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
11130,ERR9979395,ERX9520370,ERS12499848,ERP139765,PRJEB54901,Single cell RNA sequencing of germ free zebrafish embryos,E-MTAB-11984,Transcriptome Analysis,The present study was conducted in the frame of the EU funded Graphene Flagship project. We previously evaluated the impact of graphene oxide GO on the gut microbiome in adult zebrafish by performing 16S rRNA gene sequencing in wild type versus AhR deficient zebrafish.  Here  we performed single cell RNA sequencing 10x Genomics on whole dissociated germ free GF zebrafish embryos exposed at 5 dpf to GO plus the microbial metabolite butyrate to gain insight into the impact on specific cell populations in GF zebrafish.,ENA FIRST PUBLIC:2022 07 22|ENA LAST UPDATE:2022 07 22,,Protocols: The generation of germ free zebrafish wild type AB followed previously established protocols [1]. In brief  2 hpf embryos were transferred to petri dishes with sterile E3 medium  supplemented with ampicillin 100 μg/mL  kanamycin 5 μg/mL and amphotericin B 250 ng/mL and incubated at 28°C. At 50% epiboly up to shield stage 6 hpf  the embryos were surface disinfected with 0.1% of polyvinylpyrroidone iodine PVP I for exactly 2 min  followed by 0.003% sterile bleach immersion for 18 min. The embryos were then rinsed with sterile E3 medium  transferred to flasks and incubated at 28°C. The viability was monitored  and sterile medium was refreshed daily. At day 4  the hatched embryos were used for the sterility validation. A day 5  germ free zebrafish were exposed to the combination of GO 30 µg/mL and butyrate 2.5 mM for 24 h. GO and BA were pre incubated for 1 h prior to the exposure. Twenty larvae were used as one replicate  four replicates  i.e. eighty larvae in total  were used for each condition. post the exposure  zebrafish larvae were dissociated for single cell suspension following the published protocol [2]. Briefly  zebrafish larvae were euthanized with 0.01% of tricaine for 5 min  collected in 1.5 mL tube  and washed with PBS for three times. The dissociation was initiated by adding 500 μL of pre warmed enzyme mix containing 460 μL of 0.25% trypsin EDTA Gibco and 40 μL of collagenase Sigma Aldrich at the concentration of 100 mg/mL  followed by mechanical dissociation using P1000 and then P200 pipette tips in heat block at 30 °C until the tissue was no longer visible about 10 min. The dissociation was then stopped by adding 800 μL DMEM Corning Cat# 10 013 CV with 10% FBS Fisher Scientific. The cell pellets were collected by centrifuging at 1000 rpm for 5 min at RT  followed by washing with PBS. The cells were next resuspended in 0.5 mL DMEM with 10% FBS. Four replicates from each condition were pooled together at this step and filtered through 40 μm nylon mesh  with an additional washing using DMEM with 10% FBS. The cell suspension was then stained with a fluorescent DNA dye DRAQ7 to exclude non viable cells Invitrogen Cat# D15106 at the dose of 3 μM for 10 min at room temperature before the fluorescence activated cell sorting BD FACSAria III  BD Biosciences  NJ  USA. The sorting was performed using a 100 microns nozzle with the flow rate of 2 and temperature control at 4 °C and gated based on forward scatter and DRAQ7. The DRAQ7 negative cells of each sample were FACS sorted into the tubes containing DMEM with 10% FBS and placed on ice immediately post the sorting. The cells were then proceeded with the single cell RNA sequencing analysis. 1. Pham LN  Kanther M  Semova I & Rawls JF. Methods for generating and colonizing gnotobiotic zebrafish. Nat. Protoc. 3  1862 1875 2008. 2. Bresciani E  Broadbridge E  Liu PP An efficient dissociation protocol for generation of single cell suspension from zebrafish embryos and larvae  MethodsX. 5  1287 1290 2018. Single cell RNA sequencing scRNA seq was performed by Eukaryotic Single Cell Genomics Facility at SciLifeLab  Stockholm. The single cells collected from FACS sorting were loaded on a 10x GemCode Single Cell Instrument 10x Genomics  Pleasanton  USA to generate single cell gel beads in emulsion GEMs using the Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 10x Genomics following the manufacture's protocol. Briefly  GEMs were generated by combining barcoded Single Cell three prime v3.1 Gel Beads  a Master Mix containing cells  and Partitioning Oil onto Chromium Next GEM Chip G. Following GEMs generation  the Gel Bead was dissolved  primers containing an Illumina TruSeq Read 1read 1 sequencing primer  16 nt 10x Barcode  12 nt unique molecular identifier UMI and 30 nt polydT sequence were released  and the co partitioned cells were lysed. The nucleic acid library construction was performed using the Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 10x Genomics  16 rxns PN 1000268 following the manufacture's protocol. post GEMs generation  primers were mixed with the cell lysate and a Master Mix containing reverse transcription RT reagents to produce barcoded  full length cDNA from polyadenylated mRNA. Silane magnetic beads were used to purify the first strand cDNA from the post GEM RT reaction mixture  which included leftover biochemical reagents and primers. Barcoded  full length cDNA was amplified via PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size. P5  P7  i7 and i5 sample indexes  and TruSeq Read 2 read 2 primer sequence were added via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries containing the P5 and P7 primers used in Illumina amplification were prepared for an estimated 5000 nuclei per sample.,Sample 2 WT GO+BA,SAMEA110401656,"Institute of Environmental Medicine, Karolinska Institutet",ENA FIRST PUBLIC:2022 07 22|ENA LAST UPDATE:2022 07 22|External Id:SAMEA110401656|INSDC center alias:Institute of Environmental Medicine  Karolinska Institutet|INSDC center name:Institute of Environmental Medicine  Karolinska Institutet|INSDC first public:2022 07 22T16:26:50Z|INSDC last update:2022 07 22T16:26:50Z|INSDC status:public|Submitter Id:E MTAB 11984:Sample 2 WT GO+BA|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|genotype:wild type genotype|individual:pool of 80 individuals|isolate:not applicable|organism part:whole organism|sample name:E MTAB 11984:Sample 2 WT GO+BA|sex:not available|stimulus:graphene oxide 30 ug/mL and butyrate 2.5 mM|strain:AB,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; Single cell RNA sequencing of germ free zebrafish embryos,E MTAB 11984:Sample 2 WT GO+BA p,Sample 2 WT GO+BA p,Single cell RNA sequencing of germ free zebrafish embryos,The generation of germ free zebrafish wild type AB followed previously established protocols [1]. In brief  2 hpf embryos were transferred to petri dishes with sterile E3 medium  supplemented with ampicillin 100 μg/mL  kanamycin 5 μg/mL and amphotericin B 250 ng/mL and incubated at 28°C. At 50% epiboly up to shield stage 6 hpf  the embryos were surface disinfected with 0.1% of polyvinylpyrroidone iodine PVP I for exactly 2 min  followed by 0.003% sterile bleach immersion for 18 min. The embryos were then rinsed with sterile E3 medium  transferred to flasks and incubated at 28°C. The viability was monitored  and sterile medium was refreshed daily. At day 4  the hatched embryos were used for the sterility validation. A day 5  germ free zebrafish were exposed to the combination of GO 30 µg/mL and butyrate 2.5 mM for 24 h. GO and BA were pre incubated for 1 h prior to the exposure. Twenty larvae were used as one replicate  four replicates  i.e. eighty larvae in total  were used for each condition. post the exposure  zebrafish larvae were dissociated for single cell suspension following the published protocol [2]. Briefly  zebrafish larvae were euthanized with 0.01% of tricaine for 5 min  collected in 1.5 mL tube  and washed with PBS for three times. The dissociation was initiated by adding 500 μL of pre warmed enzyme mix containing 460 μL of 0.25% trypsin EDTA Gibco and 40 μL of collagenase Sigma Aldrich at the concentration of 100 mg/mL  followed by mechanical dissociation using P1000 and then P200 pipette tips in heat block at 30 °C until the tissue was no longer visible about 10 min. The dissociation was then stopped by adding 800 μL DMEM Corning Cat# 10 013 CV with 10% FBS Fisher Scientific. The cell pellets were collected by centrifuging at 1000 rpm for 5 min at RT  followed by washing with PBS. The cells were next resuspended in 0.5 mL DMEM with 10% FBS. Four replicates from each condition were pooled together at this step and filtered through 40 μm nylon mesh  with an additional washing using DMEM with 10% FBS. The cell suspension was then stained with a fluorescent DNA dye DRAQ7 to exclude non viable cells Invitrogen Cat# D15106 at the dose of 3 μM for 10 min at room temperature before the fluorescence activated cell sorting BD FACSAria III  BD Biosciences  NJ  USA. The sorting was performed using a 100 microns nozzle with the flow rate of 2 and temperature control at 4 °C and gated based on forward scatter and DRAQ7. The DRAQ7 negative cells of each sample were FACS sorted into the tubes containing DMEM with 10% FBS and placed on ice immediately post the sorting. The cells were then proceeded with the single cell RNA sequencing analysis. 1. Pham LN  Kanther M  Semova I & Rawls JF. Methods for generating and colonizing gnotobiotic zebrafish. Nat. Protoc. 3  1862 1875 2008. 2. Bresciani E  Broadbridge E  Liu PP An efficient dissociation protocol for generation of single cell suspension from zebrafish embryos and larvae  MethodsX. 5  1287 1290 2018. Single cell RNA sequencing scRNA seq was performed by Eukaryotic Single Cell Genomics Facility at SciLifeLab  Stockholm. The single cells collected from FACS sorting were loaded on a 10x GemCode Single Cell Instrument 10x Genomics  Pleasanton  USA to generate single cell gel beads in emulsion GEMs using the Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 10x Genomics following the manufacture's protocol.  Briefly  GEMs were generated by combining barcoded Single Cell three prime v3.1 Gel Beads  a Master Mix containing cells  and Partitioning Oil onto Chromium Next GEM Chip G. Following GEMs generation  the Gel Bead was dissolved  primers containing an Illumina TruSeq Read 1read 1 sequencing primer  16 nt 10x Barcode  12 nt unique molecular identifier UMI and 30 nt polydT sequence were released  and the co partitioned cells were lysed.  The nucleic acid library construction was performed using the Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 10x Genomics  16 rxns PN 1000268 following the manufacture's protocol. post GEMs generation  primers were mixed with the cell lysate and a Master Mix containing reverse transcription RT reagents to produce barcoded  full length cDNA from polyadenylated mRNA. Silane magnetic beads were used to purify the first strand cDNA from the post GEM RT reaction mixture  which included leftover biochemical reagents and primers. Barcoded  full length cDNA was amplified via PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size. P5  P7  i7 and i5 sample indexes  and TruSeq Read 2 read 2 primer sequence were added via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries containing the P5 and P7 primers used in Illumina amplification were prepared for an estimated 5000 nuclei per sample.,Experimental Factor: stimulus:graphene oxide 30 ug/mL and butyrate 2.5 mM,AMPLICON,TRANSCRIPTOMIC SINGLE CELL,size fractionation,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP139765,Illumina NovaSeq 6000 paired end sequencing; Single cell RNA sequencing of germ free zebrafish embryos,ENA FIRST PUBLIC:2022 07 22|ENA LAST UPDATE:2022 07 22,P22202_7002_S2_L002_R1_001.fastq.gz P22202_7002_S2_L002_R2_001.fastq.gz,fastq fastq,18144406998.0,153766161.0,E MTAB 11984:P22202 7002 S2 L002,0:28 1:90,A:5277424121;C:3880928155;G:4118706097;T:4866649878;N:698747,28,90,,,5277424121,3880928155,4118706097,4866649878,698747,ERX9520370,ERS12499848,ERA16483151,"Institute of Environmental Medicine, Karolinska Institutet|European Nucleotide Archive","Institute of Environmental Medicine, Karolinska Institutet|European Nucleotide Archive",2,0.0109,0.90145,0.0053,0.21373,0.98746,0.79423,0.41198,0.54447,28,90,T,B,sc-like readlen,illumina,novaseq_era,full_length,size_fractionation,trueseq,sc,single_cell_droplet,10x,,Sweden,2022-07-22,Multi-stage,Embryo,Whole Organism,All anatomical structures
11131,ERR9979394,ERX9520370,ERS12499848,ERP139765,PRJEB54901,Single cell RNA sequencing of germ free zebrafish embryos,E-MTAB-11984,Transcriptome Analysis,The present study was conducted in the frame of the EU funded Graphene Flagship project. We previously evaluated the impact of graphene oxide GO on the gut microbiome in adult zebrafish by performing 16S rRNA gene sequencing in wild type versus AhR deficient zebrafish.  Here  we performed single cell RNA sequencing 10x Genomics on whole dissociated germ free GF zebrafish embryos exposed at 5 dpf to GO plus the microbial metabolite butyrate to gain insight into the impact on specific cell populations in GF zebrafish.,ENA FIRST PUBLIC:2022 07 22|ENA LAST UPDATE:2022 07 22,,Protocols: The generation of germ free zebrafish wild type AB followed previously established protocols [1]. In brief  2 hpf embryos were transferred to petri dishes with sterile E3 medium  supplemented with ampicillin 100 μg/mL  kanamycin 5 μg/mL and amphotericin B 250 ng/mL and incubated at 28°C. At 50% epiboly up to shield stage 6 hpf  the embryos were surface disinfected with 0.1% of polyvinylpyrroidone iodine PVP I for exactly 2 min  followed by 0.003% sterile bleach immersion for 18 min. The embryos were then rinsed with sterile E3 medium  transferred to flasks and incubated at 28°C. The viability was monitored  and sterile medium was refreshed daily. At day 4  the hatched embryos were used for the sterility validation. A day 5  germ free zebrafish were exposed to the combination of GO 30 µg/mL and butyrate 2.5 mM for 24 h. GO and BA were pre incubated for 1 h prior to the exposure. Twenty larvae were used as one replicate  four replicates  i.e. eighty larvae in total  were used for each condition. post the exposure  zebrafish larvae were dissociated for single cell suspension following the published protocol [2]. Briefly  zebrafish larvae were euthanized with 0.01% of tricaine for 5 min  collected in 1.5 mL tube  and washed with PBS for three times. The dissociation was initiated by adding 500 μL of pre warmed enzyme mix containing 460 μL of 0.25% trypsin EDTA Gibco and 40 μL of collagenase Sigma Aldrich at the concentration of 100 mg/mL  followed by mechanical dissociation using P1000 and then P200 pipette tips in heat block at 30 °C until the tissue was no longer visible about 10 min. The dissociation was then stopped by adding 800 μL DMEM Corning Cat# 10 013 CV with 10% FBS Fisher Scientific. The cell pellets were collected by centrifuging at 1000 rpm for 5 min at RT  followed by washing with PBS. The cells were next resuspended in 0.5 mL DMEM with 10% FBS. Four replicates from each condition were pooled together at this step and filtered through 40 μm nylon mesh  with an additional washing using DMEM with 10% FBS. The cell suspension was then stained with a fluorescent DNA dye DRAQ7 to exclude non viable cells Invitrogen Cat# D15106 at the dose of 3 μM for 10 min at room temperature before the fluorescence activated cell sorting BD FACSAria III  BD Biosciences  NJ  USA. The sorting was performed using a 100 microns nozzle with the flow rate of 2 and temperature control at 4 °C and gated based on forward scatter and DRAQ7. The DRAQ7 negative cells of each sample were FACS sorted into the tubes containing DMEM with 10% FBS and placed on ice immediately post the sorting. The cells were then proceeded with the single cell RNA sequencing analysis. 1. Pham LN  Kanther M  Semova I & Rawls JF. Methods for generating and colonizing gnotobiotic zebrafish. Nat. Protoc. 3  1862 1875 2008. 2. Bresciani E  Broadbridge E  Liu PP An efficient dissociation protocol for generation of single cell suspension from zebrafish embryos and larvae  MethodsX. 5  1287 1290 2018. Single cell RNA sequencing scRNA seq was performed by Eukaryotic Single Cell Genomics Facility at SciLifeLab  Stockholm. The single cells collected from FACS sorting were loaded on a 10x GemCode Single Cell Instrument 10x Genomics  Pleasanton  USA to generate single cell gel beads in emulsion GEMs using the Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 10x Genomics following the manufacture's protocol. Briefly  GEMs were generated by combining barcoded Single Cell three prime v3.1 Gel Beads  a Master Mix containing cells  and Partitioning Oil onto Chromium Next GEM Chip G. Following GEMs generation  the Gel Bead was dissolved  primers containing an Illumina TruSeq Read 1read 1 sequencing primer  16 nt 10x Barcode  12 nt unique molecular identifier UMI and 30 nt polydT sequence were released  and the co partitioned cells were lysed. The nucleic acid library construction was performed using the Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 10x Genomics  16 rxns PN 1000268 following the manufacture's protocol. post GEMs generation  primers were mixed with the cell lysate and a Master Mix containing reverse transcription RT reagents to produce barcoded  full length cDNA from polyadenylated mRNA. Silane magnetic beads were used to purify the first strand cDNA from the post GEM RT reaction mixture  which included leftover biochemical reagents and primers. Barcoded  full length cDNA was amplified via PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size. P5  P7  i7 and i5 sample indexes  and TruSeq Read 2 read 2 primer sequence were added via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries containing the P5 and P7 primers used in Illumina amplification were prepared for an estimated 5000 nuclei per sample.,Sample 2 WT GO+BA,SAMEA110401656,"Institute of Environmental Medicine, Karolinska Institutet",ENA FIRST PUBLIC:2022 07 22|ENA LAST UPDATE:2022 07 22|External Id:SAMEA110401656|INSDC center alias:Institute of Environmental Medicine  Karolinska Institutet|INSDC center name:Institute of Environmental Medicine  Karolinska Institutet|INSDC first public:2022 07 22T16:26:50Z|INSDC last update:2022 07 22T16:26:50Z|INSDC status:public|Submitter Id:E MTAB 11984:Sample 2 WT GO+BA|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|genotype:wild type genotype|individual:pool of 80 individuals|isolate:not applicable|organism part:whole organism|sample name:E MTAB 11984:Sample 2 WT GO+BA|sex:not available|stimulus:graphene oxide 30 ug/mL and butyrate 2.5 mM|strain:AB,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; Single cell RNA sequencing of germ free zebrafish embryos,E MTAB 11984:Sample 2 WT GO+BA p,Sample 2 WT GO+BA p,Single cell RNA sequencing of germ free zebrafish embryos,The generation of germ free zebrafish wild type AB followed previously established protocols [1]. In brief  2 hpf embryos were transferred to petri dishes with sterile E3 medium  supplemented with ampicillin 100 μg/mL  kanamycin 5 μg/mL and amphotericin B 250 ng/mL and incubated at 28°C. At 50% epiboly up to shield stage 6 hpf  the embryos were surface disinfected with 0.1% of polyvinylpyrroidone iodine PVP I for exactly 2 min  followed by 0.003% sterile bleach immersion for 18 min. The embryos were then rinsed with sterile E3 medium  transferred to flasks and incubated at 28°C. The viability was monitored  and sterile medium was refreshed daily. At day 4  the hatched embryos were used for the sterility validation. A day 5  germ free zebrafish were exposed to the combination of GO 30 µg/mL and butyrate 2.5 mM for 24 h. GO and BA were pre incubated for 1 h prior to the exposure. Twenty larvae were used as one replicate  four replicates  i.e. eighty larvae in total  were used for each condition. post the exposure  zebrafish larvae were dissociated for single cell suspension following the published protocol [2]. Briefly  zebrafish larvae were euthanized with 0.01% of tricaine for 5 min  collected in 1.5 mL tube  and washed with PBS for three times. The dissociation was initiated by adding 500 μL of pre warmed enzyme mix containing 460 μL of 0.25% trypsin EDTA Gibco and 40 μL of collagenase Sigma Aldrich at the concentration of 100 mg/mL  followed by mechanical dissociation using P1000 and then P200 pipette tips in heat block at 30 °C until the tissue was no longer visible about 10 min. The dissociation was then stopped by adding 800 μL DMEM Corning Cat# 10 013 CV with 10% FBS Fisher Scientific. The cell pellets were collected by centrifuging at 1000 rpm for 5 min at RT  followed by washing with PBS. The cells were next resuspended in 0.5 mL DMEM with 10% FBS. Four replicates from each condition were pooled together at this step and filtered through 40 μm nylon mesh  with an additional washing using DMEM with 10% FBS. The cell suspension was then stained with a fluorescent DNA dye DRAQ7 to exclude non viable cells Invitrogen Cat# D15106 at the dose of 3 μM for 10 min at room temperature before the fluorescence activated cell sorting BD FACSAria III  BD Biosciences  NJ  USA. The sorting was performed using a 100 microns nozzle with the flow rate of 2 and temperature control at 4 °C and gated based on forward scatter and DRAQ7. The DRAQ7 negative cells of each sample were FACS sorted into the tubes containing DMEM with 10% FBS and placed on ice immediately post the sorting. The cells were then proceeded with the single cell RNA sequencing analysis. 