{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where technology = \"celseq\" and tissue_curation_coarse = \"All anatomical structures\"", "rows": [[10060, "ERR4795364", "ERX4665135", "ERS5281176", "ERP124847", "PRJEB41113", "Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma", "E-MTAB-9727", "Transcriptome Analysis", "The mesothelium forms epithelial membranes that line the bodies cavities and surround the internal organs. Mesothelia widely contribute to organ homeostasis and regeneration and their dysregulation can result in congenital anomalies of the viscera ventral wall defects and mesothelioma tumors. Nonetheless the embryonic ontogeny and developmental regulation of mesothelium formation has remained uncharted. Here we combine genetic lineage tracing in toto live imaging and single cell transcriptomics in zebrafish to track mesothelial progenitor origins from the lateral plate mesoderm LPM. Our single cell analysis uncovers a post gastrulation gene expression signature centered on hand2 that delineates distinct progenitor populations within the forming LPM. Combining gene expression analysis and imaging of transgenic reporter zebrafish embryos we chart the origin of mesothelial progenitors to the lateral most hand2 expressing LPM and confirm evolutionary conservation in mouse. Our time lapse imaging of transgenic hand2 reporter embryos captures zebrafish mesothelium formation documenting the coordinated cell movements that form pericardium and visceral and parietal peritoneum. We establish that the primordial germ cells migrate associated with the forming mesothelium as ventral migration boundary. Functionally hand2 mutants fail to close the ventral mesothelium due to perturbed migration of mesothelium progenitors. Analyzing mouse and human mesothelioma tumors hypothesized to emerge from transformed mesothelium we find de novo expression of LPM associated transcription factors and in particular of Hand2 indicating the re initiation of a developmental transcriptional program in mesothelioma. Taken together our work outlines a genetic and developmental signature of mesothelial origins centered around Hand2 contributing to our understanding of mesothelial pathologies and mesothelioma.", "ENA FIRST PUBLIC:2022 01 14|ENA LAST UPDATE:2022 01 14", null, "Protocols: Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3 without xxx glutamine and sodium pyruvate Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently they were incubated for another 5 min. Cells were filtered through a 35 \u03bcm cell strainer Falcon round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing the cells were resuspended in 1X PBS. drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al. 2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 \u03bcl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch a 4 bp random molecular barcode UMI a cell specific barcode the 5\u2032Illumina TruSeq small RNA kit adaptor and a T7 promoter provided by Single Cell Discoveries. post sorting the plates were immediately placed on ice and stored at \u221280\u00b0C. In brief ERCC Spike in RNA 0.02 \u03bcL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse transcription and second strand synthesis reagents were dispensed using the Nanodrop II GC biotech. post generation of cDNA from the original mRNA all cells from one plate were pooled and the pooled sample was amplified linearly with in vitro transcription. The amplified RNA was then reverse transcribed to cDNA using a random hexamer primers Hashimshony et al. 2016. To generate sequencing libraries RPI series index primers were used for library PCR.", "Sample 4", "E MTAB 9727:Sample 4", null, "isolate:not applicable|organism:Danio rerio|sex:mixed|age:10|developmental stage:tailbud stage|organism part:lateral plate mesoderm plate|genotype:drl:mCherry|ENA FIRST PUBLIC:2021 04 01|ENA LAST UPDATE:2021 09 01", null, null, null, null, null, null, null, null, "NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma", "E MTAB 9727:Sample 4 s", "Sample 4 s", "Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma", "Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3 without xxx glutamine and sodium pyruvate Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently they were incubated for another 5 min. Cells were filtered through a 35 \u03bcm cell strainer Falcon round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing the cells were resuspended in 1X PBS. drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al. 2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 \u03bcl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch a 4 bp random molecular barcode UMI a cell specific barcode the 5\u2032Illumina TruSeq small RNA kit adaptor and a T7 promoter provided by Single Cell Discoveries. post sorting the plates were immediately placed on ice and stored at \u221280\u00b0C. In brief ERCC Spike in RNA 0.02 \u03bcL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse transcription and second strand synthesis reagents were dispensed using the Nanodrop II GC biotech. post generation of cDNA from the original mRNA all cells from one plate were pooled and the pooled sample was amplified linearly with in vitro transcription. The amplified RNA was then reverse transcribed to cDNA using a random hexamer primers Hashimshony et al. 2016. To generate sequencing libraries RPI series index primers were used for library PCR.", "Experimental Factor: replicate:lateral plate mesoderm plate 4", "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "RANDOM", "SINGLE", "ILLUMINA", "NextSeq 500", null, "ERP124847", "NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma", "ENA FIRST PUBLIC:2022 01 14|ENA LAST UPDATE:2022 01 14", "SN4_AH2TW3BGX5_S1_R1_cat.fastq.gz", "fastq", 5410723202.0, 71707309.0, "E MTAB 9727:Sample 4", "0:75.46 1:0", "A:1330416803;C:531269504;G:734031980;T:2814959249;N:45666", 75, 0, null, null, 1330416803, 531269504, 734031980, 2814959249, 45666, "ERX4665135", "ERS5281176", "ERA3048543", "University of Zurich|European Nucleotide Archive", "University of Zurich|European Nucleotide Archive", 1, 0.33614, null, 0.21532, null, 0.99019, null, 0.41002, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Switzerland", "2021-04-01", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [10061, "ERR4795365", "ERX4665135", "ERS5281176", "ERP124847", "PRJEB41113", "Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma", "E-MTAB-9727", "Transcriptome Analysis", "The mesothelium forms epithelial membranes that line the bodies cavities and surround the internal organs. Mesothelia widely contribute to organ homeostasis and regeneration and their dysregulation can result in congenital anomalies of the viscera ventral wall defects and mesothelioma tumors. Nonetheless the embryonic ontogeny and developmental regulation of mesothelium formation has remained uncharted. Here we combine genetic lineage tracing in toto live imaging and single cell transcriptomics in zebrafish to track mesothelial progenitor origins from the lateral plate mesoderm LPM. Our single cell analysis uncovers a post gastrulation gene expression signature centered on hand2 that delineates distinct progenitor populations within the forming LPM. Combining gene expression analysis and imaging of transgenic reporter zebrafish embryos we chart the origin of mesothelial progenitors to the lateral most hand2 expressing LPM and confirm evolutionary conservation in mouse. Our time lapse imaging of transgenic hand2 reporter embryos captures zebrafish mesothelium formation documenting the coordinated cell movements that form pericardium and visceral and parietal peritoneum. We establish that the primordial germ cells migrate associated with the forming mesothelium as ventral migration boundary. Functionally hand2 mutants fail to close the ventral mesothelium due to perturbed migration of mesothelium progenitors. Analyzing mouse and human mesothelioma tumors hypothesized to emerge from transformed mesothelium we find de novo expression of LPM associated transcription factors and in particular of Hand2 indicating the re initiation of a developmental transcriptional program in mesothelioma. Taken together our work outlines a genetic and developmental signature of mesothelial origins centered around Hand2 contributing to our understanding of mesothelial pathologies and mesothelioma.", "ENA FIRST PUBLIC:2022 01 14|ENA LAST UPDATE:2022 01 14", null, "Protocols: Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3 without xxx glutamine and sodium pyruvate Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently they were incubated for another 5 min. Cells were filtered through a 35 \u03bcm cell strainer Falcon round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing the cells were resuspended in 1X PBS. drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al. 2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 \u03bcl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch a 4 bp random molecular barcode UMI a cell specific barcode the 5\u2032Illumina TruSeq small RNA kit adaptor and a T7 promoter provided by Single Cell Discoveries. post sorting the plates were immediately placed on ice and stored at \u221280\u00b0C. In brief ERCC Spike in RNA 0.02 \u03bcL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse transcription and second strand synthesis reagents were dispensed using the Nanodrop II GC biotech. post generation of cDNA from the original mRNA all cells from one plate were pooled and the pooled sample was amplified linearly with in vitro transcription. The amplified RNA was then reverse transcribed to cDNA using a random hexamer primers Hashimshony et al. 2016. To generate sequencing libraries RPI series index primers were used for library PCR.", "Sample 4", "E MTAB 9727:Sample 4", null, "isolate:not applicable|organism:Danio rerio|sex:mixed|age:10|developmental stage:tailbud stage|organism part:lateral plate mesoderm plate|genotype:drl:mCherry|ENA FIRST PUBLIC:2021 04 01|ENA LAST UPDATE:2021 09 01", null, null, null, null, null, null, null, null, "NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma", "E MTAB 9727:Sample 4 s", "Sample 4 s", "Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma", "Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3 without xxx glutamine and sodium pyruvate Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently they were incubated for another 5 min. Cells were filtered through a 35 \u03bcm cell strainer Falcon round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing the cells were resuspended in 1X PBS. drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al. 2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 \u03bcl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch a 4 bp random molecular barcode UMI a cell specific barcode the 5\u2032Illumina TruSeq small RNA kit adaptor and a T7 promoter provided by Single Cell Discoveries. post sorting the plates were immediately placed on ice and stored at \u221280\u00b0C. In brief ERCC Spike in RNA 0.02 \u03bcL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse transcription and second strand synthesis reagents were dispensed using the Nanodrop II GC biotech. post generation of cDNA from the original mRNA all cells from one plate were pooled and the pooled sample was amplified linearly with in vitro transcription. The amplified RNA was then reverse transcribed to cDNA using a random hexamer primers Hashimshony et al. 2016. To generate sequencing libraries RPI series index primers were used for library PCR.", "Experimental Factor: replicate:lateral plate mesoderm plate 4", "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "RANDOM", "SINGLE", "ILLUMINA", "NextSeq 500", null, "ERP124847", "NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma", "ENA FIRST PUBLIC:2022 01 14|ENA LAST UPDATE:2022 01 14", "SN4_AH2TW3BGX5_S1_R2_cat.fastq.gz", "fastq", 5414184547.0, 71707309.0, "E MTAB 9727:Sample 4 1", "0:0 1:75.50", "A:1582938104;C:1052565419;G:1177180395;T:1600161662;N:1338967", 0, 75, null, null, 1582938104, 1052565419, 1177180395, 1600161662, 1338967, "ERX4665135", "ERS5281176", "ERA3048543", "University of Zurich|European Nucleotide Archive", "University of Zurich|European Nucleotide Archive", 1, 0.84976, null, 0.28521, null, 0.85038, null, 0.5124, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Switzerland", "2021-04-01", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [10062, "ERR4795362", "ERX4665134", "ERS5281175", "ERP124847", "PRJEB41113", "Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma", "E-MTAB-9727", "Transcriptome Analysis", "The mesothelium forms epithelial membranes that line the bodies cavities and surround the internal organs. Mesothelia widely contribute to organ homeostasis and regeneration and their dysregulation can result in congenital anomalies of the viscera ventral wall defects and mesothelioma tumors. Nonetheless the embryonic ontogeny and developmental regulation of mesothelium formation has remained uncharted. Here we combine genetic lineage tracing in toto live imaging and single cell transcriptomics in zebrafish to track mesothelial progenitor origins from the lateral plate mesoderm LPM. Our single cell analysis uncovers a post gastrulation gene expression signature centered on hand2 that delineates distinct progenitor populations within the forming LPM. Combining gene expression analysis and imaging of transgenic reporter zebrafish embryos we chart the origin of mesothelial progenitors to the lateral most hand2 expressing LPM and confirm evolutionary conservation in mouse. Our time lapse imaging of transgenic hand2 reporter embryos captures zebrafish mesothelium formation documenting the coordinated cell movements that form pericardium and visceral and parietal peritoneum. We establish that the primordial germ cells migrate associated with the forming mesothelium as ventral migration boundary. Functionally hand2 mutants fail to close the ventral mesothelium due to perturbed migration of mesothelium progenitors. Analyzing mouse and human mesothelioma tumors hypothesized to emerge from transformed mesothelium we find de novo expression of LPM associated transcription factors and in particular of Hand2 indicating the re initiation of a developmental transcriptional program in mesothelioma. Taken together our work outlines a genetic and developmental signature of mesothelial origins centered around Hand2 contributing to our understanding of mesothelial pathologies and mesothelioma.", "ENA FIRST PUBLIC:2022 01 14|ENA LAST UPDATE:2022 01 14", null, "Protocols: Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3 without xxx glutamine and sodium pyruvate Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently they were incubated for another 5 min. Cells were filtered through a 35 \u03bcm cell strainer Falcon round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing the cells were resuspended in 1X PBS. drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al. 2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 \u03bcl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch a 4 bp random molecular barcode UMI a cell specific barcode the 5\u2032Illumina TruSeq small RNA kit adaptor and a T7 promoter provided by Single Cell Discoveries. post sorting the plates were immediately placed on ice and stored at \u221280\u00b0C. In brief ERCC Spike in RNA 0.02 \u03bcL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse transcription and second strand synthesis reagents were dispensed using the Nanodrop II GC biotech. post generation of cDNA from the original mRNA all cells from one plate were pooled and the pooled sample was amplified linearly with in vitro transcription. The amplified RNA was then reverse transcribed to cDNA using a random hexamer primers Hashimshony et al. 2016. To generate sequencing libraries RPI series index primers were used for library PCR.", "Sample 3", "E MTAB 9727:Sample 3", null, "isolate:not applicable|organism:Danio rerio|sex:mixed|age:10|developmental stage:tailbud stage|organism part:lateral plate mesoderm plate|genotype:drl:mCherry|ENA FIRST PUBLIC:2021 04 01|ENA LAST UPDATE:2021 09 01", null, null, null, null, null, null, null, null, "NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma", "E MTAB 9727:Sample 3 s", "Sample 3 s", "Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma", "Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3 without xxx glutamine and sodium pyruvate Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently they were incubated for another 5 min. Cells were filtered through a 35 \u03bcm cell strainer Falcon round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing the cells were resuspended in 1X PBS. drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al. 2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 \u03bcl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch a 4 bp random molecular barcode UMI a cell specific barcode the 5\u2032Illumina TruSeq small RNA kit adaptor and a T7 promoter provided by Single Cell Discoveries. post sorting the plates were immediately placed on ice and stored at \u221280\u00b0C. In brief ERCC Spike in RNA 0.02 \u03bcL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse transcription and second strand synthesis reagents were dispensed using the Nanodrop II GC biotech. post generation of cDNA from the original mRNA all cells from one plate were pooled and the pooled sample was amplified linearly with in vitro transcription. The amplified RNA was then reverse transcribed to cDNA using a random hexamer primers Hashimshony et al. 2016. To generate sequencing libraries RPI series index primers were used for library PCR.", "Experimental Factor: replicate:lateral plate mesoderm plate 3", "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "RANDOM", "SINGLE", "ILLUMINA", "NextSeq 500", null, "ERP124847", "NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma", "ENA FIRST PUBLIC:2022 01 14|ENA LAST UPDATE:2022 01 14", "SN3_AHY3WGBGX3_S7_R1_cat.fastq.gz", "fastq", 4823193891.0, 63965519.0, "E MTAB 9727:Sample 3", "0:75.40 1:0", "A:1323978162;C:446831209;G:581746343;T:2470114091;N:524086", 75, 0, null, null, 1323978162, 446831209, 581746343, 2470114091, 524086, "ERX4665134", "ERS5281175", "ERA3048543", "University of Zurich|European Nucleotide Archive", "University of Zurich|European Nucleotide Archive", 1, 0.36549, null, 0.19722, null, 0.95552, null, 0.4702, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Switzerland", "2021-04-01", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [10063, "ERR4795363", "ERX4665134", "ERS5281175", "ERP124847", "PRJEB41113", "Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma", "E-MTAB-9727", "Transcriptome Analysis", "The mesothelium forms epithelial membranes that line the bodies cavities and surround the internal organs. Mesothelia widely contribute to organ homeostasis and regeneration and their dysregulation can result in congenital anomalies of the viscera ventral wall defects and mesothelioma tumors. Nonetheless the embryonic ontogeny and developmental regulation of mesothelium formation has remained uncharted. Here we combine genetic lineage tracing in toto live imaging and single cell transcriptomics in zebrafish to track mesothelial progenitor origins from the lateral plate mesoderm LPM. Our single cell analysis uncovers a post gastrulation gene expression signature centered on hand2 that delineates distinct progenitor populations within the forming LPM. Combining gene expression analysis and imaging of transgenic reporter zebrafish embryos we chart the origin of mesothelial progenitors to the lateral most hand2 expressing LPM and confirm evolutionary conservation in mouse. Our time lapse imaging of transgenic hand2 reporter embryos captures zebrafish mesothelium formation documenting the coordinated cell movements that form pericardium and visceral and parietal peritoneum. We establish that the primordial germ cells migrate associated with the forming mesothelium as ventral migration boundary. Functionally hand2 mutants fail to close the ventral mesothelium due to perturbed migration of mesothelium progenitors. Analyzing mouse and human mesothelioma tumors hypothesized to emerge from transformed mesothelium we find de novo expression of LPM associated transcription factors and in particular of Hand2 indicating the re initiation of a developmental transcriptional program in mesothelioma. Taken together our work outlines a genetic and developmental signature of mesothelial origins centered around Hand2 contributing to our understanding of mesothelial pathologies and mesothelioma.", "ENA FIRST PUBLIC:2022 01 14|ENA LAST UPDATE:2022 01 14", null, "Protocols: Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3 without xxx glutamine and sodium pyruvate Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently they were incubated for another 5 min. Cells were filtered through a 35 \u03bcm cell strainer Falcon round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing the cells were resuspended in 1X PBS. drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al. 2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 \u03bcl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch a 4 bp random molecular barcode UMI a cell specific barcode the 5\u2032Illumina TruSeq small RNA kit adaptor and a T7 promoter provided by Single Cell Discoveries. post sorting the plates were immediately placed on ice and stored at \u221280\u00b0C. In brief ERCC Spike in RNA 0.02 \u03bcL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse transcription and second strand synthesis reagents were dispensed using the Nanodrop II GC biotech. post generation of cDNA from the original mRNA all cells from one plate were pooled and the pooled sample was amplified linearly with in vitro transcription. The amplified RNA was then reverse transcribed to cDNA using a random hexamer primers Hashimshony et al. 2016. To generate sequencing libraries RPI series index primers were used for library PCR.", "Sample 3", "E MTAB 9727:Sample 3", null, "isolate:not applicable|organism:Danio rerio|sex:mixed|age:10|developmental stage:tailbud stage|organism part:lateral plate mesoderm plate|genotype:drl:mCherry|ENA FIRST PUBLIC:2021 04 01|ENA LAST UPDATE:2021 09 01", null, null, null, null, null, null, null, null, "NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma", "E MTAB 9727:Sample 3 s", "Sample 3 s", "Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma", "Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3 without xxx glutamine and sodium pyruvate Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently they were incubated for another 5 min. Cells were filtered through a 35 \u03bcm cell strainer Falcon round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing the cells were resuspended in 1X PBS. drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al. 2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 \u03bcl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch a 4 bp random molecular barcode UMI a cell specific barcode the 