{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where devstage_curation = \"Gastrula\" and experiment.library_selection = \"RANDOM\"", "rows": [[8088, "ERR034127", "ERX012653", "ERS032268", "ERP000635", "PRJEB2512", "The Zebrafish transcriptome during early development", "KI-BN-JKE-DRERIO-RNASEQ-2011", "Transcriptome Analysis", "Background: Zebrafish Danio rerio is an important model for the study of early vertebrate development. The transition from fertilized egg to embryo is accompanied by a multitude of changes in gene expression and the transcriptional events that underlie these processes have not been fully characterized. In this study we use RNA Seq to characterize and compare the transcriptome of four early developmental stages in zebrafish on a global scale. Results: An average of 79M total reads were detected from the different stages. Out of the total number of reads 65% 73% reads were successfully mapped to the zebrafish genome and 36% 44% out of those were uniquely mapped. The total number of detected unique gene transcripts was 11187 of which 10096 of these were already present at 1 cell stage. The largest number of common transcripts was observed between 1 cell stage and 16 cell stage. An enrichment of gene transcripts with molecular functions of DNA binding protein folding and processing as well as metal ion binding was observed with progression of development. To confirm our RNA Seq results and to further investigate the developmental expression of specific genes the transcript levels of a subset of genes were analyzed using TaqMan\u00ae array micro fluidic card TLDA. Conclusion: Clustering analysis of the detected transcripts show a majority of gene transcripts being present at steady levels with a minority of the gene transcripts clustering as increasing or decreasing in expression during development. Developmental stages pre MBT were similar when comparing highly expressed genes whereas 50% epiboly stage differed from the earlier three stages in highly expressed genes number of uniquely expressed genes and enrichment of GO molecular functions.", null, null, "RNA extracted from zebrafish embryo at 50% epiboly stage", "zebrafish embryo 50 epiboly", "SAMEA791629", "Department of Biosciences and Nutrition, Karolinska Institutet, Sweden", "ENA first public:2011 06 09|ENA last update:2018 03 08|External Id:SAMEA791629|INSDC center alias:KI BN|INSDC center name:Department of Biosciences and Nutrition Karolinska Institutet Sweden|INSDC first public:2011 06 09T11:04:10Z|INSDC last update:2018 03 08T15:26:39Z|INSDC status:public|Submitter Id:KI BN JKE DRERIO RNASEQ 2011 50epiboly|common name:zebrafish|sample name:KI BN JKE DRERIO RNASEQ 2011 50epiboly|sex:mixed|strain:Tuebingen", null, null, null, null, null, null, null, null, "Transcriptome profiling of early zebrafish development", "KI BN JKE DRERIO RNASEQ 2011 50epiboly", "JKE Drerio rna seq", "Transcriptome profiling of 50% epiboly stages of zebrafish embryos.", "Total RNA was extracted from approximately 150 embryos per developmental stage using Trireagent Sigma Aldrich. The total RNA was then processed further according to the Small RNA Expression Kit Applied Biosystems.", null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ABI_SOLID", "AB SOLiD System 3.0", "500Application ReadForward1", "ERP000635", "AB SOLiD System 3.0 sequencing; Transcriptome profiling of early zebrafish development", "ENA FIRST PUBLIC:2011 06 09|ENA LAST UPDATE:2018 11 16", "KI-BN-JKE-DRERIO-RNASEQ-2011-50epiboly.csfasta.gz KI-BN-JKE-DRERIO-RNASEQ-2011-50epiboly_QV.qual.gz", "SOLiD_native SOLiD_native", 3929903550.0, 78598071.0, "KI BN JKE DRERIO RNASEQ 2011 50epiboly", "0:50", null, 50, null, null, null, null, null, null, null, null, "ERX012653", "ERS032268", "ERA029959", "KI-BN|Department of Biosciences and Nutrition", "Department of Biosciences and Nutrition, Karolinska