1. Pham LN  Kanther M  Semova I & Rawls JF. Methods for generating and colonizing gnotobiotic zebrafish. Nat. Protoc. 3  1862 1875 2008. 2. Bresciani E  Broadbridge E  Liu PP An efficient dissociation protocol for generation of single cell suspension from zebrafish embryos and larvae  MethodsX. 5  1287 1290 2018. Single cell RNA sequencing scRNA seq was performed by Eukaryotic Single Cell Genomics Facility at SciLifeLab  Stockholm. The single cells collected from FACS sorting were loaded on a 10x GemCode Single Cell Instrument 10x Genomics  Pleasanton  USA to generate single cell gel beads in emulsion GEMs using the Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 10x Genomics following the manufacture's protocol.  Briefly  GEMs were generated by combining barcoded Single Cell three prime v3.1 Gel Beads  a Master Mix containing cells  and Partitioning Oil onto Chromium Next GEM Chip G. Following GEMs generation  the Gel Bead was dissolved  primers containing an Illumina TruSeq Read 1read 1 sequencing primer  16 nt 10x Barcode  12 nt unique molecular identifier UMI and 30 nt polydT sequence were released  and the co partitioned cells were lysed.  The nucleic acid library construction was performed using the Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 10x Genomics  16 rxns PN 1000268 following the manufacture's protocol. post GEMs generation  primers were mixed with the cell lysate and a Master Mix containing reverse transcription RT reagents to produce barcoded  full length cDNA from polyadenylated mRNA. Silane magnetic beads were used to purify the first strand cDNA from the post GEM RT reaction mixture  which included leftover biochemical reagents and primers. Barcoded  full length cDNA was amplified via PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size. P5  P7  i7 and i5 sample indexes  and TruSeq Read 2 read 2 primer sequence were added via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries containing the P5 and P7 primers used in Illumina amplification were prepared for an estimated 5000 nuclei per sample.,Experimental Factor: stimulus:graphene oxide 30 ug/mL and butyrate 2.5 mM,AMPLICON,TRANSCRIPTOMIC SINGLE CELL,size fractionation,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP139765,Illumina NovaSeq 6000 paired end sequencing; Single cell RNA sequencing of germ free zebrafish embryos,ENA FIRST PUBLIC:2022 07 22|ENA LAST UPDATE:2022 07 22,P22202_7002_S2_L001_R1_001.fastq.gz P22202_7002_S2_L001_R2_001.fastq.gz,fastq fastq,18458951574.0,156431793.0,E MTAB 11984:P22202 7002 S2 L001,0:28 1:90,A:5372920926;C:3946687814;G:4185647697;T:4953205454;N:489683,28,90,,,5372920926,3946687814,4185647697,4953205454,489683,ERX9520370,ERS12499848,ERA16483151,"Institute of Environmental Medicine, Karolinska Institutet|European Nucleotide Archive","Institute of Environmental Medicine, Karolinska Institutet|European Nucleotide Archive",2,0.01037,0.90168,0.0048,0.21246,0.98752,0.79297,0.42601,0.54996,28,90,T,B,sc-like readlen,illumina,novaseq_era,full_length,size_fractionation,trueseq,sc,single_cell_droplet,10x,,Sweden,2022-07-22,Multi-stage,Embryo,Whole Organism,All anatomical structures
11132,ERR9979392,ERX9520369,ERS12499847,ERP139765,PRJEB54901,Single cell RNA sequencing of germ free zebrafish embryos,E-MTAB-11984,Transcriptome Analysis,The present study was conducted in the frame of the EU funded Graphene Flagship project. We previously evaluated the impact of graphene oxide GO on the gut microbiome in adult zebrafish by performing 16S rRNA gene sequencing in wild type versus AhR deficient zebrafish.  Here  we performed single cell RNA sequencing 10x Genomics on whole dissociated germ free GF zebrafish embryos exposed at 5 dpf to GO plus the microbial metabolite butyrate to gain insight into the impact on specific cell populations in GF zebrafish.,ENA FIRST PUBLIC:2022 07 22|ENA LAST UPDATE:2022 07 22,,Protocols: The generation of germ free zebrafish wild type AB followed previously established protocols [1]. In brief  2 hpf embryos were transferred to petri dishes with sterile E3 medium  supplemented with ampicillin 100 μg/mL  kanamycin 5 μg/mL and amphotericin B 250 ng/mL and incubated at 28°C. At 50% epiboly up to shield stage 6 hpf  the embryos were surface disinfected with 0.1% of polyvinylpyrroidone iodine PVP I for exactly 2 min  followed by 0.003% sterile bleach immersion for 18 min. The embryos were then rinsed with sterile E3 medium  transferred to flasks and incubated at 28°C. The viability was monitored  and sterile medium was refreshed daily. At day 4  the hatched embryos were used for the sterility validation. A day 5  germ free zebrafish were exposed to the combination of GO 30 µg/mL and butyrate 2.5 mM for 24 h. GO and BA were pre incubated for 1 h prior to the exposure. Twenty larvae were used as one replicate  four replicates  i.e. eighty larvae in total  were used for each condition. post the exposure  zebrafish larvae were dissociated for single cell suspension following the published protocol [2]. Briefly  zebrafish larvae were euthanized with 0.01% of tricaine for 5 min  collected in 1.5 mL tube  and washed with PBS for three times. The dissociation was initiated by adding 500 μL of pre warmed enzyme mix containing 460 μL of 0.25% trypsin EDTA Gibco and 40 μL of collagenase Sigma Aldrich at the concentration of 100 mg/mL  followed by mechanical dissociation using P1000 and then P200 pipette tips in heat block at 30 °C until the tissue was no longer visible about 10 min. The dissociation was then stopped by adding 800 μL DMEM Corning Cat# 10 013 CV with 10% FBS Fisher Scientific. The cell pellets were collected by centrifuging at 1000 rpm for 5 min at RT  followed by washing with PBS. The cells were next resuspended in 0.5 mL DMEM with 10% FBS. Four replicates from each condition were pooled together at this step and filtered through 40 μm nylon mesh  with an additional washing using DMEM with 10% FBS. The cell suspension was then stained with a fluorescent DNA dye DRAQ7 to exclude non viable cells Invitrogen Cat# D15106 at the dose of 3 μM for 10 min at room temperature before the fluorescence activated cell sorting BD FACSAria III  BD Biosciences  NJ  USA. The sorting was performed using a 100 microns nozzle with the flow rate of 2 and temperature control at 4 °C and gated based on forward scatter and DRAQ7. The DRAQ7 negative cells of each sample were FACS sorted into the tubes containing DMEM with 10% FBS and placed on ice immediately post the sorting. The cells were then proceeded with the single cell RNA sequencing analysis. 1. Pham LN  Kanther M  Semova I & Rawls JF. Methods for generating and colonizing gnotobiotic zebrafish. Nat. Protoc. 3  1862 1875 2008. 2. Bresciani E  Broadbridge E  Liu PP An efficient dissociation protocol for generation of single cell suspension from zebrafish embryos and larvae  MethodsX. 5  1287 1290 2018. Single cell RNA sequencing scRNA seq was performed by Eukaryotic Single Cell Genomics Facility at SciLifeLab  Stockholm. The single cells collected from FACS sorting were loaded on a 10x GemCode Single Cell Instrument 10x Genomics  Pleasanton  USA to generate single cell gel beads in emulsion GEMs using the Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 10x Genomics following the manufacture's protocol. Briefly  GEMs were generated by combining barcoded Single Cell three prime v3.1 Gel Beads  a Master Mix containing cells  and Partitioning Oil onto Chromium Next GEM Chip G. Following GEMs generation  the Gel Bead was dissolved  primers containing an Illumina TruSeq Read 1read 1 sequencing primer  16 nt 10x Barcode  12 nt unique molecular identifier UMI and 30 nt polydT sequence were released  and the co partitioned cells were lysed. The nucleic acid library construction was performed using the Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 10x Genomics  16 rxns PN 1000268 following the manufacture's protocol. post GEMs generation  primers were mixed with the cell lysate and a Master Mix containing reverse transcription RT reagents to produce barcoded  full length cDNA from polyadenylated mRNA. Silane magnetic beads were used to purify the first strand cDNA from the post GEM RT reaction mixture  which included leftover biochemical reagents and primers. Barcoded  full length cDNA was amplified via PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size. P5  P7  i7 and i5 sample indexes  and TruSeq Read 2 read 2 primer sequence were added via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries containing the P5 and P7 primers used in Illumina amplification were prepared for an estimated 5000 nuclei per sample.,Sample 1 WT control,SAMEA110401655,"Institute of Environmental Medicine, Karolinska Institutet",ENA FIRST PUBLIC:2022 07 22|ENA LAST UPDATE:2022 07 22|External Id:SAMEA110401655|INSDC center alias:Institute of Environmental Medicine  Karolinska Institutet|INSDC center name:Institute of Environmental Medicine  Karolinska Institutet|INSDC first public:2022 07 22T16:26:50Z|INSDC last update:2022 07 22T16:26:50Z|INSDC status:public|Submitter Id:E MTAB 11984:Sample 1 WT control|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|genotype:wild type genotype|individual:pool of 80 individuals|isolate:not applicable|organism part:whole organism|sample name:E MTAB 11984:Sample 1 WT control|sex:not available|stimulus:n1|strain:AB,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; Single cell RNA sequencing of germ free zebrafish embryos,E MTAB 11984:Sample 1 WT control p,Sample 1 WT control p,Single cell RNA sequencing of germ free zebrafish embryos,The generation of germ free zebrafish wild type AB followed previously established protocols [1]. In brief  2 hpf embryos were transferred to petri dishes with sterile E3 medium  supplemented with ampicillin 100 μg/mL  kanamycin 5 μg/mL and amphotericin B 250 ng/mL and incubated at 28°C. At 50% epiboly up to shield stage 6 hpf  the embryos were surface disinfected with 0.1% of polyvinylpyrroidone iodine PVP I for exactly 2 min  followed by 0.003% sterile bleach immersion for 18 min. The embryos were then rinsed with sterile E3 medium  transferred to flasks and incubated at 28°C. The viability was monitored  and sterile medium was refreshed daily. At day 4  the hatched embryos were used for the sterility validation. A day 5  germ free zebrafish were exposed to the combination of GO 30 µg/mL and butyrate 2.5 mM for 24 h. GO and BA were pre incubated for 1 h prior to the exposure. Twenty larvae were used as one replicate  four replicates  i.e. eighty larvae in total  were used for each condition. post the exposure  zebrafish larvae were dissociated for single cell suspension following the published protocol [2]. Briefly  zebrafish larvae were euthanized with 0.01% of tricaine for 5 min  collected in 1.5 mL tube  and washed with PBS for three times. The dissociation was initiated by adding 500 μL of pre warmed enzyme mix containing 460 μL of 0.25% trypsin EDTA Gibco and 40 μL of collagenase Sigma Aldrich at the concentration of 100 mg/mL  followed by mechanical dissociation using P1000 and then P200 pipette tips in heat block at 30 °C until the tissue was no longer visible about 10 min. The dissociation was then stopped by adding 800 μL DMEM Corning Cat# 10 013 CV with 10% FBS Fisher Scientific. The cell pellets were collected by centrifuging at 1000 rpm for 5 min at RT  followed by washing with PBS. The cells were next resuspended in 0.5 mL DMEM with 10% FBS. Four replicates from each condition were pooled together at this step and filtered through 40 μm nylon mesh  with an additional washing using DMEM with 10% FBS. The cell suspension was then stained with a fluorescent DNA dye DRAQ7 to exclude non viable cells Invitrogen Cat# D15106 at the dose of 3 μM for 10 min at room temperature before the fluorescence activated cell sorting BD FACSAria III  BD Biosciences  NJ  USA. The sorting was performed using a 100 microns nozzle with the flow rate of 2 and temperature control at 4 °C and gated based on forward scatter and DRAQ7. The DRAQ7 negative cells of each sample were FACS sorted into the tubes containing DMEM with 10% FBS and placed on ice immediately post the sorting. The cells were then proceeded with the single cell RNA sequencing analysis. 1. Pham LN  Kanther M  Semova I & Rawls JF. Methods for generating and colonizing gnotobiotic zebrafish. Nat. Protoc. 3  1862 1875 2008. 2. Bresciani E  Broadbridge E  Liu PP An efficient dissociation protocol for generation of single cell suspension from zebrafish embryos and larvae  MethodsX. 5  1287 1290 2018. Single cell RNA sequencing scRNA seq was performed by Eukaryotic Single Cell Genomics Facility at SciLifeLab  Stockholm. The single cells collected from FACS sorting were loaded on a 10x GemCode Single Cell Instrument 10x Genomics  Pleasanton  USA to generate single cell gel beads in emulsion GEMs using the Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 10x Genomics following the manufacture's protocol.  Briefly  GEMs were generated by combining barcoded Single Cell three prime v3.1 Gel Beads  a Master Mix containing cells  and Partitioning Oil onto Chromium Next GEM Chip G. Following GEMs generation  the Gel Bead was dissolved  primers containing an Illumina TruSeq Read 1read 1 sequencing primer  16 nt 10x Barcode  12 nt unique molecular identifier UMI and 30 nt polydT sequence were released  and the co partitioned cells were lysed.  The nucleic acid library construction was performed using the Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 10x Genomics  16 rxns PN 1000268 following the manufacture's protocol. post GEMs generation  primers were mixed with the cell lysate and a Master Mix containing reverse transcription RT reagents to produce barcoded  full length cDNA from polyadenylated mRNA. Silane magnetic beads were used to purify the first strand cDNA from the post GEM RT reaction mixture  which included leftover biochemical reagents and primers. Barcoded  full length cDNA was amplified via PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size. P5  P7  i7 and i5 sample indexes  and TruSeq Read 2 read 2 primer sequence were added via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries containing the P5 and P7 primers used in Illumina amplification were prepared for an estimated 5000 nuclei per sample.,Experimental Factor: stimulus:n1,AMPLICON,TRANSCRIPTOMIC SINGLE CELL,size fractionation,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP139765,Illumina NovaSeq 6000 paired end sequencing; Single cell RNA sequencing of germ free zebrafish embryos,ENA FIRST PUBLIC:2022 07 22|ENA LAST UPDATE:2022 07 22,P22202_7001_S1_L001_R1_001.fastq.gz P22202_7001_S1_L001_R2_001.fastq.gz,fastq fastq,19396994226.0,164381307.0,E MTAB 11984:P22202 7001 S1 L001,0:28 1:90,A:5665199484;C:4091196594;G:4415211076;T:5224866754;N:520318,28,90,,,5665199484,4091196594,4415211076,5224866754,520318,ERX9520369,ERS12499847,ERA16483151,"Institute of Environmental Medicine, Karolinska Institutet|European Nucleotide Archive","Institute of Environmental Medicine, Karolinska Institutet|European Nucleotide Archive",2,0.01093,0.89238,0.00557,0.232,0.98764,0.79444,0.40806,0.54781,28,90,T,B,sc-like readlen,illumina,novaseq_era,full_length,size_fractionation,trueseq,sc,single_cell_droplet,10x,,Sweden,2022-07-22,Multi-stage,Embryo,Whole Organism,All anatomical structures
11133,ERR9979393,ERX9520369,ERS12499847,ERP139765,PRJEB54901,Single cell RNA sequencing of germ free zebrafish embryos,E-MTAB-11984,Transcriptome Analysis,The present study was conducted in the frame of the EU funded Graphene Flagship project. We previously evaluated the impact of graphene oxide GO on the gut microbiome in adult zebrafish by performing 16S rRNA gene sequencing in wild type versus AhR deficient zebrafish.  Here  we performed single cell RNA sequencing 10x Genomics on whole dissociated germ free GF zebrafish embryos exposed at 5 dpf to GO plus the microbial metabolite butyrate to gain insight into the impact on specific cell populations in GF zebrafish.,ENA FIRST PUBLIC:2022 07 22|ENA LAST UPDATE:2022 07 22,,Protocols: The generation of germ free zebrafish wild type AB followed previously established protocols [1]. In brief  2 hpf embryos were transferred to petri dishes with sterile E3 medium  supplemented with ampicillin 100 μg/mL  kanamycin 5 μg/mL and amphotericin B 250 ng/mL and incubated at 28°C. At 50% epiboly up to shield stage 6 hpf  the embryos were surface disinfected with 0.1% of polyvinylpyrroidone iodine PVP I for exactly 2 min  followed by 0.003% sterile bleach immersion for 18 min. The embryos were then rinsed with sterile E3 medium  transferred to flasks and incubated at 28°C. The viability was monitored  and sterile medium was refreshed daily. At day 4  the hatched embryos were used for the sterility validation. A day 5  germ free zebrafish were exposed to the combination of GO 30 µg/mL and butyrate 2.5 mM for 24 h. GO and BA were pre incubated for 1 h prior to the exposure. Twenty larvae were used as one replicate  four replicates  i.e. eighty larvae in total  were used for each condition. post the exposure  zebrafish larvae were dissociated for single cell suspension following the published protocol [2]. Briefly  zebrafish larvae were euthanized with 0.01% of tricaine for 5 min  collected in 1.5 mL tube  and washed with PBS for three times. The dissociation was initiated by adding 500 μL of pre warmed enzyme mix containing 460 μL of 0.25% trypsin EDTA Gibco and 40 μL of collagenase Sigma Aldrich at the concentration of 100 mg/mL  followed by mechanical dissociation using P1000 and then P200 pipette tips in heat block at 30 °C until the tissue was no longer visible about 10 min. The dissociation was then stopped by adding 800 μL DMEM Corning Cat# 10 013 CV with 10% FBS Fisher Scientific. The cell pellets were collected by centrifuging at 1000 rpm for 5 min at RT  followed by washing with PBS. The cells were next resuspended in 0.5 mL DMEM with 10% FBS. Four replicates from each condition were pooled together at this step and filtered through 40 μm nylon mesh  with an additional washing using DMEM with 10% FBS. The cell suspension was then stained with a fluorescent DNA dye DRAQ7 to exclude non viable cells Invitrogen Cat# D15106 at the dose of 3 μM for 10 min at room temperature before the fluorescence activated cell sorting BD FACSAria III  BD Biosciences  NJ  USA. The sorting was performed using a 100 microns nozzle with the flow rate of 2 and temperature control at 4 °C and gated based on forward scatter and DRAQ7. The DRAQ7 negative cells of each sample were FACS sorted into the tubes containing DMEM with 10% FBS and placed on ice immediately post the sorting. The cells were then proceeded with the single cell RNA sequencing analysis. 1. Pham LN  Kanther M  Semova I & Rawls JF. Methods for generating and colonizing gnotobiotic zebrafish. Nat. Protoc. 3  1862 1875 2008. 2. Bresciani E  Broadbridge E  Liu PP An efficient dissociation protocol for generation of single cell suspension from zebrafish embryos and larvae  MethodsX. 