rowid,run.accession,experiment.accession,sample.accession,study.accession,bioproject,study.title,study.alias,study.type,study.abstract,study.attributes,study.PMIDs,sample.description,sample.title,sample.alias,sample.centername,sample.attributes,GEOsample.title,GEOsample.dataprocessing,GEOsample.source,GEOsample.treatmentprotocol,GEOsample.extractprotocol,GEOsample.growthprotocol,GEOsample.characteristics,GEOsample.accession,experiment.title,experiment.alias,experiment.library_name,experiment.design_description,experiment.library_construction_protocol,experiment.attributes,experiment.library_strategy,experiment.library_source,experiment.library_selection,experiment.library_layout,experiment.platform,experiment.instrument_model,experiment.spot_descriptor,experiment.study_ref,run.title,run.attributes,run.filename,run.semantic_name,run.total_bases,run.total_spots,run.alias,run.read_lengths,run.base_counts,run.r1_length,run.r2_length,run.r3_length,run.r4_length,run.Acount,run.Ccount,run.Gcount,run.Tcount,run.Ncount,run.experiment,run.pool_member,submission.accession,submission.srasource,submission.bioprojectsource,seqdetective.n_mates,seqdetective.mapping_rate.mate1,seqdetective.mapping_rate.mate2,seqdetective.nofeature_rate.mate1,seqdetective.nofeature_rate.mate2,seqdetective.sparsity.mate1,seqdetective.sparsity.mate2,seqdetective.pos_strand_rate.mate1,seqdetective.pos_strand_rate.mate2,seqdetective.readlen.mate1,seqdetective.readlen.mate2,seqdetective.judgement.mate1,seqdetective.judgement.mate2,seqdetective.judgement.reason,platform_family,instrument_generation,read_bias,selection_class,prep_kit,sc_or_bulk,tech_class,technology,tech_variant,submission.bioprojectsource.country,earliest_date,devstage_curation,devstage_curation_coarse,tissue_curation,tissue_curation_coarse
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,,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 μm 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 μl 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′Illumina 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 −80°C.  In brief  ERCC Spike in RNA 0.02 μL 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,,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,,,,,,,,,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 μm 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 μl 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′Illumina 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 −80°C.  In brief  ERCC Spike in RNA 0.02 μL 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,,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,,,1330416803,531269504,734031980,2814959249,45666,ERX4665135,ERS5281176,ERA3048543,University of Zurich|European Nucleotide Archive,University of Zurich|European Nucleotide Archive,1,0.33614,,0.21532,,0.99019,,0.41002,,76,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,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,,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 μm 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 μl 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′Illumina 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 −80°C.  In brief  ERCC Spike in RNA 0.02 μL 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,,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,,,,,,,,,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 μm 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 μl 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′Illumina 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 −80°C.  In brief  ERCC Spike in RNA 0.02 μL 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,,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,,,1582938104,1052565419,1177180395,1600161662,1338967,ERX4665135,ERS5281176,ERA3048543,University of Zurich|European Nucleotide Archive,University of Zurich|European Nucleotide Archive,1,0.84976,,0.28521,,0.85038,,0.5124,,75,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,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,,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 μm 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 μl 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′Illumina 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 −80°C.  In brief  ERCC Spike in RNA 0.02 μL 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,,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,,,,,,,,,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 μm 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 μl 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′Illumina 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 −80°C.  In brief  ERCC Spike in RNA 0.02 μL 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,,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,,,1323978162,446831209,581746343,2470114091,524086,ERX4665134,ERS5281175,ERA3048543,University of Zurich|European Nucleotide Archive,University of Zurich|European Nucleotide Archive,1,0.36549,,0.19722,,0.95552,,0.4702,,76,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,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,,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 μm 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 μl 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′Illumina 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 −80°C.  In brief  ERCC Spike in RNA 0.02 μL 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,,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,,,,,,,,,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 μm 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 μl 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′Illumina 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 −80°C.  In brief  ERCC Spike in RNA 0.02 μL 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,,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,,,1434099697,964508763,893584575,1534727600,1968756,ERX4665134,ERS5281175,ERA3048543,University of Zurich|European Nucleotide Archive,University of Zurich|European Nucleotide Archive,1,0.85811,,0.26231,,0.82731,,0.48618,,76,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,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,,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 μm 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 μl 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′Illumina 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 −80°C.  In brief  ERCC Spike in RNA 0.02 μL 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,,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,,,,,,,,,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 μm 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 μl 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′Illumina 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 −80°C.  In brief  ERCC Spike in RNA 0.02 μL 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,,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,,,1526486973,558020193,717587491,2795646081,630655,ERX4665133,ERS5281174,ERA3048543,University of Zurich|European Nucleotide Archive,University of Zurich|European Nucleotide Archive,1,0.28059,,0.19252,,0.96404,,0.4874,,75,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,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,,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 μm 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 μl 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′Illumina 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 −80°C.  In brief  ERCC Spike in RNA 0.02 μL 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,,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,,,,,,,,,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 μm 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 μl 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′Illumina 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 −80°C.  In brief  ERCC Spike in RNA 0.02 μL 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,,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,,,1850568176,1035622971,1071138281,1640475883,2346060,ERX4665133,ERS5281174,ERA3048543,University of Zurich|European Nucleotide Archive,University of Zurich|European Nucleotide Archive,1,0.7679,,0.30371,,0.82651,,0.43401,,75,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,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,,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 μm 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 μl 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′Illumina 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 −80°C.  In brief  ERCC Spike in RNA 0.02 μL 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,,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,,,,,,,,,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 μm 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 μl 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′Illumina 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 −80°C.  In brief  ERCC Spike in RNA 0.02 μL 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,,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,,,1330744174,451622042,591151500,2622422664,561936,ERX4665132,ERS5281173,ERA3048543,University of Zurich|European Nucleotide Archive,University of Zurich|European Nucleotide Archive,1,0.29754,,0.17671,,0.9669,,0.45463,,75,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,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,,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 μm 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 μl 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′Illumina 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 −80°C.  In brief  ERCC Spike in RNA 0.02 μL 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,,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,,,,,,,,,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 μm 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 μl 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′Illumina 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 −80°C.  In brief  ERCC Spike in RNA 0.02 μL 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,,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,,,1591945117,933968124,986108614,1485824022,2062512,ERX4665132,ERS5281173,ERA3048543,University of Zurich|European Nucleotide Archive,University of Zurich|European Nucleotide Archive,1,0.81333,,0.2466,,0.83027,,0.51572,,75,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Switzerland,2021-04-01,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
32370,SRR29180530,SRX24700714,SRS21428245,SRP509851,PRJNA1116337,Ioxynil and diethylstilbestrol disrupt vascular and heart development in zebrafish,PRJNA1116337,Other,Endocrine disruption is one of the consequences of industrialization and chemicals released into theenvironment have a profound impact on organisms. Waterborne micromolar concentrations of ioxynil IOX and diethylstilbestrol DES in fish affect the development of the heart  vasculature and thyroid gland.,,,,,DES,,isolate:exposure to DES|age:48 hpf|dev stage:embryos|collection date:2018 06|geo loc name:Portugal|sex:pooled male and female|tissue:embryos|treatment:exposure to DES|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of DES treated,DES,DES,Sequencing the transcriptomes of zebrafish embryos of DES treated,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP509851,,,DES_TAAGGC_L001_R1_001.fastq.gz DES_TAAGGC_L001_R2_001.fastq.gz,fastq fastq,9169560000.0,30565200.0,DES TAAGGC L001 R1 001.fastq.gz,0:150 1:150,A:2545096687;C:2037322055;G:2024787099;T:2562124529;N:229630,150,150,,,2545096687,2037322055,2024787099,2562124529,229630,SRX24700714,SRS21428245,SRA1878028,Shanghai Ocean University|College of Fisheries and Life Science,Shanghai Ocean University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2024-05-25,Hatching,Embryo,Embryo Imprecise,All anatomical structures
32371,SRR29180531,SRX24700713,SRS21428246,SRP509851,PRJNA1116337,Ioxynil and diethylstilbestrol disrupt vascular and heart development in zebrafish,PRJNA1116337,Other,Endocrine disruption is one of the consequences of industrialization and chemicals released into theenvironment have a profound impact on organisms. Waterborne micromolar concentrations of ioxynil IOX and diethylstilbestrol DES in fish affect the development of the heart  vasculature and thyroid gland.,,,,,IOX,,isolate:exposure to IOX|age:48 hpf|dev stage:embryos|collection date:2018 06|geo loc name:Portugal|sex:pooled male and female|tissue:embryos|treatment:exposure to IOX|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of IOX treated,IOX,IOX,Sequencing the transcriptomes of zebrafish embryos of IOX treated,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP509851,,,IOX_CGTACT_L001_R1_001.fastq.gz IOX_CGTACT_L001_R2_001.fastq.gz,fastq fastq,9547157100.0,31823857.0,IOX CGTACT L001 R1 001.fastq.gz,0:150 1:150,A:2631030736;C:2146265744;G:2124421595;T:2645201596;N:237429,150,150,,,2631030736,2146265744,2124421595,2645201596,237429,SRX24700713,SRS21428246,SRA1878028,Shanghai Ocean University|College of Fisheries and Life Science,Shanghai Ocean University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2024-05-25,Hatching,Embryo,Embryo Imprecise,All anatomical structures
32372,SRR29180532,SRX24700712,SRS21428244,SRP509851,PRJNA1116337,Ioxynil and diethylstilbestrol disrupt vascular and heart development in zebrafish,PRJNA1116337,Other,Endocrine disruption is one of the consequences of industrialization and chemicals released into theenvironment have a profound impact on organisms. Waterborne micromolar concentrations of ioxynil IOX and diethylstilbestrol DES in fish affect the development of the heart  vasculature and thyroid gland.,,,,,CTR,,isolate:control|age:48 hpf|dev stage:embryos|collection date:2018 06|geo loc name:Portugal|sex:pooled male and female|tissue:embryos|treatment:control|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of CTR treated,CTR,CTR,Sequencing the transcriptomes of zebrafish embryos of control,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP509851,,,CTR_AGGCAG_L001_R1_001.fastq.gz CTR_AGGCAG_L001_R2_001.fastq.gz,fastq fastq,9602954100.0,32009847.0,CTR AGGCAG L001 R1 001.fastq.gz,0:150 1:150,A:2637866848;C:2169057233;G:2152906664;T:2642882530;N:240825,150,150,,,2637866848,2169057233,2152906664,2642882530,240825,SRX24700712,SRS21428244,SRA1878028,Shanghai Ocean University|College of Fisheries and Life Science,Shanghai Ocean University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2024-05-25,Hatching,Embryo,Embryo Imprecise,All anatomical structures
39911,SRR2255651,SRX1187765,SRS1056695,SRP063370,PRJNA294819,Danio rerio PFOS FL transcriptome project,PRJNA294819,Other,,,,,,TRAPPC11 Mutant2,,breed:not applicable|strain:not applicable|age:6 dpf provider:not applicable|sex:not collected|tissue:embryro|treatment:TRAPPC11 Mutant2|BioSampleModel:Model organism or animal,,,,,,,,,TRAPPC11 Mutant2,TRAPPC11 Mutant2,TRAPPC11 Mutant2,cDNA library from 300 ng of total RNA were constructed from two biological replicates using the TruSeq Stranded RNA LT Sample Prep Kit Illumina. The cDNA library was prepared according to the manufacturer’s instruction as previously described Gu et al.  2015. Briefly  Index barcodes were first ligated for identification of individual samples. mRNA was purified from the total RNA using poly T oligo attached magnetic beads Illumina  San Diego  USA  follows by random fragmentation using divalent cations at 94?C for 1 min. First and second strand cDNAs were synthesized using random oligonucleotides and SuperScript II  followed by DNA polymerase I and RNase H. Exonuclease/polymerase was used to produce blunted overhangs. Illumina PE adapter oligonucleotides were ligated to the cDNA post 3’ end adenylation. DNA fragments were enriched by 15 cycles of PCR reaction. The libraries were purified using the AMPure XP and were quantified using KAPA Library Quantification Kits.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina MiSeq,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP063370,,,fattyliver2_S6_L001_R1_001.fastq.gz fattyliver2_S6_L001_R2_001.fastq.gz,fastq fastq,836752562.0,5540752.0,TRAPPC11 Mutant2,0:75.54 1:75.48,A:219401421;C:198252489;G:195663968;T:223211242;N:223442,75,75,,,219401421,198252489,195663968,223211242,223442,SRX1187765,SRS1056695,SRA295687,The Chinese University of Hong Kong,The Chinese University of Hong Kong,2,0.96204,0.96259,0.05777,0.05527,0.74142,0.74089,0.47566,0.47333,75,52,B,B,biological fallback assumption,illumina,miseq,unknown,random_priming,trueseq,bulk,unknown,unknown,,China,2016-09-05,Larval,Larval,Embryo Imprecise,All anatomical structures
