131191: Danio rerio RNAseq 3dpf mut2; Danio rerio; RNA Seq	GSM3131191		1	RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	GEO Accession:GSM3131191	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2000	SRP144601		Ring1b-3dpf-replicate2-12246_R1.fastq.gz Ring1b-3dpf-replicate2-12246_R2.fastq.gz	fastq fastq	1428569856.0	17006784.0	GSM3131191 r1	0:42 1:42	A:375553518;C:323985274;G:352887011;T:376064416;N:79637	42	42	375553518	323985274	352887011	376064416	79637	SRX4041443	SRS3258933	SRA699717	GEO	Molecular Biology, Radboud University	2	0.80267	0.81635	0.42059	0.41851	0.67598	0.67564	0.46878	0.47374	42	42	B	B	biological fallback assumption	illumina	hiseq_era	unknown	rrna_depletion	ribozero	sc	single_cell_plate	celseq	Netherlands	2018-05-04	Larval	Larval	Whole Organism	All anatomical structures
48254	48254	SRR7119798	SRX4041442	SRS3258921	SRP144601	PRJNA459724	The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis	GSE114038	Other	Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1 2 3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos wild types and rnf2 mutants 8 and 7 replicates respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1 2 dpf and 3 dpf Danio rerio dissected hearts wild types 9 13 and 10 replicates respectively and rnf2 mutants 8 9 and 9 replicates respectively		pubmed:30867528	Danio rerio RNAseq 3dpf mut1	GSM3131190	tissue:whole embryo\|strain:TU/TLF mixed background\|cell type:whole embryo\|age:3 dpf\|genotype:rnf2 /	Danio rerio RNAseq 3dpf mut1	RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format	whole embryo		RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	Zebrafish Danio rerio were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al. 1995.	strain:TU/TLF mixed background\|cell type:whole embryo\|age:3 dpf\|genotype:rnf2 /	GSM3131190	GSM3131190: Danio rerio RNAseq 3dpf mut1; Danio rerio; RNA Seq	GSM3131190		1	RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	GEO Accession:GSM3131190	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2000	SRP144601		Ring1b-3dpf-replicate1-12245_R1.fastq.gz Ring1b-3dpf-replicate1-12245_R2.fastq.gz	fastq fastq	1619814000.0	19283500.0	GSM3131190 r1	0:42 1:42	A:434648048;C:363147668;G:388048793;T:433881736;N:87755	42	42	434648048	363147668	388048793	433881736	87755	SRX4041442	SRS3258921	SRA699717	GEO	Molecular Biology, Radboud University	2	0.79912	0.81304	0.45971	0.46081	0.67556	0.6759	0.46577	0.46988	42	42	B	B	biological fallback assumption	illumina	hiseq_era	unknown	rrna_depletion	ribozero	sc	single_cell_plate	celseq	Netherlands	2018-05-04	Larval	Larval	Whole Organism	All anatomical structures
48255	48255	SRR7119797	SRX4041441	SRS3258932	SRP144601	PRJNA459724	The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis	GSE114038	Other	Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1 2 3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos wild types and rnf2 mutants 8 and 7 replicates respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1 2 dpf and 3 dpf Danio rerio dissected hearts wild types 9 13 and 10 replicates respectively and rnf2 mutants 8 9 and 9 replicates respectively		pubmed:30867528	Danio rerio RNAseq 3dpf wt13	GSM3131189	tissue:whole embryo\|strain:TLF\|cell type:whole embryo\|age:3 dpf\|genotype:wild type	Danio rerio RNAseq 3dpf wt13	RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format	whole embryo		RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	Zebrafish Danio rerio were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al. 1995.	strain:TLF\|cell type:whole embryo\|age:3 dpf\|genotype:wild type	GSM3131189	GSM3131189: Danio rerio RNAseq 3dpf wt13; Danio rerio; RNA Seq	GSM3131189		1	RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	GEO Accession:GSM3131189	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2000	SRP144601		NDC-TLF-3dpf-repl13-13287_R1.fastq.gz NDC-TLF-3dpf-repl13-13287_R2.fastq.gz	fastq fastq	1535721936.0	18282404.0	GSM3131189 r1	0:42 1:42	A:403114263;C:355464889;G:362868285;T:413725995;N:548504	42	42	403114263	355464889	362868285	413725995	548504	SRX4041441	SRS3258932	SRA699717	GEO	Molecular Biology, Radboud University	2	0.89271	0.90739	0.24124	0.23374	0.67292	0.67349	0.45333	0.45657	42	42	B	B	biological fallback assumption	illumina	hiseq_era	unknown	rrna_depletion	ribozero	sc	single_cell_plate	celseq	Netherlands	2018-05-04	Larval	Larval	Whole Organism	All anatomical structures
48256	48256	SRR7119796	SRX4041440	SRS3258920	SRP144601	PRJNA459724	The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis	GSE114038	Other	Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1 2 3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos wild types and rnf2 mutants 8 and 7 replicates respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1 2 dpf and 3 dpf Danio rerio dissected hearts wild types 9 13 and 10 replicates respectively and rnf2 mutants 8 9 and 9 replicates respectively		pubmed:30867528	Danio rerio RNAseq 3dpf wt12	GSM3131188	tissue:whole embryo\|strain:TLF\|cell type:whole embryo\|age:3 dpf\|genotype:wild type	Danio rerio RNAseq 3dpf wt12	RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format	whole embryo		RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	Zebrafish Danio rerio were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al. 1995.	strain:TLF\|cell type:whole embryo\|age:3 dpf\|genotype:wild type	GSM3131188	GSM3131188: Danio rerio RNAseq 3dpf wt12; Danio rerio; RNA Seq	GSM3131188		1	RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	GEO Accession:GSM3131188	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2000	SRP144601		NDC-TLF-3dpf-repl12-13286_R1.fastq.gz NDC-TLF-3dpf-repl12-13286_R2.fastq.gz	fastq fastq	1296768900.0	15437725.0	GSM3131188 r1	0:42 1:42	A:342053865;C:298842079;G:305530839;T:349875429;N:466688	42	42	342053865	298842079	305530839	349875429	466688	SRX4041440	SRS3258920	SRA699717	GEO	Molecular Biology, Radboud University	2	0.88405	0.90076	0.25686	0.24808	0.67365	0.67156	0.44757	0.45604	42	42	B	B	biological fallback assumption	illumina	hiseq_era	unknown	rrna_depletion	ribozero	sc	single_cell_plate	celseq	Netherlands	2018-05-04	Larval	Larval	Whole Organism	All anatomical structures
48257	48257	SRR7119795	SRX4041439	SRS3258919	SRP144601	PRJNA459724	The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis	GSE114038	Other	Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1 2 3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos wild types and rnf2 mutants 8 and 7 replicates respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1 2 dpf and 3 dpf Danio rerio dissected hearts wild types 9 13 and 10 replicates respectively and rnf2 mutants 8 9 and 9 replicates respectively		pubmed:30867528	Danio rerio RNAseq 3dpf wt11	GSM3131187	tissue:whole embryo\|strain:TLF\|cell type:whole embryo\|age:3 dpf\|genotype:wild type	Danio rerio RNAseq 3dpf wt11	RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format	whole embryo		RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	Zebrafish Danio rerio were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al. 1995.	strain:TLF\|cell type:whole embryo\|age:3 dpf\|genotype:wild type	GSM3131187	GSM3131187: Danio rerio RNAseq 3dpf wt11; Danio rerio; RNA Seq	GSM3131187		1	RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	GEO Accession:GSM3131187	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2000	SRP144601		NDC-TLF-3dpf-repl11-13285_R1.fastq.gz NDC-TLF-3dpf-repl11-13285_R2.fastq.gz	fastq fastq	2485819560.0	29593090.0	GSM3131187 r1	0:42 1:42	A:637012348;C:587468873;G:621718352;T:638709810;N:910177	42	42	637012348	587468873	621718352	638709810	910177	SRX4041439	SRS3258919	SRA699717	GEO	Molecular Biology, Radboud University	2	0.81173	0.83081	0.26441	0.27241	0.69572	0.69863	0.46814	0.46844	42	42	B	B	biological fallback assumption	illumina	hiseq_era	unknown	rrna_depletion	ribozero	sc	single_cell_plate	celseq	Netherlands	2018-05-04	Larval	Larval	Whole Organism	All anatomical structures
48258	48258	SRR7119794	SRX4041438	SRS3258918	SRP144601	PRJNA459724	The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis	GSE114038	Other	Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1 2 3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos wild types and rnf2 mutants 8 and 7 replicates respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1 2 dpf and 3 dpf Danio rerio dissected hearts wild types 9 13 and 10 replicates respectively and rnf2 mutants 8 9 and 9 replicates respectively		pubmed:30867528	Danio rerio RNAseq 3dpf wt5	GSM3131186	tissue:whole embryo\|strain:TLF\|cell type:whole embryo\|age:3 dpf\|genotype:wild type	Danio rerio RNAseq 3dpf wt5	RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format	whole embryo		RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	Zebrafish Danio rerio were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al. 1995.	strain:TLF\|cell type:whole embryo\|age:3 dpf\|genotype:wild type	GSM3131186	GSM3131186: Danio rerio RNAseq 3dpf wt5; Danio rerio; RNA Seq	GSM3131186		1	RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	GEO Accession:GSM3131186	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2000	SRP144601		NDC-TLF-3dpf-repl5-13284_R1.fastq.gz NDC-TLF-3dpf-repl5-13284_R2.fastq.gz	fastq fastq	854422548.0	10171697.0	GSM3131186 r1	0:42 1:42	A:227799696;C:189132544;G:207116976;T:230065989;N:307343	42	42	227799696	189132544	207116976	230065989	307343	SRX4041438	SRS3258918	SRA699717	GEO	Molecular Biology, Radboud University	2	0.8869	0.89921	0.29991	0.30201	0.67259	0.67466	0.43395	0.45782	42	42	B	B	biological fallback assumption	illumina	hiseq_era	unknown	rrna_depletion	ribozero	sc	single_cell_plate	celseq	Netherlands	2018-05-04	Larval	Larval	Whole Organism	All anatomical structures
