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
30769,SRR28348935,SRX23954961,SRS20755382,SRP495323,PRJNA1088158,Protein profiling of zebrafish embryos unmasks regulatory layers during early embryogenesis.,GSE261646,Transcriptome Analysis,The maternal to zygotic transition is crucial in embryonic development  marked by the degradation of maternally provided mRNAs and initiation of zygotic gene expression. However  the changes occurring at the protein level during this transition remain unclear. Here  we conducted protein profiling throughout zebrafish embryogenesis using quantitative mass spectrometry  integrating transcriptomics and translatomics datasets. Our data shows that unlike RNA changes  protein changes are less dynamic. Further  increases in protein levels correlate with mRNA translation  whereas declines in protein levels do not  suggesting active protein degradation processes. Interestingly  proteins from pure zygotic genes are present at fertilization  challenging existing mRNA based gene classifications. As a proof of concept  we utilized CRISPR Cas13d to target znf281b mRNA  a gene whose protein significantly accumulates within the first two hpf  demonstrating its crucial role in development. Consequently  our protein profiling  coupled with CRISPR Cas13d  offers a new approach to unravel maternal mRNAs function during embryonic development. Overall design: Two biological replicate samples containing 50 zebrafish oocytes per stage were collected by pairing females in natural matings to ''purge'' mature eggs and used to establish an oogenesis time line. Fish were euthanized and ovaries harvested within 1–11 days post purging dpp. Stage I and II oocytes were collected at 1–2 dpp  stage III oocytes germinal vesicle in central position at 4–7 dpp  and stage IV oocytes germinal vesicle asymmetrically located at 8–10 dpp. Oocyte isolations were based on73  and conducted in isolation medium Leibovitz L 15 Sigma Aldrich #L5520 plus Collagenase I and II depending on the stages as follows. Stages I and II were isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130 and 3 mg/mL Collagenase II Gibco 17101015. Stage III was isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130. Stage IV was isolated by mechanical stripping with forceps and needle without xxx use of Collagenases. Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer's protocols. Three biological replicate samples containing 20 dechorionated zebrafish embryos were snap frozen in TRIzol Invitrogen #15596026. Four time points of embryonic development were included: 1 cell stage 0 hpf  hpf  2 hpf  4 hpf  and 6 hpf. RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer's protocols.,,pubmed:39302832,,Zebrafish Embryo  2hpf  rep3,GSM8147858,,source name:Whole embryo|tissue:Whole embryo|developmental stage:2hpf|genotype:AB  TF and TLF|geo loc name:missing|collection date:missing,Zebrafish Embryo  2hpf  rep3,Raw reads from zebrafish oocytes stages I IV and embryos 0   2   4   and 6 hpf were demultiplexed into FASTQ format allowing up to one mismatch using Illumina bcl convert 3.10.5. Reads were aligned to UCSC genome danRer11 with STAR aligner version 2.7.3a  using Ensembl 106 gene models. Counts were converted to TPM values using RSEM version v1.3.0 and all subsequent analysis was done using TPM. Assembly: danRer11 Ensembl 106 gene models Supplementary files format and content: comma separated files with TPMs from all replicates,Whole embryo,,Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer’s protocols. 0   2   4  and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer’s protocols. Ribo dep Stranded RNA Seq Zebrafish embryos 0   2   4   and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA  as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer’s directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598  and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled  quantified  and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing  Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA  as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer’s instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina  Cat. No. 20020598  and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized  pooled  and sequenced on a NextSeq 500 instrument Illumina  as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing  Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files.,,tissue:Whole embryo|developmental stage:2hpf|genotype:AB  TF and TLF,GSM8147858,GSM8147858: Zebrafish Embryo  2hpf  rep3; Danio rerio; RNA Seq,GSM8147858 r1,GSM8147858,1,Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer's protocols. 0   2   4  and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer's protocols. Ribo dep Stranded RNA Seq Zebrafish embryos 0   2   4   and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA  as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer's directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598  and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled  quantified  and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing  Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA  as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer's instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina  Cat. No. 20020598  and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized  pooled  and sequenced on a NextSeq 500 instrument Illumina  as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing  Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP495323,,,s_2hpf_3.fastq,fastq,1748504032.0,23006632.0,GSM8147858 r1,0:76,A:420580006;C:434589498;G:408972977;T:484281127;N:80424,76,,,,420580006,434589498,408972977,484281127,80424,SRX23954961,SRS20755382,SRA1824599,"Computational Biology, Stowers Institute for Medical Research","Computational Biology, Stowers Institute for Medical Research",,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,trueseq,bulk,bulk,bulk,,United States,2024-03-14,Cleavage,Embryo,Whole Organism,All anatomical structures
30770,SRR28348936,SRX23954960,SRS20755381,SRP495323,PRJNA1088158,Protein profiling of zebrafish embryos unmasks regulatory layers during early embryogenesis.,GSE261646,Transcriptome Analysis,The maternal to zygotic transition is crucial in embryonic development  marked by the degradation of maternally provided mRNAs and initiation of zygotic gene expression. However  the changes occurring at the protein level during this transition remain unclear. Here  we conducted protein profiling throughout zebrafish embryogenesis using quantitative mass spectrometry  integrating transcriptomics and translatomics datasets. Our data shows that unlike RNA changes  protein changes are less dynamic. Further  increases in protein levels correlate with mRNA translation  whereas declines in protein levels do not  suggesting active protein degradation processes. Interestingly  proteins from pure zygotic genes are present at fertilization  challenging existing mRNA based gene classifications. As a proof of concept  we utilized CRISPR Cas13d to target znf281b mRNA  a gene whose protein significantly accumulates within the first two hpf  demonstrating its crucial role in development. Consequently  our protein profiling  coupled with CRISPR Cas13d  offers a new approach to unravel maternal mRNAs function during embryonic development. Overall design: Two biological replicate samples containing 50 zebrafish oocytes per stage were collected by pairing females in natural matings to ''purge'' mature eggs and used to establish an oogenesis time line. Fish were euthanized and ovaries harvested within 1–11 days post purging dpp. Stage I and II oocytes were collected at 1–2 dpp  stage III oocytes germinal vesicle in central position at 4–7 dpp  and stage IV oocytes germinal vesicle asymmetrically located at 8–10 dpp. Oocyte isolations were based on73  and conducted in isolation medium Leibovitz L 15 Sigma Aldrich #L5520 plus Collagenase I and II depending on the stages as follows. Stages I and II were isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130 and 3 mg/mL Collagenase II Gibco 17101015. Stage III was isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130. Stage IV was isolated by mechanical stripping with forceps and needle without xxx use of Collagenases. Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer's protocols. Three biological replicate samples containing 20 dechorionated zebrafish embryos were snap frozen in TRIzol Invitrogen #15596026. Four time points of embryonic development were included: 1 cell stage 0 hpf  hpf  2 hpf  4 hpf  and 6 hpf. RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer's protocols.,,pubmed:39302832,,Zebrafish Embryo  2hpf  rep2,GSM8147857,,source name:Whole embryo|tissue:Whole embryo|developmental stage:2hpf|genotype:AB  TF and TLF|geo loc name:missing|collection date:missing,Zebrafish Embryo  2hpf  rep2,Raw reads from zebrafish oocytes stages I IV and embryos 0   2   4   and 6 hpf were demultiplexed into FASTQ format allowing up to one mismatch using Illumina bcl convert 3.10.5. Reads were aligned to UCSC genome danRer11 with STAR aligner version 2.7.3a  using Ensembl 106 gene models. Counts were converted to TPM values using RSEM version v1.3.0 and all subsequent analysis was done using TPM. Assembly: danRer11 Ensembl 106 gene models Supplementary files format and content: comma separated files with TPMs from all replicates,Whole embryo,,Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer’s protocols. 0   2   4  and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer’s protocols. Ribo dep Stranded RNA Seq Zebrafish embryos 0   2   4   and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA  as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer’s directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598  and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled  quantified  and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing  Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA  as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer’s instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina  Cat. No. 20020598  and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized  pooled  and sequenced on a NextSeq 500 instrument Illumina  as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing  Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files.,,tissue:Whole embryo|developmental stage:2hpf|genotype:AB  TF and TLF,GSM8147857,GSM8147857: Zebrafish Embryo  2hpf  rep2; Danio rerio; RNA Seq,GSM8147857 r1,GSM8147857,1,Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer's protocols. 0   2   4  and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer's protocols. Ribo dep Stranded RNA Seq Zebrafish embryos 0   2   4   and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA  as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer's directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598  and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled  quantified  and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing  Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA  as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer's instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina  Cat. No. 20020598  and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized  pooled  and sequenced on a NextSeq 500 instrument Illumina  as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing  Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP495323,,,s_2hpf_2.fastq,fastq,1578919456.0,20775256.0,GSM8147857 r1,0:76,A:380440230;C:393721925;G:368114931;T:436571104;N:71266,76,,,,380440230,393721925,368114931,436571104,71266,SRX23954960,SRS20755381,SRA1824599,"Computational Biology, Stowers Institute for Medical Research","Computational Biology, Stowers Institute for Medical Research",,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,trueseq,bulk,bulk,bulk,,United States,2024-03-14,Cleavage,Embryo,Whole Organism,All anatomical structures
30771,SRR28348937,SRX23954959,SRS20755380,SRP495323,PRJNA1088158,Protein profiling of zebrafish embryos unmasks regulatory layers during early embryogenesis.,GSE261646,Transcriptome Analysis,The maternal to zygotic transition is crucial in embryonic development  marked by the degradation of maternally provided mRNAs and initiation of zygotic gene expression. However  the changes occurring at the protein level during this transition remain unclear. Here  we conducted protein profiling throughout zebrafish embryogenesis using quantitative mass spectrometry  integrating transcriptomics and translatomics datasets. Our data shows that unlike RNA changes  protein changes are less dynamic. Further  increases in protein levels correlate with mRNA translation  whereas declines in protein levels do not  suggesting active protein degradation processes. Interestingly  proteins from pure zygotic genes are present at fertilization  challenging existing mRNA based gene classifications. As a proof of concept  we utilized CRISPR Cas13d to target znf281b mRNA  a gene whose protein significantly accumulates within the first two hpf  demonstrating its crucial role in development. Consequently  our protein profiling  coupled with CRISPR Cas13d  offers a new approach to unravel maternal mRNAs function during embryonic development. Overall design: Two biological replicate samples containing 50 zebrafish oocytes per stage were collected by pairing females in natural matings to ''purge'' mature eggs and used to establish an oogenesis time line. Fish were euthanized and ovaries harvested within 1–11 days post purging dpp. Stage I and II oocytes were collected at 1–2 dpp  stage III oocytes germinal vesicle in central position at 4–7 dpp  and stage IV oocytes germinal vesicle asymmetrically located at 8–10 dpp. Oocyte isolations were based on73  and conducted in isolation medium Leibovitz L 15 Sigma Aldrich #L5520 plus Collagenase I and II depending on the stages as follows. Stages I and II were isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130 and 3 mg/mL Collagenase II Gibco 17101015. Stage III was isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130. Stage IV was isolated by mechanical stripping with forceps and needle without xxx use of Collagenases. Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer's protocols. Three biological replicate samples containing 20 dechorionated zebrafish embryos were snap frozen in TRIzol Invitrogen #15596026. Four time points of embryonic development were included: 1 cell stage 0 hpf  hpf  2 hpf  4 hpf  and 6 hpf. RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer's protocols.,,pubmed:39302832,,Zebrafish Embryo  2hpf  rep1,GSM8147856,,source name:Whole embryo|tissue:Whole embryo|developmental stage:2hpf|genotype:AB  TF and TLF|geo loc name:missing|collection date:missing,Zebrafish Embryo  2hpf  rep1,Raw reads from zebrafish oocytes stages I IV and embryos 0   2   4   and 6 hpf were demultiplexed into FASTQ format allowing up to one mismatch using Illumina bcl convert 3.10.5. Reads were aligned to UCSC genome danRer11 with STAR aligner version 2.7.3a  using Ensembl 106 gene models. Counts were converted to TPM values using RSEM version v1.3.0 and all subsequent analysis was done using TPM. Assembly: danRer11 Ensembl 106 gene models Supplementary files format and content: comma separated files with TPMs from all replicates,Whole embryo,,Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer’s protocols. 0   2   4  and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer’s protocols. Ribo dep Stranded RNA Seq Zebrafish embryos 0   2   4   and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA  as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer’s directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598  and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled  quantified  and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing  Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA  as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer’s instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina  Cat. No. 20020598  and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized  pooled  and sequenced on a NextSeq 500 instrument Illumina  as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing  Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files.,,tissue:Whole embryo|developmental stage:2hpf|genotype:AB  TF and TLF,GSM8147856,GSM8147856: Zebrafish Embryo  2hpf  rep1; Danio rerio; RNA Seq,GSM8147856 r1,GSM8147856,1,Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer's protocols. 0   2   4  and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer's protocols. Ribo dep Stranded RNA Seq Zebrafish embryos 0   2   4   and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA  as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer's directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598  and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled  quantified  and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing  Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA  as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer's instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina  Cat. No. 20020598  and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized  pooled  and sequenced on a NextSeq 500 instrument Illumina  as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing  Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP495323,,,s_2hpf_1.fastq,fastq,1730435412.0,22768887.0,GSM8147856 r1,0:76,A:420026952;C:428388301;G:403718608;T:478219805;N:81746,76,,,,420026952,428388301,403718608,478219805,81746,SRX23954959,SRS20755380,SRA1824599,"Computational Biology, Stowers Institute for Medical Research","Computational Biology, Stowers Institute for Medical Research",,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,trueseq,bulk,bulk,bulk,,United States,2024-03-14,Cleavage,Embryo,Whole Organism,All anatomical structures
32033,SRR28976522,SRX24505963,SRS21254128,SRP506702,PRJNA1109723,rbm24a is an organizer component of germ plasm to determine germ cell fate,GSE267086,Other,The  formation of germ cells is a critical issue for the continuation of species. A large group of animals follow a preformation strategy to generate their primordial germ cells PGCs. They produce a set of localized maternal mRNAs and proteins to form phase separated germ plasm that functions as the PGC determinants  but the mechanisms underlying the assembly of germ plasm is poorly understood. This study identifies Rbm24a as an enssential localized germ plasm protein component that controls the formation of large and functional germ plasm granules. Rbm24a is complexed with Buc and interacts with germ plasm mRNAs  which determines the specific grasp of germ plasm mRNAs into the phase separated aggregates. Rbm24a absent granules fail to undergo kinesin dependent transport towards the cleavage furrows  where small particles fuse into large ones. The loss of maternal rbm24a causes the complete degradation of germ plasm components and the disappearance of PGCs  resulting in totally sterile animals. Our work establishes that Rbm24 is a critical nucleating organizer component of germ plasm  highlighting an emerging common mechanism to read and recruit RNA component into phase separated condensates. Overall design: To elucidate the comprehensive RNA binding landscape of Rbm24a in zebrafish  we employed RIP seq analysis on both rbm24a GFP knock in and wild type zebrafish.,,,,Zebrafish  RIP seq  Rbm24a Knock in IP,GSM8259538,,source name:whole embryo|tissue:whole embryo|developmental stage:4 cell stage|cell type:embryonic cell|genotype:Rbm24a Knock in|antibody:GFP|geo loc name:missing|collection date:missing,Zebrafish  RIP seq  Rbm24a Knock in IP,Each library was amplified by a 15 cycle PCR  and 150 bp paired end sequencing was subjected to Illumina Nova seq 6000 to obtain the raw data. Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes raw counts for each Sample Supplementary files format and content: Bigwig file for each Sample,whole embryo,,Total RNAs were extracted from WT and Mrbm24a embryos at 4 cell sphere 24 hpf stage  using TRIzol reagent Invitrogen  and were precipitated by cold isopropanol 50%  v/v in the presence of carrier glycogen 20 µg/each sample. 1 μg total RNA was used for following library preparation. The polyA mRNA isolation was performed  using OligodT beads. The mRNA and RIP IP RNA fragmentation was performed using divalent cations and high  temperature. Priming was performed using Random Primers. First strand cDNA and the second strand  cDNA were synthesized. The purified double stranded cDNA was then treated 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 DNA Clean Beads. Each sample was then amplified by  PCR using P5 and P7 primers and the PCR products were validated.  Then libraries with different indexs were multiplexed and loaded on an Illumina Nova seq 6000 instrument for sequencing using a 2x150 paired end PE configuration according to  manufacturer’s instructions.,Zebrafish embryos were maintained in 1/3x Ringer's at 28.5C,tissue:whole embryo|developmental stage:4 cell stage|cell type:embryonic cell|genotype:Rbm24a Knock in|antibody:GFP,GSM8259538,GSM8259538: Zebrafish  RIP seq  Rbm24a Knock in IP; Danio rerio; RIP Seq,GSM8259538 r1,GSM8259538,1,Total RNAs were extracted from WT and Mrbm24a embryos at 4 cell sphere 24 hpf stage  using TRIzol reagent Invitrogen  and were precipitated by cold isopropanol 50%  v/v in the presence of carrier glycogen 20 µg/each sample. 1 μg total RNA was used for following library preparation. The polyA mRNA isolation was performed  using OligodT beads. The mRNA and RIP IP RNA fragmentation was performed using divalent cations and high  temperature. Priming was performed using Random Primers. First strand cDNA and the second strand  cDNA were synthesized. The purified double stranded cDNA was then treated 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 DNA Clean Beads. Each sample was then amplified by  PCR using P5 and P7 primers and the PCR products were validated.  Then libraries with different indexs were multiplexed and loaded on an Illumina Nova seq 6000 instrument for sequencing using a 2x150 paired end PE configuration according to  manufacturer's instructions.,,RIP-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP506702,,,RIP_KI_IP_R2.fq.gz RIP_KI_IP_R1.fq.gz,fastq fastq,6457893104.0,21383752.0,GSM8259538 r1,0:151 1:151,A:975588225;C:2019180290;G:2469634919;T:992947702;N:541968,151,151,,,975588225,2019180290,2469634919,992947702,541968,SRX24505963,SRS21254128,SRA1863578,"Ang Li, College of Life Sciences, shandong university","Ang Li, College of Life Sciences, shandong university",2,0.90304,0.86018,0.20083,0.20471,0.96382,0.96743,0.96102,0.98876,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,bulk,bulk,,China,2024-05-09,Cleavage,Embryo,Whole Organism,All anatomical structures