5\u2032Illumina TruSeq small RNA kit adaptor and a T7 promoter provided by Single Cell Discoveries. post sorting the plates were immediately placed on ice and stored at \u221280\u00b0C. In brief ERCC Spike in RNA 0.02 \u03bcL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse transcription and second strand synthesis reagents were dispensed using the Nanodrop II GC biotech. post generation of cDNA from the original mRNA all cells from one plate were pooled and the pooled sample was amplified linearly with in vitro transcription. The amplified RNA was then reverse transcribed to cDNA using a random hexamer primers Hashimshony et al. 2016. To generate sequencing libraries RPI series index primers were used for library PCR.", "Experimental Factor: replicate:lateral plate mesoderm plate 3", "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "RANDOM", "SINGLE", "ILLUMINA", "NextSeq 500", null, "ERP124847", "NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma", "ENA FIRST PUBLIC:2022 01 14|ENA LAST UPDATE:2022 01 14", "SN3_AHY3WGBGX3_S7_R2_cat.fastq.gz", "fastq", 4828889391.0, 63965519.0, "E MTAB 9727:Sample 3 1", "0:0 1:75.49", "A:1434099697;C:964508763;G:893584575;T:1534727600;N:1968756", 0, 75, null, null, 1434099697, 964508763, 893584575, 1534727600, 1968756, "ERX4665134", "ERS5281175", "ERA3048543", "University of Zurich|European Nucleotide Archive", "University of Zurich|European Nucleotide Archive", 1, 0.85811, null, 0.26231, null, 0.82731, null, 0.48618, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Switzerland", "2021-04-01", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [10064, "ERR4795360", "ERX4665133", "ERS5281174", "ERP124847", "PRJEB41113", "Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma", "E-MTAB-9727", "Transcriptome Analysis", "The mesothelium forms epithelial membranes that line the bodies cavities and surround the internal organs. Mesothelia widely contribute to organ homeostasis and regeneration and their dysregulation can result in congenital anomalies of the viscera ventral wall defects and mesothelioma tumors. Nonetheless the embryonic ontogeny and developmental regulation of mesothelium formation has remained uncharted. Here we combine genetic lineage tracing in toto live imaging and single cell transcriptomics in zebrafish to track mesothelial progenitor origins from the lateral plate mesoderm LPM. Our single cell analysis uncovers a post gastrulation gene expression signature centered on hand2 that delineates distinct progenitor populations within the forming LPM. Combining gene expression analysis and imaging of transgenic reporter zebrafish embryos we chart the origin of mesothelial progenitors to the lateral most hand2 expressing LPM and confirm evolutionary conservation in mouse. Our time lapse imaging of transgenic hand2 reporter embryos captures zebrafish mesothelium formation documenting the coordinated cell movements that form pericardium and visceral and parietal peritoneum. We establish that the primordial germ cells migrate associated with the forming mesothelium as ventral migration boundary. Functionally hand2 mutants fail to close the ventral mesothelium due to perturbed migration of mesothelium progenitors. Analyzing mouse and human mesothelioma tumors hypothesized to emerge from transformed mesothelium we find de novo expression of LPM associated transcription factors and in particular of Hand2 indicating the re initiation of a developmental transcriptional program in mesothelioma. Taken together our work outlines a genetic and developmental signature of mesothelial origins centered around Hand2 contributing to our understanding of mesothelial pathologies and mesothelioma.", "ENA FIRST PUBLIC:2022 01 14|ENA LAST UPDATE:2022 01 14", null, "Protocols: Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3 without xxx glutamine and sodium pyruvate Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently they were incubated for another 5 min. Cells were filtered through a 35 \u03bcm cell strainer Falcon round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing the cells were resuspended in 1X PBS. drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al. 2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 \u03bcl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch a 4 bp random molecular barcode UMI a cell specific barcode the 5\u2032Illumina TruSeq small RNA kit adaptor and a T7 promoter provided by Single Cell Discoveries. post sorting the plates were immediately placed on ice and stored at \u221280\u00b0C. In brief ERCC Spike in RNA 0.02 \u03bcL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse transcription and second strand synthesis reagents were dispensed using the Nanodrop II GC biotech. post generation of cDNA from the original mRNA all cells from one plate were pooled and the pooled sample was amplified linearly with in vitro transcription. The amplified RNA was then reverse transcribed to cDNA using a random hexamer primers Hashimshony et al. 2016. To generate sequencing libraries RPI series index primers were used for library PCR.", "Sample 2", "E MTAB 9727:Sample 2", null, "isolate:not applicable|organism:Danio rerio|sex:mixed|age:10|developmental stage:tailbud stage|organism part:lateral plate mesoderm plate|genotype:drl:mCherry|ENA FIRST PUBLIC:2021 04 01|ENA LAST UPDATE:2021 09 01", null, null, null, null, null, null, null, null, "NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma", "E MTAB 9727:Sample 2 s", "Sample 2 s", "Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma", "Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3 without xxx glutamine and sodium pyruvate Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently they were incubated for another 5 min. Cells were filtered through a 35 \u03bcm cell strainer Falcon round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing the cells were resuspended in 1X PBS. drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al. 2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 \u03bcl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch a 4 bp random molecular barcode UMI a cell specific barcode the 5\u2032Illumina TruSeq small RNA kit adaptor and a T7 promoter provided by Single Cell Discoveries. post sorting the plates were immediately placed on ice and stored at \u221280\u00b0C. In brief ERCC Spike in RNA 0.02 \u03bcL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse transcription and second strand synthesis reagents were dispensed using the Nanodrop II GC biotech. post generation of cDNA from the original mRNA all cells from one plate were pooled and the pooled sample was amplified linearly with in vitro transcription. The amplified RNA was then reverse transcribed to cDNA using a random hexamer primers Hashimshony et al. 2016. To generate sequencing libraries RPI series index primers were used for library PCR.", "Experimental Factor: replicate:lateral plate mesoderm plate 2", "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "RANDOM", "SINGLE", "ILLUMINA", "NextSeq 500", null, "ERP124847", "NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma", "ENA FIRST PUBLIC:2022 01 14|ENA LAST UPDATE:2022 01 14", "SN2_AHY3WGBGX3_S6_R1_cat.fastq.gz", "fastq", 5598371393.0, 74235388.0, "E MTAB 9727:Sample 2", "0:75.41 1:0", "A:1526486973;C:558020193;G:717587491;T:2795646081;N:630655", 75, 0, null, null, 1526486973, 558020193, 717587491, 2795646081, 630655, "ERX4665133", "ERS5281174", "ERA3048543", "University of Zurich|European Nucleotide Archive", "University of Zurich|European Nucleotide Archive", 1, 0.28059, null, 0.19252, null, 0.96404, null, 0.4874, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Switzerland", "2021-04-01", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [10065, "ERR4795361", "ERX4665133", "ERS5281174", "ERP124847", "PRJEB41113", "Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma", "E-MTAB-9727", "Transcriptome Analysis", "The mesothelium forms epithelial membranes that line the bodies cavities and surround the internal organs. Mesothelia widely contribute to organ homeostasis and regeneration and their dysregulation can result in congenital anomalies of the viscera ventral wall defects and mesothelioma tumors. Nonetheless the embryonic ontogeny and developmental regulation of mesothelium formation has remained uncharted. Here we combine genetic lineage tracing in toto live imaging and single cell transcriptomics in zebrafish to track mesothelial progenitor origins from the lateral plate mesoderm LPM. Our single cell analysis uncovers a post gastrulation gene expression signature centered on hand2 that delineates distinct progenitor populations within the forming LPM. Combining gene expression analysis and imaging of transgenic reporter zebrafish embryos we chart the origin of mesothelial progenitors to the lateral most hand2 expressing LPM and confirm evolutionary conservation in mouse. Our time lapse imaging of transgenic hand2 reporter embryos captures zebrafish mesothelium formation documenting the coordinated cell movements that form pericardium and visceral and parietal peritoneum. We establish that the primordial germ cells migrate associated with the forming mesothelium as ventral migration boundary. Functionally hand2 mutants fail to close the ventral mesothelium due to perturbed migration of mesothelium progenitors. Analyzing mouse and human mesothelioma tumors hypothesized to emerge from transformed mesothelium we find de novo expression of LPM associated transcription factors and in particular of Hand2 indicating the re initiation of a developmental transcriptional program in mesothelioma. Taken together our work outlines a genetic and developmental signature of mesothelial origins centered around Hand2 contributing to our understanding of mesothelial pathologies and mesothelioma.", "ENA FIRST PUBLIC:2022 01 14|ENA LAST UPDATE:2022 01 14", null, "Protocols: Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3 without xxx glutamine and sodium pyruvate Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently they were incubated for another 5 min. Cells were filtered through a 35 \u03bcm cell strainer Falcon round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing the cells were resuspended in 1X PBS. drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al. 2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 \u03bcl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch a 4 bp random molecular barcode UMI a cell specific barcode the 5\u2032Illumina TruSeq small RNA kit adaptor and a T7 promoter provided by Single Cell Discoveries. post sorting the plates were immediately placed on ice and stored at \u221280\u00b0C. In brief ERCC Spike in RNA 0.02 \u03bcL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse transcription and second strand synthesis reagents were dispensed using the Nanodrop II GC biotech. post generation of cDNA from the original mRNA all cells from one plate were pooled and the pooled sample was amplified linearly with in vitro transcription. The amplified RNA was then reverse transcribed to cDNA using a random hexamer primers Hashimshony et al. 2016. To generate sequencing libraries RPI series index primers were used for library PCR.", "Sample 2", "E MTAB 9727:Sample 2", null, "isolate:not applicable|organism:Danio rerio|sex:mixed|age:10|developmental stage:tailbud stage|organism part:lateral plate mesoderm plate|genotype:drl:mCherry|ENA FIRST PUBLIC:2021 04 01|ENA LAST UPDATE:2021 09 01", null, null, null, null, null, null, null, null, "NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma", "E MTAB 9727:Sample 2 s", "Sample 2 s", "Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma", "Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3 without xxx glutamine and sodium pyruvate Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently they were incubated for another 5 min. Cells were filtered through a 35 \u03bcm cell strainer Falcon round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing the cells were resuspended in 1X PBS. drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al. 2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 \u03bcl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch a 4 bp random molecular barcode UMI a cell specific barcode the 5\u2032Illumina TruSeq small RNA kit adaptor and a T7 promoter provided by Single Cell Discoveries. post sorting the plates were immediately placed on ice and stored at \u221280\u00b0C. In brief ERCC Spike in RNA 0.02 \u03bcL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse transcription and second strand synthesis reagents were dispensed using the Nanodrop II GC biotech. post generation of cDNA from the original mRNA all cells from one plate were pooled and the pooled sample was amplified linearly with in vitro transcription. The amplified RNA was then reverse transcribed to cDNA using a random hexamer primers Hashimshony et al. 2016. To generate sequencing libraries RPI series index primers were used for library PCR.", "Experimental Factor: replicate:lateral plate mesoderm plate 2", "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "RANDOM", "SINGLE", "ILLUMINA", "NextSeq 500", null, "ERP124847", "NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma", "ENA FIRST PUBLIC:2022 01 14|ENA LAST UPDATE:2022 01 14", "SN2_AHY3WGBGX3_S6_R2_cat.fastq.gz", "fastq", 5600151371.0, 74235388.0, "E MTAB 9727:Sample 2 1", "0:0 1:75.44", "A:1850568176;C:1035622971;G:1071138281;T:1640475883;N:2346060", 0, 75, null, null, 1850568176, 1035622971, 1071138281, 1640475883, 2346060, "ERX4665133", "ERS5281174", "ERA3048543", "University of Zurich|European Nucleotide Archive", "University of Zurich|European Nucleotide Archive", 1, 0.7679, null, 0.30371, null, 0.82651, null, 0.43401, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Switzerland", "2021-04-01", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [10066, "ERR4795358", "ERX4665132", "ERS5281173", "ERP124847", "PRJEB41113", "Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma", "E-MTAB-9727", "Transcriptome Analysis", "The mesothelium forms epithelial membranes that line the bodies cavities and surround the internal organs. Mesothelia widely contribute to organ homeostasis and regeneration and their dysregulation can result in congenital anomalies of the viscera ventral wall defects and mesothelioma tumors. Nonetheless the embryonic ontogeny and developmental regulation of mesothelium formation has remained uncharted. Here we combine genetic lineage tracing in toto live imaging and single cell transcriptomics in zebrafish to track mesothelial progenitor origins from the lateral plate mesoderm LPM. Our single cell analysis uncovers a post gastrulation gene expression signature centered on hand2 that delineates distinct progenitor populations within the forming LPM. Combining gene expression analysis and imaging of transgenic reporter zebrafish embryos we chart the origin of mesothelial progenitors to the lateral most hand2 expressing LPM and confirm evolutionary conservation in mouse. Our time lapse imaging of transgenic hand2 reporter embryos captures zebrafish mesothelium formation documenting the coordinated cell movements that form pericardium and visceral and parietal peritoneum. We establish that the primordial germ cells migrate associated with the forming mesothelium as ventral migration boundary. Functionally hand2 mutants fail to close the ventral mesothelium due to perturbed migration of mesothelium progenitors. Analyzing mouse and human mesothelioma tumors hypothesized to emerge from transformed mesothelium we find de novo expression of LPM associated transcription factors and in particular of Hand2 indicating the re initiation of a developmental transcriptional program in mesothelioma. Taken together our work outlines a genetic and developmental signature of mesothelial origins centered around Hand2 contributing to our understanding of mesothelial pathologies and mesothelioma.", "ENA FIRST PUBLIC:2022 01 14|ENA LAST UPDATE:2022 01 14", null, "Protocols: Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3 without xxx glutamine and sodium pyruvate Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently they were incubated for another 5 min. Cells were filtered through a 35 \u03bcm cell strainer Falcon round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing the cells were resuspended in 1X PBS. drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al. 2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 \u03bcl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch a 4 bp random molecular barcode UMI a cell specific barcode the 5\u2032Illumina TruSeq small RNA kit adaptor and a T7 promoter provided by Single Cell Discoveries. post sorting the plates were immediately placed on ice and stored at \u221280\u00b0C. In brief ERCC Spike in RNA 0.02 \u03bcL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse transcription and second strand synthesis reagents were dispensed using the Nanodrop II GC biotech. post generation of cDNA from the original mRNA all cells from one plate were pooled and the pooled sample was amplified linearly with in vitro transcription. The amplified RNA was then reverse transcribed to cDNA using a random hexamer primers Hashimshony et al. 2016. To generate sequencing libraries RPI series index primers were used for library PCR.", "Sample 1", "E MTAB 9727:Sample 1", null, "isolate:not applicable|organism:Danio rerio|sex:mixed|age:10|developmental stage:tailbud stage|organism part:lateral plate mesoderm plate|genotype:drl:mCherry|ENA FIRST PUBLIC:2021 04 01|ENA LAST UPDATE:2021 09 01", null, null, null, null, null, null, null, null, "NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma", "E MTAB 9727:Sample 1 s", "Sample 1 s", "Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma", "Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3 without xxx glutamine and sodium pyruvate Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently they were incubated for another 5 min. Cells were filtered through a 35 \u03bcm cell strainer Falcon round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing the cells were resuspended in 1X PBS. drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al. 2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 \u03bcl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch a 4 bp random molecular barcode UMI a cell specific barcode the 5\u2032Illumina TruSeq small RNA kit adaptor and a T7 promoter provided by Single Cell Discoveries. post sorting the plates were immediately placed on ice and stored at \u221280\u00b0C. In brief ERCC Spike in RNA 0.02 \u03bcL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse transcription and second strand synthesis reagents were dispensed using the Nanodrop II GC biotech. post generation of cDNA from the original mRNA all cells from one plate were pooled and the pooled sample was amplified linearly with in vitro transcription. The amplified RNA was then reverse transcribed to cDNA using a random hexamer primers Hashimshony et al. 2016. To generate sequencing libraries RPI series index primers were used for library PCR.", "Experimental Factor: replicate:lateral plate mesoderm plate 1", "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "RANDOM", "SINGLE", "ILLUMINA", "NextSeq 500", null, "ERP124847", "NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma", "ENA FIRST PUBLIC:2022 01 14|ENA LAST UPDATE:2022 01 14", "SN1_AHY3WGBGX3_S5_R1_cat.fastq.gz", "fastq", 4996502316.0, 66258508.0, "E MTAB 9727:Sample 1", "0:75.41 1:0", "A:1330744174;C:451622042;G:591151500;T:2622422664;N:561936", 75, 0, null, null, 1330744174, 451622042, 591151500, 2622422664, 561936, "ERX4665132", "ERS5281173", "ERA3048543", "University of Zurich|European Nucleotide Archive", "University of Zurich|European Nucleotide Archive", 1, 0.29754, null, 0.17671, null, 0.9669, null, 0.45463, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Switzerland", "2021-04-01", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [10067, "ERR4795359", "ERX4665132", "ERS5281173", "ERP124847", "PRJEB41113", "Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma", "E-MTAB-9727", "Transcriptome Analysis", "The mesothelium forms epithelial membranes that line the bodies cavities and surround the internal organs. Mesothelia widely contribute to organ homeostasis and regeneration and their dysregulation can result in congenital anomalies of the viscera ventral wall defects and mesothelioma tumors. Nonetheless the embryonic ontogeny and developmental regulation of mesothelium formation has remained uncharted. Here we combine genetic lineage tracing in toto live imaging and single cell transcriptomics in zebrafish to track mesothelial progenitor origins from the lateral plate mesoderm LPM. Our single cell analysis uncovers a post gastrulation gene expression signature centered on hand2 that delineates distinct progenitor populations within the forming LPM. Combining gene expression analysis and imaging of transgenic reporter zebrafish embryos we chart the origin of mesothelial progenitors to the lateral most hand2 expressing LPM and confirm evolutionary conservation in mouse. Our time lapse imaging of transgenic hand2 reporter embryos captures zebrafish mesothelium formation documenting the coordinated cell movements that form pericardium and visceral and parietal peritoneum. We establish that the primordial germ cells migrate associated with the forming mesothelium as ventral migration boundary. Functionally hand2 mutants fail to close the ventral mesothelium due to perturbed migration of mesothelium progenitors. Analyzing mouse and human mesothelioma tumors hypothesized to emerge from transformed mesothelium we find de novo expression of LPM associated transcription factors and in particular of Hand2 indicating the re initiation of a developmental transcriptional program in mesothelioma. Taken together our work outlines a genetic and developmental signature of mesothelial origins centered around Hand2 contributing to our understanding of mesothelial pathologies and mesothelioma.", "ENA FIRST PUBLIC:2022 01 14|ENA LAST UPDATE:2022 01 14", null, "Protocols: Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3 without xxx glutamine and sodium pyruvate Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently they were incubated for another 5 min. Cells were filtered through a 35 \u03bcm cell strainer Falcon round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing the cells were resuspended in 1X PBS. drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al. 2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 \u03bcl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch a 4 bp random molecular barcode UMI a cell specific barcode the 5\u2032Illumina TruSeq small RNA kit adaptor and a T7 promoter provided by Single Cell Discoveries. post sorting the plates were immediately placed on ice and stored at \u221280\u00b0C. In brief ERCC Spike in RNA 0.02 \u03bcL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse transcription and second strand synthesis reagents were