Institutet, Sweden", 1, 0.60757, null, 0.09893, null, 0.94899, null, 0.77821, null, 50, null, "B", null, "usable mapping rate", "legacy", "early", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "Sweden", "2011-06-09", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [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"], [51275, "SRR8663328", "SRX5460025", "SRS4433915", "SRP187415", "PRJNA525392", "Whole transcriptome bisufilte sequencing for multiple species [Zebrafish]", "GSE127779", "Other", "We applied a robust experimental and computational framework to identify mRNA m5C sites with high specificity in multiple species. Overall design: RNA BS seq of mRNA for multiple species.", "parent bioproject:PRJNA525389", "pubmed:35513466", null, "ZF 10hpf rep2", "GSM3638669", null, "source name:embryo|tissue:embryo|developmental stage:10 hpf|strain:wild type AB fish", "ZF 10hpf rep2", "Basecalls performed using illumina bcl2fastq 2.17. Adapters were trimmed with cutadapt. Adapter trimmed reads were quality trimmed with Trimmomatic. Clean reads were firstly mapped to the genome and then transcriptome with hisat2 2.10 Pileup was performed using samtools API pysam. Customized scripts were used to call m5C sites from samples Genome build: Zv9.78 Supplementary files format and content: CSV files recording the coverage m5C level P value for m5C sites", "embryo", null, "For the embryonic stages 200 embryos were collected and for the larval stage 150 larvae were collected. Total RNA was isolated with TRIzol reagent and Direct zol RNA MiniPrep kit. Polyadenylated RNA was separated from total RNA using Oligo dT Magnetic Beads Vazyme. 100ng 1\u03bcg of polyadenylated RNA was converted using the EZ RNA methylation kit Zymo Research with modified high stringency conversion conditions. The quantity of the converted RNA was determined by Qubit. 20ng converted RNA was fragmented into 150200 nt fragments by incubation at 94 \u00b0C for 8min in fragmentation buffer NEBNext Ultra II Directional RNA Library Prep Kit NEB. The fragmented RNA was then used for library construction following the manufacturer\u2019s protocol NEBNext Ultra II Directional RNA Library Prep Kit NEB.", "Embryos were reared at 28.5 \u00b0C and all experiments and observations were performed as close to this temperature as possible.", "tissue:embryo|developmental stage:10 hpf|strain:wild type AB fish", "GSM3638669", "GSM3638669: ZF 10hpf rep2; Danio rerio; Bisulfite Seq", "GSM3638669", null, "1", "For the embryonic stages 200 embryos were collected and for the larval stage 150 larvae were collected. Total RNA was isolated with TRIzol reagent and Direct zol RNA MiniPrep kit. Polyadenylated RNA was separated from total RNA using Oligo dT Magnetic Beads Vazyme. 100ng 1\u03bcg of polyadenylated RNA was converted using the EZ RNA methylation kit Zymo Research with modified high stringency conversion conditions. The quantity of the converted RNA was determined by Qubit. 20ng converted RNA was fragmented into 150200 nt fragments by incubation at 94 \u00b0C for 8min in fragmentation buffer NEBNext Ultra II Directional RNA Library Prep Kit NEB. The fragmented RNA was then used for library construction following the manufacturer's protocol NEBNext Ultra II Directional RNA Library Prep Kit NEB.", "GEO Accession:GSM3638669", "Bisulfite-Seq", "TRANSCRIPTOMIC", "RANDOM", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP187415", null, null, null, null, 18449316900.0, 61497723.0, "GSM3638669 r1", "0:150 1:150", "A:6508135454;C:2695665097;G:2948776234;T:6296104735;N:635380", 150, 150, null, null, 6508135454, 2695665097, 2948776234, 6296104735, 635380, "SRX5460025", "SRS4433915", "SRA855736", "GEO", "Sun Yat-sen University", 2, 0.00092, 0.00073, 0.00035, 0.00017, 0.99931, 0.99933, 0.66019, 0.6129, 150, 150, "T", "T", "mates < 9% mapping