32034,SRR28976523,SRX24505962,SRS21254127,SRP506702,PRJNA1109723,rbm24a is an organizer component of germ plasm to determine germ cell fate,GSE267086,Other,The  formation of germ cells is a critical issue for the continuation of species. A large group of animals follow a preformation strategy to generate their primordial germ cells PGCs. They produce a set of localized maternal mRNAs and proteins to form phase separated germ plasm that functions as the PGC determinants  but the mechanisms underlying the assembly of germ plasm is poorly understood. This study identifies Rbm24a as an enssential localized germ plasm protein component that controls the formation of large and functional germ plasm granules. Rbm24a is complexed with Buc and interacts with germ plasm mRNAs  which determines the specific grasp of germ plasm mRNAs into the phase separated aggregates. Rbm24a absent granules fail to undergo kinesin dependent transport towards the cleavage furrows  where small particles fuse into large ones. The loss of maternal rbm24a causes the complete degradation of germ plasm components and the disappearance of PGCs  resulting in totally sterile animals. Our work establishes that Rbm24 is a critical nucleating organizer component of germ plasm  highlighting an emerging common mechanism to read and recruit RNA component into phase separated condensates. Overall design: To elucidate the comprehensive RNA binding landscape of Rbm24a in zebrafish  we employed RIP seq analysis on both rbm24a GFP knock in and wild type zebrafish.,,,,Zebrafish  RIP seq  wild type IP,GSM8259537,,source name:whole embryo|tissue:whole embryo|developmental stage:4 cell stage|cell type:embryonic cell|genotype:wild type|antibody:GFP|geo loc name:missing|collection date:missing,Zebrafish  RIP seq  wild type IP,Each library was amplified by a 15 cycle PCR  and 150 bp paired end sequencing was subjected to Illumina Nova seq 6000 to obtain the raw data. Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes raw counts for each Sample Supplementary files format and content: Bigwig file for each Sample,whole embryo,,Total RNAs were extracted from WT and Mrbm24a embryos at 4 cell sphere 24 hpf stage  using TRIzol reagent Invitrogen  and were precipitated by cold isopropanol 50%  v/v in the presence of carrier glycogen 20 µg/each sample. 1 μg total RNA was used for following library preparation. The polyA mRNA isolation was performed  using OligodT beads. The mRNA and RIP IP RNA fragmentation was performed using divalent cations and high  temperature. Priming was performed using Random Primers. First strand cDNA and the second strand  cDNA were synthesized. The purified double stranded cDNA was then treated 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 DNA Clean Beads. Each sample was then amplified by  PCR using P5 and P7 primers and the PCR products were validated.  Then libraries with different indexs were multiplexed and loaded on an Illumina Nova seq 6000 instrument for sequencing using a 2x150 paired end PE configuration according to  manufacturer’s instructions.,Zebrafish embryos were maintained in 1/3x Ringer's at 28.5C,tissue:whole embryo|developmental stage:4 cell stage|cell type:embryonic cell|genotype:wild type|antibody:GFP,GSM8259537,GSM8259537: Zebrafish  RIP seq  wild type IP; Danio rerio; RIP Seq,GSM8259537 r1,GSM8259537,1,Total RNAs were extracted from WT and Mrbm24a embryos at 4 cell sphere 24 hpf stage  using TRIzol reagent Invitrogen  and were precipitated by cold isopropanol 50%  v/v in the presence of carrier glycogen 20 µg/each sample. 1 μg total RNA was used for following library preparation. The polyA mRNA isolation was performed  using OligodT beads. The mRNA and RIP IP RNA fragmentation was performed using divalent cations and high  temperature. Priming was performed using Random Primers. First strand cDNA and the second strand  cDNA were synthesized. The purified double stranded cDNA was then treated 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 DNA Clean Beads. Each sample was then amplified by  PCR using P5 and P7 primers and the PCR products were validated.  Then libraries with different indexs were multiplexed and loaded on an Illumina Nova seq 6000 instrument for sequencing using a 2x150 paired end PE configuration according to  manufacturer's instructions.,,RIP-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP506702,,,RIP_WT_IP_R2.fq.gz RIP_WT_IP_R1.fq.gz,fastq fastq,4501412680.0,14905340.0,GSM8259537 r1,0:151 1:151,A:651609366;C:1285679784;G:1901211768;T:662533141;N:378621,151,151,,,651609366,1285679784,1901211768,662533141,378621,SRX24505962,SRS21254127,SRA1863578,"Ang Li, College of Life Sciences, shandong university","Ang Li, College of Life Sciences, shandong university",2,0.96426,0.81361,0.26579,0.2253,0.97784,0.97806,0.8699,0.93379,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,bulk,bulk,,China,2024-05-09,Cleavage,Embryo,Whole Organism,All anatomical structures
32035,SRR28976524,SRX24505961,SRS21254126,SRP506702,PRJNA1109723,rbm24a is an organizer component of germ plasm to determine germ cell fate,GSE267086,Other,The  formation of germ cells is a critical issue for the continuation of species. A large group of animals follow a preformation strategy to generate their primordial germ cells PGCs. They produce a set of localized maternal mRNAs and proteins to form phase separated germ plasm that functions as the PGC determinants  but the mechanisms underlying the assembly of germ plasm is poorly understood. This study identifies Rbm24a as an enssential localized germ plasm protein component that controls the formation of large and functional germ plasm granules. Rbm24a is complexed with Buc and interacts with germ plasm mRNAs  which determines the specific grasp of germ plasm mRNAs into the phase separated aggregates. Rbm24a absent granules fail to undergo kinesin dependent transport towards the cleavage furrows  where small particles fuse into large ones. The loss of maternal rbm24a causes the complete degradation of germ plasm components and the disappearance of PGCs  resulting in totally sterile animals. Our work establishes that Rbm24 is a critical nucleating organizer component of germ plasm  highlighting an emerging common mechanism to read and recruit RNA component into phase separated condensates. Overall design: To elucidate the comprehensive RNA binding landscape of Rbm24a in zebrafish  we employed RIP seq analysis on both rbm24a GFP knock in and wild type zebrafish.,,,,Zebrafish  RIP seq  Rbm24a Knock in input,GSM8259536,,source name:whole embryo|tissue:whole embryo|developmental stage:4 cell stage|cell type:embryonic cell|genotype:Rbm24a Knock in|antibody:input|geo loc name:missing|collection date:missing,Zebrafish  RIP seq  Rbm24a Knock in input,Each library was amplified by a 15 cycle PCR  and 150 bp paired end sequencing was subjected to Illumina Nova seq 6000 to obtain the raw data. Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes raw counts for each Sample Supplementary files format and content: Bigwig file for each Sample,whole embryo,,Total RNAs were extracted from WT and Mrbm24a embryos at 4 cell sphere 24 hpf stage  using TRIzol reagent Invitrogen  and were precipitated by cold isopropanol 50%  v/v in the presence of carrier glycogen 20 µg/each sample. 1 μg total RNA was used for following library preparation. The polyA mRNA isolation was performed  using OligodT beads. The mRNA and RIP IP RNA fragmentation was performed using divalent cations and high  temperature. Priming was performed using Random Primers. First strand cDNA and the second strand  cDNA were synthesized. The purified double stranded cDNA was then treated 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 DNA Clean Beads. Each sample was then amplified by  PCR using P5 and P7 primers and the PCR products were validated.  Then libraries with different indexs were multiplexed and loaded on an Illumina Nova seq 6000 instrument for sequencing using a 2x150 paired end PE configuration according to  manufacturer’s instructions.,Zebrafish embryos were maintained in 1/3x Ringer's at 28.5C,tissue:whole embryo|developmental stage:4 cell stage|cell type:embryonic cell|genotype:Rbm24a Knock in|antibody:input,GSM8259536,GSM8259536: Zebrafish  RIP seq  Rbm24a Knock in input; Danio rerio; RIP Seq,GSM8259536 r1,GSM8259536,1,Total RNAs were extracted from WT and Mrbm24a embryos at 4 cell sphere 24 hpf stage  using TRIzol reagent Invitrogen  and were precipitated by cold isopropanol 50%  v/v in the presence of carrier glycogen 20 µg/each sample. 1 μg total RNA was used for following library preparation. The polyA mRNA isolation was performed  using OligodT beads. The mRNA and RIP IP RNA fragmentation was performed using divalent cations and high  temperature. Priming was performed using Random Primers. First strand cDNA and the second strand  cDNA were synthesized. The purified double stranded cDNA was then treated 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 DNA Clean Beads. Each sample was then amplified by  PCR using P5 and P7 primers and the PCR products were validated.  Then libraries with different indexs were multiplexed and loaded on an Illumina Nova seq 6000 instrument for sequencing using a 2x150 paired end PE configuration according to  manufacturer's instructions.,,RIP-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP506702,,,RIP_KI_Input_R2.fq.gz RIP_KI_Input_R1.fq.gz,fastq fastq,9539398726.0,31587413.0,GSM8259536 r1,0:151 1:151,A:2233069830;C:2078359171;G:3009942870;T:2217201959;N:824896,151,151,,,2233069830,2078359171,3009942870,2217201959,824896,SRX24505961,SRS21254126,SRA1863578,"Ang Li, College of Life Sciences, shandong university","Ang Li, College of Life Sciences, shandong university",2,0.90112,0.81448,0.02415,0.01993,0.79287,0.79807,0.47884,0.48186,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,bulk,bulk,,China,2024-05-09,Cleavage,Embryo,Whole Organism,All anatomical structures
32036,SRR28976525,SRX24505960,SRS21254125,SRP506702,PRJNA1109723,rbm24a is an organizer component of germ plasm to determine germ cell fate,GSE267086,Other,The  formation of germ cells is a critical issue for the continuation of species. A large group of animals follow a preformation strategy to generate their primordial germ cells PGCs. They produce a set of localized maternal mRNAs and proteins to form phase separated germ plasm that functions as the PGC determinants  but the mechanisms underlying the assembly of germ plasm is poorly understood. This study identifies Rbm24a as an enssential localized germ plasm protein component that controls the formation of large and functional germ plasm granules. Rbm24a is complexed with Buc and interacts with germ plasm mRNAs  which determines the specific grasp of germ plasm mRNAs into the phase separated aggregates. Rbm24a absent granules fail to undergo kinesin dependent transport towards the cleavage furrows  where small particles fuse into large ones. The loss of maternal rbm24a causes the complete degradation of germ plasm components and the disappearance of PGCs  resulting in totally sterile animals. Our work establishes that Rbm24 is a critical nucleating organizer component of germ plasm  highlighting an emerging common mechanism to read and recruit RNA component into phase separated condensates. Overall design: To elucidate the comprehensive RNA binding landscape of Rbm24a in zebrafish  we employed RIP seq analysis on both rbm24a GFP knock in and wild type zebrafish.,,,,Zebrafish  RIP seq  wild type input,GSM8259535,,source name:whole embryo|tissue:whole embryo|developmental stage:4 cell stage|cell type:embryonic cell|genotype:wild type|antibody:input|geo loc name:missing|collection date:missing,Zebrafish  RIP seq  wild type input,Each library was amplified by a 15 cycle PCR  and 150 bp paired end sequencing was subjected to Illumina Nova seq 6000 to obtain the raw data. Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes raw counts for each Sample Supplementary files format and content: Bigwig file for each Sample,whole embryo,,Total RNAs were extracted from WT and Mrbm24a embryos at 4 cell sphere 24 hpf stage  using TRIzol reagent Invitrogen  and were precipitated by cold isopropanol 50%  v/v in the presence of carrier glycogen 20 µg/each sample. 1 μg total RNA was used for following library preparation. The polyA mRNA isolation was performed  using OligodT beads. The mRNA and RIP IP RNA fragmentation was performed using divalent cations and high  temperature. Priming was performed using Random Primers. First strand cDNA and the second strand  cDNA were synthesized. The purified double stranded cDNA was then treated 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 DNA Clean Beads. Each sample was then amplified by  PCR using P5 and P7 primers and the PCR products were validated.  Then libraries with different indexs were multiplexed and loaded on an Illumina Nova seq 6000 instrument for sequencing using a 2x150 paired end PE configuration according to  manufacturer’s instructions.,Zebrafish embryos were maintained in 1/3x Ringer's at 28.5C,tissue:whole embryo|developmental stage:4 cell stage|cell type:embryonic cell|genotype:wild type|antibody:input,GSM8259535,GSM8259535: Zebrafish  RIP seq  wild type input; Danio rerio; RIP Seq,GSM8259535 r1,GSM8259535,1,Total RNAs were extracted from WT and Mrbm24a embryos at 4 cell sphere 24 hpf stage  using TRIzol reagent Invitrogen  and were precipitated by cold isopropanol 50%  v/v in the presence of carrier glycogen 20 µg/each sample. 1 μg total RNA was used for following library preparation. The polyA mRNA isolation was performed  using OligodT beads. The mRNA and RIP IP RNA fragmentation was performed using divalent cations and high  temperature. Priming was performed using Random Primers. First strand cDNA and the second strand  cDNA were synthesized. The purified double stranded cDNA was then treated 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 DNA Clean Beads. Each sample was then amplified by  PCR using P5 and P7 primers and the PCR products were validated.  Then libraries with different indexs were multiplexed and loaded on an Illumina Nova seq 6000 instrument for sequencing using a 2x150 paired end PE configuration according to  manufacturer's instructions.,,RIP-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP506702,,,RIP_WT_Input_R2.fq.gz RIP_WT_Input_R1.fq.gz,fastq fastq,14180410302.0,46955001.0,GSM8259535 r1,0:151 1:151,A:3380011534;C:2883841476;G:4593876270;T:3321465622;N:1215400,151,151,,,3380011534,2883841476,4593876270,3321465622,1215400,SRX24505960,SRS21254125,SRA1863578,"Ang Li, College of Life Sciences, shandong university","Ang Li, College of Life Sciences, shandong university",2,0.86497,0.64685,0.04432,0.02854,0.79324,0.8031,0.52927,0.53304,151,151,B,B,mate2-mate1 similar by mapping diff,illumina,novaseq_era,unknown,poly_a,unknown,bulk,bulk,bulk,,China,2024-05-09,Cleavage,Embryo,Whole Organism,All anatomical structures
34036,SRR31033345,SRX26418807,SRS22938440,SRP539223,PRJNA1174207,Rbm24 dictates mRNA recruitment for germ plasm assembly,GSE279756,Transcriptome Analysis,Ribonucleoprotein RNP granules are the most common membrane less biomolecular condensates. However  the mechanisms underlying their assembly are largely unknown. The aggregation of germ plasm determines the fate of primordial germ cells PGCs and serves as a model for RNP granule assembly. Here  we show that maternal RNA binding protein Rbm24a is the key factor governing specific sorting of mRNAs. Mechanistically  Rbm24a complexes with Buc and interacts to dictate the specific grasp of germ plasm mRNAs into phase separated condensates. Germ plasm particles lacking Rbm24a and mRNAs fail to undergo kinesin dependent transport towards the cleavage furrows where small granules fuse into large aggregates. Therefore  the loss of maternal Rbm24a causes a complete degradation of germ plasm and the disappearance of PGCs. These findings demonstrate that Rbm24a functions as a nucleating organizer of the germ plasm  highlighting an emerging mechanism for RNA binding proteins in reading and recruiting RNA components into the phase separated protein scaffold. Overall design: To examine the global transcriptome alterations following the loss of maternal Rbm24a  we conducted bulk RNA seq analysis on Mrbm24a and their sibling embyos at 4 cell  sphere stage and 24 hpf.,,,,Zebrafish  Riboseq  M 4cell 5,GSM8579730,,source name:whole embryo|tissue:whole embryo|Stage:4 cell stage|cell type:embryonic cell|genotype:Mrbm24a|geo loc name:missing|collection date:missing,Zebrafish  Riboseq  M 4cell 5,Each library was amplified by a 11 cycle PCR  and 150 bp paired end sequencing was subjected to Illumina HiSeq 2000 to obtain the raw data. Assembly: GRCz10 Supplementary files format and content: tab delimited text file includes raw counts for each Sample Supplementary files format and content: tab delimited text file includes FPKM values for each Sample,whole embryo,,Total RNAs were extracted from WT and Mrbm24a embryos at 4 cell sphere 24 hpf stage  using TRIzol reagent Invitrogen  and were precipitated by cold isopropanol 50%  v/v in the presence of carrier glycogen 20 µg/each sample. 1 μg total RNA was used for following library preparation. The polyA mRNA isolation was performed using OligodT beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated 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 DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Illumina HiSeq/ Illumina Novaseq/ MGI2000 instrument for sequencing using a 2x150 paired end PE configuration according to manufacturer’s instructions.,Zebrafish embryos were maintained in 1/3x Ringer's at 28.5C,tissue:whole embryo|Stage:4 cell stage|cell type:embryonic cell|genotype:Mrbm24a,GSM8579730,GSM8579730: Zebrafish  Riboseq  M 4cell 5; Danio rerio; RNA Seq,GSM8579730 r1,GSM8579730,1,Total RNAs were extracted from WT and Mrbm24a embryos at 4 cell sphere 24 hpf stage  using TRIzol reagent Invitrogen  and were precipitated by cold isopropanol 50%  v/v in the presence of carrier glycogen 20 µg/each sample. 1 μg total RNA was used for following library preparation. The polyA mRNA isolation was performed using OligodT beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated 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 DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Illumina HiSeq/ Illumina Novaseq/ MGI2000 instrument for sequencing using a 2x150 paired end PE configuration according to manufacturer's instructions.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP539223,,,M-4cell-5_L1_1.fq.gz M-4cell-5_L1_2.fq.gz,fastq fastq,5643278100.0,18810927.0,GSM8579730 r1,0:150 1:150,A:1555401034;C:1268722567;G:1323837426;T:1495279385;N:37688,150,150,,,1555401034,1268722567,1323837426,1495279385,37688,SRX26418807,SRS22938440,SRA1993092,Shandong university,Shandong university,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,bulk,bulk,,China,2024-10-17,Cleavage,Embryo,Whole Organism,All anatomical structures