dispensed using the Nanodrop II GC biotech. post generation of cDNA from the original mRNA all cells from one plate were pooled and the pooled sample was amplified linearly with in vitro transcription. The amplified RNA was then reverse transcribed to cDNA using a random hexamer primers Hashimshony et al. 2016. To generate sequencing libraries RPI series index primers were used for library PCR.", "Sample 1", "E MTAB 9727:Sample 1", null, "isolate:not applicable|organism:Danio rerio|sex:mixed|age:10|developmental stage:tailbud stage|organism part:lateral plate mesoderm plate|genotype:drl:mCherry|ENA FIRST PUBLIC:2021 04 01|ENA LAST UPDATE:2021 09 01", null, null, null, null, null, null, null, null, "NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma", "E MTAB 9727:Sample 1 s", "Sample 1 s", "Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma", "Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3 without xxx glutamine and sodium pyruvate Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently they were incubated for another 5 min. Cells were filtered through a 35 \u03bcm cell strainer Falcon round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing the cells were resuspended in 1X PBS. drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al. 2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 \u03bcl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch a 4 bp random molecular barcode UMI a cell specific barcode the 5\u2032Illumina TruSeq small RNA kit adaptor and a T7 promoter provided by Single Cell Discoveries. post sorting the plates were immediately placed on ice and stored at \u221280\u00b0C. In brief ERCC Spike in RNA 0.02 \u03bcL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse transcription and second strand synthesis reagents were dispensed using the Nanodrop II GC biotech. post generation of cDNA from the original mRNA all cells from one plate were pooled and the pooled sample was amplified linearly with in vitro transcription. The amplified RNA was then reverse transcribed to cDNA using a random hexamer primers Hashimshony et al. 2016. To generate sequencing libraries RPI series index primers were used for library PCR.", "Experimental Factor: replicate:lateral plate mesoderm plate 1", "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "RANDOM", "SINGLE", "ILLUMINA", "NextSeq 500", null, "ERP124847", "NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma", "ENA FIRST PUBLIC:2022 01 14|ENA LAST UPDATE:2022 01 14", "SN1_AHY3WGBGX3_S5_R2_cat.fastq.gz", "fastq", 4999908389.0, 66258508.0, "E MTAB 9727:Sample 1 1", "0:0 1:75.46", "A:1591945117;C:933968124;G:986108614;T:1485824022;N:2062512", 0, 75, null, null, 1591945117, 933968124, 986108614, 1485824022, 2062512, "ERX4665132", "ERS5281173", "ERA3048543", "University of Zurich|European Nucleotide Archive", "University of Zurich|European Nucleotide Archive", 1, 0.81333, null, 0.2466, null, 0.83027, null, 0.51572, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Switzerland", "2021-04-01", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [30508, "SRR27764648", "SRX23429609", "SRS20284060", "SRP486518", "PRJNA1070582", "Gene expression profile of neighboring cells of cells with unfit Wnt morphogen gradient during cell competition", "GSE254439", "Transcriptome Analysis", "Morphogen signalling forms an activity gradient and instructs cell identities in a signalling strength dependent manner to pattern developing tissues. However developing tissues also undergo dynamic morphogenesis which may produce cells with unfit morphogen signalling and consequent noisy morphogen gradient. Here we show that a cell competition related system corrects such noisy morphogen gradients. Zebrafish imaging analyses of the Wnt/\u00df catenin signalling gradient which acts as a morphogen to establish embryonic anterior posterior patterning revealed that unfit cells with abnormal Wnt/\u00df catenin activity spontaneously appear and produce noise in the gradient. Communication between unfit and neighbouring fit cells via cadherin proteins stimulates apoptosis of the unfit cells by activating Smad signalling and reactive oxygen species production. This unfit cell elimination is required for proper Wnt/\u00df catenin gradient formation and consequent anterior posterior patterning. Because this gradient controls patterning not only in the embryo but also in adult tissues this system may support tissue robustness and disease prevention. Overall design: \u00df catCA constitutive active form of \u00df catenin expressing GFP+ cells or \u00dfcatCA unexpressing GFP cells from \u00df catCA mosaically introduced zebrafish early embryos were sorted by FACS cell sorter. Total RNAs were extracted and analyzed by RNA seq.", null, "pubmed:39546611", null, "Mosaic GFP control GFP min lot2", "GSM8042248", null, "source name:early embryonic cell|strain:AB|tissue:early embryonic cell|developmental stage:9 hpf loc name:missing|collection date:missing", "Mosaic GFP control GFP min lot2", "Sequenced reads were mapped to the GRCz10 reference genome using Bowtie2 ver. 2.3.1. UMI counts were extracted per HTSeq ver. 0.6.1 from the CEL Seq2 pipeline. Assembly: GRCz10 Supplementary files format and content: Tab delimited text file for expression data normalized by regularized logarithm.", "early embryonic cell", null, "Cells were dissolved in TRIzol reagent Invitrogen and extracted. Samples were prepared according to the CEL Seq2 protocol described in Hashimshony et al. Geneome Biology 2016. Libraries preparation was performed according to the published CEL Seq2 protocol.", null, "strain:AB|tissue:early embryonic cell|developmental stage:9 hpf", "GSM8042248", "GSM8042248: Mosaic GFP control GFP min lot2; Danio rerio; RNA Seq", "GSM8042248 r1", "GSM8042248", "1", "Cells were dissolved in TRIzol reagent Invitrogen and extracted. Samples were prepared according to the CEL Seq2 protocol described in Hashimshony et al. Geneome Biology 2016. Libraries preparation was performed according to the published CEL Seq2 protocol.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 1500", null, "SRP486518", null, null, "Mosaic_GFP_control_GFP_min_lot2.fastq.gz", "fastq", 7474464.0, 207624.0, "GSM8042248 r1", "0:36", "A:1796571;C:1274347;G:1548876;T:2854637;N:33", 36, null, null, null, 1796571, 1274347, 1548876, 2854637, 33, "SRX23429609", "SRS20284060", "SRA1793856", "Department of Homeostatic Regulation, Research Institute for Microbial Diseases, Osaka University", "Department of Homeostatic Regulation, Research Institute for Microbial Diseases, Osaka University", 1, 0.82922, null, 0.20207, null, 0.86143, null, 0.54661, null, 36, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Japan", "2024-01-29", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [30509, "SRR27764649", "SRX23429608", "SRS20284059", "SRP486518", "PRJNA1070582", "Gene expression profile of neighboring cells of cells with unfit Wnt morphogen gradient during cell competition", "GSE254439", "Transcriptome Analysis", "Morphogen signalling forms an activity gradient and instructs cell identities in a signalling strength dependent manner to pattern developing tissues. However developing tissues also undergo dynamic morphogenesis which may produce cells with unfit morphogen signalling and consequent noisy morphogen gradient. Here we show that a cell competition related system corrects such noisy morphogen gradients. Zebrafish imaging analyses of the Wnt/\u00df catenin signalling gradient which acts as a morphogen to establish embryonic anterior posterior patterning revealed that unfit cells with abnormal Wnt/\u00df catenin activity spontaneously appear and produce noise in the gradient. Communication between unfit and neighbouring fit cells via cadherin proteins stimulates apoptosis of the unfit cells by activating Smad signalling and reactive oxygen species production. This unfit cell elimination is required for proper Wnt/\u00df catenin gradient formation and consequent anterior posterior patterning. Because this gradient controls patterning not only in the embryo but also in adult tissues this system may support tissue robustness and disease prevention. Overall design: \u00df catCA constitutive active form of \u00df catenin expressing GFP+ cells or \u00dfcatCA unexpressing GFP cells from \u00df catCA mosaically introduced zebrafish early embryos were sorted by FACS cell sorter. Total RNAs were extracted and analyzed by RNA seq.", null, "pubmed:39546611", null, "Mosaic GFP control GFP min lot1", "GSM8042247", null, "source name:early embryonic cell|strain:AB|tissue:early embryonic cell|developmental stage:9 hpf loc name:missing|collection date:missing", "Mosaic GFP control GFP min lot1", "Sequenced reads were mapped to the GRCz10 reference genome using Bowtie2 ver. 2.3.1. UMI counts were extracted per HTSeq ver. 0.6.1 from the CEL Seq2 pipeline. Assembly: GRCz10 Supplementary files format and content: Tab delimited text file for expression data normalized by regularized logarithm.", "early embryonic cell", null, "Cells were dissolved in TRIzol reagent Invitrogen and extracted. Samples were prepared according to the CEL Seq2 protocol described in Hashimshony et al. Geneome Biology 2016. Libraries preparation was performed according to the published CEL Seq2 protocol.", null, "strain:AB|tissue:early embryonic cell|developmental stage:9 hpf", "GSM8042247", "GSM8042247: Mosaic GFP control GFP min lot1; Danio rerio; RNA Seq", "GSM8042247 r1", "GSM8042247", "1", "Cells were dissolved in TRIzol reagent Invitrogen and extracted. Samples were prepared according to the CEL Seq2 protocol described in Hashimshony et al. Geneome Biology 2016. Libraries preparation was performed according to the published CEL Seq2 protocol.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 1500", null, "SRP486518", null, null, "Mosaic_GFP_control_GFP_min_lot1.fastq.gz", "fastq", 8256240.0, 229340.0, "GSM8042247 r1", "0:36", "A:1947003;C:1345938;G:1692065;T:3271133;N:101", 36, null, null, null, 1947003, 1345938, 1692065, 3271133, 101, "SRX23429608", "SRS20284059", "SRA1793856", "Department of Homeostatic Regulation, Research Institute for Microbial Diseases, Osaka University", "Department of Homeostatic Regulation, Research Institute for Microbial Diseases, Osaka University", 1, 0.83305, null, 0.17754, null, 0.8619, null, 0.61474, null, 36, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Japan", "2024-01-29", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [30510, "SRR27764650", "SRX23429607", "SRS20284058", "SRP486518", "PRJNA1070582", "Gene expression profile of neighboring cells of cells with unfit Wnt morphogen gradient during cell competition", "GSE254439", "Transcriptome Analysis", "Morphogen signalling forms an activity gradient and instructs cell identities in a signalling strength dependent manner to pattern developing tissues. However developing tissues also undergo dynamic morphogenesis which may produce cells with unfit morphogen signalling and consequent noisy morphogen gradient. Here we show that a cell competition related system corrects such noisy morphogen gradients. Zebrafish imaging analyses of the Wnt/\u00df catenin signalling gradient which acts as a morphogen to establish embryonic anterior posterior patterning revealed that unfit cells with abnormal Wnt/\u00df catenin activity spontaneously appear and produce noise in the gradient. Communication between unfit and neighbouring fit cells via cadherin proteins stimulates apoptosis of the unfit cells by activating Smad signalling and reactive oxygen species production. This unfit cell elimination is required for proper Wnt/\u00df catenin gradient formation and consequent anterior posterior patterning. Because this gradient controls patterning not only in the embryo but also in adult tissues this system may support tissue robustness and disease prevention. Overall design: \u00df catCA constitutive active form of \u00df catenin expressing GFP+ cells or \u00dfcatCA unexpressing GFP cells from \u00df catCA mosaically introduced zebrafish early embryos were sorted by FACS cell sorter. Total RNAs were extracted and analyzed by RNA seq.", null, "pubmed:39546611", null, "Mosaic beta catCA GFP min lot2", "GSM8042246", null, "source name:early embryonic cell|strain:AB|tissue:early embryonic cell|developmental stage:9 hpf loc name:missing|collection date:missing", "Mosaic beta catCA GFP min lot2", "Sequenced reads were mapped to the GRCz10 reference genome using Bowtie2 ver. 2.3.1. UMI counts were extracted per HTSeq ver. 0.6.1 from the CEL Seq2 pipeline. Assembly: GRCz10 Supplementary files format and content: Tab delimited text file for expression data normalized by regularized logarithm.", "early embryonic cell", null, "Cells were dissolved in TRIzol reagent Invitrogen and extracted. Samples were prepared according to the CEL Seq2 protocol described in Hashimshony et al. Geneome Biology 2016. Libraries preparation was performed according to the published CEL Seq2 protocol.", null, "strain:AB|tissue:early embryonic cell|developmental stage:9 hpf", "GSM8042246", "GSM8042246: Mosaic beta catCA GFP min lot2; Danio rerio; RNA Seq", "GSM8042246 r1", "GSM8042246", "1", "Cells were dissolved in TRIzol reagent Invitrogen and extracted. Samples were prepared according to the CEL Seq2 protocol described in Hashimshony et al. Geneome Biology 2016. Libraries preparation was performed according to the published CEL Seq2 protocol.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 1500", null, "SRP486518", null, null, "Mosaic_beta-catCA_GFP_min_lot2.fastq.gz", "fastq", 856836.0, 23801.0, "GSM8042246 r1", "0:36", "A:217589;C:147419;G:175612;T:316201;N:15", 36, null, null, null, 217589, 147419, 175612, 316201, 15, "SRX23429607", "SRS20284058", "SRA1793856", "Department of Homeostatic Regulation, Research Institute for Microbial Diseases, Osaka University", "Department of Homeostatic Regulation, Research Institute for Microbial Diseases, Osaka University", 1, 0.82481, null, 0.28434, null, 0.95371, null, 0.61551, null, 36, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Japan", "2024-01-29", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [30511, "SRR27764651", "SRX23429606", "SRS20284057", "SRP486518", "PRJNA1070582", "Gene expression profile of neighboring cells of cells with unfit Wnt morphogen gradient during cell competition", "GSE254439", "Transcriptome Analysis", "Morphogen signalling forms an activity gradient and instructs cell identities in a signalling strength dependent manner to pattern developing tissues. However developing tissues also undergo dynamic morphogenesis which may produce cells with unfit morphogen signalling and consequent noisy morphogen gradient. Here we show that a cell competition related system corrects such noisy morphogen gradients. Zebrafish imaging analyses of the Wnt/\u00df catenin signalling gradient which acts as a morphogen to establish embryonic anterior posterior patterning revealed that unfit cells with abnormal Wnt/\u00df catenin activity spontaneously appear and produce noise in the gradient. Communication between unfit and neighbouring fit cells via cadherin proteins stimulates apoptosis of the unfit cells by activating Smad signalling and reactive oxygen species production. This unfit cell elimination is required for proper Wnt/\u00df catenin gradient formation and consequent anterior posterior patterning. Because this gradient controls patterning not only in the embryo but also in adult tissues this system may support tissue robustness and disease prevention. Overall design: \u00df catCA constitutive active form of \u00df catenin expressing GFP+ cells or \u00dfcatCA unexpressing GFP cells from \u00df catCA mosaically introduced zebrafish early embryos were sorted by FACS cell sorter. Total RNAs were extracted and analyzed by RNA seq.", null, "pubmed:39546611", null, "Mosaic beta catCA GFP min lot1", "GSM8042245", null, "source name:early embryonic cell|strain:AB|tissue:early embryonic cell|developmental stage:9 hpf loc name:missing|collection date:missing", "Mosaic beta catCA GFP min lot1", "Sequenced reads were mapped to the GRCz10 reference genome using Bowtie2 ver. 2.3.1. UMI counts were extracted per HTSeq ver. 0.6.1 from the CEL Seq2 pipeline. Assembly: GRCz10 Supplementary files format and content: Tab delimited text file for expression data normalized by regularized logarithm.", "early embryonic cell", null, "Cells were dissolved in TRIzol reagent Invitrogen and extracted. Samples were prepared according to the CEL Seq2 protocol described in Hashimshony et al. Geneome Biology 2016. Libraries preparation was performed according to the published CEL Seq2 protocol.", null, "strain:AB|tissue:early embryonic cell|developmental stage:9 hpf", "GSM8042245", "GSM8042245: Mosaic beta catCA GFP min lot1; Danio rerio; RNA Seq", "GSM8042245 r1", "GSM8042245", "1", "Cells were dissolved in TRIzol reagent Invitrogen and extracted. Samples were prepared according to the CEL Seq2 protocol described in Hashimshony et al. Geneome Biology 2016. Libraries preparation was performed according to the published CEL Seq2 protocol.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 1500", null, "SRP486518", null, null, "Mosaic_beta-catCA_GFP_min_lot1.fastq.gz", "fastq", 7181388.0, 199483.0, "GSM8042245 r1", "0:36", "A:1744919;C:1207643;G:1456829;T:2771919;N:78", 36, null, null, null, 1744919, 1207643, 1456829, 2771919, 78, "SRX23429606", "SRS20284057", "SRA1793856", "Department of Homeostatic Regulation, Research Institute for Microbial Diseases, Osaka University", "Department of Homeostatic Regulation, Research Institute for Microbial Diseases, Osaka University", 1, 0.83629, null, 0.16823, null, 0.84774, null, 0.64548, null, 36, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Japan", "2024-01-29", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38073, "SRR1531483", "SRX665263", "SRS670077", "SRP045064", "PRJNA256975", "Genome wide RNA tomography in the zebrafish embryo", "GSE59873", "Other", "Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches using for example in situ hybridization can provide spatial information about gene expression but are limited to analyzing one or a few genes at a time. Here we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage 10 somites 15 somites 18 somites and mouse forelimbs E10.5 we cryosectioned samples extracted RNA from the individual sections and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al. Cell Reports 2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.", null, "pubmed:25417113", null, "18 somites stage straightened secti1d tail to head", "GSM1448820", null, "tissue:deyolked embryo head removed|Stage:18 somites|sectioning direction:tail to head|section thickness:24 \u00b5m|embedding strategy:deyolked and straightened embryo", "18 somites stage straightened secti1d tail to head", "Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al. Cell Reports 2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections", "deyolked embryo head removed", "Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned and individual slices were transferred to Eppendorf tubes on dry ice.", "RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012", null, "Stage:18 somites|sectioning direction:tail to head|section thickness:24 \u00b5m|embedding strategy:deyolked and straightened embryo", "GSM1448820", "GSM1448820: 18 somites stage straightened secti1d tail to head; Danio rerio; RNA Seq", "GSM1448820", null, "1", "RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012", "GEO Accession:GSM1448820", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP045064", null, null, "dr_18ss_TH_R2.fastq.gz dr_18ss_TH_R1.fastq.gz", "fastq fastq", 15779230884.0, 154698342.0, "GSM1448820 r1", "0:51 1:51", "A:3451000604;C:2392800593;G:2522666152;T:7412137093;N:626442", 51, 51, null, null, 3451000604, 2392800593, 2522666152, 7412137093, 626442, "SRX665263", "SRS670077", "SRA177126", "GEO", "Hubrecht Institute", 2, 0.11555, 0.70031, 0.08647, 0.12212, 0.98238, 0.78946, 0.48905, 0.5514, 51, 51, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2014-07-29", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38074, "SRR1531482", "SRX665262", "SRS670076", "SRP045064", "PRJNA256975", "Genome wide RNA tomography in the zebrafish embryo", "GSE59873", "Other", "Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches using for example in situ hybridization can provide spatial information about gene expression but are limited to analyzing one or a few genes at a time. Here we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage 10 somites 15 somites 18 somites and mouse forelimbs E10.5 we cryosectioned samples extracted RNA from the individual sections and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al. Cell Reports 2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.", null, "pubmed:25417113", null, "15 somites stage straightened secti1d tail to head replicate", "GSM1448819", null, "tissue:deyolked embryo|Stage:15 somites|sectioning direction:tail to head|section thickness:18 \u00b5m|embedding strategy:deyolked and straightened embryo", "15 somites stage straightened secti1d tail to head replicate", "Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al. Cell Reports 2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections", "deyolked embryo", "Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned and individual slices were transferred to Eppendorf tubes on dry ice.", "RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012", null, "Stage:15 somites|sectioning direction:tail to head|section thickness:18 \u00b5m|embedding strategy:deyolked and straightened embryo", "GSM1448819", "GSM1448819: 15 somites stage straightened secti1d tail to head replicate; Danio rerio; RNA Seq", "GSM1448819", null, "1", "RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012", "GEO Accession:GSM1448819", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP045064", null, null, "dr_15ss_TH2_R2.fastq.gz dr_15ss_TH2_R1.fastq.gz", "fastq fastq", 4502603442.0, 44143171.0, "GSM1448819 r1", "0:51 1:51", "A:1010801791;C:688133305;G:712006267;T:2047960758;N:43701321", 51, 51, null, null, 1010801791, 688133305, 712006267, 2047960758, 43701321, "SRX665262", "SRS670076", "SRA177126", "GEO", "Hubrecht Institute", 2, 0.0903, 0.78618, 0.08054, 0.12953, 0.98703, 0.78046, 0.53574, 0.52775, 51, 51, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2014-07-29", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38075, "SRR1531481", "SRX665261", "SRS670075", "SRP045064", "PRJNA256975", "Genome wide RNA tomography in the zebrafish embryo", "GSE59873", "Other", "Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches using for example in situ hybridization can provide spatial information about gene expression but are limited to analyzing one or a few genes at a time. Here we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage 10 somites 15 somites 18 somites and mouse forelimbs E10.5 we cryosectioned samples extracted RNA from the individual sections and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al. Cell Reports 2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.", null, "pubmed:25417113", null, "sections 97 108 for samples dr 15ss TH and dr 15ss HT", "GSM1448818", null, "tissue:deyolked embryo|Stage:15 somites|sectioning direction:head to tail and tail to head|section thickness:18 \u00b5m|embedding strategy:deyolked and straightened embryo", "sections 97 108 for samples dr 15ss TH and dr 15ss HT", "Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al. Cell Reports 2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections", "deyolked embryo", "Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned and individual slices were transferred to Eppendorf tubes on dry ice.", "RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. 