48259	48259	SRR7119793	SRX4041437	SRS3258917	SRP144601	PRJNA459724	The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis	GSE114038	Other	Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1 2 3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos wild types and rnf2 mutants 8 and 7 replicates respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1 2 dpf and 3 dpf Danio rerio dissected hearts wild types 9 13 and 10 replicates respectively and rnf2 mutants 8 9 and 9 replicates respectively		pubmed:30867528	Danio rerio RNAseq 3dpf wt4	GSM3131185	tissue:whole embryo\|strain:TLF\|cell type:whole embryo\|age:3 dpf\|genotype:wild type	Danio rerio RNAseq 3dpf wt4	RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format	whole embryo		RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	Zebrafish Danio rerio were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al. 1995.	strain:TLF\|cell type:whole embryo\|age:3 dpf\|genotype:wild type	GSM3131185	GSM3131185: Danio rerio RNAseq 3dpf wt4; Danio rerio; RNA Seq	GSM3131185		1	RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	GEO Accession:GSM3131185	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2000	SRP144601		NDC-TLF-3dpf-repl4-13283_R1.fastq.gz NDC-TLF-3dpf-repl4-13283_R2.fastq.gz	fastq fastq	1884789312.0	22437968.0	GSM3131185 r1	0:42 1:42	A:516338681;C:420191388;G:421311695;T:526266145;N:681403	42	42	516338681	420191388	421311695	526266145	681403	SRX4041437	SRS3258917	SRA699717	GEO	Molecular Biology, Radboud University	2	0.89533	0.90768	0.30891	0.30384	0.66492	0.66636	0.44687	0.45358	42	42	B	B	biological fallback assumption	illumina	hiseq_era	unknown	rrna_depletion	ribozero	sc	single_cell_plate	celseq	Netherlands	2018-05-04	Larval	Larval	Whole Organism	All anatomical structures
48260	48260	SRR7119792	SRX4041436	SRS3258916	SRP144601	PRJNA459724	The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis	GSE114038	Other	Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1 2 3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos wild types and rnf2 mutants 8 and 7 replicates respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1 2 dpf and 3 dpf Danio rerio dissected hearts wild types 9 13 and 10 replicates respectively and rnf2 mutants 8 9 and 9 replicates respectively		pubmed:30867528	Danio rerio RNAseq 3dpf wt3	GSM3131184	tissue:whole embryo\|strain:TLF\|cell type:whole embryo\|age:3 dpf\|genotype:wild type	Danio rerio RNAseq 3dpf wt3	RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format	whole embryo		RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	Zebrafish Danio rerio were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al. 1995.	strain:TLF\|cell type:whole embryo\|age:3 dpf\|genotype:wild type	GSM3131184	GSM3131184: Danio rerio RNAseq 3dpf wt3; Danio rerio; RNA Seq	GSM3131184		1	RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	GEO Accession:GSM3131184	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2000	SRP144601		TLF-3dpf-replicate3-12250_R1.fastq.gz TLF-3dpf-replicate3-12250_R2.fastq.gz	fastq fastq	1781685444.0	21210541.0	GSM3131184 r1	0:42 1:42	A:454462414;C:421206578;G:449348079;T:456572027;N:96346	42	42	454462414	421206578	449348079	456572027	96346	SRX4041436	SRS3258916	SRA699717	GEO	Molecular Biology, Radboud University	2	0.77224	0.79091	0.333	0.33343	0.67229	0.67265	0.46461	0.47357	42	42	B	B	biological fallback assumption	illumina	hiseq_era	unknown	rrna_depletion	ribozero	sc	single_cell_plate	celseq	Netherlands	2018-05-04	Larval	Larval	Whole Organism	All anatomical structures
48261	48261	SRR7119790	SRX4041435	SRS3258915	SRP144601	PRJNA459724	The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis	GSE114038	Other	Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1 2 3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos wild types and rnf2 mutants 8 and 7 replicates respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1 2 dpf and 3 dpf Danio rerio dissected hearts wild types 9 13 and 10 replicates respectively and rnf2 mutants 8 9 and 9 replicates respectively		pubmed:30867528	Danio rerio RNAseq 3dpf wt2	GSM3131183	tissue:whole embryo\|strain:TLF\|cell type:whole embryo\|age:3 dpf\|genotype:wild type	Danio rerio RNAseq 3dpf wt2	RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format	whole embryo		RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	Zebrafish Danio rerio were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al. 1995.	strain:TLF\|cell type:whole embryo\|age:3 dpf\|genotype:wild type	GSM3131183	GSM3131183: Danio rerio RNAseq 3dpf wt2; Danio rerio; RNA Seq	GSM3131183		1	RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	GEO Accession:GSM3131183	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2000	SRP144601		TLF-3dpf-replicate2-12249_R1.fastq.gz TLF-3dpf-replicate2-12249_R2.fastq.gz	fastq fastq	1548027852.0	18428903.0	GSM3131183 r1	0:42 1:42	A:396847823;C:364731299;G:388571797;T:397788001;N:88932	42	42	396847823	364731299	388571797	397788001	88932	SRX4041435	SRS3258915	SRA699717	GEO	Molecular Biology, Radboud University	2	0.79516	0.81734	0.30973	0.3124	0.67095	0.67381	0.45609	0.4615	42	42	B	B	biological fallback assumption	illumina	hiseq_era	unknown	rrna_depletion	ribozero	sc	single_cell_plate	celseq	Netherlands	2018-05-04	Larval	Larval	Whole Organism	All anatomical structures
48262	48262	SRR7119789	SRX4041434	SRS3258914	SRP144601	PRJNA459724	The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis	GSE114038	Other	Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1 2 3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos wild types and rnf2 mutants 8 and 7 replicates respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1 2 dpf and 3 dpf Danio rerio dissected hearts wild types 9 13 and 10 replicates respectively and rnf2 mutants 8 9 and 9 replicates respectively		pubmed:30867528	Danio rerio RNAseq 3dpf wt1	GSM3131182	tissue:whole embryo\|strain:TLF\|cell type:whole embryo\|age:3 dpf\|genotype:wild type	Danio rerio RNAseq 3dpf wt1	RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format	whole embryo		RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	Zebrafish Danio rerio were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al. 1995.	strain:TLF\|cell type:whole embryo\|age:3 dpf\|genotype:wild type	GSM3131182	GSM3131182: Danio rerio RNAseq 3dpf wt1; Danio rerio; RNA Seq	GSM3131182		1	RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	GEO Accession:GSM3131182	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2000	SRP144601		TLF-3dpf-replicate1-12248_R1.fastq.gz TLF-3dpf-replicate1-12248_R2.fastq.gz	fastq fastq	1443284556.0	17181959.0	GSM3131182 r1	0:42 1:42	A:371226822;C:343019970;G:358627075;T:370330892;N:79797	42	42	371226822	343019970	358627075	370330892	79797	SRX4041434	SRS3258914	SRA699717	GEO	Molecular Biology, Radboud University	2	0.82734	0.83906	0.35561	0.35376	0.68816	0.69112	0.53167	0.53342	42	42	B	B	biological fallback assumption	illumina	hiseq_era	unknown	rrna_depletion	ribozero	sc	single_cell_plate	celseq	Netherlands	2018-05-04	Larval	Larval	Whole Organism	All anatomical structures
64110	64110	SRR14270307	SRX10631968	SRS8728218	SRP315277	PRJNA722846	Shp1 protein tyrosine phosphatase function in the early development of the hematopoietic system of zebrafish	GSE172292	Transcriptome Analysis	We developed a ptpn6 knock out zebrafish and found a disruption in the early development of the hematopoietic system. Marcrophage subpopulation size en numbers of macrophage progenitors differ between mutants and siblings. Overall design: 5dpf zebrafish embryos were dissociated and FACS sorted. Macrophages mpeg were sorted in 384 well plates.			PB 04	GSM5252012	tissue:Whole embryo\|developmental stage:5 dpf\|sort day:2\|genotype:Ptpn6 siblings	PB 04	Well numbers X001 X384 in .TranscriptCounts.tsv refer to well numbers of the 384 well plate in the following order: A1 to A24 B1 to B24 until P24. The right mate of each read pair was mapped to the ensemble of all gene loci. Reads mapping to multiple loci were discarded. During sequencing Read 1 was assigned 26/75 base pairs and was used for identification of the Illumina library barcode cel barcode and UMI. R2 was assigned 60/75* base pairs and used to map to the reference transcriptome of Zv9 with BWA Anders and Huber 2010. Data was demultiplexed as described in Grün et al. 2014. Mapping and generation of count tables was automated using the MapAndGo script1. https://github.com/anna alemany/transcriptomics/tree/master/mapandgo Tabular separated file indicating number of transcripts per section obtained as previously described Grün Dominic Lennart Kester and Alexander Van Oudenaarden. "Validation of noise models for single cell transcriptomics." Nature methods 11.6 2014: 637. We refer to transcripts as unique molecules based on UMI correction. coutc files contain number of reads coutb files contain number of observed UMI and coutt files contain number of unique UMI corrected transcripts per gene per cell The left read contains the barcode information: the first eight bases correspond to a cell specific barcode* followed by a 6bp unique molecular identifier UMI. The remainder of the left read contains a polyT stretch followed by a number <40 of transcript derived bases. Read 1 was not used for quantification. Supplementary files format and content: cell specific barcodes are specified in the file “cel seq2 barcodes.csv” Genome build: zV9 Danio Rerio	Whole embryo		Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols		developmental stage:5 dpf\|sort day:2\|genotype:Ptpn6 siblings	GSM5252012	GSM5252012: PB 04; Danio rerio; RNA Seq	GSM5252012		1	Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM5252012	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP315277		HUB-PB-004_HK7YNBGXB_S2_L001_R1_001.fastq.gz HUB-PB-004_HK7YNBGXB_S2_L001_R2_001.fastq.gz	fastq fastq	986010210.0	11465235.0	GSM5252012 r1	0:26 1:60	A:254263542;C:174689279;G:187203726;T:369678029;N:175634	26	60	254263542	174689279	187203726	369678029	175634	SRX10631968	SRS8728218	SRA1220139	GEO	Hubrecht Institute	2	0.12751	0.84787	0.11742	0.27807	0.99261	0.83319	0.57778	0.58131	26	60	T	B	sc-like readlen	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Netherlands	2021-04-19	Larval	Larval	Whole Organism	All anatomical structures