34037,SRR31033351,SRX26418806,SRS22938443,SRP539223,PRJNA1174207,Rbm24 dictates mRNA recruitment for germ plasm assembly,GSE279756,Transcriptome Analysis,Ribonucleoprotein RNP granules are the most common membrane less biomolecular condensates. However  the mechanisms underlying their assembly are largely unknown. The aggregation of germ plasm determines the fate of primordial germ cells PGCs and serves as a model for RNP granule assembly. Here  we show that maternal RNA binding protein Rbm24a is the key factor governing specific sorting of mRNAs. Mechanistically  Rbm24a complexes with Buc and interacts to dictate the specific grasp of germ plasm mRNAs into phase separated condensates. Germ plasm particles lacking Rbm24a and mRNAs fail to undergo kinesin dependent transport towards the cleavage furrows where small granules fuse into large aggregates. Therefore  the loss of maternal Rbm24a causes a complete degradation of germ plasm and the disappearance of PGCs. These findings demonstrate that Rbm24a functions as a nucleating organizer of the germ plasm  highlighting an emerging mechanism for RNA binding proteins in reading and recruiting RNA components into the phase separated protein scaffold. Overall design: To examine the global transcriptome alterations following the loss of maternal Rbm24a  we conducted bulk RNA seq analysis on Mrbm24a and their sibling embyos at 4 cell  sphere stage and 24 hpf.,,,,Zebrafish  Riboseq  M 4cell 4,GSM8579729,,source name:whole embryo|tissue:whole embryo|Stage:4 cell stage|cell type:embryonic cell|genotype:Mrbm24a|geo loc name:missing|collection date:missing,Zebrafish  Riboseq  M 4cell 4,Each library was amplified by a 11 cycle PCR  and 150 bp paired end sequencing was subjected to Illumina HiSeq 2000 to obtain the raw data. Assembly: GRCz10 Supplementary files format and content: tab delimited text file includes raw counts for each Sample Supplementary files format and content: tab delimited text file includes FPKM values for each Sample,whole embryo,,Total RNAs were extracted from WT and Mrbm24a embryos at 4 cell sphere 24 hpf stage  using TRIzol reagent Invitrogen  and were precipitated by cold isopropanol 50%  v/v in the presence of carrier glycogen 20 µg/each sample. 1 μg total RNA was used for following library preparation. The polyA mRNA isolation was performed using OligodT beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated 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 DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Illumina HiSeq/ Illumina Novaseq/ MGI2000 instrument for sequencing using a 2x150 paired end PE configuration according to manufacturer’s instructions.,Zebrafish embryos were maintained in 1/3x Ringer's at 28.5C,tissue:whole embryo|Stage:4 cell stage|cell type:embryonic cell|genotype:Mrbm24a,GSM8579729,GSM8579729: Zebrafish  Riboseq  M 4cell 4; Danio rerio; RNA Seq,GSM8579729 r1,GSM8579729,1,Total RNAs were extracted from WT and Mrbm24a embryos at 4 cell sphere 24 hpf stage  using TRIzol reagent Invitrogen  and were precipitated by cold isopropanol 50%  v/v in the presence of carrier glycogen 20 µg/each sample. 1 μg total RNA was used for following library preparation. The polyA mRNA isolation was performed using OligodT beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated 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 DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Illumina HiSeq/ Illumina Novaseq/ MGI2000 instrument for sequencing using a 2x150 paired end PE configuration according to manufacturer's instructions.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP539223,,,M-4cell-4_L1_1.fq.gz M-4cell-4_L1_2.fq.gz,fastq fastq,6607232100.0,22024107.0,GSM8579729 r1,0:150 1:150,A:1825603885;C:1480833466;G:1538474482;T:1762276005;N:44262,150,150,,,1825603885,1480833466,1538474482,1762276005,44262,SRX26418806,SRS22938443,SRA1993092,Shandong university,Shandong university,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,bulk,bulk,,China,2024-10-17,Cleavage,Embryo,Whole Organism,All anatomical structures
34038,SRR31033346,SRX26418805,SRS22938438,SRP539223,PRJNA1174207,Rbm24 dictates mRNA recruitment for germ plasm assembly,GSE279756,Transcriptome Analysis,Ribonucleoprotein RNP granules are the most common membrane less biomolecular condensates. However  the mechanisms underlying their assembly are largely unknown. The aggregation of germ plasm determines the fate of primordial germ cells PGCs and serves as a model for RNP granule assembly. Here  we show that maternal RNA binding protein Rbm24a is the key factor governing specific sorting of mRNAs. Mechanistically  Rbm24a complexes with Buc and interacts to dictate the specific grasp of germ plasm mRNAs into phase separated condensates. Germ plasm particles lacking Rbm24a and mRNAs fail to undergo kinesin dependent transport towards the cleavage furrows where small granules fuse into large aggregates. Therefore  the loss of maternal Rbm24a causes a complete degradation of germ plasm and the disappearance of PGCs. These findings demonstrate that Rbm24a functions as a nucleating organizer of the germ plasm  highlighting an emerging mechanism for RNA binding proteins in reading and recruiting RNA components into the phase separated protein scaffold. Overall design: To examine the global transcriptome alterations following the loss of maternal Rbm24a  we conducted bulk RNA seq analysis on Mrbm24a and their sibling embyos at 4 cell  sphere stage and 24 hpf.,,,,Zebrafish  Riboseq  M 4cell 3,GSM8579728,,source name:whole embryo|tissue:whole embryo|Stage:4 cell stage|cell type:embryonic cell|genotype:Mrbm24a|geo loc name:missing|collection date:missing,Zebrafish  Riboseq  M 4cell 3,Each library was amplified by a 11 cycle PCR  and 150 bp paired end sequencing was subjected to Illumina HiSeq 2000 to obtain the raw data. Assembly: GRCz10 Supplementary files format and content: tab delimited text file includes raw counts for each Sample Supplementary files format and content: tab delimited text file includes FPKM values for each Sample,whole embryo,,Total RNAs were extracted from WT and Mrbm24a embryos at 4 cell sphere 24 hpf stage  using TRIzol reagent Invitrogen  and were precipitated by cold isopropanol 50%  v/v in the presence of carrier glycogen 20 µg/each sample. 1 μg total RNA was used for following library preparation. The polyA mRNA isolation was performed using OligodT beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated 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 DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Illumina HiSeq/ Illumina Novaseq/ MGI2000 instrument for sequencing using a 2x150 paired end PE configuration according to manufacturer’s instructions.,Zebrafish embryos were maintained in 1/3x Ringer's at 28.5C,tissue:whole embryo|Stage:4 cell stage|cell type:embryonic cell|genotype:Mrbm24a,GSM8579728,GSM8579728: Zebrafish  Riboseq  M 4cell 3; Danio rerio; RNA Seq,GSM8579728 r1,GSM8579728,1,Total RNAs were extracted from WT and Mrbm24a embryos at 4 cell sphere 24 hpf stage  using TRIzol reagent Invitrogen  and were precipitated by cold isopropanol 50%  v/v in the presence of carrier glycogen 20 µg/each sample. 1 μg total RNA was used for following library preparation. The polyA mRNA isolation was performed using OligodT beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated 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 DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Illumina HiSeq/ Illumina Novaseq/ MGI2000 instrument for sequencing using a 2x150 paired end PE configuration according to manufacturer's instructions.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP539223,,,M-4cell-3_L1_1.fq.gz M-4cell-3_L1_2.fq.gz,fastq fastq,7948794900.0,26495983.0,GSM8579728 r1,0:150 1:150,A:2183592013;C:1794605656;G:1863773539;T:2106770087;N:53605,150,150,,,2183592013,1794605656,1863773539,2106770087,53605,SRX26418805,SRS22938438,SRA1993092,Shandong university,Shandong university,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,bulk,bulk,,China,2024-10-17,Cleavage,Embryo,Whole Organism,All anatomical structures
34039,SRR31033350,SRX26418804,SRS22938441,SRP539223,PRJNA1174207,Rbm24 dictates mRNA recruitment for germ plasm assembly,GSE279756,Transcriptome Analysis,Ribonucleoprotein RNP granules are the most common membrane less biomolecular condensates. However  the mechanisms underlying their assembly are largely unknown. The aggregation of germ plasm determines the fate of primordial germ cells PGCs and serves as a model for RNP granule assembly. Here  we show that maternal RNA binding protein Rbm24a is the key factor governing specific sorting of mRNAs. Mechanistically  Rbm24a complexes with Buc and interacts to dictate the specific grasp of germ plasm mRNAs into phase separated condensates. Germ plasm particles lacking Rbm24a and mRNAs fail to undergo kinesin dependent transport towards the cleavage furrows where small granules fuse into large aggregates. Therefore  the loss of maternal Rbm24a causes a complete degradation of germ plasm and the disappearance of PGCs. These findings demonstrate that Rbm24a functions as a nucleating organizer of the germ plasm  highlighting an emerging mechanism for RNA binding proteins in reading and recruiting RNA components into the phase separated protein scaffold. Overall design: To examine the global transcriptome alterations following the loss of maternal Rbm24a  we conducted bulk RNA seq analysis on Mrbm24a and their sibling embyos at 4 cell  sphere stage and 24 hpf.,,,,Zebrafish  Riboseq  M 4cell 2,GSM8579727,,source name:whole embryo|tissue:whole embryo|Stage:4 cell stage|cell type:embryonic cell|genotype:Mrbm24a|geo loc name:missing|collection date:missing,Zebrafish  Riboseq  M 4cell 2,Each library was amplified by a 11 cycle PCR  and 150 bp paired end sequencing was subjected to Illumina HiSeq 2000 to obtain the raw data. Assembly: GRCz10 Supplementary files format and content: tab delimited text file includes raw counts for each Sample Supplementary files format and content: tab delimited text file includes FPKM values for each Sample,whole embryo,,Total RNAs were extracted from WT and Mrbm24a embryos at 4 cell sphere 24 hpf stage  using TRIzol reagent Invitrogen  and were precipitated by cold isopropanol 50%  v/v in the presence of carrier glycogen 20 µg/each sample. 1 μg total RNA was used for following library preparation. The polyA mRNA isolation was performed using OligodT beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated 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 DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Illumina HiSeq/ Illumina Novaseq/ MGI2000 instrument for sequencing using a 2x150 paired end PE configuration according to manufacturer’s instructions.,Zebrafish embryos were maintained in 1/3x Ringer's at 28.5C,tissue:whole embryo|Stage:4 cell stage|cell type:embryonic cell|genotype:Mrbm24a,GSM8579727,GSM8579727: Zebrafish  Riboseq  M 4cell 2; Danio rerio; RNA Seq,GSM8579727 r1,GSM8579727,1,Total RNAs were extracted from WT and Mrbm24a embryos at 4 cell sphere 24 hpf stage  using TRIzol reagent Invitrogen  and were precipitated by cold isopropanol 50%  v/v in the presence of carrier glycogen 20 µg/each sample. 1 μg total RNA was used for following library preparation. The polyA mRNA isolation was performed using OligodT beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated 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 DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Illumina HiSeq/ Illumina Novaseq/ MGI2000 instrument for sequencing using a 2x150 paired end PE configuration according to manufacturer's instructions.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP539223,,,M-4cell-2_L1_1.fq.gz M-4cell-2_L1_2.fq.gz,fastq fastq,7036510200.0,23455034.0,GSM8579727 r1,0:150 1:150,A:1830698676;C:1686461802;G:1754202163;T:1765099649;N:47910,150,150,,,1830698676,1686461802,1754202163,1765099649,47910,SRX26418804,SRS22938441,SRA1993092,Shandong university,Shandong university,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,bulk,bulk,,China,2024-10-17,Cleavage,Embryo,Whole Organism,All anatomical structures
34047,SRR31033355,SRX26418796,SRS22938428,SRP539223,PRJNA1174207,Rbm24 dictates mRNA recruitment for germ plasm assembly,GSE279756,Transcriptome Analysis,Ribonucleoprotein RNP granules are the most common membrane less biomolecular condensates. However  the mechanisms underlying their assembly are largely unknown. The aggregation of germ plasm determines the fate of primordial germ cells PGCs and serves as a model for RNP granule assembly. Here  we show that maternal RNA binding protein Rbm24a is the key factor governing specific sorting of mRNAs. Mechanistically  Rbm24a complexes with Buc and interacts to dictate the specific grasp of germ plasm mRNAs into phase separated condensates. Germ plasm particles lacking Rbm24a and mRNAs fail to undergo kinesin dependent transport towards the cleavage furrows where small granules fuse into large aggregates. Therefore  the loss of maternal Rbm24a causes a complete degradation of germ plasm and the disappearance of PGCs. These findings demonstrate that Rbm24a functions as a nucleating organizer of the germ plasm  highlighting an emerging mechanism for RNA binding proteins in reading and recruiting RNA components into the phase separated protein scaffold. Overall design: To examine the global transcriptome alterations following the loss of maternal Rbm24a  we conducted bulk RNA seq analysis on Mrbm24a and their sibling embyos at 4 cell  sphere stage and 24 hpf.,,,,Zebrafish  RNAseq  Sibling 4cell 4,GSM8579719,,source name:whole embryo|tissue:whole embryo|Stage:4 cell stage|cell type:embryonic cell|genotype:wild type|geo loc name:missing|collection date:missing,Zebrafish  RNAseq  Sibling 4cell 4,Each library was amplified by a 11 cycle PCR  and 150 bp paired end sequencing was subjected to Illumina HiSeq 2000 to obtain the raw data. Assembly: GRCz10 Supplementary files format and content: tab delimited text file includes raw counts for each Sample Supplementary files format and content: tab delimited text file includes FPKM values for each Sample,whole embryo,,Total RNAs were extracted from WT and Mrbm24a embryos at 4 cell sphere 24 hpf stage  using TRIzol reagent Invitrogen  and were precipitated by cold isopropanol 50%  v/v in the presence of carrier glycogen 20 µg/each sample. 1 μg total RNA was used for following library preparation. The polyA mRNA isolation was performed using OligodT beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated 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 DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Illumina HiSeq/ Illumina Novaseq/ MGI2000 instrument for sequencing using a 2x150 paired end PE configuration according to manufacturer’s instructions.,Zebrafish embryos were maintained in 1/3x Ringer's at 28.5C,tissue:whole embryo|Stage:4 cell stage|cell type:embryonic cell|genotype:wild type,GSM8579719,GSM8579719: Zebrafish  RNAseq  Sibling 4cell 4; Danio rerio; RNA Seq,GSM8579719 r1,GSM8579719,1,Total RNAs were extracted from WT and Mrbm24a embryos at 4 cell sphere 24 hpf stage  using TRIzol reagent Invitrogen  and were precipitated by cold isopropanol 50%  v/v in the presence of carrier glycogen 20 µg/each sample. 1 μg total RNA was used for following library preparation. The polyA mRNA isolation was performed using OligodT beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated 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 DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Illumina HiSeq/ Illumina Novaseq/ MGI2000 instrument for sequencing using a 2x150 paired end PE configuration according to manufacturer's instructions.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP539223,,,Sibling-4cell-4_L1_1.fq.gz Sibling-4cell-4_L1_2.fq.gz,fastq fastq,7424662500.0,24748875.0,GSM8579719 r1,0:150 1:150,A:2045351766;C:1671617139;G:1731338149;T:1976305596;N:49850,150,150,,,2045351766,1671617139,1731338149,1976305596,49850,SRX26418796,SRS22938428,SRA1993092,Shandong university,Shandong university,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,bulk,bulk,,China,2024-10-17,Cleavage,Embryo,Whole Organism,All anatomical structures
34048,SRR31033358,SRX26418795,SRS22938431,SRP539223,PRJNA1174207,Rbm24 dictates mRNA recruitment for germ plasm assembly,GSE279756,Transcriptome Analysis,Ribonucleoprotein RNP granules are the most common membrane less biomolecular condensates. However  the mechanisms underlying their assembly are largely unknown. The aggregation of germ plasm determines the fate of primordial germ cells PGCs and serves as a model for RNP granule assembly. Here  we show that maternal RNA binding protein Rbm24a is the key factor governing specific sorting of mRNAs. Mechanistically  Rbm24a complexes with Buc and interacts to dictate the specific grasp of germ plasm mRNAs into phase separated condensates. Germ plasm particles lacking Rbm24a and mRNAs fail to undergo kinesin dependent transport towards the cleavage furrows where small granules fuse into large aggregates. Therefore  the loss of maternal Rbm24a causes a complete degradation of germ plasm and the disappearance of PGCs. These findings demonstrate that Rbm24a functions as a nucleating organizer of the germ plasm  highlighting an emerging mechanism for RNA binding proteins in reading and recruiting RNA components into the phase separated protein scaffold. Overall design: To examine the global transcriptome alterations following the loss of maternal Rbm24a  we conducted bulk RNA seq analysis on Mrbm24a and their sibling embyos at 4 cell  sphere stage and 24 hpf.,,,,Zebrafish  RNAseq  Sibling 4cell 2,GSM8579718,,source name:whole embryo|tissue:whole embryo|Stage:4 cell stage|cell type:embryonic cell|genotype:wild type|geo loc name:missing|collection date:missing,Zebrafish  RNAseq  Sibling 4cell 2,Each library was amplified by a 11 cycle PCR  and 150 bp paired end sequencing was subjected to Illumina HiSeq 2000 to obtain the raw data. Assembly: GRCz10 Supplementary files format and content: tab delimited text file includes raw counts for each Sample Supplementary files format and content: tab delimited text file includes FPKM values for each Sample,whole embryo,,Total RNAs were extracted from WT and Mrbm24a embryos at 4 cell sphere 24 hpf stage  using TRIzol reagent Invitrogen  and were precipitated by cold isopropanol 50%  v/v in the presence of carrier glycogen 20 µg/each sample. 1 μg total RNA was used for following library preparation. The polyA mRNA isolation was performed using OligodT beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated 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 DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Illumina HiSeq/ Illumina Novaseq/ MGI2000 instrument for sequencing using a 2x150 paired end PE configuration according to manufacturer’s instructions.,Zebrafish embryos were maintained in 1/3x Ringer's at 28.5C,tissue:whole embryo|Stage:4 cell stage|cell type:embryonic cell|genotype:wild type,GSM8579718,GSM8579718: Zebrafish  RNAseq  Sibling 4cell 2; Danio rerio; RNA Seq,GSM8579718 r1,GSM8579718,1,Total RNAs were extracted from WT and Mrbm24a embryos at 4 cell sphere 24 hpf stage  using TRIzol reagent Invitrogen  and were precipitated by cold isopropanol 50%  v/v in the presence of carrier glycogen 20 µg/each sample. 1 μg total RNA was used for following library preparation. The polyA mRNA isolation was performed using OligodT beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated 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 DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Illumina HiSeq/ Illumina Novaseq/ MGI2000 instrument for sequencing using a 2x150 paired end PE configuration according to manufacturer's instructions.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP539223,,,Sibling-4cell-2_L1_1.fq.gz Sibling-4cell-2_L1_2.fq.gz,fastq fastq,6484454400.0,21614848.0,GSM8579718 r1,0:150 1:150,A:1701212104;C:1544478776;G:1597991536;T:1640728663;N:43321,150,150,,,1701212104,1544478776,1597991536,1640728663,43321,SRX26418795,SRS22938431,SRA1993092,Shandong university,Shandong university,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,bulk,bulk,,China,2024-10-17,Cleavage,Embryo,Whole Organism,All anatomical structures