39912,SRR2255629,SRX1187764,SRS1056694,SRP063370,PRJNA294819,Danio rerio PFOS FL transcriptome project,PRJNA294819,Other,,,,,,TRAPPC11 Mutant1,,breed:not applicable|strain:not applicable|age:6 dpf provider:not applicable|sex:not collected|tissue:embryro|treatment:TRAPPC11 Mutant1|BioSampleModel:Model organism or animal,,,,,,,,,TRAPPC11 Mutant1,TRAPPC11 Mutant1,TRAPPC11 Mutant1,cDNA library from 300 ng of total RNA were constructed from two biological replicates using the TruSeq Stranded RNA LT Sample Prep Kit Illumina. The cDNA library was prepared according to the manufacturer’s instruction as previously described Gu et al.  2015. Briefly  Index barcodes were first ligated for identification of individual samples. mRNA was purified from the total RNA using poly T oligo attached magnetic beads Illumina  San Diego  USA  follows by random fragmentation using divalent cations at 94?C for 1 min. First and second strand cDNAs were synthesized using random oligonucleotides and SuperScript II  followed by DNA polymerase I and RNase H. Exonuclease/polymerase was used to produce blunted overhangs. Illumina PE adapter oligonucleotides were ligated to the cDNA post 3’ end adenylation. DNA fragments were enriched by 15 cycles of PCR reaction. The libraries were purified using the AMPure XP and were quantified using KAPA Library Quantification Kits.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina MiSeq,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP063370,,,fattyliver1_S5_L001_R1_001.fastq.gz fattyliver1_S5_L001_R2_001.fastq.gz,fastq fastq,752730180.0,4984563.0,TRAPPC11 Mutant1,0:75.53 1:75.48,A:201453785;C:174638707;G:171041330;T:205386632;N:209726,75,75,,,201453785,174638707,171041330,205386632,209726,SRX1187764,SRS1056694,SRA295687,The Chinese University of Hong Kong,The Chinese University of Hong Kong,2,0.95653,0.95631,0.07274,0.06976,0.70573,0.70664,0.49403,0.49925,74,76,B,B,biological fallback assumption,illumina,miseq,unknown,random_priming,trueseq,bulk,unknown,unknown,,China,2015-09-05,Larval,Larval,Embryo Imprecise,All anatomical structures
39913,SRR2255628,SRX1187763,SRS1056693,SRP063370,PRJNA294819,Danio rerio PFOS FL transcriptome project,PRJNA294819,Other,,,,,,PFOS2,,breed:not applicable|strain:not applicable|age:6 dpf provider:not applicable|sex:not collected|tissue:embryro|treatment:PFOS2|BioSampleModel:Model organism or animal,,,,,,,,,PFOS2,PFOS2,PFOS2,cDNA library from 300 ng of total RNA were constructed from two biological replicates using the TruSeq Stranded RNA LT Sample Prep Kit Illumina. The cDNA library was prepared according to the manufacturer’s instruction as previously described Gu et al.  2015. Briefly  Index barcodes were first ligated for identification of individual samples. mRNA was purified from the total RNA using poly T oligo attached magnetic beads Illumina  San Diego  USA  follows by random fragmentation using divalent cations at 94?C for 1 min. First and second strand cDNAs were synthesized using random oligonucleotides and SuperScript II  followed by DNA polymerase I and RNase H. Exonuclease/polymerase was used to produce blunted overhangs. Illumina PE adapter oligonucleotides were ligated to the cDNA post 3’ end adenylation. DNA fragments were enriched by 15 cycles of PCR reaction. The libraries were purified using the AMPure XP and were quantified using KAPA Library Quantification Kits.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina MiSeq,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP063370,,,PFOS2_S4_L001_R1_001.fastq.gz PFOS2_S4_L001_R2_001.fastq.gz,fastq fastq,660339622.0,4372724.0,PFOS2,0:75.53 1:75.48,A:174477377;C:155458423;G:152138367;T:178072878;N:192577,75,75,,,174477377,155458423,152138367,178072878,192577,SRX1187763,SRS1056693,SRA295687,The Chinese University of Hong Kong,The Chinese University of Hong Kong,2,0.95841,0.95943,0.06213,0.06061,0.71664,0.71717,0.49605,0.5046,76,52,B,B,biological fallback assumption,illumina,miseq,unknown,random_priming,trueseq,bulk,unknown,unknown,,China,2016-09-05,Larval,Larval,Embryo Imprecise,All anatomical structures
39914,SRR2255627,SRX1187762,SRS1056692,SRP063370,PRJNA294819,Danio rerio PFOS FL transcriptome project,PRJNA294819,Other,,,,,,PFOS1,,breed:not applicable|strain:not applicable|age:6 dpf provider:not applicable|sex:not collected|tissue:embryro|treatment:PFOS1|BioSampleModel:Model organism or animal,,,,,,,,,PFOS1,PFOS1,PFOS1,cDNA library from 300 ng of total RNA were constructed from two biological replicates using the TruSeq Stranded RNA LT Sample Prep Kit Illumina. The cDNA library was prepared according to the manufacturer’s instruction as previously described Gu et al.  2015. Briefly  Index barcodes were first ligated for identification of individual samples. mRNA was purified from the total RNA using poly T oligo attached magnetic beads Illumina  San Diego  USA  follows by random fragmentation using divalent cations at 94?C for 1 min. First and second strand cDNAs were synthesized using random oligonucleotides and SuperScript II  followed by DNA polymerase I and RNase H. Exonuclease/polymerase was used to produce blunted overhangs. Illumina PE adapter oligonucleotides were ligated to the cDNA post 3’ end adenylation. DNA fragments were enriched by 15 cycles of PCR reaction. The libraries were purified using the AMPure XP and were quantified using KAPA Library Quantification Kits.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina MiSeq,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP063370,,,PFOS1_S3_L001_R1_001.fastq.gz PFOS1_S3_L001_R2_001.fastq.gz,fastq fastq,791950817.0,5244084.0,PFOS1,0:75.53 1:75.48,A:207476025;C:187690975;G:185784999;T:210781701;N:217117,75,75,,,207476025,187690975,185784999,210781701,217117,SRX1187762,SRS1056692,SRA295687,The Chinese University of Hong Kong,The Chinese University of Hong Kong,2,0.96195,0.96213,0.051,0.04857,0.7386,0.73927,0.49669,0.49151,76,53,B,B,biological fallback assumption,illumina,miseq,unknown,random_priming,trueseq,bulk,unknown,unknown,,China,2016-09-05,Larval,Larval,Embryo Imprecise,All anatomical structures
39915,SRR2255626,SRX1187761,SRS1056691,SRP063370,PRJNA294819,Danio rerio PFOS FL transcriptome project,PRJNA294819,Other,,,,,,DMSO2,,breed:not applicable|strain:not applicable|age:6 dpf provider:not applicable|sex:not collected|tissue:embryro|treatment:DMSO2|BioSampleModel:Model organism or animal,,,,,,,,,DMSO2,DMSO2,DMSO2,cDNA library from 300 ng of total RNA were constructed from two biological replicates using the TruSeq Stranded RNA LT Sample Prep Kit Illumina. The cDNA library was prepared according to the manufacturer’s instruction as previously described Gu et al.  2015. Briefly  Index barcodes were first ligated for identification of individual samples. mRNA was purified from the total RNA using poly T oligo attached magnetic beads Illumina  San Diego  USA  follows by random fragmentation using divalent cations at 94?C for 1 min. First and second strand cDNAs were synthesized using random oligonucleotides and SuperScript II  followed by DNA polymerase I and RNase H. Exonuclease/polymerase was used to produce blunted overhangs. Illumina PE adapter oligonucleotides were ligated to the cDNA post 3’ end adenylation. DNA fragments were enriched by 15 cycles of PCR reaction. The libraries were purified using the AMPure XP and were quantified using KAPA Library Quantification Kits.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina MiSeq,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP063370,,,DMSO2_S2_L001_R1_001.fastq.gz DMSO2_S2_L001_R2_001.fastq.gz,fastq fastq,847975709.0,5615263.0,DMSO2,0:75.53 1:75.48,A:222828293;C:200598370;G:196827420;T:227477582;N:244044,75,75,,,222828293,200598370,196827420,227477582,244044,SRX1187761,SRS1056691,SRA295687,The Chinese University of Hong Kong,The Chinese University of Hong Kong,2,0.95825,0.95852,0.06376,0.06156,0.71224,0.71313,0.49629,0.49076,76,76,B,B,biological fallback assumption,illumina,miseq,unknown,random_priming,trueseq,bulk,unknown,unknown,,China,2016-09-05,Larval,Larval,Embryo Imprecise,All anatomical structures
39916,SRR2255625,SRX1187760,SRS1056690,SRP063370,PRJNA294819,Danio rerio PFOS FL transcriptome project,PRJNA294819,Other,,,,,,DMSO1,,breed:not applicable|strain:not applicable|age:6 dpf provider:not applicable|sex:not collected|tissue:embryro|treatment:DMSO1|BioSampleModel:Model organism or animal,,,,,,,,,DMSO1,DMSO1,DMSO1,cDNA library from 300 ng of total RNA were constructed from two biological replicates using the TruSeq Stranded RNA LT Sample Prep Kit Illumina. The cDNA library was prepared according to the manufacturer’s instruction as previously described Gu et al.  2015. Briefly  Index barcodes were first ligated for identification of individual samples. mRNA was purified from the total RNA using poly T oligo attached magnetic beads Illumina  San Diego  USA  follows by random fragmentation using divalent cations at 94?C for 1 min. First and second strand cDNAs were synthesized using random oligonucleotides and SuperScript II  followed by DNA polymerase I and RNase H. Exonuclease/polymerase was used to produce blunted overhangs. Illumina PE adapter oligonucleotides were ligated to the cDNA post 3’ end adenylation. DNA fragments were enriched by 15 cycles of PCR reaction. The libraries were purified using the AMPure XP and were quantified using KAPA Library Quantification Kits.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina MiSeq,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP063370,,,DMSO1_S1_L001_R1_001.fastq.gz DMSO1_S1_L001_R2_001.fastq.gz,fastq fastq,825003413.0,5463030.0,DMSO1,0:75.53 1:75.48,A:217714985;C:193454273;G:192078021;T:221527657;N:228477,75,75,,,217714985,193454273,192078021,221527657,228477,SRX1187760,SRS1056690,SRA295687,The Chinese University of Hong Kong,The Chinese University of Hong Kong,2,0.96443,0.9657,0.05205,0.04878,0.76581,0.76465,0.49046,0.47298,76,54,B,B,biological fallback assumption,illumina,miseq,unknown,random_priming,trueseq,bulk,unknown,unknown,,China,2016-09-05,Larval,Larval,Embryo Imprecise,All anatomical structures
42301,SRR5579865,SRX2837982,SRS2212147,SRP107584,PRJNA387320,Danio rerio 1207 Raw sequence reads,PRJNA387320,Other,,,,,,1207 2,,breed:not applicable|strain:not applicable|age:1 month|biomaterial provider:not applicable|sex:not collected|tissue:Embyro|treatment:1207 2|BioSampleModel:Model organism or animal,,,,,,,,,2002 2,1207 2 S1 L001,1207 2 S1 L001,The embryos were subjected to RNA isolation. Ten embryos per group n = 10 from wild type control embryos  n = 10 from mibnn2002 mutants and n = 10 from mibta52b mutants were used to prepare a pooled RNA sample. Three biological replicates per group were prepared. Total RNA from pooled samples was extracted by using the mirVanaTM RNA isolation kit Applied Biosystems according to the manufacturer’s protocol as previously described. RNA quality was assessed by using the Agilent 2100 Bioanalyzer system and samples with a RNA Integrity Number RIN greater than 8 were used for RNA library construction.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina MiSeq,,SRP107584,,,,,1531873131.0,5203504.0,1207 2 S2 L001 2 paired.fq.gz,0:148.34 1:146.06,A:384469512;C:380138079;G:381661689;T:385603823;N:28,148,146,,,384469512,380138079,381661689,385603823,28,SRX2837982,SRS2212147,SRA563090,The Chinese University of Hong Kong|School of Life Sciences,The Chinese University of Hong Kong,2,0.97313,0.97391,0.03931,0.03966,0.73675,0.74186,0.47243,0.47819,151,150,B,B,biological fallback assumption,illumina,miseq,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2017-05-20,Juvenile,Juvenile,Embryo Imprecise,All anatomical structures
42302,SRR5579866,SRX2837981,SRS2212146,SRP107584,PRJNA387320,Danio rerio 1207 Raw sequence reads,PRJNA387320,Other,,,,,,1207 1,,breed:not applicable|strain:not applicable|age:1 month|biomaterial provider:not applicable|sex:not collected|tissue:Embyro|treatment:1207 1|BioSampleModel:Model organism or animal,,,,,,,,,2002 1,1207 1 S1 L001,1207 1 S1 L001,The embryos were subjected to RNA isolation. Ten embryos per group n = 10 from wild type control embryos  n = 10 from mibnn2002 mutants and n = 10 from mibta52b mutants were used to prepare a pooled RNA sample. Three biological replicates per group were prepared. Total RNA from pooled samples was extracted by using the mirVanaTM RNA isolation kit Applied Biosystems according to the manufacturer’s protocol as previously described. RNA quality was assessed by using the Agilent 2100 Bioanalyzer system and samples with a RNA Integrity Number RIN greater than 8 were used for RNA library construction.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina MiSeq,,SRP107584,,,,,1250178633.0,4243308.0,1207 1 S1 L001 2 paired.fq.gz,0:148.83 1:145.79,A:314820390;C:308887372;G:310674271;T:315796566;N:34,148,145,,,314820390,308887372,310674271,315796566,34,SRX2837981,SRS2212146,SRA563090,The Chinese University of Hong Kong|School of Life Sciences,The Chinese University of Hong Kong,2,0.97174,0.9719,0.04506,0.04505,0.73154,0.73683,0.4817,0.48252,150,148,B,B,biological fallback assumption,illumina,miseq,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2017-05-20,Juvenile,Juvenile,Embryo Imprecise,All anatomical structures
42303,SRR5579867,SRX2837980,SRS2212145,SRP107584,PRJNA387320,Danio rerio 1207 Raw sequence reads,PRJNA387320,Other,,,,,,AB 1,,breed:not applicable|strain:not applicable|age:1 month|biomaterial provider:not applicable|sex:not collected|tissue:Embyro|treatment:AB1|BioSampleModel:Model organism or animal,,,,,,,,,WT1,AB1 S1 L001,AB1 S1 L001,The embryos were subjected to RNA isolation. Ten embryos per group n = 10 from wild type control embryos  n = 10 from mibnn2002 mutants and n = 10 from mibta52b mutants were used to prepare a pooled RNA sample. Three biological replicates per group were prepared. Total RNA from pooled samples was extracted by using the mirVanaTM RNA isolation kit Applied Biosystems according to the manufacturer’s protocol as previously described. RNA quality was assessed by using the Agilent 2100 Bioanalyzer system and samples with a RNA Integrity Number RIN greater than 8 were used for RNA library construction.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina MiSeq,,SRP107584,,,,,1819768909.0,6190653.0,AB1 S1 L001 2 paired.fq.gz,0:148.08 1:145.88,A:465877977;C:442905762;G:444673127;T:466312043;N:0,148,145,,,465877977,442905762,444673127,466312043,0,SRX2837980,SRS2212145,SRA563090,The Chinese University of Hong Kong|School of Life Sciences,The Chinese University of Hong Kong,2,0.97169,0.97078,0.03527,0.03575,0.72823,0.73338,0.48283,0.48226,151,151,B,B,biological fallback assumption,illumina,miseq,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2017-05-20,Juvenile,Juvenile,Embryo Imprecise,All anatomical structures