64111	64111	SRR14270308	SRX10631968	SRS8728218	SRP315277	PRJNA722846	Shp1 protein tyrosine phosphatase function in the early development of the hematopoietic system of zebrafish	GSE172292	Transcriptome Analysis	We developed a ptpn6 knock out zebrafish and found a disruption in the early development of the hematopoietic system. Marcrophage subpopulation size en numbers of macrophage progenitors differ between mutants and siblings. Overall design: 5dpf zebrafish embryos were dissociated and FACS sorted. Macrophages mpeg were sorted in 384 well plates.			PB 04	GSM5252012	tissue:Whole embryo\|developmental stage:5 dpf\|sort day:2\|genotype:Ptpn6 siblings	PB 04	Well numbers X001 X384 in .TranscriptCounts.tsv refer to well numbers of the 384 well plate in the following order: A1 to A24 B1 to B24 until P24. The right mate of each read pair was mapped to the ensemble of all gene loci. Reads mapping to multiple loci were discarded. During sequencing Read 1 was assigned 26/75 base pairs and was used for identification of the Illumina library barcode cel barcode and UMI. R2 was assigned 60/75* base pairs and used to map to the reference transcriptome of Zv9 with BWA Anders and Huber 2010. Data was demultiplexed as described in Grün et al. 2014. Mapping and generation of count tables was automated using the MapAndGo script1. https://github.com/anna alemany/transcriptomics/tree/master/mapandgo Tabular separated file indicating number of transcripts per section obtained as previously described Grün Dominic Lennart Kester and Alexander Van Oudenaarden. "Validation of noise models for single cell transcriptomics." Nature methods 11.6 2014: 637. We refer to transcripts as unique molecules based on UMI correction. coutc files contain number of reads coutb files contain number of observed UMI and coutt files contain number of unique UMI corrected transcripts per gene per cell The left read contains the barcode information: the first eight bases correspond to a cell specific barcode* followed by a 6bp unique molecular identifier UMI. The remainder of the left read contains a polyT stretch followed by a number <40 of transcript derived bases. Read 1 was not used for quantification. Supplementary files format and content: cell specific barcodes are specified in the file “cel seq2 barcodes.csv” Genome build: zV9 Danio Rerio	Whole embryo		Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols		developmental stage:5 dpf\|sort day:2\|genotype:Ptpn6 siblings	GSM5252012	GSM5252012: PB 04; Danio rerio; RNA Seq	GSM5252012		1	Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM5252012	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP315277		HUB-PB-004_HK7YNBGXB_S2_L002_R1_001.fastq.gz HUB-PB-004_HK7YNBGXB_S2_L002_R2_001.fastq.gz	fastq fastq	975991726.0	11348741.0	GSM5252012 r2	0:26 1:60	A:249739805;C:171614646;G:190634015;T:363955671;N:47589	26	60	249739805	171614646	190634015	363955671	47589	SRX10631968	SRS8728218	SRA1220139	GEO	Hubrecht Institute	2	0.12666	0.84406	0.11676	0.27662	0.99226	0.834	0.57962	0.58473	26	60	T	B	sc-like readlen	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Netherlands	2021-04-19	Larval	Larval	Whole Organism	All anatomical structures
64112	64112	SRR14270309	SRX10631968	SRS8728218	SRP315277	PRJNA722846	Shp1 protein tyrosine phosphatase function in the early development of the hematopoietic system of zebrafish	GSE172292	Transcriptome Analysis	We developed a ptpn6 knock out zebrafish and found a disruption in the early development of the hematopoietic system. Marcrophage subpopulation size en numbers of macrophage progenitors differ between mutants and siblings. Overall design: 5dpf zebrafish embryos were dissociated and FACS sorted. Macrophages mpeg were sorted in 384 well plates.			PB 04	GSM5252012	tissue:Whole embryo\|developmental stage:5 dpf\|sort day:2\|genotype:Ptpn6 siblings	PB 04	Well numbers X001 X384 in .TranscriptCounts.tsv refer to well numbers of the 384 well plate in the following order: A1 to A24 B1 to B24 until P24. The right mate of each read pair was mapped to the ensemble of all gene loci. Reads mapping to multiple loci were discarded. During sequencing Read 1 was assigned 26/75 base pairs and was used for identification of the Illumina library barcode cel barcode and UMI. R2 was assigned 60/75* base pairs and used to map to the reference transcriptome of Zv9 with BWA Anders and Huber 2010. Data was demultiplexed as described in Grün et al. 2014. Mapping and generation of count tables was automated using the MapAndGo script1. https://github.com/anna alemany/transcriptomics/tree/master/mapandgo Tabular separated file indicating number of transcripts per section obtained as previously described Grün Dominic Lennart Kester and Alexander Van Oudenaarden. "Validation of noise models for single cell transcriptomics." Nature methods 11.6 2014: 637. We refer to transcripts as unique molecules based on UMI correction. coutc files contain number of reads coutb files contain number of observed UMI and coutt files contain number of unique UMI corrected transcripts per gene per cell The left read contains the barcode information: the first eight bases correspond to a cell specific barcode* followed by a 6bp unique molecular identifier UMI. The remainder of the left read contains a polyT stretch followed by a number <40 of transcript derived bases. Read 1 was not used for quantification. Supplementary files format and content: cell specific barcodes are specified in the file “cel seq2 barcodes.csv” Genome build: zV9 Danio Rerio	Whole embryo		Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols		developmental stage:5 dpf\|sort day:2\|genotype:Ptpn6 siblings	GSM5252012	GSM5252012: PB 04; Danio rerio; RNA Seq	GSM5252012		1	Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM5252012	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP315277		HUB-PB-004_HK7YNBGXB_S2_L003_R1_001.fastq.gz HUB-PB-004_HK7YNBGXB_S2_L003_R2_001.fastq.gz	fastq fastq	994435888.0	11563208.0	GSM5252012 r3	0:26 1:60	A:256651271;C:176213474;G:188991919;T:372487332;N:91892	26	60	256651271	176213474	188991919	372487332	91892	SRX10631968	SRS8728218	SRA1220139	GEO	Hubrecht Institute	2	0.1295	0.84813	0.11934	0.27808	0.99168	0.83514	0.56162	0.58665	26	60	T	B	sc-like readlen	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Netherlands	2021-04-19	Larval	Larval	Whole Organism	All anatomical structures
64113	64113	SRR14270310	SRX10631968	SRS8728218	SRP315277	PRJNA722846	Shp1 protein tyrosine phosphatase function in the early development of the hematopoietic system of zebrafish	GSE172292	Transcriptome Analysis	We developed a ptpn6 knock out zebrafish and found a disruption in the early development of the hematopoietic system. Marcrophage subpopulation size en numbers of macrophage progenitors differ between mutants and siblings. Overall design: 5dpf zebrafish embryos were dissociated and FACS sorted. Macrophages mpeg were sorted in 384 well plates.			PB 04	GSM5252012	tissue:Whole embryo\|developmental stage:5 dpf\|sort day:2\|genotype:Ptpn6 siblings	PB 04	Well numbers X001 X384 in .TranscriptCounts.tsv refer to well numbers of the 384 well plate in the following order: A1 to A24 B1 to B24 until P24. The right mate of each read pair was mapped to the ensemble of all gene loci. Reads mapping to multiple loci were discarded. During sequencing Read 1 was assigned 26/75 base pairs and was used for identification of the Illumina library barcode cel barcode and UMI. R2 was assigned 60/75* base pairs and used to map to the reference transcriptome of Zv9 with BWA Anders and Huber 2010. Data was demultiplexed as described in Grün et al. 2014. Mapping and generation of count tables was automated using the MapAndGo script1. https://github.com/anna alemany/transcriptomics/tree/master/mapandgo Tabular separated file indicating number of transcripts per section obtained as previously described Grün Dominic Lennart Kester and Alexander Van Oudenaarden. "Validation of noise models for single cell transcriptomics." Nature methods 11.6 2014: 637. We refer to transcripts as unique molecules based on UMI correction. coutc files contain number of reads coutb files contain number of observed UMI and coutt files contain number of unique UMI corrected transcripts per gene per cell The left read contains the barcode information: the first eight bases correspond to a cell specific barcode* followed by a 6bp unique molecular identifier UMI. The remainder of the left read contains a polyT stretch followed by a number <40 of transcript derived bases. Read 1 was not used for quantification. Supplementary files format and content: cell specific barcodes are specified in the file “cel seq2 barcodes.csv” Genome build: zV9 Danio Rerio	Whole embryo		Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols		developmental stage:5 dpf\|sort day:2\|genotype:Ptpn6 siblings	GSM5252012	GSM5252012: PB 04; Danio rerio; RNA Seq	GSM5252012		1	Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM5252012	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP315277		HUB-PB-004_HK7YNBGXB_S2_L004_R1_001.fastq.gz HUB-PB-004_HK7YNBGXB_S2_L004_R2_001.fastq.gz	fastq fastq	987289202.0	11480107.0	GSM5252012 r4	0:26 1:60	A:252872859;C:173815065;G:192358026;T:368206452;N:36800	26	60	252872859	173815065	192358026	368206452	36800	SRX10631968	SRS8728218	SRA1220139	GEO	Hubrecht Institute	2	0.12769	0.84325	0.11776	0.27506	0.99235	0.83293	0.54807	0.58503	26	60	T	B	sc-like readlen	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Netherlands	2021-04-19	Larval	Larval	Whole Organism	All anatomical structures