34049,SRR31033356,SRX26418794,SRS22938430,SRP539223,PRJNA1174207,Rbm24 dictates mRNA recruitment for germ plasm assembly,GSE279756,Transcriptome Analysis,Ribonucleoprotein RNP granules are the most common membrane less biomolecular condensates. However  the mechanisms underlying their assembly are largely unknown. The aggregation of germ plasm determines the fate of primordial germ cells PGCs and serves as a model for RNP granule assembly. Here  we show that maternal RNA binding protein Rbm24a is the key factor governing specific sorting of mRNAs. Mechanistically  Rbm24a complexes with Buc and interacts to dictate the specific grasp of germ plasm mRNAs into phase separated condensates. Germ plasm particles lacking Rbm24a and mRNAs fail to undergo kinesin dependent transport towards the cleavage furrows where small granules fuse into large aggregates. Therefore  the loss of maternal Rbm24a causes a complete degradation of germ plasm and the disappearance of PGCs. These findings demonstrate that Rbm24a functions as a nucleating organizer of the germ plasm  highlighting an emerging mechanism for RNA binding proteins in reading and recruiting RNA components into the phase separated protein scaffold. Overall design: To examine the global transcriptome alterations following the loss of maternal Rbm24a  we conducted bulk RNA seq analysis on Mrbm24a and their sibling embyos at 4 cell  sphere stage and 24 hpf.,,,,Zebrafish  RNAseq  Sibling 4cell 1,GSM8579717,,source name:whole embryo|tissue:whole embryo|Stage:4 cell stage|cell type:embryonic cell|genotype:wild type|geo loc name:missing|collection date:missing,Zebrafish  RNAseq  Sibling 4cell 1,Each library was amplified by a 11 cycle PCR  and 150 bp paired end sequencing was subjected to Illumina HiSeq 2000 to obtain the raw data. Assembly: GRCz10 Supplementary files format and content: tab delimited text file includes raw counts for each Sample Supplementary files format and content: tab delimited text file includes FPKM values for each Sample,whole embryo,,Total RNAs were extracted from WT and Mrbm24a embryos at 4 cell sphere 24 hpf stage  using TRIzol reagent Invitrogen  and were precipitated by cold isopropanol 50%  v/v in the presence of carrier glycogen 20 µg/each sample. 1 μg total RNA was used for following library preparation. The polyA mRNA isolation was performed using OligodT beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated 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 DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Illumina HiSeq/ Illumina Novaseq/ MGI2000 instrument for sequencing using a 2x150 paired end PE configuration according to manufacturer’s instructions.,Zebrafish embryos were maintained in 1/3x Ringer's at 28.5C,tissue:whole embryo|Stage:4 cell stage|cell type:embryonic cell|genotype:wild type,GSM8579717,GSM8579717: Zebrafish  RNAseq  Sibling 4cell 1; Danio rerio; RNA Seq,GSM8579717 r1,GSM8579717,1,Total RNAs were extracted from WT and Mrbm24a embryos at 4 cell sphere 24 hpf stage  using TRIzol reagent Invitrogen  and were precipitated by cold isopropanol 50%  v/v in the presence of carrier glycogen 20 µg/each sample. 1 μg total RNA was used for following library preparation. The polyA mRNA isolation was performed using OligodT beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated 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 DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Illumina HiSeq/ Illumina Novaseq/ MGI2000 instrument for sequencing using a 2x150 paired end PE configuration according to manufacturer's instructions.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP539223,,,Sibling-4cell-1_L1_1.fq.gz Sibling-4cell-1_L1_2.fq.gz,fastq fastq,8126999700.0,27089999.0,GSM8579717 r1,0:150 1:150,A:2195769442;C:1872416059;G:1934390760;T:2124367874;N:55565,150,150,,,2195769442,1872416059,1934390760,2124367874,55565,SRX26418794,SRS22938430,SRA1993092,Shandong university,Shandong university,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,bulk,bulk,,China,2024-10-17,Cleavage,Embryo,Whole Organism,All anatomical structures
38352,SRR1785164,SRX864135,SRS834996,SRP053099,PRJNA274362,Transcriptomics analysis of gene expression in 10 embryo development stages of Danio rerio,GSE65556,Transcriptome Analysis,RNA was isolated from Danio embryo cells using the TRIzol Invitrogen reagent by following the company manual. For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100. All samples showed a RIN RNA integrity number of higher than 9. Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 Illumina  San Diego  CA  USA according to the manufacturer's protocol.The libraries were sequenced using HiSeq2000 Illumina in single read mode  creating reads with a length of 101 bp. Sequencing chemistry v2 Illumina was used and samples were multiplexed in two samples per lane. Overall design: Examination of gene expressive levels in embryo development of Danio,,,,64 cell rep1,GSM1600040,,tissue:Danio embryo cells|developmental stage:embryo|cell type:64 cell,64 cell rep1,Reads were aligned to theZv9 genome assembly using TopHat v2.0.9 For each sample  RPKM was computed as the number of reads which map per kilobase of exon model per million mapped reads for each gene. Genome build: Zv9 Supplementary files format and content: RPKM for each gene in each development stage,Danio embryo cells,,RNA was isolated from Danio cells using the TRIzol Invitrogen reagent by following the company manual. For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100 Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 Illumina  San Diego  CA  USA according to the manufacturer’s protocol.The libraries were sequenced using HiSeq2000 Illumina in single read mode  creating reads with a length of 50 bp.,,developmental stage:embryo|cell type:64 cell,GSM1600040,GSM1600040: 64 cell rep1; Danio rerio; RNA Seq,GSM1600040,,1,RNA was isolated from Danio cells using the TRIzol Invitrogen reagent by following the company manual. For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100 Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 Illumina  San Diego  CA  USA according to the manufacturer’s protocol.The libraries were sequenced using HiSeq2000 Illumina in single read mode  creating reads with a length of 50 bp.,GEO Accession:GSM1600040,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP053099,,,W6T_1.fastq.gz,fastq,8895665799.0,88075899.0,GSM1600040 r1,0:101,A:2214065560;C:2252759233;G:2253964784;T:2174045976;N:830246,101,,,,2214065560,2252759233,2253964784,2174045976,830246,SRX864135,SRS834996,SRA236187,GEO,Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS),1,0.96228,,0.0252,,0.77481,,0.4855,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,bulk,bulk,,China,2015-02-03,Cleavage,Embryo,Embryo Imprecise,All anatomical structures
38353,SRR1785163,SRX864134,SRS834991,SRP053099,PRJNA274362,Transcriptomics analysis of gene expression in 10 embryo development stages of Danio rerio,GSE65556,Transcriptome Analysis,RNA was isolated from Danio embryo cells using the TRIzol Invitrogen reagent by following the company manual. For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100. All samples showed a RIN RNA integrity number of higher than 9. Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 Illumina  San Diego  CA  USA according to the manufacturer's protocol.The libraries were sequenced using HiSeq2000 Illumina in single read mode  creating reads with a length of 101 bp. Sequencing chemistry v2 Illumina was used and samples were multiplexed in two samples per lane. Overall design: Examination of gene expressive levels in embryo development of Danio,,,,16 cell rep1,GSM1600039,,tissue:Danio embryo cells|developmental stage:embryo|cell type:16 cell,16 cell rep1,Reads were aligned to theZv9 genome assembly using TopHat v2.0.9 For each sample  RPKM was computed as the number of reads which map per kilobase of exon model per million mapped reads for each gene. Genome build: Zv9 Supplementary files format and content: RPKM for each gene in each development stage,Danio embryo cells,,RNA was isolated from Danio cells using the TRIzol Invitrogen reagent by following the company manual. For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100 Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 Illumina  San Diego  CA  USA according to the manufacturer’s protocol.The libraries were sequenced using HiSeq2000 Illumina in single read mode  creating reads with a length of 50 bp.,,developmental stage:embryo|cell type:16 cell,GSM1600039,GSM1600039: 16 cell rep1; Danio rerio; RNA Seq,GSM1600039,,1,RNA was isolated from Danio cells using the TRIzol Invitrogen reagent by following the company manual. For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100 Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 Illumina  San Diego  CA  USA according to the manufacturer’s protocol.The libraries were sequenced using HiSeq2000 Illumina in single read mode  creating reads with a length of 50 bp.,GEO Accession:GSM1600039,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP053099,,,W5T_1.fastq.gz,fastq,8981816880.0,88928880.0,GSM1600039 r1,0:101,A:2337146004;C:2178908640;G:2150713936;T:2314829776;N:218524,101,,,,2337146004,2178908640,2150713936,2314829776,218524,SRX864134,SRS834991,SRA236187,GEO,Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS),1,0.94918,,0.02746,,0.76264,,0.50197,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,bulk,bulk,,China,2015-02-03,Cleavage,Embryo,Embryo Imprecise,All anatomical structures
38354,SRR1785162,SRX864133,SRS834990,SRP053099,PRJNA274362,Transcriptomics analysis of gene expression in 10 embryo development stages of Danio rerio,GSE65556,Transcriptome Analysis,RNA was isolated from Danio embryo cells using the TRIzol Invitrogen reagent by following the company manual. For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100. All samples showed a RIN RNA integrity number of higher than 9. Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 Illumina  San Diego  CA  USA according to the manufacturer's protocol.The libraries were sequenced using HiSeq2000 Illumina in single read mode  creating reads with a length of 101 bp. Sequencing chemistry v2 Illumina was used and samples were multiplexed in two samples per lane. Overall design: Examination of gene expressive levels in embryo development of Danio,,,,4 cell rep1,GSM1600038,,tissue:Danio embryo cells|developmental stage:embryo|cell type:4 cell,4 cell rep1,Reads were aligned to theZv9 genome assembly using TopHat v2.0.9 For each sample  RPKM was computed as the number of reads which map per kilobase of exon model per million mapped reads for each gene. Genome build: Zv9 Supplementary files format and content: RPKM for each gene in each development stage,Danio embryo cells,,RNA was isolated from Danio cells using the TRIzol Invitrogen reagent by following the company manual. For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100 Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 Illumina  San Diego  CA  USA according to the manufacturer’s protocol.The libraries were sequenced using HiSeq2000 Illumina in single read mode  creating reads with a length of 50 bp.,,developmental stage:embryo|cell type:4 cell,GSM1600038,GSM1600038: 4 cell rep1; Danio rerio; RNA Seq,GSM1600038,,1,RNA was isolated from Danio cells using the TRIzol Invitrogen reagent by following the company manual. For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100 Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 Illumina  San Diego  CA  USA according to the manufacturer’s protocol.The libraries were sequenced using HiSeq2000 Illumina in single read mode  creating reads with a length of 50 bp.,GEO Accession:GSM1600038,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP053099,,,W4T_1.fastq.gz,fastq,13975600381.0,138372281.0,GSM1600038 r1,0:101,A:3535785422;C:3493456274;G:3501455121;T:3443583783;N:1319781,101,,,,3535785422,3493456274,3501455121,3443583783,1319781,SRX864133,SRS834990,SRA236187,GEO,Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS),1,0.96034,,0.01453,,0.80397,,0.48159,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,bulk,bulk,,China,2015-02-03,Cleavage,Embryo,Embryo Imprecise,All anatomical structures
47627,SRR6784681,SRX3744219,SRS3000688,SRP133517,PRJNA436017,Maternal mRNA degradation by TUT4 and TUT7 in the zebrafish maternal to zygotic transition,GSE111152,Transcriptome Analysis,During the maternal to zygotic transition MZT  maternal RNAs are actively degraded and replaced by newly synthesized zygotic transcripts in a highly coordinated manner. However  it remains largely unknown how maternal mRNA decay is triggered in early vertebrate embryos. Here  through genome wide profiling of RNA abundance and three prime modification  we show that uridylation is induced at the onset of maternal mRNA clearance. The temporal control of uridylation is conserved in vertebrates. When the homologs of terminal uridylyltransferases TUT4 and TUT7 TUT4/7 are depleted in zebrafish and Xenopus  maternal mRNA clearance is significantly delayed  leading to developmental defects during gastrulation. Short tailed mRNAs are selectively uridylated by TUT4/7  with the highly uridylated transcripts degraded faster during the MZT than those with unmodified polyA tails. Our study demonstrates that uridylation plays a crucial role in timely mRNA degradation  thereby allowing the progression of early development. Overall design: Examination of zebrafish embryos injected with control or TUT4/7 morpholinos at 1 cell stage. RNA seq libraries were prepared at different time points across the MZT period. Three experimental sets  rs1a  rs2b  and rs2   were conducted independently.,,pubmed:29625039,,Zebrafish 2 hpf whole embryo injected with TUT47MO Exp. ID: rs1a,GSM3024073,,tissue:Zebrafish whole embryo|hpf translation blocking  TUT7 translation blocking|strain:AB,Zebrafish 2 hpf whole embryo injected with TUT47MO Exp. ID: rs1a,"The sequences were basecalled by Illumina RTA embedded in NextSeq Control Software 1.3.2 by the standard workflow. Sequenced reads from RNA seq data were mapped to the GRCz10 genome with RefSeq release 104 annotations above using STAR 2.5.3a via RSEM 2.1.31. The gene level quantifications were performed using RSEM with the default options for strand specific and paired end RNA seq. The ""rs1a"" set of our libraries was between sample normalized using RUV seq 1.10.0. The standard workflow suggested by RUV seq did not work due to the global changes of maternal transcripts following the progression of embryogenesis. Instead  we first chose a subset of spike in RNAs that have ≥ 256 “expected counts” of reads in at least 90% of samples. Then  the counts were normalized by the RUVg algorithm k = 1. The geometric means of the normalized counts were used as size factors for the scale normalization of all other RNAs. The ERCC spike in reads in our second RNA seq dataset were too unreliable to be used as references. Even the raw read counts mappable to the reference spike in sequences were significantly out of the linear correlations between any two samples. As a workaround  we picked the internal controls from the first set to find genes that express more than 500 normalized reads with ≤ 0.2 of the log2 largest difference between two samples. Fourteen genes satisfied the criteria to become a set of internal controls. The internal reference genes were used in place of spike in RNAs for processing counts by the modified indirect RUVg approach. Genome build: GRCz10 Supplementary files format and content: comma separated text file include RUVg normalized rs1a and rs1b or TPM normalized rs2 values for each sample.",Zebrafish whole embryo,Approximately 1 nl of the solution containing TUT4/7 or control morpholinos was injected into wild type zebrafish embryos at xxx cell stage.,For each sample  embryos were collected and total RNA was extracted with TRIzol Invitrogen. The samples were spiked in with ERCC RNA Spike In Mix Ambion for normalization purpose. The quality of total RNA was checked by Agilent Bioanalyzer 2100 Agilent. Ribosomal RNA was depleted from total RNA using Ribo Zero Gold kit Epicentre. RNA  seq libraries were constructed using TruSeq stranded total RNA library prep kit Illumina and sequenced in Illumina Nextseq 500 v2  to yield paired end 76nt reads.,Zebrafish embryos were obtained by the natural mating of wild type AB strain and grown in embryo medium at 28.5˚C. Embryos were staged according to standard morphological criteria.,hpf translation blocking  TUT7 translation blocking|strain:AB,GSM3024073,GSM3024073: Zebrafish 2 hpf whole embryo injected with TUT47MO Exp. ID: rs1a; Danio rerio; RNA Seq,GSM3024073,,1,For each sample  embryos were collected and total RNA was extracted with TRIzol Invitrogen. The samples were spiked in with ERCC RNA Spike In Mix Ambion for normalization purpose. The quality of total RNA was checked by Agilent Bioanalyzer 2100 Agilent. Ribosomal RNA was depleted from total RNA using Ribo Zero Gold kit Epicentre. RNA  seq libraries were constructed using TruSeq stranded total RNA library prep kit Illumina and sequenced in Illumina Nextseq 500 v2  to yield paired end 76nt reads.,GEO Accession:GSM3024073,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP133517,,,rs1a-TUT47MO-2hpf_R1.fastq.gz rs1a-TUT47MO-2hpf_R2.fastq.gz,fastq fastq,4923239400.0,32821596.0,GSM3024073 r1,0:75 1:75,A:1261575170;C:1199162847;G:1197287478;T:1262521450;N:2692455,75,75,,,1261575170,1199162847,1197287478,1262521450,2692455,SRX3744219,SRS3000688,SRA662359,GEO,"Narry Kim Lab, Center for RNA Research, Institute for Basic Science",2,0.95618,0.96009,0.06558,0.06236,0.75426,0.75595,0.546,0.53355,75,75,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,ribozero,bulk,bulk,bulk,,South Korea,2018-02-26,Cleavage,Embryo,Whole Organism,All anatomical structures
47630,SRR6784678,SRX3744216,SRS3000685,SRP133517,PRJNA436017,Maternal mRNA degradation by TUT4 and TUT7 in the zebrafish maternal to zygotic transition,GSE111152,Transcriptome Analysis,During the maternal to zygotic transition MZT  maternal RNAs are actively degraded and replaced by newly synthesized zygotic transcripts in a highly coordinated manner. However  it remains largely unknown how maternal mRNA decay is triggered in early vertebrate embryos. Here  through genome wide profiling of RNA abundance and three prime modification  we show that uridylation is induced at the onset of maternal mRNA clearance. The temporal control of uridylation is conserved in vertebrates. When the homologs of terminal uridylyltransferases TUT4 and TUT7 TUT4/7 are depleted in zebrafish and Xenopus  maternal mRNA clearance is significantly delayed  leading to developmental defects during gastrulation. Short tailed mRNAs are selectively uridylated by TUT4/7  with the highly uridylated transcripts degraded faster during the MZT than those with unmodified polyA tails. Our study demonstrates that uridylation plays a crucial role in timely mRNA degradation  thereby allowing the progression of early development. Overall design: Examination of zebrafish embryos injected with control or TUT4/7 morpholinos at 1 cell stage. RNA seq libraries were prepared at different time points across the MZT period. Three experimental sets  rs1a  rs2b  and rs2   were conducted independently.,,pubmed:29625039,,Zebrafish 2 hpf whole embryo injected with TUT7MO Exp. ID: rs1a,GSM3024070,,tissue:Zebrafish whole embryo|hpf translation blocking|strain:AB,Zebrafish 2 hpf whole embryo injected with TUT7MO Exp. ID: rs1a,"The sequences were basecalled by Illumina RTA embedded in NextSeq Control Software 1.3.2 by the standard workflow. Sequenced reads from RNA seq data were mapped to the GRCz10 genome with RefSeq release 104 annotations above using STAR 2.5.3a via RSEM 2.1.31. The gene level quantifications were performed using RSEM with the default options for strand specific and paired end RNA seq. The ""rs1a"" set of our libraries was between sample normalized using RUV seq 1.10.0. The standard workflow suggested by RUV seq did not work due to the global changes of maternal transcripts following the progression of embryogenesis. Instead  we first chose a subset of spike in RNAs that have ≥ 256 “expected counts” of reads in at least 90% of samples. Then  the counts were normalized by the RUVg algorithm k = 1. The geometric means of the normalized counts were used as size factors for the scale normalization of all other RNAs. The ERCC spike in reads in our second RNA seq dataset were too unreliable to be used as references. Even the raw read counts mappable to the reference spike in sequences were significantly out of the linear correlations between any two samples. As a workaround  we picked the internal controls from the first set to find genes that express more than 500 normalized reads with ≤ 0.2 of the log2 largest difference between two samples. Fourteen genes satisfied the criteria to become a set of internal controls. The internal reference genes were used in place of spike in RNAs for processing counts by the modified indirect RUVg approach. Genome build: GRCz10 Supplementary files format and content: comma separated text file include RUVg normalized rs1a and rs1b or TPM normalized rs2 values for each sample.",Zebrafish whole embryo,Approximately 1 nl of the solution containing TUT4/7 or control morpholinos was injected into wild type zebrafish embryos at xxx cell stage.,For each sample  embryos were collected and total RNA was extracted with TRIzol Invitrogen. The samples were spiked in with ERCC RNA Spike In Mix Ambion for normalization purpose. The quality of total RNA was checked by Agilent Bioanalyzer 2100 Agilent. Ribosomal RNA was depleted from total RNA using Ribo Zero Gold kit Epicentre. RNA  seq libraries were constructed using TruSeq stranded total RNA library prep kit Illumina and sequenced in Illumina Nextseq 500 v2  to yield paired end 76nt reads.,Zebrafish embryos were obtained by the natural mating of wild type AB strain and grown in embryo medium at 28.5˚C. Embryos were staged according to standard morphological criteria.,hpf translation blocking|strain:AB,GSM3024070,GSM3024070: Zebrafish 2 hpf whole embryo injected with TUT7MO Exp. ID: rs1a; Danio rerio; RNA Seq,GSM3024070,,1,For each sample  embryos were collected and total RNA was extracted with TRIzol Invitrogen. The samples were spiked in with ERCC RNA Spike In Mix Ambion for normalization purpose. The quality of total RNA was checked by Agilent Bioanalyzer 2100 Agilent. Ribosomal RNA was depleted from total RNA using Ribo Zero Gold kit Epicentre. RNA  seq libraries were constructed using TruSeq stranded total RNA library prep kit Illumina and sequenced in Illumina Nextseq 500 v2  to yield paired end 76nt reads.,GEO Accession:GSM3024070,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP133517,,,rs1a-TUT7MO-2hpf_R2.fastq.gz rs1a-TUT7MO-2hpf_R1.fastq.gz,fastq fastq,3983969250.0,26559795.0,GSM3024070 r1,0:75 1:75,A:1014145452;C:978176901;G:976339602;T:1013200417;N:2106878,75,75,,,1014145452,978176901,976339602,1013200417,2106878,SRX3744216,SRS3000685,SRA662359,GEO,"Narry Kim Lab, Center for RNA Research, Institute for Basic Science",2,0.95552,0.95939,0.07086,0.06779,0.75808,0.76019,0.61441,0.61969,75,75,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,ribozero,bulk,bulk,bulk,,South Korea,2018-02-26,Cleavage,Embryo,Whole Organism,All anatomical structures