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Cell Reports 2012", "GEO Accession:GSM1448818", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP045064", null, null, "dr_15ss_TH97-108_HT97-108_R2.fastq.gz dr_15ss_TH97-108_HT97-108_R1.fastq.gz", "fastq fastq", 472071606.0, 4628153.0, "GSM1448818 r1", "0:51 1:51", "A:108013079;C:76852222;G:73612321;T:208300498;N:5293486", 51, 51, null, null, 108013079, 76852222, 73612321, 208300498, 5293486, "SRX665261", "SRS670075", "SRA177126", "GEO", "Hubrecht Institute", 2, 0.06997, 0.71056, 0.06103, 0.12966, 0.9865, 0.79446, 0.53118, 0.53673, 51, 51, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2014-07-29", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38076, "SRR1531480", "SRX665260", "SRS670074", "SRP045064", "PRJNA256975", "Genome wide RNA tomography in the zebrafish embryo", "GSE59873", "Other", "Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches using for example in situ hybridization can provide spatial information about gene expression but are limited to analyzing one or a few genes at a time. Here we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage 10 somites 15 somites 18 somites and mouse forelimbs E10.5 we cryosectioned samples extracted RNA from the individual sections and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al. Cell Reports 2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.", null, "pubmed:25417113", null, "15 somites stage straightened secti1d tail to head", "GSM1448817", null, "tissue:deyolked embryo|Stage:15 somites|sectioning direction:tail to head|section thickness:18 \u00b5m|embedding strategy:deyolked and straightened embryo", "15 somites stage straightened secti1d tail to head", "Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al. Cell Reports 2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections", "deyolked embryo", "Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned and individual slices were transferred to Eppendorf tubes on dry ice.", "RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012", null, "Stage:15 somites|sectioning direction:tail to head|section thickness:18 \u00b5m|embedding strategy:deyolked and straightened embryo", "GSM1448817", "GSM1448817: 15 somites stage straightened secti1d tail to head; Danio rerio; RNA Seq", "GSM1448817", null, "1", "RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012", "GEO Accession:GSM1448817", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP045064", null, null, "dr_15ss_TH_R1.fastq.gz dr_15ss_TH_R2.fastq.gz", "fastq fastq", 3381229314.0, 33149307.0, "GSM1448817 r1", "0:51 1:51", "A:806003850;C:517726785;G:527487361;T:1491678004;N:38333314", 51, 51, null, null, 806003850, 517726785, 527487361, 1491678004, 38333314, "SRX665260", "SRS670074", "SRA177126", "GEO", "Hubrecht Institute", 2, 0.06812, 0.69273, 0.05849, 0.1511, 0.98502, 0.7834, 0.47808, 0.53868, 51, 51, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2014-07-29", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38077, "SRR1531479", "SRX665259", "SRS670073", "SRP045064", "PRJNA256975", "Genome wide RNA tomography in the zebrafish embryo", "GSE59873", "Other", "Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches using for example in situ hybridization can provide spatial information about gene expression but are limited to analyzing one or a few genes at a time. Here we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage 10 somites 15 somites 18 somites and mouse forelimbs E10.5 we cryosectioned samples extracted RNA from the individual sections and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al. Cell Reports 2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.", null, "pubmed:25417113", null, "15 somites stage straightened secti1d head to tail", "GSM1448816", null, "tissue:deyolked embryo|Stage:15 somites|sectioning direction:head to tail|section thickness:18 \u00b5m|embedding strategy:deyolked and straightened embryo", "15 somites stage straightened secti1d head to tail", "Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al. Cell Reports 2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections", "deyolked embryo", "Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned and individual slices were transferred to Eppendorf tubes on dry ice.", "RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012", null, "Stage:15 somites|sectioning direction:head to tail|section thickness:18 \u00b5m|embedding strategy:deyolked and straightened embryo", "GSM1448816", "GSM1448816: 15 somites stage straightened secti1d head to tail; Danio rerio; RNA Seq", "GSM1448816", null, "1", "RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012", "GEO Accession:GSM1448816", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP045064", null, null, "dr_15ss_HT_R1.fastq.gz dr_15ss_HT_R2.fastq.gz", "fastq fastq", 3476174076.0, 34080138.0, "GSM1448816 r1", "0:51 1:51", "A:800519794;C:540890287;G:554165272;T:1542680760;N:37917963", 51, 51, null, null, 800519794, 540890287, 554165272, 1542680760, 37917963, "SRX665259", "SRS670073", "SRA177126", "GEO", "Hubrecht Institute", 2, 0.06769, 0.70036, 0.05945, 0.13184, 0.98849, 0.79026, 0.50058, 0.57003, 51, 51, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2014-07-29", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [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.", null, "pubmed:25417113", null, "15 somite stage secti1d from right to left", "GSM1448815", null, "tissue:whole embryo|Stage:15 somites|sectioning direction:right left|section thickness:18 \u00b5m|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", null, "Stage:15 somites|sectioning direction:right left|section thickness:18 \u00b5m|embedding strategy:intact embryo", "GSM1448815", "GSM1448815: 15 somite stage secti1d from right to left; Danio rerio; RNA Seq", "GSM1448815", null, "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", null, "SRP045064", null, null, "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, null, null, 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", null, "Netherlands", "2014-07-29", "Segmentation", "Embryo", "Whole Organism", "All anatomical structures"], [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.", null, "pubmed:25417113", null, "15 somite stage secti1d from right to left", "GSM1448815", null, "tissue:whole embryo|Stage:15 somites|sectioning direction:right left|section thickness:18 \u00b5m|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", null, "Stage:15 somites|sectioning direction:right left|section thickness:18 \u00b5m|embedding strategy:intact embryo", "GSM1448815", "GSM1448815: 15 somite stage secti1d from right to left; Danio rerio; RNA Seq", "GSM1448815", null, "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", null, "SRP045064", null, "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, null, null, 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", null, "Netherlands", "2014-07-29", "Segmentation", "Embryo", "Whole Organism", "All anatomical structures"], [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.", null, "pubmed:25417113", null, "15 somite stage secti1d from left to right", "GSM1448814", null, "tissue:whole embryo|Stage:15 somites|sectioning direction:left right|section thickness:18 \u00b5m|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", null, "Stage:15 somites|sectioning direction:left right|section thickness:18 \u00b5m|embedding strategy:intact embryo", "GSM1448814", "GSM1448814: 15 somite stage secti1d from left to right; Danio rerio; RNA Seq", "GSM1448814", null, "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", null, "SRP045064", null, null, "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, null, null, 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", null, "Netherlands", "2014-07-29", "Segmentation", "Embryo", "Whole Organism", "All anatomical structures"], [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.", null, "pubmed:25417113", null, "15 somite stage secti1d from left to right", "GSM1448814", null, "tissue:whole embryo|Stage:15 somites|sectioning direction:left right|section thickness:18 \u00b5m|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", null, "Stage:15 somites|sectioning direction:left right|section thickness:18 \u00b5m|embedding strategy:intact embryo", "GSM1448814", "GSM1448814: 15 somite stage secti1d from left to right; Danio rerio; RNA Seq", "GSM1448814", null, "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", null, "SRP045064", null, "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, null, null, 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", null, "Netherlands", "2014-07-29", "Segmentation", "Embryo", "Whole Organism", "All anatomical structures"], [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.", null, "pubmed:25417113", null, "15 somite stage secti1d from dorsal to ventral end", "GSM1448813", null, "tissue:whole embryo|Stage:15 somites|sectioning direction:dorsal ventral|section thickness:18 \u00b5m|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", null, "Stage:15 somites|sectioning direction:dorsal ventral|section thickness:18 \u00b5m|embedding strategy:intact embryo", "GSM1448813", "GSM1448813: 15 somite stage secti1d from dorsal to ventral end; Danio rerio; RNA Seq", "GSM1448813", null, "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", null, "SRP045064", null, null, "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, null, null, 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", null, "Netherlands", "2014-07-29", "Segmentation", "Embryo", "Whole Organism", "All anatomical structures"], [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.", null, "pubmed:25417113", null, "15 somite stage secti1d from dorsal to ventral end", "GSM1448813", null, "tissue:whole embryo|Stage:15 somites|sectioning direction:dorsal ventral|section thickness:18 \u00b5m|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", null, "Stage:15 somites|sectioning direction:dorsal ventral|section thickness:18 \u00b5m|embedding strategy:intact embryo", "GSM1448813", "GSM1448813: 15 somite stage secti1d from dorsal to ventral end; Danio rerio; RNA Seq", "GSM1448813", null, "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", null, "SRP045064", null, "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, null, null, 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", null, "Netherlands", "2014-07-29", "Segmentation", "Embryo", "Whole Organism", "All anatomical structures"], [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.", null, "pubmed:25417113", null, "15 somite stage secti1d from ventral to dorsal end", "GSM1448812", null, "tissue:whole embryo|Stage:15 somites|sectioning direction:ventral dorsal|section thickness:18 \u00b5m|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", null, "Stage:15 somites|sectioning direction:ventral dorsal|section thickness:18 \u00b5m|embedding strategy:intact embryo", "GSM1448812", "GSM1448812: 15 somite stage secti1d from ventral to dorsal end; Danio rerio; RNA Seq", "GSM1448812", null, "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", null, "SRP045064", null, null, "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, null, null, 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", null, "Netherlands", "2014-07-29", "Segmentation", "Embryo", "Whole Organism", "All anatomical structures"], [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.", null, "pubmed:25417113", null, "15 somite stage secti1d from ventral to dorsal end", "GSM1448812", null, "tissue:whole embryo|Stage:15 somites|sectioning direction:ventral dorsal|section thickness:18 \u00b5m|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", null, "Stage:15 somites|sectioning direction:ventral dorsal|section thickness:18 \u00b5m|embedding strategy:intact embryo", "GSM1448812", "GSM1448812: 15 somite stage secti1d from ventral to dorsal end; Danio rerio; RNA Seq", "GSM1448812", null, "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", null, "SRP045064", null, "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, null, null, 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", null, "Netherlands", "2014-07-29", "Segmentation", "Embryo", "Whole Organism", "All anatomical structures"], [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.", null, "pubmed:25417113", null, "15 somite stage secti1d from posterior to anterior end", "GSM1448811", null, "tissue:whole embryo|Stage:15 somites|sectioning direction:posterior anterior|section thickness:18 \u00b5m|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", null, "Stage:15 somites|sectioning direction:posterior anterior|section thickness:18 \u00b5m|embedding strategy:intact embryo", "GSM1448811", "GSM1448811: 15 somite stage secti1d from posterior to anterior end; Danio rerio; RNA Seq", "GSM1448811", null, "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", null, "SRP045064", null, null, "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, null, null, 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", null, "Netherlands", "2014-07-29", "Segmentation", "Embryo", "Whole Organism", "All anatomical structures"], [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.", null, "pubmed:25417113", null, "15 somite stage secti1d from anterior to posterior end", "GSM1448810", null, "tissue:whole embryo|Stage:15 somites|sectioning direction:anterior posterior|section thickness:18 \u00b5m|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", null, "Stage:15 somites|sectioning direction:anterior posterior|section thickness:18 \u00b5m|embedding strategy:intact embryo", "GSM1448810", "GSM1448810: 15 somite stage secti1d from anterior to posterior end; Danio rerio; RNA Seq", "GSM1448810", null, "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", null, "SRP045064", null, null, "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, null, null, 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", null, "Netherlands", "2014-07-29", "Segmentation", "Embryo", "Whole Organism", "All anatomical structures"], [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.", null, "pubmed:25417113", null, "10 somite stage secti1d from right to left", "GSM1448809", null, "tissue:whole embryo|Stage:10 somites|sectioning direction:right left|section thickness:18 \u00b5m|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. 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Cell Reports 2012", "GEO Accession:GSM1448809", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP045064", null, null, "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, null, null, 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", null, "Netherlands", "2014-07-29", "Segmentation", "Embryo", "Whole Organism", "All anatomical structures"], [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.", null, "pubmed:25417113", null, "10 somite stage secti1d from left to right", "GSM1448808", null, "tissue:whole embryo|Stage:10 somites|sectioning direction:left right|section thickness:18 \u00b5m|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. 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Cell Reports 2012", "GEO Accession:GSM1448808", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP045064", null, null, "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, null, null, 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", null, "Netherlands", "2014-07-29", "Segmentation", "Embryo", "Whole Organism", "All anatomical structures"], [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.", null, "pubmed:25417113", null, "10 somite stage secti1d from dorsal to ventral end", "GSM1448807", null, "tissue:whole embryo|Stage:10 somites|sectioning direction:dorsal ventral|section thickness:18 \u00b5m|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. 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Cell Reports 2012", "GEO Accession:GSM1448807", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP045064", null, null, "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, null, null, 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", null, "Netherlands", "2014-07-29", "Segmentation", "Embryo", "Whole Organism", "All anatomical structures"], [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.", null, "pubmed:25417113", null, "10 somite stage secti1d from dorsal to ventral end", "GSM1448807", null, "tissue:whole embryo|Stage:10 somites|sectioning direction:dorsal ventral|section thickness:18 \u00b5m|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", null, "Stage:10 somites|sectioning direction:dorsal ventral|section thickness:18 \u00b5m|embedding strategy:intact embryo", "GSM1448807", "GSM1448807: 10 somite stage secti1d from dorsal to ventral end; Danio rerio; RNA Seq", "GSM1448807", null, "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", null, "SRP045064", null, "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, null, null, 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", null, "Netherlands", "2014-07-29", "Segmentation", "Embryo", "Whole Organism", "All anatomical structures"], [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.", null, "pubmed:25417113", null, "10 somite stage secti1d from ventral to dorsal end", "GSM1448806", null, "tissue:whole embryo|Stage:10 somites|sectioning direction:ventral dorsal|section thickness:18 \u00b5m|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. 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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.", null, "pubmed:25417113", null, "10 somite stage secti1d from ventral to dorsal end", "GSM1448806", null, "tissue:whole embryo|Stage:10 somites|sectioning direction:ventral dorsal|section thickness:18 \u00b5m|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. 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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.", null, "pubmed:25417113", null, "10 somite stage secti1d from posterior to anterior end", "GSM1448805", null, "tissue:whole embryo|Stage:10 somites|sectioning direction:anterior posterior|section thickness:18 \u00b5m|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", null, "Stage:10 somites|sectioning direction:anterior posterior|section thickness:18 \u00b5m|embedding strategy:intact embryo", "GSM1448805", "GSM1448805: 10 somite stage secti1d from posterior to anterior end; Danio rerio; RNA Seq", "GSM1448805", null, "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", null, "SRP045064", null, null, "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, null, null, 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", null, "Netherlands", "2014-07-29", "Segmentation", "Embryo", "Whole Organism", "All anatomical structures"], [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.", null, "pubmed:25417113", null, "10 somite stage secti1d from posterior to anterior end", "GSM1448805", null, "tissue:whole embryo|Stage:10 somites|sectioning direction:anterior posterior|section thickness:18 \u00b5m|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. 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Cell Reports 2012", "GEO Accession:GSM1448805", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP045064", null, "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, null, null, 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", null, "Netherlands", "2014-07-29", "Segmentation", "Embryo", "Whole Organism", "All anatomical structures"], [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.", null, "pubmed:25417113", null, "10 somite stage secti1d from anterior to posterior end replicate", "GSM1448804", null, "tissue:whole embryo|Stage:10 somites|sectioning direction:anterior posterior|section thickness:18 \u00b5m|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", null, "Stage:10 somites|sectioning direction:anterior posterior|section thickness:18 \u00b5m|embedding strategy:intact embryo", "GSM1448804", "GSM1448804: 10 somite stage secti1d from anterior to posterior end replicate; Danio rerio; RNA Seq", "GSM1448804", null, "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", null, "SRP045064", null, null, "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, null, null, 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", null, "Netherlands", "2014-07-29", "Segmentation", "Embryo", "Whole Organism", "All anatomical structures"], [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.", null, "pubmed:25417113", null, "10 somite stage secti1d from anterior to posterior end", "GSM1448803", null, "tissue:whole embryo|Stage:10 somites|sectioning direction:anterior posterior|section thickness:18 \u00b5m|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", null, "Stage:10 somites|sectioning direction:anterior posterior|section thickness:18 \u00b5m|embedding strategy:intact embryo", "GSM1448803", "GSM1448803: 10 somite stage secti1d from anterior to posterior end; Danio rerio; RNA Seq", "GSM1448803", null, "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", null, "SRP045064", null, null, "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, null, null, 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", null, "Netherlands", "2014-07-29", "Segmentation", "Embryo", "Whole Organism", "All anatomical structures"], [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.", null, "pubmed:25417113", null, "10 somite stage secti1d from anterior to posterior end", "GSM1448803", null, "tissue:whole embryo|Stage:10 somites|sectioning direction:anterior posterior|section thickness:18 \u00b5m|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", null, "Stage:10 somites|sectioning direction:anterior posterior|section thickness:18 \u00b5m|embedding strategy:intact embryo", "GSM1448803", "GSM1448803: 10 somite stage secti1d from anterior to posterior end; Danio rerio; RNA Seq", "GSM1448803", null, "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", null, "SRP045064", null, "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, null, null, 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", null, "Netherlands", "2014-07-29", "Segmentation", "Embryo", "Whole Organism", "All anatomical structures"], [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.", null, "pubmed:25417113", null, "shield stage secti1d from dorsal to ventral end replicate", "GSM1448802", null, "tissue:whole embryo|Stage:shield stage|sectioning direction:dorsal ventral|section thickness:18 \u00b5m|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", null, "Stage:shield stage|sectioning direction:dorsal ventral|section thickness:18 \u00b5m|embedding strategy:intact embryo", "GSM1448802", "GSM1448802: shield stage secti1d from dorsal to ventral end replicate; Danio rerio; RNA Seq", "GSM1448802", null, "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", null, "SRP045064", null, null, "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, null, null, 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", null, "Netherlands", "2014-07-29", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [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.", null, "pubmed:25417113", null, "shield stage secti1d from dorsal to ventral end", "GSM1448801", null, "tissue:whole embryo|Stage:shield stage|sectioning direction:dorsal ventral|section thickness:18 \u00b5m|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. 