42304,SRR5579868,SRX2837979,SRS2212143,SRP107584,PRJNA387320,Danio rerio 1207 Raw sequence reads,PRJNA387320,Other,,,,,,1207 3,,breed:not applicable|strain:not applicable|age:1 month|biomaterial provider:not applicable|sex:not collected|tissue:Embyro|treatment:1207 3|BioSampleModel:Model organism or animal,,,,,,,,,2002 3,1207 3 S1 L001,1207 3 S1 L001,The embryos were subjected to RNA isolation. Ten embryos per group n = 10 from wild type control embryos  n = 10 from mibnn2002 mutants and n = 10 from mibta52b mutants were used to prepare a pooled RNA sample. Three biological replicates per group were prepared. Total RNA from pooled samples was extracted by using the mirVanaTM RNA isolation kit Applied Biosystems according to the manufacturer’s protocol as previously described. RNA quality was assessed by using the Agilent 2100 Bioanalyzer system and samples with a RNA Integrity Number RIN greater than 8 were used for RNA library construction.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina MiSeq,,SRP107584,,,,,1045991851.0,3554741.0,1207 3 S3 L001 2 paired.fq.gz,0:148.38 1:145.87,A:263998819;C:257909132;G:259440555;T:264643331;N:14,148,145,,,263998819,257909132,259440555,264643331,14,SRX2837979,SRS2212143,SRA563090,The Chinese University of Hong Kong|School of Life Sciences,The Chinese University of Hong Kong,2,0.97252,0.97273,0.0409,0.04037,0.74213,0.74574,0.48248,0.48634,151,151,B,B,biological fallback assumption,illumina,miseq,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2017-05-20,Juvenile,Juvenile,Embryo Imprecise,All anatomical structures
42305,SRR5579869,SRX2837978,SRS2212142,SRP107584,PRJNA387320,Danio rerio 1207 Raw sequence reads,PRJNA387320,Other,,,,,,AB 3,,breed:not applicable|strain:not applicable|age:1 month|biomaterial provider:not applicable|sex:not collected|tissue:Embyro|treatment:AB3|BioSampleModel:Model organism or animal,,,,,,,,,WT3,AB3 S1 L001,AB3 S1 L001,The embryos were subjected to RNA isolation. Ten embryos per group n = 10 from wild type control embryos  n = 10 from mibnn2002 mutants and n = 10 from mibta52b mutants were used to prepare a pooled RNA sample. Three biological replicates per group were prepared. Total RNA from pooled samples was extracted by using the mirVanaTM RNA isolation kit Applied Biosystems according to the manufacturer’s protocol as previously described. RNA quality was assessed by using the Agilent 2100 Bioanalyzer system and samples with a RNA Integrity Number RIN greater than 8 were used for RNA library construction.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina MiSeq,,SRP107584,,,,,1126218531.0,3826972.0,AB3 S3 L001 1 paired.fq.gz,0:148.46 1:145.83,A:285650942;C:276774884;G:276765238;T:287027467;N:0,148,145,,,285650942,276774884,276765238,287027467,0,SRX2837978,SRS2212142,SRA563090,The Chinese University of Hong Kong|School of Life Sciences,The Chinese University of Hong Kong,2,0.97355,0.97389,0.03977,0.04012,0.71999,0.72506,0.47576,0.4728,149,151,B,B,biological fallback assumption,illumina,miseq,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2017-05-20,Juvenile,Juvenile,Embryo Imprecise,All anatomical structures
42306,SRR5579870,SRX2837977,SRS2212144,SRP107584,PRJNA387320,Danio rerio 1207 Raw sequence reads,PRJNA387320,Other,,,,,,AB 2,,breed:not applicable|strain:not applicable|age:1 month|biomaterial provider:not applicable|sex:not collected|tissue:Embyro|treatment:AB2|BioSampleModel:Model organism or animal,,,,,,,,,WT2,AB2 S1 L001,AB2 S1 L001,The embryos were subjected to RNA isolation. Ten embryos per group n = 10 from wild type control embryos  n = 10 from mibnn2002 mutants and n = 10 from mibta52b mutants were used to prepare a pooled RNA sample. Three biological replicates per group were prepared. Total RNA from pooled samples was extracted by using the mirVanaTM RNA isolation kit Applied Biosystems according to the manufacturer’s protocol as previously described. RNA quality was assessed by using the Agilent 2100 Bioanalyzer system and samples with a RNA Integrity Number RIN greater than 8 were used for RNA library construction.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina MiSeq,,SRP107584,,,,,1716453669.0,5815815.0,AB2 S2 L001 1 paired.fq.gz,0:148.63 1:146.50,A:430519895;C:426826400;G:426635292;T:432472082;N:0,148,146,,,430519895,426826400,426635292,432472082,0,SRX2837977,SRS2212144,SRA563090,The Chinese University of Hong Kong|School of Life Sciences,The Chinese University of Hong Kong,2,0.97735,0.97725,0.02854,0.02833,0.73196,0.73484,0.48256,0.4861,151,151,B,B,biological fallback assumption,illumina,miseq,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2017-05-20,Juvenile,Juvenile,Embryo Imprecise,All anatomical structures
51269,SRR8663334,SRX5460031,SRS4433921,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,,ZF 48hpf rep2,GSM3638675,,source name:embryo|tissue:embryo|developmental stage:48 hpf|strain:wild type AB fish,ZF 48hpf 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,,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 1μg 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 °C 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.,Embryos were reared at 28.5 °C and all experiments and observations were performed as close to this temperature as possible.,tissue:embryo|developmental stage:48 hpf|strain:wild type AB fish,GSM3638675,GSM3638675: ZF 48hpf rep2; Danio rerio; Bisulfite Seq,GSM3638675,,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 1μg 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 °C 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:GSM3638675,Bisulfite-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP187415,,,,,21257043600.0,70856812.0,GSM3638675 r1,0:150 1:150,A:7462169931;C:3151216767;G:3428144480;T:7214024902;N:1487520,150,150,,,7462169931,3151216767,3428144480,7214024902,1487520,SRX5460031,SRS4433921,SRA855736,GEO,Sun Yat-sen University,2,0.00062,0.00055,0.00017,0.00013,0.99949,0.99945,0.67901,0.75362,150,150,T,T,mates < 9% mapping rate,illumina,hiseq_era,full_length,random_priming,nebnext,bulk,unknown,unknown,,China,2019-03-04,Hatching,Embryo,Embryo Imprecise,All anatomical structures
51270,SRR8663333,SRX5460030,SRS4433920,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,,ZF 48hpf rep1,GSM3638674,,source name:embryo|tissue:embryo|developmental stage:48 hpf|strain:wild type AB fish,ZF 48hpf 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,,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 1μg 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 °C 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.,Embryos were reared at 28.5 °C and all experiments and observations were performed as close to this temperature as possible.,tissue:embryo|developmental stage:48 hpf|strain:wild type AB fish,GSM3638674,GSM3638674: ZF 48hpf rep1; Danio rerio; Bisulfite Seq,GSM3638674,,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 1μg 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 °C 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:GSM3638674,Bisulfite-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP187415,,,,,20408177400.0,68027258.0,GSM3638674 r1,0:150 1:150,A:6990585654;C:3225159172;G:3562240517;T:6628764661;N:1427396,150,150,,,6990585654,3225159172,3562240517,6628764661,1427396,SRX5460030,SRS4433920,SRA855736,GEO,Sun Yat-sen University,2,0.0009,0.00071,0.0003,0.00019,0.99928,0.99941,0.6,0.64367,150,150,T,T,mates < 9% mapping rate,illumina,hiseq_era,full_length,random_priming,nebnext,bulk,unknown,unknown,,China,2019-03-04,Hatching,Embryo,Embryo Imprecise,All anatomical structures
51271,SRR8663332,SRX5460029,SRS4433919,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,,ZF 24hpf rep2,GSM3638673,,source name:embryo|tissue:embryo|developmental stage:24 hpf|strain:wild type AB fish,ZF 24hpf 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,,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 1μg 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 °C 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.,Embryos were reared at 28.5 °C and all experiments and observations were performed as close to this temperature as possible.,tissue:embryo|developmental stage:24 hpf|strain:wild type AB fish,GSM3638673,GSM3638673: ZF 24hpf rep2; Danio rerio; Bisulfite Seq,GSM3638673,,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 1μg 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 °C 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:GSM3638673,Bisulfite-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP187415,,,,,21961409700.0,73204699.0,GSM3638673 r1,0:150 1:150,A:7568027843;C:3406881222;G:3795216487;T:7190249641;N:1034507,150,150,,,7568027843,3406881222,3795216487,7190249641,1034507,SRX5460029,SRS4433919,SRA855736,GEO,Sun Yat-sen University,2,0.00082,0.0007,0.00032,0.00023,0.99945,0.99947,0.65517,0.65,150,150,T,T,mates < 9% mapping rate,illumina,hiseq_era,full_length,random_priming,nebnext,bulk,unknown,unknown,,China,2019-03-04,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
51272,SRR8663331,SRX5460028,SRS4433918,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,,ZF 24hpf rep1,GSM3638672,,source name:embryo|tissue:embryo|developmental stage:24 hpf|strain:wild type AB fish,ZF 24hpf 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,,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 1μg 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 °C 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.,Embryos were reared at 28.5 °C and all experiments and observations were performed as close to this temperature as possible.,tissue:embryo|developmental stage:24 hpf|strain:wild type AB fish,GSM3638672,GSM3638672: ZF 24hpf rep1; Danio rerio; Bisulfite Seq,GSM3638672,,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 1μg 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 °C 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:GSM3638672,Bisulfite-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP187415,,,,,22998615300.0,76662051.0,GSM3638672 r1,0:150 1:150,A:7938674920;C:3553518327;G:3950127781;T:7555207157;N:1087115,150,150,,,7938674920,3553518327,3950127781,7555207157,1087115,SRX5460028,SRS4433918,SRA855736,GEO,Sun Yat-sen University,2,0.00076,0.00067,0.00027,0.00021,0.99926,0.99937,0.53658,0.58666,150,150,T,T,mates < 9% mapping rate,illumina,hiseq_era,full_length,random_priming,nebnext,bulk,unknown,unknown,,China,2019-03-04,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
51273,SRR8663330,SRX5460027,SRS4433917,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,,ZF 16hpf rep2,GSM3638671,,source name:embryo|tissue:embryo|developmental stage:16 hpf|strain:wild type AB fish,ZF 16hpf 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,,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 1μg 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 °C 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.,Embryos were reared at 28.5 °C and all experiments and observations were performed as close to this temperature as possible.,tissue:embryo|developmental stage:16 hpf|strain:wild type AB fish,GSM3638671,GSM3638671: ZF 16hpf rep2; Danio rerio; Bisulfite Seq,GSM3638671,,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 1μg 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 °C 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:GSM3638671,Bisulfite-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP187415,,,,,25701246300.0,85670821.0,GSM3638671 r1,0:150 1:150,A:8976132831;C:3855344207;G:4201042226;T:8667517583;N:1209453,150,150,,,8976132831,3855344207,4201042226,8667517583,1209453,SRX5460027,SRS4433917,SRA855736,GEO,Sun Yat-sen University,2,0.00117,0.00107,0.00036,0.00034,0.99928,0.99941,0.73571,0.75206,150,150,T,T,mates < 9% mapping rate,illumina,hiseq_era,full_length,random_priming,nebnext,bulk,unknown,unknown,,China,2019-03-04,Segmentation,Embryo,Embryo Imprecise,All anatomical structures
51274,SRR8663329,SRX5460026,SRS4433916,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,,ZF 16hpf rep1,GSM3638670,,source name:embryo|tissue:embryo|developmental stage:16 hpf|strain:wild type AB fish,ZF 16hpf 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,,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 1μg 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 °C 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.,Embryos were reared at 28.5 °C and all experiments and observations were performed as close to this temperature as possible.,tissue:embryo|developmental stage:16 hpf|strain:wild type AB fish,GSM3638670,GSM3638670: ZF 16hpf rep1; Danio rerio; Bisulfite Seq,GSM3638670,,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 1μg 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 °C 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:GSM3638670,Bisulfite-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP187415,,,,,21585057600.0,71950192.0,GSM3638670 r1,0:150 1:150,A:7493903581;C:3312864799;G:3567558230;T:7209728977;N:1002013,150,150,,,7493903581,3312864799,3567558230,7209728977,1002013,SRX5460026,SRS4433916,SRA855736,GEO,Sun Yat-sen University,2,0.00125,0.00119,0.00039,0.00034,0.99945,0.99947,0.7551,0.76865,150,150,T,T,mates < 9% mapping rate,illumina,hiseq_era,full_length,random_priming,nebnext,bulk,unknown,unknown,,China,2019-03-04,Segmentation,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,,ZF 10hpf rep2,GSM3638669,,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,,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 1μg 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 °C 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.,Embryos were reared at 28.5 °C 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,,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 1μg 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 °C 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,,SRP187415,,,,,18449316900.0,61497723.0,GSM3638669 r1,0:150 1:150,A:6508135454;C:2695665097;G:2948776234;T:6296104735;N:635380,150,150,,,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,,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,,ZF 10hpf rep1,GSM3638668,,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,,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 1μg 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 °C 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.,Embryos were reared at 28.5 °C 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,,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 1μg 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 °C 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,,SRP187415,,,,,35064552300.0,116881841.0,GSM3638668 r1,0:150 1:150,A:12442483305;C:5073538954;G:5489080636;T:12058238019;N:1211386,150,150,,,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,,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,,ZF 8hpf rep2,GSM3638667,,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,,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 1μg 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 °C 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.,Embryos were reared at 28.5 °C 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,,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 1μg 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 °C 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,,SRP187415,,,,,14346635400.0,47822118.0,GSM3638667 r1,0:150 1:150,A:5096565523;C:2082957184;G:2242869596;T:4923737869;N:505228,150,150,,,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,,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,,ZF 8hpf rep1,GSM3638666,,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,,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 1μg 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 °C 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.,Embryos were reared at 28.5 °C 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,,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 1μg 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 °C 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,,SRP187415,,,,,22564435500.0,75214785.0,GSM3638666 r1,0:150 1:150,A:8037530388;C:3263669666;G:3467393764;T:7794998569;N:843113,150,150,,,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,,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,,ZF 6hpf rep2,GSM3638665,,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,,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 1μg 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 °C 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.,Embryos were reared at 28.5 °C 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,,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 1μg 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 °C 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,,SRP187415,,,,,15663840300.0,52212801.0,GSM3638665 r1,0:150 1:150,A:5036459488;C:2768054214;G:3109386160;T:4747198752;N:2741686,150,150,,,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,,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,,ZF 6hpf rep1,GSM3638664,,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,,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 1μg 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 °C 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.,Embryos were reared at 28.5 °C 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,,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 1μg 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 °C 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,,SRP187415,,,,,13146289500.0,43820965.0,GSM3638664 r1,0:150 1:150,A:4440608717;C:2140855274;G:2250243580;T:4312362152;N:2219777,150,150,,,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,,China,2019-03-04,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