47633,SRR6784675,SRX3744213,SRS3000682,SRP133517,PRJNA436017,Maternal mRNA degradation by TUT4 and TUT7 in the zebrafish maternal to zygotic transition,GSE111152,Transcriptome Analysis,During the maternal to zygotic transition MZT  maternal RNAs are actively degraded and replaced by newly synthesized zygotic transcripts in a highly coordinated manner. However  it remains largely unknown how maternal mRNA decay is triggered in early vertebrate embryos. Here  through genome wide profiling of RNA abundance and three prime modification  we show that uridylation is induced at the onset of maternal mRNA clearance. The temporal control of uridylation is conserved in vertebrates. When the homologs of terminal uridylyltransferases TUT4 and TUT7 TUT4/7 are depleted in zebrafish and Xenopus  maternal mRNA clearance is significantly delayed  leading to developmental defects during gastrulation. Short tailed mRNAs are selectively uridylated by TUT4/7  with the highly uridylated transcripts degraded faster during the MZT than those with unmodified polyA tails. Our study demonstrates that uridylation plays a crucial role in timely mRNA degradation  thereby allowing the progression of early development. Overall design: Examination of zebrafish embryos injected with control or TUT4/7 morpholinos at 1 cell stage. RNA seq libraries were prepared at different time points across the MZT period. Three experimental sets  rs1a  rs2b  and rs2   were conducted independently.,,pubmed:29625039,,Zebrafish 2 hpf whole embryo injected with TUT4MO Exp. ID: rs1a,GSM3024067,,tissue:Zebrafish whole embryo|hpf translation blocking|strain:AB,Zebrafish 2 hpf whole embryo injected with TUT4MO Exp. ID: rs1a,"The sequences were basecalled by Illumina RTA embedded in NextSeq Control Software 1.3.2 by the standard workflow. Sequenced reads from RNA seq data were mapped to the GRCz10 genome with RefSeq release 104 annotations above using STAR 2.5.3a via RSEM 2.1.31. The gene level quantifications were performed using RSEM with the default options for strand specific and paired end RNA seq. The ""rs1a"" set of our libraries was between sample normalized using RUV seq 1.10.0. The standard workflow suggested by RUV seq did not work due to the global changes of maternal transcripts following the progression of embryogenesis. Instead  we first chose a subset of spike in RNAs that have ≥ 256 “expected counts” of reads in at least 90% of samples. Then  the counts were normalized by the RUVg algorithm k = 1. The geometric means of the normalized counts were used as size factors for the scale normalization of all other RNAs. The ERCC spike in reads in our second RNA seq dataset were too unreliable to be used as references. Even the raw read counts mappable to the reference spike in sequences were significantly out of the linear correlations between any two samples. As a workaround  we picked the internal controls from the first set to find genes that express more than 500 normalized reads with ≤ 0.2 of the log2 largest difference between two samples. Fourteen genes satisfied the criteria to become a set of internal controls. The internal reference genes were used in place of spike in RNAs for processing counts by the modified indirect RUVg approach. Genome build: GRCz10 Supplementary files format and content: comma separated text file include RUVg normalized rs1a and rs1b or TPM normalized rs2 values for each sample.",Zebrafish whole embryo,Approximately 1 nl of the solution containing TUT4/7 or control morpholinos was injected into wild type zebrafish embryos at xxx cell stage.,For each sample  embryos were collected and total RNA was extracted with TRIzol Invitrogen. The samples were spiked in with ERCC RNA Spike In Mix Ambion for normalization purpose. The quality of total RNA was checked by Agilent Bioanalyzer 2100 Agilent. Ribosomal RNA was depleted from total RNA using Ribo Zero Gold kit Epicentre. RNA  seq libraries were constructed using TruSeq stranded total RNA library prep kit Illumina and sequenced in Illumina Nextseq 500 v2  to yield paired end 76nt reads.,Zebrafish embryos were obtained by the natural mating of wild type AB strain and grown in embryo medium at 28.5˚C. Embryos were staged according to standard morphological criteria.,hpf translation blocking|strain:AB,GSM3024067,GSM3024067: Zebrafish 2 hpf whole embryo injected with TUT4MO Exp. ID: rs1a; Danio rerio; RNA Seq,GSM3024067,,1,For each sample  embryos were collected and total RNA was extracted with TRIzol Invitrogen. The samples were spiked in with ERCC RNA Spike In Mix Ambion for normalization purpose. The quality of total RNA was checked by Agilent Bioanalyzer 2100 Agilent. Ribosomal RNA was depleted from total RNA using Ribo Zero Gold kit Epicentre. RNA  seq libraries were constructed using TruSeq stranded total RNA library prep kit Illumina and sequenced in Illumina Nextseq 500 v2  to yield paired end 76nt reads.,GEO Accession:GSM3024067,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP133517,,,rs1a-TUT4MO-2hpf_R1.fastq.gz rs1a-TUT4MO-2hpf_R2.fastq.gz,fastq fastq,5214480150.0,34763201.0,GSM3024067 r1,0:75 1:75,A:1328615159;C:1278427609;G:1268574347;T:1336043947;N:2819088,75,75,,,1328615159,1278427609,1268574347,1336043947,2819088,SRX3744213,SRS3000682,SRA662359,GEO,"Narry Kim Lab, Center for RNA Research, Institute for Basic Science",2,0.95603,0.95974,0.07255,0.06963,0.7569,0.75883,0.53751,0.52285,75,75,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,ribozero,bulk,bulk,bulk,,South Korea,2018-02-26,Cleavage,Embryo,Whole Organism,All anatomical structures
47636,SRR6784672,SRX3744210,SRS3000679,SRP133517,PRJNA436017,Maternal mRNA degradation by TUT4 and TUT7 in the zebrafish maternal to zygotic transition,GSE111152,Transcriptome Analysis,During the maternal to zygotic transition MZT  maternal RNAs are actively degraded and replaced by newly synthesized zygotic transcripts in a highly coordinated manner. However  it remains largely unknown how maternal mRNA decay is triggered in early vertebrate embryos. Here  through genome wide profiling of RNA abundance and three prime modification  we show that uridylation is induced at the onset of maternal mRNA clearance. The temporal control of uridylation is conserved in vertebrates. When the homologs of terminal uridylyltransferases TUT4 and TUT7 TUT4/7 are depleted in zebrafish and Xenopus  maternal mRNA clearance is significantly delayed  leading to developmental defects during gastrulation. Short tailed mRNAs are selectively uridylated by TUT4/7  with the highly uridylated transcripts degraded faster during the MZT than those with unmodified polyA tails. Our study demonstrates that uridylation plays a crucial role in timely mRNA degradation  thereby allowing the progression of early development. Overall design: Examination of zebrafish embryos injected with control or TUT4/7 morpholinos at 1 cell stage. RNA seq libraries were prepared at different time points across the MZT period. Three experimental sets  rs1a  rs2b  and rs2   were conducted independently.,,pubmed:29625039,,Zebrafish 2 hpf whole embryo injected with ConMO Exp. ID: rs1a,GSM3024064,,tissue:Zebrafish whole embryo|hpf,Zebrafish 2 hpf whole embryo injected with ConMO Exp. ID: rs1a,"The sequences were basecalled by Illumina RTA embedded in NextSeq Control Software 1.3.2 by the standard workflow. Sequenced reads from RNA seq data were mapped to the GRCz10 genome with RefSeq release 104 annotations above using STAR 2.5.3a via RSEM 2.1.31. The gene level quantifications were performed using RSEM with the default options for strand specific and paired end RNA seq. The ""rs1a"" set of our libraries was between sample normalized using RUV seq 1.10.0. The standard workflow suggested by RUV seq did not work due to the global changes of maternal transcripts following the progression of embryogenesis. Instead  we first chose a subset of spike in RNAs that have ≥ 256 “expected counts” of reads in at least 90% of samples. Then  the counts were normalized by the RUVg algorithm k = 1. The geometric means of the normalized counts were used as size factors for the scale normalization of all other RNAs. The ERCC spike in reads in our second RNA seq dataset were too unreliable to be used as references. Even the raw read counts mappable to the reference spike in sequences were significantly out of the linear correlations between any two samples. As a workaround  we picked the internal controls from the first set to find genes that express more than 500 normalized reads with ≤ 0.2 of the log2 largest difference between two samples. Fourteen genes satisfied the criteria to become a set of internal controls. The internal reference genes were used in place of spike in RNAs for processing counts by the modified indirect RUVg approach. Genome build: GRCz10 Supplementary files format and content: comma separated text file include RUVg normalized rs1a and rs1b or TPM normalized rs2 values for each sample.",Zebrafish whole embryo,Approximately 1 nl of the solution containing TUT4/7 or control morpholinos was injected into wild type zebrafish embryos at xxx cell stage.,For each sample  embryos were collected and total RNA was extracted with TRIzol Invitrogen. The samples were spiked in with ERCC RNA Spike In Mix Ambion for normalization purpose. The quality of total RNA was checked by Agilent Bioanalyzer 2100 Agilent. Ribosomal RNA was depleted from total RNA using Ribo Zero Gold kit Epicentre. RNA  seq libraries were constructed using TruSeq stranded total RNA library prep kit Illumina and sequenced in Illumina Nextseq 500 v2  to yield paired end 76nt reads.,Zebrafish embryos were obtained by the natural mating of wild type AB strain and grown in embryo medium at 28.5˚C. Embryos were staged according to standard morphological criteria.,hpf,GSM3024064,GSM3024064: Zebrafish 2 hpf whole embryo injected with ConMO Exp. ID: rs1a; Danio rerio; RNA Seq,GSM3024064,,1,For each sample  embryos were collected and total RNA was extracted with TRIzol Invitrogen. The samples were spiked in with ERCC RNA Spike In Mix Ambion for normalization purpose. The quality of total RNA was checked by Agilent Bioanalyzer 2100 Agilent. Ribosomal RNA was depleted from total RNA using Ribo Zero Gold kit Epicentre. RNA  seq libraries were constructed using TruSeq stranded total RNA library prep kit Illumina and sequenced in Illumina Nextseq 500 v2  to yield paired end 76nt reads.,GEO Accession:GSM3024064,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP133517,,,rs1a-ConMO-2hpf_R2.fastq.gz rs1a-ConMO-2hpf_R1.fastq.gz,fastq fastq,3633282150.0,24221881.0,GSM3024064 r1,0:75 1:75,A:932255307;C:884564592;G:885445672;T:929026330;N:1990249,75,75,,,932255307,884564592,885445672,929026330,1990249,SRX3744210,SRS3000679,SRA662359,GEO,"Narry Kim Lab, Center for RNA Research, Institute for Basic Science",2,0.95724,0.961,0.06104,0.05762,0.75507,0.75735,0.59479,0.6042,75,75,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,ribozero,bulk,bulk,bulk,,South Korea,2018-02-26,Cleavage,Embryo,Whole Organism,All anatomical structures
56049,SRR10836768,SRX7508628,SRS5949020,SRP239626,PRJNA599208,Genome wide localization of RNAs during early zebrafish development,GSE143208,Transcriptome Analysis,We employed transcriptomics methods to examine RNAs from the nuclear and cytosolic fractions from zebrafish embryos at different stages of development. The RNA seq revealed spatial and temporal regulation of lncRNA expression during zebrafish development. Overall design: Localization of RNAs in the nuclear and cytosolic fractions of zebrafish embryonic cells in the 64 Cell  256 Cell  1000 Cell  Dome and Shield stages of development.,,pubmed:33795334,,64 cell Cyt,GSM4252149,,source name:64Cell stage embryo|tissue:zebrafish embryos|developmental stage:64 cell|fraction:Cytosolic,64 cell Cyt,RNA seq reads were trimmed using the Trimmomatic v0.27 and then mapped to the Zv9 genome using STAR v2.6.0a with parameters  p8 Transcript per million TPM was calculated using the Stringtie and Ballgown program Genome build: Zv9 Supplementary files format and content: tab delimited TPM files for all stages,64Cell stage embryo,Dechorionated embryos were then washed twice with 1 X PBS Phosphate buffer solution  ThermoFisher. RLN buffer was added to the tube containing embryos and the yolk sac disrupted releasing the cells in the buffer. This was then incubated on ice for 5 mins and centrifuged. The resulting supernatant was collected and labelled as the cytosolic fraction. The pellet was washed twice with 200 µL of RLN buffer and finally  collected and labelled as the nuclear fraction.,RNA was extracted using the Rneasy mini kit Sequencing libraries were prepared using the TruSeq Stranded Total RNA library Prep kit with the Illumina Ribo Zero rRNA removal kit Human Mouse Rat.,Wild type male and female zebrafish AB strain were set up in breeding tanks overnight and the eggs were collected the next day as soon as 10 min they were laid important to get synchronised embryos. About 100 500 depending upon the stage embryos were collected for each developmental stage 64 cell  256 cell  1000 cell  shield  24hpf  50hpf. The embryos were treated with Pronase protease from Streptomyces griseus  Sigma Aldrich to remove the chorion  1mL of Pronase working solution 1mg/mL was added to 2 3 ml of fish water containing embryos.,tissue:zebrafish embryos|developmental stage:64 cell|fraction:Cytosolic,GSM4252149,GSM4252149: 64 cell Cyt; Danio rerio; RNA Seq,GSM4252149,,1,RNA was extracted using the Rneasy mini kit Sequencing libraries were prepared using the TruSeq Stranded Total RNA library Prep kit with the Illumina Ribo Zero rRNA removal kit Human Mouse Rat.,GEO Accession:GSM4252149,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP239626,,,64-Cell-C2_L001_R2_001.fastq.gz 64-Cell-C2_L001_R1_001.fastq.gz,fastq fastq,1336151488.0,8851356.0,GSM4252149 r1,0:75.53 1:75.42,A:340311530;C:320422478;G:333939387;T:341176473;N:301620,75,75,,,340311530,320422478,333939387,341176473,301620,SRX7508628,SRS5949020,SRA1020776,GEO,"School of Biosciences, University of Birmingham",2,0.94359,0.94497,0.05405,0.0519,0.75386,0.75643,0.56525,0.43294,76,75,B,B,biological fallback assumption,illumina,nextseq,unknown,rrna_depletion,ribozero,bulk,bulk,bulk,,United Kingdom,2020-01-06,Cleavage,Embryo,Embryo Imprecise,All anatomical structures
56050,SRR10836769,SRX7508628,SRS5949020,SRP239626,PRJNA599208,Genome wide localization of RNAs during early zebrafish development,GSE143208,Transcriptome Analysis,We employed transcriptomics methods to examine RNAs from the nuclear and cytosolic fractions from zebrafish embryos at different stages of development. The RNA seq revealed spatial and temporal regulation of lncRNA expression during zebrafish development. Overall design: Localization of RNAs in the nuclear and cytosolic fractions of zebrafish embryonic cells in the 64 Cell  256 Cell  1000 Cell  Dome and Shield stages of development.,,pubmed:33795334,,64 cell Cyt,GSM4252149,,source name:64Cell stage embryo|tissue:zebrafish embryos|developmental stage:64 cell|fraction:Cytosolic,64 cell Cyt,RNA seq reads were trimmed using the Trimmomatic v0.27 and then mapped to the Zv9 genome using STAR v2.6.0a with parameters  p8 Transcript per million TPM was calculated using the Stringtie and Ballgown program Genome build: Zv9 Supplementary files format and content: tab delimited TPM files for all stages,64Cell stage embryo,Dechorionated embryos were then washed twice with 1 X PBS Phosphate buffer solution  ThermoFisher. RLN buffer was added to the tube containing embryos and the yolk sac disrupted releasing the cells in the buffer. This was then incubated on ice for 5 mins and centrifuged. The resulting supernatant was collected and labelled as the cytosolic fraction. The pellet was washed twice with 200 µL of RLN buffer and finally  collected and labelled as the nuclear fraction.,RNA was extracted using the Rneasy mini kit Sequencing libraries were prepared using the TruSeq Stranded Total RNA library Prep kit with the Illumina Ribo Zero rRNA removal kit Human Mouse Rat.,Wild type male and female zebrafish AB strain were set up in breeding tanks overnight and the eggs were collected the next day as soon as 10 min they were laid important to get synchronised embryos. About 100 500 depending upon the stage embryos were collected for each developmental stage 64 cell  256 cell  1000 cell  shield  24hpf  50hpf. The embryos were treated with Pronase protease from Streptomyces griseus  Sigma Aldrich to remove the chorion  1mL of Pronase working solution 1mg/mL was added to 2 3 ml of fish water containing embryos.,tissue:zebrafish embryos|developmental stage:64 cell|fraction:Cytosolic,GSM4252149,GSM4252149: 64 cell Cyt; Danio rerio; RNA Seq,GSM4252149,,1,RNA was extracted using the Rneasy mini kit Sequencing libraries were prepared using the TruSeq Stranded Total RNA library Prep kit with the Illumina Ribo Zero rRNA removal kit Human Mouse Rat.,GEO Accession:GSM4252149,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP239626,,,64-Cell-C2_L002_R1_001.fastq.gz 64-Cell-C2_L002_R2_001.fastq.gz,fastq fastq,1307072541.0,8658827.0,GSM4252149 r2,0:75.53 1:75.42,A:333132687;C:313198956;G:326763649;T:333629976;N:347273,75,75,,,333132687,313198956,326763649,333629976,347273,SRX7508628,SRS5949020,SRA1020776,GEO,"School of Biosciences, University of Birmingham",2,0.94527,0.94545,0.05438,0.0525,0.75369,0.75666,0.56642,0.56431,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,rrna_depletion,ribozero,bulk,bulk,bulk,,United Kingdom,2020-01-06,Cleavage,Embryo,Embryo Imprecise,All anatomical structures
56051,SRR10836770,SRX7508628,SRS5949020,SRP239626,PRJNA599208,Genome wide localization of RNAs during early zebrafish development,GSE143208,Transcriptome Analysis,We employed transcriptomics methods to examine RNAs from the nuclear and cytosolic fractions from zebrafish embryos at different stages of development. The RNA seq revealed spatial and temporal regulation of lncRNA expression during zebrafish development. Overall design: Localization of RNAs in the nuclear and cytosolic fractions of zebrafish embryonic cells in the 64 Cell  256 Cell  1000 Cell  Dome and Shield stages of development.,,pubmed:33795334,,64 cell Cyt,GSM4252149,,source name:64Cell stage embryo|tissue:zebrafish embryos|developmental stage:64 cell|fraction:Cytosolic,64 cell Cyt,RNA seq reads were trimmed using the Trimmomatic v0.27 and then mapped to the Zv9 genome using STAR v2.6.0a with parameters  p8 Transcript per million TPM was calculated using the Stringtie and Ballgown program Genome build: Zv9 Supplementary files format and content: tab delimited TPM files for all stages,64Cell stage embryo,Dechorionated embryos were then washed twice with 1 X PBS Phosphate buffer solution  ThermoFisher. RLN buffer was added to the tube containing embryos and the yolk sac disrupted releasing the cells in the buffer. This was then incubated on ice for 5 mins and centrifuged. The resulting supernatant was collected and labelled as the cytosolic fraction. The pellet was washed twice with 200 µL of RLN buffer and finally  collected and labelled as the nuclear fraction.,RNA was extracted using the Rneasy mini kit Sequencing libraries were prepared using the TruSeq Stranded Total RNA library Prep kit with the Illumina Ribo Zero rRNA removal kit Human Mouse Rat.,Wild type male and female zebrafish AB strain were set up in breeding tanks overnight and the eggs were collected the next day as soon as 10 min they were laid important to get synchronised embryos. About 100 500 depending upon the stage embryos were collected for each developmental stage 64 cell  256 cell  1000 cell  shield  24hpf  50hpf. The embryos were treated with Pronase protease from Streptomyces griseus  Sigma Aldrich to remove the chorion  1mL of Pronase working solution 1mg/mL was added to 2 3 ml of fish water containing embryos.,tissue:zebrafish embryos|developmental stage:64 cell|fraction:Cytosolic,GSM4252149,GSM4252149: 64 cell Cyt; Danio rerio; RNA Seq,GSM4252149,,1,RNA was extracted using the Rneasy mini kit Sequencing libraries were prepared using the TruSeq Stranded Total RNA library Prep kit with the Illumina Ribo Zero rRNA removal kit Human Mouse Rat.,GEO Accession:GSM4252149,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP239626,,,64-Cell-C2_L003_R1_001.fastq.gz 64-Cell-C2_L003_R2_001.fastq.gz,fastq fastq,1334001642.0,8836838.0,GSM4252149 r3,0:75.53 1:75.43,A:340290874;C:321032534;G:330640484;T:341840555;N:197195,75,75,,,340290874,321032534,330640484,341840555,197195,SRX7508628,SRS5949020,SRA1020776,GEO,"School of Biosciences, University of Birmingham",2,0.94327,0.94457,0.05449,0.0522,0.7527,0.75528,0.56043,0.55555,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,rrna_depletion,ribozero,bulk,bulk,bulk,,United Kingdom,2020-01-06,Cleavage,Embryo,Embryo Imprecise,All anatomical structures