5  1287 1290 2018. Single cell RNA sequencing scRNA seq was performed by Eukaryotic Single Cell Genomics Facility at SciLifeLab  Stockholm. The single cells collected from FACS sorting were loaded on a 10x GemCode Single Cell Instrument 10x Genomics  Pleasanton  USA to generate single cell gel beads in emulsion GEMs using the Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 10x Genomics following the manufacture's protocol. Briefly  GEMs were generated by combining barcoded Single Cell three prime v3.1 Gel Beads  a Master Mix containing cells  and Partitioning Oil onto Chromium Next GEM Chip G. Following GEMs generation  the Gel Bead was dissolved  primers containing an Illumina TruSeq Read 1read 1 sequencing primer  16 nt 10x Barcode  12 nt unique molecular identifier UMI and 30 nt polydT sequence were released  and the co partitioned cells were lysed. The nucleic acid library construction was performed using the Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 10x Genomics  16 rxns PN 1000268 following the manufacture's protocol. post GEMs generation  primers were mixed with the cell lysate and a Master Mix containing reverse transcription RT reagents to produce barcoded  full length cDNA from polyadenylated mRNA. Silane magnetic beads were used to purify the first strand cDNA from the post GEM RT reaction mixture  which included leftover biochemical reagents and primers. Barcoded  full length cDNA was amplified via PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size. P5  P7  i7 and i5 sample indexes  and TruSeq Read 2 read 2 primer sequence were added via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries containing the P5 and P7 primers used in Illumina amplification were prepared for an estimated 5000 nuclei per sample.,Sample 1 WT control,SAMEA110401655,"Institute of Environmental Medicine, Karolinska Institutet",ENA FIRST PUBLIC:2022 07 22|ENA LAST UPDATE:2022 07 22|External Id:SAMEA110401655|INSDC center alias:Institute of Environmental Medicine  Karolinska Institutet|INSDC center name:Institute of Environmental Medicine  Karolinska Institutet|INSDC first public:2022 07 22T16:26:50Z|INSDC last update:2022 07 22T16:26:50Z|INSDC status:public|Submitter Id:E MTAB 11984:Sample 1 WT control|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|genotype:wild type genotype|individual:pool of 80 individuals|isolate:not applicable|organism part:whole organism|sample name:E MTAB 11984:Sample 1 WT control|sex:not available|stimulus:n1|strain:AB,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; Single cell RNA sequencing of germ free zebrafish embryos,E MTAB 11984:Sample 1 WT control p,Sample 1 WT control p,Single cell RNA sequencing of germ free zebrafish embryos,The generation of germ free zebrafish wild type AB followed previously established protocols [1]. In brief  2 hpf embryos were transferred to petri dishes with sterile E3 medium  supplemented with ampicillin 100 μg/mL  kanamycin 5 μg/mL and amphotericin B 250 ng/mL and incubated at 28°C. At 50% epiboly up to shield stage 6 hpf  the embryos were surface disinfected with 0.1% of polyvinylpyrroidone iodine PVP I for exactly 2 min  followed by 0.003% sterile bleach immersion for 18 min. The embryos were then rinsed with sterile E3 medium  transferred to flasks and incubated at 28°C. The viability was monitored  and sterile medium was refreshed daily. At day 4  the hatched embryos were used for the sterility validation. A day 5  germ free zebrafish were exposed to the combination of GO 30 µg/mL and butyrate 2.5 mM for 24 h. GO and BA were pre incubated for 1 h prior to the exposure. Twenty larvae were used as one replicate  four replicates  i.e. eighty larvae in total  were used for each condition. post the exposure  zebrafish larvae were dissociated for single cell suspension following the published protocol [2]. Briefly  zebrafish larvae were euthanized with 0.01% of tricaine for 5 min  collected in 1.5 mL tube  and washed with PBS for three times. The dissociation was initiated by adding 500 μL of pre warmed enzyme mix containing 460 μL of 0.25% trypsin EDTA Gibco and 40 μL of collagenase Sigma Aldrich at the concentration of 100 mg/mL  followed by mechanical dissociation using P1000 and then P200 pipette tips in heat block at 30 °C until the tissue was no longer visible about 10 min. The dissociation was then stopped by adding 800 μL DMEM Corning Cat# 10 013 CV with 10% FBS Fisher Scientific. The cell pellets were collected by centrifuging at 1000 rpm for 5 min at RT  followed by washing with PBS. The cells were next resuspended in 0.5 mL DMEM with 10% FBS. Four replicates from each condition were pooled together at this step and filtered through 40 μm nylon mesh  with an additional washing using DMEM with 10% FBS. The cell suspension was then stained with a fluorescent DNA dye DRAQ7 to exclude non viable cells Invitrogen Cat# D15106 at the dose of 3 μM for 10 min at room temperature before the fluorescence activated cell sorting BD FACSAria III  BD Biosciences  NJ  USA. The sorting was performed using a 100 microns nozzle with the flow rate of 2 and temperature control at 4 °C and gated based on forward scatter and DRAQ7. The DRAQ7 negative cells of each sample were FACS sorted into the tubes containing DMEM with 10% FBS and placed on ice immediately post the sorting. The cells were then proceeded with the single cell RNA sequencing analysis. 1. Pham LN  Kanther M  Semova I & Rawls JF. Methods for generating and colonizing gnotobiotic zebrafish. Nat. Protoc. 3  1862 1875 2008. 2. Bresciani E  Broadbridge E  Liu PP An efficient dissociation protocol for generation of single cell suspension from zebrafish embryos and larvae  MethodsX. 5  1287 1290 2018. Single cell RNA sequencing scRNA seq was performed by Eukaryotic Single Cell Genomics Facility at SciLifeLab  Stockholm. The single cells collected from FACS sorting were loaded on a 10x GemCode Single Cell Instrument 10x Genomics  Pleasanton  USA to generate single cell gel beads in emulsion GEMs using the Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 10x Genomics following the manufacture's protocol.  Briefly  GEMs were generated by combining barcoded Single Cell three prime v3.1 Gel Beads  a Master Mix containing cells  and Partitioning Oil onto Chromium Next GEM Chip G. Following GEMs generation  the Gel Bead was dissolved  primers containing an Illumina TruSeq Read 1read 1 sequencing primer  16 nt 10x Barcode  12 nt unique molecular identifier UMI and 30 nt polydT sequence were released  and the co partitioned cells were lysed.  The nucleic acid library construction was performed using the Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 10x Genomics  16 rxns PN 1000268 following the manufacture's protocol. post GEMs generation  primers were mixed with the cell lysate and a Master Mix containing reverse transcription RT reagents to produce barcoded  full length cDNA from polyadenylated mRNA. Silane magnetic beads were used to purify the first strand cDNA from the post GEM RT reaction mixture  which included leftover biochemical reagents and primers. Barcoded  full length cDNA was amplified via PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size. P5  P7  i7 and i5 sample indexes  and TruSeq Read 2 read 2 primer sequence were added via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries containing the P5 and P7 primers used in Illumina amplification were prepared for an estimated 5000 nuclei per sample.,Experimental Factor: stimulus:n1,AMPLICON,TRANSCRIPTOMIC SINGLE CELL,size fractionation,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP139765,Illumina NovaSeq 6000 paired end sequencing; Single cell RNA sequencing of germ free zebrafish embryos,ENA FIRST PUBLIC:2022 07 22|ENA LAST UPDATE:2022 07 22,P22202_7001_S1_L002_R1_001.fastq.gz P22202_7001_S1_L002_R2_001.fastq.gz,fastq fastq,19063958224.0,161558968.0,E MTAB 11984:P22202 7001 S1 L002,0:28 1:90,A:5563588848;C:4022930643;G:4344549562;T:5132136743;N:752428,28,90,,,5563588848,4022930643,4344549562,5132136743,752428,ERX9520369,ERS12499847,ERA16483151,"Institute of Environmental Medicine, Karolinska Institutet|European Nucleotide Archive","Institute of Environmental Medicine, Karolinska Institutet|European Nucleotide Archive",2,0.01118,0.89308,0.00573,0.23128,0.98737,0.79354,0.39264,0.54552,28,90,T,B,sc-like readlen,illumina,novaseq_era,full_length,size_fractionation,trueseq,sc,single_cell_droplet,10x,,Sweden,2022-07-22,Multi-stage,Embryo,Whole Organism,All anatomical structures
11134,ERR9981089,ERX9522049,ERS12503451,ERP139797,PRJEB54930,Single cell RNA sequencing of lck GFP transgenic zebrafish,E-MTAB-11991,Transcriptome Analysis,The present study was conducted in the frame of the EU funded Graphene Flagship project. The aim is to evaluate the impact of graphene oxide GO on the innate immune system using zebrafish as a model. We previously performed single cell RNA sequencing of germ free zebrafish embryos exposed to GO plus the microbial metabolite butyrate BA. Here  we performed a follow up experiment using germ free lck GFP transgenic fish in which the zebrafish were exposed to GO plus BA at xxx dpf. The embryos were then dissociated and subsequently sorted on lck and submitted for single cell RNA sequencing using 10x Genomics.,ENA FIRST PUBLIC:2022 07 23|ENA LAST UPDATE:2022 07 23,,Protocols: The generation of germ free Tglck:GFP zebrafish followed previously established protocols [1]. In brief  2 hpf embryos were transferred to petri dishes with sterile E3 medium  supplemented with ampicillin 100 μg/mL  kanamycin 5 μg/mL and amphotericin B 250 ng/mL and incubated at 28°C. At 50% epiboly up to shield stage 6 hpf  the embryos were surface disinfected with 0.1% of polyvinylpyrroidone iodine PVP I for exactly 2 min  followed by 0.003% sterile bleach immersion for 18 min. The embryos were then rinsed with sterile E3 medium  transferred to flasks and incubated at 28°C. The viability was monitored  and sterile medium was refreshed daily. At day 4  the hatched embryos were used for the sterility validation. A day 5  germ free Tglck:GFP zebrafish were exposed to the combination of GO 30 µg/mL and butyrate 2.5 mM for 24 h. GO and BA were pre incubated for 1 h prior to the exposure. Fifty larvae were used as one replicate  four replicates  i.e. two hundred larvae in total  were used for each condition. post the exposure  zebrafish larvae were dissociated for single cell suspension following the published protocol [2]. Briefly  zebrafish larvae were euthanized with 0.01% of tricaine for 5 min  collected in 1.5 mL tube  and washed with PBS for three times. The dissociation was initiated by adding 500 μL of pre warmed enzyme mix containing 460 μL of 0.25% trypsin EDTA Gibco and 40 μL of collagenase Sigma Aldrich at the concentration of 100 mg/mL  followed by mechanical dissociation using P1000 and then P200 pipette tips in heat block at 30 °C until the tissue was no longer visible about 10 min. The dissociation was then stopped by adding 800 μL DMEM Corning Cat# 10 013 CV with 10% FBS Fisher Scientific. The cell pellets were collected by centrifuging at 1000 rpm for 5 min at RT  followed by washing with PBS. The cells were next resuspended in 0.5 mL DMEM with 10% FBS. Four replicates from each condition were pooled together at this step and filtered through 40 μm nylon mesh  with an additional washing using DMEM with 10% FBS. The cell suspension was then stained with a fluorescent DNA dye DRAQ7 to exclude non viable cells Invitrogen Cat# D15106 at the dose of 3 μM for 10 min at room temperature before the fluorescence activated cell sorting BD FACSAria III  BD Biosciences  NJ  USA. The sorting was performed using a 100 microns nozzle with the flow rate of 2 and temperature control at 4 °C and gated based on forward scatter and DRAQ7. The DRAQ7 lck+ cells of each sample were FACS sorted into the tubes containing DMEM with 10% FBS and placed on ice immediately post the sorting. The cells were then proceeded with the single cell RNA sequencing analysis. 1. Pham LN  Kanther M  Semova I & Rawls JF. Methods for generating and colonizing gnotobiotic zebrafish. Nat. Protoc. 3  1862 1875 2008. 2. Bresciani E  Broadbridge E  Liu PP An efficient dissociation protocol for generation of single cell suspension from zebrafish embryos and larvae  MethodsX. 5  1287 1290 2018. Single cell RNA sequencing scRNA seq was performed by Eukaryotic Single Cell Genomics Facility at SciLifeLab  Stockholm. The single cells collected from FACS sorting were loaded on a 10x GemCode Single Cell Instrument 10x Genomics  Pleasanton  USA to generate single cell gel beads in emulsion GEMs using the Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 10x Genomics following the manufacture's protocol. Briefly  GEMs were generated by combining barcoded Single Cell three prime v3.1 Gel Beads  a Master Mix containing cells  and Partitioning Oil onto Chromium Next GEM Chip G. Following GEMs generation  the Gel Bead was dissolved  primers containing an Illumina TruSeq Read 1read 1 sequencing primer  16 nt 10x Barcode  12 nt unique molecular identifier UMI and 30 nt polydT sequence were released  and the co partitioned cells were lysed. The nucleic acid library construction was performed using the Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 10x Genomics  16 rxns PN 1000268 following the manufacture's protocol. post GEMs generation  primers were mixed with the cell lysate and a Master Mix containing reverse transcription RT reagents to produce barcoded  full length cDNA from polyadenylated mRNA. Silane magnetic beads were used to purify the first strand cDNA from the post GEM RT reaction mixture  which included leftover biochemical reagents and primers. Barcoded  full length cDNA was amplified via PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size. P5  P7  i7 and i5 sample indexes  and TruSeq Read 2 read 2 primer sequence were added via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries containing the P5 and P7 primers used in Illumina amplification were prepared for an estimated 5000 nuclei per sample.,Sample 1 lck control,SAMEA110406305,"Institute of Environmental Medicine, Karolinska Institutet",ENA FIRST PUBLIC:2022 07 23|ENA LAST UPDATE:2022 07 23|External Id:SAMEA110406305|INSDC center alias:Institute of Environmental Medicine  Karolinska Institutet|INSDC center name:Institute of Environmental Medicine  Karolinska Institutet|INSDC first public:2022 07 23T04:33:35Z|INSDC last update:2022 07 23T04:33:35Z|INSDC status:public|Submitter Id:E MTAB 11991:Sample 1 lck control|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larva|disease:normal|genotype:wild type genotype|isolate:not applicable|organism part:whole organism|sample name:E MTAB 11991:Sample 1 lck control|strain:Tglck:GFP,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; Single cell RNA sequencing of lck GFP transgenic zebrafish,E MTAB 11991:Sample 1 lck control p,Sample 1 lck control p,Single cell RNA sequencing of lck GFP transgenic zebrafish,The generation of germ free Tglck:GFP zebrafish followed previously established protocols [1]. In brief  2 hpf embryos were transferred to petri dishes with sterile E3 medium  supplemented with ampicillin 100 μg/mL  kanamycin 5 μg/mL and amphotericin B 250 ng/mL and incubated at 28°C. At 50% epiboly up to shield stage 6 hpf  the embryos were surface disinfected with 0.1% of polyvinylpyrroidone iodine PVP I for exactly 2 min  followed by 0.003% sterile bleach immersion for 18 min. The embryos were then rinsed with sterile E3 medium  transferred to flasks and incubated at 28°C. The viability was monitored  and sterile medium was refreshed daily. At day 4  the hatched embryos were used for the sterility validation. A day 5  germ free Tglck:GFP zebrafish were exposed to the combination of GO 30 µg/mL and butyrate 2.5 mM for 24 h. GO and BA were pre incubated for 1 h prior to the exposure. Fifty larvae were used as one replicate  four replicates  i.e. two hundred larvae in total  were used for each condition. post the exposure  zebrafish larvae were dissociated for single cell suspension following the published protocol [2]. Briefly  zebrafish larvae were euthanized with 0.01% of tricaine for 5 min  collected in 1.5 mL tube  and washed with PBS for three times. The dissociation was initiated by adding 500 μL of pre warmed enzyme mix containing 460 μL of 0.25% trypsin EDTA Gibco and 40 μL of collagenase Sigma Aldrich at the concentration of 100 mg/mL  followed by mechanical dissociation using P1000 and then P200 pipette tips in heat block at 30 °C until the tissue was no longer visible about 10 min. The dissociation was then stopped by adding 800 μL DMEM Corning Cat# 10 013 CV with 10% FBS Fisher Scientific. The cell pellets were collected by centrifuging at 1000 rpm for 5 min at RT  followed by washing with PBS. The cells were next resuspended in 0.5 mL DMEM with 10% FBS. Four replicates from each condition were pooled together at this step and filtered through 40 μm nylon mesh  with an additional washing using DMEM with 10% FBS. The cell suspension was then stained with a fluorescent DNA dye DRAQ7 to exclude non viable cells Invitrogen Cat# D15106 at the dose of 3 μM for 10 min at room temperature before the fluorescence activated cell sorting BD FACSAria III  BD Biosciences  NJ  USA. The sorting was performed using a 100 microns nozzle with the flow rate of 2 and temperature control at 4 °,Experimental Factor: stimulus:n1,AMPLICON,TRANSCRIPTOMIC SINGLE CELL,size fractionation,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP139797,Illumina NovaSeq 6000 paired end sequencing; Single cell RNA sequencing of lck GFP transgenic zebrafish,ENA FIRST PUBLIC:2022 07 23|ENA LAST UPDATE:2022 07 23,P25452_2002_S2_L001_R1_001.fastq.gz P25452_2002_S2_L001_R2_001.fastq.gz,fastq fastq,60177283876.0,509976982.0,E MTAB 11991:P25452 2002 S2 L001,0:28 1:90,A:17254566438;C:13547211711;G:14188233429;T:15185192817;N:2079481,28,90,,,17254566438,13547211711,14188233429,15185192817,2079481,ERX9522049,ERS12503451,ERA16488297,"Institute of Environmental Medicine, Karolinska Institutet|European Nucleotide Archive","Institute of Environmental Medicine, Karolinska Institutet|European Nucleotide Archive",2,0.00671,0.93031,0.00231,0.11028,0.9932,0.82227,0.30887,0.58272,28,90,T,B,sc-like readlen,illumina,novaseq_era,full_length,size_fractionation,trueseq,sc,single_cell_droplet,10x,,Sweden,2022-07-23,Larval,Larval,Whole Organism,All anatomical structures
11135,ERR9981090,ERX9522049,ERS12503451,ERP139797,PRJEB54930,Single cell RNA sequencing of lck GFP transgenic zebrafish,E-MTAB-11991,Transcriptome Analysis,The present study was conducted in the frame of the EU funded Graphene Flagship project. The aim is to evaluate the impact of graphene oxide GO on the innate immune system using zebrafish as a model. We previously performed single cell RNA sequencing of germ free zebrafish embryos exposed to GO plus the microbial metabolite butyrate BA. Here  we performed a follow up experiment using germ free lck GFP transgenic fish in which the zebrafish were exposed to GO plus BA at xxx dpf. The embryos were then dissociated and subsequently sorted on lck and submitted for single cell RNA sequencing using 10x Genomics.,ENA FIRST PUBLIC:2022 07 23|ENA LAST UPDATE:2022 07 23,,Protocols: The generation of germ free Tglck:GFP zebrafish followed previously established protocols [1]. In brief  2 hpf embryos were transferred to petri dishes with sterile E3 medium  supplemented with ampicillin 100 μg/mL  kanamycin 5 μg/mL and amphotericin B 250 ng/mL and incubated at 28°C. At 50% epiboly up to shield stage 6 hpf  the embryos were surface disinfected with 0.1% of polyvinylpyrroidone iodine PVP I for exactly 2 min  followed by 0.003% sterile bleach immersion for 18 min. The embryos were then rinsed with sterile E3 medium  transferred to flasks and incubated at 28°C. The viability was monitored  and sterile medium was refreshed daily. At day 4  the hatched embryos were used for the sterility validation. A day 5  germ free Tglck:GFP zebrafish were exposed to the combination of GO 30 µg/mL and butyrate 2.5 mM for 24 h. GO and BA were pre incubated for 1 h prior to the exposure. Fifty larvae were used as one replicate  four replicates  i.e. two hundred larvae in total  were used for each condition. post the exposure  zebrafish larvae were dissociated for single cell suspension following the published protocol [2]. Briefly  zebrafish larvae were euthanized with 0.01% of tricaine for 5 min  collected in 1.5 mL tube  and washed with PBS for three times. The dissociation was initiated by adding 500 μL of pre warmed enzyme mix containing 460 μL of 0.25% trypsin EDTA Gibco and 40 μL of collagenase Sigma Aldrich at the concentration of 100 mg/mL  followed by mechanical dissociation using P1000 and then P200 pipette tips in heat block at 30 °C until the tissue was no longer visible about 10 min. The dissociation was then stopped by adding 800 μL DMEM Corning Cat# 10 013 CV with 10% FBS Fisher Scientific. The cell pellets were collected by centrifuging at 1000 rpm for 5 min at RT  followed by washing with PBS. The cells were next resuspended in 0.5 mL DMEM with 10% FBS. Four replicates from each condition were pooled together at this step and filtered through 40 μm nylon mesh  with an additional washing using DMEM with 10% FBS. The cell suspension was then stained with a fluorescent DNA dye DRAQ7 to exclude non viable cells Invitrogen Cat# D15106 at the dose of 3 μM for 10 min at room temperature before the fluorescence activated cell sorting BD FACSAria III  BD Biosciences  NJ  USA. The sorting was performed using a 100 microns nozzle with the flow rate of 2 and temperature control at 4 °C and gated based on forward scatter and DRAQ7. The DRAQ7 lck+ cells of each sample were FACS sorted into the tubes containing DMEM with 10% FBS and placed on ice immediately post the sorting. The cells were then proceeded with the single cell RNA sequencing analysis. 1. Pham LN  Kanther M  Semova I & Rawls JF. Methods for generating and colonizing gnotobiotic zebrafish. Nat. Protoc. 3  1862 1875 2008. 2. Bresciani E  Broadbridge E  Liu PP An efficient dissociation protocol for generation of single cell suspension from zebrafish embryos and larvae  MethodsX. 