rate", "illumina", "hiseq_era", "full_length", "random_priming", "nebnext", "bulk", "unknown", "unknown", null, "China", "2019-03-04", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [51276, "SRR8663327", "SRX5460024", "SRS4433914", "SRP187415", "PRJNA525392", "Whole transcriptome bisufilte sequencing for multiple species [Zebrafish]", "GSE127779", "Other", "We applied a robust experimental and computational framework to identify mRNA m5C sites with high specificity in multiple species. Overall design: RNA BS seq of mRNA for multiple species.", "parent bioproject:PRJNA525389", "pubmed:35513466", null, "ZF 10hpf rep1", "GSM3638668", null, "source name:embryo|tissue:embryo|developmental stage:10 hpf|strain:wild type AB fish", "ZF 10hpf rep1", "Basecalls performed using illumina bcl2fastq 2.17. Adapters were trimmed with cutadapt. Adapter trimmed reads were quality trimmed with Trimmomatic. Clean reads were firstly mapped to the genome and then transcriptome with hisat2 2.10 Pileup was performed using samtools API pysam. Customized scripts were used to call m5C sites from samples Genome build: Zv9.78 Supplementary files format and content: CSV files recording the coverage m5C level P value for m5C sites", "embryo", null, "For the embryonic stages 200 embryos were collected and for the larval stage 150 larvae were collected. Total RNA was isolated with TRIzol reagent and Direct zol RNA MiniPrep kit. Polyadenylated RNA was separated from total RNA using Oligo dT Magnetic Beads Vazyme. 100ng 1\u03bcg of polyadenylated RNA was converted using the EZ RNA methylation kit Zymo Research with modified high stringency conversion conditions. The quantity of the converted RNA was determined by Qubit. 20ng converted RNA was fragmented into 150200 nt fragments by incubation at 94 \u00b0C for 8min in fragmentation buffer NEBNext Ultra II Directional RNA Library Prep Kit NEB. The fragmented RNA was then used for library construction following the manufacturer\u2019s protocol NEBNext Ultra II Directional RNA Library Prep Kit NEB.", "Embryos were reared at 28.5 \u00b0C and all experiments and observations were performed as close to this temperature as possible.", "tissue:embryo|developmental stage:10 hpf|strain:wild type AB fish", "GSM3638668", "GSM3638668: ZF 10hpf rep1; Danio rerio; Bisulfite Seq", "GSM3638668", null, "1", "For the embryonic stages 200 embryos were collected and for the larval stage 150 larvae were collected. Total RNA was isolated with TRIzol reagent and Direct zol RNA MiniPrep kit. Polyadenylated RNA was separated from total RNA using Oligo dT Magnetic Beads Vazyme. 100ng 1\u03bcg of polyadenylated RNA was converted using the EZ RNA methylation kit Zymo Research with modified high stringency conversion conditions. The quantity of the converted RNA was determined by Qubit. 20ng converted RNA was fragmented into 150200 nt fragments by incubation at 94 \u00b0C for 8min in fragmentation buffer NEBNext Ultra II Directional RNA Library Prep Kit NEB. The fragmented RNA was then used for library construction following the manufacturer's protocol NEBNext Ultra II Directional RNA Library Prep Kit NEB.", "GEO Accession:GSM3638668", "Bisulfite-Seq", "TRANSCRIPTOMIC", "RANDOM", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP187415", null, null, null, null, 35064552300.0, 116881841.0, "GSM3638668 r1", "0:150 1:150", "A:12442483305;C:5073538954;G:5489080636;T:12058238019;N:1211386", 150, 150, null, null, 12442483305, 5073538954, 5489080636, 12058238019, 1211386, "SRX5460024", "SRS4433914", "SRA855736", "GEO", "Sun Yat-sen University", 2, 0.0009, 0.00072, 0.00028, 0.00019, 0.99926, 0.99945, 0.61403, 0.67045, 150, 150, "T", "T", "mates < 9% mapping rate", "illumina", "hiseq_era", "full_length", "random_priming", "nebnext", "bulk", "unknown", "unknown", null, "China", "2019-03-04", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [51277, "SRR8663326", "SRX5460023", "SRS4433913", "SRP187415", "PRJNA525392", "Whole