56052,SRR10836771,SRX7508628,SRS5949020,SRP239626,PRJNA599208,Genome wide localization of RNAs during early zebrafish development,GSE143208,Transcriptome Analysis,We employed transcriptomics methods to examine RNAs from the nuclear and cytosolic fractions from zebrafish embryos at different stages of development. The RNA seq revealed spatial and temporal regulation of lncRNA expression during zebrafish development. Overall design: Localization of RNAs in the nuclear and cytosolic fractions of zebrafish embryonic cells in the 64 Cell  256 Cell  1000 Cell  Dome and Shield stages of development.,,pubmed:33795334,,64 cell Cyt,GSM4252149,,source name:64Cell stage embryo|tissue:zebrafish embryos|developmental stage:64 cell|fraction:Cytosolic,64 cell Cyt,RNA seq reads were trimmed using the Trimmomatic v0.27 and then mapped to the Zv9 genome using STAR v2.6.0a with parameters  p8 Transcript per million TPM was calculated using the Stringtie and Ballgown program Genome build: Zv9 Supplementary files format and content: tab delimited TPM files for all stages,64Cell stage embryo,Dechorionated embryos were then washed twice with 1 X PBS Phosphate buffer solution  ThermoFisher. RLN buffer was added to the tube containing embryos and the yolk sac disrupted releasing the cells in the buffer. This was then incubated on ice for 5 mins and centrifuged. The resulting supernatant was collected and labelled as the cytosolic fraction. The pellet was washed twice with 200 µL of RLN buffer and finally  collected and labelled as the nuclear fraction.,RNA was extracted using the Rneasy mini kit Sequencing libraries were prepared using the TruSeq Stranded Total RNA library Prep kit with the Illumina Ribo Zero rRNA removal kit Human Mouse Rat.,Wild type male and female zebrafish AB strain were set up in breeding tanks overnight and the eggs were collected the next day as soon as 10 min they were laid important to get synchronised embryos. About 100 500 depending upon the stage embryos were collected for each developmental stage 64 cell  256 cell  1000 cell  shield  24hpf  50hpf. The embryos were treated with Pronase protease from Streptomyces griseus  Sigma Aldrich to remove the chorion  1mL of Pronase working solution 1mg/mL was added to 2 3 ml of fish water containing embryos.,tissue:zebrafish embryos|developmental stage:64 cell|fraction:Cytosolic,GSM4252149,GSM4252149: 64 cell Cyt; Danio rerio; RNA Seq,GSM4252149,,1,RNA was extracted using the Rneasy mini kit Sequencing libraries were prepared using the TruSeq Stranded Total RNA library Prep kit with the Illumina Ribo Zero rRNA removal kit Human Mouse Rat.,GEO Accession:GSM4252149,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP239626,,,64-Cell-C2_L004_R1_001.fastq.gz 64-Cell-C2_L004_R2_001.fastq.gz,fastq fastq,1305961821.0,8651139.0,GSM4252149 r4,0:75.53 1:75.43,A:333312907;C:314516495;G:323171918;T:334776318;N:184183,75,75,,,333312907,314516495,323171918,334776318,184183,SRX7508628,SRS5949020,SRA1020776,GEO,"School of Biosciences, University of Birmingham",2,0.94385,0.94476,0.05394,0.05188,0.75246,0.75597,0.56098,0.56649,76,74,B,B,biological fallback assumption,illumina,nextseq,unknown,rrna_depletion,ribozero,bulk,bulk,bulk,,United Kingdom,2020-01-06,Cleavage,Embryo,Embryo Imprecise,All anatomical structures
56053,SRR10836764,SRX7508627,SRS5949019,SRP239626,PRJNA599208,Genome wide localization of RNAs during early zebrafish development,GSE143208,Transcriptome Analysis,We employed transcriptomics methods to examine RNAs from the nuclear and cytosolic fractions from zebrafish embryos at different stages of development. The RNA seq revealed spatial and temporal regulation of lncRNA expression during zebrafish development. Overall design: Localization of RNAs in the nuclear and cytosolic fractions of zebrafish embryonic cells in the 64 Cell  256 Cell  1000 Cell  Dome and Shield stages of development.,,pubmed:33795334,,64 cell Nuc,GSM4252148,,source name:64Cell stage embryo|tissue:zebrafish embryos|developmental stage:64 cell|fraction:Nuclear,64 cell Nuc,RNA seq reads were trimmed using the Trimmomatic v0.27 and then mapped to the Zv9 genome using STAR v2.6.0a with parameters  p8 Transcript per million TPM was calculated using the Stringtie and Ballgown program Genome build: Zv9 Supplementary files format and content: tab delimited TPM files for all stages,64Cell stage embryo,Dechorionated embryos were then washed twice with 1 X PBS Phosphate buffer solution  ThermoFisher. RLN buffer was added to the tube containing embryos and the yolk sac disrupted releasing the cells in the buffer. This was then incubated on ice for 5 mins and centrifuged. The resulting supernatant was collected and labelled as the cytosolic fraction. The pellet was washed twice with 200 µL of RLN buffer and finally  collected and labelled as the nuclear fraction.,RNA was extracted using the Rneasy mini kit Sequencing libraries were prepared using the TruSeq Stranded Total RNA library Prep kit with the Illumina Ribo Zero rRNA removal kit Human Mouse Rat.,Wild type male and female zebrafish AB strain were set up in breeding tanks overnight and the eggs were collected the next day as soon as 10 min they were laid important to get synchronised embryos. About 100 500 depending upon the stage embryos were collected for each developmental stage 64 cell  256 cell  1000 cell  shield  24hpf  50hpf. The embryos were treated with Pronase protease from Streptomyces griseus  Sigma Aldrich to remove the chorion  1mL of Pronase working solution 1mg/mL was added to 2 3 ml of fish water containing embryos.,tissue:zebrafish embryos|developmental stage:64 cell|fraction:Nuclear,GSM4252148,GSM4252148: 64 cell Nuc; Danio rerio; RNA Seq,GSM4252148,,1,RNA was extracted using the Rneasy mini kit Sequencing libraries were prepared using the TruSeq Stranded Total RNA library Prep kit with the Illumina Ribo Zero rRNA removal kit Human Mouse Rat.,GEO Accession:GSM4252148,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP239626,,,64-Cell-N2_L001_R2_001.fastq.gz 64-Cell-N2_L001_R1_001.fastq.gz,fastq fastq,1321005353.0,8750201.0,GSM4252148 r1,0:75.58 1:75.39,A:354789098;C:303898641;G:309341474;T:352687283;N:288857,75,75,,,354789098,303898641,309341474,352687283,288857,SRX7508627,SRS5949019,SRA1020776,GEO,"School of Biosciences, University of Birmingham",2,0.94588,0.94437,0.03564,0.03357,0.78384,0.7864,0.76529,0.75993,75,76,B,B,biological fallback assumption,illumina,nextseq,unknown,rrna_depletion,ribozero,bulk,bulk,bulk,,United Kingdom,2020-01-06,Cleavage,Embryo,Embryo Imprecise,All anatomical structures
56054,SRR10836765,SRX7508627,SRS5949019,SRP239626,PRJNA599208,Genome wide localization of RNAs during early zebrafish development,GSE143208,Transcriptome Analysis,We employed transcriptomics methods to examine RNAs from the nuclear and cytosolic fractions from zebrafish embryos at different stages of development. The RNA seq revealed spatial and temporal regulation of lncRNA expression during zebrafish development. Overall design: Localization of RNAs in the nuclear and cytosolic fractions of zebrafish embryonic cells in the 64 Cell  256 Cell  1000 Cell  Dome and Shield stages of development.,,pubmed:33795334,,64 cell Nuc,GSM4252148,,source name:64Cell stage embryo|tissue:zebrafish embryos|developmental stage:64 cell|fraction:Nuclear,64 cell Nuc,RNA seq reads were trimmed using the Trimmomatic v0.27 and then mapped to the Zv9 genome using STAR v2.6.0a with parameters  p8 Transcript per million TPM was calculated using the Stringtie and Ballgown program Genome build: Zv9 Supplementary files format and content: tab delimited TPM files for all stages,64Cell stage embryo,Dechorionated embryos were then washed twice with 1 X PBS Phosphate buffer solution  ThermoFisher. RLN buffer was added to the tube containing embryos and the yolk sac disrupted releasing the cells in the buffer. This was then incubated on ice for 5 mins and centrifuged. The resulting supernatant was collected and labelled as the cytosolic fraction. The pellet was washed twice with 200 µL of RLN buffer and finally  collected and labelled as the nuclear fraction.,RNA was extracted using the Rneasy mini kit Sequencing libraries were prepared using the TruSeq Stranded Total RNA library Prep kit with the Illumina Ribo Zero rRNA removal kit Human Mouse Rat.,Wild type male and female zebrafish AB strain were set up in breeding tanks overnight and the eggs were collected the next day as soon as 10 min they were laid important to get synchronised embryos. About 100 500 depending upon the stage embryos were collected for each developmental stage 64 cell  256 cell  1000 cell  shield  24hpf  50hpf. The embryos were treated with Pronase protease from Streptomyces griseus  Sigma Aldrich to remove the chorion  1mL of Pronase working solution 1mg/mL was added to 2 3 ml of fish water containing embryos.,tissue:zebrafish embryos|developmental stage:64 cell|fraction:Nuclear,GSM4252148,GSM4252148: 64 cell Nuc; Danio rerio; RNA Seq,GSM4252148,,1,RNA was extracted using the Rneasy mini kit Sequencing libraries were prepared using the TruSeq Stranded Total RNA library Prep kit with the Illumina Ribo Zero rRNA removal kit Human Mouse Rat.,GEO Accession:GSM4252148,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP239626,,,64-Cell-N2_L002_R1_001.fastq.gz 64-Cell-N2_L002_R2_001.fastq.gz,fastq fastq,1295035725.0,8578355.0,GSM4252148 r2,0:75.58 1:75.39,A:347982975;C:297790857;G:303257309;T:345677742;N:326842,75,75,,,347982975,297790857,303257309,345677742,326842,SRX7508627,SRS5949019,SRA1020776,GEO,"School of Biosciences, University of Birmingham",2,0.94664,0.94481,0.03501,0.03387,0.7839,0.7866,0.76555,0.76373,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,rrna_depletion,ribozero,bulk,bulk,bulk,,United Kingdom,2020-01-06,Cleavage,Embryo,Embryo Imprecise,All anatomical structures
56055,SRR10836766,SRX7508627,SRS5949019,SRP239626,PRJNA599208,Genome wide localization of RNAs during early zebrafish development,GSE143208,Transcriptome Analysis,We employed transcriptomics methods to examine RNAs from the nuclear and cytosolic fractions from zebrafish embryos at different stages of development. The RNA seq revealed spatial and temporal regulation of lncRNA expression during zebrafish development. Overall design: Localization of RNAs in the nuclear and cytosolic fractions of zebrafish embryonic cells in the 64 Cell  256 Cell  1000 Cell  Dome and Shield stages of development.,,pubmed:33795334,,64 cell Nuc,GSM4252148,,source name:64Cell stage embryo|tissue:zebrafish embryos|developmental stage:64 cell|fraction:Nuclear,64 cell Nuc,RNA seq reads were trimmed using the Trimmomatic v0.27 and then mapped to the Zv9 genome using STAR v2.6.0a with parameters  p8 Transcript per million TPM was calculated using the Stringtie and Ballgown program Genome build: Zv9 Supplementary files format and content: tab delimited TPM files for all stages,64Cell stage embryo,Dechorionated embryos were then washed twice with 1 X PBS Phosphate buffer solution  ThermoFisher. RLN buffer was added to the tube containing embryos and the yolk sac disrupted releasing the cells in the buffer. This was then incubated on ice for 5 mins and centrifuged. The resulting supernatant was collected and labelled as the cytosolic fraction. The pellet was washed twice with 200 µL of RLN buffer and finally  collected and labelled as the nuclear fraction.,RNA was extracted using the Rneasy mini kit Sequencing libraries were prepared using the TruSeq Stranded Total RNA library Prep kit with the Illumina Ribo Zero rRNA removal kit Human Mouse Rat.,Wild type male and female zebrafish AB strain were set up in breeding tanks overnight and the eggs were collected the next day as soon as 10 min they were laid important to get synchronised embryos. About 100 500 depending upon the stage embryos were collected for each developmental stage 64 cell  256 cell  1000 cell  shield  24hpf  50hpf. The embryos were treated with Pronase protease from Streptomyces griseus  Sigma Aldrich to remove the chorion  1mL of Pronase working solution 1mg/mL was added to 2 3 ml of fish water containing embryos.,tissue:zebrafish embryos|developmental stage:64 cell|fraction:Nuclear,GSM4252148,GSM4252148: 64 cell Nuc; Danio rerio; RNA Seq,GSM4252148,,1,RNA was extracted using the Rneasy mini kit Sequencing libraries were prepared using the TruSeq Stranded Total RNA library Prep kit with the Illumina Ribo Zero rRNA removal kit Human Mouse Rat.,GEO Accession:GSM4252148,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP239626,,,64-Cell-N2_L003_R1_001.fastq.gz 64-Cell-N2_L003_R2_001.fastq.gz,fastq fastq,1319910505.0,8742742.0,GSM4252148 r3,0:75.58 1:75.39,A:354921477;C:304429084;G:307177632;T:353201339;N:180973,75,75,,,354921477,304429084,307177632,353201339,180973,SRX7508627,SRS5949019,SRA1020776,GEO,"School of Biosciences, University of Birmingham",2,0.9463,0.94449,0.03579,0.034,0.78336,0.78589,0.76473,0.76049,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,rrna_depletion,ribozero,bulk,bulk,bulk,,United Kingdom,2020-01-06,Cleavage,Embryo,Embryo Imprecise,All anatomical structures
56056,SRR10836767,SRX7508627,SRS5949019,SRP239626,PRJNA599208,Genome wide localization of RNAs during early zebrafish development,GSE143208,Transcriptome Analysis,We employed transcriptomics methods to examine RNAs from the nuclear and cytosolic fractions from zebrafish embryos at different stages of development. The RNA seq revealed spatial and temporal regulation of lncRNA expression during zebrafish development. Overall design: Localization of RNAs in the nuclear and cytosolic fractions of zebrafish embryonic cells in the 64 Cell  256 Cell  1000 Cell  Dome and Shield stages of development.,,pubmed:33795334,,64 cell Nuc,GSM4252148,,source name:64Cell stage embryo|tissue:zebrafish embryos|developmental stage:64 cell|fraction:Nuclear,64 cell Nuc,RNA seq reads were trimmed using the Trimmomatic v0.27 and then mapped to the Zv9 genome using STAR v2.6.0a with parameters  p8 Transcript per million TPM was calculated using the Stringtie and Ballgown program Genome build: Zv9 Supplementary files format and content: tab delimited TPM files for all stages,64Cell stage embryo,Dechorionated embryos were then washed twice with 1 X PBS Phosphate buffer solution  ThermoFisher. RLN buffer was added to the tube containing embryos and the yolk sac disrupted releasing the cells in the buffer. This was then incubated on ice for 5 mins and centrifuged. The resulting supernatant was collected and labelled as the cytosolic fraction. The pellet was washed twice with 200 µL of RLN buffer and finally  collected and labelled as the nuclear fraction.,RNA was extracted using the Rneasy mini kit Sequencing libraries were prepared using the TruSeq Stranded Total RNA library Prep kit with the Illumina Ribo Zero rRNA removal kit Human Mouse Rat.,Wild type male and female zebrafish AB strain were set up in breeding tanks overnight and the eggs were collected the next day as soon as 10 min they were laid important to get synchronised embryos. About 100 500 depending upon the stage embryos were collected for each developmental stage 64 cell  256 cell  1000 cell  shield  24hpf  50hpf. The embryos were treated with Pronase protease from Streptomyces griseus  Sigma Aldrich to remove the chorion  1mL of Pronase working solution 1mg/mL was added to 2 3 ml of fish water containing embryos.,tissue:zebrafish embryos|developmental stage:64 cell|fraction:Nuclear,GSM4252148,GSM4252148: 64 cell Nuc; Danio rerio; RNA Seq,GSM4252148,,1,RNA was extracted using the Rneasy mini kit Sequencing libraries were prepared using the TruSeq Stranded Total RNA library Prep kit with the Illumina Ribo Zero rRNA removal kit Human Mouse Rat.,GEO Accession:GSM4252148,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP239626,,,64-Cell-N2_L004_R1_001.fastq.gz 64-Cell-N2_L004_R2_001.fastq.gz,fastq fastq,1295847653.0,8583386.0,GSM4252148 r4,0:75.58 1:75.39,A:348646646;C:299056047;G:301226476;T:346747021;N:171463,75,75,,,348646646,299056047,301226476,346747021,171463,SRX7508627,SRS5949019,SRA1020776,GEO,"School of Biosciences, University of Birmingham",2,0.93863,0.94342,0.03587,0.03418,0.78435,0.78754,0.76226,0.76112,75,76,B,B,biological fallback assumption,illumina,nextseq,unknown,rrna_depletion,ribozero,bulk,bulk,bulk,,United Kingdom,2020-01-06,Cleavage,Embryo,Embryo Imprecise,All anatomical structures
65768,SRR15600910,SRX11898432,SRS9909614,SRP333957,PRJNA757460,Adar mediated A to I editing is required for establishment of embryonic body axes in zebrafish,GSE182714,Other,Adar mediated A to I editing is required for establishment of embryonic body axes in zebrafish. To assess the effect of Adar KD and OE  uninjected wild type and embryos injected with 1 ng of adar MO or 50 pg of adar mRNA were kept until desired developmental stage: 128 cell or 50% epiboly. Two replicates of 20 pooled embryos from each time point were isolated for RNA extraction. For the analysis at 12 hpf  a separate batch of uninjected control  as well as Adar KD and OE samples were generated in three replicates. Overall design: Parental DNA was extracted from one individual male and female fishes from tail fin clipping  together with RNA from their offspring at 16 cell  3.5 hpf  and 5.3 hpf stages. For each time point  at least 20 embryos were pooled for RNA extraction. To assess the effect of Adar KD and OE  uninjected wild type and embryos injected with 1 ng of adar MO or 50 pg of adar mRNA were kept until desired developmental stage: 128 cell or 50% epiboly. Two replicates of 20 pooled embryos from each time point were isolated for RNA extraction. For the analysis at 12 hpf  a separate batch of uninjected control  as well as Adar KD and OE samples were generated in three replicates. Total RNA was extracted using TRIzol LS Thermo Fisher Scientific  USA and cleaned up on the Qiagen Rneasy Mini column Qiagen  USA. Quality control of extracted RNA was performed using the 2200 TapeStation system from Agilent Technologies USA. To avoid the bias caused by cytoplasmic polyadenylation during early embryonic stages  total RNA was rRNA depleted using Ribo Zero Magnetic Gold Kit Human  Mouse  Rat; Epicenter.  cDNA synthesis for Next Generation Sequencing NGS was performed by SMARTer Stranded RNA seq kit  Clontech Laboratories  USA as recommended by the manufacturer. Paired end sequencing 2 × 75 bp reads was performed with NextSeq 500 Illumina  USA.,,pubmed:36127363,,Offspring 16 cell,GSM5535043,,source name:whole zebrafish embryo|strain:WT ABTL|tissue:whole embryo|developmental stage:16 cell,Offspring 16 cell,Basecalling was performed by Illumina RTA 1.18.61. Files were translated into demultiplexed FASTQ files by Illumina bcl2fastq2 2.16.10. Low quality sequences and adapter content were trimmed with cutadapt v. 2.4. Reads were aligned to the zebrafish genome assembly GRCz10  using STAR v2.7.7a and samtools v1.11 Expression quantification was performed using HTSeq v0.11.2 Differential expression was performed using DESeq2 R v3.6.3 Putative RNA editing sites based on DNA  and RNA seq input were detected using REDiscover https://github.com/lpryszcz/REDiscover. Options  q 15  Q 20  were used  i.e. a minimal mapping quality of 15 and a minimal base call quality of 20 were required. Sites that were not homozygous between female and male samples were excluded from the analysis. Alternative alleles were only called when they were present in at least 20% of RNA reads. For simplicity  sites with more than one alternative allele were excluded from the analysis. Genome build: GRCz10  Supplementary files format and content: tab delimited file format,whole zebrafish embryo,To assess the effect of Adar KD and OE  uninjected wild type and embryos injected with 1 ng of adar MO or 50 pg of adar mRNA were kept until desired developmental stage.,Parental genomic DNA was extracted from adult fin clippings of an individual male and female zebrafish of wild type ABTL background. For the rest of the samples  20 pooled embryos from each time point were isolated for RNA extraction. Total RNA was extracted using TRIzol LS Thermo Fisher Scientific  USA and cleaned up on the Qiagen Rneasy Mini column Qiagen  USA. Quality control of extracted RNA was performed using the 2200 TapeStation system from Agilent Technologies USA. To avoid the bias caused by cytoplasmic polyadenylation during early embryonic stages Winata et al.  2018  total RNA was rRNA depleted using Ribo Zero Magnetic Gold Kit Human  Mouse  Rat; Epicenter.  For the 7 dpf samples  total RNA was subjected to mRNA enrichment using  NEBNext PolyA mRNA Magnetic Isolation Module E7490  NEB. genomic DNA library was constructed using Nextera XT Illumina  USA using standard protocol; cDNA synthesis was performed by SMARTer Stranded RNA seq kit Clontech Laboratories  USA as recommended by the manufacturer. For the 7 dpf samples  library was constructed using TruSeq Stranded Total RNA library preparation kit Illumina  USA.,Zebrafish embryos were maintained according to standard protocol Westerfield et al.  2000 and staged according to standard morphological criteria Kimmel et al.  1995.,strain:WT ABTL|tissue:whole embryo|developmental stage:16 cell,GSM5535043,GSM5535043: Offspring 16 cell; Danio rerio; RNA Seq,GSM5535043,,1,Parental genomic DNA was extracted from adult fin clippings of an individual male and female zebrafish of wild type ABTL background. For the rest of the samples  20 pooled embryos from each time point were isolated for RNA extraction. Total RNA was extracted using TRIzol LS Thermo Fisher Scientific  USA and cleaned up on the Qiagen Rneasy Mini column Qiagen  USA. Quality control of extracted RNA was performed using the 2200 TapeStation system from Agilent Technologies USA. To avoid the bias caused by cytoplasmic polyadenylation during early embryonic stages Winata et al.  2018  total RNA was rRNA depleted using Ribo Zero Magnetic Gold Kit Human  Mouse  Rat; Epicenter. genomic DNA library was constructed using Nextera XT Illumina  USA using standard protocol; cDNA synthesis was performed by SMARTer Stranded RNA seq kit Clontech Laboratories  USA as recommended by the manufacturer.,GEO Accession:GSM5535043,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP333957,,,4-16c_S1_L001_R1_001.fastq.gz 4-16c_S1_L001_R2_001.fastq.gz,fastq fastq,2339644031.0,15494096.0,GSM5535043 r1,0:75.50 1:75.50,A:616099047;C:571909359;G:557245477;T:593689312;N:700836,75,75,,,616099047,571909359,557245477,593689312,700836,SRX11898432,SRS9909614,SRA1283368,GEO,"Zebrafish Developmental Genomics, International Institute of Molecular and Cell Biology in Warsaw",2,0.94716,0.94797,0.05051,0.05038,0.75939,0.76189,0.48192,0.48054,76,76,B,B,biological fallback assumption,illumina,nextseq,full_length,rrna_depletion,ribozero,bulk,bulk,bulk,,Poland,2021-08-24,Cleavage,Embryo,Whole Organism,All anatomical structures