51281,SRR8663322,SRX5460019,SRS4433909,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,,ZF 4hpf rep2,GSM3638663,,source name:embryo|tissue:embryo|developmental stage:4 hpf|strain:wild type AB fish,ZF 4hpf 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,,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 1μg 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 °C 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.,Embryos were reared at 28.5 °C and all experiments and observations were performed as close to this temperature as possible.,tissue:embryo|developmental stage:4 hpf|strain:wild type AB fish,GSM3638663,GSM3638663: ZF 4hpf rep2; Danio rerio; Bisulfite Seq,GSM3638663,,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 1μg 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 °C 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:GSM3638663,Bisulfite-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP187415,,,,,14505809700.0,48352699.0,GSM3638663 r1,0:150 1:150,A:4877194269;C:2388898572;G:2560124505;T:4676340810;N:3251544,150,150,,,4877194269,2388898572,2560124505,4676340810,3251544,SRX5460019,SRS4433909,SRA855736,GEO,Sun Yat-sen University,2,0.00065,0.00045,0.00027,0.00016,0.99928,0.99945,0.46376,0.54166,150,150,T,T,mates < 9% mapping rate,illumina,hiseq_era,full_length,random_priming,nebnext,bulk,unknown,unknown,,China,2019-03-04,Blastula,Embryo,Embryo Imprecise,All anatomical structures
51282,SRR8663321,SRX5460018,SRS4433908,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,,ZF 4hpf rep1,GSM3638662,,source name:embryo|tissue:embryo|developmental stage:4 hpf|strain:wild type AB fish,ZF 4hpf 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,,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 1μg 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 °C 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.,Embryos were reared at 28.5 °C and all experiments and observations were performed as close to this temperature as possible.,tissue:embryo|developmental stage:4 hpf|strain:wild type AB fish,GSM3638662,GSM3638662: ZF 4hpf rep1; Danio rerio; Bisulfite Seq,GSM3638662,,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 1μg 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 °C 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:GSM3638662,Bisulfite-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP187415,,,,,13666257000.0,45554190.0,GSM3638662 r1,0:150 1:150,A:4616947793;C:2221382014;G:2373430205;T:4451384606;N:3112382,150,150,,,4616947793,2221382014,2373430205,4451384606,3112382,SRX5460018,SRS4433908,SRA855736,GEO,Sun Yat-sen University,2,0.00094,0.00054,0.00044,0.00022,0.99928,0.99939,0.38888,0.50943,150,150,T,T,mates < 9% mapping rate,illumina,hiseq_era,full_length,random_priming,nebnext,bulk,unknown,unknown,,China,2019-03-04,Blastula,Embryo,Embryo Imprecise,All anatomical structures
51283,SRR8663320,SRX5460017,SRS4433907,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,,ZF 2hpf rep2,GSM3638661,,source name:embryo|tissue:embryo|developmental stage:2 hpf|strain:wild type AB fish,ZF 2hpf 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,,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 1μg 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 °C 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.,Embryos were reared at 28.5 °C and all experiments and observations were performed as close to this temperature as possible.,tissue:embryo|developmental stage:2 hpf|strain:wild type AB fish,GSM3638661,GSM3638661: ZF 2hpf rep2; Danio rerio; Bisulfite Seq,GSM3638661,,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 1μg 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 °C 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:GSM3638661,Bisulfite-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP187415,,,,,14619051000.0,48730170.0,GSM3638661 r1,0:150 1:150,A:4888878605;C:2423468919;G:2611005028;T:4692396498;N:3301950,150,150,,,4888878605,2423468919,2611005028,4692396498,3301950,SRX5460017,SRS4433907,SRA855736,GEO,Sun Yat-sen University,2,0.00069,0.00053,0.00032,0.00019,0.99943,0.99953,0.28358,0.375,150,150,T,T,mates < 9% mapping rate,illumina,hiseq_era,full_length,random_priming,nebnext,bulk,unknown,unknown,,China,2019-03-04,Cleavage,Embryo,Embryo Imprecise,All anatomical structures
51284,SRR8663319,SRX5460016,SRS4433906,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,,ZF 2hpf rep1,GSM3638660,,source name:embryo|tissue:embryo|developmental stage:2 hpf|strain:wild type AB fish,ZF 2hpf 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,,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 1μg 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 °C 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.,Embryos were reared at 28.5 °C and all experiments and observations were performed as close to this temperature as possible.,tissue:embryo|developmental stage:2 hpf|strain:wild type AB fish,GSM3638660,GSM3638660: ZF 2hpf rep1; Danio rerio; Bisulfite Seq,GSM3638660,,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 1μg 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 °C 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:GSM3638660,Bisulfite-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP187415,,,,,13281290400.0,44270968.0,GSM3638660 r1,0:150 1:150,A:4501039678;C:2150810078;G:2278027624;T:4348527287;N:2885733,150,150,,,4501039678,2150810078,2278027624,4348527287,2885733,SRX5460016,SRS4433906,SRA855736,GEO,Sun Yat-sen University,2,0.00064,0.00039,0.00025,0.00013,0.99949,0.99963,0.46478,0.63414,150,150,T,T,mates < 9% mapping rate,illumina,hiseq_era,full_length,random_priming,nebnext,bulk,unknown,unknown,,China,2019-03-04,Cleavage,Embryo,Embryo Imprecise,All anatomical structures
51285,SRR8663318,SRX5460015,SRS4433905,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,,ZF 0hpf rep2,GSM3638659,,source name:embryo|tissue:embryo|developmental stage:0 hpf|strain:wild type AB fish,ZF 0hpf 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,,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 1μg 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 °C 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.,Embryos were reared at 28.5 °C and all experiments and observations were performed as close to this temperature as possible.,tissue:embryo|developmental stage:0 hpf|strain:wild type AB fish,GSM3638659,GSM3638659: ZF 0hpf rep2; Danio rerio; Bisulfite Seq,GSM3638659,,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 1μg 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 °C 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:GSM3638659,Bisulfite-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP187415,,,,,11732143200.0,39107144.0,GSM3638659 r1,0:150 1:150,A:4048603242;C:1827111316;G:1904770606;T:3949005244;N:2652792,150,150,,,4048603242,1827111316,1904770606,3949005244,2652792,SRX5460015,SRS4433905,SRA855736,GEO,Sun Yat-sen University,2,0.00152,0.00115,0.00043,0.00016,0.99928,0.99943,0.24509,0.81645,150,150,T,T,mates < 9% mapping rate,illumina,hiseq_era,full_length,random_priming,nebnext,bulk,unknown,unknown,,China,2019-03-04,Zygote,Embryo,Embryo Imprecise,All anatomical structures
51286,SRR8663317,SRX5460014,SRS4433904,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,,ZF 0hpf rep1,GSM3638658,,source name:embryo|tissue:embryo|developmental stage:0 hpf|strain:wild type AB fish,ZF 0hpf 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,,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 1μg 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 °C 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.,Embryos were reared at 28.5 °C and all experiments and observations were performed as close to this temperature as possible.,tissue:embryo|developmental stage:0 hpf|strain:wild type AB fish,GSM3638658,GSM3638658: ZF 0hpf rep1; Danio rerio; Bisulfite Seq,GSM3638658,,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 1μg 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 °C 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:GSM3638658,Bisulfite-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP187415,,,,,9931664700.0,33105549.0,GSM3638658 r1,0:150 1:150,A:3401474427;C:1566218806;G:1670547045;T:3291140367;N:2284055,150,150,,,3401474427,1566218806,1670547045,3291140367,2284055,SRX5460014,SRS4433904,SRA855736,GEO,Sun Yat-sen University,2,0.00196,0.00154,0.00071,0.00027,0.99928,0.99935,0.80263,0.85024,150,150,T,T,mates < 9% mapping rate,illumina,hiseq_era,full_length,random_priming,nebnext,bulk,unknown,unknown,,China,2019-03-04,Zygote,Embryo,Embryo Imprecise,All anatomical structures
51318,SRR8735311,SRX5528099,SRS4494644,SRP188580,PRJNA527366,Characterization of the key role of dachshund b in the development of the pancreatic islet in zebrafish Danio rerio,PRJNA527366,Other,In this study  we characterized the function of dachb  the zebrafish homologue of human DACH1  in developing zebrafish embryos. Morpholino MO  mediated knock down of dachb resulted in impaired islet cell development  with a significant decrease in both the ß cell and islet cell numbers.,,,,,sample1,,strain:NA|isolate:NA|breed:NA|cultivar:NA|ecotype:NA|age:NA|dev stage:NA|sex:NA|tissue:embryos|genotype:Un injected|id:1|BioSampleModel:Model organism or animal,,,,,,,,,Un injected1,1,1,rRNA depletion,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP188580,,,1_2.fastq.gz 1_1.fastq.gz,fastq fastq,6454568216.0,31953308.0,1 1.fastq.gz,0:101 1:101,A:1711842196;C:1499359338;G:1512713745;T:1727020570;N:3632367,101,101,,,1711842196,1499359338,1512713745,1727020570,3632367,SRX5528099,SRS4494644,SRA861332,The Chinese University of Hong Kong|Department of Medicine and Therapeutics,The Chinese University of Hong Kong,2,0.92197,0.92401,0.20455,0.20573,0.72452,0.72943,0.63778,0.63469,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2020-01-27,Undetermined,Embryo,Embryo Imprecise,All anatomical structures
51319,SRR8735312,SRX5528098,SRS4494643,SRP188580,PRJNA527366,Characterization of the key role of dachshund b in the development of the pancreatic islet in zebrafish Danio rerio,PRJNA527366,Other,In this study  we characterized the function of dachb  the zebrafish homologue of human DACH1  in developing zebrafish embryos. Morpholino MO  mediated knock down of dachb resulted in impaired islet cell development  with a significant decrease in both the ß cell and islet cell numbers.,,,,,sample2,,strain:NA|isolate:NA|breed:NA|cultivar:NA|ecotype:NA|age:NA|dev stage:NA|sex:NA|tissue:embryos|genotype:p53MO|id:2|BioSampleModel:Model organism or animal,,,,,,,,,p53MO2,2,2,rRNA depletion,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP188580,,,2_2.fastq.gz 2_1.fastq.gz,fastq fastq,7923312236.0,39224318.0,2 1.fastq.gz,0:101 1:101,A:2115145426;C:1843204267;G:1845223955;T:2117945529;N:1793059,101,101,,,2115145426,1843204267,1845223955,2117945529,1793059,SRX5528098,SRS4494643,SRA861332,The Chinese University of Hong Kong|Department of Medicine and Therapeutics,The Chinese University of Hong Kong,2,0.93137,0.93358,0.18665,0.18693,0.7025,0.70421,0.55171,0.55971,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2019-03-16,Undetermined,Embryo,Embryo Imprecise,All anatomical structures
51320,SRR8735313,SRX5528097,SRS4494642,SRP188580,PRJNA527366,Characterization of the key role of dachshund b in the development of the pancreatic islet in zebrafish Danio rerio,PRJNA527366,Other,In this study  we characterized the function of dachb  the zebrafish homologue of human DACH1  in developing zebrafish embryos. Morpholino MO  mediated knock down of dachb resulted in impaired islet cell development  with a significant decrease in both the ß cell and islet cell numbers.,,,,,sample3,,strain:NA|isolate:NA|breed:NA|cultivar:NA|ecotype:NA|age:NA|dev stage:NA|sex:NA|tissue:embryos|genotype:p53MO dachbMOss|id:3|BioSampleModel:Model organism or animal,,,,,,,,,p53MO dachbMOss3,3,3,rRNA depletion,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP188580,,,3_2.fastq.gz 3_1.fastq.gz,fastq fastq,7167410460.0,35482230.0,3 1.fastq.gz,0:101 1:101,A:1924009959;C:1637729174;G:1671772822;T:1929836302;N:4062203,101,101,,,1924009959,1637729174,1671772822,1929836302,4062203,SRX5528097,SRS4494642,SRA861332,The Chinese University of Hong Kong|Department of Medicine and Therapeutics,The Chinese University of Hong Kong,2,0.91551,0.91609,0.20076,0.20036,0.70956,0.71244,0.62871,0.62479,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2020-01-27,Undetermined,Embryo,Embryo Imprecise,All anatomical structures
51321,SRR8735314,SRX5528096,SRS4494641,SRP188580,PRJNA527366,Characterization of the key role of dachshund b in the development of the pancreatic islet in zebrafish Danio rerio,PRJNA527366,Other,In this study  we characterized the function of dachb  the zebrafish homologue of human DACH1  in developing zebrafish embryos. Morpholino MO  mediated knock down of dachb resulted in impaired islet cell development  with a significant decrease in both the ß cell and islet cell numbers.,,,,,sample4,,strain:NA|isolate:NA|breed:NA|cultivar:NA|ecotype:NA|age:NA|dev stage:NA|sex:NA|tissue:embryos|genotype:Un injected|id:4|BioSampleModel:Model organism or animal,,,,,,,,,Un injected4,4,4,rRNA depletion,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP188580,,,4_1.fastq.gz 4_2.fastq.gz,fastq fastq,7730990460.0,38272230.0,4 1.fastq.gz,0:101 1:101,A:2077362460;C:1785598181;G:1793240660;T:2073032897;N:1756262,101,101,,,2077362460,1785598181,1793240660,2073032897,1756262,SRX5528096,SRS4494641,SRA861332,The Chinese University of Hong Kong|Department of Medicine and Therapeutics,The Chinese University of Hong Kong,2,0.93365,0.93546,0.1884,0.18821,0.70299,0.70364,0.57943,0.5807,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2020-01-27,Undetermined,Embryo,Embryo Imprecise,All anatomical structures
51322,SRR8735315,SRX5528095,SRS4494640,SRP188580,PRJNA527366,Characterization of the key role of dachshund b in the development of the pancreatic islet in zebrafish Danio rerio,PRJNA527366,Other,In this study  we characterized the function of dachb  the zebrafish homologue of human DACH1  in developing zebrafish embryos. Morpholino MO  mediated knock down of dachb resulted in impaired islet cell development  with a significant decrease in both the ß cell and islet cell numbers.,,,,,sample5,,strain:NA|isolate:NA|breed:NA|cultivar:NA|ecotype:NA|age:NA|dev stage:NA|sex:NA|tissue:embryos|genotype:p53MO|id:5|BioSampleModel:Model organism or animal,,,,,,,,,p53MO5,5,5,rRNA depletion,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP188580,,,5_1.fastq.gz 5_2.fastq.gz,fastq fastq,6268848608.0,31033904.0,5 1.fastq.gz,0:101 1:101,A:1714288048;C:1406856986;G:1416719545;T:1727415480;N:3568549,101,101,,,1714288048,1406856986,1416719545,1727415480,3568549,SRX5528095,SRS4494640,SRA861332,The Chinese University of Hong Kong|Department of Medicine and Therapeutics,The Chinese University of Hong Kong,2,0.91571,0.91742,0.22322,0.2243,0.71187,0.71417,0.63484,0.63493,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2020-01-27,Undetermined,Embryo,Embryo Imprecise,All anatomical structures