64114	64114	SRR14270303	SRX10631967	SRS8728217	SRP315277	PRJNA722846	Shp1 protein tyrosine phosphatase function in the early development of the hematopoietic system of zebrafish	GSE172292	Transcriptome Analysis	We developed a ptpn6 knock out zebrafish and found a disruption in the early development of the hematopoietic system. Marcrophage subpopulation size en numbers of macrophage progenitors differ between mutants and siblings. Overall design: 5dpf zebrafish embryos were dissociated and FACS sorted. Macrophages mpeg were sorted in 384 well plates.			PB 03	GSM5252011	tissue:Whole embryo\|developmental stage:5 dpf\|sort day:2\|genotype:Ptpn6 mutants	PB 03	Well numbers X001 X384 in .TranscriptCounts.tsv refer to well numbers of the 384 well plate in the following order: A1 to A24 B1 to B24 until P24. The right mate of each read pair was mapped to the ensemble of all gene loci. Reads mapping to multiple loci were discarded. During sequencing Read 1 was assigned 26/75 base pairs and was used for identification of the Illumina library barcode cel barcode and UMI. R2 was assigned 60/75* base pairs and used to map to the reference transcriptome of Zv9 with BWA Anders and Huber 2010. Data was demultiplexed as described in Grün et al. 2014. Mapping and generation of count tables was automated using the MapAndGo script1. https://github.com/anna alemany/transcriptomics/tree/master/mapandgo Tabular separated file indicating number of transcripts per section obtained as previously described Grün Dominic Lennart Kester and Alexander Van Oudenaarden. "Validation of noise models for single cell transcriptomics." Nature methods 11.6 2014: 637. We refer to transcripts as unique molecules based on UMI correction. coutc files contain number of reads coutb files contain number of observed UMI and coutt files contain number of unique UMI corrected transcripts per gene per cell The left read contains the barcode information: the first eight bases correspond to a cell specific barcode* followed by a 6bp unique molecular identifier UMI. The remainder of the left read contains a polyT stretch followed by a number <40 of transcript derived bases. Read 1 was not used for quantification. Supplementary files format and content: cell specific barcodes are specified in the file “cel seq2 barcodes.csv” Genome build: zV9 Danio Rerio	Whole embryo		Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols		developmental stage:5 dpf\|sort day:2\|genotype:Ptpn6 mutants	GSM5252011	GSM5252011: PB 03; Danio rerio; RNA Seq	GSM5252011		1	Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM5252011	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP315277		HUB-PB-003_HK7YNBGXB_S1_L001_R1_001.fastq.gz HUB-PB-003_HK7YNBGXB_S1_L001_R2_001.fastq.gz	fastq fastq	661428924.0	7691034.0	GSM5252011 r1	0:26 1:60	A:168215613;C:118730788;G:123898534;T:250464451;N:119538	26	60	168215613	118730788	123898534	250464451	119538	SRX10631967	SRS8728217	SRA1220139	GEO	Hubrecht Institute	2	0.12504	0.87398	0.11693	0.30041	0.99366	0.83197	0.58977	0.57713	26	60	T	B	sc-like readlen	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Netherlands	2021-04-19	Larval	Larval	Whole Organism	All anatomical structures
64115	64115	SRR14270304	SRX10631967	SRS8728217	SRP315277	PRJNA722846	Shp1 protein tyrosine phosphatase function in the early development of the hematopoietic system of zebrafish	GSE172292	Transcriptome Analysis	We developed a ptpn6 knock out zebrafish and found a disruption in the early development of the hematopoietic system. Marcrophage subpopulation size en numbers of macrophage progenitors differ between mutants and siblings. Overall design: 5dpf zebrafish embryos were dissociated and FACS sorted. Macrophages mpeg were sorted in 384 well plates.			PB 03	GSM5252011	tissue:Whole embryo\|developmental stage:5 dpf\|sort day:2\|genotype:Ptpn6 mutants	PB 03	Well numbers X001 X384 in .TranscriptCounts.tsv refer to well numbers of the 384 well plate in the following order: A1 to A24 B1 to B24 until P24. The right mate of each read pair was mapped to the ensemble of all gene loci. Reads mapping to multiple loci were discarded. During sequencing Read 1 was assigned 26/75 base pairs and was used for identification of the Illumina library barcode cel barcode and UMI. R2 was assigned 60/75* base pairs and used to map to the reference transcriptome of Zv9 with BWA Anders and Huber 2010. Data was demultiplexed as described in Grün et al. 2014. Mapping and generation of count tables was automated using the MapAndGo script1. https://github.com/anna alemany/transcriptomics/tree/master/mapandgo Tabular separated file indicating number of transcripts per section obtained as previously described Grün Dominic Lennart Kester and Alexander Van Oudenaarden. "Validation of noise models for single cell transcriptomics." Nature methods 11.6 2014: 637. We refer to transcripts as unique molecules based on UMI correction. coutc files contain number of reads coutb files contain number of observed UMI and coutt files contain number of unique UMI corrected transcripts per gene per cell The left read contains the barcode information: the first eight bases correspond to a cell specific barcode* followed by a 6bp unique molecular identifier UMI. The remainder of the left read contains a polyT stretch followed by a number <40 of transcript derived bases. Read 1 was not used for quantification. Supplementary files format and content: cell specific barcodes are specified in the file “cel seq2 barcodes.csv” Genome build: zV9 Danio Rerio	Whole embryo		Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols		developmental stage:5 dpf\|sort day:2\|genotype:Ptpn6 mutants	GSM5252011	GSM5252011: PB 03; Danio rerio; RNA Seq	GSM5252011		1	Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM5252011	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP315277		HUB-PB-003_HK7YNBGXB_S1_L002_R1_001.fastq.gz HUB-PB-003_HK7YNBGXB_S1_L002_R2_001.fastq.gz	fastq fastq	654078332.0	7605562.0	GSM5252011 r2	0:26 1:60	A:165061544;C:116595826;G:125951842;T:246436661;N:32459	26	60	165061544	116595826	125951842	246436661	32459	SRX10631967	SRS8728217	SRA1220139	GEO	Hubrecht Institute	2	0.12397	0.86829	0.11601	0.29962	0.99332	0.83128	0.6489	0.5784	26	60	T	B	sc-like readlen	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Netherlands	2021-04-19	Larval	Larval	Whole Organism	All anatomical structures
64116	64116	SRR14270305	SRX10631967	SRS8728217	SRP315277	PRJNA722846	Shp1 protein tyrosine phosphatase function in the early development of the hematopoietic system of zebrafish	GSE172292	Transcriptome Analysis	We developed a ptpn6 knock out zebrafish and found a disruption in the early development of the hematopoietic system. Marcrophage subpopulation size en numbers of macrophage progenitors differ between mutants and siblings. Overall design: 5dpf zebrafish embryos were dissociated and FACS sorted. Macrophages mpeg were sorted in 384 well plates.			PB 03	GSM5252011	tissue:Whole embryo\|developmental stage:5 dpf\|sort day:2\|genotype:Ptpn6 mutants	PB 03	Well numbers X001 X384 in .TranscriptCounts.tsv refer to well numbers of the 384 well plate in the following order: A1 to A24 B1 to B24 until P24. The right mate of each read pair was mapped to the ensemble of all gene loci. Reads mapping to multiple loci were discarded. During sequencing Read 1 was assigned 26/75 base pairs and was used for identification of the Illumina library barcode cel barcode and UMI. R2 was assigned 60/75* base pairs and used to map to the reference transcriptome of Zv9 with BWA Anders and Huber 2010. Data was demultiplexed as described in Grün et al. 2014. Mapping and generation of count tables was automated using the MapAndGo script1. https://github.com/anna alemany/transcriptomics/tree/master/mapandgo Tabular separated file indicating number of transcripts per section obtained as previously described Grün Dominic Lennart Kester and Alexander Van Oudenaarden. "Validation of noise models for single cell transcriptomics." Nature methods 11.6 2014: 637. We refer to transcripts as unique molecules based on UMI correction. coutc files contain number of reads coutb files contain number of observed UMI and coutt files contain number of unique UMI corrected transcripts per gene per cell The left read contains the barcode information: the first eight bases correspond to a cell specific barcode* followed by a 6bp unique molecular identifier UMI. The remainder of the left read contains a polyT stretch followed by a number <40 of transcript derived bases. Read 1 was not used for quantification. Supplementary files format and content: cell specific barcodes are specified in the file “cel seq2 barcodes.csv” Genome build: zV9 Danio Rerio	Whole embryo		Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols		developmental stage:5 dpf\|sort day:2\|genotype:Ptpn6 mutants	GSM5252011	GSM5252011: PB 03; Danio rerio; RNA Seq	GSM5252011		1	Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM5252011	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP315277		HUB-PB-003_HK7YNBGXB_S1_L003_R1_001.fastq.gz HUB-PB-003_HK7YNBGXB_S1_L003_R2_001.fastq.gz	fastq fastq	665757906.0	7741371.0	GSM5252011 r3	0:26 1:60	A:169318159;C:119549188;G:124847058;T:251982052;N:61449	26	60	169318159	119549188	124847058	251982052	61449	SRX10631967	SRS8728217	SRA1220139	GEO	Hubrecht Institute	2	0.12459	0.87418	0.11646	0.30014	0.99364	0.83175	0.65756	0.58002	26	60	T	B	sc-like readlen	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Netherlands	2021-04-19	Larval	Larval	Whole Organism	All anatomical structures