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Cell Reports 2012", "GEO Accession:GSM1448801", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP045064", null, null, "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, null, null, 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", null, "Netherlands", "2014-07-29", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [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.", null, "pubmed:25417113", null, "shield stage secti1d from dorsal to ventral end", "GSM1448801", null, "tissue:whole embryo|Stage:shield stage|sectioning direction:dorsal ventral|section thickness:18 \u00b5m|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. 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Cell Reports 2012", "GEO Accession:GSM1448801", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP045064", null, "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, null, null, 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", null, "Netherlands", "2014-07-29", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [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.", null, "pubmed:25417113", null, "shield stage secti1d from ventral to dorsal end", "GSM1448800", null, "tissue:whole embryo|Stage:shield stage|sectioning direction:ventral dorsal|section thickness:18 \u00b5m|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. 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Cell Reports 2012", "GEO Accession:GSM1448800", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP045064", null, null, "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, null, null, 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", null, "Netherlands", "2014-07-29", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [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.", null, "pubmed:25417113", null, "shield stage secti1d from ventral to dorsal end", "GSM1448800", null, "tissue:whole embryo|Stage:shield stage|sectioning direction:ventral dorsal|section thickness:18 \u00b5m|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. 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Cell Reports 2012", "GEO Accession:GSM1448800", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP045064", null, "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", null, null, null, null, null, null, null, null, null, null, null, "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", null, "Netherlands", "2014-07-29", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [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.", null, "pubmed:25417113", null, "shield stage secti1d from right to left", "GSM1448799", null, "tissue:whole embryo|Stage:shield stage|sectioning direction:right left|section thickness:18 \u00b5m|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. 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Cell Reports 2012", "GEO Accession:GSM1448799", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP045064", null, null, "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, null, null, 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", null, "Netherlands", "2014-07-29", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [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.", null, "pubmed:25417113", null, "shield stage secti1d from right to left", "GSM1448799", null, "tissue:whole embryo|Stage:shield stage|sectioning direction:right left|section thickness:18 \u00b5m|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. 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Cell Reports 2012", "GEO Accession:GSM1448799", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP045064", null, "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, null, null, 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", null, "Netherlands", "2014-07-29", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [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.", null, "pubmed:25417113", null, "shield stage secti1d from left to right", "GSM1448798", null, "tissue:whole embryo|Stage:shield stage|sectioning direction:left right|section thickness:18 \u00b5m|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. 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Cell Reports 2012", "GEO Accession:GSM1448798", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP045064", null, null, "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, null, null, 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", null, "Netherlands", "2014-07-29", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [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.", null, "pubmed:25417113", null, "shield stage secti1d from left to right", "GSM1448798", null, "tissue:whole embryo|Stage:shield stage|sectioning direction:left right|section thickness:18 \u00b5m|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", null, "Stage:shield stage|sectioning direction:left right|section thickness:18 \u00b5m|embedding strategy:intact embryo", "GSM1448798", "GSM1448798: shield stage secti1d from left to right; Danio rerio; RNA Seq", "GSM1448798", null, "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", null, "SRP045064", null, "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, null, null, 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", null, "Netherlands", "2014-07-29", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [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.", null, "pubmed:25417113", null, "shield stage secti1d from vegetal to animal pole replicate", "GSM1448797", null, "tissue:whole embryo|Stage:shield stage|sectioning direction:vegetal animal|section thickness:18 \u00b5m|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", null, "Stage:shield stage|sectioning direction:vegetal animal|section thickness:18 \u00b5m|embedding strategy:intact embryo", "GSM1448797", "GSM1448797: shield stage secti1d from vegetal to animal pole replicate; Danio rerio; RNA Seq", "GSM1448797", null, "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", null, "SRP045064", null, null, "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, null, null, 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", null, "Netherlands", "2014-07-29", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [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.", null, "pubmed:25417113", null, "shield stage secti1d from vegetal to animal pole", "GSM1448796", null, "tissue:whole embryo|Stage:shield stage|sectioning direction:vegetal animal|section thickness:18 \u00b5m|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", null, "Stage:shield stage|sectioning direction:vegetal animal|section thickness:18 \u00b5m|embedding strategy:intact embryo", "GSM1448796", "GSM1448796: shield stage secti1d from vegetal to animal pole; Danio rerio; RNA Seq", "GSM1448796", null, "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", null, "SRP045064", null, null, "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, null, null, 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", null, "Netherlands", "2014-07-29", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [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.", null, "pubmed:25417113", null, "shield stage secti1d from vegetal to animal pole", "GSM1448796", null, "tissue:whole embryo|Stage:shield stage|sectioning direction:vegetal animal|section thickness:18 \u00b5m|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", null, "Stage:shield stage|sectioning direction:vegetal animal|section thickness:18 \u00b5m|embedding strategy:intact embryo", "GSM1448796", "GSM1448796: shield stage secti1d from vegetal to animal pole; Danio rerio; RNA Seq", "GSM1448796", null, "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", null, "SRP045064", null, "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, null, null, 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", null, "Netherlands", "2014-07-29", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [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.", null, "pubmed:25417113", null, "shield stage secti1d from animal to vegetal pole", "GSM1448795", null, "tissue:whole embryo|Stage:shield stage|sectioning direction:animal vegetal|section thickness:18 \u00b5m|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", null, "Stage:shield stage|sectioning direction:animal vegetal|section thickness:18 \u00b5m|embedding strategy:intact embryo", "GSM1448795", "GSM1448795: shield stage secti1d from animal to vegetal pole; Danio rerio; RNA Seq", "GSM1448795", null, "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", null, "SRP045064", null, null, "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, null, null, 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", null, "Netherlands", "2014-07-29", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [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.", null, "pubmed:25417113", null, "shield stage secti1d from animal to vegetal pole", "GSM1448795", null, "tissue:whole embryo|Stage:shield stage|sectioning direction:animal vegetal|section thickness:18 \u00b5m|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", null, "Stage:shield stage|sectioning direction:animal vegetal|section thickness:18 \u00b5m|embedding strategy:intact embryo", "GSM1448795", "GSM1448795: shield stage secti1d from animal to vegetal pole; Danio rerio; RNA Seq", "GSM1448795", null, "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", null, "SRP045064", null, "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, null, null, 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", null, "Netherlands", "2014-07-29", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [38122, "SRR1555598", "SRX684706", "SRS687823", "SRP045679", "PRJNA258656", "Danio rerio high resolution developmental transcriptomic time course", "GSE60619", "Transcriptome Analysis", "Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This \u201cphylotypic stage\u201d has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a \u2018zootypic\u2019 stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples", "parent bioproject:PRJNA287810", "pubmed:26886793", null, "Metazome ZF timecourse sample 0106", "GSM1483841", null, "tissue:single embryo", "Metazome ZF timecourse sample 0106", "Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix", "single embryo", null, "RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.", "zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.", "time min post fertilization:4240", "GSM1483841", "GSM1483841: Metazome ZF timecourse sample 0106; Danio rerio; RNA Seq", "GSM1483841", null, "1", "RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.", "GEO Accession:GSM1483841", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP045679", null, null, "Metazome_ZF_timecourse_sample_0106.fastq.gz", "fastq", 3911705.0, 111763.0, "GSM1483841 r1", "0:35", "A:1100064;C:790487;G:836206;T:1169251;N:15697", 35, null, null, null, 1100064, 790487, 836206, 1169251, 15697, "SRX684706", "SRS687823", "SRA179995", "GEO", "Yanai, Biology, Technion - Israel Institute of Technology", 1, 0.72414, null, 0.09461, null, 0.96725, null, 0.4942, null, 35, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Israel", "2014-08-21", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38123, "SRR1555597", "SRX684705", "SRS687821", "SRP045679", "PRJNA258656", "Danio rerio high resolution developmental transcriptomic time course", "GSE60619", "Transcriptome Analysis", "Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This \u201cphylotypic stage\u201d has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a \u2018zootypic\u2019 stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples", "parent bioproject:PRJNA287810", "pubmed:26886793", null, "Metazome ZF timecourse sample 0105", "GSM1483840", null, "tissue:single embryo", "Metazome ZF timecourse sample 0105", "Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix", "single embryo", null, "RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.", "zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.", "time min post fertilization:4200", "GSM1483840", "GSM1483840: Metazome ZF timecourse sample 0105; Danio rerio; RNA Seq", "GSM1483840", null, "1", "RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.", "GEO Accession:GSM1483840", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP045679", null, null, "Metazome_ZF_timecourse_sample_0105.fastq.gz", "fastq", 32877145.0, 939347.0, "GSM1483840 r1", "0:35", "A:9524894;C:6625944;G:6696548;T:9953576;N:76183", 35, null, null, null, 9524894, 6625944, 6696548, 9953576, 76183, "SRX684705", "SRS687821", "SRA179995", "GEO", "Yanai, Biology, Technion - Israel Institute of Technology", 1, 0.74436, null, 0.07095, null, 0.88201, null, 0.47612, null, 35, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Israel", "2014-08-21", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38124, "SRR1555596", "SRX684704", "SRS687822", "SRP045679", "PRJNA258656", "Danio rerio high resolution developmental transcriptomic time course", "GSE60619", "Transcriptome Analysis", "Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This \u201cphylotypic stage\u201d has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a \u2018zootypic\u2019 stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples", "parent bioproject:PRJNA287810", "pubmed:26886793", null, "Metazome ZF timecourse sample 0104", "GSM1483839", null, "tissue:single embryo", "Metazome ZF timecourse sample 0104", "Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix", "single embryo", null, "RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.", "zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.", "time min post fertilization:4160", "GSM1483839", "GSM1483839: Metazome ZF timecourse sample 0104; Danio rerio; RNA Seq", "GSM1483839", null, "1", "RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.", "GEO Accession:GSM1483839", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP045679", null, null, "Metazome_ZF_timecourse_sample_0104.fastq.gz", "fastq", 83810020.0, 2394572.0, "GSM1483839 r1", "0:35", "A:24075610;C:16799998;G:16694424;T:25967423;N:272565", 35, null, null, null, 24075610, 16799998, 16694424, 25967423, 272565, "SRX684704", "SRS687822", "SRA179995", "GEO", "Yanai, Biology, Technion - Israel Institute of Technology", 1, 0.7588, null, 0.07993, null, 0.84449, null, 0.49785, null, 35, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Israel", "2014-08-21", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38125, "SRR1555595", "SRX684703", "SRS687820", "SRP045679", "PRJNA258656", "Danio rerio high resolution developmental transcriptomic time course", "GSE60619", "Transcriptome Analysis", "Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This \u201cphylotypic stage\u201d has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a \u2018zootypic\u2019 stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples", "parent bioproject:PRJNA287810", "pubmed:26886793", null, "Metazome ZF timecourse sample 0103", "GSM1483838", null, "tissue:single embryo", "Metazome ZF timecourse sample 0103", "Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix", "single embryo", null, "RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.", "zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.", "time min post fertilization:4120", "GSM1483838", "GSM1483838: Metazome ZF timecourse sample 0103; Danio rerio; RNA Seq", "GSM1483838", null, "1", "RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.", "GEO Accession:GSM1483838", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP045679", null, null, "Metazome_ZF_timecourse_sample_0103.fastq.gz", "fastq", 98206150.0, 2805890.0, "GSM1483838 r1", "0:35", "A:28361916;C:19232789;G:19589483;T:30798968;N:222994", 35, null, null, null, 28361916, 19232789, 19589483, 30798968, 222994, "SRX684703", "SRS687820", "SRA179995", "GEO", "Yanai, Biology, Technion - Israel Institute of Technology", 1, 0.75509, null, 0.13429, null, 0.81117, null, 0.49102, null, 35, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Israel", "2014-08-21", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38126, "SRR1555594", "SRX684702", "SRS687819", "SRP045679", "PRJNA258656", "Danio rerio high resolution developmental transcriptomic time course", "GSE60619", "Transcriptome Analysis", "Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This \u201cphylotypic stage\u201d has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a \u2018zootypic\u2019 stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples", "parent bioproject:PRJNA287810", "pubmed:26886793", null, "Metazome ZF timecourse sample 0102", "GSM1483837", null, "tissue:single embryo", "Metazome ZF timecourse sample 0102", "Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix", "single embryo", null, "RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.", "zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.", "time min post fertilization:4080", "GSM1483837", "GSM1483837: Metazome ZF timecourse sample 0102; Danio rerio; RNA Seq", "GSM1483837", null, "1", "RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.", "GEO Accession:GSM1483837", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP045679", null, null, "Metazome_ZF_timecourse_sample_0102.fastq.gz", "fastq", 192817835.0, 5509081.0, "GSM1483837 r1", "0:35", "A:55969077;C:36880901;G:37835921;T:61101558;N:1030378", 35, null, null, null, 55969077, 36880901, 37835921, 61101558, 1030378, "SRX684702", "SRS687819", "SRA179995", "GEO", "Yanai, Biology, Technion - Israel Institute of Technology", 1, 0.73387, null, 0.17245, null, 0.80164, null, 0.48657, null, 35, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Israel", "2014-08-21", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38127, "SRR1555593", "SRX684701", "SRS687818", "SRP045679", "PRJNA258656", "Danio rerio high resolution developmental transcriptomic time course", "GSE60619", "Transcriptome Analysis", "Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This \u201cphylotypic stage\u201d has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a \u2018zootypic\u2019 stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples", "parent bioproject:PRJNA287810", "pubmed:26886793", null, "Metazome ZF timecourse sample 0101", "GSM1483836", null, "tissue:single embryo", "Metazome ZF timecourse sample 0101", "Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix", "single embryo", null, "RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.", "zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.", "time min post fertilization:4040", "GSM1483836", "GSM1483836: Metazome ZF timecourse sample 0101; Danio rerio; RNA Seq", "GSM1483836", null, "1", "RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.", "GEO Accession:GSM1483836", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP045679", null, null, "Metazome_ZF_timecourse_sample_0101.fastq.gz", "fastq", 374339455.0, 10695413.0, "GSM1483836 r1", "0:35", "A:112191846;C:73679996;G:73185024;T:114766825;N:515764", 35, null, null, null, 112191846, 73679996, 73185024, 114766825, 515764, "SRX684701", "SRS687818", "SRA179995", "GEO", "Yanai, Biology, Technion - Israel Institute of Technology", 1, 0.83131, null, 0.16618, null, 0.77812, null, 0.49895, null, 35, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Israel", "2014-08-21", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38128, "SRR1555592", "SRX684700", "SRS687816", "SRP045679", "PRJNA258656", "Danio rerio high resolution developmental transcriptomic time course", "GSE60619", "Transcriptome Analysis", "Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This \u201cphylotypic stage\u201d has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a \u2018zootypic\u2019 stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples", "parent bioproject:PRJNA287810", "pubmed:26886793", null, "Metazome ZF timecourse sample 0100", "GSM1483835", null, "tissue:single embryo", "Metazome ZF timecourse sample 0100", "Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix", "single embryo", null, "RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.", "zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.", "time min post fertilization:4000", "GSM1483835", "GSM1483835: Metazome ZF timecourse sample 0100; Danio rerio; RNA Seq", "GSM1483835", null, "1", "RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.", "GEO Accession:GSM1483835", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP045679", null, null, "Metazome_ZF_timecourse_sample_0100.fastq.gz", "fastq", 15239420.0, 435412.0, "GSM1483835 r1", "0:35", "A:4361241;C:3088134;G:3269084;T:4498093;N:22868", 35, null, null, null, 4361241, 3088134, 3269084, 4498093, 22868, "SRX684700", "SRS687816", "SRA179995", "GEO", "Yanai, Biology, Technion - Israel Institute of Technology", 1, 0.7702, null, 0.17879, null, 0.92904, null, 0.505, null, 35, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Israel", "2014-08-21", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38129, "SRR1555591", "SRX684699", "SRS687817", "SRP045679", "PRJNA258656", "Danio rerio high resolution developmental transcriptomic time course", "GSE60619", "Transcriptome Analysis", "Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This \u201cphylotypic stage\u201d has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a \u2018zootypic\u2019 stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples", "parent bioproject:PRJNA287810", "pubmed:26886793", null, "Metazome ZF timecourse sample 0099", "GSM1483834", null, "tissue:single embryo", "Metazome ZF timecourse sample 0099", "Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix", "single embryo", null, "RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.", "zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.", "time min post fertilization:3960", "GSM1483834", "GSM1483834: Metazome ZF timecourse sample 0099; Danio rerio; RNA Seq", "GSM1483834", null, "1", "RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.", "GEO Accession:GSM1483834", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP045679", null, null, "Metazome_ZF_timecourse_sample_0099.fastq.gz", "fastq", 