51323,SRR8735316,SRX5528094,SRS4494639,SRP188580,PRJNA527366,Characterization of the key role of dachshund b in the development of the pancreatic islet in zebrafish Danio rerio,PRJNA527366,Other,In this study  we characterized the function of dachb  the zebrafish homologue of human DACH1  in developing zebrafish embryos. Morpholino MO  mediated knock down of dachb resulted in impaired islet cell development  with a significant decrease in both the ß cell and islet cell numbers.,,,,,sample6,,strain:NA|isolate:NA|breed:NA|cultivar:NA|ecotype:NA|age:NA|dev stage:NA|sex:NA|tissue:embryos|genotype:p53MO dachbMOss|id:6|BioSampleModel:Model organism or animal,,,,,,,,,p53MO dachbMOss6,6,6,rRNA depletion,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP188580,,,6_1.fastq.gz 6_2.fastq.gz,fastq fastq,7551147638.0,37381919.0,6 1.fastq.gz,0:101 1:101,A:2055603662;C:1718965994;G:1723927649;T:2050926435;N:1723898,101,101,,,2055603662,1718965994,1723927649,2050926435,1723898,SRX5528094,SRS4494639,SRA861332,The Chinese University of Hong Kong|Department of Medicine and Therapeutics,The Chinese University of Hong Kong,2,0.92834,0.93211,0.19289,0.19294,0.697,0.69895,0.60804,0.60183,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2020-01-27,Undetermined,Embryo,Embryo Imprecise,All anatomical structures
51324,SRR8735317,SRX5528093,SRS4494638,SRP188580,PRJNA527366,Characterization of the key role of dachshund b in the development of the pancreatic islet in zebrafish Danio rerio,PRJNA527366,Other,In this study  we characterized the function of dachb  the zebrafish homologue of human DACH1  in developing zebrafish embryos. Morpholino MO  mediated knock down of dachb resulted in impaired islet cell development  with a significant decrease in both the ß cell and islet cell numbers.,,,,,sample7,,strain:NA|isolate:NA|breed:NA|cultivar:NA|ecotype:NA|age:NA|dev stage:NA|sex:NA|tissue:embryos|genotype:Un injected|id:7|BioSampleModel:Model organism or animal,,,,,,,,,Un injected7,7,7,rRNA depletion,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP188580,,,7_1.fastq.gz 7_2.fastq.gz,fastq fastq,8054903318.0,39875759.0,7 1.fastq.gz,0:101 1:101,A:2179527852;C:1844086452;G:1846868174;T:2182591371;N:1829469,101,101,,,2179527852,1844086452,1846868174,2182591371,1829469,SRX5528093,SRS4494638,SRA861332,The Chinese University of Hong Kong|Department of Medicine and Therapeutics,The Chinese University of Hong Kong,2,0.93087,0.93266,0.20658,0.20582,0.70465,0.70656,0.5697,0.57048,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2020-01-27,Undetermined,Embryo,Embryo Imprecise,All anatomical structures
51325,SRR8735318,SRX5528092,SRS4494637,SRP188580,PRJNA527366,Characterization of the key role of dachshund b in the development of the pancreatic islet in zebrafish Danio rerio,PRJNA527366,Other,In this study  we characterized the function of dachb  the zebrafish homologue of human DACH1  in developing zebrafish embryos. Morpholino MO  mediated knock down of dachb resulted in impaired islet cell development  with a significant decrease in both the ß cell and islet cell numbers.,,,,,sample8,,strain:NA|isolate:NA|breed:NA|cultivar:NA|ecotype:NA|age:NA|dev stage:NA|sex:NA|tissue:embryos|genotype:p53MO dachbMOss|id:8|BioSampleModel:Model organism or animal,,,,,,,,,p53MO dachbMOss8,8,8,rRNA depletion,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP188580,,,8_1.fastq.gz 8_2.fastq.gz,fastq fastq,7770765472.0,38469136.0,8 1.fastq.gz,0:101 1:101,A:2070852269;C:1791977628;G:1814751519;T:2088768678;N:4415378,101,101,,,2070852269,1791977628,1814751519,2088768678,4415378,SRX5528092,SRS4494637,SRA861332,The Chinese University of Hong Kong|Department of Medicine and Therapeutics,The Chinese University of Hong Kong,2,0.91409,0.9159,0.23811,0.23792,0.71804,0.72088,0.66221,0.66365,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2020-01-27,Undetermined,Embryo,Embryo Imprecise,All anatomical structures
53387,SRR9849850,SRX6604478,SRS5169417,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.,,,,,64h,,cultivar:Danio rerio|age:64hpf stage:hatching|sex:not determined|tissue:not applicable|BioSampleModel:Model organism or animal,,,,,,,,,circRNA 64h 2,64h 2,64h 2,circRNA sequence using embryo from zebrafish 64 hpf,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP216580,,,64h-1_Clean_1.fq.gz 64h-1_Clean_2.fq.gz,fastq fastq,12070643714.0,40313092.0,64h 1 Clean 1.fq.gz,0:149.71 1:149.71,A:3237260307;C:2738447871;G:2833701504;T:3260078610;N:1155422,149,149,,,3237260307,2738447871,2833701504,3260078610,1155422,SRX6604478,SRS5169417,SRA927972,Guangxi Academy of Fishery Sciences|Guangxi Academy of Fishery Sciences,Guangxi Academy of Fishery Sciences,2,0.83609,0.83872,0.41826,0.41667,0.77557,0.78397,0.47577,0.47371,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2019-07-27,Hatching,Embryo,Embryo Imprecise,All anatomical structures
53388,SRR9849851,SRX6604477,SRS5169416,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.,,,,,56h,,cultivar:Danio rerio|age:56hpf stage:hatching|sex:not determined|tissue:not applicable|BioSampleModel:Model organism or animal,,,,,,,,,circRNA 56h 2,56h 2,56h 2,circRNA sequence using embryo from zebrafish 56 hpf,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP216580,,,56h-1_Clean_1.fq.gz 56h-1_Clean_2.fq.gz,fastq fastq,12652509916.0,42236972.0,56h 1 Clean 1.fq.gz,0:149.78 1:149.78,A:3143250045;C:3111652116;G:3204244162;T:3192159623;N:1203970,149,149,,,3143250045,3111652116,3204244162,3192159623,1203970,SRX6604477,SRS5169416,SRA927972,Guangxi Academy of Fishery Sciences|Guangxi Academy of Fishery Sciences,Guangxi Academy of Fishery Sciences,2,0.75422,0.75589,0.33145,0.32138,0.8242,0.82911,0.44098,0.47205,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2019-07-27,Hatching,Embryo,Embryo Imprecise,All anatomical structures
53389,SRR9849852,SRX6604476,SRS5169417,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.,,,,,64h,,cultivar:Danio rerio|age:64hpf stage:hatching|sex:not determined|tissue:not applicable|BioSampleModel:Model organism or animal,,,,,,,,,circRNA 64h 1,64h 1,64h 1,circRNA sequence using embryo from zebrafish 64 hpf,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP216580,,,BN2-438_L4_7008.R1.clean.fastq.gz BN2-438_L4_7008.R2.clean.fastq.gz,fastq fastq,10065278400.0,33550928.0,BN2 438 L4 7008.R1.clean.fastq.gz,0:150 1:150,A:1866703079;C:2946459459;G:3062616963;T:2188863630;N:635269,150,150,,,1866703079,2946459459,3062616963,2188863630,635269,SRX6604476,SRS5169417,SRA927972,Guangxi Academy of Fishery Sciences|Guangxi Academy of Fishery Sciences,Guangxi Academy of Fishery Sciences,2,0.9213,0.9133,0.81853,0.81548,0.96639,0.96741,0.46951,0.49212,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2019-07-27,Hatching,Embryo,Embryo Imprecise,All anatomical structures
53390,SRR9849853,SRX6604475,SRS5169415,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.,,,,,40h,,cultivar:Danio rerio|age:40hpf stage:pharyngula|sex:not determined|tissue:not applicable|BioSampleModel:Model organism or animal,,,,,,,,,circRNA 40h 2,40h 2,40h 2,circRNA sequence using embryo from zebrafish 40 hpf,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP216580,,,40h-1_Clean_1.fq.gz 40h-1_Clean_2.fq.gz,fastq fastq,13039776756.0,43496055.0,40h 1 Clean 1.fq.gz,0:149.90 1:149.90,A:3288491359;C:3163780126;G:3276849759;T:3309186789;N:1468723,149,149,,,3288491359,3163780126,3276849759,3309186789,1468723,SRX6604475,SRS5169415,SRA927972,Guangxi Academy of Fishery Sciences|Guangxi Academy of Fishery Sciences,Guangxi Academy of Fishery Sciences,2,0.7816,0.78295,0.30782,0.30455,0.81148,0.82091,0.45266,0.46863,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2019-07-27,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
53391,SRR9849854,SRX6604474,SRS5169416,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.,,,,,56h,,cultivar:Danio rerio|age:56hpf stage:hatching|sex:not determined|tissue:not applicable|BioSampleModel:Model organism or animal,,,,,,,,,circRNA 56h 1,56h 1,56h 1,circRNA sequence using embryo from zebrafish 56 hpf,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP216580,,,BN2-437_L4_7007.R1.clean.fastq.gz BN2-437_L4_7007.R2.clean.fastq.gz,fastq fastq,7808518800.0,26028396.0,BN2 437 L4 7007.R1.clean.fastq.gz,0:150 1:150,A:1446244174;C:2292471599;G:2377378733;T:1691933018;N:491276,150,150,,,1446244174,2292471599,2377378733,1691933018,491276,SRX6604474,SRS5169416,SRA927972,Guangxi Academy of Fishery Sciences|Guangxi Academy of Fishery Sciences,Guangxi Academy of Fishery Sciences,2,0.90958,0.89969,0.83016,0.82404,0.9641,0.96558,0.44242,0.44176,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2019-07-27,Hatching,Embryo,Embryo Imprecise,All anatomical structures
53392,SRR9849855,SRX6604473,SRS5169409,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.,,,,,24h,,cultivar:Danio rerio|age:24hpf stage:segmentation|sex:not determined|tissue:not applicable|BioSampleModel:Model organism or animal,,,,,,,,,circRNA 24h 2,24h 2,24h 2,circRNA sequence using embryo from zebrafish 24 hpf,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP216580,,,24h-2_Clean_1.fq.gz 24h-2_Clean_2.fq.gz,fastq fastq,14034181236.0,46814505.0,24h 2 Clean 1.fq.gz,0:149.89 1:149.89,A:3573271889;C:3370553727;G:3504868393;T:3583897705;N:1589522,149,149,,,3573271889,3370553727,3504868393,3583897705,1589522,SRX6604473,SRS5169409,SRA927972,Guangxi Academy of Fishery Sciences|Guangxi Academy of Fishery Sciences,Guangxi Academy of Fishery Sciences,2,0.6799,0.67993,0.30195,0.29636,0.82453,0.83489,0.46929,0.47455,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2019-07-27,Multi-stage,Embryo,Embryo Imprecise,All anatomical structures
53393,SRR9849856,SRX6604472,SRS5169415,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.,,,,,40h,,cultivar:Danio rerio|age:40hpf stage:pharyngula|sex:not determined|tissue:not applicable|BioSampleModel:Model organism or animal,,,,,,,,,circRNA 40h 1,40h 1,40h 1,circRNA sequence using embryo from zebrafish 40 hpf,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP216580,,,BN2-435_L4_7005.R1.clean.fastq.gz BN2-435_L4_7005.R2.clean.fastq.gz,fastq fastq,7253248500.0,24177495.0,BN2 435 L4 7005.R1.clean.fastq.gz,0:150 1:150,A:1410890545;C:2084999879;G:2163487041;T:1593413760;N:457275,150,150,,,1410890545,2084999879,2163487041,1593413760,457275,SRX6604472,SRS5169415,SRA927972,Guangxi Academy of Fishery Sciences|Guangxi Academy of Fishery Sciences,Guangxi Academy of Fishery Sciences,2,0.87864,0.86461,0.70089,0.69415,0.94899,0.95221,0.45413,0.48608,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2019-07-27,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
53394,SRR9849857,SRX6604471,SRS5169414,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.,,,,,12h,,cultivar:Danio rerio|age:12hpf stage:segmentation|sex:not determined|tissue:not applicable|BioSampleModel:Model organism or animal,,,,,,,,,circRNA 12h 2,12h 2,12h 2,circRNA sequence using embryo from zebrafish 12 hpf,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP216580,,,12h-1_Clean_1.fq.gz 12h-1_Clean_2.fq.gz,fastq fastq,9760537114.0,32612820.0,12h 1 Clean 1.fq.gz,0:149.64 1:149.64,A:2537269193;C:2297094668;G:2379024620;T:2546216364;N:932269,149,149,,,2537269193,2297094668,2379024620,2546216364,932269,SRX6604471,SRS5169414,SRA927972,Guangxi Academy of Fishery Sciences|Guangxi Academy of Fishery Sciences,Guangxi Academy of Fishery Sciences,2,0.75204,0.75144,0.34914,0.3456,0.79444,0.80298,0.47617,0.47647,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2019-07-27,Segmentation,Embryo,Embryo Imprecise,All anatomical structures
53395,SRR9849858,SRX6604470,SRS5169410,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.,,,,,16h,,cultivar:Danio rerio|age:16hpf stage:segmentation|sex:not determined|tissue:not applicable|BioSampleModel:Model organism or animal,,,,,,,,,circRNA 16h 1,16h 1,16h 1,circRNA sequence using embryo from zebrafish 16 hpf,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP216580,,,BN2-430_L3_56.R1.clean.fastq.gz BN2-430_L3_56.R2.clean.fastq.gz,fastq fastq,11290204500.0,37634015.0,BN2 430 L3 56.R1.clean.fastq.gz,0:150 1:150,A:2002607987;C:3409827596;G:3508023598;T:2368035468;N:1709851,150,150,,,2002607987,3409827596,3508023598,2368035468,1709851,SRX6604470,SRS5169410,SRA927972,Guangxi Academy of Fishery Sciences|Guangxi Academy of Fishery Sciences,Guangxi Academy of Fishery Sciences,2,0.91788,0.9101,0.83385,0.81588,0.98462,0.9847,0.87183,0.87504,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2019-07-27,Segmentation,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.,,,,,8h,,cultivar:Danio rerio|age:8hpf stage:gastrula|sex:not determined|tissue:not applicable|BioSampleModel:Model organism or animal,,,,,,,,,circRNA 8h 2,8h 2,8h 2,circRNA sequence using embryo from zebrafish 8 hpf,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP216580,,,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,,,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,,China,2019-07-27,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
53397,SRR9849860,SRX6604468,SRS5169414,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.,,,,,12h,,cultivar:Danio rerio|age:12hpf stage:segmentation|sex:not determined|tissue:not applicable|BioSampleModel:Model organism or animal,,,,,,,,,circRNA 12h 1,12h 1,12h 1,circRNA sequence using embryo from zebrafish 12 hpf,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP216580,,,BN2-429_L3_55.R1.clean.fastq.gz BN2-429_L3_55.R2.clean.fastq.gz,fastq fastq,9471315300.0,31571051.0,BN2 429 L3 55.R1.clean.fastq.gz,0:150 1:150,A:1671591116;C:2907243262;G:3000871353;T:1890180659;N:1428910,150,150,,,1671591116,2907243262,3000871353,1890180659,1428910,SRX6604468,SRS5169414,SRA927972,Guangxi Academy of Fishery Sciences|Guangxi Academy of Fishery Sciences,Guangxi Academy of Fishery Sciences,2,0.76551,0.7596,0.58436,0.57204,0.9853,0.98567,0.95092,0.95274,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2019-07-27,Segmentation,Embryo,Embryo Imprecise,All anatomical structures
53398,SRR9849861,SRX6604467,SRS5169413,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.,,,,,4h,,cultivar:Danio rerio|age:4hpf stage:bastula|sex:not determined|tissue:not applicable|BioSampleModel:Model organism or animal,,,,,,,,,circRNA 4h 1,4h 1,4h 1,circRNA sequence using embryo from zebrafish 4 hpf,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP216580,,,BN2-427_L3_53.R1.clean.fastq.gz BN2-427_L3_53.R2.clean.fastq.gz,fastq fastq,10733190600.0,35777302.0,BN2 427 L3 53.R1.clean.fastq.gz,0:150 1:150,A:1899542444;C:3199739789;G:3296303811;T:2336021248;N:1583308,150,150,,,1899542444,3199739789,3296303811,2336021248,1583308,SRX6604467,SRS5169413,SRA927972,Guangxi Academy of Fishery Sciences|Guangxi Academy of Fishery Sciences,Guangxi Academy of Fishery Sciences,2,0.84333,0.8387,0.65527,0.64575,0.97634,0.97737,0.70606,0.63009,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2019-07-27,Blastula,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.,,,,,8h,,cultivar:Danio rerio|age:8hpf stage:gastrula|sex:not determined|tissue:not applicable|BioSampleModel:Model organism or animal,,,,,,,,,circRNA 8h 1,8h 1,8h 1,circRNA sequence using embryo from zebrafish 8 hpf,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP216580,,,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,,,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,,China,2019-07-27,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