5  1287 1290 2018. Single cell RNA sequencing scRNA seq was performed by Eukaryotic Single Cell Genomics Facility at SciLifeLab  Stockholm. The single cells collected from FACS sorting were loaded on a 10x GemCode Single Cell Instrument 10x Genomics  Pleasanton  USA to generate single cell gel beads in emulsion GEMs using the Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 10x Genomics following the manufacture's protocol. Briefly  GEMs were generated by combining barcoded Single Cell three prime v3.1 Gel Beads  a Master Mix containing cells  and Partitioning Oil onto Chromium Next GEM Chip G. Following GEMs generation  the Gel Bead was dissolved  primers containing an Illumina TruSeq Read 1read 1 sequencing primer  16 nt 10x Barcode  12 nt unique molecular identifier UMI and 30 nt polydT sequence were released  and the co partitioned cells were lysed. The nucleic acid library construction was performed using the Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 10x Genomics  16 rxns PN 1000268 following the manufacture's protocol. post GEMs generation  primers were mixed with the cell lysate and a Master Mix containing reverse transcription RT reagents to produce barcoded  full length cDNA from polyadenylated mRNA. Silane magnetic beads were used to purify the first strand cDNA from the post GEM RT reaction mixture  which included leftover biochemical reagents and primers. Barcoded  full length cDNA was amplified via PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size. P5  P7  i7 and i5 sample indexes  and TruSeq Read 2 read 2 primer sequence were added via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries containing the P5 and P7 primers used in Illumina amplification were prepared for an estimated 5000 nuclei per sample.,Sample 1 lck control,SAMEA110406305,"Institute of Environmental Medicine, Karolinska Institutet",ENA FIRST PUBLIC:2022 07 23|ENA LAST UPDATE:2022 07 23|External Id:SAMEA110406305|INSDC center alias:Institute of Environmental Medicine  Karolinska Institutet|INSDC center name:Institute of Environmental Medicine  Karolinska Institutet|INSDC first public:2022 07 23T04:33:35Z|INSDC last update:2022 07 23T04:33:35Z|INSDC status:public|Submitter Id:E MTAB 11991:Sample 1 lck control|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larva|disease:normal|genotype:wild type genotype|isolate:not applicable|organism part:whole organism|sample name:E MTAB 11991:Sample 1 lck control|strain:Tglck:GFP,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; Single cell RNA sequencing of lck GFP transgenic zebrafish,E MTAB 11991:Sample 1 lck control p,Sample 1 lck control p,Single cell RNA sequencing of lck GFP transgenic zebrafish,The generation of germ free Tglck:GFP zebrafish followed previously established protocols [1]. In brief  2 hpf embryos were transferred to petri dishes with sterile E3 medium  supplemented with ampicillin 100 μg/mL  kanamycin 5 μg/mL and amphotericin B 250 ng/mL and incubated at 28°C. At 50% epiboly up to shield stage 6 hpf  the embryos were surface disinfected with 0.1% of polyvinylpyrroidone iodine PVP I for exactly 2 min  followed by 0.003% sterile bleach immersion for 18 min. The embryos were then rinsed with sterile E3 medium  transferred to flasks and incubated at 28°C. The viability was monitored  and sterile medium was refreshed daily. At day 4  the hatched embryos were used for the sterility validation. A day 5  germ free Tglck:GFP zebrafish were exposed to the combination of GO 30 µg/mL and butyrate 2.5 mM for 24 h. GO and BA were pre incubated for 1 h prior to the exposure. Fifty larvae were used as one replicate  four replicates  i.e. two hundred larvae in total  were used for each condition. post the exposure  zebrafish larvae were dissociated for single cell suspension following the published protocol [2]. Briefly  zebrafish larvae were euthanized with 0.01% of tricaine for 5 min  collected in 1.5 mL tube  and washed with PBS for three times. The dissociation was initiated by adding 500 μL of pre warmed enzyme mix containing 460 μL of 0.25% trypsin EDTA Gibco and 40 μL of collagenase Sigma Aldrich at the concentration of 100 mg/mL  followed by mechanical dissociation using P1000 and then P200 pipette tips in heat block at 30 °C until the tissue was no longer visible about 10 min. The dissociation was then stopped by adding 800 μL DMEM Corning Cat# 10 013 CV with 10% FBS Fisher Scientific. The cell pellets were collected by centrifuging at 1000 rpm for 5 min at RT  followed by washing with PBS. The cells were next resuspended in 0.5 mL DMEM with 10% FBS. Four replicates from each condition were pooled together at this step and filtered through 40 μm nylon mesh  with an additional washing using DMEM with 10% FBS. The cell suspension was then stained with a fluorescent DNA dye DRAQ7 to exclude non viable cells Invitrogen Cat# D15106 at the dose of 3 μM for 10 min at room temperature before the fluorescence activated cell sorting BD FACSAria III  BD Biosciences  NJ  USA. The sorting was performed using a 100 microns nozzle with the flow rate of 2 and temperature control at 4 °,Experimental Factor: stimulus:n1,AMPLICON,TRANSCRIPTOMIC SINGLE CELL,size fractionation,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP139797,Illumina NovaSeq 6000 paired end sequencing; Single cell RNA sequencing of lck GFP transgenic zebrafish,ENA FIRST PUBLIC:2022 07 23|ENA LAST UPDATE:2022 07 23,P25452_2002_S2_L002_R1_001.fastq.gz P25452_2002_S2_L002_R2_001.fastq.gz,fastq fastq,60597886144.0,513541408.0,E MTAB 11991:P25452 2002 S2 L002,0:28 1:90,A:17368154358;C:13649089056;G:14296037620;T:15282869484;N:1735626,28,90,,,17368154358,13649089056,14296037620,15282869484,1735626,ERX9522049,ERS12503451,ERA16488297,"Institute of Environmental Medicine, Karolinska Institutet|European Nucleotide Archive","Institute of Environmental Medicine, Karolinska Institutet|European Nucleotide Archive",2,0.00656,0.92899,0.00211,0.11059,0.99334,0.82335,0.32311,0.57644,28,90,T,B,sc-like readlen,illumina,novaseq_era,full_length,size_fractionation,trueseq,sc,single_cell_droplet,10x,,Sweden,2022-07-23,Larval,Larval,Whole Organism,All anatomical structures
11136,ERR9981087,ERX9522048,ERS12503450,ERP139797,PRJEB54930,Single cell RNA sequencing of lck GFP transgenic zebrafish,E-MTAB-11991,Transcriptome Analysis,The present study was conducted in the frame of the EU funded Graphene Flagship project. The aim is to evaluate the impact of graphene oxide GO on the innate immune system using zebrafish as a model. We previously performed single cell RNA sequencing of germ free zebrafish embryos exposed to GO plus the microbial metabolite butyrate BA. Here  we performed a follow up experiment using germ free lck GFP transgenic fish in which the zebrafish were exposed to GO plus BA at xxx dpf. The embryos were then dissociated and subsequently sorted on lck and submitted for single cell RNA sequencing using 10x Genomics.,ENA FIRST PUBLIC:2022 07 23|ENA LAST UPDATE:2022 07 23,,Protocols: The generation of germ free Tglck:GFP zebrafish followed previously established protocols [1]. In brief  2 hpf embryos were transferred to petri dishes with sterile E3 medium  supplemented with ampicillin 100 μg/mL  kanamycin 5 μg/mL and amphotericin B 250 ng/mL and incubated at 28°C. At 50% epiboly up to shield stage 6 hpf  the embryos were surface disinfected with 0.1% of polyvinylpyrroidone iodine PVP I for exactly 2 min  followed by 0.003% sterile bleach immersion for 18 min. The embryos were then rinsed with sterile E3 medium  transferred to flasks and incubated at 28°C. The viability was monitored  and sterile medium was refreshed daily. At day 4  the hatched embryos were used for the sterility validation. A day 5  germ free Tglck:GFP zebrafish were exposed to the combination of GO 30 µg/mL and butyrate 2.5 mM for 24 h. GO and BA were pre incubated for 1 h prior to the exposure. Fifty larvae were used as one replicate  four replicates  i.e. two hundred larvae in total  were used for each condition. post the exposure  zebrafish larvae were dissociated for single cell suspension following the published protocol [2]. Briefly  zebrafish larvae were euthanized with 0.01% of tricaine for 5 min  collected in 1.5 mL tube  and washed with PBS for three times. The dissociation was initiated by adding 500 μL of pre warmed enzyme mix containing 460 μL of 0.25% trypsin EDTA Gibco and 40 μL of collagenase Sigma Aldrich at the concentration of 100 mg/mL  followed by mechanical dissociation using P1000 and then P200 pipette tips in heat block at 30 °C until the tissue was no longer visible about 10 min. The dissociation was then stopped by adding 800 μL DMEM Corning Cat# 10 013 CV with 10% FBS Fisher Scientific. The cell pellets were collected by centrifuging at 1000 rpm for 5 min at RT  followed by washing with PBS. The cells were next resuspended in 0.5 mL DMEM with 10% FBS. Four replicates from each condition were pooled together at this step and filtered through 40 μm nylon mesh  with an additional washing using DMEM with 10% FBS. The cell suspension was then stained with a fluorescent DNA dye DRAQ7 to exclude non viable cells Invitrogen Cat# D15106 at the dose of 3 μM for 10 min at room temperature before the fluorescence activated cell sorting BD FACSAria III  BD Biosciences  NJ  USA. The sorting was performed using a 100 microns nozzle with the flow rate of 2 and temperature control at 4 °C and gated based on forward scatter and DRAQ7. The DRAQ7 lck+ cells of each sample were FACS sorted into the tubes containing DMEM with 10% FBS and placed on ice immediately post the sorting. The cells were then proceeded with the single cell RNA sequencing analysis. 1. Pham LN  Kanther M  Semova I & Rawls JF. Methods for generating and colonizing gnotobiotic zebrafish. Nat. Protoc. 3  1862 1875 2008. 2. Bresciani E  Broadbridge E  Liu PP An efficient dissociation protocol for generation of single cell suspension from zebrafish embryos and larvae  MethodsX. 5  1287 1290 2018. Single cell RNA sequencing scRNA seq was performed by Eukaryotic Single Cell Genomics Facility at SciLifeLab  Stockholm. The single cells collected from FACS sorting were loaded on a 10x GemCode Single Cell Instrument 10x Genomics  Pleasanton  USA to generate single cell gel beads in emulsion GEMs using the Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 10x Genomics following the manufacture's protocol. Briefly  GEMs were generated by combining barcoded Single Cell three prime v3.1 Gel Beads  a Master Mix containing cells  and Partitioning Oil onto Chromium Next GEM Chip G. Following GEMs generation  the Gel Bead was dissolved  primers containing an Illumina TruSeq Read 1read 1 sequencing primer  16 nt 10x Barcode  12 nt unique molecular identifier UMI and 30 nt polydT sequence were released  and the co partitioned cells were lysed. The nucleic acid library construction was performed using the Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 10x Genomics  16 rxns PN 1000268 following the manufacture's protocol. post GEMs generation  primers were mixed with the cell lysate and a Master Mix containing reverse transcription RT reagents to produce barcoded  full length cDNA from polyadenylated mRNA. Silane magnetic beads were used to purify the first strand cDNA from the post GEM RT reaction mixture  which included leftover biochemical reagents and primers. Barcoded  full length cDNA was amplified via PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size. P5  P7  i7 and i5 sample indexes  and TruSeq Read 2 read 2 primer sequence were added via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries containing the P5 and P7 primers used in Illumina amplification were prepared for an estimated 5000 nuclei per sample.,Sample 2 lck GO+BA,SAMEA110406304,"Institute of Environmental Medicine, Karolinska Institutet",ENA FIRST PUBLIC:2022 07 23|ENA LAST UPDATE:2022 07 23|External Id:SAMEA110406304|INSDC center alias:Institute of Environmental Medicine  Karolinska Institutet|INSDC center name:Institute of Environmental Medicine  Karolinska Institutet|INSDC first public:2022 07 23T04:33:35Z|INSDC last update:2022 07 23T04:33:35Z|INSDC status:public|Submitter Id:E MTAB 11991:Sample 2 lck GO+BA|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larva|disease:normal|genotype:wild type genotype|isolate:not applicable|organism part:whole organism|sample name:E MTAB 11991:Sample 2 lck GO+BA|strain:Tglck:GFP,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; Single cell RNA sequencing of lck GFP transgenic zebrafish,E MTAB 11991:Sample 2 lck GO+BA p,Sample 2 lck GO+BA p,Single cell RNA sequencing of lck GFP transgenic zebrafish,The generation of germ free Tglck:GFP zebrafish followed previously established protocols [1]. In brief  2 hpf embryos were transferred to petri dishes with sterile E3 medium  supplemented with ampicillin 100 μg/mL  kanamycin 5 μg/mL and amphotericin B 250 ng/mL and incubated at 28°C. At 50% epiboly up to shield stage 6 hpf  the embryos were surface disinfected with 0.1% of polyvinylpyrroidone iodine PVP I for exactly 2 min  followed by 0.003% sterile bleach immersion for 18 min. The embryos were then rinsed with sterile E3 medium  transferred to flasks and incubated at 28°C. The viability was monitored  and sterile medium was refreshed daily. At day 4  the hatched embryos were used for the sterility validation. A day 5  germ free Tglck:GFP zebrafish were exposed to the combination of GO 30 µg/mL and butyrate 2.5 mM for 24 h. GO and BA were pre incubated for 1 h prior to the exposure. Fifty larvae were used as one replicate  four replicates  i.e. two hundred larvae in total  were used for each condition. post the exposure  zebrafish larvae were dissociated for single cell suspension following the published protocol [2]. Briefly  zebrafish larvae were euthanized with 0.01% of tricaine for 5 min  collected in 1.5 mL tube  and washed with PBS for three times. The dissociation was initiated by adding 500 μL of pre warmed enzyme mix containing 460 μL of 0.25% trypsin EDTA Gibco and 40 μL of collagenase Sigma Aldrich at the concentration of 100 mg/mL  followed by mechanical dissociation using P1000 and then P200 pipette tips in heat block at 30 °C until the tissue was no longer visible about 10 min. The dissociation was then stopped by adding 800 μL DMEM Corning Cat# 10 013 CV with 10% FBS Fisher Scientific. The cell pellets were collected by centrifuging at 1000 rpm for 5 min at RT  followed by washing with PBS. The cells were next resuspended in 0.5 mL DMEM with 10% FBS. Four replicates from each condition were pooled together at this step and filtered through 40 μm nylon mesh  with an additional washing using DMEM with 10% FBS. The cell suspension was then stained with a fluorescent DNA dye DRAQ7 to exclude non viable cells Invitrogen Cat# D15106 at the dose of 3 μM for 10 min at room temperature before the fluorescence activated cell sorting BD FACSAria III  BD Biosciences  NJ  USA. The sorting was performed using a 100 microns nozzle with the flow rate of 2 and temperature control at 4 °C and gated based on forward scatter and DRAQ7. The DRAQ7 lck+ cells of each sample were FACS sorted into the tubes containing DMEM with 10% FBS and placed on ice immediately post the sorting. The cells were then proceeded with the single cell RNA sequencing analysis. 1. Pham LN  Kanther M  Semova I & Rawls JF. Methods for generating and colonizing gnotobiotic zebrafish. Nat. Protoc. 3  1862 1875 2008. 2. Bresciani E  Broadbridge E  Liu PP An efficient dissociation protocol for generation of single cell suspension from zebrafish embryos and larvae  MethodsX. 5  1287 1290 2018. Single cell RNA sequencing scRNA seq was performed by Eukaryotic Single Cell Genomics Facility at SciLifeLab  Stockholm. The single cells collected from FACS sorting were loaded on a 10x GemCode Single Cell Instrument 10x Genomics  Pleasanton  USA to generate single cell gel beads in emulsion GEMs using the Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 10x Genomics following the manufacture's protocol.  Briefly  GEMs were generated by combining barcoded Single Cell three prime v3.1 Gel Beads  a Master Mix containing cells  and Partitioning Oil onto Chromium Next GEM Chip G. Following GEMs generation  the Gel Bead was dissolved  primers containing an Illumina TruSeq Read 1read 1 sequencing primer  16 nt 10x Barcode  12 nt unique molecular identifier UMI and 30 nt polydT sequence were released  and the co partitioned cells were lysed. The nucleic acid library construction was performed using the Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 10x Genomics  16 rxns PN 1000268 following the manufacture's protocol. post GEMs generation  primers were mixed with the cell lysate and a Master Mix containing reverse transcription RT reagents to produce barcoded  full length cDNA from polyadenylated mRNA. Silane magnetic beads were used to purify the first strand cDNA from the post GEM RT reaction mixture  which included leftover biochemical reagents and primers. Barcoded  full length cDNA was amplified via PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size. P5  P7  i7 and i5 sample indexes  and TruSeq Read 2 read 2 primer sequence were added via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries containing the P5 and P7 primers used in Illumina amplification were prepared for an estimated 5000 nuclei per sample.,Experimental Factor: stimulus:graphene oxide  30 microgram per milliliter|Experimental Factor: compound:butyrate|Experimental Factor: dose:2.5,AMPLICON,TRANSCRIPTOMIC SINGLE CELL,size fractionation,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP139797,Illumina NovaSeq 6000 paired end sequencing; Single cell RNA sequencing of lck GFP transgenic zebrafish,ENA FIRST PUBLIC:2022 07 23|ENA LAST UPDATE:2022 07 23,P25452_2001_S1_L001_R1_001.fastq.gz P25452_2001_S1_L001_R2_001.fastq.gz,fastq fastq,20866120186.0,176831527.0,E MTAB 11991:P25452 2001 S1 L001,0:28 1:90,A:5933525376;C:4737179804;G:5025711080;T:5168983880;N:720046,28,90,,,5933525376,4737179804,5025711080,5168983880,720046,ERX9522048,ERS12503450,ERA16488297,"Institute of Environmental Medicine, Karolinska Institutet|European Nucleotide Archive","Institute of Environmental Medicine, Karolinska Institutet|European Nucleotide Archive",2,0.00805,0.92622,0.00259,0.11842,0.99302,0.83027,0.2729,0.57699,28,90,T,B,sc-like readlen,illumina,novaseq_era,full_length,size_fractionation,trueseq,sc,single_cell_droplet,10x,,Sweden,2022-07-23,Larval,Larval,Whole Organism,All anatomical structures