64117	64117	SRR14270306	SRX10631967	SRS8728217	SRP315277	PRJNA722846	Shp1 protein tyrosine phosphatase function in the early development of the hematopoietic system of zebrafish	GSE172292	Transcriptome Analysis	We developed a ptpn6 knock out zebrafish and found a disruption in the early development of the hematopoietic system. Marcrophage subpopulation size en numbers of macrophage progenitors differ between mutants and siblings. Overall design: 5dpf zebrafish embryos were dissociated and FACS sorted. Macrophages mpeg were sorted in 384 well plates.			PB 03	GSM5252011	tissue:Whole embryo\|developmental stage:5 dpf\|sort day:2\|genotype:Ptpn6 mutants	PB 03	Well numbers X001 X384 in .TranscriptCounts.tsv refer to well numbers of the 384 well plate in the following order: A1 to A24 B1 to B24 until P24. The right mate of each read pair was mapped to the ensemble of all gene loci. Reads mapping to multiple loci were discarded. During sequencing Read 1 was assigned 26/75 base pairs and was used for identification of the Illumina library barcode cel barcode and UMI. R2 was assigned 60/75* base pairs and used to map to the reference transcriptome of Zv9 with BWA Anders and Huber 2010. Data was demultiplexed as described in Grün et al. 2014. Mapping and generation of count tables was automated using the MapAndGo script1. https://github.com/anna alemany/transcriptomics/tree/master/mapandgo Tabular separated file indicating number of transcripts per section obtained as previously described Grün Dominic Lennart Kester and Alexander Van Oudenaarden. "Validation of noise models for single cell transcriptomics." Nature methods 11.6 2014: 637. We refer to transcripts as unique molecules based on UMI correction. coutc files contain number of reads coutb files contain number of observed UMI and coutt files contain number of unique UMI corrected transcripts per gene per cell The left read contains the barcode information: the first eight bases correspond to a cell specific barcode* followed by a 6bp unique molecular identifier UMI. The remainder of the left read contains a polyT stretch followed by a number <40 of transcript derived bases. Read 1 was not used for quantification. Supplementary files format and content: cell specific barcodes are specified in the file “cel seq2 barcodes.csv” Genome build: zV9 Danio Rerio	Whole embryo		Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols		developmental stage:5 dpf\|sort day:2\|genotype:Ptpn6 mutants	GSM5252011	GSM5252011: PB 03; Danio rerio; RNA Seq	GSM5252011		1	Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM5252011	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP315277		HUB-PB-003_HK7YNBGXB_S1_L004_R1_001.fastq.gz HUB-PB-003_HK7YNBGXB_S1_L004_R2_001.fastq.gz	fastq fastq	661920070.0	7696745.0	GSM5252011 r4	0:26 1:60	A:167185610;C:118130816;G:127099698;T:249480399;N:23547	26	60	167185610	118130816	127099698	249480399	23547	SRX10631967	SRS8728217	SRA1220139	GEO	Hubrecht Institute	2	0.12331	0.86845	0.11548	0.29839	0.99379	0.83299	0.65741	0.57156	26	60	T	B	sc-like readlen	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Netherlands	2021-04-19	Larval	Larval	Whole Organism	All anatomical structures
64118	64118	SRR14270299	SRX10631966	SRS8728216	SRP315277	PRJNA722846	Shp1 protein tyrosine phosphatase function in the early development of the hematopoietic system of zebrafish	GSE172292	Transcriptome Analysis	We developed a ptpn6 knock out zebrafish and found a disruption in the early development of the hematopoietic system. Marcrophage subpopulation size en numbers of macrophage progenitors differ between mutants and siblings. Overall design: 5dpf zebrafish embryos were dissociated and FACS sorted. Macrophages mpeg were sorted in 384 well plates.			PB 02	GSM5252010	tissue:Whole embryo\|developmental stage:5 dpf\|sort day:1\|genotype:Ptpn6 siblings A H and ptpn6 mutants I P	PB 02	Well numbers X001 X384 in .TranscriptCounts.tsv refer to well numbers of the 384 well plate in the following order: A1 to A24 B1 to B24 until P24. The right mate of each read pair was mapped to the ensemble of all gene loci. Reads mapping to multiple loci were discarded. During sequencing Read 1 was assigned 26/75 base pairs and was used for identification of the Illumina library barcode cel barcode and UMI. R2 was assigned 60/75* base pairs and used to map to the reference transcriptome of Zv9 with BWA Anders and Huber 2010. Data was demultiplexed as described in Grün et al. 2014. Mapping and generation of count tables was automated using the MapAndGo script1. https://github.com/anna alemany/transcriptomics/tree/master/mapandgo Tabular separated file indicating number of transcripts per section obtained as previously described Grün Dominic Lennart Kester and Alexander Van Oudenaarden. "Validation of noise models for single cell transcriptomics." Nature methods 11.6 2014: 637. We refer to transcripts as unique molecules based on UMI correction. coutc files contain number of reads coutb files contain number of observed UMI and coutt files contain number of unique UMI corrected transcripts per gene per cell The left read contains the barcode information: the first eight bases correspond to a cell specific barcode* followed by a 6bp unique molecular identifier UMI. The remainder of the left read contains a polyT stretch followed by a number <40 of transcript derived bases. Read 1 was not used for quantification. Supplementary files format and content: cell specific barcodes are specified in the file “cel seq2 barcodes.csv” Genome build: zV9 Danio Rerio	Whole embryo		Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols		developmental stage:5 dpf\|sort day:1\|genotype:Ptpn6 siblings A H and ptpn6 mutants I P	GSM5252010	GSM5252010: PB 02; Danio rerio; RNA Seq	GSM5252010		1	Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM5252010	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP315277		HUB-PB-002_HC2CGBGX9_S2_L001_R1_001.fastq.gz HUB-PB-002_HC2CGBGX9_S2_L001_R2_001.fastq.gz	fastq fastq	1024663168.0	11914688.0	GSM5252010 r1	0:26 1:60	A:262697623;C:189686514;G:197838515;T:373069804;N:1370712	26	60	262697623	189686514	197838515	373069804	1370712	SRX10631966	SRS8728216	SRA1220139	GEO	Hubrecht Institute	2	0.10374	0.86353	0.09639	0.38098	0.98845	0.85251	0.6156	0.62881	26	60	T	B	sc-like readlen	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Netherlands	2021-04-19	Larval	Larval	Whole Organism	All anatomical structures
64119	64119	SRR14270300	SRX10631966	SRS8728216	SRP315277	PRJNA722846	Shp1 protein tyrosine phosphatase function in the early development of the hematopoietic system of zebrafish	GSE172292	Transcriptome Analysis	We developed a ptpn6 knock out zebrafish and found a disruption in the early development of the hematopoietic system. Marcrophage subpopulation size en numbers of macrophage progenitors differ between mutants and siblings. Overall design: 5dpf zebrafish embryos were dissociated and FACS sorted. Macrophages mpeg were sorted in 384 well plates.			PB 02	GSM5252010	tissue:Whole embryo\|developmental stage:5 dpf\|sort day:1\|genotype:Ptpn6 siblings A H and ptpn6 mutants I P	PB 02	Well numbers X001 X384 in .TranscriptCounts.tsv refer to well numbers of the 384 well plate in the following order: A1 to A24 B1 to B24 until P24. The right mate of each read pair was mapped to the ensemble of all gene loci. Reads mapping to multiple loci were discarded. During sequencing Read 1 was assigned 26/75 base pairs and was used for identification of the Illumina library barcode cel barcode and UMI. R2 was assigned 60/75* base pairs and used to map to the reference transcriptome of Zv9 with BWA Anders and Huber 2010. Data was demultiplexed as described in Grün et al. 2014. Mapping and generation of count tables was automated using the MapAndGo script1. https://github.com/anna alemany/transcriptomics/tree/master/mapandgo Tabular separated file indicating number of transcripts per section obtained as previously described Grün Dominic Lennart Kester and Alexander Van Oudenaarden. "Validation of noise models for single cell transcriptomics." Nature methods 11.6 2014: 637. We refer to transcripts as unique molecules based on UMI correction. coutc files contain number of reads coutb files contain number of observed UMI and coutt files contain number of unique UMI corrected transcripts per gene per cell The left read contains the barcode information: the first eight bases correspond to a cell specific barcode* followed by a 6bp unique molecular identifier UMI. The remainder of the left read contains a polyT stretch followed by a number <40 of transcript derived bases. Read 1 was not used for quantification. Supplementary files format and content: cell specific barcodes are specified in the file “cel seq2 barcodes.csv” Genome build: zV9 Danio Rerio	Whole embryo		Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols		developmental stage:5 dpf\|sort day:1\|genotype:Ptpn6 siblings A H and ptpn6 mutants I P	GSM5252010	GSM5252010: PB 02; Danio rerio; RNA Seq	GSM5252010		1	Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM5252010	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP315277		HUB-PB-002_HC2CGBGX9_S2_L002_R1_001.fastq.gz HUB-PB-002_HC2CGBGX9_S2_L002_R2_001.fastq.gz	fastq fastq	1151014712.0	13383892.0	GSM5252010 r2	0:26 1:60	A:293550204;C:211235441;G:227184907;T:417646165;N:1397995	26	60	293550204	211235441	227184907	417646165	1397995	SRX10631966	SRS8728216	SRA1220139	GEO	Hubrecht Institute	2	0.10311	0.8584	0.09562	0.37934	0.98867	0.85549	0.63997	0.62958	26	60	T	B	sc-like readlen	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Netherlands	2021-04-19	Larval	Larval	Whole Organism	All anatomical structures