transcriptome bisufilte sequencing for multiple species [Zebrafish]", "GSE127779", "Other", "We applied a robust experimental and computational framework to identify mRNA m5C sites with high specificity in multiple species. Overall design: RNA BS seq of mRNA for multiple species.", "parent bioproject:PRJNA525389", "pubmed:35513466", null, "ZF 8hpf rep2", "GSM3638667", null, "source name:embryo|tissue:embryo|developmental stage:8 hpf|strain:wild type AB fish", "ZF 8hpf rep2", "Basecalls performed using illumina bcl2fastq 2.17. Adapters were trimmed with cutadapt. Adapter trimmed reads were quality trimmed with Trimmomatic. Clean reads were firstly mapped to the genome and then transcriptome with hisat2 2.10 Pileup was performed using samtools API pysam. Customized scripts were used to call m5C sites from samples Genome build: Zv9.78 Supplementary files format and content: CSV files recording the coverage m5C level P value for m5C sites", "embryo", null, "For the embryonic stages 200 embryos were collected and for the larval stage 150 larvae were collected. Total RNA was isolated with TRIzol reagent and Direct zol RNA MiniPrep kit. Polyadenylated RNA was separated from total RNA using Oligo dT Magnetic Beads Vazyme. 100ng 1\u03bcg of polyadenylated RNA was converted using the EZ RNA methylation kit Zymo Research with modified high stringency conversion conditions. The quantity of the converted RNA was determined by Qubit. 20ng converted RNA was fragmented into 150200 nt fragments by incubation at 94 \u00b0C for 8min in fragmentation buffer NEBNext Ultra II Directional RNA Library Prep Kit NEB. The fragmented RNA was then used for library construction following the manufacturer\u2019s protocol NEBNext Ultra II Directional RNA Library Prep Kit NEB.", "Embryos were reared at 28.5 \u00b0C and all experiments and observations were performed as close to this temperature as possible.", "tissue:embryo|developmental stage:8 hpf|strain:wild type AB fish", "GSM3638667", "GSM3638667: ZF 8hpf rep2; Danio rerio; Bisulfite Seq", "GSM3638667", null, "1", "For the embryonic stages 200 embryos were collected and for the larval stage 150 larvae were collected. Total RNA was isolated with TRIzol reagent and Direct zol RNA MiniPrep kit. Polyadenylated RNA was separated from total RNA using Oligo dT Magnetic Beads Vazyme. 100ng 1\u03bcg of polyadenylated RNA was converted using the EZ RNA methylation kit Zymo Research with modified high stringency conversion conditions. The quantity of the converted RNA was determined by Qubit. 20ng converted RNA was fragmented into 150200 nt fragments by incubation at 94 \u00b0C for 8min in fragmentation buffer NEBNext Ultra II Directional RNA Library Prep Kit NEB. The fragmented RNA was then used for library construction following the manufacturer's protocol NEBNext Ultra II Directional RNA Library Prep Kit NEB.", "GEO Accession:GSM3638667", "Bisulfite-Seq", "TRANSCRIPTOMIC", "RANDOM", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP187415", null, null, null, null, 14346635400.0, 47822118.0, "GSM3638667 r1", "0:150 1:150", "A:5096565523;C:2082957184;G:2242869596;T:4923737869;N:505228", 150, 150, null, null, 5096565523, 2082957184, 2242869596, 4923737869, 505228, "SRX5460023", "SRS4433913", "SRA855736", "GEO", "Sun Yat-sen University", 2, 0.00107, 0.00102, 0.00035, 0.00021, 0.99884, 0.99884, 0.61068, 0.71428, 150, 150, "T", "T", "mates < 9% mapping rate", "illumina", "hiseq_era", "full_length", "random_priming", "nebnext", "bulk", "unknown", "unknown", null, "China", "2019-03-04", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [51278, "SRR8663325", "SRX5460022", "SRS4433912", "SRP187415", "PRJNA525392", "Whole transcriptome bisufilte sequencing for multiple species [Zebrafish]", "GSE127779", "Other", "We applied a robust experimental and computational