53400,SRR9849863,SRX6604465,SRS5169411,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.,,,,,0h,,cultivar:Danio rerio|age:0hpf stage:zygote|sex:not determined|tissue:not applicable|BioSampleModel:Model organism or animal,,,,,,,,,circRNA 0h 1,0h 1,0h 1,circRNA sequence using embryo from zebrafish 0 hpf,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP216580,,,BN2-426_L3_52.R1.clean.fastq.gz BN2-426_L3_52.R2.clean.fastq.gz,fastq fastq,15572807100.0,51909357.0,BN2 426 L3 52.R1.clean.fastq.gz,0:150 1:150,A:2605617359;C:4885017797;G:5011849012;T:3067990728;N:2332204,150,150,,,2605617359,4885017797,5011849012,3067990728,2332204,SRX6604465,SRS5169411,SRA927972,Guangxi Academy of Fishery Sciences|Guangxi Academy of Fishery Sciences,Guangxi Academy of Fishery Sciences,2,0.78804,0.77444,0.56081,0.54686,0.93348,0.93545,0.77104,0.62239,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2019-07-27,Zygote,Embryo,Embryo Imprecise,All anatomical structures
53401,SRR9849864,SRX6604464,SRS5169411,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.,,,,,0h,,cultivar:Danio rerio|age:0hpf stage:zygote|sex:not determined|tissue:not applicable|BioSampleModel:Model organism or animal,,,,,,,,,circRNA 0h 2,0h 2,0h 2,circRNA sequence using embryo from zebrafish 0 hpf,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP216580,,,0h_Clean_1.fq.gz 0h_Clean_2.fq.gz,fastq fastq,17258783034.0,57614191.0,0h Clean 1.fq.gz,0:149.78 1:149.78,A:3915507312;C:4601222856;G:4762519500;T:3977299451;N:2233915,149,149,,,3915507312,4601222856,4762519500,3977299451,2233915,SRX6604464,SRS5169411,SRA927972,Guangxi Academy of Fishery Sciences|Guangxi Academy of Fishery Sciences,Guangxi Academy of Fishery Sciences,2,0.82486,0.82843,0.16023,0.14824,0.79971,0.80348,0.48785,0.48902,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2019-07-27,Zygote,Embryo,Embryo Imprecise,All anatomical structures
53402,SRR9849865,SRX6604463,SRS5169410,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.,,,,,16h,,cultivar:Danio rerio|age:16hpf stage:segmentation|sex:not determined|tissue:not applicable|BioSampleModel:Model organism or animal,,,,,,,,,circRNA 16h 2,16h 2,16h 2,circRNA sequence using embryo from zebrafish 16 hpf,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP216580,,,16h-1_Clean_1.fq.gz 16h-1_Clean_2.fq.gz,fastq fastq,13746008148.0,45914536.0,16h 1 Clean 1.fq.gz,0:149.69 1:149.69,A:3633911267;C:3175232398;G:3288410708;T:3647163703;N:1290072,149,149,,,3633911267,3175232398,3288410708,3647163703,1290072,SRX6604463,SRS5169410,SRA927972,Guangxi Academy of Fishery Sciences|Guangxi Academy of Fishery Sciences,Guangxi Academy of Fishery Sciences,2,0.76446,0.76939,0.32701,0.32679,0.80537,0.8116,0.47029,0.4846,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2019-07-27,Segmentation,Embryo,Embryo Imprecise,All anatomical structures
53403,SRR9849866,SRX6604462,SRS5169409,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.,,,,,24h,,cultivar:Danio rerio|age:24hpf stage:segmentation|sex:not determined|tissue:not applicable|BioSampleModel:Model organism or animal,,,,,,,,,circRNA 24h 1,24h 1,24h 1,circRNA sequence using embryo from zebrafish 24 hpf,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP216580,,,BN2-432_L3_7002.R1.clean.fastq.gz BN2-432_L3_7002.R2.clean.fastq.gz,fastq fastq,4964505000.0,16548350.0,BN2 432 L3 7002.R1.clean.fastq.gz,0:150 1:150,A:869476377;C:1551985326;G:1601622154;T:940673581;N:747562,150,150,,,869476377,1551985326,1601622154,940673581,747562,SRX6604462,SRS5169409,SRA927972,Guangxi Academy of Fishery Sciences|Guangxi Academy of Fishery Sciences,Guangxi Academy of Fishery Sciences,2,0.90699,0.90038,0.67002,0.65836,0.98528,0.98557,0.90533,0.8368,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2019-07-27,Multi-stage,Embryo,Embryo Imprecise,All anatomical structures
55447,SRR10436022,SRX7131796,SRS5640788,SRP229649,PRJNA588137,rnf213a knockout zebrafish Transcriptome or Gene expression,PRJNA588137,Transcriptome Analysis,To explore the downstream molecules of rnf213a  we conducted transcriptome sequencing to detect differentially expressed genes DEGs between +2bp rnf213a /  mutant and wild type zebrafish at 72hpf and 120hpf.,,,,,2bp 120hpf,,strain:rnf213a mutant|dev stage:120hpf|sex:pooled male and female|tissue:whole mount embryos|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: whole mount embryos,rnf213a 8,rnf213a 8,The polyA mRNA isolation was performed using NEBNext PolyA mRNA Magnetic Isolation Module NEB or Ribo Zero rRNA removal Kit illumina. The mRNA fragmentation and priming was performed using NEBNext First Strand Synthesis Reaction Buffer and NEBNext Random Primers. First strand cDNA was synthesized using ProtoScript II Reverse Transcriptase and the second strand cDNA was synthesized using Second Strand Synthesis Enzyme Mix. The purified double stranded cDNAby AxyPrep Mag PCR Clean up Axygenwas then treated with End Prep Enzyme Mix to repair both ends and add a dA tailing in one reaction  followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using AxyPrep Mag PCR Clean up Axygen  and fragments of 360 bp with the approximate insert size of 300 bp were recovered. Each sample was then amplified by PCR for 11 cycles using P5 and P7 primers  with both primers carrying sequences which can anneal with flow cell to perform bridge PCR and P7 primer carrying a six base index allowing for multiplexing. The PCR products were cleaned up using AxyPrep Mag PCR Clean up Axygen  validated using an Agilent 2100 Bioanalyzer Agilent Technologies  Palo Alto  CA  USA  and quantified by Qubit 2.0 Fluorometer Invitrogen  Carlsbad  CA  USA.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,HiSeq X Ten,,SRP229649,,,rnf213a_8,fastq,4982904300.0,33219362.0,rnf213a 8.gz,0:0 1:150,A:1324339848;C:1163795168;G:1165190242;T:1329576411;N:2631,0,150,,,1324339848,1163795168,1165190242,1329576411,2631,SRX7131796,SRS5640788,SRA993760,First affiliated hospital of Sun Yat-sen university|neurology,First affiliated hospital of Sun Yat-sen university,1,0.92735,,0.08973,,0.66523,,0.48455,,150,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,nebnext,bulk,unknown,unknown,,China,2019-11-13,Larval,Larval,Embryo Imprecise,All anatomical structures
55448,SRR10436027,SRX7131795,SRS5640788,SRP229649,PRJNA588137,rnf213a knockout zebrafish Transcriptome or Gene expression,PRJNA588137,Transcriptome Analysis,To explore the downstream molecules of rnf213a  we conducted transcriptome sequencing to detect differentially expressed genes DEGs between +2bp rnf213a /  mutant and wild type zebrafish at 72hpf and 120hpf.,,,,,2bp 120hpf,,strain:rnf213a mutant|dev stage:120hpf|sex:pooled male and female|tissue:whole mount embryos|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: whole mount embryos,rnf213a 7,rnf213a 7,The polyA mRNA isolation was performed using NEBNext PolyA mRNA Magnetic Isolation Module NEB or Ribo Zero rRNA removal Kit illumina. The mRNA fragmentation and priming was performed using NEBNext First Strand Synthesis Reaction Buffer and NEBNext Random Primers. First strand cDNA was synthesized using ProtoScript II Reverse Transcriptase and the second strand cDNA was synthesized using Second Strand Synthesis Enzyme Mix. The purified double stranded cDNAby AxyPrep Mag PCR Clean up Axygenwas then treated with End Prep Enzyme Mix to repair both ends and add a dA tailing in one reaction  followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using AxyPrep Mag PCR Clean up Axygen  and fragments of 360 bp with the approximate insert size of 300 bp were recovered. Each sample was then amplified by PCR for 11 cycles using P5 and P7 primers  with both primers carrying sequences which can anneal with flow cell to perform bridge PCR and P7 primer carrying a six base index allowing for multiplexing. The PCR products were cleaned up using AxyPrep Mag PCR Clean up Axygen  validated using an Agilent 2100 Bioanalyzer Agilent Technologies  Palo Alto  CA  USA  and quantified by Qubit 2.0 Fluorometer Invitrogen  Carlsbad  CA  USA.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,HiSeq X Ten,,SRP229649,,,rnf213a_7,fastq,4982904300.0,33219362.0,rnf213a 7.gz,0:150 1:0,A:1334481379;C:1157336743;G:1153222575;T:1337750420;N:113183,150,0,,,1334481379,1157336743,1153222575,1337750420,113183,SRX7131795,SRS5640788,SRA993760,First affiliated hospital of Sun Yat-sen university|neurology,First affiliated hospital of Sun Yat-sen university,1,0.92697,,0.08859,,0.6522,,0.47736,,150,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,nebnext,bulk,unknown,unknown,,China,2019-11-13,Larval,Larval,Embryo Imprecise,All anatomical structures
55449,SRR10436023,SRX7131794,SRS5640787,SRP229649,PRJNA588137,rnf213a knockout zebrafish Transcriptome or Gene expression,PRJNA588137,Transcriptome Analysis,To explore the downstream molecules of rnf213a  we conducted transcriptome sequencing to detect differentially expressed genes DEGs between +2bp rnf213a /  mutant and wild type zebrafish at 72hpf and 120hpf.,,,,,normal 120hpf,,strain:wild type|dev stage:120hpf|sex:pooled male and female|tissue:whole mount embryos|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: whole mount embryos,rnf213a 6,rnf213a 6,The polyA mRNA isolation was performed using NEBNext PolyA mRNA Magnetic Isolation Module NEB or Ribo Zero rRNA removal Kit illumina. The mRNA fragmentation and priming was performed using NEBNext First Strand Synthesis Reaction Buffer and NEBNext Random Primers. First strand cDNA was synthesized using ProtoScript II Reverse Transcriptase and the second strand cDNA was synthesized using Second Strand Synthesis Enzyme Mix. The purified double stranded cDNAby AxyPrep Mag PCR Clean up Axygenwas then treated with End Prep Enzyme Mix to repair both ends and add a dA tailing in one reaction  followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using AxyPrep Mag PCR Clean up Axygen  and fragments of 360 bp with the approximate insert size of 300 bp were recovered. Each sample was then amplified by PCR for 11 cycles using P5 and P7 primers  with both primers carrying sequences which can anneal with flow cell to perform bridge PCR and P7 primer carrying a six base index allowing for multiplexing. The PCR products were cleaned up using AxyPrep Mag PCR Clean up Axygen  validated using an Agilent 2100 Bioanalyzer Agilent Technologies  Palo Alto  CA  USA  and quantified by Qubit 2.0 Fluorometer Invitrogen  Carlsbad  CA  USA.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,HiSeq X Ten,,SRP229649,,,rnf213a_6,fastq,4604017500.0,30693450.0,rnf213a 6.gz,0:0 1:150,A:1223063228;C:1075059595;G:1073833007;T:1232058851;N:2819,0,150,,,1223063228,1075059595,1073833007,1232058851,2819,SRX7131794,SRS5640787,SRA993760,First affiliated hospital of Sun Yat-sen university|neurology,First affiliated hospital of Sun Yat-sen university,1,0.9235,,0.09498,,0.66827,,0.47851,,150,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,nebnext,bulk,unknown,unknown,,China,2019-11-13,Larval,Larval,Embryo Imprecise,All anatomical structures
55450,SRR10436026,SRX7131793,SRS5640787,SRP229649,PRJNA588137,rnf213a knockout zebrafish Transcriptome or Gene expression,PRJNA588137,Transcriptome Analysis,To explore the downstream molecules of rnf213a  we conducted transcriptome sequencing to detect differentially expressed genes DEGs between +2bp rnf213a /  mutant and wild type zebrafish at 72hpf and 120hpf.,,,,,normal 120hpf,,strain:wild type|dev stage:120hpf|sex:pooled male and female|tissue:whole mount embryos|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: whole mount embryos,rnf213a 5,rnf213a 5,The polyA mRNA isolation was performed using NEBNext PolyA mRNA Magnetic Isolation Module NEB or Ribo Zero rRNA removal Kit illumina. The mRNA fragmentation and priming was performed using NEBNext First Strand Synthesis Reaction Buffer and NEBNext Random Primers. First strand cDNA was synthesized using ProtoScript II Reverse Transcriptase and the second strand cDNA was synthesized using Second Strand Synthesis Enzyme Mix. The purified double stranded cDNAby AxyPrep Mag PCR Clean up Axygenwas then treated with End Prep Enzyme Mix to repair both ends and add a dA tailing in one reaction  followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using AxyPrep Mag PCR Clean up Axygen  and fragments of 360 bp with the approximate insert size of 300 bp were recovered. Each sample was then amplified by PCR for 11 cycles using P5 and P7 primers  with both primers carrying sequences which can anneal with flow cell to perform bridge PCR and P7 primer carrying a six base index allowing for multiplexing. The PCR products were cleaned up using AxyPrep Mag PCR Clean up Axygen  validated using an Agilent 2100 Bioanalyzer Agilent Technologies  Palo Alto  CA  USA  and quantified by Qubit 2.0 Fluorometer Invitrogen  Carlsbad  CA  USA.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,HiSeq X Ten,,SRP229649,,,rnf213a_5,fastq,4604017500.0,30693450.0,rnf213a 5.gz,0:150 1:0,A:1233642245;C:1066547157;G:1063728944;T:1239996010;N:103144,150,0,,,1233642245,1066547157,1063728944,1239996010,103144,SRX7131793,SRS5640787,SRA993760,First affiliated hospital of Sun Yat-sen university|neurology,First affiliated hospital of Sun Yat-sen university,1,0.9238,,0.09388,,0.6549,,0.4787,,150,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,nebnext,bulk,unknown,unknown,,China,2019-11-13,Larval,Larval,Embryo Imprecise,All anatomical structures
55451,SRR10436024,SRX7131792,SRS5640786,SRP229649,PRJNA588137,rnf213a knockout zebrafish Transcriptome or Gene expression,PRJNA588137,Transcriptome Analysis,To explore the downstream molecules of rnf213a  we conducted transcriptome sequencing to detect differentially expressed genes DEGs between +2bp rnf213a /  mutant and wild type zebrafish at 72hpf and 120hpf.,,,,,2bp 72hpf,,strain:rnf213a mutant|dev stage:72hpf|sex:pooled male and female|tissue:whole mount embryos|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: whole mount embryos,rnf213a 4,rnf213a 4,The polyA mRNA isolation was performed using NEBNext PolyA mRNA Magnetic Isolation Module NEB or Ribo Zero rRNA removal Kit illumina. The mRNA fragmentation and priming was performed using NEBNext First Strand Synthesis Reaction Buffer and NEBNext Random Primers. First strand cDNA was synthesized using ProtoScript II Reverse Transcriptase and the second strand cDNA was synthesized using Second Strand Synthesis Enzyme Mix. The purified double stranded cDNAby AxyPrep Mag PCR Clean up Axygenwas then treated with End Prep Enzyme Mix to repair both ends and add a dA tailing in one reaction  followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using AxyPrep Mag PCR Clean up Axygen  and fragments of 360 bp with the approximate insert size of 300 bp were recovered. Each sample was then amplified by PCR for 11 cycles using P5 and P7 primers  with both primers carrying sequences which can anneal with flow cell to perform bridge PCR and P7 primer carrying a six base index allowing for multiplexing. The PCR products were cleaned up using AxyPrep Mag PCR Clean up Axygen  validated using an Agilent 2100 Bioanalyzer Agilent Technologies  Palo Alto  CA  USA  and quantified by Qubit 2.0 Fluorometer Invitrogen  Carlsbad  CA  USA.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,HiSeq X Ten,,SRP229649,,,rnf213a_4,fastq,3640003350.0,24266689.0,rnf213a 4.gz,0:0 1:150,A:957485805;C:856078896;G:866344396;T:959578628;N:515625,0,150,,,957485805,856078896,866344396,959578628,515625,SRX7131792,SRS5640786,SRA993760,First affiliated hospital of Sun Yat-sen university|neurology,First affiliated hospital of Sun Yat-sen university,1,0.93507,,0.08252,,0.67186,,0.4731,,150,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,nebnext,bulk,unknown,unknown,,China,2019-11-13,Larval,Larval,Embryo Imprecise,All anatomical structures