64120	64120	SRR14270301	SRX10631966	SRS8728216	SRP315277	PRJNA722846	Shp1 protein tyrosine phosphatase function in the early development of the hematopoietic system of zebrafish	GSE172292	Transcriptome Analysis	We developed a ptpn6 knock out zebrafish and found a disruption in the early development of the hematopoietic system. Marcrophage subpopulation size en numbers of macrophage progenitors differ between mutants and siblings. Overall design: 5dpf zebrafish embryos were dissociated and FACS sorted. Macrophages mpeg were sorted in 384 well plates.			PB 02	GSM5252010	tissue:Whole embryo\|developmental stage:5 dpf\|sort day:1\|genotype:Ptpn6 siblings A H and ptpn6 mutants I P	PB 02	Well numbers X001 X384 in .TranscriptCounts.tsv refer to well numbers of the 384 well plate in the following order: A1 to A24 B1 to B24 until P24. The right mate of each read pair was mapped to the ensemble of all gene loci. Reads mapping to multiple loci were discarded. During sequencing Read 1 was assigned 26/75 base pairs and was used for identification of the Illumina library barcode cel barcode and UMI. R2 was assigned 60/75* base pairs and used to map to the reference transcriptome of Zv9 with BWA Anders and Huber 2010. Data was demultiplexed as described in Grün et al. 2014. Mapping and generation of count tables was automated using the MapAndGo script1. https://github.com/anna alemany/transcriptomics/tree/master/mapandgo Tabular separated file indicating number of transcripts per section obtained as previously described Grün Dominic Lennart Kester and Alexander Van Oudenaarden. "Validation of noise models for single cell transcriptomics." Nature methods 11.6 2014: 637. We refer to transcripts as unique molecules based on UMI correction. coutc files contain number of reads coutb files contain number of observed UMI and coutt files contain number of unique UMI corrected transcripts per gene per cell The left read contains the barcode information: the first eight bases correspond to a cell specific barcode* followed by a 6bp unique molecular identifier UMI. The remainder of the left read contains a polyT stretch followed by a number <40 of transcript derived bases. Read 1 was not used for quantification. Supplementary files format and content: cell specific barcodes are specified in the file “cel seq2 barcodes.csv” Genome build: zV9 Danio Rerio	Whole embryo		Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols		developmental stage:5 dpf\|sort day:1\|genotype:Ptpn6 siblings A H and ptpn6 mutants I P	GSM5252010	GSM5252010: PB 02; Danio rerio; RNA Seq	GSM5252010		1	Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM5252010	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP315277		HUB-PB-002_HC2CGBGX9_S2_L003_R1_001.fastq.gz HUB-PB-002_HC2CGBGX9_S2_L003_R2_001.fastq.gz	fastq fastq	1092543398.0	12703993.0	GSM5252010 r3	0:26 1:60	A:280238069;C:201736459;G:211013214;T:398695330;N:860326	26	60	280238069	201736459	211013214	398695330	860326	SRX10631966	SRS8728216	SRA1220139	GEO	Hubrecht Institute	2	0.10355	0.86382	0.09588	0.38224	0.98863	0.85429	0.65257	0.63065	26	60	T	B	sc-like readlen	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Netherlands	2021-04-19	Larval	Larval	Whole Organism	All anatomical structures
64121	64121	SRR14270302	SRX10631966	SRS8728216	SRP315277	PRJNA722846	Shp1 protein tyrosine phosphatase function in the early development of the hematopoietic system of zebrafish	GSE172292	Transcriptome Analysis	We developed a ptpn6 knock out zebrafish and found a disruption in the early development of the hematopoietic system. Marcrophage subpopulation size en numbers of macrophage progenitors differ between mutants and siblings. Overall design: 5dpf zebrafish embryos were dissociated and FACS sorted. Macrophages mpeg were sorted in 384 well plates.			PB 02	GSM5252010	tissue:Whole embryo\|developmental stage:5 dpf\|sort day:1\|genotype:Ptpn6 siblings A H and ptpn6 mutants I P	PB 02	Well numbers X001 X384 in .TranscriptCounts.tsv refer to well numbers of the 384 well plate in the following order: A1 to A24 B1 to B24 until P24. The right mate of each read pair was mapped to the ensemble of all gene loci. Reads mapping to multiple loci were discarded. During sequencing Read 1 was assigned 26/75 base pairs and was used for identification of the Illumina library barcode cel barcode and UMI. R2 was assigned 60/75* base pairs and used to map to the reference transcriptome of Zv9 with BWA Anders and Huber 2010. Data was demultiplexed as described in Grün et al. 2014. Mapping and generation of count tables was automated using the MapAndGo script1. https://github.com/anna alemany/transcriptomics/tree/master/mapandgo Tabular separated file indicating number of transcripts per section obtained as previously described Grün Dominic Lennart Kester and Alexander Van Oudenaarden. "Validation of noise models for single cell transcriptomics." Nature methods 11.6 2014: 637. We refer to transcripts as unique molecules based on UMI correction. coutc files contain number of reads coutb files contain number of observed UMI and coutt files contain number of unique UMI corrected transcripts per gene per cell The left read contains the barcode information: the first eight bases correspond to a cell specific barcode* followed by a 6bp unique molecular identifier UMI. The remainder of the left read contains a polyT stretch followed by a number <40 of transcript derived bases. Read 1 was not used for quantification. Supplementary files format and content: cell specific barcodes are specified in the file “cel seq2 barcodes.csv” Genome build: zV9 Danio Rerio	Whole embryo		Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols		developmental stage:5 dpf\|sort day:1\|genotype:Ptpn6 siblings A H and ptpn6 mutants I P	GSM5252010	GSM5252010: PB 02; Danio rerio; RNA Seq	GSM5252010		1	Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM5252010	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP315277		HUB-PB-002_HC2CGBGX9_S2_L004_R1_001.fastq.gz HUB-PB-002_HC2CGBGX9_S2_L004_R2_001.fastq.gz	fastq fastq	1196112682.0	13908287.0	GSM5252010 r4	0:26 1:60	A:305645133;C:219310697;G:235825599;T:434540271;N:790982	26	60	305645133	219310697	235825599	434540271	790982	SRX10631966	SRS8728216	SRA1220139	GEO	Hubrecht Institute	2	0.10383	0.85683	0.09599	0.38181	0.9881	0.85648	0.60938	0.62233	26	60	T	B	sc-like readlen	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Netherlands	2021-04-19	Larval	Larval	Whole Organism	All anatomical structures
69930	69930	SRR22318718	SRX18291979	SRS15783401	SRP374955	PRJNA837586	Labelling transcriptional response to dissociation using SLAMseq	GSE202880	Other	Transcriptional response to dissociation is known to cause artefacts in single cell data sets. We used 4sU to label newly made transcripts during dissociation in order to to later remove them from the data set Overall design: 10mM 4sU was added to the dissociation buffer while the samples were enzymatically dissociated for 30 min. A 4sU injected control was added to the zebrafish samples to identify high turnover genes	parent bioproject:PRJNA837863	pubmed:36573354	larvae cold dissociated rep 3	GSM6735818	tissue:whole larvae 48hpf\|cell type:whole larvae 48hpf\|genotype:WT\|treatment:30 min 4sU during dissociation\|time:48hpf	larvae cold dissociated rep 3	Demultiplexing bcl2fastq v2.19 CELseq barcodes demultiplexed using custom code https://github.com/anikaneuschulz/CELseq3 demultiplex mapping using STAR v2.7.3a aggregation of mutation information and calculation of labeling rates per gene / in bulk using custom code https://github.com/anikaneuschulz/MTglob pipeline genome build/assembly: dr11.95 processed data files format and content: Tab delimited mutation rates per gene	whole larvae 48hpf		10 anesthetized larvae were washed twice in ice cold HBSS Life Technologies GmbH #14175095 and resuspended in 200µl psychrophilic protease mix 1x Native Bacillus licheniformis Protease Creative Enzymes #NATE 0633 in HBSS 10 mM 4sU and incubated on ice for 30 min. Dissociation was aided by pipetting up and down with a 200 µl tip 25 times every 5 minutes. Enzymes were inactivated by adding 15 µl 10% BSA Sigma Aldrich; #A4503 before spinning down and resuspending the cells in TRIzol RNA was extracted using TRIzol Chloroform Isopropanol according to the manufacturer’s instructions. Iodiacetamide Treatment was carried out on extracted RNA in 50% DMSO as described in Herzog et. Al 2017 https://doi.org/10.1038/nmeth.4435. libraries for RNA seq were prepared following a CELseq protocol as published in Holler & Junker 2019 https://doi.org/10.1007/978 1 4939 9009 2 9. Sequencing adapters were switched – Insert is in read 1!		cell type:whole larvae 48hpf\|genotype:WT\|treatment:30 min 4sU during dissociation\|time:48hpf	GSM6735818	GSM6735818: larvae cold dissociated rep 3; Danio rerio; RNA Seq	GSM6735818 r1	GSM6735818	1	10 anesthetized larvae were washed twice in ice cold HBSS Life Technologies GmbH #14175095 and resuspended in 200µl psychrophilic protease mix 1x Native Bacillus licheniformis Protease Creative Enzymes #NATE 0633 in HBSS 10 mM 4sU and incubated on ice for 30 min. Dissociation was aided by pipetting up and down with a 200 µl tip 25 times every 5 minutes. Enzymes were inactivated by adding 15 µl 10% BSA Sigma Aldrich; #A4503 before spinning down and resuspending the cells in TRIzol RNA was extracted using TRIzol Chloroform Isopropanol according to the manufacturer's instructions. Iodiacetamide Treatment was carried out on extracted RNA in 50% DMSO as described in Herzog et. Al 2017 https://doi.org/10.1038/nmeth.4435. libraries for RNA seq were prepared following a CELseq protocol as published in Holler & Junker 2019 https://doi.org/10.1007/978 1 4939 9009 2 9. Sequencing adapters were switched – Insert is in read 1!		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP374955	assembly:dr11.95	l_cold_dissociated_3_R1.fastq.gz l_cold_dissociated_3_R2.fastq.gz	fastq fastq	1990371450.0	13269143.0	GSM6735818 r1	0:120 1:30	A:566370443;C:348995823;G:430419075;T:644554767;N:31342	120	30	566370443	348995823	430419075	644554767	31342	SRX18291979	SRS15783401	SRA1542250	Junker, Max-Delbrück-Center for Molecular Medicine	Junker, Max-Delbrück-Center for Molecular Medicine	2	0.76687	0.27949	0.20883	0.27941	0.84124	0.99989	0.56374	1.0	120	30	B	T	mate2 technical by mapping diff	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Germany	2022-11-17	Multi-stage	Multi-stage	Whole Organism	All anatomical structures