284196500.0, 8119900.0, "GSM1483834 r1", "0:35", "A:81991733;C:57440756;G:58362818;T:86010858;N:390335", 35, null, null, null, 81991733, 57440756, 58362818, 86010858, 390335, "SRX684699", "SRS687817", "SRA179995", "GEO", "Yanai, Biology, Technion - Israel Institute of Technology", 1, 0.81284, null, 0.1715, null, 0.78468, null, 0.49472, null, 35, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Israel", "2014-08-21", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38130, "SRR1555590", "SRX684698", "SRS687815", "SRP045679", "PRJNA258656", "Danio rerio high resolution developmental transcriptomic time course", "GSE60619", "Transcriptome Analysis", "Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This \u201cphylotypic stage\u201d has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a \u2018zootypic\u2019 stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples", "parent bioproject:PRJNA287810", "pubmed:26886793", null, "Metazome ZF timecourse sample 0098", "GSM1483833", null, "tissue:single embryo", "Metazome ZF timecourse sample 0098", "Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix", "single embryo", null, "RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.", "zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.", "time min post fertilization:3920", "GSM1483833", "GSM1483833: Metazome ZF timecourse sample 0098; Danio rerio; RNA Seq", "GSM1483833", null, "1", "RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.", "GEO Accession:GSM1483833", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP045679", null, null, "Metazome_ZF_timecourse_sample_0098.fastq.gz", "fastq", 244245015.0, 6978429.0, "GSM1483833 r1", "0:35", "A:70141725;C:48500061;G:50748992;T:74478239;N:375998", 35, null, null, null, 70141725, 48500061, 50748992, 74478239, 375998, "SRX684698", "SRS687815", "SRA179995", "GEO", "Yanai, Biology, Technion - Israel Institute of Technology", 1, 0.79668, null, 0.17718, null, 0.79271, null, 0.45966, null, 35, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Israel", "2014-08-21", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38131, "SRR1555589", "SRX684697", "SRS687814", "SRP045679", "PRJNA258656", "Danio rerio high resolution developmental transcriptomic time course", "GSE60619", "Transcriptome Analysis", "Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This \u201cphylotypic stage\u201d has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a \u2018zootypic\u2019 stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples", "parent bioproject:PRJNA287810", "pubmed:26886793", null, "Metazome ZF timecourse sample 0097", "GSM1483832", null, "tissue:single embryo", "Metazome ZF timecourse sample 0097", "Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix", "single embryo", null, "RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.", "zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.", "time min post fertilization:3880", "GSM1483832", "GSM1483832: Metazome ZF timecourse sample 0097; Danio rerio; RNA Seq", "GSM1483832", null, "1", "RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.", "GEO Accession:GSM1483832", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP045679", null, null, "Metazome_ZF_timecourse_sample_0097.fastq.gz", "fastq", 215347510.0, 6152786.0, "GSM1483832 r1", "0:35", "A:62928172;C:42420829;G:43902946;T:65803342;N:292221", 35, null, null, null, 62928172, 42420829, 43902946, 65803342, 292221, "SRX684697", "SRS687814", "SRA179995", "GEO", "Yanai, Biology, Technion - Israel Institute of Technology", 1, 0.80605, null, 0.17396, null, 0.78873, null, 0.50241, null, 35, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Israel", "2014-08-21", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38132, "SRR1555588", "SRX684696", "SRS687813", "SRP045679", "PRJNA258656", "Danio rerio high resolution developmental transcriptomic time course", "GSE60619", "Transcriptome Analysis", "Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This \u201cphylotypic stage\u201d has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a \u2018zootypic\u2019 stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples", "parent bioproject:PRJNA287810", "pubmed:26886793", null, "Metazome ZF timecourse sample 0096", "GSM1483831", null, "tissue:single embryo", "Metazome ZF timecourse sample 0096", "Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix", "single embryo", null, "RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.", "zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.", "time min post fertilization:3840", "GSM1483831", "GSM1483831: Metazome ZF timecourse sample 0096; Danio rerio; RNA Seq", "GSM1483831", null, "1", "RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.", "GEO Accession:GSM1483831", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP045679", null, null, "Metazome_ZF_timecourse_sample_0096.fastq.gz", "fastq", 13992230.0, 399778.0, "GSM1483831 r1", "0:35", "A:4077402;C:2837417;G:2856511;T:4200750;N:20150", 35, null, null, null, 4077402, 2837417, 2856511, 4200750, 20150, "SRX684696", "SRS687813", "SRA179995", "GEO", "Yanai, Biology, Technion - Israel Institute of Technology", 1, 0.77543, null, 0.14778, null, 0.93288, null, 0.48967, null, 35, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Israel", "2014-08-21", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38133, "SRR1555587", "SRX684695", "SRS687811", "SRP045679", "PRJNA258656", "Danio rerio high resolution developmental transcriptomic time course", "GSE60619", "Transcriptome Analysis", "Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This \u201cphylotypic stage\u201d has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a \u2018zootypic\u2019 stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples", "parent bioproject:PRJNA287810", "pubmed:26886793", null, "Metazome ZF timecourse sample 0095", "GSM1483830", null, "tissue:single embryo", "Metazome ZF timecourse sample 0095", "Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix", "single embryo", null, "RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.", "zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.", "time min post fertilization:3800", "GSM1483830", "GSM1483830: Metazome ZF timecourse sample 0095; Danio rerio; RNA Seq", "GSM1483830", null, "1", "RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.", "GEO Accession:GSM1483830", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP045679", null, null, "Metazome_ZF_timecourse_sample_0095.fastq.gz", "fastq", 290151435.0, 8290041.0, "GSM1483830 r1", "0:35", "A:86694666;C:56953853;G:57315219;T:88811589;N:376108", 35, null, null, null, 86694666, 56953853, 57315219, 88811589, 376108, "SRX684695", "SRS687811", "SRA179995", "GEO", "Yanai, Biology, Technion - Israel Institute of Technology", 1, 0.79098, null, 0.18155, null, 0.79034, null, 0.51338, null, 35, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Israel", "2014-08-21", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38134, "SRR1555586", "SRX684694", "SRS687810", "SRP045679", "PRJNA258656", "Danio rerio high resolution developmental transcriptomic time course", "GSE60619", "Transcriptome Analysis", "Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This \u201cphylotypic stage\u201d has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a \u2018zootypic\u2019 stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples", "parent bioproject:PRJNA287810", "pubmed:26886793", null, "Metazome ZF timecourse sample 0094", "GSM1483829", null, "tissue:single embryo", "Metazome ZF timecourse sample 0094", "Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix", "single embryo", null, "RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.", "zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.", "time min post fertilization:3760", "GSM1483829", "GSM1483829: Metazome ZF timecourse sample 0094; Danio rerio; RNA Seq", "GSM1483829", null, "1", "RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.", "GEO Accession:GSM1483829", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP045679", null, null, "Metazome_ZF_timecourse_sample_0094.fastq.gz", "fastq", 645422925.0, 18440655.0, "GSM1483829 r1", "0:35", "A:186408265;C:127218686;G:131406509;T:199399112;N:990353", 35, null, null, null, 186408265, 127218686, 131406509, 199399112, 990353, "SRX684694", "SRS687810", "SRA179995", "GEO", "Yanai, Biology, Technion - Israel Institute of Technology", 1, 0.81184, null, 0.15572, null, 0.78496, null, 0.48733, null, 35, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Israel", "2014-08-21", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38135, "SRR1555585", "SRX684693", "SRS687812", "SRP045679", "PRJNA258656", "Danio rerio high resolution developmental transcriptomic time course", "GSE60619", "Transcriptome Analysis", "Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This \u201cphylotypic stage\u201d has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a \u2018zootypic\u2019 stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples", "parent bioproject:PRJNA287810", "pubmed:26886793", null, "Metazome ZF timecourse sample 0093", "GSM1483828", null, "tissue:single embryo", "Metazome ZF timecourse sample 0093", "Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix", "single embryo", null, "RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.", "zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.", "time min post fertilization:3720", "GSM1483828", "GSM1483828: Metazome ZF timecourse sample 0093; Danio rerio; RNA Seq", "GSM1483828", null, "1", "RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.", "GEO Accession:GSM1483828", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP045679", null, null, "Metazome_ZF_timecourse_sample_0093.fastq.gz", "fastq", 82574205.0, 2359263.0, "GSM1483828 r1", "0:35", "A:24239984;C:16625180;G:16309055;T:25123568;N:276418", 35, null, null, null, 24239984, 16625180, 16309055, 25123568, 276418, "SRX684693", "SRS687812", "SRA179995", "GEO", "Yanai, Biology, Technion - Israel Institute of Technology", 1, 0.75557, null, 0.14554, null, 0.82205, null, 0.49736, null, 35, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Israel", "2014-08-21", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38136, "SRR1555584", "SRX684692", "SRS687809", "SRP045679", "PRJNA258656", "Danio rerio high resolution developmental transcriptomic time course", "GSE60619", "Transcriptome Analysis", "Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This \u201cphylotypic stage\u201d has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a \u2018zootypic\u2019 stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples", "parent bioproject:PRJNA287810", "pubmed:26886793", null, "Metazome ZF timecourse sample 0092", "GSM1483827", null, "tissue:single embryo", "Metazome ZF timecourse sample 0092", "Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix", "single embryo", null, "RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.", "zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.", "time min post fertilization:3680", "GSM1483827", "GSM1483827: Metazome ZF timecourse sample 0092; Danio rerio; RNA Seq", "GSM1483827", null, "1", "RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.", "GEO Accession:GSM1483827", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP045679", null, null, "Metazome_ZF_timecourse_sample_0092.fastq.gz", "fastq", 72186905.0, 2062483.0, "GSM1483827 r1", "0:35", "A:21349438;C:14361391;G:14472348;T:21766197;N:237531", 35, null, null, null, 21349438, 14361391, 14472348, 21766197, 237531, "SRX684692", "SRS687809", "SRA179995", "GEO", "Yanai, Biology, Technion - Israel Institute of Technology", 1, 0.74348, null, 0.13614, null, 0.8309, null, 0.51328, null, 35, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Israel", "2014-08-21", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38137, "SRR1555583", "SRX684691", "SRS687808", "SRP045679", "PRJNA258656", "Danio rerio high resolution developmental transcriptomic time course", "GSE60619", "Transcriptome Analysis", "Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This \u201cphylotypic stage\u201d has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a \u2018zootypic\u2019 stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples", "parent bioproject:PRJNA287810", "pubmed:26886793", null, "Metazome ZF timecourse sample 0091", "GSM1483826", null, "tissue:single embryo", "Metazome ZF timecourse sample 0091", "Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix", "single embryo", null, "RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.", "zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.", "time min post fertilization:3640", "GSM1483826", "GSM1483826: Metazome ZF timecourse sample 0091; Danio rerio; RNA Seq", "GSM1483826", null, "1", "RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.", "GEO Accession:GSM1483826", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP045679", null, null, "Metazome_ZF_timecourse_sample_0091.fastq.gz", "fastq", 18405940.0, 525884.0, "GSM1483826 r1", "0:35", "A:5374937;C:3766785;G:3774551;T:5451369;N:38298", 35, null, null, null, 5374937, 3766785, 3774551, 5451369, 38298, "SRX684691", "SRS687808", "SRA179995", "GEO", "Yanai, Biology, Technion - Israel Institute of Technology", 1, 0.74005, null, 0.11089, null, 0.91494, null, 0.49823, null, 35, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Israel", "2014-08-21", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38138, "SRR1555582", "SRX684690", "SRS687807", "SRP045679", "PRJNA258656", "Danio rerio high resolution developmental transcriptomic time course", "GSE60619", "Transcriptome Analysis", "Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This \u201cphylotypic stage\u201d has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a \u2018zootypic\u2019 stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples", "parent bioproject:PRJNA287810", "pubmed:26886793", null, "Metazome ZF timecourse sample 0090", "GSM1483825", null, "tissue:single embryo", "Metazome ZF timecourse sample 0090", "Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix", "single embryo", null, "RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.", "zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.", "time min post fertilization:3600", "GSM1483825", "GSM1483825: Metazome ZF timecourse sample 0090; Danio rerio; RNA Seq", "GSM1483825", null, "1", "RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.", "GEO Accession:GSM1483825", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP045679", null, null, "Metazome_ZF_timecourse_sample_0090.fastq.gz", "fastq", 141938265.0, 4055379.0, "GSM1483825 r1", "0:35", "A:41371650;C:28115945;G:29356068;T:42485478;N:609124", 35, null, null, null, 41371650, 28115945, 29356068, 42485478, 609124, "SRX684690", "SRS687807", "SRA179995", "GEO", "Yanai, Biology, Technion - Israel Institute of Technology", 1, 0.71151, null, 0.17711, null, 0.82789, null, 0.52369, null, 35, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Israel", "2014-08-21", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38139, "SRR1555581", "SRX684689", "SRS687806", "SRP045679", "PRJNA258656", "Danio rerio high resolution developmental transcriptomic time course", "GSE60619", "Transcriptome Analysis", "Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This \u201cphylotypic stage\u201d has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a \u2018zootypic\u2019 stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples", "parent bioproject:PRJNA287810", "pubmed:26886793", null, "Metazome ZF timecourse sample 0089", "GSM1483824", null, "tissue:single embryo", "Metazome ZF timecourse sample 0089", "Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix", "single embryo", null, "RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.", "zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.", "time min post fertilization:3560", "GSM1483824", "GSM1483824: Metazome ZF timecourse sample 0089; Danio rerio; RNA Seq", "GSM1483824", null, "1", "RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.", "GEO Accession:GSM1483824", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP045679", null, null, "Metazome_ZF_timecourse_sample_0089.fastq.gz", "fastq", 99569015.0, 2844829.0, "GSM1483824 r1", "0:35", "A:28763571;C:20065085;G:19332839;T:31088193;N:319327", 35, null, null, null, 28763571, 20065085, 19332839, 31088193, 319327, "SRX684689", "SRS687806", "SRA179995", "GEO", "Yanai, Biology, Technion - Israel Institute of Technology", 1, 0.74177, null, 0.13103, null, 0.81854, null, 0.51184, null, 35, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Israel", "2014-08-21", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38140, "SRR1555580", "SRX684688", "SRS687805", "SRP045679", "PRJNA258656", "Danio rerio high resolution developmental transcriptomic time course", "GSE60619", "Transcriptome Analysis", "Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This \u201cphylotypic stage\u201d has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a \u2018zootypic\u2019 stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples", "parent bioproject:PRJNA287810", "pubmed:26886793", null, "Metazome ZF timecourse sample 0088", "GSM1483823", null, "tissue:single embryo", "Metazome ZF timecourse sample 0088", "Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix", "single embryo", null, "RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.", "zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.", "time min post fertilization:3520", "GSM1483823", "GSM1483823: Metazome ZF timecourse sample 0088; Danio rerio; RNA Seq", "GSM1483823", null, "1", "RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.", "GEO Accession:GSM1483823", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP045679", null, null, "Metazome_ZF_timecourse_sample_0088.fastq.gz", "fastq", 168790055.0, 4822573.0, "GSM1483823 r1", "0:35", "A:49034449;C:32785565;G:33439918;T:52997820;N:532303", 35, null, null, null, 49034449, 32785565, 33439918, 52997820, 532303, "SRX684688", "SRS687805", "SRA179995", "GEO", "Yanai, Biology, Technion - Israel Institute of Technology", 1, 0.73454, null, 0.15775, null, 0.8047, null, 0.50587, null, 35, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Israel", "2014-08-21", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38141, "SRR1555579", "SRX684687", "SRS687803", "SRP045679", "PRJNA258656", "Danio rerio high resolution developmental transcriptomic time course", "GSE60619", "Transcriptome Analysis", "Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This \u201cphylotypic stage\u201d has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a \u2018zootypic\u2019 stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples", "parent bioproject:PRJNA287810", "pubmed:26886793", null, "Metazome ZF timecourse sample 0087", "GSM1483822", null, "tissue:single embryo", "Metazome ZF timecourse sample 0087", "Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix", "single embryo", null, "RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.", "zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.", "time min post fertilization:3480", "GSM1483822", "GSM1483822: Metazome ZF timecourse sample 0087; Danio rerio; RNA Seq", "GSM1483822", null, "1", "RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.", "GEO Accession:GSM1483822", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP045679", null, null, "Metazome_ZF_timecourse_sample_0087.fastq.gz", "fastq", 83155975.0, 2375885.0, "GSM1483822 r1", "0:35", "A:23985678;C:16871573;G:17048421;T:25086100;N:164203", 35, null, null, null, 23985678, 16871573, 17048421, 25086100, 164203, "SRX684687", "SRS687803", "SRA179995", "GEO", "Yanai, Biology, Technion - Israel Institute of Technology", 1, 0.75055, null, 0.10258, null, 0.83952, null, 0.49914, null, 35, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Israel", "2014-08-21", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38142, "SRR1555578", "SRX684686", "SRS687804", "SRP045679", "PRJNA258656", "Danio rerio high resolution developmental transcriptomic time course", "GSE60619", "Transcriptome Analysis", "Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This \u201cphylotypic stage\u201d has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a \u2018zootypic\u2019 stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples", "parent bioproject:PRJNA287810", "pubmed:26886793", null, "Metazome ZF timecourse sample 0086", "GSM1483821", null, "tissue:single embryo", "Metazome ZF timecourse sample 0086", "Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix", "single embryo", null, "RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.", "zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.", "time min post fertilization:3440", "GSM1483821", "GSM1483821: Metazome ZF timecourse sample 0086; Danio rerio; RNA Seq", "GSM1483821", null, "1", "RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.", "GEO Accession:GSM1483821", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP045679", null, null, "Metazome_ZF_timecourse_sample_0086.fastq.gz", "fastq", 36772155.0, 1050633.0, "GSM1483821 r1", "0:35", "A:10536765;C:7377251;G:7701105;T:11014088;N:142946", 35, null, null, null, 10536765, 7377251, 7701105, 11014088, 142946, "SRX684686", "SRS687804", "SRA179995", "GEO", "Yanai, Biology, Technion - Israel Institute of Technology", 1, 0.745, null, 0.08312, null, 0.88209, null, 0.52632, null, 35, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Israel", "2014-08-21", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38143, "SRR1555577", "SRX684685", "SRS687802", "SRP045679", "PRJNA258656", "Danio rerio high resolution developmental transcriptomic time course", "GSE60619", "Transcriptome Analysis", "Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This \u201cphylotypic stage\u201d has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a \u2018zootypic\u2019 stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples", "parent bioproject:PRJNA287810", "pubmed:26886793", null, "Metazome ZF timecourse sample 0085", "GSM1483820", null, "tissue:single embryo", "Metazome ZF timecourse sample 0085", "Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix", "single embryo", null, "RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.", "zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.", "time min post fertilization:3400", "GSM1483820", "GSM1483820: Metazome ZF timecourse sample 0085; Danio rerio; RNA Seq", "GSM1483820", null, "1", "RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.", "GEO Accession:GSM1483820", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP045679", null, null, "Metazome_ZF_timecourse_sample_0085.fastq.gz", "fastq", 142281650.0, 4065190.0, "GSM1483820 r1", "0:35", "A:41238155;C:28228882;G:28727190;T:43901346;N:186077", 35, null, null, null, 41238155, 28228882, 28727190, 43901346, 186077, "SRX684685", "SRS687802", "SRA179995", "GEO", "Yanai, Biology, Technion - Israel Institute of Technology", 1, 0.80695, null, 0.14045, null, 0.80361, null, 0.5, null, 35, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Israel", "2014-08-21", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38144, "SRR1555576", "SRX684684", "SRS687800", "SRP045679", "PRJNA258656", "Danio rerio high resolution developmental transcriptomic time course", "GSE60619", "Transcriptome Analysis", "Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This \u201cphylotypic stage\u201d has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a \u2018zootypic\u2019 stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples", "parent bioproject:PRJNA287810", "pubmed:26886793", null, "Metazome ZF timecourse sample 0084", "GSM1483819", null, "tissue:single embryo", "Metazome ZF timecourse sample 0084", "Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix", "single embryo", null, "RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.", "zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.", "time min post fertilization:3360", "GSM1483819", "GSM1483819: Metazome ZF timecourse sample 0084; Danio rerio; RNA Seq", "GSM1483819", null, "1", "RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.", "GEO Accession:GSM1483819", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP045679", null, null, "Metazome_ZF_timecourse_sample_0084.fastq.gz", "fastq", 147589295.0, 4216837.0, "GSM1483819 r1", "0:35", "A:42100013;C:30125860;G:31767504;T:43391728;N:204190", 35, null, null, null, 42100013, 30125860, 31767504, 43391728, 204190, "SRX684684", "SRS687800", "SRA179995", "GEO", "Yanai, Biology, Technion - Israel Institute of Technology", 1, 0.80373, null, 0.08661, null, 0.83157, null, 0.51923, null, 35, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Israel", "2014-08-21", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38145, "SRR1555575", "SRX684683", "SRS687801", "SRP045679", "PRJNA258656", "Danio rerio high resolution developmental transcriptomic time course", "GSE60619", "Transcriptome Analysis", "Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This \u201cphylotypic stage\u201d has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a \u2018zootypic\u2019 stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples", "parent bioproject:PRJNA287810", "pubmed:26886793", null, "Metazome ZF timecourse sample 0083", "GSM1483818", null, "tissue:single embryo", "Metazome ZF timecourse sample 0083", "Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix", "single embryo", null, "RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.", "zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.", "time min post fertilization:3320", "GSM1483818", "GSM1483818: Metazome ZF timecourse sample 0083; Danio rerio; RNA Seq", "GSM1483818", null, "1", "RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.", "GEO Accession:GSM1483818", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP045679", null, null, "Metazome_ZF_timecourse_sample_0083.fastq.gz", "fastq", 147243985.0, 4206971.0, "GSM1483818 r1", "0:35", "A:42533757;C:29874233;G:30500611;T:44132167;N:203217", 35, null, null, null, 42533757, 29874233, 30500611, 44132167, 203217, "SRX684683", "SRS687801", "SRA179995", "GEO", "Yanai, Biology, Technion - Israel Institute of Technology", 1, 0.80738, null, 0.08642, null, 0.82219, null, 0.49396, null, 35, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Israel", "2014-08-21", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38146, "SRR1555574", "SRX684682", "SRS687799", "SRP045679", "PRJNA258656", "Danio rerio high resolution developmental transcriptomic time course", "GSE60619", "Transcriptome Analysis", "Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This \u201cphylotypic stage\u201d has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a \u2018zootypic\u2019 stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples", "parent bioproject:PRJNA287810", "pubmed:26886793", null, "Metazome ZF timecourse sample 0082", "GSM1483817", null, "tissue:single embryo", "Metazome ZF timecourse sample 0082", "Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix", "single embryo", null, "RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.", "zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.", "time min post fertilization:3280", "GSM1483817", "GSM1483817: Metazome ZF timecourse sample 0082; Danio rerio; RNA Seq", "GSM1483817", null, "1", "RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.", "GEO Accession:GSM1483817", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP045679", null, null, "Metazome_ZF_timecourse_sample_0082.fastq.gz", "fastq", 96747735.0, 2764221.0, "GSM1483817 r1", "0:35", "A:26768730;C:19578598;G:21713242;T:28549716;N:137449", 35, null, null, null, 26768730, 19578598, 21713242, 28549716, 137449, "SRX684682", "SRS687799", "SRA179995", "GEO", "Yanai, Biology, Technion - Israel Institute of Technology", 1, 0.80738, null, 0.09417, null, 0.85167, null, 0.50713, null, 35, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Israel", "2014-08-21", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38147, "SRR1555573", "SRX684681", "SRS687798", "SRP045679", "PRJNA258656", "Danio rerio high resolution developmental transcriptomic time course", "GSE60619", "Transcriptome Analysis", "Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This \u201cphylotypic stage\u201d has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a \u2018zootypic\u2019 stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples", "parent bioproject:PRJNA287810", "pubmed:26886793", null, "Metazome ZF timecourse sample 0081", "GSM1483816", null, "tissue:single embryo", "Metazome ZF timecourse sample 0081", "Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix", "single embryo", null, "RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.", "zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.", "time min post fertilization:3240", "GSM1483816", "GSM1483816: Metazome ZF timecourse sample 0081; Danio rerio; RNA Seq", "GSM1483816", null, "1", "RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.", "GEO Accession:GSM1483816", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP045679", null, null, "Metazome_ZF_timecourse_sample_0081.fastq.gz", "fastq", 158402895.0, 4525797.0, "GSM1483816 r1", "0:35", "A:46939694;C:31610300;G:32050592;T:47571349;N:230960", 35, null, null, null, 46939694, 31610300, 32050592, 47571349, 230960, "SRX684681", "SRS687798", "SRA179995", "GEO", "Yanai, Biology, Technion - Israel Institute of Technology", 1, 0.78709, null, 0.11916, null, 0.82351, null, 0.48714, null, 35, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Israel", "2014-08-21", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38148, "SRR1555572", "SRX684680", "SRS687797", "SRP045679", "PRJNA258656", "Danio rerio high resolution developmental transcriptomic time course", "GSE60619", "Transcriptome Analysis", "Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This \u201cphylotypic stage\u201d has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a \u2018zootypic\u2019 stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples", "parent bioproject:PRJNA287810", "pubmed:26886793", null, "Metazome ZF timecourse sample 0080", "GSM1483815", null, "tissue:single embryo", "Metazome ZF timecourse sample 0080", "Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix", "single embryo", null, "RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.", "zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.", "time min post fertilization:3200", "GSM1483815", "GSM1483815: Metazome ZF timecourse sample 0080; Danio rerio; RNA Seq", "GSM1483815", null, "1", "RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.", "GEO Accession:GSM1483815", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP045679", null, null, "Metazome_ZF_timecourse_sample_0080.fastq.gz", "fastq", 1432375.0, 40925.0, "GSM1483815 r1", "0:35", "A:422951;C:297837;G:308257;T:400778;N:2552", 35, null, null, null, 422951, 297837, 308257, 400778, 2552, "SRX684680", "SRS687797", "SRA179995", "GEO", "Yanai, Biology, Technion - Israel Institute of Technology", 1, 0.7103, null, 0.12471, null, 0.9811, null, 0.57619, null, 35, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Israel", "2014-08-21", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38149, "SRR1555571", "SRX684679", "SRS687796", "SRP045679", "PRJNA258656", "Danio rerio high resolution developmental transcriptomic time course", "GSE60619", "Transcriptome Analysis", "Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This \u201cphylotypic stage\u201d has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a \u2018zootypic\u2019 stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples", "parent bioproject:PRJNA287810", "pubmed:26886793", null, "Metazome ZF timecourse sample 0079", "GSM1483814", null, "tissue:single embryo", "Metazome ZF timecourse sample 0079", "Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix", "single embryo", null, "RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.", "zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.", "time min post fertilization:3160", "GSM1483814", "GSM1483814: Metazome ZF timecourse sample 0079; Danio rerio; RNA Seq", "GSM1483814", null, "1", "RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.", "GEO Accession:GSM1483814", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP045679", null, null, "Metazome_ZF_timecourse_sample_0079.fastq.gz", "fastq", 171937640.0, 4912504.0, "GSM1483814 r1", "0:35", "A:49235964;C:34067309;G:35846095;T:52553397;N:234875", 35, null, null, null, 49235964, 34067309, 35846095, 52553397, 234875, "SRX684679", "SRS687796", "SRA179995", "GEO", "Yanai, Biology, Technion - Israel Institute of Technology", 1, 0.79389, null, 0.14252, null, 0.81107, null, 0.50474, null, 35, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Israel", "2014-08-21", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38150, "SRR1555570", "SRX684678", "SRS687795", "SRP045679", "PRJNA258656", "Danio rerio high resolution developmental transcriptomic time course", "GSE60619", "Transcriptome Analysis", "Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This \u201cphylotypic stage\u201d has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a \u2018zootypic\u2019 stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples", "parent bioproject:PRJNA287810", "pubmed:26886793", null, "Metazome ZF timecourse sample 0078", "GSM1483813", null, "tissue:single embryo", "Metazome ZF timecourse sample 0078", "Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix", "single embryo", null, "RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.", "zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.", "time min post fertilization:3120", "GSM1483813", "GSM1483813: Metazome ZF timecourse sample 0078; Danio rerio; RNA Seq", "GSM1483813", null, "1", "RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.", "GEO Accession:GSM1483813", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP045679", null, null, "Metazome_ZF_timecourse_sample_0078.fastq.gz", "fastq", 220246950.0, 6292770.0, "GSM1483813 r1", "0:35", "A:63723749;C:43666354;G:45504302;T:67009596;N:342949", 35, null, null, null, 63723749, 43666354, 45504302, 67009596, 342949, "SRX684678", "SRS687795", "SRA179995", "GEO", "Yanai, Biology, Technion - Israel Institute of Technology", 1, 0.80813, null, 0.1512, null, 0.80174, null, 0.49937, null, 35, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Israel", "2014-08-21", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38151, "SRR1555569", "SRX684677", "SRS687794", "SRP045679", "PRJNA258656", "Danio rerio high resolution developmental transcriptomic time course", "GSE60619", "Transcriptome Analysis", "Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This \u201cphylotypic stage\u201d has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a \u2018zootypic\u2019 stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples", "parent bioproject:PRJNA287810", "pubmed:26886793", null, "Metazome ZF timecourse sample 0077", "GSM1483812", null, "tissue:single embryo", "Metazome ZF timecourse sample 0077", "Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix", "single embryo", null, "RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.", "zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.", "time min post fertilization:3080", "GSM1483812", "GSM1483812: Metazome ZF timecourse sample 0077; Danio rerio; RNA Seq", "GSM1483812", null, "1", "RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.", "GEO Accession:GSM1483812", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP045679", null, null, "Metazome_ZF_timecourse_sample_0077.fastq.gz", "fastq", 93138675.0, 2661105.0, "GSM1483812 r1", "0:35", "A:27102533;C:18314712;G:18498218;T:29006764;N:216448", 35, null, null, null, 27102533, 18314712, 18498218, 29006764, 216448, "SRX684677", "SRS687794", "SRA179995", "GEO", "Yanai, Biology, Technion - Israel Institute of Technology", 1, 0.75818, null, 0.11499, null, 0.81572, null, 0.50169, null, 35, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Israel", "2014-08-21", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38152, "SRR1555568", "SRX684676", "SRS687793", "SRP045679", "PRJNA258656", "Danio rerio high resolution developmental transcriptomic time course", "GSE60619", "Transcriptome Analysis", "Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This \u201cphylotypic stage\u201d has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a \u2018zootypic\u2019 stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples", "parent bioproject:PRJNA287810", "pubmed:26886793", null, "Metazome ZF timecourse sample 0076", "GSM1483811", null, "tissue:single embryo", "Metazome ZF timecourse sample 0076", "Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix", "single embryo", null, "RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.", "zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.", "time min post fertilization:3040", "GSM1483811", "GSM1483811: Metazome ZF timecourse sample 0076; Danio rerio; RNA Seq", "GSM1483811", null, "1", "RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.", "GEO Accession:GSM1483811", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP045679", null, null, "Metazome_ZF_timecourse_sample_0076.fastq.gz", "fastq", 118512415.0, 3386069.0, "GSM1483811 r1", "0:35", "A:33806370;C:23395934;G:24547522;T:36374942;N:387647", 35, null, null, null, 33806370, 23395934, 24547522, 36374942, 387647, "SRX684676", "SRS687793", "SRA179995", "GEO", "Yanai, Biology, Technion - Israel Institute of Technology", 1, 0.75326, null, 0.1088, null, 0.81667, null, 0.49341, null, 35, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Israel", "2014-08-21", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38153, "SRR1555567", "SRX684675", "SRS687792", "SRP045679", "PRJNA258656", "Danio rerio high resolution developmental transcriptomic time course", "GSE60619", "Transcriptome Analysis", "Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This \u201cphylotypic stage\u201d has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a \u2018zootypic\u2019 stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples", "parent bioproject:PRJNA287810", "pubmed:26886793", null, "Metazome ZF timecourse sample 0075", "GSM1483810", null, "tissue:single embryo", "Metazome ZF timecourse sample 0075", "Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix", "single embryo", null, "RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.", "zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.", "time min post fertilization:3000", "GSM1483810", "GSM1483810: Metazome ZF timecourse sample 0075; Danio rerio; RNA Seq", "GSM1483810", null, "1", "RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.", "GEO Accession:GSM1483810", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP045679", null, null, "Metazome_ZF_timecourse_sample_0075.fastq.gz", "fastq", 2520525.0, 72015.0, "GSM1483810 r1", "0:35", "A:818327;C:420638;G:441967;T:833315;N:6278", 35, null, null, null, 818327, 420638, 441967, 833315, 6278, "SRX684675", "SRS687792", "SRA179995", "GEO", "Yanai, Biology, Technion - Israel Institute of Technology", 1, 0.7119, null, 0.22445, null, 0.97368, null, 0.51561, null, 35, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Israel", "2014-08-21", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38154, "SRR1555566", "SRX684674", "SRS687791", "SRP045679", "PRJNA258656", "Danio rerio high resolution developmental transcriptomic time course", "GSE60619", "Transcriptome Analysis", "Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This \u201cphylotypic stage\u201d has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a \u2018zootypic\u2019 stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples", "parent bioproject:PRJNA287810", "pubmed:26886793", null, "Metazome ZF timecourse sample 0074", "GSM1483809", null, "tissue:single embryo", "Metazome ZF timecourse sample 0074", "Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix", "single embryo", null, "RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.", "zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.", "time min post fertilization:2960", "GSM1483809", "GSM1483809: Metazome ZF timecourse sample 0074; Danio rerio; RNA Seq", "GSM1483809", null, "1", "RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.", "GEO Accession:GSM1483809", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP045679", null, null, "Metazome_ZF_timecourse_sample_0074.fastq.gz", "fastq", 95385710.0, 2725306.0, "GSM1483809 r1", "0:35", "A:27032549;C:18681500;G:19490852;T:29708978;N:471831", 35, null, null, null, 27032549, 18681500, 19490852, 29708978, 471831, "SRX684674", "SRS687791", "SRA179995", "GEO", "Yanai, Biology, Technion - Israel Institute of Technology", 1, 0.75216, null, 0.09004, null, 0.83469, null, 0.48768, null, 35, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Israel", "2014-08-21", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38155, "SRR1555565", "SRX684673", "SRS687790", "SRP045679", "PRJNA258656", "Danio rerio high resolution developmental transcriptomic time course", "GSE60619", "Transcriptome Analysis", "Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This \u201cphylotypic stage\u201d has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a \u2018zootypic\u2019 stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples", "parent bioproject:PRJNA287810", "pubmed:26886793", null, "Metazome ZF timecourse sample 0073", "GSM1483808", null, "tissue:single embryo", "Metazome ZF timecourse sample 0073", "Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix", "single embryo", null, "RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.", "zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.", "time min post fertilization:2920", "GSM1483808", "GSM1483808: Metazome ZF timecourse sample 0073; Danio rerio; RNA Seq", "GSM1483808", null, "1", "RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.", "GEO Accession:GSM1483808", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP045679", null, null, "Metazome_ZF_timecourse_sample_0073.fastq.gz", "fastq", 149165835.0, 4261881.0, "GSM1483808 r1", "0:35", "A:42991931;C:29913953;G:30117935;T:45803552;N:338464", 35, null, null, null, 42991931, 29913953, 30117935, 45803552, 338464, "SRX684673", "SRS687790", "SRA179995", "GEO", "Yanai, Biology, Technion - Israel Institute of Technology", 1, 0.76488, null, 0.10545, null, 0.80586, null, 0.5046, null, 35, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Israel", "2014-08-21", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38156, "SRR1555564", "SRX684672", "SRS687789", "SRP045679", "PRJNA258656", "Danio rerio high resolution developmental transcriptomic time course", "GSE60619", "Transcriptome Analysis", "Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This \u201cphylotypic stage\u201d has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a \u2018zootypic\u2019 stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples", "parent bioproject:PRJNA287810", "pubmed:26886793", null, "Metazome ZF timecourse sample 0072", "GSM1483807", null, "tissue:single embryo", "Metazome ZF timecourse sample 0072", "Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix", "single embryo", null, "RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.", "zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.", "time min post fertilization:2880", "GSM1483807", "GSM1483807: Metazome ZF timecourse sample 0072; Danio rerio; RNA Seq", "GSM1483807", null, "1", "RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.", "GEO Accession:GSM1483807", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP045679", null, null, "Metazome_ZF_timecourse_sample_0072.fastq.gz", "fastq", 203829675.0, 5823705.0, "GSM1483807 r1", "0:35", "A:61171233;C:40047517;G:44515900;T:57461403;N:633622", 35, null, null, null, 61171233, 40047517, 44515900, 57461403, 633622, "SRX684672", "SRS687789", "SRA179995", "GEO", "Yanai, Biology, Technion - Israel Institute of Technology", 1, 0.65225, null, 0.10254, null, 0.82014, null, 0.50437, null, 35, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Israel", "2014-08-21", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38157, "SRR1555563", "SRX684671", "SRS687788", "SRP045679", "PRJNA258656", "Danio rerio high resolution developmental transcriptomic time course", "GSE60619", "Transcriptome Analysis", "Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This \u201cphylotypic stage\u201d has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a \u2018zootypic\u2019 stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples", "parent bioproject:PRJNA287810", "pubmed:26886793", null, "Metazome ZF timecourse sample 0071", "GSM1483806", null, "tissue:single embryo", "Metazome ZF timecourse sample 0071", "Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix", "single embryo", null, "RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.", "zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.", "time min post fertilization:2840", "GSM1483806", "GSM1483806: Metazome ZF timecourse sample 0071; Danio rerio; RNA Seq", "GSM1483806", null, "1", "RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.", "GEO Accession:GSM1483806", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP045679", null, null, "Metazome_ZF_timecourse_sample_0071.fastq.gz", "fastq", 107894360.0, 3082696.0, "GSM1483806 r1", "0:35", "A:30475809;C:22092085;G:22685204;T:32400616;N:240646", 35, null, null, null, 30475809, 22092085, 22685204, 32400616, 240646, "SRX684671", "SRS687788", "SRA179995", "GEO", "Yanai, Biology, Technion - Israel Institute of Technology", 1, 0.77637, null, 0.10375, null, 0.81574, null, 0.50918, null, 35, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Israel", "2014-08-21", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38158, "SRR1555562", "SRX684670", "SRS687787", "SRP045679", "PRJNA258656", "Danio rerio high resolution developmental transcriptomic time course", "GSE60619", "Transcriptome Analysis", "Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This \u201cphylotypic stage\u201d has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a \u2018zootypic\u2019 stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples", "parent