11137,ERR9981088,ERX9522048,ERS12503450,ERP139797,PRJEB54930,Single cell RNA sequencing of lck GFP transgenic zebrafish,E-MTAB-11991,Transcriptome Analysis,The present study was conducted in the frame of the EU funded Graphene Flagship project. The aim is to evaluate the impact of graphene oxide GO on the innate immune system using zebrafish as a model. We previously performed single cell RNA sequencing of germ free zebrafish embryos exposed to GO plus the microbial metabolite butyrate BA. Here  we performed a follow up experiment using germ free lck GFP transgenic fish in which the zebrafish were exposed to GO plus BA at xxx dpf. The embryos were then dissociated and subsequently sorted on lck and submitted for single cell RNA sequencing using 10x Genomics.,ENA FIRST PUBLIC:2022 07 23|ENA LAST UPDATE:2022 07 23,,Protocols: The generation of germ free Tglck:GFP zebrafish followed previously established protocols [1]. In brief  2 hpf embryos were transferred to petri dishes with sterile E3 medium  supplemented with ampicillin 100 μg/mL  kanamycin 5 μg/mL and amphotericin B 250 ng/mL and incubated at 28°C. At 50% epiboly up to shield stage 6 hpf  the embryos were surface disinfected with 0.1% of polyvinylpyrroidone iodine PVP I for exactly 2 min  followed by 0.003% sterile bleach immersion for 18 min. The embryos were then rinsed with sterile E3 medium  transferred to flasks and incubated at 28°C. The viability was monitored  and sterile medium was refreshed daily. At day 4  the hatched embryos were used for the sterility validation. A day 5  germ free Tglck:GFP zebrafish were exposed to the combination of GO 30 µg/mL and butyrate 2.5 mM for 24 h. GO and BA were pre incubated for 1 h prior to the exposure. Fifty larvae were used as one replicate  four replicates  i.e. two hundred larvae in total  were used for each condition. post the exposure  zebrafish larvae were dissociated for single cell suspension following the published protocol [2]. Briefly  zebrafish larvae were euthanized with 0.01% of tricaine for 5 min  collected in 1.5 mL tube  and washed with PBS for three times. The dissociation was initiated by adding 500 μL of pre warmed enzyme mix containing 460 μL of 0.25% trypsin EDTA Gibco and 40 μL of collagenase Sigma Aldrich at the concentration of 100 mg/mL  followed by mechanical dissociation using P1000 and then P200 pipette tips in heat block at 30 °C until the tissue was no longer visible about 10 min. The dissociation was then stopped by adding 800 μL DMEM Corning Cat# 10 013 CV with 10% FBS Fisher Scientific. The cell pellets were collected by centrifuging at 1000 rpm for 5 min at RT  followed by washing with PBS. The cells were next resuspended in 0.5 mL DMEM with 10% FBS. Four replicates from each condition were pooled together at this step and filtered through 40 μm nylon mesh  with an additional washing using DMEM with 10% FBS. The cell suspension was then stained with a fluorescent DNA dye DRAQ7 to exclude non viable cells Invitrogen Cat# D15106 at the dose of 3 μM for 10 min at room temperature before the fluorescence activated cell sorting BD FACSAria III  BD Biosciences  NJ  USA. The sorting was performed using a 100 microns nozzle with the flow rate of 2 and temperature control at 4 °C and gated based on forward scatter and DRAQ7. The DRAQ7 lck+ cells of each sample were FACS sorted into the tubes containing DMEM with 10% FBS and placed on ice immediately post the sorting. The cells were then proceeded with the single cell RNA sequencing analysis. 1. Pham LN  Kanther M  Semova I & Rawls JF. Methods for generating and colonizing gnotobiotic zebrafish. Nat. Protoc. 3  1862 1875 2008. 2. Bresciani E  Broadbridge E  Liu PP An efficient dissociation protocol for generation of single cell suspension from zebrafish embryos and larvae  MethodsX. 5  1287 1290 2018. Single cell RNA sequencing scRNA seq was performed by Eukaryotic Single Cell Genomics Facility at SciLifeLab  Stockholm. The single cells collected from FACS sorting were loaded on a 10x GemCode Single Cell Instrument 10x Genomics  Pleasanton  USA to generate single cell gel beads in emulsion GEMs using the Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 10x Genomics following the manufacture's protocol. Briefly  GEMs were generated by combining barcoded Single Cell three prime v3.1 Gel Beads  a Master Mix containing cells  and Partitioning Oil onto Chromium Next GEM Chip G. Following GEMs generation  the Gel Bead was dissolved  primers containing an Illumina TruSeq Read 1read 1 sequencing primer  16 nt 10x Barcode  12 nt unique molecular identifier UMI and 30 nt polydT sequence were released  and the co partitioned cells were lysed. The nucleic acid library construction was performed using the Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 10x Genomics  16 rxns PN 1000268 following the manufacture's protocol. post GEMs generation  primers were mixed with the cell lysate and a Master Mix containing reverse transcription RT reagents to produce barcoded  full length cDNA from polyadenylated mRNA. Silane magnetic beads were used to purify the first strand cDNA from the post GEM RT reaction mixture  which included leftover biochemical reagents and primers. Barcoded  full length cDNA was amplified via PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size. P5  P7  i7 and i5 sample indexes  and TruSeq Read 2 read 2 primer sequence were added via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries containing the P5 and P7 primers used in Illumina amplification were prepared for an estimated 5000 nuclei per sample.,Sample 2 lck GO+BA,SAMEA110406304,"Institute of Environmental Medicine, Karolinska Institutet",ENA FIRST PUBLIC:2022 07 23|ENA LAST UPDATE:2022 07 23|External Id:SAMEA110406304|INSDC center alias:Institute of Environmental Medicine  Karolinska Institutet|INSDC center name:Institute of Environmental Medicine  Karolinska Institutet|INSDC first public:2022 07 23T04:33:35Z|INSDC last update:2022 07 23T04:33:35Z|INSDC status:public|Submitter Id:E MTAB 11991:Sample 2 lck GO+BA|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larva|disease:normal|genotype:wild type genotype|isolate:not applicable|organism part:whole organism|sample name:E MTAB 11991:Sample 2 lck GO+BA|strain:Tglck:GFP,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; Single cell RNA sequencing of lck GFP transgenic zebrafish,E MTAB 11991:Sample 2 lck GO+BA p,Sample 2 lck GO+BA p,Single cell RNA sequencing of lck GFP transgenic zebrafish,The generation of germ free Tglck:GFP zebrafish followed previously established protocols [1]. In brief  2 hpf embryos were transferred to petri dishes with sterile E3 medium  supplemented with ampicillin 100 μg/mL  kanamycin 5 μg/mL and amphotericin B 250 ng/mL and incubated at 28°C. At 50% epiboly up to shield stage 6 hpf  the embryos were surface disinfected with 0.1% of polyvinylpyrroidone iodine PVP I for exactly 2 min  followed by 0.003% sterile bleach immersion for 18 min. The embryos were then rinsed with sterile E3 medium  transferred to flasks and incubated at 28°C. The viability was monitored  and sterile medium was refreshed daily. At day 4  the hatched embryos were used for the sterility validation. A day 5  germ free Tglck:GFP zebrafish were exposed to the combination of GO 30 µg/mL and butyrate 2.5 mM for 24 h. GO and BA were pre incubated for 1 h prior to the exposure. Fifty larvae were used as one replicate  four replicates  i.e. two hundred larvae in total  were used for each condition. post the exposure  zebrafish larvae were dissociated for single cell suspension following the published protocol [2]. Briefly  zebrafish larvae were euthanized with 0.01% of tricaine for 5 min  collected in 1.5 mL tube  and washed with PBS for three times. The dissociation was initiated by adding 500 μL of pre warmed enzyme mix containing 460 μL of 0.25% trypsin EDTA Gibco and 40 μL of collagenase Sigma Aldrich at the concentration of 100 mg/mL  followed by mechanical dissociation using P1000 and then P200 pipette tips in heat block at 30 °C until the tissue was no longer visible about 10 min. The dissociation was then stopped by adding 800 μL DMEM Corning Cat# 10 013 CV with 10% FBS Fisher Scientific. The cell pellets were collected by centrifuging at 1000 rpm for 5 min at RT  followed by washing with PBS. The cells were next resuspended in 0.5 mL DMEM with 10% FBS. Four replicates from each condition were pooled together at this step and filtered through 40 μm nylon mesh  with an additional washing using DMEM with 10% FBS. The cell suspension was then stained with a fluorescent DNA dye DRAQ7 to exclude non viable cells Invitrogen Cat# D15106 at the dose of 3 μM for 10 min at room temperature before the fluorescence activated cell sorting BD FACSAria III  BD Biosciences  NJ  USA. The sorting was performed using a 100 microns nozzle with the flow rate of 2 and temperature control at 4 °C and gated based on forward scatter and DRAQ7. The DRAQ7 lck+ cells of each sample were FACS sorted into the tubes containing DMEM with 10% FBS and placed on ice immediately post the sorting. The cells were then proceeded with the single cell RNA sequencing analysis. 1. Pham LN  Kanther M  Semova I & Rawls JF. Methods for generating and colonizing gnotobiotic zebrafish. Nat. Protoc. 3  1862 1875 2008. 2. Bresciani E  Broadbridge E  Liu PP An efficient dissociation protocol for generation of single cell suspension from zebrafish embryos and larvae  MethodsX. 5  1287 1290 2018. Single cell RNA sequencing scRNA seq was performed by Eukaryotic Single Cell Genomics Facility at SciLifeLab  Stockholm. The single cells collected from FACS sorting were loaded on a 10x GemCode Single Cell Instrument 10x Genomics  Pleasanton  USA to generate single cell gel beads in emulsion GEMs using the Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 10x Genomics following the manufacture's protocol.  Briefly  GEMs were generated by combining barcoded Single Cell three prime v3.1 Gel Beads  a Master Mix containing cells  and Partitioning Oil onto Chromium Next GEM Chip G. Following GEMs generation  the Gel Bead was dissolved  primers containing an Illumina TruSeq Read 1read 1 sequencing primer  16 nt 10x Barcode  12 nt unique molecular identifier UMI and 30 nt polydT sequence were released  and the co partitioned cells were lysed. The nucleic acid library construction was performed using the Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 10x Genomics  16 rxns PN 1000268 following the manufacture's protocol. post GEMs generation  primers were mixed with the cell lysate and a Master Mix containing reverse transcription RT reagents to produce barcoded  full length cDNA from polyadenylated mRNA. Silane magnetic beads were used to purify the first strand cDNA from the post GEM RT reaction mixture  which included leftover biochemical reagents and primers. Barcoded  full length cDNA was amplified via PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size. P5  P7  i7 and i5 sample indexes  and TruSeq Read 2 read 2 primer sequence were added via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries containing the P5 and P7 primers used in Illumina amplification were prepared for an estimated 5000 nuclei per sample.,Experimental Factor: stimulus:graphene oxide  30 microgram per milliliter|Experimental Factor: compound:butyrate|Experimental Factor: dose:2.5,AMPLICON,TRANSCRIPTOMIC SINGLE CELL,size fractionation,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP139797,Illumina NovaSeq 6000 paired end sequencing; Single cell RNA sequencing of lck GFP transgenic zebrafish,ENA FIRST PUBLIC:2022 07 23|ENA LAST UPDATE:2022 07 23,P25452_2001_S1_L002_R1_001.fastq.gz P25452_2001_S1_L002_R2_001.fastq.gz,fastq fastq,21068682172.0,178548154.0,E MTAB 11991:P25452 2001 S1 L002,0:28 1:90,A:5987758267;C:4786100132;G:5078292970;T:5215926275;N:604528,28,90,,,5987758267,4786100132,5078292970,5215926275,604528,ERX9522048,ERS12503450,ERA16488297,"Institute of Environmental Medicine, Karolinska Institutet|European Nucleotide Archive","Institute of Environmental Medicine, Karolinska Institutet|European Nucleotide Archive",2,0.00813,0.92702,0.00264,0.11874,0.99283,0.82737,0.30228,0.56929,28,90,T,B,sc-like readlen,illumina,novaseq_era,full_length,size_fractionation,trueseq,sc,single_cell_droplet,10x,,Sweden,2022-07-23,Larval,Larval,Whole Organism,All anatomical structures
15081,ERR12476478,ERX11852299,ERS17743543,ERP156655,PRJEB71869,Effects of paternal starvation in the offspring development of zebrafish,33b9d14c-4211-4249-aede-f0f021d197e6,Other,Dietary restriction in the form of fasting is a putative key to a healthier and longer life  but these benefits may come at a trade off with reproductive fitness and may affect the following generations. The potential inter  and transgenerational effects of long term fasting and starvation are particularly poorly understood in vertebrates when they originate from the paternal line. We utilised the externally fertilising zebrafish amenable to a split egg clutch design to explore the male specific effects of fasting/starvation on fertility and fitness of offspring independently of maternal contribution. Eighteen days of fasting resulted in reduced fertility in exposed males. While average offspring survival was not affected  we detected increased larval growth rate in F1 offspring from starved males and more malformed embryos at 24 hpf in F2 offspring produced by F1 offspring from starved males. Comparing the transcriptomes of F1 embryos sired by starved and fed fathers revealed robust and reproducible increased expression of muscle composition genes but lower expression of lipid metabolism and lysosome genes in embryos from starved fathers. A large proportion of these genes showed enrichment in the yolk syncytial layer suggesting gene regulatory responses associated with metabolism of nutrients through paternal effects on extra embryonic tissues which are loaded with maternal factors. We compared the embryo transcriptomes to published adult transcriptome datasets and found comparable repressive effects of starvation on metabolism associated genes. These similarities suggest a physiologically relevant  directed and potentially adaptive response transmitted by the father  independently from the offspring's nutritional state  which was defined by the mother.,ENA FIRST PUBLIC:2024 01 15|ENA LAST UPDATE:2024 01 15,,24 hpf embryo collected at 1242 from a cross with a starved father,1242D Starved,1242SD,,organism:Danio rerio|collection date:2018 02 02|scientific name:Danio rerio|common name:zebrafish|geographic location country and/or sea:Sweden,,,,,,,,,NextSeq 500 sequencing,ena EXPERIMENT TAB 15 01 2024 21:42:36:201 277053,1242SD,1,,,RNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,NextSeq 500,,ERP156655,NextSeq 500 sequencing,ENA FIRST PUBLIC:2024 01 22|ENA LAST UPDATE:2024 01 22,1242SD_S14_L003_R1_001.fastq.gz,fastq,95457398.0,1268859.0,ena RUN TAB 15 01 2024 21:42:36:202 277054,0:75.23,A:33339157;C:18598733;G:20350072;T:23148005;N:21431,75,,,,33339157,18598733,20350072,23148005,21431,ERX11852299,ERS17743543,ERA27788968,University of Birmingham|European Nucleotide Archive,University of Birmingham,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,size_fractionation,unknown,bulk,unknown,unknown,,United Kingdom,2024-01-15,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
25277,SRR30160454,SRX25627658,SRS22272474,SRP457111,PRJNA1009808,Dynamics of the zebrafish tRNAome during the maternal to zygotic transition [tRNA Seq],GSE241754,Transcriptome Analysis,Time course analysis of tRNA abundance during zebrafish early embryonic development. Overall design: Wild type TLAB strain zebrafish embryos were grown in standard housing conditions.Unfertilized eggs 0 hpf were collected or embryos were staged and collected at consecutive developmental time points  namelyat the 256 cell 2.5 hpf  1000 cell 3 hpf  sphere 4 hpf  shield 6 hpf and bud 10 hpf stages. Eggs and embryos were either flash frozen in liquid nitrogen or immediately processed. Samples were used for western blotting analysis  polysome profiling  ribosome profiling or mRNA and tRNA sequencing for investigating the regulation of tRNA gene expression and translational status during early zebrafish embryogenesis.,parent bioproject:PRJNA1009800,pubmed:39402326,,WT bud 10 hpf charged tRNA seqrep 3,GSM8441306,,tissue:10 hpf embryos|cell type:10 hpf embryos|geo loc name:missing|collection date:missing,WT bud 10 hpf charged tRNA seqrep 3,Read demultiplexing and adapter trimming performed with cutadapt v3.5  where bases were quality trimmed from five prime and three prime ends using a phred score cutoff of 30. Only trimmed reads were retained  and reads sorter than 10 bases were discarded. An additional round of trimming was performed to remove 5’ RN nucleotides introduced by circularization from the RT primer. Reads were processed with the mim tRNAseq computational pipeline v1.3.8 using the parameters:   species Drer   cluster id 0.93   threads 40   min cov 0.001   deconv cov ratio 0.4   max mismatches 0.075   remap   remap mismatches 0.075    max multi 10 max multi 6   remap   remap mismatches 0.075   crosstalks. Assembly: GRCz11 Supplementary files format and content: csv; mim tRNAseq generated CCA proportions,10 hpf embryos,,Total RNA from D.rerio embryos collected at the sphere 4 hpf or bud 10 hpf stage was extracted with TRIZOL under mild acidic conditions to preserve tRNA charging and  subjected to oxidation and beta elimination Behrens and Nedialkova  2022. tRNA seq libraries were prepared using the mim tRNAseq workflow Behrens and Nedialkova  2022 and sequenced on an Illumina NovaSeq 6000 platform.,,cell type:10 hpf embryos,GSM8441306,GSM8441306: WT bud 10 hpf charged tRNA seqrep 3; Danio rerio; ncRNA Seq,GSM8441306 r1,GSM8441306,1,Total RNA from D.rerio embryos collected at the sphere 4 hpf or bud 10 hpf stage was extracted with TRIZOL under mild acidic conditions to preserve tRNA charging and  subjected to oxidation and beta elimination Behrens and Nedialkova  2022. tRNA seq libraries were prepared using the mim tRNAseq workflow Behrens and Nedialkova  2022 and sequenced on an Illumina NovaSeq 6000 platform.,,ncRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP457111,,,10hpf_aa_rep3.fastq.gz,fastq,193965330.0,3367323.0,GSM8441306 r1,0:57.60,A:36799299;C:55100074;G:53758955;T:48306966;N:36,57,,,,36799299,55100074,53758955,48306966,36,SRX25627658,SRS22272474,SRA1941998,Max Planck Institute of Biochemistry,Max Planck Institute of Biochemistry,1,0.34405,,0.05049,,0.89471,,0.46469,,88,,B,,usable mapping rate,illumina,novaseq_era,5prime,size_fractionation,unknown,bulk,unknown,unknown,,Germany,2024-08-05,Multi-stage,Embryo,Embryo Imprecise,All anatomical structures
25278,SRR30160455,SRX25627657,SRS22272473,SRP457111,PRJNA1009808,Dynamics of the zebrafish tRNAome during the maternal to zygotic transition [tRNA Seq],GSE241754,Transcriptome Analysis,Time course analysis of tRNA abundance during zebrafish early embryonic development. Overall design: Wild type TLAB strain zebrafish embryos were grown in standard housing conditions.Unfertilized eggs 0 hpf were collected or embryos were staged and collected at consecutive developmental time points  namelyat the 256 cell 2.5 hpf  1000 cell 3 hpf  sphere 4 hpf  shield 6 hpf and bud 10 hpf stages. Eggs and embryos were either flash frozen in liquid nitrogen or immediately processed. Samples were used for western blotting analysis  polysome profiling  ribosome profiling or mRNA and tRNA sequencing for investigating the regulation of tRNA gene expression and translational status during early zebrafish embryogenesis.,parent bioproject:PRJNA1009800,pubmed:39402326,,WT bud 10 hpf charged tRNA seqrep 2,GSM8441305,,tissue:10 hpf embryos|cell type:10 hpf embryos|geo loc name:missing|collection date:missing,WT bud 10 hpf charged tRNA seqrep 2,Read demultiplexing and adapter trimming performed with cutadapt v3.5  where bases were quality trimmed from five prime and three prime ends using a phred score cutoff of 30. Only trimmed reads were retained  and reads sorter than 10 bases were discarded. An additional round of trimming was performed to remove 5’ RN nucleotides introduced by circularization from the RT primer. Reads were processed with the mim tRNAseq computational pipeline v1.3.8 using the parameters:   species Drer   cluster id 0.93   threads 40   min cov 0.001   deconv cov ratio 0.4   max mismatches 0.075   remap   remap mismatches 0.075    max multi 10 max multi 6   remap   remap mismatches 0.075   crosstalks. Assembly: GRCz11 Supplementary files format and content: csv; mim tRNAseq generated CCA proportions,10 hpf embryos,,Total RNA from D.rerio embryos collected at the sphere 4 hpf or bud 10 hpf stage was extracted with TRIZOL under mild acidic conditions to preserve tRNA charging and  subjected to oxidation and beta elimination Behrens and Nedialkova  2022. tRNA seq libraries were prepared using the mim tRNAseq workflow Behrens and Nedialkova  2022 and sequenced on an Illumina NovaSeq 6000 platform.,,cell type:10 hpf embryos,GSM8441305,GSM8441305: WT bud 10 hpf charged tRNA seqrep 2; Danio rerio; ncRNA Seq,GSM8441305 r1,GSM8441305,1,Total RNA from D.rerio embryos collected at the sphere 4 hpf or bud 10 hpf stage was extracted with TRIZOL under mild acidic conditions to preserve tRNA charging and  subjected to oxidation and beta elimination Behrens and Nedialkova  2022. tRNA seq libraries were prepared using the mim tRNAseq workflow Behrens and Nedialkova  2022 and sequenced on an Illumina NovaSeq 6000 platform.,,ncRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP457111,,,10hpf_aa_rep2.fastq.gz,fastq,138524715.0,2369009.0,GSM8441305 r1,0:58.47,A:26396279;C:39139297;G:38459048;T:34530060;N:31,58,,,,26396279,39139297,38459048,34530060,31,SRX25627657,SRS22272473,SRA1941998,Max Planck Institute of Biochemistry,Max Planck Institute of Biochemistry,1,0.35458,,0.05179,,0.89424,,0.46401,,74,,B,,usable mapping rate,illumina,novaseq_era,5prime,size_fractionation,unknown,bulk,unknown,unknown,,Germany,2024-08-05,Multi-stage,Embryo,Embryo Imprecise,All anatomical structures