69931	69931	SRR22318719	SRX18291978	SRS15783400	SRP374955	PRJNA837586	Labelling transcriptional response to dissociation using SLAMseq	GSE202880	Other	Transcriptional response to dissociation is known to cause artefacts in single cell data sets. We used 4sU to label newly made transcripts during dissociation in order to to later remove them from the data set Overall design: 10mM 4sU was added to the dissociation buffer while the samples were enzymatically dissociated for 30 min. A 4sU injected control was added to the zebrafish samples to identify high turnover genes	parent bioproject:PRJNA837863	pubmed:36573354	larvae cold dissociated rep 2	GSM6735817	tissue:whole larvae 48hpf\|cell type:whole larvae 48hpf\|genotype:WT\|treatment:30 min 4sU during dissociation\|time:48hpf	larvae cold dissociated rep 2	Demultiplexing bcl2fastq v2.19 CELseq barcodes demultiplexed using custom code https://github.com/anikaneuschulz/CELseq3 demultiplex mapping using STAR v2.7.3a aggregation of mutation information and calculation of labeling rates per gene / in bulk using custom code https://github.com/anikaneuschulz/MTglob pipeline genome build/assembly: dr11.95 processed data files format and content: Tab delimited mutation rates per gene	whole larvae 48hpf		10 anesthetized larvae were washed twice in ice cold HBSS Life Technologies GmbH #14175095 and resuspended in 200µl psychrophilic protease mix 1x Native Bacillus licheniformis Protease Creative Enzymes #NATE 0633 in HBSS 10 mM 4sU and incubated on ice for 30 min. Dissociation was aided by pipetting up and down with a 200 µl tip 25 times every 5 minutes. Enzymes were inactivated by adding 15 µl 10% BSA Sigma Aldrich; #A4503 before spinning down and resuspending the cells in TRIzol RNA was extracted using TRIzol Chloroform Isopropanol according to the manufacturer’s instructions. Iodiacetamide Treatment was carried out on extracted RNA in 50% DMSO as described in Herzog et. Al 2017 https://doi.org/10.1038/nmeth.4435. libraries for RNA seq were prepared following a CELseq protocol as published in Holler & Junker 2019 https://doi.org/10.1007/978 1 4939 9009 2 9. Sequencing adapters were switched – Insert is in read 1!		cell type:whole larvae 48hpf\|genotype:WT\|treatment:30 min 4sU during dissociation\|time:48hpf	GSM6735817	GSM6735817: larvae cold dissociated rep 2; Danio rerio; RNA Seq	GSM6735817 r1	GSM6735817	1	10 anesthetized larvae were washed twice in ice cold HBSS Life Technologies GmbH #14175095 and resuspended in 200µl psychrophilic protease mix 1x Native Bacillus licheniformis Protease Creative Enzymes #NATE 0633 in HBSS 10 mM 4sU and incubated on ice for 30 min. Dissociation was aided by pipetting up and down with a 200 µl tip 25 times every 5 minutes. Enzymes were inactivated by adding 15 µl 10% BSA Sigma Aldrich; #A4503 before spinning down and resuspending the cells in TRIzol RNA was extracted using TRIzol Chloroform Isopropanol according to the manufacturer's instructions. Iodiacetamide Treatment was carried out on extracted RNA in 50% DMSO as described in Herzog et. Al 2017 https://doi.org/10.1038/nmeth.4435. libraries for RNA seq were prepared following a CELseq protocol as published in Holler & Junker 2019 https://doi.org/10.1007/978 1 4939 9009 2 9. Sequencing adapters were switched – Insert is in read 1!		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP374955	assembly:dr11.95	l_cold_dissociated_2_R1.fastq.gz l_cold_dissociated_2_R2.fastq.gz	fastq fastq	2041072800.0	13607152.0	GSM6735817 r1	0:120 1:30	A:601835074;C:343437646;G:389096220;T:706671485;N:32375	120	30	601835074	343437646	389096220	706671485	32375	SRX18291978	SRS15783400	SRA1542250	Junker, Max-Delbrück-Center for Molecular Medicine	Junker, Max-Delbrück-Center for Molecular Medicine	2	0.77047	0.00385	0.20012	0.00362	0.83165	0.99985	0.52587	0.275	120	30	B	T	mate2 technical by mapping diff	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Germany	2022-11-17	Multi-stage	Multi-stage	Whole Organism	All anatomical structures
69932	69932	SRR22318720	SRX18291977	SRS15783399	SRP374955	PRJNA837586	Labelling transcriptional response to dissociation using SLAMseq	GSE202880	Other	Transcriptional response to dissociation is known to cause artefacts in single cell data sets. We used 4sU to label newly made transcripts during dissociation in order to to later remove them from the data set Overall design: 10mM 4sU was added to the dissociation buffer while the samples were enzymatically dissociated for 30 min. A 4sU injected control was added to the zebrafish samples to identify high turnover genes	parent bioproject:PRJNA837863	pubmed:36573354	larvae cold dissociated rep 1	GSM6735816	tissue:whole larvae 48hpf\|cell type:whole larvae 48hpf\|genotype:WT\|treatment:30 min 4sU during dissociation\|time:48hpf	larvae cold dissociated rep 1	Demultiplexing bcl2fastq v2.19 CELseq barcodes demultiplexed using custom code https://github.com/anikaneuschulz/CELseq3 demultiplex mapping using STAR v2.7.3a aggregation of mutation information and calculation of labeling rates per gene / in bulk using custom code https://github.com/anikaneuschulz/MTglob pipeline genome build/assembly: dr11.95 processed data files format and content: Tab delimited mutation rates per gene	whole larvae 48hpf		10 anesthetized larvae were washed twice in ice cold HBSS Life Technologies GmbH #14175095 and resuspended in 200µl psychrophilic protease mix 1x Native Bacillus licheniformis Protease Creative Enzymes #NATE 0633 in HBSS 10 mM 4sU and incubated on ice for 30 min. Dissociation was aided by pipetting up and down with a 200 µl tip 25 times every 5 minutes. Enzymes were inactivated by adding 15 µl 10% BSA Sigma Aldrich; #A4503 before spinning down and resuspending the cells in TRIzol RNA was extracted using TRIzol Chloroform Isopropanol according to the manufacturer’s instructions. Iodiacetamide Treatment was carried out on extracted RNA in 50% DMSO as described in Herzog et. Al 2017 https://doi.org/10.1038/nmeth.4435. libraries for RNA seq were prepared following a CELseq protocol as published in Holler & Junker 2019 https://doi.org/10.1007/978 1 4939 9009 2 9. Sequencing adapters were switched – Insert is in read 1!		cell type:whole larvae 48hpf\|genotype:WT\|treatment:30 min 4sU during dissociation\|time:48hpf	GSM6735816	GSM6735816: larvae cold dissociated rep 1; Danio rerio; RNA Seq	GSM6735816 r1	GSM6735816	1	10 anesthetized larvae were washed twice in ice cold HBSS Life Technologies GmbH #14175095 and resuspended in 200µl psychrophilic protease mix 1x Native Bacillus licheniformis Protease Creative Enzymes #NATE 0633 in HBSS 10 mM 4sU and incubated on ice for 30 min. Dissociation was aided by pipetting up and down with a 200 µl tip 25 times every 5 minutes. Enzymes were inactivated by adding 15 µl 10% BSA Sigma Aldrich; #A4503 before spinning down and resuspending the cells in TRIzol RNA was extracted using TRIzol Chloroform Isopropanol according to the manufacturer's instructions. Iodiacetamide Treatment was carried out on extracted RNA in 50% DMSO as described in Herzog et. Al 2017 https://doi.org/10.1038/nmeth.4435. libraries for RNA seq were prepared following a CELseq protocol as published in Holler & Junker 2019 https://doi.org/10.1007/978 1 4939 9009 2 9. Sequencing adapters were switched – Insert is in read 1!		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP374955	assembly:dr11.95	l_cold_dissociated_1_R1.fastq.gz l_cold_dissociated_1_R2.fastq.gz	fastq fastq	1962457800.0	13083052.0	GSM6735816 r1	0:120 1:30	A:567899843;C:333628477;G:414722974;T:646176418;N:30088	120	30	567899843	333628477	414722974	646176418	30088	SRX18291977	SRS15783399	SRA1542250	Junker, Max-Delbrück-Center for Molecular Medicine	Junker, Max-Delbrück-Center for Molecular Medicine	2	0.77763	0.22483	0.24862	0.22308	0.84228	0.99985	0.61067	0.02236	120	30	B	T	mate2 technical by mapping diff	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Germany	2022-11-17	Multi-stage	Multi-stage	Whole Organism	All anatomical structures