framework to identify mRNA m5C sites with high specificity in multiple species. Overall design: RNA BS seq of mRNA for multiple species.", "parent bioproject:PRJNA525389", "pubmed:35513466", null, "ZF 8hpf rep1", "GSM3638666", null, "source name:embryo|tissue:embryo|developmental stage:8 hpf|strain:wild type AB fish", "ZF 8hpf rep1", "Basecalls performed using illumina bcl2fastq 2.17. Adapters were trimmed with cutadapt. Adapter trimmed reads were quality trimmed with Trimmomatic. Clean reads were firstly mapped to the genome and then transcriptome with hisat2 2.10 Pileup was performed using samtools API pysam. Customized scripts were used to call m5C sites from samples Genome build: Zv9.78 Supplementary files format and content: CSV files recording the coverage m5C level P value for m5C sites", "embryo", null, "For the embryonic stages 200 embryos were collected and for the larval stage 150 larvae were collected. Total RNA was isolated with TRIzol reagent and Direct zol RNA MiniPrep kit. Polyadenylated RNA was separated from total RNA using Oligo dT Magnetic Beads Vazyme. 100ng 1\u03bcg of polyadenylated RNA was converted using the EZ RNA methylation kit Zymo Research with modified high stringency conversion conditions. The quantity of the converted RNA was determined by Qubit. 20ng converted RNA was fragmented into 150200 nt fragments by incubation at 94 \u00b0C for 8min in fragmentation buffer NEBNext Ultra II Directional RNA Library Prep Kit NEB. The fragmented RNA was then used for library construction following the manufacturer\u2019s protocol NEBNext Ultra II Directional RNA Library Prep Kit NEB.", "Embryos were reared at 28.5 \u00b0C and all experiments and observations were performed as close to this temperature as possible.", "tissue:embryo|developmental stage:8 hpf|strain:wild type AB fish", "GSM3638666", "GSM3638666: ZF 8hpf rep1; Danio rerio; Bisulfite Seq", "GSM3638666", null, "1", "For the embryonic stages 200 embryos were collected and for the larval stage 150 larvae were collected. Total RNA was isolated with TRIzol reagent and Direct zol RNA MiniPrep kit. Polyadenylated RNA was separated from total RNA using Oligo dT Magnetic Beads Vazyme. 100ng 1\u03bcg of polyadenylated RNA was converted using the EZ RNA methylation kit Zymo Research with modified high stringency conversion conditions. The quantity of the converted RNA was determined by Qubit. 20ng converted RNA was fragmented into 150200 nt fragments by incubation at 94 \u00b0C for 8min in fragmentation buffer NEBNext Ultra II Directional RNA Library Prep Kit NEB. The fragmented RNA was then used for library construction following the manufacturer's protocol NEBNext Ultra II Directional RNA Library Prep Kit NEB.", "GEO Accession:GSM3638666", "Bisulfite-Seq", "TRANSCRIPTOMIC", "RANDOM", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP187415", null, null, null, null, 22564435500.0, 75214785.0, "GSM3638666 r1", "0:150 1:150", "A:8037530388;C:3263669666;G:3467393764;T:7794998569;N:843113", 150, 150, null, null, 8037530388, 3263669666, 3467393764, 7794998569, 843113, "SRX5460022", "SRS4433912", "SRA855736", "GEO", "Sun Yat-sen University", 2, 0.00089, 0.00082, 0.00026, 0.0002, 0.99939, 0.99939, 0.71171, 0.73267, 150, 150, "T", "T", "mates < 9% mapping rate", "illumina", "hiseq_era", "full_length", "random_priming", "nebnext", "bulk", "unknown", "unknown", null, "China", "2019-03-04", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [51279, "SRR8663324", "SRX5460021", "SRS4433911", "SRP187415", "PRJNA525392", "Whole transcriptome bisufilte sequencing for multiple species [Zebrafish]", "GSE127779", "Other", "We applied a robust experimental and computational framework to identify mRNA m5C sites with high specificity in multiple species. Overall design: RNA BS seq of mRNA for multiple species.", "parent bioproject:PRJNA525389", "pubmed:35513466", null, "ZF 