25279,SRR30160456,SRX25627656,SRS22272472,SRP457111,PRJNA1009808,Dynamics of the zebrafish tRNAome during the maternal to zygotic transition [tRNA Seq],GSE241754,Transcriptome Analysis,Time course analysis of tRNA abundance during zebrafish early embryonic development. Overall design: Wild type TLAB strain zebrafish embryos were grown in standard housing conditions.Unfertilized eggs 0 hpf were collected or embryos were staged and collected at consecutive developmental time points  namelyat the 256 cell 2.5 hpf  1000 cell 3 hpf  sphere 4 hpf  shield 6 hpf and bud 10 hpf stages. Eggs and embryos were either flash frozen in liquid nitrogen or immediately processed. Samples were used for western blotting analysis  polysome profiling  ribosome profiling or mRNA and tRNA sequencing for investigating the regulation of tRNA gene expression and translational status during early zebrafish embryogenesis.,parent bioproject:PRJNA1009800,pubmed:39402326,,WT bud 10 hpf charged tRNA seqrep 1,GSM8441304,,tissue:10 hpf embryos|cell type:10 hpf embryos|geo loc name:missing|collection date:missing,WT bud 10 hpf charged tRNA seqrep 1,Read demultiplexing and adapter trimming performed with cutadapt v3.5  where bases were quality trimmed from five prime and three prime ends using a phred score cutoff of 30. Only trimmed reads were retained  and reads sorter than 10 bases were discarded. An additional round of trimming was performed to remove 5’ RN nucleotides introduced by circularization from the RT primer. Reads were processed with the mim tRNAseq computational pipeline v1.3.8 using the parameters:   species Drer   cluster id 0.93   threads 40   min cov 0.001   deconv cov ratio 0.4   max mismatches 0.075   remap   remap mismatches 0.075    max multi 10 max multi 6   remap   remap mismatches 0.075   crosstalks. Assembly: GRCz11 Supplementary files format and content: csv; mim tRNAseq generated CCA proportions,10 hpf embryos,,Total RNA from D.rerio embryos collected at the sphere 4 hpf or bud 10 hpf stage was extracted with TRIZOL under mild acidic conditions to preserve tRNA charging and  subjected to oxidation and beta elimination Behrens and Nedialkova  2022. tRNA seq libraries were prepared using the mim tRNAseq workflow Behrens and Nedialkova  2022 and sequenced on an Illumina NovaSeq 6000 platform.,,cell type:10 hpf embryos,GSM8441304,GSM8441304: WT bud 10 hpf charged tRNA seqrep 1; Danio rerio; ncRNA Seq,GSM8441304 r1,GSM8441304,1,Total RNA from D.rerio embryos collected at the sphere 4 hpf or bud 10 hpf stage was extracted with TRIZOL under mild acidic conditions to preserve tRNA charging and  subjected to oxidation and beta elimination Behrens and Nedialkova  2022. tRNA seq libraries were prepared using the mim tRNAseq workflow Behrens and Nedialkova  2022 and sequenced on an Illumina NovaSeq 6000 platform.,,ncRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP457111,,,10hpf_aa_rep1.fastq.gz,fastq,54473618.0,946419.0,GSM8441304 r1,0:57.56,A:10345022;C:15413782;G:15135500;T:13579304;N:10,57,,,,10345022,15413782,15135500,13579304,10,SRX25627656,SRS22272472,SRA1941998,Max Planck Institute of Biochemistry,Max Planck Institute of Biochemistry,1,0.36103,,0.0515,,0.89227,,0.4748,,81,,B,,usable mapping rate,illumina,novaseq_era,5prime,size_fractionation,unknown,bulk,unknown,unknown,,Germany,2024-08-05,Multi-stage,Embryo,Embryo Imprecise,All anatomical structures
25280,SRR30160457,SRX25627655,SRS22272471,SRP457111,PRJNA1009808,Dynamics of the zebrafish tRNAome during the maternal to zygotic transition [tRNA Seq],GSE241754,Transcriptome Analysis,Time course analysis of tRNA abundance during zebrafish early embryonic development. Overall design: Wild type TLAB strain zebrafish embryos were grown in standard housing conditions.Unfertilized eggs 0 hpf were collected or embryos were staged and collected at consecutive developmental time points  namelyat the 256 cell 2.5 hpf  1000 cell 3 hpf  sphere 4 hpf  shield 6 hpf and bud 10 hpf stages. Eggs and embryos were either flash frozen in liquid nitrogen or immediately processed. Samples were used for western blotting analysis  polysome profiling  ribosome profiling or mRNA and tRNA sequencing for investigating the regulation of tRNA gene expression and translational status during early zebrafish embryogenesis.,parent bioproject:PRJNA1009800,pubmed:39402326,,WT sphere 4 hpf charged tRNA seqrep 3,GSM8441303,,tissue:4 hpf embryos|cell type:4 hpf embryos|geo loc name:missing|collection date:missing,WT sphere 4 hpf charged tRNA seqrep 3,Read demultiplexing and adapter trimming performed with cutadapt v3.5  where bases were quality trimmed from five prime and three prime ends using a phred score cutoff of 30. Only trimmed reads were retained  and reads sorter than 10 bases were discarded. An additional round of trimming was performed to remove 5’ RN nucleotides introduced by circularization from the RT primer. Reads were processed with the mim tRNAseq computational pipeline v1.3.8 using the parameters:   species Drer   cluster id 0.93   threads 40   min cov 0.001   deconv cov ratio 0.4   max mismatches 0.075   remap   remap mismatches 0.075    max multi 10 max multi 6   remap   remap mismatches 0.075   crosstalks. Assembly: GRCz11 Supplementary files format and content: csv; mim tRNAseq generated CCA proportions,4 hpf embryos,,Total RNA from D.rerio embryos collected at the sphere 4 hpf or bud 10 hpf stage was extracted with TRIZOL under mild acidic conditions to preserve tRNA charging and  subjected to oxidation and beta elimination Behrens and Nedialkova  2022. tRNA seq libraries were prepared using the mim tRNAseq workflow Behrens and Nedialkova  2022 and sequenced on an Illumina NovaSeq 6000 platform.,,cell type:4 hpf embryos,GSM8441303,GSM8441303: WT sphere 4 hpf charged tRNA seqrep 3; Danio rerio; ncRNA Seq,GSM8441303 r1,GSM8441303,1,Total RNA from D.rerio embryos collected at the sphere 4 hpf or bud 10 hpf stage was extracted with TRIZOL under mild acidic conditions to preserve tRNA charging and  subjected to oxidation and beta elimination Behrens and Nedialkova  2022. tRNA seq libraries were prepared using the mim tRNAseq workflow Behrens and Nedialkova  2022 and sequenced on an Illumina NovaSeq 6000 platform.,,ncRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP457111,,,4hpf_aa_rep3.fastq.gz,fastq,100810543.0,1747597.0,GSM8441303 r1,0:57.69,A:20466558;C:28054923;G:26849246;T:25439798;N:18,57,,,,20466558,28054923,26849246,25439798,18,SRX25627655,SRS22272471,SRA1941998,Max Planck Institute of Biochemistry,Max Planck Institute of Biochemistry,1,0.36374,,0.06294,,0.87316,,0.54642,,39,,B,,usable mapping rate,illumina,novaseq_era,5prime,size_fractionation,unknown,bulk,unknown,unknown,,Germany,2024-08-05,Multi-stage,Embryo,Embryo Imprecise,All anatomical structures
25281,SRR30160458,SRX25627654,SRS22272470,SRP457111,PRJNA1009808,Dynamics of the zebrafish tRNAome during the maternal to zygotic transition [tRNA Seq],GSE241754,Transcriptome Analysis,Time course analysis of tRNA abundance during zebrafish early embryonic development. Overall design: Wild type TLAB strain zebrafish embryos were grown in standard housing conditions.Unfertilized eggs 0 hpf were collected or embryos were staged and collected at consecutive developmental time points  namelyat the 256 cell 2.5 hpf  1000 cell 3 hpf  sphere 4 hpf  shield 6 hpf and bud 10 hpf stages. Eggs and embryos were either flash frozen in liquid nitrogen or immediately processed. Samples were used for western blotting analysis  polysome profiling  ribosome profiling or mRNA and tRNA sequencing for investigating the regulation of tRNA gene expression and translational status during early zebrafish embryogenesis.,parent bioproject:PRJNA1009800,pubmed:39402326,,WT sphere 4 hpf charged tRNA seqrep 2,GSM8441302,,tissue:4 hpf embryos|cell type:4 hpf embryos|geo loc name:missing|collection date:missing,WT sphere 4 hpf charged tRNA seqrep 2,Read demultiplexing and adapter trimming performed with cutadapt v3.5  where bases were quality trimmed from five prime and three prime ends using a phred score cutoff of 30. Only trimmed reads were retained  and reads sorter than 10 bases were discarded. An additional round of trimming was performed to remove 5’ RN nucleotides introduced by circularization from the RT primer. Reads were processed with the mim tRNAseq computational pipeline v1.3.8 using the parameters:   species Drer   cluster id 0.93   threads 40   min cov 0.001   deconv cov ratio 0.4   max mismatches 0.075   remap   remap mismatches 0.075    max multi 10 max multi 6   remap   remap mismatches 0.075   crosstalks. Assembly: GRCz11 Supplementary files format and content: csv; mim tRNAseq generated CCA proportions,4 hpf embryos,,Total RNA from D.rerio embryos collected at the sphere 4 hpf or bud 10 hpf stage was extracted with TRIZOL under mild acidic conditions to preserve tRNA charging and  subjected to oxidation and beta elimination Behrens and Nedialkova  2022. tRNA seq libraries were prepared using the mim tRNAseq workflow Behrens and Nedialkova  2022 and sequenced on an Illumina NovaSeq 6000 platform.,,cell type:4 hpf embryos,GSM8441302,GSM8441302: WT sphere 4 hpf charged tRNA seqrep 2; Danio rerio; ncRNA Seq,GSM8441302 r1,GSM8441302,1,Total RNA from D.rerio embryos collected at the sphere 4 hpf or bud 10 hpf stage was extracted with TRIZOL under mild acidic conditions to preserve tRNA charging and  subjected to oxidation and beta elimination Behrens and Nedialkova  2022. tRNA seq libraries were prepared using the mim tRNAseq workflow Behrens and Nedialkova  2022 and sequenced on an Illumina NovaSeq 6000 platform.,,ncRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP457111,,,4hpf_aa_rep2.fastq.gz,fastq,121662759.0,2046536.0,GSM8441302 r1,0:59.45,A:24519095;C:33689156;G:32726095;T:30728382;N:31,59,,,,24519095,33689156,32726095,30728382,31,SRX25627654,SRS22272470,SRA1941998,Max Planck Institute of Biochemistry,Max Planck Institute of Biochemistry,1,0.3726,,0.06263,,0.87136,,0.55584,,31,,B,,usable mapping rate,illumina,novaseq_era,5prime,size_fractionation,unknown,bulk,unknown,unknown,,Germany,2024-08-05,Multi-stage,Embryo,Embryo Imprecise,All anatomical structures
25282,SRR30160459,SRX25627653,SRS22272469,SRP457111,PRJNA1009808,Dynamics of the zebrafish tRNAome during the maternal to zygotic transition [tRNA Seq],GSE241754,Transcriptome Analysis,Time course analysis of tRNA abundance during zebrafish early embryonic development. Overall design: Wild type TLAB strain zebrafish embryos were grown in standard housing conditions.Unfertilized eggs 0 hpf were collected or embryos were staged and collected at consecutive developmental time points  namelyat the 256 cell 2.5 hpf  1000 cell 3 hpf  sphere 4 hpf  shield 6 hpf and bud 10 hpf stages. Eggs and embryos were either flash frozen in liquid nitrogen or immediately processed. Samples were used for western blotting analysis  polysome profiling  ribosome profiling or mRNA and tRNA sequencing for investigating the regulation of tRNA gene expression and translational status during early zebrafish embryogenesis.,parent bioproject:PRJNA1009800,pubmed:39402326,,WT sphere 4 hpf charged tRNA seqrep 1,GSM8441301,,tissue:4 hpf embryos|cell type:4 hpf embryos|geo loc name:missing|collection date:missing,WT sphere 4 hpf charged tRNA seqrep 1,Read demultiplexing and adapter trimming performed with cutadapt v3.5  where bases were quality trimmed from five prime and three prime ends using a phred score cutoff of 30. Only trimmed reads were retained  and reads sorter than 10 bases were discarded. An additional round of trimming was performed to remove 5’ RN nucleotides introduced by circularization from the RT primer. Reads were processed with the mim tRNAseq computational pipeline v1.3.8 using the parameters:   species Drer   cluster id 0.93   threads 40   min cov 0.001   deconv cov ratio 0.4   max mismatches 0.075   remap   remap mismatches 0.075    max multi 10 max multi 6   remap   remap mismatches 0.075   crosstalks. Assembly: GRCz11 Supplementary files format and content: csv; mim tRNAseq generated CCA proportions,4 hpf embryos,,Total RNA from D.rerio embryos collected at the sphere 4 hpf or bud 10 hpf stage was extracted with TRIZOL under mild acidic conditions to preserve tRNA charging and  subjected to oxidation and beta elimination Behrens and Nedialkova  2022. tRNA seq libraries were prepared using the mim tRNAseq workflow Behrens and Nedialkova  2022 and sequenced on an Illumina NovaSeq 6000 platform.,,cell type:4 hpf embryos,GSM8441301,GSM8441301: WT sphere 4 hpf charged tRNA seqrep 1; Danio rerio; ncRNA Seq,GSM8441301 r1,GSM8441301,1,Total RNA from D.rerio embryos collected at the sphere 4 hpf or bud 10 hpf stage was extracted with TRIZOL under mild acidic conditions to preserve tRNA charging and  subjected to oxidation and beta elimination Behrens and Nedialkova  2022. tRNA seq libraries were prepared using the mim tRNAseq workflow Behrens and Nedialkova  2022 and sequenced on an Illumina NovaSeq 6000 platform.,,ncRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP457111,,,4hpf_aa_rep1.fastq.gz,fastq,124990980.0,2116213.0,GSM8441301 r1,0:59.06,A:25487542;C:34621140;G:33284460;T:31597816;N:22,59,,,,25487542,34621140,33284460,31597816,22,SRX25627653,SRS22272469,SRA1941998,Max Planck Institute of Biochemistry,Max Planck Institute of Biochemistry,1,0.36013,,0.05967,,0.87387,,0.55002,,44,,B,,usable mapping rate,illumina,novaseq_era,5prime,size_fractionation,unknown,bulk,unknown,unknown,,Germany,2024-08-05,Multi-stage,Embryo,Embryo Imprecise,All anatomical structures
25283,SRR25764121,SRX21486801,SRS18719093,SRP457111,PRJNA1009808,Dynamics of the zebrafish tRNAome during the maternal to zygotic transition [tRNA Seq],GSE241754,Transcriptome Analysis,Time course analysis of tRNA abundance during zebrafish early embryonic development. Overall design: Wild type TLAB strain zebrafish embryos were grown in standard housing conditions.Unfertilized eggs 0 hpf were collected or embryos were staged and collected at consecutive developmental time points  namelyat the 256 cell 2.5 hpf  1000 cell 3 hpf  sphere 4 hpf  shield 6 hpf and bud 10 hpf stages. Eggs and embryos were either flash frozen in liquid nitrogen or immediately processed. Samples were used for western blotting analysis  polysome profiling  ribosome profiling or mRNA and tRNA sequencing for investigating the regulation of tRNA gene expression and translational status during early zebrafish embryogenesis.,parent bioproject:PRJNA1009800,pubmed:39402326,,WT bud 10 hpf tRNA seq rep2,GSM7734782,,source name:Gastrula|strain:TLAB strain|tissue:Gastrula|developmental stage:Bud 10 hpf|genotype:WT|geo loc name:missing|collection date:missing,WT bud 10 hpf tRNA seq rep2,Read demultiplexing and adapter trimming performed with cutadapt v3.5  where bases were quality trimmed from five prime and three prime ends using a phred score cutoff of 30. Only trimmed reads were retained  and reads sorter than 10 bases were discarded. An additional round of trimming was performed to remove 5’ RN nucleotides introduced by circularization from the RT primer. Reads were processed with the mim tRNAseq computational pipeline v1.2 using the parameters   species Drer   cluster id 0.93   min cov 0.001   max mismatches 0.075   control condition Egg   deconv cov ratio 0.4   remap mismatches 0.075. Additional DESeq2 analysis was performed by excluding unsplit tRNA clusters  and on read counts summed by isotype. Assembly: GRCz11 Supplementary files format and content: csv; mim tRNAseq generated tRNA transcript resad counts,Gastrula,unperturbed growth conditions in E3 medium for zebrafish embryos.,50 whole embryos were collected per sample and immediately lysed in 800uL LiDS/LET buffer5% Lithium dodecyl sulfate in 20 mM Tris HCl pH=7.4  100 mM LiCl  2 mM EDTA  5 mM DTT  pH 7.4. tRNA seq libraries were prepared using the mim tRNAseq workflow Behrens 2021  2022 and sequenced on an Illumina NextSeq 500 platform. mim tRNAseq,Embryos were grown in standard housing conditions namely28°C at a 14/10 hour light/dark cycle.,strain:TLAB strain|tissue:Gastrula|developmental stage:Bud 10 hpf|genotype:WT,GSM7734782,GSM7734782: WT bud 10 hpf tRNA seq rep2; Danio rerio; ncRNA Seq,GSM7734782 r1,GSM7734782,1,50 whole embryos were collected per sample and immediately lysed in 800uL LiDS/LET buffer5% Lithium dodecyl sulfate in 20 mM Tris HCl pH=7.4  100 mM LiCl  2 mM EDTA  5 mM DTT  pH 7.4. tRNA seq libraries were prepared using the mim tRNAseq workflow Behrens 2021  2022 and sequenced on an Illumina NextSeq 500 platform. mim tRNAseq,,ncRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,NextSeq 500,,SRP457111,,,WT_tRNA_bud_2.fastq.gz,fastq,278145656.0,4215107.0,GSM7734782 r1,0:65.99,A:52499947;C:77161357;G:79314034;T:69169753;N:565,65,,,,52499947,77161357,79314034,69169753,565,SRX21486801,SRS18719093,SRA1700461,"Mechanisms of Protein Biogenesis, Max Planck Institute for Biochemistry",Max Planck Institute of Biochemistry,1,0.31888,,0.01661,,0.92348,,0.40156,,75,,B,,usable mapping rate,illumina,nextseq,5prime,size_fractionation,unknown,bulk,unknown,unknown,,Germany,2023-08-28,Gastrula,Embryo,Whole Organism,All anatomical structures
25284,SRR25764122,SRX21486800,SRS18719092,SRP457111,PRJNA1009808,Dynamics of the zebrafish tRNAome during the maternal to zygotic transition [tRNA Seq],GSE241754,Transcriptome Analysis,Time course analysis of tRNA abundance during zebrafish early embryonic development. Overall design: Wild type TLAB strain zebrafish embryos were grown in standard housing conditions.Unfertilized eggs 0 hpf were collected or embryos were staged and collected at consecutive developmental time points  namelyat the 256 cell 2.5 hpf  1000 cell 3 hpf  sphere 4 hpf  shield 6 hpf and bud 10 hpf stages. Eggs and embryos were either flash frozen in liquid nitrogen or immediately processed. Samples were used for western blotting analysis  polysome profiling  ribosome profiling or mRNA and tRNA sequencing for investigating the regulation of tRNA gene expression and translational status during early zebrafish embryogenesis.,parent bioproject:PRJNA1009800,pubmed:39402326,,WT bud 10 hpf tRNA seq rep1,GSM7734781,,source name:Gastrula|strain:TLAB strain|tissue:Gastrula|developmental stage:Bud 10 hpf|genotype:WT|geo loc name:missing|collection date:missing,WT bud 10 hpf tRNA seq rep1,Read demultiplexing and adapter trimming performed with cutadapt v3.5  where bases were quality trimmed from five prime and three prime ends using a phred score cutoff of 30. Only trimmed reads were retained  and reads sorter than 10 bases were discarded. An additional round of trimming was performed to remove 5’ RN nucleotides introduced by circularization from the RT primer. Reads were processed with the mim tRNAseq computational pipeline v1.2 using the parameters   species Drer   cluster id 0.93   min cov 0.001   max mismatches 0.075   control condition Egg   deconv cov ratio 0.4   remap mismatches 0.075. Additional DESeq2 analysis was performed by excluding unsplit tRNA clusters  and on read counts summed by isotype. Assembly: GRCz11 Supplementary files format and content: csv; mim tRNAseq generated tRNA transcript resad counts,Gastrula,unperturbed growth conditions in E3 medium for zebrafish embryos.,50 whole embryos were collected per sample and immediately lysed in 800uL LiDS/LET buffer5% Lithium dodecyl sulfate in 20 mM Tris HCl pH=7.4  100 mM LiCl  2 mM EDTA  5 mM DTT  pH 7.4. tRNA seq libraries were prepared using the mim tRNAseq workflow Behrens 2021  2022 and sequenced on an Illumina NextSeq 500 platform. mim tRNAseq,Embryos were grown in standard housing conditions namely28°C at a 14/10 hour light/dark cycle.,strain:TLAB strain|tissue:Gastrula|developmental stage:Bud 10 hpf|genotype:WT,GSM7734781,GSM7734781: WT bud 10 hpf tRNA seq rep1; Danio rerio; ncRNA Seq,GSM7734781 r1,GSM7734781,1,50 whole embryos were collected per sample and immediately lysed in 800uL LiDS/LET buffer5% Lithium dodecyl sulfate in 20 mM Tris HCl pH=7.4  100 mM LiCl  2 mM EDTA  5 mM DTT  pH 7.4. tRNA seq libraries were prepared using the mim tRNAseq workflow Behrens 2021  2022 and sequenced on an Illumina NextSeq 500 platform. mim tRNAseq,,ncRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,NextSeq 500,,SRP457111,,,WT_tRNA_bud_1.fastq.gz,fastq,385514625.0,5770392.0,GSM7734781 r1,0:66.81,A:73305393;C:107155246;G:109793285;T:95259823;N:878,66,,,,73305393,107155246,109793285,95259823,878,SRX21486800,SRS18719092,SRA1700461,"Mechanisms of Protein Biogenesis, Max Planck Institute for Biochemistry",Max Planck Institute of Biochemistry,1,0.33213,,0.01782,,0.92354,,0.42724,,39,,B,,usable mapping rate,illumina,nextseq,5prime,size_fractionation,unknown,bulk,unknown,unknown,,Germany,2023-08-28,Gastrula,Embryo,Whole Organism,All anatomical structures