69933	69933	SRR19178789	SRX15244119	SRS12977047	SRP374955	PRJNA837586	Labelling transcriptional response to dissociation using SLAMseq	GSE202880	Other	Transcriptional response to dissociation is known to cause artefacts in single cell data sets. We used 4sU to label newly made transcripts during dissociation in order to to later remove them from the data set Overall design: 10mM 4sU was added to the dissociation buffer while the samples were enzymatically dissociated for 30 min. A 4sU injected control was added to the zebrafish samples to identify high turnover genes	parent bioproject:PRJNA837863	pubmed:36573354	larvae homogenized	GSM6135030	tissue:whole larvae 48hpf\|cell type:whole larvae 48hpf\|genotype:WT\|treatment:homogenized\|age:48hpf	larvae homogenized	Demultiplexing bcl2fastq v2.19 CELseq barcodes demultiplexed using custom code https://github.com/anikaneuschulz/CELseq3 demultiplex mapping using STAR v2.7.3a aggregation of mutation information and calculation of labeling rates per gene / in bulk using custom code https://github.com/anikaneuschulz/MTglob pipeline genome build/assembly: dr11.95 processed data files format and content: Tab delimited mutation rates per gene	whole larvae 48hpf		10 larvae were anesthesized on ice and homogenized in TRIzol RNA was extracted using TRIzol Chloroform Isopropanol according to the manufacturer’s instructions. Iodiacetamide Treatment was carried out on extracted RNA in 50% DMSO as described in Herzog et. Al 2017 https://doi.org/10.1038/nmeth.4435. libraries for RNA seq were prepared following a CELseq protocol as published in Holler & Junker 2019 https://doi.org/10.1007/978 1 4939 9009 2 9. Sequencing adapters were switched – Insert is in read 1!		cell type:whole larvae 48hpf\|genotype:WT\|treatment:homogenized\|age:48hpf	GSM6135030	GSM6135030: larvae homogenized; Danio rerio; RNA Seq	GSM6135030 r1	GSM6135030	1	10 larvae were anesthesized on ice and homogenized in TRIzol RNA was extracted using TRIzol Chloroform Isopropanol according to the manufacturer's instructions. Iodiacetamide Treatment was carried out on extracted RNA in 50% DMSO as described in Herzog et. Al 2017 https://doi.org/10.1038/nmeth.4435. libraries for RNA seq were prepared following a CELseq protocol as published in Holler & Junker 2019 https://doi.org/10.1007/978 1 4939 9009 2 9. Sequencing adapters were switched – Insert is in read 1!		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP374955		l_homogenised_R1.fastq.gz l_homogenised_R2.fastq.gz	fastq fastq	2128952100.0	14193014.0	GSM6135030 r1	0:120 1:30	A:640803723;C:366701707;G:389171070;T:732243074;N:32526	120	30	640803723	366701707	389171070	732243074	32526	SRX15244119	SRS12977047	SRA1419460	Junker, Max-Delbrück-Center for Molecular Medicine	Junker, Max-Delbrück-Center for Molecular Medicine	2	0.74632	0.19814	0.18356	0.19806	0.8454	0.99975	0.49504	0.58333	120	30	B	T	mate2 technical by mapping diff	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Germany	2022-05-12	Hatching	Embryo	Whole Organism	All anatomical structures
69934	69934	SRR19178790	SRX15244118	SRS12977046	SRP374955	PRJNA837586	Labelling transcriptional response to dissociation using SLAMseq	GSE202880	Other	Transcriptional response to dissociation is known to cause artefacts in single cell data sets. We used 4sU to label newly made transcripts during dissociation in order to to later remove them from the data set Overall design: 10mM 4sU was added to the dissociation buffer while the samples were enzymatically dissociated for 30 min. A 4sU injected control was added to the zebrafish samples to identify high turnover genes	parent bioproject:PRJNA837863	pubmed:36573354	larvae injected	GSM6135029	tissue:whole larvae 48hpf\|cell type:whole larvae 48hpf\|genotype:WT\|treatment:30 min 4sU injected\|age:48hpf	larvae injected	Demultiplexing bcl2fastq v2.19 CELseq barcodes demultiplexed using custom code https://github.com/anikaneuschulz/CELseq3 demultiplex mapping using STAR v2.7.3a aggregation of mutation information and calculation of labeling rates per gene / in bulk using custom code https://github.com/anikaneuschulz/MTglob pipeline genome build/assembly: dr11.95 processed data files format and content: Tab delimited mutation rates per gene	whole larvae 48hpf		10 larvae injected with 5nl 4sU 100mM in 10 mM Tris•HCl pH 7.4 Carl Roth with Dextran fluorescein Thermo Fisher Scientific #7136 were incubated at 28°C for 30 minutes anesthesized on ice and homogenized in TRIzol RNA was extracted using TRIzol Chloroform Isopropanol according to the manufacturer’s instructions. Iodiacetamide Treatment was carried out on extracted RNA in 50% DMSO as described in Herzog et. Al 2017 https://doi.org/10.1038/nmeth.4435. libraries for RNA seq were prepared following a CELseq protocol as published in Holler & Junker 2019 https://doi.org/10.1007/978 1 4939 9009 2 9. Sequencing adapters were switched – Insert is in read 1!		cell type:whole larvae 48hpf\|genotype:WT\|treatment:30 min 4sU injected\|age:48hpf	GSM6135029	GSM6135029: larvae injected; Danio rerio; RNA Seq	GSM6135029 r1	GSM6135029	1	10 larvae injected with 5nl 4sU 100mM in 10 mM Tris•HCl pH 7.4 Carl Roth with Dextran fluorescein Thermo Fisher Scientific #7136 were incubated at 28°C for 30 minutes anesthesized on ice and homogenized in TRIzol RNA was extracted using TRIzol Chloroform Isopropanol according to the manufacturer's instructions. Iodiacetamide Treatment was carried out on extracted RNA in 50% DMSO as described in Herzog et. Al 2017 https://doi.org/10.1038/nmeth.4435. libraries for RNA seq were prepared following a CELseq protocol as published in Holler & Junker 2019 https://doi.org/10.1007/978 1 4939 9009 2 9. Sequencing adapters were switched – Insert is in read 1!		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP374955		l_injected_R1.fastq.gz l_injected_R2.fastq.gz	fastq fastq	1235050200.0	8233668.0	GSM6135029 r1	0:120 1:30	A:378943760;C:185923499;G:307183410;T:362956267;N:43264	120	30	378943760	185923499	307183410	362956267	43264	SRX15244118	SRS12977046	SRA1419460	Junker, Max-Delbrück-Center for Molecular Medicine	Junker, Max-Delbrück-Center for Molecular Medicine	2	0.65413	0.25162	0.12157	0.25153	0.8757	0.99969	0.58973	0.66666	120	30	B	T	mate2 technical by mapping diff	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Germany	2022-05-12	Hatching	Embryo	Whole Organism	All anatomical structures
69935	69935	SRR19178791	SRX15244117	SRS12977045	SRP374955	PRJNA837586	Labelling transcriptional response to dissociation using SLAMseq	GSE202880	Other	Transcriptional response to dissociation is known to cause artefacts in single cell data sets. We used 4sU to label newly made transcripts during dissociation in order to to later remove them from the data set Overall design: 10mM 4sU was added to the dissociation buffer while the samples were enzymatically dissociated for 30 min. A 4sU injected control was added to the zebrafish samples to identify high turnover genes	parent bioproject:PRJNA837863	pubmed:36573354	larvae dissociated	GSM6135028	tissue:whole larvae 48hpf\|cell type:whole larvae 48hpf\|genotype:WT\|treatment:30 min 4sU during dissociation\|age:48hpf	larvae dissociated	Demultiplexing bcl2fastq v2.19 CELseq barcodes demultiplexed using custom code https://github.com/anikaneuschulz/CELseq3 demultiplex mapping using STAR v2.7.3a aggregation of mutation information and calculation of labeling rates per gene / in bulk using custom code https://github.com/anikaneuschulz/MTglob pipeline genome build/assembly: dr11.95 processed data files format and content: Tab delimited mutation rates per gene	whole larvae 48hpf		10 anaesthetized larvae were washed twice in ice cold HBSS Life Technologies GmbH #14175095 and resuspended in 500 l TryplE Mix 1xTrypleE Life Technologies GmbH #A1217701 in HBSS 1mM EDTA pH 8 Molekula #900493 10 mM 4sU Merck Chemicals GmbH #T4509 for labelled sample and incubated at 37°C for 30 min. Enzymes were inactivated by adding 15 µl 10% BSA Sigma Aldrich; #A4503 before spinning down and resuspending the cells in TRIzol RNA was extracted using TRIzol Chloroform Isopropanol according to the manufacturer’s instructions. Iodiacetamide Treatment was carried out on extracted RNA in 50% DMSO as described in Herzog et. Al 2017 https://doi.org/10.1038/nmeth.4435. libraries for RNA seq were prepared following a CELseq protocol as published in Holler & Junker 2019 https://doi.org/10.1007/978 1 4939 9009 2 9. Sequencing adapters were switched – Insert is in read 1!		cell type:whole larvae 48hpf\|genotype:WT\|treatment:30 min 4sU during dissociation\|age:48hpf	GSM6135028	GSM6135028: larvae dissociated; Danio rerio; RNA Seq	GSM6135028 r1	GSM6135028	1	10 anaesthetized larvae were washed twice in ice cold HBSS Life Technologies GmbH #14175095 and resuspended in 500 l TryplE Mix 1xTrypleE Life Technologies GmbH #A1217701 in HBSS 1mM EDTA pH 8 Molekula #900493 10 mM 4sU Merck Chemicals GmbH #T4509 for labelled sample and incubated at 37°C for 30 min. Enzymes were inactivated by adding 15 µl 10% BSA Sigma Aldrich; #A4503 before spinning down and resuspending the cells in TRIzol RNA was extracted using TRIzol Chloroform Isopropanol according to the manufacturer's instructions. Iodiacetamide Treatment was carried out on extracted RNA in 50% DMSO as described in Herzog et. Al 2017 https://doi.org/10.1038/nmeth.4435. libraries for RNA seq were prepared following a CELseq protocol as published in Holler & Junker 2019 https://doi.org/10.1007/978 1 4939 9009 2 9. Sequencing adapters were switched – Insert is in read 1!		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP374955		l_dissociated_R1.fastq.gz l_dissociated_R2.fastq.gz	fastq fastq	4372680900.0	29151206.0	GSM6135028 r1	0:120 1:30	A:1175420304;C:813779631;G:1060557968;T:1322855814;N:67183	120	30	1175420304	813779631	1060557968	1322855814	67183	SRX15244117	SRS12977045	SRA1419460	Junker, Max-Delbrück-Center for Molecular Medicine	Junker, Max-Delbrück-Center for Molecular Medicine	2	0.76655	0.00411	0.1812	0.00398	0.85273	0.99987	0.57504	0.0909	120	30	B	T	mate2 technical by mapping diff	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	Germany	2022-05-12	Hatching	Embryo	Whole Organism	All anatomical structures

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