6hpf rep2", "GSM3638665", null, "source name:embryo|tissue:embryo|developmental stage:6 hpf|strain:wild type AB fish", "ZF 6hpf rep2", "Basecalls performed using illumina bcl2fastq 2.17. Adapters were trimmed with cutadapt. Adapter trimmed reads were quality trimmed with Trimmomatic. Clean reads were firstly mapped to the genome and then transcriptome with hisat2 2.10 Pileup was performed using samtools API pysam. Customized scripts were used to call m5C sites from samples Genome build: Zv9.78 Supplementary files format and content: CSV files recording the coverage m5C level P value for m5C sites", "embryo", null, "For the embryonic stages 200 embryos were collected and for the larval stage 150 larvae were collected. Total RNA was isolated with TRIzol reagent and Direct zol RNA MiniPrep kit. Polyadenylated RNA was separated from total RNA using Oligo dT Magnetic Beads Vazyme. 100ng 1\u03bcg of polyadenylated RNA was converted using the EZ RNA methylation kit Zymo Research with modified high stringency conversion conditions. The quantity of the converted RNA was determined by Qubit. 20ng converted RNA was fragmented into 150200 nt fragments by incubation at 94 \u00b0C for 8min in fragmentation buffer NEBNext Ultra II Directional RNA Library Prep Kit NEB. The fragmented RNA was then used for library construction following the manufacturer\u2019s protocol NEBNext Ultra II Directional RNA Library Prep Kit NEB.", "Embryos were reared at 28.5 \u00b0C and all experiments and observations were performed as close to this temperature as possible.", "tissue:embryo|developmental stage:6 hpf|strain:wild type AB fish", "GSM3638665", "GSM3638665: ZF 6hpf rep2; Danio rerio; Bisulfite Seq", "GSM3638665", null, "1", "For the embryonic stages 200 embryos were collected and for the larval stage 150 larvae were collected. Total RNA was isolated with TRIzol reagent and Direct zol RNA MiniPrep kit. Polyadenylated RNA was separated from total RNA using Oligo dT Magnetic Beads Vazyme. 100ng 1\u03bcg of polyadenylated RNA was converted using the EZ RNA methylation kit Zymo Research with modified high stringency conversion conditions. The quantity of the converted RNA was determined by Qubit. 20ng converted RNA was fragmented into 150200 nt fragments by incubation at 94 \u00b0C for 8min in fragmentation buffer NEBNext Ultra II Directional RNA Library Prep Kit NEB. The fragmented RNA was then used for library construction following the manufacturer's protocol NEBNext Ultra II Directional RNA Library Prep Kit NEB.", "GEO Accession:GSM3638665", "Bisulfite-Seq", "TRANSCRIPTOMIC", "RANDOM", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP187415", null, null, null, null, 15663840300.0, 52212801.0, "GSM3638665 r1", "0:150 1:150", "A:5036459488;C:2768054214;G:3109386160;T:4747198752;N:2741686", 150, 150, null, null, 5036459488, 2768054214, 3109386160, 4747198752, 2741686, "SRX5460021", "SRS4433911", "SRA855736", "GEO", "Sun Yat-sen University", 2, 0.00121, 0.0008, 0.00062, 0.00035, 0.99922, 0.99924, 0.41509, 0.40789, 150, 150, "T", "T", "mates < 9% mapping rate", "illumina", "hiseq_era", "full_length", "random_priming", "nebnext", "bulk", "unknown", "unknown", null, "China", "2019-03-04", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [51280, "SRR8663323", "SRX5460020", "SRS4433910", "SRP187415", "PRJNA525392", "Whole transcriptome bisufilte sequencing for multiple species [Zebrafish]", "GSE127779", "Other", "We applied a robust experimental and computational framework to identify mRNA m5C sites with high specificity in multiple species. Overall design: RNA BS seq of mRNA for multiple species.", "parent bioproject:PRJNA525389", "pubmed:35513466", null, "ZF 6hpf rep1", "GSM3638664", null, "source name:embryo|tissue:embryo|developmental stage:6 hpf|strain:wild type AB fish", "ZF 6hpf rep1", "Basecalls performed using illumina bcl2fastq 