55452,SRR10436025,SRX7131791,SRS5640786,SRP229649,PRJNA588137,rnf213a knockout zebrafish Transcriptome or Gene expression,PRJNA588137,Transcriptome Analysis,To explore the downstream molecules of rnf213a  we conducted transcriptome sequencing to detect differentially expressed genes DEGs between +2bp rnf213a /  mutant and wild type zebrafish at 72hpf and 120hpf.,,,,,2bp 72hpf,,strain:rnf213a mutant|dev stage:72hpf|sex:pooled male and female|tissue:whole mount embryos|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: whole mount embryos,rnf213a 3,rnf213a 3,The polyA mRNA isolation was performed using NEBNext PolyA mRNA Magnetic Isolation Module NEB or Ribo Zero rRNA removal Kit illumina. The mRNA fragmentation and priming was performed using NEBNext First Strand Synthesis Reaction Buffer and NEBNext Random Primers. First strand cDNA was synthesized using ProtoScript II Reverse Transcriptase and the second strand cDNA was synthesized using Second Strand Synthesis Enzyme Mix. The purified double stranded cDNAby AxyPrep Mag PCR Clean up Axygenwas then treated with End Prep Enzyme Mix to repair both ends and add a dA tailing in one reaction  followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using AxyPrep Mag PCR Clean up Axygen  and fragments of 360 bp with the approximate insert size of 300 bp were recovered. Each sample was then amplified by PCR for 11 cycles using P5 and P7 primers  with both primers carrying sequences which can anneal with flow cell to perform bridge PCR and P7 primer carrying a six base index allowing for multiplexing. The PCR products were cleaned up using AxyPrep Mag PCR Clean up Axygen  validated using an Agilent 2100 Bioanalyzer Agilent Technologies  Palo Alto  CA  USA  and quantified by Qubit 2.0 Fluorometer Invitrogen  Carlsbad  CA  USA.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,HiSeq X Ten,,SRP229649,,,rnf213a_3,fastq,3640003350.0,24266689.0,rnf213a 3.gz,0:150 1:0,A:959700410;C:857785674;G:859574997;T:962707972;N:234297,150,0,,,959700410,857785674,859574997,962707972,234297,SRX7131791,SRS5640786,SRA993760,First affiliated hospital of Sun Yat-sen university|neurology,First affiliated hospital of Sun Yat-sen university,1,0.93504,,0.08216,,0.66541,,0.4721,,150,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,nebnext,bulk,unknown,unknown,,China,2019-11-13,Larval,Larval,Embryo Imprecise,All anatomical structures
55453,SRR10436028,SRX7131790,SRS5640785,SRP229649,PRJNA588137,rnf213a knockout zebrafish Transcriptome or Gene expression,PRJNA588137,Transcriptome Analysis,To explore the downstream molecules of rnf213a  we conducted transcriptome sequencing to detect differentially expressed genes DEGs between +2bp rnf213a /  mutant and wild type zebrafish at 72hpf and 120hpf.,,,,,normal 72hpf,,strain:wild type|dev stage:72hpf|sex:pooled male and female|tissue:whole mount embryos|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: whole mount embryos,rnf213a 2,rnf213a 2,The polyA mRNA isolation was performed using NEBNext PolyA mRNA Magnetic Isolation Module NEB or Ribo Zero rRNA removal Kit illumina. The mRNA fragmentation and priming was performed using NEBNext First Strand Synthesis Reaction Buffer and NEBNext Random Primers. First strand cDNA was synthesized using ProtoScript II Reverse Transcriptase and the second strand cDNA was synthesized using Second Strand Synthesis Enzyme Mix. The purified double stranded cDNAby AxyPrep Mag PCR Clean up Axygenwas then treated with End Prep Enzyme Mix to repair both ends and add a dA tailing in one reaction  followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using AxyPrep Mag PCR Clean up Axygen  and fragments of 360 bp with the approximate insert size of 300 bp were recovered. Each sample was then amplified by PCR for 11 cycles using P5 and P7 primers  with both primers carrying sequences which can anneal with flow cell to perform bridge PCR and P7 primer carrying a six base index allowing for multiplexing. The PCR products were cleaned up using AxyPrep Mag PCR Clean up Axygen  validated using an Agilent 2100 Bioanalyzer Agilent Technologies  Palo Alto  CA  USA  and quantified by Qubit 2.0 Fluorometer Invitrogen  Carlsbad  CA  USA.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,HiSeq X Ten,,SRP229649,,,rnf213a_2,fastq,3592044900.0,23946966.0,rnf213a 2.gz,0:0 1:150,A:950382154;C:839432686;G:850391648;T:951328573;N:509839,0,150,,,950382154,839432686,850391648,951328573,509839,SRX7131790,SRS5640785,SRA993760,First affiliated hospital of Sun Yat-sen university|neurology,First affiliated hospital of Sun Yat-sen university,1,0.93222,,0.09138,,0.66087,,0.48076,,150,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,nebnext,bulk,unknown,unknown,,China,2019-11-13,Larval,Larval,Embryo Imprecise,All anatomical structures
55454,SRR10436029,SRX7131789,SRS5640785,SRP229649,PRJNA588137,rnf213a knockout zebrafish Transcriptome or Gene expression,PRJNA588137,Transcriptome Analysis,To explore the downstream molecules of rnf213a  we conducted transcriptome sequencing to detect differentially expressed genes DEGs between +2bp rnf213a /  mutant and wild type zebrafish at 72hpf and 120hpf.,,,,,normal 72hpf,,strain:wild type|dev stage:72hpf|sex:pooled male and female|tissue:whole mount embryos|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: whole mount embryos,rnf213a 1,rnf213a 1,The polyA mRNA isolation was performed using NEBNext PolyA mRNA Magnetic Isolation Module NEB or Ribo Zero rRNA removal Kit illumina. The mRNA fragmentation and priming was performed using NEBNext First Strand Synthesis Reaction Buffer and NEBNext Random Primers. First strand cDNA was synthesized using ProtoScript II Reverse Transcriptase and the second strand cDNA was synthesized using Second Strand Synthesis Enzyme Mix. The purified double stranded cDNAby AxyPrep Mag PCR Clean up Axygenwas then treated with End Prep Enzyme Mix to repair both ends and add a dA tailing in one reaction  followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using AxyPrep Mag PCR Clean up Axygen  and fragments of 360 bp with the approximate insert size of 300 bp were recovered. Each sample was then amplified by PCR for 11 cycles using P5 and P7 primers  with both primers carrying sequences which can anneal with flow cell to perform bridge PCR and P7 primer carrying a six base index allowing for multiplexing. The PCR products were cleaned up using AxyPrep Mag PCR Clean up Axygen  validated using an Agilent 2100 Bioanalyzer Agilent Technologies  Palo Alto  CA  USA  and quantified by Qubit 2.0 Fluorometer Invitrogen  Carlsbad  CA  USA.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,HiSeq X Ten,,SRP229649,,,rnf213a_1,fastq,3592044900.0,23946966.0,rnf213a 1.gz,0:150 1:0,A:952165099;C:842448366;G:843305876;T:953891694;N:233865,150,0,,,952165099,842448366,843305876,953891694,233865,SRX7131789,SRS5640785,SRA993760,First affiliated hospital of Sun Yat-sen university|neurology,First affiliated hospital of Sun Yat-sen university,1,0.93128,,0.09035,,0.65445,,0.47792,,150,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,nebnext,bulk,unknown,unknown,,China,2019-11-13,Larval,Larval,Embryo Imprecise,All anatomical structures
57192,SRR11267487,SRX7874167,SRS6282472,SRP252014,PRJNA611476,RNAseq between mutant and wild type zebrafish at different developmental stages,PRJNA611476,Other,,,,,,2D wt 4,,strain:Abtu|ecotype:wild type|dev stage:2dpf|sex:missing|tissue:embryos|replicate:biological replicate 4|BioSampleModel:Model organism or animal,,,,,,,,,2dpf wild type replicate 4,2D wt 4,2D wt 4,common method,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP252014,,,s-2D-W4_RRA127644-V_2.fq.gz s-2D-W4_RRA127644-V_1.fq.gz,fastq fastq,8446821000.0,28156070.0,s 2D W4 RRA127644 V 1.fq.gz,0:150 1:150,A:2097825166;C:2140144849;G:2138243343;T:2070561208;N:46434,150,150,,,2097825166,2140144849,2138243343,2070561208,46434,SRX7874167,SRS6282472,SRA1052323,Sun Yat-sen University|College of Life Sciences,Sun Yat-sen University,2,0.96179,0.9619,0.03544,0.03525,0.73484,0.73476,0.46149,0.46378,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2020-03-09,Hatching,Embryo,Embryo Imprecise,All anatomical structures
57193,SRR11267488,SRX7874166,SRS6282471,SRP252014,PRJNA611476,RNAseq between mutant and wild type zebrafish at different developmental stages,PRJNA611476,Other,,,,,,2D wt 3,,strain:Abtu|ecotype:wild type|dev stage:2dpf|sex:missing|tissue:embryos|replicate:biological replicate 3|BioSampleModel:Model organism or animal,,,,,,,,,2dpf wild type replicate 3,2D wt 3,2D wt 3,common method,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP252014,,,s-2D-W3_RRA127643-V_2.fq.gz s-2D-W3_RRA127643-V_1.fq.gz,fastq fastq,7574668800.0,25248896.0,s 2D W3 RRA127643 V 1.fq.gz,0:150 1:150,A:1965967840;C:1838044502;G:1837157311;T:1933458605;N:40542,150,150,,,1965967840,1838044502,1837157311,1933458605,40542,SRX7874166,SRS6282471,SRA1052323,Sun Yat-sen University|College of Life Sciences,Sun Yat-sen University,2,0.94714,0.94809,0.06053,0.06005,0.70601,0.7066,0.44616,0.4478,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2020-03-09,Hatching,Embryo,Embryo Imprecise,All anatomical structures
57194,SRR11267489,SRX7874165,SRS6282470,SRP252014,PRJNA611476,RNAseq between mutant and wild type zebrafish at different developmental stages,PRJNA611476,Other,,,,,,2D wt 2,,strain:Abtu|ecotype:wild type|dev stage:2dpf|sex:missing|tissue:embryos|replicate:biological replicate 2|BioSampleModel:Model organism or animal,,,,,,,,,2dpf wild type replicate 2,2D wt 2,2D wt 2,common method,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP252014,,,s-2D-W2_RRA127642-V_1.fq.gz s-2D-W2_RRA127642-V_2.fq.gz,fastq fastq,6972507000.0,23241690.0,s 2D W2 RRA127642 V 1.fq.gz,0:150 1:150,A:1813207623;C:1690998145;G:1687754190;T:1780508001;N:39041,150,150,,,1813207623,1690998145,1687754190,1780508001,39041,SRX7874165,SRS6282470,SRA1052323,Sun Yat-sen University|College of Life Sciences,Sun Yat-sen University,2,0.94999,0.95119,0.05951,0.0596,0.7077,0.70778,0.45098,0.44895,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2020-03-09,Hatching,Embryo,Embryo Imprecise,All anatomical structures
57195,SRR11267490,SRX7874164,SRS6282468,SRP252014,PRJNA611476,RNAseq between mutant and wild type zebrafish at different developmental stages,PRJNA611476,Other,,,,,,2D wt 1,,strain:Abtu|ecotype:wild type|dev stage:2dpf|sex:missing|tissue:embryos|replicate:biological replicate 1|BioSampleModel:Model organism or animal,,,,,,,,,2dpf wild type replicate 1,2D wt 1,2D wt 1,common method,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP252014,,,s-2D-W1_RRA127641-V_1.fq.gz s-2D-W1_RRA127641-V_2.fq.gz,fastq fastq,7527697800.0,25092326.0,s 2D W1 RRA127641 V 1.fq.gz,0:150 1:150,A:1939383301;C:1841967572;G:1840198678;T:1906107300;N:40949,150,150,,,1939383301,1841967572,1840198678,1906107300,40949,SRX7874164,SRS6282468,SRA1052323,Sun Yat-sen University|College of Life Sciences,Sun Yat-sen University,2,0.93028,0.93025,0.05585,0.05522,0.71163,0.71281,0.45427,0.45339,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2020-03-09,Hatching,Embryo,Embryo Imprecise,All anatomical structures
57196,SRR11267491,SRX7874163,SRS6282469,SRP252014,PRJNA611476,RNAseq between mutant and wild type zebrafish at different developmental stages,PRJNA611476,Other,,,,,,2D mut 6,,strain:Abtu|ecotype:mutant|dev stage:2dpf|sex:missing|tissue:embryos|replicate:biological replicate 6|BioSampleModel:Model organism or animal,,,,,,,,,2dpf mutant replicate 6,2D mut 6,2D mut 6,common method,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP252014,,,s-2D-MU6_RRA127640-V_1.fq.gz s-2D-MU6_RRA127640-V_2.fq.gz,fastq fastq,7468400400.0,24894668.0,s 2D MU6 RRA127640 V 1.fq.gz,0:150 1:150,A:1831861636;C:1917846110;G:1910771652;T:1807881608;N:39394,150,150,,,1831861636,1917846110,1910771652,1807881608,39394,SRX7874163,SRS6282469,SRA1052323,Sun Yat-sen University|College of Life Sciences,Sun Yat-sen University,2,0.96824,0.96912,0.02823,0.02789,0.76116,0.76086,0.46225,0.46104,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2020-03-09,Hatching,Embryo,Embryo Imprecise,All anatomical structures
57205,SRR11267500,SRX7874154,SRS6282459,SRP252014,PRJNA611476,RNAseq between mutant and wild type zebrafish at different developmental stages,PRJNA611476,Other,,,,,,2D mut 5,,strain:Abtu|ecotype:mutant|dev stage:2dpf|sex:missing|tissue:embryos|replicate:biological replicate 5|BioSampleModel:Model organism or animal,,,,,,,,,2dpf mutant replicate 5,2D mut 5,2D mut 5,common method,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP252014,,,s-2D-MU5_RRA127639-V_1.fq.gz s-2D-MU5_RRA127639-V_2.fq.gz,fastq fastq,7610707500.0,25369025.0,s 2D MU5 RRA127639 V 1.fq.gz,0:150 1:150,A:1916314949;C:1902998959;G:1903573416;T:1887778592;N:41584,150,150,,,1916314949,1902998959,1903573416,1887778592,41584,SRX7874154,SRS6282459,SRA1052323,Sun Yat-sen University|College of Life Sciences,Sun Yat-sen University,2,0.95723,0.95704,0.04362,0.04378,0.7231,0.72196,0.45408,0.45325,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2020-03-09,Hatching,Embryo,Embryo Imprecise,All anatomical structures
57216,SRR11267511,SRX7874143,SRS6282448,SRP252014,PRJNA611476,RNAseq between mutant and wild type zebrafish at different developmental stages,PRJNA611476,Other,,,,,,2D mut 4,,strain:Abtu|ecotype:mutant|dev stage:2dpf|sex:missing|tissue:embryos|replicate:biological replicate 4|BioSampleModel:Model organism or animal,,,,,,,,,2dpf mutant replicate 4,2D mut 4,2D mut 4,common method,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP252014,,,s-2D-MU4_RRA127638-V_2.fq.gz s-2D-MU4_RRA127638-V_1.fq.gz,fastq fastq,7971688200.0,26572294.0,s 2D MU4 RRA127638 V 1.fq.gz,0:150 1:150,A:1975296205;C:2025572304;G:2026332631;T:1944443854;N:43206,150,150,,,1975296205,2025572304,2026332631,1944443854,43206,SRX7874143,SRS6282448,SRA1052323,Sun Yat-sen University|College of Life Sciences,Sun Yat-sen University,2,0.96253,0.96256,0.03284,0.03254,0.75057,0.75079,0.45472,0.45579,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2020-03-09,Hatching,Embryo,Embryo Imprecise,All anatomical structures
57223,SRR11267518,SRX7874136,SRS6282441,SRP252014,PRJNA611476,RNAseq between mutant and wild type zebrafish at different developmental stages,PRJNA611476,Other,,,,,,4D wt 6,,strain:Abtu|ecotype:wild type|dev stage:4dpf|sex:missing|tissue:embryos|replicate:biological replicate 6|BioSampleModel:Model organism or animal,,,,,,,,,4dpf wild type replicate 6,4D wt 6,4D wt 6,common method,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP252014,,,s-4DW6_RRA129726-V_1.fq.gz s-4DW6_RRA129726-V_2.fq.gz,fastq fastq,6290868600.0,20969562.0,s 4DW6 RRA129726 V 1.fq.gz,0:150 1:150,A:1602921878;C:1557114242;G:1554419087;T:1576298561;N:114832,150,150,,,1602921878,1557114242,1554419087,1576298561,114832,SRX7874136,SRS6282441,SRA1052323,Sun Yat-sen University|College of Life Sciences,Sun Yat-sen University,2,0.95859,0.95923,0.04563,0.04591,0.70828,0.70865,0.45792,0.46969,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2020-03-09,Larval,Larval,Embryo Imprecise,All anatomical structures
57224,SRR11267519,SRX7874135,SRS6282439,SRP252014,PRJNA611476,RNAseq between mutant and wild type zebrafish at different developmental stages,PRJNA611476,Other,,,,,,4D wt 5,,strain:Abtu|ecotype:wild type|dev stage:4dpf|sex:missing|tissue:embryos|replicate:biological replicate 5|BioSampleModel:Model organism or animal,,,,,,,,,4dpf wild type replicate 5,4D wt 5,4D wt 5,common method,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP252014,,,s-4DW5_RRA129725-V_2.fq.gz s-4DW5_RRA129725-V_1.fq.gz,fastq fastq,6521328900.0,21737763.0,s 4DW5 RRA129725 V 1.fq.gz,0:150 1:150,A:1655910947;C:1620499741;G:1616133473;T:1628664792;N:119947,150,150,,,1655910947,1620499741,1616133473,1628664792,119947,SRX7874135,SRS6282439,SRA1052323,Sun Yat-sen University|College of Life Sciences,Sun Yat-sen University,2,0.96275,0.96347,0.03156,0.03162,0.72068,0.71979,0.47386,0.47433,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2020-03-09,Larval,Larval,Embryo Imprecise,All anatomical structures
57225,SRR11267520,SRX7874134,SRS6282438,SRP252014,PRJNA611476,RNAseq between mutant and wild type zebrafish at different developmental stages,PRJNA611476,Other,,,,,,4D wt 4,,strain:Abtu|ecotype:wild type|dev stage:4dpf|sex:missing|tissue:embryos|replicate:biological replicate 4|BioSampleModel:Model organism or animal,,,,,,,,,4dpf wild type replicate 4,4D wt 4,4D wt 4,common method,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP252014,,,s-4DW4_RRA129724-V_2.fq.gz s-4DW4_RRA129724-V_1.fq.gz,fastq fastq,5854878600.0,19516262.0,s 4DW4 RRA129724 V 1.fq.gz,0:150 1:150,A:1516513397;C:1423158456;G:1421167843;T:1493933378;N:105526,150,150,,,1516513397,1423158456,1421167843,1493933378,105526,SRX7874134,SRS6282438,SRA1052323,Sun Yat-sen University|College of Life Sciences,Sun Yat-sen University,2,0.95398,0.95372,0.05409,0.05408,0.69193,0.69043,0.47544,0.47498,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2020-03-09,Larval,Larval,Embryo Imprecise,All anatomical structures