25285,SRR25764123,SRX21486799,SRS18719098,SRP457111,PRJNA1009808,Dynamics of the zebrafish tRNAome during the maternal to zygotic transition [tRNA Seq],GSE241754,Transcriptome Analysis,Time course analysis of tRNA abundance during zebrafish early embryonic development. Overall design: Wild type TLAB strain zebrafish embryos were grown in standard housing conditions.Unfertilized eggs 0 hpf were collected or embryos were staged and collected at consecutive developmental time points  namelyat the 256 cell 2.5 hpf  1000 cell 3 hpf  sphere 4 hpf  shield 6 hpf and bud 10 hpf stages. Eggs and embryos were either flash frozen in liquid nitrogen or immediately processed. Samples were used for western blotting analysis  polysome profiling  ribosome profiling or mRNA and tRNA sequencing for investigating the regulation of tRNA gene expression and translational status during early zebrafish embryogenesis.,parent bioproject:PRJNA1009800,pubmed:39402326,,WT shield 6 hpf tRNA seq rep2,GSM7734780,,source name:Gastrula|strain:TLAB strain|tissue:Gastrula|developmental stage:Shield 6 hpf|genotype:WT|geo loc name:missing|collection date:missing,WT shield 6 hpf tRNA seq rep2,Read demultiplexing and adapter trimming performed with cutadapt v3.5  where bases were quality trimmed from five prime and three prime ends using a phred score cutoff of 30. Only trimmed reads were retained  and reads sorter than 10 bases were discarded. An additional round of trimming was performed to remove 5’ RN nucleotides introduced by circularization from the RT primer. Reads were processed with the mim tRNAseq computational pipeline v1.2 using the parameters   species Drer   cluster id 0.93   min cov 0.001   max mismatches 0.075   control condition Egg   deconv cov ratio 0.4   remap mismatches 0.075. Additional DESeq2 analysis was performed by excluding unsplit tRNA clusters  and on read counts summed by isotype. Assembly: GRCz11 Supplementary files format and content: csv; mim tRNAseq generated tRNA transcript resad counts,Gastrula,unperturbed growth conditions in E3 medium for zebrafish embryos.,50 whole embryos were collected per sample and immediately lysed in 800uL LiDS/LET buffer5% Lithium dodecyl sulfate in 20 mM Tris HCl pH=7.4  100 mM LiCl  2 mM EDTA  5 mM DTT  pH 7.4. tRNA seq libraries were prepared using the mim tRNAseq workflow Behrens 2021  2022 and sequenced on an Illumina NextSeq 500 platform. mim tRNAseq,Embryos were grown in standard housing conditions namely28°C at a 14/10 hour light/dark cycle.,strain:TLAB strain|tissue:Gastrula|developmental stage:Shield 6 hpf|genotype:WT,GSM7734780,GSM7734780: WT shield 6 hpf tRNA seq rep2; Danio rerio; ncRNA Seq,GSM7734780 r1,GSM7734780,1,50 whole embryos were collected per sample and immediately lysed in 800uL LiDS/LET buffer5% Lithium dodecyl sulfate in 20 mM Tris HCl pH=7.4  100 mM LiCl  2 mM EDTA  5 mM DTT  pH 7.4. tRNA seq libraries were prepared using the mim tRNAseq workflow Behrens 2021  2022 and sequenced on an Illumina NextSeq 500 platform. mim tRNAseq,,ncRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,NextSeq 500,,SRP457111,,,WT_tRNA_shield_2.fastq.gz,fastq,469031736.0,7421688.0,GSM7734780 r1,0:63.20,A:90257219;C:130440728;G:130549302;T:117783411;N:1076,63,,,,90257219,130440728,130549302,117783411,1076,SRX21486799,SRS18719098,SRA1700461,"Mechanisms of Protein Biogenesis, Max Planck Institute for Biochemistry",Max Planck Institute of Biochemistry,1,0.29535,,0.02113,,0.91528,,0.43824,,37,,B,,usable mapping rate,illumina,nextseq,5prime,size_fractionation,unknown,bulk,unknown,unknown,,Germany,2023-08-28,Gastrula,Embryo,Whole Organism,All anatomical structures
25286,SRR25764124,SRX21486798,SRS18719100,SRP457111,PRJNA1009808,Dynamics of the zebrafish tRNAome during the maternal to zygotic transition [tRNA Seq],GSE241754,Transcriptome Analysis,Time course analysis of tRNA abundance during zebrafish early embryonic development. Overall design: Wild type TLAB strain zebrafish embryos were grown in standard housing conditions.Unfertilized eggs 0 hpf were collected or embryos were staged and collected at consecutive developmental time points  namelyat the 256 cell 2.5 hpf  1000 cell 3 hpf  sphere 4 hpf  shield 6 hpf and bud 10 hpf stages. Eggs and embryos were either flash frozen in liquid nitrogen or immediately processed. Samples were used for western blotting analysis  polysome profiling  ribosome profiling or mRNA and tRNA sequencing for investigating the regulation of tRNA gene expression and translational status during early zebrafish embryogenesis.,parent bioproject:PRJNA1009800,pubmed:39402326,,WT shield 6 hpf tRNA seq rep1,GSM7734779,,source name:Gastrula|strain:TLAB strain|tissue:Gastrula|developmental stage:Shield 6 hpf|genotype:WT|geo loc name:missing|collection date:missing,WT shield 6 hpf tRNA seq rep1,Read demultiplexing and adapter trimming performed with cutadapt v3.5  where bases were quality trimmed from five prime and three prime ends using a phred score cutoff of 30. Only trimmed reads were retained  and reads sorter than 10 bases were discarded. An additional round of trimming was performed to remove 5’ RN nucleotides introduced by circularization from the RT primer. Reads were processed with the mim tRNAseq computational pipeline v1.2 using the parameters   species Drer   cluster id 0.93   min cov 0.001   max mismatches 0.075   control condition Egg   deconv cov ratio 0.4   remap mismatches 0.075. Additional DESeq2 analysis was performed by excluding unsplit tRNA clusters  and on read counts summed by isotype. Assembly: GRCz11 Supplementary files format and content: csv; mim tRNAseq generated tRNA transcript resad counts,Gastrula,unperturbed growth conditions in E3 medium for zebrafish embryos.,50 whole embryos were collected per sample and immediately lysed in 800uL LiDS/LET buffer5% Lithium dodecyl sulfate in 20 mM Tris HCl pH=7.4  100 mM LiCl  2 mM EDTA  5 mM DTT  pH 7.4. tRNA seq libraries were prepared using the mim tRNAseq workflow Behrens 2021  2022 and sequenced on an Illumina NextSeq 500 platform. mim tRNAseq,Embryos were grown in standard housing conditions namely28°C at a 14/10 hour light/dark cycle.,strain:TLAB strain|tissue:Gastrula|developmental stage:Shield 6 hpf|genotype:WT,GSM7734779,GSM7734779: WT shield 6 hpf tRNA seq rep1; Danio rerio; ncRNA Seq,GSM7734779 r1,GSM7734779,1,50 whole embryos were collected per sample and immediately lysed in 800uL LiDS/LET buffer5% Lithium dodecyl sulfate in 20 mM Tris HCl pH=7.4  100 mM LiCl  2 mM EDTA  5 mM DTT  pH 7.4. tRNA seq libraries were prepared using the mim tRNAseq workflow Behrens 2021  2022 and sequenced on an Illumina NextSeq 500 platform. mim tRNAseq,,ncRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,NextSeq 500,,SRP457111,,,WT_tRNA_shield_1.fastq.gz,fastq,487207771.0,7521930.0,GSM7734779 r1,0:64.77,A:94654510;C:134893975;G:135716906;T:121941280;N:1100,64,,,,94654510,134893975,135716906,121941280,1100,SRX21486798,SRS18719100,SRA1700461,"Mechanisms of Protein Biogenesis, Max Planck Institute for Biochemistry",Max Planck Institute of Biochemistry,1,0.30664,,0.02274,,0.91297,,0.46012,,79,,B,,usable mapping rate,illumina,nextseq,5prime,size_fractionation,unknown,bulk,unknown,unknown,,Germany,2023-08-28,Gastrula,Embryo,Whole Organism,All anatomical structures
25287,SRR25764125,SRX21486797,SRS18719094,SRP457111,PRJNA1009808,Dynamics of the zebrafish tRNAome during the maternal to zygotic transition [tRNA Seq],GSE241754,Transcriptome Analysis,Time course analysis of tRNA abundance during zebrafish early embryonic development. Overall design: Wild type TLAB strain zebrafish embryos were grown in standard housing conditions.Unfertilized eggs 0 hpf were collected or embryos were staged and collected at consecutive developmental time points  namelyat the 256 cell 2.5 hpf  1000 cell 3 hpf  sphere 4 hpf  shield 6 hpf and bud 10 hpf stages. Eggs and embryos were either flash frozen in liquid nitrogen or immediately processed. Samples were used for western blotting analysis  polysome profiling  ribosome profiling or mRNA and tRNA sequencing for investigating the regulation of tRNA gene expression and translational status during early zebrafish embryogenesis.,parent bioproject:PRJNA1009800,pubmed:39402326,,WT sphere 4 hpf tRNA seq rep2,GSM7734778,,source name:Blastula|strain:TLAB strain|tissue:Blastula|developmental stage:Sphere 4 hpf|genotype:WT|geo loc name:missing|collection date:missing,WT sphere 4 hpf tRNA seq rep2,Read demultiplexing and adapter trimming performed with cutadapt v3.5  where bases were quality trimmed from five prime and three prime ends using a phred score cutoff of 30. Only trimmed reads were retained  and reads sorter than 10 bases were discarded. An additional round of trimming was performed to remove 5’ RN nucleotides introduced by circularization from the RT primer. Reads were processed with the mim tRNAseq computational pipeline v1.2 using the parameters   species Drer   cluster id 0.93   min cov 0.001   max mismatches 0.075   control condition Egg   deconv cov ratio 0.4   remap mismatches 0.075. Additional DESeq2 analysis was performed by excluding unsplit tRNA clusters  and on read counts summed by isotype. Assembly: GRCz11 Supplementary files format and content: csv; mim tRNAseq generated tRNA transcript resad counts,Blastula,unperturbed growth conditions in E3 medium for zebrafish embryos.,50 whole embryos were collected per sample and immediately lysed in 800uL LiDS/LET buffer5% Lithium dodecyl sulfate in 20 mM Tris HCl pH=7.4  100 mM LiCl  2 mM EDTA  5 mM DTT  pH 7.4. tRNA seq libraries were prepared using the mim tRNAseq workflow Behrens 2021  2022 and sequenced on an Illumina NextSeq 500 platform. mim tRNAseq,Embryos were grown in standard housing conditions namely28°C at a 14/10 hour light/dark cycle.,strain:TLAB strain|tissue:Blastula|developmental stage:Sphere 4 hpf|genotype:WT,GSM7734778,GSM7734778: WT sphere 4 hpf tRNA seq rep2; Danio rerio; ncRNA Seq,GSM7734778 r1,GSM7734778,1,50 whole embryos were collected per sample and immediately lysed in 800uL LiDS/LET buffer5% Lithium dodecyl sulfate in 20 mM Tris HCl pH=7.4  100 mM LiCl  2 mM EDTA  5 mM DTT  pH 7.4. tRNA seq libraries were prepared using the mim tRNAseq workflow Behrens 2021  2022 and sequenced on an Illumina NextSeq 500 platform. mim tRNAseq,,ncRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,NextSeq 500,,SRP457111,,,WT_tRNA_sphere_2.fastq.gz,fastq,196089572.0,2998867.0,GSM7734778 r1,0:65.39,A:39134451;C:53803100;G:53602781;T:49548779;N:461,65,,,,39134451,53803100,53602781,49548779,461,SRX21486797,SRS18719094,SRA1700461,"Mechanisms of Protein Biogenesis, Max Planck Institute for Biochemistry",Max Planck Institute of Biochemistry,1,0.28808,,0.01959,,0.91553,,0.47742,,78,,B,,usable mapping rate,illumina,nextseq,5prime,size_fractionation,unknown,bulk,unknown,unknown,,Germany,2023-08-28,Blastula,Embryo,Whole Organism,All anatomical structures
25288,SRR25764126,SRX21486796,SRS18719096,SRP457111,PRJNA1009808,Dynamics of the zebrafish tRNAome during the maternal to zygotic transition [tRNA Seq],GSE241754,Transcriptome Analysis,Time course analysis of tRNA abundance during zebrafish early embryonic development. Overall design: Wild type TLAB strain zebrafish embryos were grown in standard housing conditions.Unfertilized eggs 0 hpf were collected or embryos were staged and collected at consecutive developmental time points  namelyat the 256 cell 2.5 hpf  1000 cell 3 hpf  sphere 4 hpf  shield 6 hpf and bud 10 hpf stages. Eggs and embryos were either flash frozen in liquid nitrogen or immediately processed. Samples were used for western blotting analysis  polysome profiling  ribosome profiling or mRNA and tRNA sequencing for investigating the regulation of tRNA gene expression and translational status during early zebrafish embryogenesis.,parent bioproject:PRJNA1009800,pubmed:39402326,,WT sphere 4 hpf tRNA seq rep1,GSM7734777,,source name:Blastula|strain:TLAB strain|tissue:Blastula|developmental stage:Sphere 4 hpf|genotype:WT|geo loc name:missing|collection date:missing,WT sphere 4 hpf tRNA seq rep1,Read demultiplexing and adapter trimming performed with cutadapt v3.5  where bases were quality trimmed from five prime and three prime ends using a phred score cutoff of 30. Only trimmed reads were retained  and reads sorter than 10 bases were discarded. An additional round of trimming was performed to remove 5’ RN nucleotides introduced by circularization from the RT primer. Reads were processed with the mim tRNAseq computational pipeline v1.2 using the parameters   species Drer   cluster id 0.93   min cov 0.001   max mismatches 0.075   control condition Egg   deconv cov ratio 0.4   remap mismatches 0.075. Additional DESeq2 analysis was performed by excluding unsplit tRNA clusters  and on read counts summed by isotype. Assembly: GRCz11 Supplementary files format and content: csv; mim tRNAseq generated tRNA transcript resad counts,Blastula,unperturbed growth conditions in E3 medium for zebrafish embryos.,50 whole embryos were collected per sample and immediately lysed in 800uL LiDS/LET buffer5% Lithium dodecyl sulfate in 20 mM Tris HCl pH=7.4  100 mM LiCl  2 mM EDTA  5 mM DTT  pH 7.4. tRNA seq libraries were prepared using the mim tRNAseq workflow Behrens 2021  2022 and sequenced on an Illumina NextSeq 500 platform. mim tRNAseq,Embryos were grown in standard housing conditions namely28°C at a 14/10 hour light/dark cycle.,strain:TLAB strain|tissue:Blastula|developmental stage:Sphere 4 hpf|genotype:WT,GSM7734777,GSM7734777: WT sphere 4 hpf tRNA seq rep1; Danio rerio; ncRNA Seq,GSM7734777 r1,GSM7734777,1,50 whole embryos were collected per sample and immediately lysed in 800uL LiDS/LET buffer5% Lithium dodecyl sulfate in 20 mM Tris HCl pH=7.4  100 mM LiCl  2 mM EDTA  5 mM DTT  pH 7.4. tRNA seq libraries were prepared using the mim tRNAseq workflow Behrens 2021  2022 and sequenced on an Illumina NextSeq 500 platform. mim tRNAseq,,ncRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,NextSeq 500,,SRP457111,,,WT_tRNA_sphere_1.fastq.gz,fastq,273027894.0,4080366.0,GSM7734777 r1,0:66.91,A:54678043;C:74713512;G:74872888;T:68762883;N:568,66,,,,54678043,74713512,74872888,68762883,568,SRX21486796,SRS18719096,SRA1700461,"Mechanisms of Protein Biogenesis, Max Planck Institute for Biochemistry",Max Planck Institute of Biochemistry,1,0.30124,,0.01877,,0.9163,,0.49987,,79,,B,,usable mapping rate,illumina,nextseq,5prime,size_fractionation,unknown,bulk,unknown,unknown,,Germany,2023-08-28,Blastula,Embryo,Whole Organism,All anatomical structures
25289,SRR25764127,SRX21486795,SRS18719097,SRP457111,PRJNA1009808,Dynamics of the zebrafish tRNAome during the maternal to zygotic transition [tRNA Seq],GSE241754,Transcriptome Analysis,Time course analysis of tRNA abundance during zebrafish early embryonic development. Overall design: Wild type TLAB strain zebrafish embryos were grown in standard housing conditions.Unfertilized eggs 0 hpf were collected or embryos were staged and collected at consecutive developmental time points  namelyat the 256 cell 2.5 hpf  1000 cell 3 hpf  sphere 4 hpf  shield 6 hpf and bud 10 hpf stages. Eggs and embryos were either flash frozen in liquid nitrogen or immediately processed. Samples were used for western blotting analysis  polysome profiling  ribosome profiling or mRNA and tRNA sequencing for investigating the regulation of tRNA gene expression and translational status during early zebrafish embryogenesis.,parent bioproject:PRJNA1009800,pubmed:39402326,,WT 1000 cell 3 hpf tRNA seq rep2,GSM7734776,,source name:Blastula|strain:TLAB strain|tissue:Blastula|developmental stage:1000 cell 3 hpf|genotype:WT|geo loc name:missing|collection date:missing,WT 1000 cell 3 hpf tRNA seq rep2,Read demultiplexing and adapter trimming performed with cutadapt v3.5  where bases were quality trimmed from five prime and three prime ends using a phred score cutoff of 30. Only trimmed reads were retained  and reads sorter than 10 bases were discarded. An additional round of trimming was performed to remove 5’ RN nucleotides introduced by circularization from the RT primer. Reads were processed with the mim tRNAseq computational pipeline v1.2 using the parameters   species Drer   cluster id 0.93   min cov 0.001   max mismatches 0.075   control condition Egg   deconv cov ratio 0.4   remap mismatches 0.075. Additional DESeq2 analysis was performed by excluding unsplit tRNA clusters  and on read counts summed by isotype. Assembly: GRCz11 Supplementary files format and content: csv; mim tRNAseq generated tRNA transcript resad counts,Blastula,unperturbed growth conditions in E3 medium for zebrafish embryos.,50 whole embryos were collected per sample and immediately lysed in 800uL LiDS/LET buffer5% Lithium dodecyl sulfate in 20 mM Tris HCl pH=7.4  100 mM LiCl  2 mM EDTA  5 mM DTT  pH 7.4. tRNA seq libraries were prepared using the mim tRNAseq workflow Behrens 2021  2022 and sequenced on an Illumina NextSeq 500 platform. mim tRNAseq,Embryos were grown in standard housing conditions namely28°C at a 14/10 hour light/dark cycle.,strain:TLAB strain|tissue:Blastula|developmental stage:1000 cell 3 hpf|genotype:WT,GSM7734776,GSM7734776: WT 1000 cell 3 hpf tRNA seq rep2; Danio rerio; ncRNA Seq,GSM7734776 r1,GSM7734776,1,50 whole embryos were collected per sample and immediately lysed in 800uL LiDS/LET buffer5% Lithium dodecyl sulfate in 20 mM Tris HCl pH=7.4  100 mM LiCl  2 mM EDTA  5 mM DTT  pH 7.4. tRNA seq libraries were prepared using the mim tRNAseq workflow Behrens 2021  2022 and sequenced on an Illumina NextSeq 500 platform. mim tRNAseq,,ncRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,NextSeq 500,,SRP457111,,,WT_tRNA_1Kcell_2.fastq.gz,fastq,240973473.0,3918764.0,GSM7734776 r1,0:61.49,A:48091658;C:66684510;G:65183534;T:61013184;N:587,61,,,,48091658,66684510,65183534,61013184,587,SRX21486795,SRS18719097,SRA1700461,"Mechanisms of Protein Biogenesis, Max Planck Institute for Biochemistry",Max Planck Institute of Biochemistry,1,0.26629,,0.02297,,0.92305,,0.48525,,79,,B,,usable mapping rate,illumina,nextseq,5prime,size_fractionation,unknown,bulk,unknown,unknown,,Germany,2023-08-28,Blastula,Embryo,Whole Organism,All anatomical structures
25290,SRR25764128,SRX21486794,SRS18719095,SRP457111,PRJNA1009808,Dynamics of the zebrafish tRNAome during the maternal to zygotic transition [tRNA Seq],GSE241754,Transcriptome Analysis,Time course analysis of tRNA abundance during zebrafish early embryonic development. Overall design: Wild type TLAB strain zebrafish embryos were grown in standard housing conditions.Unfertilized eggs 0 hpf were collected or embryos were staged and collected at consecutive developmental time points  namelyat the 256 cell 2.5 hpf  1000 cell 3 hpf  sphere 4 hpf  shield 6 hpf and bud 10 hpf stages. Eggs and embryos were either flash frozen in liquid nitrogen or immediately processed. Samples were used for western blotting analysis  polysome profiling  ribosome profiling or mRNA and tRNA sequencing for investigating the regulation of tRNA gene expression and translational status during early zebrafish embryogenesis.,parent bioproject:PRJNA1009800,pubmed:39402326,,WT 1000 cell 3 hpf tRNA seq rep1,GSM7734775,,source name:Blastula|strain:TLAB strain|tissue:Blastula|developmental stage:1000 cell 3 hpf|genotype:WT|geo loc name:missing|collection date:missing,WT 1000 cell 3 hpf tRNA seq rep1,Read demultiplexing and adapter trimming performed with cutadapt v3.5  where bases were quality trimmed from five prime and three prime ends using a phred score cutoff of 30. Only trimmed reads were retained  and reads sorter than 10 bases were discarded. An additional round of trimming was performed to remove 5’ RN nucleotides introduced by circularization from the RT primer. Reads were processed with the mim tRNAseq computational pipeline v1.2 using the parameters   species Drer   cluster id 0.93   min cov 0.001   max mismatches 0.075   control condition Egg   deconv cov ratio 0.4   remap mismatches 0.075. Additional DESeq2 analysis was performed by excluding unsplit tRNA clusters  and on read counts summed by isotype. Assembly: GRCz11 Supplementary files format and content: csv; mim tRNAseq generated tRNA transcript resad counts,Blastula,unperturbed growth conditions in E3 medium for zebrafish embryos.,50 whole embryos were collected per sample and immediately lysed in 800uL LiDS/LET buffer5% Lithium dodecyl sulfate in 20 mM Tris HCl pH=7.4  100 mM LiCl  2 mM EDTA  5 mM DTT  pH 7.4. tRNA seq libraries were prepared using the mim tRNAseq workflow Behrens 2021  2022 and sequenced on an Illumina NextSeq 500 platform. mim tRNAseq,Embryos were grown in standard housing conditions namely28°C at a 14/10 hour light/dark cycle.,strain:TLAB strain|tissue:Blastula|developmental stage:1000 cell 3 hpf|genotype:WT,GSM7734775,GSM7734775: WT 1000 cell 3 hpf tRNA seq rep1; Danio rerio; ncRNA Seq,GSM7734775 r1,GSM7734775,1,50 whole embryos were collected per sample and immediately lysed in 800uL LiDS/LET buffer5% Lithium dodecyl sulfate in 20 mM Tris HCl pH=7.4  100 mM LiCl  2 mM EDTA  5 mM DTT  pH 7.4. tRNA seq libraries were prepared using the mim tRNAseq workflow Behrens 2021  2022 and sequenced on an Illumina NextSeq 500 platform. mim tRNAseq,,ncRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,NextSeq 500,,SRP457111,,,WT_tRNA_1Kcell_1.fastq.gz,fastq,153597915.0,2445091.0,GSM7734775 r1,0:62.82,A:30905842;C:42377268;G:41639937;T:38674503;N:365,62,,,,30905842,42377268,41639937,38674503,365,SRX21486794,SRS18719095,SRA1700461,"Mechanisms of Protein Biogenesis, Max Planck Institute for Biochemistry",Max Planck Institute of Biochemistry,1,0.27317,,0.02516,,0.92454,,0.49385,,77,,B,,usable mapping rate,illumina,nextseq,5prime,size_fractionation,unknown,bulk,unknown,unknown,,Germany,2023-08-28,Blastula,Embryo,Whole Organism,All anatomical structures