2.17. Adapters were trimmed with cutadapt. Adapter trimmed reads were quality trimmed with Trimmomatic. Clean reads were firstly mapped to the genome and then transcriptome with hisat2 2.10 Pileup was performed using samtools API pysam. Customized scripts were used to call m5C sites from samples Genome build: Zv9.78 Supplementary files format and content: CSV files recording the coverage m5C level P value for m5C sites", "embryo", null, "For the embryonic stages 200 embryos were collected and for the larval stage 150 larvae were collected. Total RNA was isolated with TRIzol reagent and Direct zol RNA MiniPrep kit. Polyadenylated RNA was separated from total RNA using Oligo dT Magnetic Beads Vazyme. 100ng 1\u03bcg of polyadenylated RNA was converted using the EZ RNA methylation kit Zymo Research with modified high stringency conversion conditions. The quantity of the converted RNA was determined by Qubit. 20ng converted RNA was fragmented into 150200 nt fragments by incubation at 94 \u00b0C for 8min in fragmentation buffer NEBNext Ultra II Directional RNA Library Prep Kit NEB. The fragmented RNA was then used for library construction following the manufacturer\u2019s protocol NEBNext Ultra II Directional RNA Library Prep Kit NEB.", "Embryos were reared at 28.5 \u00b0C and all experiments and observations were performed as close to this temperature as possible.", "tissue:embryo|developmental stage:6 hpf|strain:wild type AB fish", "GSM3638664", "GSM3638664: ZF 6hpf rep1; Danio rerio; Bisulfite Seq", "GSM3638664", null, "1", "For the embryonic stages 200 embryos were collected and for the larval stage 150 larvae were collected. Total RNA was isolated with TRIzol reagent and Direct zol RNA MiniPrep kit. Polyadenylated RNA was separated from total RNA using Oligo dT Magnetic Beads Vazyme. 100ng 1\u03bcg of polyadenylated RNA was converted using the EZ RNA methylation kit Zymo Research with modified high stringency conversion conditions. The quantity of the converted RNA was determined by Qubit. 20ng converted RNA was fragmented into 150200 nt fragments by incubation at 94 \u00b0C for 8min in fragmentation buffer NEBNext Ultra II Directional RNA Library Prep Kit NEB. The fragmented RNA was then used for library construction following the manufacturer's protocol NEBNext Ultra II Directional RNA Library Prep Kit NEB.", "GEO Accession:GSM3638664", "Bisulfite-Seq", "TRANSCRIPTOMIC", "RANDOM", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP187415", null, null, null, null, 13146289500.0, 43820965.0, "GSM3638664 r1", "0:150 1:150", "A:4440608717;C:2140855274;G:2250243580;T:4312362152;N:2219777", 150, 150, null, null, 4440608717, 2140855274, 2250243580, 4312362152, 2219777, "SRX5460020", "SRS4433910", "SRA855736", "GEO", "Sun Yat-sen University", 2, 0.00073, 0.00047, 0.00038, 0.00014, 0.99945, 0.99941, 0.32812, 0.5, 150, 150, "T", "T", "mates < 9% mapping rate", "illumina", "hiseq_era", "full_length", "random_priming", "nebnext", "bulk", "unknown", "unknown", null, "China", "2019-03-04", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [52242, "SRR9047069", "SRX5823596", "SRS4751717", "SRP198207", "PRJNA542583", "Migrasomes provide regional cues for organ morphogenesis during zebrafish gastrulation", "PRJNA542583", "Other", "Our study shows that migrasomes are signaling organelles which provide specific biochemical information to coordinate organ morphogenesis.", null, null, null, "stdMO PBS", "stdMO PBS", null, "strain:Tu|isolate:primary cell|dev stage:gastrulation|sex:not determined|tissue:embryo|collection date:2016 11 13|genotype:wild type|geo loc name:China: Beijing|sample type:embryos|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "tspan RNA seq", "uniprot", "uniprot", "RNA seq", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "BGISEQ", "BGISEQ-500", null, "SRP198207", null, null, "161214_I137_FCHF7TTBBXX_L2_WHFISclfRAAARAAPEI-203_1.fq.gz", "fastq", 