57226,SRR11267521,SRX7874133,SRS6282440,SRP252014,PRJNA611476,RNAseq between mutant and wild type zebrafish at different developmental stages,PRJNA611476,Other,,,,,,4D wt 3,,strain:Abtu|ecotype:wild type|dev stage:4dpf|sex:missing|tissue:embryos|replicate:biological replicate 3|BioSampleModel:Model organism or animal,,,,,,,,,4dpf wild type replicate 3,4D wt 3,4D wt 3,common method,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP252014,,,s-4DW3_RRA129723-V_1.fq.gz s-4DW3_RRA129723-V_2.fq.gz,fastq fastq,6420460500.0,21401535.0,s 4DW3 RRA129723 V 1.fq.gz,0:150 1:150,A:1657978157;C:1569027011;G:1567167327;T:1626170930;N:117075,150,150,,,1657978157,1569027011,1567167327,1626170930,117075,SRX7874133,SRS6282440,SRA1052323,Sun Yat-sen University|College of Life Sciences,Sun Yat-sen University,2,0.9553,0.95688,0.04567,0.04609,0.70076,0.70201,0.47195,0.47051,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2020-03-09,Larval,Larval,Embryo Imprecise,All anatomical structures
57227,SRR11267522,SRX7874132,SRS6282437,SRP252014,PRJNA611476,RNAseq between mutant and wild type zebrafish at different developmental stages,PRJNA611476,Other,,,,,,2D mut 3,,strain:Abtu|ecotype:mutant|dev stage:2dpf|sex:missing|tissue:embryos|replicate:biological replicate 3|BioSampleModel:Model organism or animal,,,,,,,,,2dpf mutant replicate 3,2D mut 3,2D mut 3,common method,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP252014,,,s-2D-MU3_RRA127637-V_1.fq.gz s-2D-MU3_RRA127637-V_2.fq.gz,fastq fastq,8159715900.0,27199053.0,s 2D MU3 RRA127637 V 1.fq.gz,0:150 1:150,A:2021631175;C:2074621188;G:2072837540;T:1990581511;N:44486,150,150,,,2021631175,2074621188,2072837540,1990581511,44486,SRX7874132,SRS6282437,SRA1052323,Sun Yat-sen University|College of Life Sciences,Sun Yat-sen University,2,0.96275,0.9634,0.02909,0.02886,0.75035,0.75035,0.46995,0.46205,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2020-03-09,Hatching,Embryo,Embryo Imprecise,All anatomical structures
57228,SRR11267523,SRX7874131,SRS6282435,SRP252014,PRJNA611476,RNAseq between mutant and wild type zebrafish at different developmental stages,PRJNA611476,Other,,,,,,4D wt 2,,strain:Abtu|ecotype:wild type|dev stage:4dpf|sex:missing|tissue:embryos|replicate:biological replicate 2|BioSampleModel:Model organism or animal,,,,,,,,,4dpf wild type replicate 2,4D wt 2,4D wt 2,common method,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP252014,,,s-4DW2_RRA129722-V_2.fq.gz s-4DW2_RRA129722-V_1.fq.gz,fastq fastq,6231414600.0,20771382.0,s 4DW2 RRA129722 V 1.fq.gz,0:150 1:150,A:1565996983;C:1561905686;G:1563088801;T:1540306966;N:116164,150,150,,,1565996983,1561905686,1563088801,1540306966,116164,SRX7874131,SRS6282435,SRA1052323,Sun Yat-sen University|College of Life Sciences,Sun Yat-sen University,2,0.96185,0.96048,0.02574,0.02597,0.7525,0.75246,0.48131,0.4798,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2020-03-09,Larval,Larval,Embryo Imprecise,All anatomical structures
57229,SRR11267524,SRX7874130,SRS6282434,SRP252014,PRJNA611476,RNAseq between mutant and wild type zebrafish at different developmental stages,PRJNA611476,Other,,,,,,4D wt 1,,strain:Abtu|ecotype:wild type|dev stage:4dpf|sex:missing|tissue:embryos|replicate:biological replicate 1|BioSampleModel:Model organism or animal,,,,,,,,,4dpf wild type replicate 1,4D wt 1,4D wt 1,common method,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP252014,,,s-4DW1_RRA129721-V_1.fq.gz s-4DW1_RRA129721-V_2.fq.gz,fastq fastq,6940311000.0,23134370.0,s 4DW1 RRA129721 V 1.fq.gz,0:150 1:150,A:1728701566;C:1758026863;G:1753262837;T:1700189966;N:129768,150,150,,,1728701566,1758026863,1753262837,1700189966,129768,SRX7874130,SRS6282434,SRA1052323,Sun Yat-sen University|College of Life Sciences,Sun Yat-sen University,2,0.96581,0.96605,0.0236,0.02384,0.75668,0.7572,0.46377,0.47497,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2020-03-09,Larval,Larval,Embryo Imprecise,All anatomical structures
57230,SRR11267525,SRX7874129,SRS6282436,SRP252014,PRJNA611476,RNAseq between mutant and wild type zebrafish at different developmental stages,PRJNA611476,Other,,,,,,4D mut 6,,strain:Abtu|ecotype:mutant|dev stage:4dpf|sex:missing|tissue:embryos|replicate:biological replicate 6|BioSampleModel:Model organism or animal,,,,,,,,,4dpf mutant replicate 6,4D mut 6,4D mut 6,common method,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP252014,,,s-4DM6_RRA129732-V_1.fq.gz s-4DM6_RRA129732-V_2.fq.gz,fastq fastq,7018647900.0,23395493.0,s 4DM6 RRA129732 V 1.fq.gz,0:150 1:150,A:1721137250;C:1803664148;G:1797589773;T:1696193598;N:63131,150,150,,,1721137250,1803664148,1797589773,1696193598,63131,SRX7874129,SRS6282436,SRA1052323,Sun Yat-sen University|College of Life Sciences,Sun Yat-sen University,2,0.9632,0.963,0.04647,0.04582,0.75469,0.75323,0.49113,0.50374,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2020-03-09,Larval,Larval,Embryo Imprecise,All anatomical structures
57231,SRR11267526,SRX7874128,SRS6282433,SRP252014,PRJNA611476,RNAseq between mutant and wild type zebrafish at different developmental stages,PRJNA611476,Other,,,,,,4D mut 5,,strain:Abtu|ecotype:mutant|dev stage:4dpf|sex:missing|tissue:embryos|replicate:biological replicate 5|BioSampleModel:Model organism or animal,,,,,,,,,4dpf mutant replicate 5,4D mut 5,4D mut 5,common method,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP252014,,,s-4DM5_RRA129731-V_1.fq.gz s-4DM5_RRA129731-V_2.fq.gz,fastq fastq,7041267300.0,23470891.0,s 4DM5 RRA129731 V 1.fq.gz,0:150 1:150,A:1820556438;C:1718486576;G:1709755419;T:1792340292;N:128575,150,150,,,1820556438,1718486576,1709755419,1792340292,128575,SRX7874128,SRS6282433,SRA1052323,Sun Yat-sen University|College of Life Sciences,Sun Yat-sen University,2,0.95631,0.95695,0.0493,0.04977,0.69777,0.69818,0.48032,0.4808,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2020-03-09,Larval,Larval,Embryo Imprecise,All anatomical structures
57232,SRR11267527,SRX7874127,SRS6282432,SRP252014,PRJNA611476,RNAseq between mutant and wild type zebrafish at different developmental stages,PRJNA611476,Other,,,,,,4D mut 4,,strain:Abtu|ecotype:mutant|dev stage:4dpf|sex:missing|tissue:embryos|replicate:biological replicate 4|BioSampleModel:Model organism or animal,,,,,,,,,4dpf mutant replicate 4,4D mut 4,4D mut 4,common method,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP252014,,,s-4DM4_RRA129730-V_1.fq.gz s-4DM4_RRA129730-V_2.fq.gz,fastq fastq,6123819300.0,20412731.0,s 4DM4 RRA129730 V 1.fq.gz,0:150 1:150,A:1588852253;C:1490446542;G:1482372430;T:1562034789;N:113286,150,150,,,1588852253,1490446542,1482372430,1562034789,113286,SRX7874127,SRS6282432,SRA1052323,Sun Yat-sen University|College of Life Sciences,Sun Yat-sen University,2,0.95504,0.95601,0.05374,0.05397,0.69607,0.69568,0.46267,0.47356,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2020-03-09,Larval,Larval,Embryo Imprecise,All anatomical structures
57233,SRR11267528,SRX7874126,SRS6282430,SRP252014,PRJNA611476,RNAseq between mutant and wild type zebrafish at different developmental stages,PRJNA611476,Other,,,,,,4D mut 3,,strain:Abtu|ecotype:mutant|dev stage:4dpf|sex:missing|tissue:embryos|replicate:biological replicate 3|BioSampleModel:Model organism or animal,,,,,,,,,4dpf mutant replicate 3,4D mut 3,4D mut 3,common method,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP252014,,,s-4DM3_RRA129729-V_1.fq.gz s-4DM3_RRA129729-V_2.fq.gz,fastq fastq,5935667700.0,19785559.0,s 4DM3 RRA129729 V 1.fq.gz,0:150 1:150,A:1528502547;C:1454741840;G:1448550625;T:1503764733;N:107955,150,150,,,1528502547,1454741840,1448550625,1503764733,107955,SRX7874126,SRS6282430,SRA1052323,Sun Yat-sen University|College of Life Sciences,Sun Yat-sen University,2,0.95331,0.95286,0.04982,0.04955,0.70104,0.70147,0.47135,0.47071,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2020-03-09,Larval,Larval,Embryo Imprecise,All anatomical structures
57234,SRR11267529,SRX7874125,SRS6282431,SRP252014,PRJNA611476,RNAseq between mutant and wild type zebrafish at different developmental stages,PRJNA611476,Other,,,,,,4D mut 2,,strain:Abtu|ecotype:mutant|dev stage:4dpf|sex:missing|tissue:embryos|replicate:biological replicate 2|BioSampleModel:Model organism or animal,,,,,,,,,4dpf mutant replicate 2,4D mut 2,4D mut 2,common method,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP252014,,,s-4DM2_RRA129728-V-W_1.fq.gz s-4DM2_RRA129728-V-W_2.fq.gz,fastq fastq,6097668000.0,20325560.0,s 4DM2 RRA129728 V W 1.fq.gz,0:150 1:150,A:1530973442;C:1532125738;G:1527770104;T:1506686977;N:111739,150,150,,,1530973442,1532125738,1527770104,1506686977,111739,SRX7874125,SRS6282431,SRA1052323,Sun Yat-sen University|College of Life Sciences,Sun Yat-sen University,2,0.9577,0.95944,0.03753,0.03769,0.73657,0.73574,0.4797,0.48662,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2020-03-09,Larval,Larval,Embryo Imprecise,All anatomical structures
57235,SRR11267530,SRX7874124,SRS6282429,SRP252014,PRJNA611476,RNAseq between mutant and wild type zebrafish at different developmental stages,PRJNA611476,Other,,,,,,4D mut 1,,strain:Abtu|ecotype:mutant|dev stage:4dpf|sex:missing|tissue:embryos|replicate:biological replicate 1|BioSampleModel:Model organism or animal,,,,,,,,,4dpf mutant replicate 1,4D mut 1,4D mut 1,common method,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP252014,,,s-4DM1_RRA129727-V_1.fq.gz s-4DM1_RRA129727-V_2.fq.gz,fastq fastq,6597863100.0,21992877.0,s 4DM1 RRA129727 V 1.fq.gz,0:150 1:150,A:1743922570;C:1570643015;G:1566383758;T:1716793707;N:120050,150,150,,,1743922570,1570643015,1566383758,1716793707,120050,SRX7874124,SRS6282429,SRA1052323,Sun Yat-sen University|College of Life Sciences,Sun Yat-sen University,2,0.94852,0.94862,0.06862,0.06874,0.67862,0.67947,0.47809,0.47844,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2020-03-09,Larval,Larval,Embryo Imprecise,All anatomical structures
57236,SRR11267531,SRX7874123,SRS6282428,SRP252014,PRJNA611476,RNAseq between mutant and wild type zebrafish at different developmental stages,PRJNA611476,Other,,,,,,2D wt 6,,strain:Abtu|ecotype:wild type|dev stage:2dpf|sex:missing|tissue:embryos|replicate:biological replicate 6|BioSampleModel:Model organism or animal,,,,,,,,,2dpf wild type replicate 6,2D wt 6,2D wt 6,common method,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP252014,,,s-2D-W6_RRA127646-V_1.fq.gz s-2D-W6_RRA127646-V_2.fq.gz,fastq fastq,7672945500.0,25576485.0,s 2D W6 RRA127646 V 1.fq.gz,0:150 1:150,A:1904102253;C:1945024582;G:1945915237;T:1877861524;N:41904,150,150,,,1904102253,1945024582,1945915237,1877861524,41904,SRX7874123,SRS6282428,SRA1052323,Sun Yat-sen University|College of Life Sciences,Sun Yat-sen University,2,0.96213,0.96229,0.02936,0.0295,0.74418,0.74428,0.46242,0.46223,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2020-03-09,Hatching,Embryo,Embryo Imprecise,All anatomical structures
57237,SRR11267532,SRX7874122,SRS6282426,SRP252014,PRJNA611476,RNAseq between mutant and wild type zebrafish at different developmental stages,PRJNA611476,Other,,,,,,2D wt 5,,strain:Abtu|ecotype:wild type|dev stage:2dpf|sex:missing|tissue:embryos|replicate:biological replicate 5|BioSampleModel:Model organism or animal,,,,,,,,,2dpf wild type replicate 5,2D wt 5,2D wt 5,common method,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP252014,,,s-2D-W5_RRA127645-V_1.fq.gz s-2D-W5_RRA127645-V_2.fq.gz,fastq fastq,6602868900.0,22009563.0,s 2D W5 RRA127645 V 1.fq.gz,0:150 1:150,A:1688419207;C:1625631997;G:1626136783;T:1662643961;N:36952,150,150,,,1688419207,1625631997,1626136783,1662643961,36952,SRX7874122,SRS6282426,SRA1052323,Sun Yat-sen University|College of Life Sciences,Sun Yat-sen University,2,0.956,0.95646,0.04794,0.04766,0.72226,0.72316,0.45044,0.44816,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2020-03-09,Hatching,Embryo,Embryo Imprecise,All anatomical structures
57238,SRR11267533,SRX7874121,SRS6282427,SRP252014,PRJNA611476,RNAseq between mutant and wild type zebrafish at different developmental stages,PRJNA611476,Other,,,,,,2D mut 2,,strain:Abtu|ecotype:mutant|dev stage:2dpf|sex:missing|tissue:embryos|replicate:biological replicate 2|BioSampleModel:Model organism or animal,,,,,,,,,2dpf mutant replicate 2,2D mut 2,2D mut 2,common method,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP252014,,,s-2D-MU2_RRA127636-V_1.fq.gz s-2D-MU2_RRA127636-V_2.fq.gz,fastq fastq,7639000500.0,25463335.0,s 2D MU2 RRA127636 V 1.fq.gz,0:150 1:150,A:1914314950;C:1916936042;G:1919603914;T:1888104180;N:41414,150,150,,,1914314950,1916936042,1919603914,1888104180,41414,SRX7874121,SRS6282427,SRA1052323,Sun Yat-sen University|College of Life Sciences,Sun Yat-sen University,2,0.95818,0.95815,0.03971,0.03906,0.72247,0.72236,0.44884,0.45872,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2020-03-09,Hatching,Embryo,Embryo Imprecise,All anatomical structures
57239,SRR11267534,SRX7874120,SRS6282425,SRP252014,PRJNA611476,RNAseq between mutant and wild type zebrafish at different developmental stages,PRJNA611476,Other,,,,,,2D mut 1,,strain:Abtu|ecotype:mutant|dev stage:2dpf|sex:missing|tissue:embryos|replicate:biological replicate 1|BioSampleModel:Model organism or animal,,,,,,,,,2dpf mutant replicate 1,2D mut 1,2D mut 1,common method,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP252014,,,s-2D-MU1_RRA127635-V_1.fq.gz s-2D-MU1_RRA127635-V_2.fq.gz,fastq fastq,7955196900.0,26517323.0,s 2D MU1 RRA127635 V 1.fq.gz,0:150 1:150,A:1980678540;C:2010190992;G:2012301601;T:1951981643;N:44124,150,150,,,1980678540,2010190992,2012301601,1951981643,44124,SRX7874120,SRS6282425,SRA1052323,Sun Yat-sen University|College of Life Sciences,Sun Yat-sen University,2,0.96174,0.96124,0.03506,0.03487,0.73866,0.73921,0.4672,0.4643,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2020-03-09,Hatching,Embryo,Embryo Imprecise,All anatomical structures
73895,SRR23312683,SRX19255357,SRS16658070,SRP420571,PRJNA929522,Transcriptomic signaling in zebrafish Danio rerio embryos exposed to environmental concentrations of glyphosate,PRJNA929522,Other,https://doi.org/10.1080/03601234.2022.2115780,,,high concentration,,D1 1000,,strain:Wilde type|age:96 hpf|sex:not applicable|tissue:complete embryos|sample type:Pool|treatment:1000|Replicate:1|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of Danio rerio,D1,D1,pool of embryos,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 1000,,SRP420571,,,10_R1_001.fastq.gz,fastq,4488415650.0,29922771.0,10 R1 001.fastq.gz,0:150 1:0,A:1238382281;C:1019437721;G:1026346198;T:1203790286;N:459164,150,0,,,1238382281,1019437721,1026346198,1203790286,459164,SRX19255357,SRS16658070,SRA1583492,Centro de Investigacion en Alimentacion y Desarrollo|Ecotoxicology,Centro de Investigacion en Alimentacion y Desarrollo,1,0.91866,,0.12395,,0.67894,,0.47111,,150,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Mexico,2023-02-02,Larval,Larval,Embryo Imprecise,All anatomical structures
73896,SRR23312684,SRX19255356,SRS16658069,SRP420571,PRJNA929522,Transcriptomic signaling in zebrafish Danio rerio embryos exposed to environmental concentrations of glyphosate,PRJNA929522,Other,https://doi.org/10.1080/03601234.2022.2115780,,,medium concentration,,C3 100,,strain:Wilde type|age:96 hpf|sex:not applicable|tissue:complete embryos|sample type:Pool|treatment:100|Replicate:3|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of Danio rerio,C3,C3,pool of embryos,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 1000,,SRP420571,,,9_R1_001.fastq.gz,fastq,5066914650.0,33779431.0,9 R1 001.fastq.gz,0:150 1:0,A:1380446646;C:1166400624;G:1173637886;T:1345919328;N:510166,150,0,,,1380446646,1166400624,1173637886,1345919328,510166,SRX19255356,SRS16658069,SRA1583492,Centro de Investigacion en Alimentacion y Desarrollo|Ecotoxicology,Centro de Investigacion en Alimentacion y Desarrollo,1,0.92353,,0.10534,,0.66718,,0.46961,,150,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Mexico,2023-02-02,Larval,Larval,Embryo Imprecise,All anatomical structures