65769,SRR15600911,SRX11898432,SRS9909614,SRP333957,PRJNA757460,Adar mediated A to I editing is required for establishment of embryonic body axes in zebrafish,GSE182714,Other,Adar mediated A to I editing is required for establishment of embryonic body axes in zebrafish. To assess the effect of Adar KD and OE  uninjected wild type and embryos injected with 1 ng of adar MO or 50 pg of adar mRNA were kept until desired developmental stage: 128 cell or 50% epiboly. Two replicates of 20 pooled embryos from each time point were isolated for RNA extraction. For the analysis at 12 hpf  a separate batch of uninjected control  as well as Adar KD and OE samples were generated in three replicates. Overall design: Parental DNA was extracted from one individual male and female fishes from tail fin clipping  together with RNA from their offspring at 16 cell  3.5 hpf  and 5.3 hpf stages. For each time point  at least 20 embryos were pooled for RNA extraction. To assess the effect of Adar KD and OE  uninjected wild type and embryos injected with 1 ng of adar MO or 50 pg of adar mRNA were kept until desired developmental stage: 128 cell or 50% epiboly. Two replicates of 20 pooled embryos from each time point were isolated for RNA extraction. For the analysis at 12 hpf  a separate batch of uninjected control  as well as Adar KD and OE samples were generated in three replicates. Total RNA was extracted using TRIzol LS Thermo Fisher Scientific  USA and cleaned up on the Qiagen Rneasy Mini column Qiagen  USA. Quality control of extracted RNA was performed using the 2200 TapeStation system from Agilent Technologies USA. To avoid the bias caused by cytoplasmic polyadenylation during early embryonic stages  total RNA was rRNA depleted using Ribo Zero Magnetic Gold Kit Human  Mouse  Rat; Epicenter.  cDNA synthesis for Next Generation Sequencing NGS was performed by SMARTer Stranded RNA seq kit  Clontech Laboratories  USA as recommended by the manufacturer. Paired end sequencing 2 × 75 bp reads was performed with NextSeq 500 Illumina  USA.,,pubmed:36127363,,Offspring 16 cell,GSM5535043,,source name:whole zebrafish embryo|strain:WT ABTL|tissue:whole embryo|developmental stage:16 cell,Offspring 16 cell,Basecalling was performed by Illumina RTA 1.18.61. Files were translated into demultiplexed FASTQ files by Illumina bcl2fastq2 2.16.10. Low quality sequences and adapter content were trimmed with cutadapt v. 2.4. Reads were aligned to the zebrafish genome assembly GRCz10  using STAR v2.7.7a and samtools v1.11 Expression quantification was performed using HTSeq v0.11.2 Differential expression was performed using DESeq2 R v3.6.3 Putative RNA editing sites based on DNA  and RNA seq input were detected using REDiscover https://github.com/lpryszcz/REDiscover. Options  q 15  Q 20  were used  i.e. a minimal mapping quality of 15 and a minimal base call quality of 20 were required. Sites that were not homozygous between female and male samples were excluded from the analysis. Alternative alleles were only called when they were present in at least 20% of RNA reads. For simplicity  sites with more than one alternative allele were excluded from the analysis. Genome build: GRCz10  Supplementary files format and content: tab delimited file format,whole zebrafish embryo,To assess the effect of Adar KD and OE  uninjected wild type and embryos injected with 1 ng of adar MO or 50 pg of adar mRNA were kept until desired developmental stage.,Parental genomic DNA was extracted from adult fin clippings of an individual male and female zebrafish of wild type ABTL background. For the rest of the samples  20 pooled embryos from each time point were isolated for RNA extraction. Total RNA was extracted using TRIzol LS Thermo Fisher Scientific  USA and cleaned up on the Qiagen Rneasy Mini column Qiagen  USA. Quality control of extracted RNA was performed using the 2200 TapeStation system from Agilent Technologies USA. To avoid the bias caused by cytoplasmic polyadenylation during early embryonic stages Winata et al.  2018  total RNA was rRNA depleted using Ribo Zero Magnetic Gold Kit Human  Mouse  Rat; Epicenter.  For the 7 dpf samples  total RNA was subjected to mRNA enrichment using  NEBNext PolyA mRNA Magnetic Isolation Module E7490  NEB. genomic DNA library was constructed using Nextera XT Illumina  USA using standard protocol; cDNA synthesis was performed by SMARTer Stranded RNA seq kit Clontech Laboratories  USA as recommended by the manufacturer. For the 7 dpf samples  library was constructed using TruSeq Stranded Total RNA library preparation kit Illumina  USA.,Zebrafish embryos were maintained according to standard protocol Westerfield et al.  2000 and staged according to standard morphological criteria Kimmel et al.  1995.,strain:WT ABTL|tissue:whole embryo|developmental stage:16 cell,GSM5535043,GSM5535043: Offspring 16 cell; Danio rerio; RNA Seq,GSM5535043,,1,Parental genomic DNA was extracted from adult fin clippings of an individual male and female zebrafish of wild type ABTL background. For the rest of the samples  20 pooled embryos from each time point were isolated for RNA extraction. Total RNA was extracted using TRIzol LS Thermo Fisher Scientific  USA and cleaned up on the Qiagen Rneasy Mini column Qiagen  USA. Quality control of extracted RNA was performed using the 2200 TapeStation system from Agilent Technologies USA. To avoid the bias caused by cytoplasmic polyadenylation during early embryonic stages Winata et al.  2018  total RNA was rRNA depleted using Ribo Zero Magnetic Gold Kit Human  Mouse  Rat; Epicenter. genomic DNA library was constructed using Nextera XT Illumina  USA using standard protocol; cDNA synthesis was performed by SMARTer Stranded RNA seq kit Clontech Laboratories  USA as recommended by the manufacturer.,GEO Accession:GSM5535043,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP333957,,,4-16c_S1_L002_R1_001.fastq.gz 4-16c_S1_L002_R2_001.fastq.gz,fastq fastq,2331084966.0,15437478.0,GSM5535043 r2,0:75.50 1:75.50,A:614855873;C:569629518;G:554714353;T:591272506;N:612716,75,75,,,614855873,569629518,554714353,591272506,612716,SRX11898432,SRS9909614,SRA1283368,GEO,"Zebrafish Developmental Genomics, International Institute of Molecular and Cell Biology in Warsaw",2,0.94727,0.94782,0.05048,0.05084,0.75883,0.76207,0.48237,0.48263,76,76,B,B,biological fallback assumption,illumina,nextseq,full_length,rrna_depletion,ribozero,bulk,bulk,bulk,,Poland,2021-08-24,Cleavage,Embryo,Whole Organism,All anatomical structures
65770,SRR15600912,SRX11898432,SRS9909614,SRP333957,PRJNA757460,Adar mediated A to I editing is required for establishment of embryonic body axes in zebrafish,GSE182714,Other,Adar mediated A to I editing is required for establishment of embryonic body axes in zebrafish. To assess the effect of Adar KD and OE  uninjected wild type and embryos injected with 1 ng of adar MO or 50 pg of adar mRNA were kept until desired developmental stage: 128 cell or 50% epiboly. Two replicates of 20 pooled embryos from each time point were isolated for RNA extraction. For the analysis at 12 hpf  a separate batch of uninjected control  as well as Adar KD and OE samples were generated in three replicates. Overall design: Parental DNA was extracted from one individual male and female fishes from tail fin clipping  together with RNA from their offspring at 16 cell  3.5 hpf  and 5.3 hpf stages. For each time point  at least 20 embryos were pooled for RNA extraction. To assess the effect of Adar KD and OE  uninjected wild type and embryos injected with 1 ng of adar MO or 50 pg of adar mRNA were kept until desired developmental stage: 128 cell or 50% epiboly. Two replicates of 20 pooled embryos from each time point were isolated for RNA extraction. For the analysis at 12 hpf  a separate batch of uninjected control  as well as Adar KD and OE samples were generated in three replicates. Total RNA was extracted using TRIzol LS Thermo Fisher Scientific  USA and cleaned up on the Qiagen Rneasy Mini column Qiagen  USA. Quality control of extracted RNA was performed using the 2200 TapeStation system from Agilent Technologies USA. To avoid the bias caused by cytoplasmic polyadenylation during early embryonic stages  total RNA was rRNA depleted using Ribo Zero Magnetic Gold Kit Human  Mouse  Rat; Epicenter.  cDNA synthesis for Next Generation Sequencing NGS was performed by SMARTer Stranded RNA seq kit  Clontech Laboratories  USA as recommended by the manufacturer. Paired end sequencing 2 × 75 bp reads was performed with NextSeq 500 Illumina  USA.,,pubmed:36127363,,Offspring 16 cell,GSM5535043,,source name:whole zebrafish embryo|strain:WT ABTL|tissue:whole embryo|developmental stage:16 cell,Offspring 16 cell,Basecalling was performed by Illumina RTA 1.18.61. Files were translated into demultiplexed FASTQ files by Illumina bcl2fastq2 2.16.10. Low quality sequences and adapter content were trimmed with cutadapt v. 2.4. Reads were aligned to the zebrafish genome assembly GRCz10  using STAR v2.7.7a and samtools v1.11 Expression quantification was performed using HTSeq v0.11.2 Differential expression was performed using DESeq2 R v3.6.3 Putative RNA editing sites based on DNA  and RNA seq input were detected using REDiscover https://github.com/lpryszcz/REDiscover. Options  q 15  Q 20  were used  i.e. a minimal mapping quality of 15 and a minimal base call quality of 20 were required. Sites that were not homozygous between female and male samples were excluded from the analysis. Alternative alleles were only called when they were present in at least 20% of RNA reads. For simplicity  sites with more than one alternative allele were excluded from the analysis. Genome build: GRCz10  Supplementary files format and content: tab delimited file format,whole zebrafish embryo,To assess the effect of Adar KD and OE  uninjected wild type and embryos injected with 1 ng of adar MO or 50 pg of adar mRNA were kept until desired developmental stage.,Parental genomic DNA was extracted from adult fin clippings of an individual male and female zebrafish of wild type ABTL background. For the rest of the samples  20 pooled embryos from each time point were isolated for RNA extraction. Total RNA was extracted using TRIzol LS Thermo Fisher Scientific  USA and cleaned up on the Qiagen Rneasy Mini column Qiagen  USA. Quality control of extracted RNA was performed using the 2200 TapeStation system from Agilent Technologies USA. To avoid the bias caused by cytoplasmic polyadenylation during early embryonic stages Winata et al.  2018  total RNA was rRNA depleted using Ribo Zero Magnetic Gold Kit Human  Mouse  Rat; Epicenter.  For the 7 dpf samples  total RNA was subjected to mRNA enrichment using  NEBNext PolyA mRNA Magnetic Isolation Module E7490  NEB. genomic DNA library was constructed using Nextera XT Illumina  USA using standard protocol; cDNA synthesis was performed by SMARTer Stranded RNA seq kit Clontech Laboratories  USA as recommended by the manufacturer. For the 7 dpf samples  library was constructed using TruSeq Stranded Total RNA library preparation kit Illumina  USA.,Zebrafish embryos were maintained according to standard protocol Westerfield et al.  2000 and staged according to standard morphological criteria Kimmel et al.  1995.,strain:WT ABTL|tissue:whole embryo|developmental stage:16 cell,GSM5535043,GSM5535043: Offspring 16 cell; Danio rerio; RNA Seq,GSM5535043,,1,Parental genomic DNA was extracted from adult fin clippings of an individual male and female zebrafish of wild type ABTL background. For the rest of the samples  20 pooled embryos from each time point were isolated for RNA extraction. Total RNA was extracted using TRIzol LS Thermo Fisher Scientific  USA and cleaned up on the Qiagen Rneasy Mini column Qiagen  USA. Quality control of extracted RNA was performed using the 2200 TapeStation system from Agilent Technologies USA. To avoid the bias caused by cytoplasmic polyadenylation during early embryonic stages Winata et al.  2018  total RNA was rRNA depleted using Ribo Zero Magnetic Gold Kit Human  Mouse  Rat; Epicenter. genomic DNA library was constructed using Nextera XT Illumina  USA using standard protocol; cDNA synthesis was performed by SMARTer Stranded RNA seq kit Clontech Laboratories  USA as recommended by the manufacturer.,GEO Accession:GSM5535043,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP333957,,,4-16c_S1_L003_R1_001.fastq.gz 4-16c_S1_L003_R2_001.fastq.gz,fastq fastq,2171629340.0,14381704.0,GSM5535043 r3,0:75.51 1:75.49,A:576474933;C:528148462;G:515750925;T:550947852;N:307168,75,75,,,576474933,528148462,515750925,550947852,307168,SRX11898432,SRS9909614,SRA1283368,GEO,"Zebrafish Developmental Genomics, International Institute of Molecular and Cell Biology in Warsaw",2,0.94477,0.94707,0.05014,0.05001,0.76136,0.7643,0.47883,0.47948,76,74,B,B,biological fallback assumption,illumina,nextseq,full_length,rrna_depletion,ribozero,bulk,bulk,bulk,,Poland,2021-08-24,Cleavage,Embryo,Whole Organism,All anatomical structures
65771,SRR15600913,SRX11898432,SRS9909614,SRP333957,PRJNA757460,Adar mediated A to I editing is required for establishment of embryonic body axes in zebrafish,GSE182714,Other,Adar mediated A to I editing is required for establishment of embryonic body axes in zebrafish. To assess the effect of Adar KD and OE  uninjected wild type and embryos injected with 1 ng of adar MO or 50 pg of adar mRNA were kept until desired developmental stage: 128 cell or 50% epiboly. Two replicates of 20 pooled embryos from each time point were isolated for RNA extraction. For the analysis at 12 hpf  a separate batch of uninjected control  as well as Adar KD and OE samples were generated in three replicates. Overall design: Parental DNA was extracted from one individual male and female fishes from tail fin clipping  together with RNA from their offspring at 16 cell  3.5 hpf  and 5.3 hpf stages. For each time point  at least 20 embryos were pooled for RNA extraction. To assess the effect of Adar KD and OE  uninjected wild type and embryos injected with 1 ng of adar MO or 50 pg of adar mRNA were kept until desired developmental stage: 128 cell or 50% epiboly. Two replicates of 20 pooled embryos from each time point were isolated for RNA extraction. For the analysis at 12 hpf  a separate batch of uninjected control  as well as Adar KD and OE samples were generated in three replicates. Total RNA was extracted using TRIzol LS Thermo Fisher Scientific  USA and cleaned up on the Qiagen Rneasy Mini column Qiagen  USA. Quality control of extracted RNA was performed using the 2200 TapeStation system from Agilent Technologies USA. To avoid the bias caused by cytoplasmic polyadenylation during early embryonic stages  total RNA was rRNA depleted using Ribo Zero Magnetic Gold Kit Human  Mouse  Rat; Epicenter.  cDNA synthesis for Next Generation Sequencing NGS was performed by SMARTer Stranded RNA seq kit  Clontech Laboratories  USA as recommended by the manufacturer. Paired end sequencing 2 × 75 bp reads was performed with NextSeq 500 Illumina  USA.,,pubmed:36127363,,Offspring 16 cell,GSM5535043,,source name:whole zebrafish embryo|strain:WT ABTL|tissue:whole embryo|developmental stage:16 cell,Offspring 16 cell,Basecalling was performed by Illumina RTA 1.18.61. Files were translated into demultiplexed FASTQ files by Illumina bcl2fastq2 2.16.10. Low quality sequences and adapter content were trimmed with cutadapt v. 2.4. Reads were aligned to the zebrafish genome assembly GRCz10  using STAR v2.7.7a and samtools v1.11 Expression quantification was performed using HTSeq v0.11.2 Differential expression was performed using DESeq2 R v3.6.3 Putative RNA editing sites based on DNA  and RNA seq input were detected using REDiscover https://github.com/lpryszcz/REDiscover. Options  q 15  Q 20  were used  i.e. a minimal mapping quality of 15 and a minimal base call quality of 20 were required. Sites that were not homozygous between female and male samples were excluded from the analysis. Alternative alleles were only called when they were present in at least 20% of RNA reads. For simplicity  sites with more than one alternative allele were excluded from the analysis. Genome build: GRCz10  Supplementary files format and content: tab delimited file format,whole zebrafish embryo,To assess the effect of Adar KD and OE  uninjected wild type and embryos injected with 1 ng of adar MO or 50 pg of adar mRNA were kept until desired developmental stage.,Parental genomic DNA was extracted from adult fin clippings of an individual male and female zebrafish of wild type ABTL background. For the rest of the samples  20 pooled embryos from each time point were isolated for RNA extraction. Total RNA was extracted using TRIzol LS Thermo Fisher Scientific  USA and cleaned up on the Qiagen Rneasy Mini column Qiagen  USA. Quality control of extracted RNA was performed using the 2200 TapeStation system from Agilent Technologies USA. To avoid the bias caused by cytoplasmic polyadenylation during early embryonic stages Winata et al.  2018  total RNA was rRNA depleted using Ribo Zero Magnetic Gold Kit Human  Mouse  Rat; Epicenter.  For the 7 dpf samples  total RNA was subjected to mRNA enrichment using  NEBNext PolyA mRNA Magnetic Isolation Module E7490  NEB. genomic DNA library was constructed using Nextera XT Illumina  USA using standard protocol; cDNA synthesis was performed by SMARTer Stranded RNA seq kit Clontech Laboratories  USA as recommended by the manufacturer. For the 7 dpf samples  library was constructed using TruSeq Stranded Total RNA library preparation kit Illumina  USA.,Zebrafish embryos were maintained according to standard protocol Westerfield et al.  2000 and staged according to standard morphological criteria Kimmel et al.  1995.,strain:WT ABTL|tissue:whole embryo|developmental stage:16 cell,GSM5535043,GSM5535043: Offspring 16 cell; Danio rerio; RNA Seq,GSM5535043,,1,Parental genomic DNA was extracted from adult fin clippings of an individual male and female zebrafish of wild type ABTL background. For the rest of the samples  20 pooled embryos from each time point were isolated for RNA extraction. Total RNA was extracted using TRIzol LS Thermo Fisher Scientific  USA and cleaned up on the Qiagen Rneasy Mini column Qiagen  USA. Quality control of extracted RNA was performed using the 2200 TapeStation system from Agilent Technologies USA. To avoid the bias caused by cytoplasmic polyadenylation during early embryonic stages Winata et al.  2018  total RNA was rRNA depleted using Ribo Zero Magnetic Gold Kit Human  Mouse  Rat; Epicenter. genomic DNA library was constructed using Nextera XT Illumina  USA using standard protocol; cDNA synthesis was performed by SMARTer Stranded RNA seq kit Clontech Laboratories  USA as recommended by the manufacturer.,GEO Accession:GSM5535043,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP333957,,,4-16c_S1_L004_R1_001.fastq.gz 4-16c_S1_L004_R2_001.fastq.gz,fastq fastq,2194036618.0,14530138.0,GSM5535043 r4,0:75.50 1:75.49,A:583398157;C:533378280;G:520236253;T:556727184;N:296744,75,75,,,583398157,533378280,520236253,556727184,296744,SRX11898432,SRS9909614,SRA1283368,GEO,"Zebrafish Developmental Genomics, International Institute of Molecular and Cell Biology in Warsaw",2,0.94501,0.94754,0.05026,0.05061,0.75954,0.76347,0.48277,0.48052,76,76,B,B,biological fallback assumption,illumina,nextseq,full_length,rrna_depletion,ribozero,bulk,bulk,bulk,,Poland,2021-08-24,Cleavage,Embryo,Whole Organism,All anatomical structures