633650654.0, 12931646.0, "161214 I137 FCHF7TTBBXX L2 WHFISclfRAAARAAPEI 203 1.fq.gz", "0:49 1:0", "A:165787428;C:152969494;G:145599180;T:169168973;N:125579", 49, 0, null, null, 165787428, 152969494, 145599180, 169168973, 125579, "SRX5823596", "SRS4751717", "SRA885639", "Tsinghua University|School of Life Sciences", "Tsinghua University", 1, 0.93004, null, 0.09559, null, 0.753, null, 0.47488, null, 49, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2019-05-30", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [53396, "SRR9849859", "SRX6604469", "SRS5169412", "SRP216580", "PRJNA556992", "Global identification of circular RNAs during zebrafish embryogenesis", "PRJNA556992", "Other", "Fertilization and embryo development guarantee the activation of totipotent zygote and tissues formation. Over past few yrs thousands of circRNAs have been identified in various animals representing a ubiquitous set of non coding RNA and conserved mechanism as essential biological functions. We sequenced RNA time series of stages with RNase R treated approach during zebrafish development in the present.", null, null, null, null, "8h", null, "cultivar:Danio rerio|age:8hpf stage:gastrula|sex:not determined|tissue:not applicable|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "circRNA 8h 2", "8h 2", "8h 2", "circRNA sequence using embryo from zebrafish 8 hpf", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP216580", null, null, "8h-1_Clean_1.fq.gz 8h-1_Clean_2.fq.gz", "fastq fastq", 10251074214.0, 34220438.0, "8h 1 Clean 1.fq.gz", "0:149.78 1:149.78", "A:2756560112;C:2322673379;G:2413816656;T:2757047449;N:976618", 149, 149, null, null, 2756560112, 2322673379, 2413816656, 2757047449, 976618, "SRX6604469", "SRS5169412", "SRA927972", "Guangxi Academy of Fishery Sciences|Guangxi Academy of Fishery Sciences", "Guangxi Academy of Fishery Sciences", 2, 0.64563, 0.64819, 0.2964, 0.2935, 0.8314, 0.84045, 0.48159, 0.45437, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2019-07-27", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [53399, "SRR9849862", "SRX6604466", "SRS5169412", "SRP216580", "PRJNA556992", "Global identification of circular RNAs during zebrafish embryogenesis", "PRJNA556992", "Other", "Fertilization and embryo development guarantee the activation of totipotent zygote and tissues formation. Over past few yrs thousands of circRNAs have been identified in various animals representing a ubiquitous set of non coding RNA and conserved mechanism as essential biological functions. We sequenced RNA time series of stages with RNase R treated approach during zebrafish development in the present.", null, null, null, null, "8h", null, "cultivar:Danio rerio|age:8hpf stage:gastrula|sex:not determined|tissue:not applicable|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "circRNA 8h 1", "8h 1", "8h 1", "circRNA sequence using embryo from zebrafish 8 hpf", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP216580", null, null, "BN2-428_L3_54.R1.clean.fastq.gz BN2-428_L3_54.R2.clean.fastq.gz", "fastq fastq", 9969874200.0, 33232914.0, "BN2 428 L3 54.R1.clean.fastq.gz", "0:150 1:150", "A:1837074577;C:2926406946;G:3018549867;T:2186360288;N:1482522", 150, 150, null, null, 1837074577, 2926406946, 3018549867, 2186360288, 1482522, "SRX6604466", "SRS5169412", "SRA927972", "Guangxi Academy of Fishery Sciences|Guangxi Academy of Fishery Sciences", "Guangxi Academy of Fishery Sciences", 2, 0.87531, 0.86035, 0.62205, 0.60979, 0.97538, 0.97621, 0.56075, 0.59936, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2019-07-27", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"]], "truncated": false, "filtered_table_rows_count": 18, "expanded_columns": [], "expandable_columns": [], "columns": ["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", 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