bioproject:PRJNA287810", "pubmed:26886793", null, "Metazome ZF timecourse sample 0070", "GSM1483805", null, "tissue:single embryo", "Metazome ZF timecourse sample 0070", "Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix", "single embryo", null, "RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.", "zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.", "time min post fertilization:2800", "GSM1483805", "GSM1483805: Metazome ZF timecourse sample 0070; Danio rerio; RNA Seq", "GSM1483805", null, "1", "RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.", "GEO Accession:GSM1483805", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP045679", null, null, "Metazome_ZF_timecourse_sample_0070.fastq.gz", "fastq", 102775820.0, 2936452.0, "GSM1483805 r1", "0:35", "A:29014067;C:20865233;G:21656956;T:30738746;N:500818", 35, null, null, null, 29014067, 20865233, 21656956, 30738746, 500818, "SRX684670", "SRS687787", "SRA179995", "GEO", "Yanai, Biology, Technion - Israel Institute of Technology", 1, 0.7643, null, 0.09535, null, 0.8325, null, 0.51201, null, 35, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Israel", "2014-08-21", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38159, "SRR1555561", "SRX684669", "SRS687786", "SRP045679", "PRJNA258656", "Danio rerio high resolution developmental transcriptomic time course", "GSE60619", "Transcriptome Analysis", "Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This \u201cphylotypic stage\u201d has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a \u2018zootypic\u2019 stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples", "parent bioproject:PRJNA287810", "pubmed:26886793", null, "Metazome ZF timecourse sample 0069", "GSM1483804", null, "tissue:single embryo", "Metazome ZF timecourse sample 0069", "Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix", "single embryo", null, "RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.", "zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.", "time min post fertilization:2760", "GSM1483804", "GSM1483804: Metazome ZF timecourse sample 0069; Danio rerio; RNA Seq", "GSM1483804", null, "1", "RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.", "GEO Accession:GSM1483804", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP045679", null, null, "Metazome_ZF_timecourse_sample_0069.fastq.gz", "fastq", 178882445.0, 5110927.0, "GSM1483804 r1", "0:35", "A:51610621;C:35847602;G:36898756;T:54275519;N:249947", 35, null, null, null, 51610621, 35847602, 36898756, 54275519, 249947, "SRX684669", "SRS687786", "SRA179995", "GEO", "Yanai, Biology, Technion - Israel Institute of Technology", 1, 0.81481, null, 0.1212, null, 0.80338, null, 0.48647, null, 35, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Israel", "2014-08-21", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38160, "SRR1555560", "SRX684668", "SRS687784", "SRP045679", "PRJNA258656", "Danio rerio high resolution developmental transcriptomic time course", "GSE60619", "Transcriptome Analysis", "Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This \u201cphylotypic stage\u201d has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a \u2018zootypic\u2019 stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples", "parent bioproject:PRJNA287810", "pubmed:26886793", null, "Metazome ZF timecourse sample 0068", "GSM1483803", null, "tissue:single embryo", "Metazome ZF timecourse sample 0068", "Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix", "single embryo", null, "RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.", "zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.", "time min post fertilization:2720", "GSM1483803", "GSM1483803: Metazome ZF timecourse sample 0068; Danio rerio; RNA Seq", "GSM1483803", null, "1", "RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.", "GEO Accession:GSM1483803", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP045679", null, null, "Metazome_ZF_timecourse_sample_0068.fastq.gz", "fastq", 289924775.0, 8283565.0, "GSM1483803 r1", "0:35", "A:85968202;C:57218562;G:58533597;T:87797178;N:407236", 35, null, null, null, 85968202, 57218562, 58533597, 87797178, 407236, "SRX684668", "SRS687784", "SRA179995", "GEO", "Yanai, Biology, Technion - Israel Institute of Technology", 1, 0.78411, null, 0.12015, null, 0.80736, null, 0.5018, null, 35, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Israel", "2014-08-21", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38161, "SRR1555559", "SRX684667", "SRS687785", "SRP045679", "PRJNA258656", "Danio rerio high resolution developmental transcriptomic time course", "GSE60619", "Transcriptome Analysis", "Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This \u201cphylotypic stage\u201d has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a \u2018zootypic\u2019 stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples", "parent bioproject:PRJNA287810", "pubmed:26886793", null, "Metazome ZF timecourse sample 0067", "GSM1483802", null, "tissue:single embryo", "Metazome ZF timecourse sample 0067", "Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix", "single embryo", null, "RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.", "zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.", "time min post fertilization:2680", "GSM1483802", "GSM1483802: Metazome ZF timecourse sample 0067; Danio rerio; RNA Seq", "GSM1483802", null, "1", "RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.", "GEO Accession:GSM1483802", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP045679", null, null, "Metazome_ZF_timecourse_sample_0067.fastq.gz", "fastq", 12717355.0, 363353.0, "GSM1483802 r1", "0:35", "A:3757539;C:2504848;G:2608725;T:3830804;N:15439", 35, null, null, null, 3757539, 2504848, 2608725, 3830804, 15439, "SRX684667", "SRS687785", "SRA179995", "GEO", "Yanai, Biology, Technion - Israel Institute of Technology", 1, 0.77835, null, 0.12605, null, 0.92604, null, 0.45926, null, 35, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Israel", "2014-08-21", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38162, "SRR1555558", "SRX684666", "SRS687783", "SRP045679", "PRJNA258656", "Danio rerio high resolution developmental transcriptomic time course", "GSE60619", "Transcriptome Analysis", "Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This \u201cphylotypic stage\u201d has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a \u2018zootypic\u2019 stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples", "parent bioproject:PRJNA287810", "pubmed:26886793", null, "Metazome ZF timecourse sample 0066", "GSM1483801", null, "tissue:single embryo", "Metazome ZF timecourse sample 0066", "Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix", "single embryo", null, "RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.", "zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.", "time min post fertilization:2640", "GSM1483801", "GSM1483801: Metazome ZF timecourse sample 0066; Danio rerio; RNA Seq", "GSM1483801", null, "1", "RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.", "GEO Accession:GSM1483801", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP045679", null, null, "Metazome_ZF_timecourse_sample_0066.fastq.gz", "fastq", 5206040.0, 148744.0, "GSM1483801 r1", "0:35", "A:1490985;C:1039675;G:1088231;T:1579040;N:8109", 35, null, null, null, 1490985, 1039675, 1088231, 1579040, 8109, "SRX684666", "SRS687783", "SRA179995", "GEO", "Yanai, Biology, Technion - Israel Institute of Technology", 1, 0.77355, null, 0.11605, null, 0.96587, null, 0.48121, null, 35, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Israel", "2014-08-21", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38163, "SRR1555557", "SRX684665", "SRS687782", "SRP045679", "PRJNA258656", "Danio rerio high resolution developmental transcriptomic time course", "GSE60619", "Transcriptome Analysis", "Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This \u201cphylotypic stage\u201d has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a \u2018zootypic\u2019 stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples", "parent bioproject:PRJNA287810", "pubmed:26886793", null, "Metazome ZF timecourse sample 0065", "GSM1483800", null, "tissue:single embryo", "Metazome ZF timecourse sample 0065", "Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix", "single embryo", null, "RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.", "zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.", "time min post fertilization:2600", "GSM1483800", "GSM1483800: Metazome ZF timecourse sample 0065; Danio rerio; RNA Seq", "GSM1483800", null, "1", "RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.", "GEO Accession:GSM1483800", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP045679", null, null, "Metazome_ZF_timecourse_sample_0065.fastq.gz", "fastq", 49543620.0, 1415532.0, "GSM1483800 r1", "0:35", "A:13699613;C:9907599;G:10751987;T:15115154;N:69267", 35, null, null, null, 13699613, 9907599, 10751987, 15115154, 69267, "SRX684665", "SRS687782", "SRA179995", "GEO", "Yanai, Biology, Technion - Israel Institute of Technology", 1, 0.81049, null, 0.12615, null, 0.86367, null, 0.51632, null, 35, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Israel", "2014-08-21", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38164, "SRR1555556", "SRX684664", "SRS687781", "SRP045679", "PRJNA258656", "Danio rerio high resolution developmental transcriptomic time course", "GSE60619", "Transcriptome Analysis", "Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This \u201cphylotypic stage\u201d has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a \u2018zootypic\u2019 stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples", "parent bioproject:PRJNA287810", "pubmed:26886793", null, "Metazome ZF timecourse sample 0064", "GSM1483799", null, "tissue:single embryo", "Metazome ZF timecourse sample 0064", "Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix", "single embryo", null, "RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.", "zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.", "time min post fertilization:2560", "GSM1483799", "GSM1483799: Metazome ZF timecourse sample 0064; Danio rerio; RNA Seq", "GSM1483799", null, "1", "RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.", "GEO Accession:GSM1483799", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP045679", null, null, "Metazome_ZF_timecourse_sample_0064.fastq.gz", "fastq", 247601200.0, 7074320.0, "GSM1483799 r1", "0:35", "A:70332996;C:49278360;G:54252598;T:73390003;N:347243", 35, null, null, null, 70332996, 49278360, 54252598, 73390003, 347243, "SRX684664", "SRS687781", "SRA179995", "GEO", "Yanai, Biology, Technion - Israel Institute of Technology", 1, 0.80448, null, 0.14935, null, 0.80975, null, 0.54749, null, 35, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Israel", "2014-08-21", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38165, "SRR1555555", "SRX684663", "SRS687779", "SRP045679", "PRJNA258656", "Danio rerio high resolution developmental transcriptomic time course", "GSE60619", "Transcriptome Analysis", "Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This \u201cphylotypic stage\u201d has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a \u2018zootypic\u2019 stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples", "parent bioproject:PRJNA287810", "pubmed:26886793", null, "Metazome ZF timecourse sample 0063", "GSM1483798", null, "tissue:single embryo", "Metazome ZF timecourse sample 0063", "Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix", "single embryo", null, "RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.", "zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.", "time min post fertilization:2520", "GSM1483798", "GSM1483798: Metazome ZF timecourse sample 0063; Danio rerio; RNA Seq", "GSM1483798", null, "1", "RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.", "GEO Accession:GSM1483798", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP045679", null, null, "Metazome_ZF_timecourse_sample_0063.fastq.gz", "fastq", 139474895.0, 3984997.0, "GSM1483798 r1", "0:35", "A:39999821;C:27945450;G:29190975;T:42159133;N:179516", 35, null, null, null, 39999821, 27945450, 29190975, 42159133, 179516, "SRX684663", "SRS687779", "SRA179995", "GEO", "Yanai, Biology, Technion - Israel Institute of Technology", 1, 0.80752, null, 0.14329, null, 0.81645, null, 0.50673, null, 35, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Israel", "2014-08-21", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38166, "SRR1555554", "SRX684662", "SRS687780", "SRP045679", "PRJNA258656", "Danio rerio high resolution developmental transcriptomic time course", "GSE60619", "Transcriptome Analysis", "Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This \u201cphylotypic stage\u201d has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a \u2018zootypic\u2019 stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples", "parent bioproject:PRJNA287810", "pubmed:26886793", null, "Metazome ZF timecourse sample 0062", "GSM1483797", null, "tissue:single embryo", "Metazome ZF timecourse sample 0062", "Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix", "single embryo", null, "RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.", "zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.", "time min post fertilization:2480", "GSM1483797", "GSM1483797: Metazome ZF timecourse sample 0062; Danio rerio; RNA Seq", "GSM1483797", null, "1", "RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.", "GEO Accession:GSM1483797", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP045679", null, null, "Metazome_ZF_timecourse_sample_0062.fastq.gz", "fastq", 177095730.0, 5059878.0, "GSM1483797 r1", "0:35", "A:50196021;C:35043121;G:37861516;T:53732194;N:262878", 35, null, null, null, 50196021, 35043121, 37861516, 53732194, 262878, "SRX684662", "SRS687780", "SRA179995", "GEO", "Yanai, Biology, Technion - Israel Institute of Technology", 1, 0.81092, null, 0.13179, null, 0.8199, null, 0.49636, null, 35, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Israel", "2014-08-21", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38167, "SRR1555553", "SRX684661", "SRS687778", "SRP045679", "PRJNA258656", "Danio rerio high resolution developmental transcriptomic time course", "GSE60619", "Transcriptome Analysis", "Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This \u201cphylotypic stage\u201d has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a \u2018zootypic\u2019 stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples", "parent bioproject:PRJNA287810", "pubmed:26886793", null, "Metazome ZF timecourse sample 0061", "GSM1483796", null, "tissue:single embryo", "Metazome ZF timecourse sample 0061", "Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix", "single embryo", null, "RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.", "zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.", "time min post fertilization:2440", "GSM1483796", "GSM1483796: Metazome ZF timecourse sample 0061; Danio rerio; RNA Seq", "GSM1483796", null, "1", "RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.", "GEO Accession:GSM1483796", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP045679", null, null, "Metazome_ZF_timecourse_sample_0061.fastq.gz", "fastq", 117262810.0, 3350366.0, "GSM1483796 r1", "0:35", "A:33678050;C:23425078;G:24368870;T:35496994;N:293818", 35, null, null, null, 33678050, 23425078, 24368870, 35496994, 293818, "SRX684661", "SRS687778", "SRA179995", "GEO", "Yanai, Biology, Technion - Israel Institute of Technology", 1, 0.71242, null, 0.11354, null, 0.83514, null, 0.51134, null, 35, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Israel", "2014-08-21", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38168, "SRR1555552", "SRX684660", "SRS687777", "SRP045679", "PRJNA258656", "Danio rerio high resolution developmental transcriptomic time course", "GSE60619", "Transcriptome Analysis", "Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This \u201cphylotypic stage\u201d has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a \u2018zootypic\u2019 stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples", "parent bioproject:PRJNA287810", "pubmed:26886793", null, "Metazome ZF timecourse sample 0060", "GSM1483795", null, "tissue:single embryo", "Metazome ZF timecourse sample 0060", "Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix", "single embryo", null, "RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.", "zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.", "time min post fertilization:2400", "GSM1483795", "GSM1483795: Metazome ZF timecourse sample 0060; Danio rerio; RNA Seq", "GSM1483795", null, "1", "RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.", "GEO Accession:GSM1483795", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP045679", null, null, "Metazome_ZF_timecourse_sample_0060.fastq.gz", "fastq", 50485225.0, 1442435.0, "GSM1483795 r1", "0:35", "A:14629070;C:9936986;G:10066758;T:15611930;N:240481", 35, null, null, null, 14629070, 9936986, 10066758, 15611930, 240481, "SRX684660", "SRS687777", "SRA179995", "GEO", "Yanai, Biology, Technion - Israel Institute of Technology", 1, 0.74045, null, 0.14214, null, 0.84703, null, 0.50639, null, 35, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Israel", "2014-08-21", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38169, "SRR1555551", "SRX684659", "SRS687776", "SRP045679", "PRJNA258656", "Danio rerio high resolution developmental transcriptomic time course", "GSE60619", "Transcriptome Analysis", "Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This \u201cphylotypic stage\u201d has recently received support from transcriptome analyses which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a \u2018zootypic\u2019 stage however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum including a segmented worm a flatworm a roundworm a water bear a fruitfly a sea urchin a zebrafish a sea anemone a sponge and a comb jelly. For each species we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples", "parent bioproject:PRJNA287810", "pubmed:26886793", null, "Metazome ZF timecourse sample 0059", "GSM1483794", null, "tissue:single embryo", "Metazome ZF timecourse sample 0059", "Libraries were sequenced on the Illumina HiSeq2000 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et a. 2012l demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix", "single embryo", null, "RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.", "zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.", "time min post fertilization:2360", "GSM1483794", "GSM1483794: Metazome ZF timecourse sample 0059; Danio rerio; RNA Seq", "GSM1483794", null, "1", "RNA was isolated using TRIzol as previously described Levin et al. 2012. The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.", "GEO Accession:GSM1483794", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP045679", null, null, "Metazome_ZF_timecourse_sample_0059.fastq.gz", "fastq", 129110905.0, 3688883.0, "GSM1483794 r1", "0:35", "A:37661404;C:25258511;G:25987964;T:39941302;N:261724", 35, null, null, null, 37661404, 25258511, 25987964, 39941302, 261724, "SRX684659", "SRS687776", "SRA179995", "GEO", "Yanai, Biology, Technion - Israel Institute of Technology", 1, 0.74152, null, 0.13117, null, 0.81749, null, 0.51022, null, 35, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Israel", "2014-08-21", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"]], "truncated": false, "filtered_table_rows_count": 355, "expanded_columns": [], "expandable_columns": [], "columns": ["rowid", "run.accession", "experiment.accession", 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"tissue_curation", "tissue_curation_coarse"], "primary_keys": [], "units": {}, "query": {"sql": "select rowid, [run.accession], [experiment.accession], [sample.accession], [study.accession], bioproject, [study.title], [study.alias], [study.type], [study.abstract], [study.attributes], [study.PMIDs], [sample.description], [sample.title], [sample.alias], [sample.centername], [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.spot_descriptor], [experiment.study_ref], [run.title], [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.r3_length], [run.r4_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, tech_variant, [submission.bioprojectsource.country], earliest_date, devstage_curation, devstage_curation_coarse, tissue_curation, tissue_curation_coarse from run_metadata where \"technology\" = :p0 and \"tissue_curation_coarse\" = :p1 order by rowid limit 101", "params": {"p0": "celseq", "p1": "All anatomical structures"}}, "facet_results": {"experiment.library_strategy": {"name": "experiment.library_strategy", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?technology=celseq&tissue_curation_coarse=All+anatomical+structures", "results": [{"value": "RNA-Seq", "label": "RNA-Seq", "count": 355, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?technology=celseq&tissue_curation_coarse=All+anatomical+structures&experiment.library_strategy=RNA-Seq", "selected": false}], "truncated": false}, "experiment.library_source": {"name": "experiment.library_source", "type": "column", "hideable": false, "toggle_url": 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"toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?technology=celseq&tissue_curation_coarse=All+anatomical+structures&experiment.library_selection=cDNA", "selected": false}, {"value": "RANDOM", "label": "RANDOM", "count": 8, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?technology=celseq&tissue_curation_coarse=All+anatomical+structures&experiment.library_selection=RANDOM", "selected": false}], "truncated": false}, "experiment.library_layout": {"name": "experiment.library_layout", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?technology=celseq&tissue_curation_coarse=All+anatomical+structures", "results": [{"value": "PAIRED", "label": "PAIRED", "count": 178, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?technology=celseq&tissue_curation_coarse=All+anatomical+structures&experiment.library_layout=PAIRED", "selected": false}, {"value": "SINGLE", "label": "SINGLE", "count": 177, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?technology=celseq&tissue_curation_coarse=All+anatomical+structures&experiment.library_layout=SINGLE", "selected": false}], "truncated": false}, "experiment.platform": {"name": "experiment.platform", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?technology=celseq&tissue_curation_coarse=All+anatomical+structures", "results": [{"value": "ILLUMINA", "label": "ILLUMINA", "count": 355, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?technology=celseq&tissue_curation_coarse=All+anatomical+structures&experiment.platform=ILLUMINA", "selected": false}], "truncated": false}, "devstage_curation_coarse": {"name": "devstage_curation_coarse", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?technology=celseq&tissue_curation_coarse=All+anatomical+structures", "results": [{"value": "Embryo", "label": "Embryo", "count": 298, "toggle_url": 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