76552,SRR25071772,SRX20825800,SRS18104437,SRP446536,PRJNA989133,Translation of zinc finger domains induces ribosome collision and Znf598 dependent mRNA decay in zebrafish [RNA seq],GSE236143,Transcriptome Analysis,Quality control of translation is crucial for maintaining cellular and organismal homeostasis. Obstacles in translation elongation induce ribosome collision  which is monitored by multiple sensor mechanisms in eukaryotes. The E3 ubiquitin ligase Znf598 recognizes collided ribosomes  triggering ribosome associated quality control RQC to rescue stalled ribosomes and no go decay NGD to degrade stall prone mRNAs. However  the impact of RQC and NGD on maintaining the translational homeostasis of endogenous mRNAs has remained unclear. In this study  we investigated the endogenous substrate mRNAs of NGD during the maternal to zygotic transition MZT of zebrafish development. RNA Seq analysis of zebrafish znf598 mutant embryos revealed that Znf598 downregulates mRNAs encoding the C2H2 type zinc finger domain C2H2 ZF during the MZT. Reporter assays and disome profiling indicated that ribosomes stall and collide while translating tandem C2H2 ZFs  leading to mRNA degradation by Znf598. Our results suggest that NGD maintains the quality of the translatome by mitigating the risk of ribosome collision at the abundantly present C2H2 ZF sequences in the vertebrate genome. Overall design: RNA seq,parent bioproject:PRJNA989127,pubmed:39636823,,znf598 knockout  1 hpf  rep3,GSM7518813,,source name:Whole embryo|tissue:Whole embryo|genotype:znf598 knockout mutant|geo loc name:missing|collection date:missing,znf598 knockout  1 hpf  rep3,Basecalling with Illumina Casava 1.8 software Analyzed using Galaxy on public server three prime adapter trimming with Fastp Alignment to genome with STAR v2.7.8a with   outFilterMismatchNmax 1   outFilterMultimapNmax 1 options Read quantitation using featureCounts v3.36.0 Assembly: GRCz11 Supplementary files format and content: text files tab separated values contain two columns: 1. gene id; 2. read counts,Whole embryo,,Total RNA was extracted using TRI Reagent Molecular Research Center and treated with DNase I. Library preparation using Ribo Zero Gold rRNA Removal Kit followed by TruSeq Stranded Total RNA Library Prep Kit Illumina,Fertilized eggs were obtained by natural breeding and developed in system water at 28.5ºC.,tissue:Whole embryo|genotype:znf598 knockout mutant,GSM7518813,GSM7518813: znf598 knockout  1 hpf  rep3; Danio rerio; RNA Seq,GSM7518813 r1,GSM7518813,1,Total RNA was extracted using TRI Reagent Molecular Research Center and treated with DNase I. Library preparation using Ribo Zero Gold rRNA Removal Kit followed by TruSeq Stranded Total RNA Library Prep Kit Illumina,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP446536,,,MZ_1h-3.fastq.gz,fastq,1806663486.0,23939526.0,GSM7518813 r1,0:75.47,A:391048740;C:497050050;G:452237261;T:466117133;N:210302,75,,,,391048740,497050050,452237261,466117133,210302,SRX20825800,SRS18104437,SRA1664576,"Department of Frontier Life Sciences, Kyoto Sangyo University","Department of Frontier Life Sciences, Kyoto Sangyo University",1,0.91375,,0.08848,,0.76506,,0.60723,,76,,B,,usable mapping rate,illumina,nextseq,unknown,rrna_depletion,ribozero,bulk,bulk,bulk,,Japan,2023-06-29,Cleavage,Embryo,Whole Organism,All anatomical structures
76553,SRR25071773,SRX20825799,SRS18104434,SRP446536,PRJNA989133,Translation of zinc finger domains induces ribosome collision and Znf598 dependent mRNA decay in zebrafish [RNA seq],GSE236143,Transcriptome Analysis,Quality control of translation is crucial for maintaining cellular and organismal homeostasis. Obstacles in translation elongation induce ribosome collision  which is monitored by multiple sensor mechanisms in eukaryotes. The E3 ubiquitin ligase Znf598 recognizes collided ribosomes  triggering ribosome associated quality control RQC to rescue stalled ribosomes and no go decay NGD to degrade stall prone mRNAs. However  the impact of RQC and NGD on maintaining the translational homeostasis of endogenous mRNAs has remained unclear. In this study  we investigated the endogenous substrate mRNAs of NGD during the maternal to zygotic transition MZT of zebrafish development. RNA Seq analysis of zebrafish znf598 mutant embryos revealed that Znf598 downregulates mRNAs encoding the C2H2 type zinc finger domain C2H2 ZF during the MZT. Reporter assays and disome profiling indicated that ribosomes stall and collide while translating tandem C2H2 ZFs  leading to mRNA degradation by Znf598. Our results suggest that NGD maintains the quality of the translatome by mitigating the risk of ribosome collision at the abundantly present C2H2 ZF sequences in the vertebrate genome. Overall design: RNA seq,parent bioproject:PRJNA989127,pubmed:39636823,,znf598 knockout  1 hpf  rep2,GSM7518812,,source name:Whole embryo|tissue:Whole embryo|genotype:znf598 knockout mutant|geo loc name:missing|collection date:missing,znf598 knockout  1 hpf  rep2,Basecalling with Illumina Casava 1.8 software Analyzed using Galaxy on public server three prime adapter trimming with Fastp Alignment to genome with STAR v2.7.8a with   outFilterMismatchNmax 1   outFilterMultimapNmax 1 options Read quantitation using featureCounts v3.36.0 Assembly: GRCz11 Supplementary files format and content: text files tab separated values contain two columns: 1. gene id; 2. read counts,Whole embryo,,Total RNA was extracted using TRI Reagent Molecular Research Center and treated with DNase I. Library preparation using Ribo Zero Gold rRNA Removal Kit followed by TruSeq Stranded Total RNA Library Prep Kit Illumina,Fertilized eggs were obtained by natural breeding and developed in system water at 28.5ºC.,tissue:Whole embryo|genotype:znf598 knockout mutant,GSM7518812,GSM7518812: znf598 knockout  1 hpf  rep2; Danio rerio; RNA Seq,GSM7518812 r1,GSM7518812,1,Total RNA was extracted using TRI Reagent Molecular Research Center and treated with DNase I. Library preparation using Ribo Zero Gold rRNA Removal Kit followed by TruSeq Stranded Total RNA Library Prep Kit Illumina,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP446536,,,MZ_1h-2.fastq.gz,fastq,1786890054.0,23678222.0,GSM7518812 r1,0:75.47,A:400615587;C:476950804;G:436028227;T:473114322;N:181114,75,,,,400615587,476950804,436028227,473114322,181114,SRX20825799,SRS18104434,SRA1664576,"Department of Frontier Life Sciences, Kyoto Sangyo University","Department of Frontier Life Sciences, Kyoto Sangyo University",1,0.933,,0.07478,,0.75728,,0.5738,,76,,B,,usable mapping rate,illumina,nextseq,unknown,rrna_depletion,ribozero,bulk,bulk,bulk,,Japan,2023-06-29,Cleavage,Embryo,Whole Organism,All anatomical structures
76554,SRR25071774,SRX20825798,SRS18104440,SRP446536,PRJNA989133,Translation of zinc finger domains induces ribosome collision and Znf598 dependent mRNA decay in zebrafish [RNA seq],GSE236143,Transcriptome Analysis,Quality control of translation is crucial for maintaining cellular and organismal homeostasis. Obstacles in translation elongation induce ribosome collision  which is monitored by multiple sensor mechanisms in eukaryotes. The E3 ubiquitin ligase Znf598 recognizes collided ribosomes  triggering ribosome associated quality control RQC to rescue stalled ribosomes and no go decay NGD to degrade stall prone mRNAs. However  the impact of RQC and NGD on maintaining the translational homeostasis of endogenous mRNAs has remained unclear. In this study  we investigated the endogenous substrate mRNAs of NGD during the maternal to zygotic transition MZT of zebrafish development. RNA Seq analysis of zebrafish znf598 mutant embryos revealed that Znf598 downregulates mRNAs encoding the C2H2 type zinc finger domain C2H2 ZF during the MZT. Reporter assays and disome profiling indicated that ribosomes stall and collide while translating tandem C2H2 ZFs  leading to mRNA degradation by Znf598. Our results suggest that NGD maintains the quality of the translatome by mitigating the risk of ribosome collision at the abundantly present C2H2 ZF sequences in the vertebrate genome. Overall design: RNA seq,parent bioproject:PRJNA989127,pubmed:39636823,,znf598 knockout  1 hpf  rep1,GSM7518811,,source name:Whole embryo|tissue:Whole embryo|genotype:znf598 knockout mutant|geo loc name:missing|collection date:missing,znf598 knockout  1 hpf  rep1,Basecalling with Illumina Casava 1.8 software Analyzed using Galaxy on public server three prime adapter trimming with Fastp Alignment to genome with STAR v2.7.8a with   outFilterMismatchNmax 1   outFilterMultimapNmax 1 options Read quantitation using featureCounts v3.36.0 Assembly: GRCz11 Supplementary files format and content: text files tab separated values contain two columns: 1. gene id; 2. read counts,Whole embryo,,Total RNA was extracted using TRI Reagent Molecular Research Center and treated with DNase I. Library preparation using Ribo Zero Gold rRNA Removal Kit followed by TruSeq Stranded Total RNA Library Prep Kit Illumina,Fertilized eggs were obtained by natural breeding and developed in system water at 28.5ºC.,tissue:Whole embryo|genotype:znf598 knockout mutant,GSM7518811,GSM7518811: znf598 knockout  1 hpf  rep1; Danio rerio; RNA Seq,GSM7518811 r1,GSM7518811,1,Total RNA was extracted using TRI Reagent Molecular Research Center and treated with DNase I. Library preparation using Ribo Zero Gold rRNA Removal Kit followed by TruSeq Stranded Total RNA Library Prep Kit Illumina,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP446536,,,MZ_1h-1.fastq.gz,fastq,1832077965.0,24286583.0,GSM7518811 r1,0:75.44,A:408821004;C:490715443;G:452431465;T:479888766;N:221287,75,,,,408821004,490715443,452431465,479888766,221287,SRX20825798,SRS18104440,SRA1664576,"Department of Frontier Life Sciences, Kyoto Sangyo University","Department of Frontier Life Sciences, Kyoto Sangyo University",1,0.91274,,0.08093,,0.76045,,0.57415,,76,,B,,usable mapping rate,illumina,nextseq,unknown,rrna_depletion,ribozero,bulk,bulk,bulk,,Japan,2023-06-29,Cleavage,Embryo,Whole Organism,All anatomical structures
76558,SRR25071778,SRX20825794,SRS18104433,SRP446536,PRJNA989133,Translation of zinc finger domains induces ribosome collision and Znf598 dependent mRNA decay in zebrafish [RNA seq],GSE236143,Transcriptome Analysis,Quality control of translation is crucial for maintaining cellular and organismal homeostasis. Obstacles in translation elongation induce ribosome collision  which is monitored by multiple sensor mechanisms in eukaryotes. The E3 ubiquitin ligase Znf598 recognizes collided ribosomes  triggering ribosome associated quality control RQC to rescue stalled ribosomes and no go decay NGD to degrade stall prone mRNAs. However  the impact of RQC and NGD on maintaining the translational homeostasis of endogenous mRNAs has remained unclear. In this study  we investigated the endogenous substrate mRNAs of NGD during the maternal to zygotic transition MZT of zebrafish development. RNA Seq analysis of zebrafish znf598 mutant embryos revealed that Znf598 downregulates mRNAs encoding the C2H2 type zinc finger domain C2H2 ZF during the MZT. Reporter assays and disome profiling indicated that ribosomes stall and collide while translating tandem C2H2 ZFs  leading to mRNA degradation by Znf598. Our results suggest that NGD maintains the quality of the translatome by mitigating the risk of ribosome collision at the abundantly present C2H2 ZF sequences in the vertebrate genome. Overall design: RNA seq,parent bioproject:PRJNA989127,pubmed:39636823,,Wild type  1 hpf  rep3,GSM7518807,,source name:Whole embryo|tissue:Whole embryo|genotype:Wild type AB strain|geo loc name:missing|collection date:missing,Wild type  1 hpf  rep3,Basecalling with Illumina Casava 1.8 software Analyzed using Galaxy on public server three prime adapter trimming with Fastp Alignment to genome with STAR v2.7.8a with   outFilterMismatchNmax 1   outFilterMultimapNmax 1 options Read quantitation using featureCounts v3.36.0 Assembly: GRCz11 Supplementary files format and content: text files tab separated values contain two columns: 1. gene id; 2. read counts,Whole embryo,,Total RNA was extracted using TRI Reagent Molecular Research Center and treated with DNase I. Library preparation using Ribo Zero Gold rRNA Removal Kit followed by TruSeq Stranded Total RNA Library Prep Kit Illumina,Fertilized eggs were obtained by natural breeding and developed in system water at 28.5ºC.,tissue:Whole embryo|genotype:Wild type AB strain,GSM7518807,GSM7518807: Wild type  1 hpf  rep3; Danio rerio; RNA Seq,GSM7518807 r1,GSM7518807,1,Total RNA was extracted using TRI Reagent Molecular Research Center and treated with DNase I. Library preparation using Ribo Zero Gold rRNA Removal Kit followed by TruSeq Stranded Total RNA Library Prep Kit Illumina,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP446536,,,AB_1h-3.fastq.gz,fastq,1980374063.0,26249180.0,GSM7518807 r1,0:75.45,A:419770511;C:554999241;G:505986927;T:499301456;N:315928,75,,,,419770511,554999241,505986927,499301456,315928,SRX20825794,SRS18104433,SRA1664576,"Department of Frontier Life Sciences, Kyoto Sangyo University","Department of Frontier Life Sciences, Kyoto Sangyo University",1,0.91737,,0.09547,,0.77404,,0.63493,,75,,B,,usable mapping rate,illumina,nextseq,unknown,rrna_depletion,ribozero,bulk,bulk,bulk,,Japan,2023-06-29,Cleavage,Embryo,Whole Organism,All anatomical structures
76559,SRR25071779,SRX20825793,SRS18104432,SRP446536,PRJNA989133,Translation of zinc finger domains induces ribosome collision and Znf598 dependent mRNA decay in zebrafish [RNA seq],GSE236143,Transcriptome Analysis,Quality control of translation is crucial for maintaining cellular and organismal homeostasis. Obstacles in translation elongation induce ribosome collision  which is monitored by multiple sensor mechanisms in eukaryotes. The E3 ubiquitin ligase Znf598 recognizes collided ribosomes  triggering ribosome associated quality control RQC to rescue stalled ribosomes and no go decay NGD to degrade stall prone mRNAs. However  the impact of RQC and NGD on maintaining the translational homeostasis of endogenous mRNAs has remained unclear. In this study  we investigated the endogenous substrate mRNAs of NGD during the maternal to zygotic transition MZT of zebrafish development. RNA Seq analysis of zebrafish znf598 mutant embryos revealed that Znf598 downregulates mRNAs encoding the C2H2 type zinc finger domain C2H2 ZF during the MZT. Reporter assays and disome profiling indicated that ribosomes stall and collide while translating tandem C2H2 ZFs  leading to mRNA degradation by Znf598. Our results suggest that NGD maintains the quality of the translatome by mitigating the risk of ribosome collision at the abundantly present C2H2 ZF sequences in the vertebrate genome. Overall design: RNA seq,parent bioproject:PRJNA989127,pubmed:39636823,,Wild type  1 hpf  rep2,GSM7518806,,source name:Whole embryo|tissue:Whole embryo|genotype:Wild type AB strain|geo loc name:missing|collection date:missing,Wild type  1 hpf  rep2,Basecalling with Illumina Casava 1.8 software Analyzed using Galaxy on public server three prime adapter trimming with Fastp Alignment to genome with STAR v2.7.8a with   outFilterMismatchNmax 1   outFilterMultimapNmax 1 options Read quantitation using featureCounts v3.36.0 Assembly: GRCz11 Supplementary files format and content: text files tab separated values contain two columns: 1. gene id; 2. read counts,Whole embryo,,Total RNA was extracted using TRI Reagent Molecular Research Center and treated with DNase I. Library preparation using Ribo Zero Gold rRNA Removal Kit followed by TruSeq Stranded Total RNA Library Prep Kit Illumina,Fertilized eggs were obtained by natural breeding and developed in system water at 28.5ºC.,tissue:Whole embryo|genotype:Wild type AB strain,GSM7518806,GSM7518806: Wild type  1 hpf  rep2; Danio rerio; RNA Seq,GSM7518806 r1,GSM7518806,1,Total RNA was extracted using TRI Reagent Molecular Research Center and treated with DNase I. Library preparation using Ribo Zero Gold rRNA Removal Kit followed by TruSeq Stranded Total RNA Library Prep Kit Illumina,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP446536,,,AB_1h-2.fastq.gz,fastq,1762189348.0,23360365.0,GSM7518806 r1,0:75.44,A:396710182;C:465399709;G:431064892;T:468813722;N:200843,75,,,,396710182,465399709,431064892,468813722,200843,SRX20825793,SRS18104432,SRA1664576,"Department of Frontier Life Sciences, Kyoto Sangyo University","Department of Frontier Life Sciences, Kyoto Sangyo University",1,0.90979,,0.06495,,0.75487,,0.47317,,76,,B,,usable mapping rate,illumina,nextseq,unknown,rrna_depletion,ribozero,bulk,bulk,bulk,,Japan,2023-06-29,Cleavage,Embryo,Whole Organism,All anatomical structures
76560,SRR25071780,SRX20825792,SRS18104431,SRP446536,PRJNA989133,Translation of zinc finger domains induces ribosome collision and Znf598 dependent mRNA decay in zebrafish [RNA seq],GSE236143,Transcriptome Analysis,Quality control of translation is crucial for maintaining cellular and organismal homeostasis. Obstacles in translation elongation induce ribosome collision  which is monitored by multiple sensor mechanisms in eukaryotes. The E3 ubiquitin ligase Znf598 recognizes collided ribosomes  triggering ribosome associated quality control RQC to rescue stalled ribosomes and no go decay NGD to degrade stall prone mRNAs. However  the impact of RQC and NGD on maintaining the translational homeostasis of endogenous mRNAs has remained unclear. In this study  we investigated the endogenous substrate mRNAs of NGD during the maternal to zygotic transition MZT of zebrafish development. RNA Seq analysis of zebrafish znf598 mutant embryos revealed that Znf598 downregulates mRNAs encoding the C2H2 type zinc finger domain C2H2 ZF during the MZT. Reporter assays and disome profiling indicated that ribosomes stall and collide while translating tandem C2H2 ZFs  leading to mRNA degradation by Znf598. Our results suggest that NGD maintains the quality of the translatome by mitigating the risk of ribosome collision at the abundantly present C2H2 ZF sequences in the vertebrate genome. Overall design: RNA seq,parent bioproject:PRJNA989127,pubmed:39636823,,Wild type  1 hpf  rep1,GSM7518805,,source name:Whole embryo|tissue:Whole embryo|genotype:Wild type AB strain|geo loc name:missing|collection date:missing,Wild type  1 hpf  rep1,Basecalling with Illumina Casava 1.8 software Analyzed using Galaxy on public server three prime adapter trimming with Fastp Alignment to genome with STAR v2.7.8a with   outFilterMismatchNmax 1   outFilterMultimapNmax 1 options Read quantitation using featureCounts v3.36.0 Assembly: GRCz11 Supplementary files format and content: text files tab separated values contain two columns: 1. gene id; 2. read counts,Whole embryo,,Total RNA was extracted using TRI Reagent Molecular Research Center and treated with DNase I. Library preparation using Ribo Zero Gold rRNA Removal Kit followed by TruSeq Stranded Total RNA Library Prep Kit Illumina,Fertilized eggs were obtained by natural breeding and developed in system water at 28.5ºC.,tissue:Whole embryo|genotype:Wild type AB strain,GSM7518805,GSM7518805: Wild type  1 hpf  rep1; Danio rerio; RNA Seq,GSM7518805 r1,GSM7518805,1,Total RNA was extracted using TRI Reagent Molecular Research Center and treated with DNase I. Library preparation using Ribo Zero Gold rRNA Removal Kit followed by TruSeq Stranded Total RNA Library Prep Kit Illumina,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP446536,,,AB_1h-1.fastq.gz,fastq,1692730103.0,22429081.0,GSM7518805 r1,0:75.47,A:387190897;C:441464631;G:408597629;T:455327744;N:149202,75,,,,387190897,441464631,408597629,455327744,149202,SRX20825792,SRS18104431,SRA1664576,"Department of Frontier Life Sciences, Kyoto Sangyo University","Department of Frontier Life Sciences, Kyoto Sangyo University",1,0.91584,,0.06124,,0.75041,,0.54867,,76,,B,,usable mapping rate,illumina,nextseq,unknown,rrna_depletion,ribozero,bulk,bulk,bulk,,Japan,2023-06-29,Cleavage,Embryo,Whole Organism,All anatomical structures