25291,SRR25764129,SRX21486793,SRS18719091,SRP457111,PRJNA1009808,Dynamics of the zebrafish tRNAome during the maternal to zygotic transition [tRNA Seq],GSE241754,Transcriptome Analysis,Time course analysis of tRNA abundance during zebrafish early embryonic development. Overall design: Wild type TLAB strain zebrafish embryos were grown in standard housing conditions.Unfertilized eggs 0 hpf were collected or embryos were staged and collected at consecutive developmental time points  namelyat the 256 cell 2.5 hpf  1000 cell 3 hpf  sphere 4 hpf  shield 6 hpf and bud 10 hpf stages. Eggs and embryos were either flash frozen in liquid nitrogen or immediately processed. Samples were used for western blotting analysis  polysome profiling  ribosome profiling or mRNA and tRNA sequencing for investigating the regulation of tRNA gene expression and translational status during early zebrafish embryogenesis.,parent bioproject:PRJNA1009800,pubmed:39402326,,WT 256 cell 2.5 hpf tRNA seq rep2,GSM7734774,,source name:Blastula|strain:TLAB strain|tissue:Blastula|developmental stage:256 cell 2.5 hpf|genotype:WT|geo loc name:missing|collection date:missing,WT 256 cell 2.5 hpf tRNA seq rep2,Read demultiplexing and adapter trimming performed with cutadapt v3.5  where bases were quality trimmed from five prime and three prime ends using a phred score cutoff of 30. Only trimmed reads were retained  and reads sorter than 10 bases were discarded. An additional round of trimming was performed to remove 5’ RN nucleotides introduced by circularization from the RT primer. Reads were processed with the mim tRNAseq computational pipeline v1.2 using the parameters   species Drer   cluster id 0.93   min cov 0.001   max mismatches 0.075   control condition Egg   deconv cov ratio 0.4   remap mismatches 0.075. Additional DESeq2 analysis was performed by excluding unsplit tRNA clusters  and on read counts summed by isotype. Assembly: GRCz11 Supplementary files format and content: csv; mim tRNAseq generated tRNA transcript resad counts,Blastula,unperturbed growth conditions in E3 medium for zebrafish embryos.,50 whole embryos were collected per sample and immediately lysed in 800uL LiDS/LET buffer5% Lithium dodecyl sulfate in 20 mM Tris HCl pH=7.4  100 mM LiCl  2 mM EDTA  5 mM DTT  pH 7.4. tRNA seq libraries were prepared using the mim tRNAseq workflow Behrens 2021  2022 and sequenced on an Illumina NextSeq 500 platform. mim tRNAseq,Embryos were grown in standard housing conditions namely28°C at a 14/10 hour light/dark cycle.,strain:TLAB strain|tissue:Blastula|developmental stage:256 cell 2.5 hpf|genotype:WT,GSM7734774,GSM7734774: WT 256 cell 2.5 hpf tRNA seq rep2; Danio rerio; ncRNA Seq,GSM7734774 r1,GSM7734774,1,50 whole embryos were collected per sample and immediately lysed in 800uL LiDS/LET buffer5% Lithium dodecyl sulfate in 20 mM Tris HCl pH=7.4  100 mM LiCl  2 mM EDTA  5 mM DTT  pH 7.4. tRNA seq libraries were prepared using the mim tRNAseq workflow Behrens 2021  2022 and sequenced on an Illumina NextSeq 500 platform. mim tRNAseq,,ncRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,NextSeq 500,,SRP457111,,,WT_tRNA_256cell_2.fastq.gz,fastq,844659062.0,13660310.0,GSM7734774 r1,0:61.83,A:165996817;C:234451560;G:230230791;T:213977958;N:1936,61,,,,165996817,234451560,230230791,213977958,1936,SRX21486793,SRS18719091,SRA1700461,"Mechanisms of Protein Biogenesis, Max Planck Institute for Biochemistry",Max Planck Institute of Biochemistry,1,0.26001,,0.01993,,0.92594,,0.45714,,61,,B,,usable mapping rate,illumina,nextseq,5prime,size_fractionation,unknown,bulk,unknown,unknown,,Germany,2023-08-28,Blastula,Embryo,Whole Organism,All anatomical structures
25292,SRR25764130,SRX21486792,SRS18719088,SRP457111,PRJNA1009808,Dynamics of the zebrafish tRNAome during the maternal to zygotic transition [tRNA Seq],GSE241754,Transcriptome Analysis,Time course analysis of tRNA abundance during zebrafish early embryonic development. Overall design: Wild type TLAB strain zebrafish embryos were grown in standard housing conditions.Unfertilized eggs 0 hpf were collected or embryos were staged and collected at consecutive developmental time points  namelyat the 256 cell 2.5 hpf  1000 cell 3 hpf  sphere 4 hpf  shield 6 hpf and bud 10 hpf stages. Eggs and embryos were either flash frozen in liquid nitrogen or immediately processed. Samples were used for western blotting analysis  polysome profiling  ribosome profiling or mRNA and tRNA sequencing for investigating the regulation of tRNA gene expression and translational status during early zebrafish embryogenesis.,parent bioproject:PRJNA1009800,pubmed:39402326,,WT 256 cell 2.5 hpf tRNA seq rep1,GSM7734773,,source name:Blastula|strain:TLAB strain|tissue:Blastula|developmental stage:256 cell 2.5 hpf|genotype:WT|geo loc name:missing|collection date:missing,WT 256 cell 2.5 hpf tRNA seq rep1,Read demultiplexing and adapter trimming performed with cutadapt v3.5  where bases were quality trimmed from five prime and three prime ends using a phred score cutoff of 30. Only trimmed reads were retained  and reads sorter than 10 bases were discarded. An additional round of trimming was performed to remove 5’ RN nucleotides introduced by circularization from the RT primer. Reads were processed with the mim tRNAseq computational pipeline v1.2 using the parameters   species Drer   cluster id 0.93   min cov 0.001   max mismatches 0.075   control condition Egg   deconv cov ratio 0.4   remap mismatches 0.075. Additional DESeq2 analysis was performed by excluding unsplit tRNA clusters  and on read counts summed by isotype. Assembly: GRCz11 Supplementary files format and content: csv; mim tRNAseq generated tRNA transcript resad counts,Blastula,unperturbed growth conditions in E3 medium for zebrafish embryos.,50 whole embryos were collected per sample and immediately lysed in 800uL LiDS/LET buffer5% Lithium dodecyl sulfate in 20 mM Tris HCl pH=7.4  100 mM LiCl  2 mM EDTA  5 mM DTT  pH 7.4. tRNA seq libraries were prepared using the mim tRNAseq workflow Behrens 2021  2022 and sequenced on an Illumina NextSeq 500 platform. mim tRNAseq,Embryos were grown in standard housing conditions namely28°C at a 14/10 hour light/dark cycle.,strain:TLAB strain|tissue:Blastula|developmental stage:256 cell 2.5 hpf|genotype:WT,GSM7734773,GSM7734773: WT 256 cell 2.5 hpf tRNA seq rep1; Danio rerio; ncRNA Seq,GSM7734773 r1,GSM7734773,1,50 whole embryos were collected per sample and immediately lysed in 800uL LiDS/LET buffer5% Lithium dodecyl sulfate in 20 mM Tris HCl pH=7.4  100 mM LiCl  2 mM EDTA  5 mM DTT  pH 7.4. tRNA seq libraries were prepared using the mim tRNAseq workflow Behrens 2021  2022 and sequenced on an Illumina NextSeq 500 platform. mim tRNAseq,,ncRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,NextSeq 500,,SRP457111,,,WT_tRNA_256cell_1.fastq.gz,fastq,215968508.0,3436266.0,GSM7734773 r1,0:62.85,A:43791388;C:59547637;G:58130851;T:54498124;N:508,62,,,,43791388,59547637,58130851,54498124,508,SRX21486792,SRS18719088,SRA1700461,"Mechanisms of Protein Biogenesis, Max Planck Institute for Biochemistry",Max Planck Institute of Biochemistry,1,0.27383,,0.02205,,0.92748,,0.46217,,71,,B,,usable mapping rate,illumina,nextseq,5prime,size_fractionation,unknown,bulk,unknown,unknown,,Germany,2023-08-28,Blastula,Embryo,Whole Organism,All anatomical structures
28490,SRR26319601,SRX22027740,SRS19100857,SRP465070,PRJNA1025141,Danio rerio Raw sequence reads,PRJNA1025141,Other,Transcriptome sequencing of A. sinensis leaf tea treated on zebrafish sleep.,,,Treatment,CX3 for transcriptome 3,CX3,,strain:AB|cultivar:WT|ecotype:China: Jiangsu|age:7 dpf|dev stage:Larvae|collection date:2022 11|geo loc name:China: Jiangsu suzhou|sex:pooled male and female|tissue:larvae|lat lon:31.32 N 120.67 E|treatment:Treatment Group|BioSampleModel:Model organism or animal,,,,,,,,,ALST3 for transcriptome 3,CX3 for transcriptome 3,CX3 for transcriptome 3,CX3 for transcriptome 3,,,RNA-Seq,TRANSCRIPTOMIC,size fractionation,PAIRED,ILLUMINA,HiSeq X Ten,,SRP465070,,,Unknown_AY803-03T0006_good_1.fq.gz Unknown_AY803-03T0006_good_2.fq.gz,fastq fastq,6255596356.0,20929531.0,Unknown AY803 03T0006 good 1.fq.gz,0:149.44 1:149.44,A:1657365560;C:1463722268;G:1467057724;T:1667269298;N:181506,149,149,,,1657365560,1463722268,1467057724,1667269298,181506,SRX22027740,SRS19100857,SRA1727563,Soochow University|School of biology & basic medical sciences,Soochow University,2,0.89228,0.91654,0.09286,0.09714,0.6588,0.65604,0.4631,0.45773,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,size_fractionation,unknown,bulk,unknown,unknown,,Unknown,2023-10-11,Larval,Larval,Whole Organism,All anatomical structures
28491,SRR26319602,SRX22027739,SRS19100854,SRP465070,PRJNA1025141,Danio rerio Raw sequence reads,PRJNA1025141,Other,Transcriptome sequencing of A. sinensis leaf tea treated on zebrafish sleep.,,,Treatment,CX2 for transcriptome 2,CX2,,strain:AB|cultivar:WT|ecotype:China: Jiangsu|age:7 dpf|dev stage:Larvae|collection date:2022 11|geo loc name:China: Jiangsu suzhou|sex:pooled male and female|tissue:larvae|lat lon:31.32 N 120.66 E|treatment:Treatment Group|BioSampleModel:Model organism or animal,,,,,,,,,ALST2 for transcriptome 2,CX2 for transcriptome 2,CX2 for transcriptome 2,CX2 for transcriptome 2,,,RNA-Seq,TRANSCRIPTOMIC,size fractionation,PAIRED,ILLUMINA,HiSeq X Ten,,SRP465070,,,Unknown_AY803-03T0005_good_1.fq.gz Unknown_AY803-03T0005_good_2.fq.gz,fastq fastq,6598066464.0,22061446.0,Unknown AY803 03T0005 good 1.fq.gz,0:149.54 1:149.54,A:1747291499;C:1543289262;G:1549193118;T:1758088368;N:204217,149,149,,,1747291499,1543289262,1549193118,1758088368,204217,SRX22027739,SRS19100854,SRA1727563,Soochow University|School of biology & basic medical sciences,Soochow University,2,0.88949,0.92148,0.08893,0.0947,0.65596,0.65228,0.46045,0.47087,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,size_fractionation,unknown,bulk,unknown,unknown,,Unknown,2023-10-11,Larval,Larval,Whole Organism,All anatomical structures
28492,SRR26319603,SRX22027738,SRS19100853,SRP465070,PRJNA1025141,Danio rerio Raw sequence reads,PRJNA1025141,Other,Transcriptome sequencing of A. sinensis leaf tea treated on zebrafish sleep.,,,Treatment,CX1 for transcriptome 1,CX1,,strain:AB|cultivar:WT|ecotype:China: Jiangsu|age:7 dpf|dev stage:Larvae|collection date:2022 11|geo loc name:China: Jiangsu suzhou|sex:pooled male and female|tissue:larvae|lat lon:31.32 N 120.65 E|treatment:Treatment Group|BioSampleModel:Model organism or animal,,,,,,,,,ALST1 for transcriptome 1,CX1 for transcriptome 1,CX1 for transcriptome 1,CX1 for transcriptome 1,,,RNA-Seq,TRANSCRIPTOMIC,size fractionation,PAIRED,ILLUMINA,HiSeq X Ten,,SRP465070,,,Unknown_AY803-03T0004_good_1.fq.gz Unknown_AY803-03T0004_good_2.fq.gz,fastq fastq,6478923586.0,21662443.0,Unknown AY803 03T0004 good 1.fq.gz,0:149.54 1:149.54,A:1712718473;C:1518937459;G:1523570227;T:1723510437;N:186990,149,149,,,1712718473,1518937459,1523570227,1723510437,186990,SRX22027738,SRS19100853,SRA1727563,Soochow University|School of biology & basic medical sciences,Soochow University,2,0.89423,0.9176,0.08944,0.09254,0.6575,0.65458,0.4693,0.46842,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,size_fractionation,unknown,bulk,unknown,unknown,,Unknown,2023-10-11,Larval,Larval,Whole Organism,All anatomical structures
28493,SRR26319604,SRX22027737,SRS19100856,SRP465070,PRJNA1025141,Danio rerio Raw sequence reads,PRJNA1025141,Other,Transcriptome sequencing of A. sinensis leaf tea treated on zebrafish sleep.,,,Control,con3 for transcriptome 3,con3,,strain:AB|cultivar:Wild type|ecotype:China: Jiangsu suzhou|age:7 dpf|dev stage:Larvae phase|collection date:2022 11|geo loc name:China: Jiangsu suzhou|sex:pooled male and female|tissue:larvae|lat lon:31.32 N 120.64 E|treatment:Control Group|BioSampleModel:Model organism or animal,,,,,,,,,con3 for transcriptome 3,con3 for transcriptome 3,con3 for transcriptome 3,con3 for transcriptome 3,,,RNA-Seq,TRANSCRIPTOMIC,size fractionation,PAIRED,ILLUMINA,HiSeq X Ten,,SRP465070,,,Unknown_AY803-03T0003_good_2.fq.gz Unknown_AY803-03T0003_good_1.fq.gz,fastq fastq,6341537566.0,21218597.0,Unknown AY803 03T0003 good 1.fq.gz,0:149.43 1:149.43,A:1679811754;C:1483631833;G:1489430825;T:1688482904;N:180250,149,149,,,1679811754,1483631833,1489430825,1688482904,180250,SRX22027737,SRS19100856,SRA1727563,Soochow University|School of biology & basic medical sciences,Soochow University,2,0.88245,0.91856,0.09069,0.09654,0.66253,0.65817,0.46245,0.46336,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,size_fractionation,unknown,bulk,unknown,unknown,,Unknown,2023-10-11,Larval,Larval,Whole Organism,All anatomical structures
28494,SRR26319605,SRX22027736,SRS19100855,SRP465070,PRJNA1025141,Danio rerio Raw sequence reads,PRJNA1025141,Other,Transcriptome sequencing of A. sinensis leaf tea treated on zebrafish sleep.,,,Control,con2 for transcriptome 2,con2,,strain:AB|cultivar:Wild type|ecotype:China: Jiangsu suzhou|age:7 dpf|dev stage:Larvae phase|collection date:2022 11|geo loc name:China: Jiangsu suzhou|sex:pooled male and female|tissue:larvae|lat lon:31.32 N 120.63 E|treatment:Control Group|BioSampleModel:Model organism or animal,,,,,,,,,con2 for transcriptome 2,con2 for transcriptome 2,con2 for transcriptome 2,con2 for transcriptome 2,,,RNA-Seq,TRANSCRIPTOMIC,size fractionation,PAIRED,ILLUMINA,HiSeq X Ten,,SRP465070,,,Unknown_AY803-03T0002_good_2.fq.gz Unknown_AY803-03T0002_good_1.fq.gz,fastq fastq,5709771178.0,19100144.0,Unknown AY803 03T0002 good 1.fq.gz,0:149.47 1:149.47,A:1505730979;C:1342843084;G:1346105868;T:1514941964;N:149283,149,149,,,1505730979,1342843084,1346105868,1514941964,149283,SRX22027736,SRS19100855,SRA1727563,Soochow University|School of biology & basic medical sciences,Soochow University,2,0.8924,0.91903,0.09155,0.09604,0.65902,0.65593,0.4634,0.46028,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,size_fractionation,unknown,bulk,unknown,unknown,,Unknown,2023-10-11,Larval,Larval,Whole Organism,All anatomical structures
28495,SRR26319606,SRX22027735,SRS19100852,SRP465070,PRJNA1025141,Danio rerio Raw sequence reads,PRJNA1025141,Other,Transcriptome sequencing of A. sinensis leaf tea treated on zebrafish sleep.,,,Control,con1 for transcriptome 1,con1,,strain:AB|cultivar:Wild type|ecotype:China: Jiangsu suzhou|age:7 dpf|dev stage:Larvae phase|collection date:2022 11|geo loc name:China: Jiangsu suzhou|sex:pooled male and female|tissue:larvae|lat lon:31.32 N 120.62 E|treatment:Control Group|BioSampleModel:Model organism or animal,,,,,,,,,con1 for transcriptome 1,con1 for transcriptome 1,con1 for transcriptome 1,con1 for transcriptome 1,,,RNA-Seq,TRANSCRIPTOMIC,size fractionation,PAIRED,ILLUMINA,HiSeq X Ten,,SRP465070,,,Unknown_AY803-03T0001_good_1.fq.gz Unknown_AY803-03T0001_good_2.fq.gz,fastq fastq,6544586118.0,21872265.0,Unknown AY803 03T0001 good 1.fq.gz,0:149.61 1:149.61,A:1731179229;C:1528367346;G:1541103688;T:1743735521;N:200334,149,149,,,1731179229,1528367346,1541103688,1743735521,200334,SRX22027735,SRS19100852,SRA1727563,Soochow University|School of biology & basic medical sciences,Soochow University,2,0.87588,0.92739,0.08683,0.09494,0.65711,0.6504,0.46774,0.47072,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,size_fractionation,unknown,bulk,unknown,unknown,,Unknown,2023-10-11,Larval,Larval,Whole Organism,All anatomical structures
29739,SRR27467672,SRX23139234,SRS20090275,SRP482074,PRJNA1061456,tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development,PRJNA1061456,Other,,,,,,Dome mock R2,,strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:5 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|treatment:mock|BioSampleModel:Model organism or animal,,,,,,,,,tRAM seq of zebrafish: embryo 5 hpf  mock  rep2,EV04009,EV04009,RNA was extracted with Trizol  tRNA isolated by size selection on denaturing polyacrylamide gel  range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment  three prime adapter ligated with T4 RNA ligase 2  reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase  using NEB Next indexed primers.,,,OTHER,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,NextSeq 500,,SRP482074,,,EV04009.R1.fastq.gz,fastq,609590940.0,4354221.0,EV04009.R1.fastq.gz,0:140,A:155062144;C:147628702;G:168099121;T:138772205;N:28768,140,,,,155062144,147628702,168099121,138772205,28768,SRX23139234,SRS20090275,SRA1781872,Medical University of Vienna|Cell and Developmental Biology,Medical University of Vienna,1,0.0,,0.0,,1.0,,,,140,,T,,under 1.2% mapping rate,illumina,nextseq,unknown,size_fractionation,nebnext,bulk,unknown,unknown,,Austria,2024-01-09,Blastula,Embryo,Whole Organism,All anatomical structures
29740,SRR27467673,SRX23139233,SRS20090278,SRP482074,PRJNA1061456,tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development,PRJNA1061456,Other,,,,,,1K cell BS R2,,strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:3 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|treatment:BS|BioSampleModel:Model organism or animal,,,,,,,,,tRAM seq of zebrafish: embryo 3 hpf  BS  rep2,EV04008,EV04008,RNA was extracted with Trizol  tRNA isolated by size selection on denaturing polyacrylamide gel  range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment  three prime adapter ligated with T4 RNA ligase 2  reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase  using NEB Next indexed primers.,,,OTHER,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,NextSeq 500,,SRP482074,,,EV04008.R1.fastq.gz,fastq,675505180.0,4825037.0,EV04008.R1.fastq.gz,0:140,A:178823976;C:121648962;G:198428643;T:176572292;N:31307,140,,,,178823976,121648962,198428643,176572292,31307,SRX23139233,SRS20090278,SRA1781872,Medical University of Vienna|Cell and Developmental Biology,Medical University of Vienna,1,0.0,,0.0,,1.0,,,,140,,T,,under 1.2% mapping rate,illumina,nextseq,unknown,size_fractionation,nebnext,bulk,unknown,unknown,,Austria,2024-01-09,Blastula,Embryo,Whole Organism,All anatomical structures
29741,SRR27467674,SRX23139232,SRS20090272,SRP482074,PRJNA1061456,tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development,PRJNA1061456,Other,,,,,,1K cell DM R2,,strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:3 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|treatment:DM|BioSampleModel:Model organism or animal,,,,,,,,,tRAM seq of zebrafish: embryo 3 hpf  DM  rep2,EV04007,EV04007,RNA was extracted with Trizol  tRNA isolated by size selection on denaturing polyacrylamide gel  range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment  three prime adapter ligated with T4 RNA ligase 2  reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase  using NEB Next indexed primers.,,,OTHER,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,NextSeq 500,,SRP482074,,,EV04007.R1.fastq.gz,fastq,702064440.0,5014746.0,EV04007.R1.fastq.gz,0:140,A:176719694;C:166467163;G:207893965;T:150951950;N:31668,140,,,,176719694,166467163,207893965,150951950,31668,SRX23139232,SRS20090272,SRA1781872,Medical University of Vienna|Cell and Developmental Biology,Medical University of Vienna,1,2e-05,,0.0,,0.99997,,1.0,,140,,T,,under 1.2% mapping rate,illumina,nextseq,unknown,size_fractionation,nebnext,bulk,unknown,unknown,,Austria,2024-01-09,Blastula,Embryo,Whole Organism,All anatomical structures
29742,SRR27467675,SRX23139231,SRS20090271,SRP482074,PRJNA1061456,tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development,PRJNA1061456,Other,,,,,,1K cell mock R2,,strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:3 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|treatment:mock|BioSampleModel:Model organism or animal,,,,,,,,,tRAM seq of zebrafish: embryo 3 hpf  mock  rep2,EV04006,EV04006,RNA was extracted with Trizol  tRNA isolated by size selection on denaturing polyacrylamide gel  range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment  three prime adapter ligated with T4 RNA ligase 2  reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase  using NEB Next indexed primers.,,,OTHER,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,NextSeq 500,,SRP482074,,,EV04006.R1.fastq.gz,fastq,664790700.0,4748505.0,EV04006.R1.fastq.gz,0:140,A:172014219;C:146545691;G:200358431;T:145840649;N:31710,140,,,,172014219,146545691,200358431,145840649,31710,SRX23139231,SRS20090271,SRA1781872,Medical University of Vienna|Cell and Developmental Biology,Medical University of Vienna,1,3e-05,,0.0,,0.99993,,1.0,,140,,T,,under 1.2% mapping rate,illumina,nextseq,unknown,size_fractionation,nebnext,bulk,unknown,unknown,,Austria,2024-01-09,Blastula,Embryo,Whole Organism,All anatomical structures
29743,SRR27467676,SRX23139230,SRS20090273,SRP482074,PRJNA1061456,tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development,PRJNA1061456,Other,,,,,,4 cell DM R2,,strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:1 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|treatment:DM|BioSampleModel:Model organism or animal,,,,,,,,,tRAM seq of zebrafish: embryo 1 hpf  DM  rep2,EV04004,EV04004,RNA was extracted with Trizol  tRNA isolated by size selection on denaturing polyacrylamide gel  range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment  three prime adapter ligated with T4 RNA ligase 2  reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase  using NEB Next indexed primers.,,,OTHER,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,NextSeq 500,,SRP482074,,,EV04004.R1.fastq.gz,fastq,895671560.0,6397654.0,EV04004.R1.fastq.gz,0:140,A:206443066;C:147067097;G:365386937;T:176734600;N:39860,140,,,,206443066,147067097,365386937,176734600,39860,SRX23139230,SRS20090273,SRA1781872,Medical University of Vienna|Cell and Developmental Biology,Medical University of Vienna,1,0.0,,0.0,,1.0,,,,140,,T,,under 1.2% mapping rate,illumina,nextseq,unknown,size_fractionation,nebnext,bulk,unknown,unknown,,Austria,2024-01-09,Cleavage,Embryo,Whole Organism,All anatomical structures
29744,SRR27467677,SRX23139229,SRS20090274,SRP482074,PRJNA1061456,tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development,PRJNA1061456,Other,,,,,,4 cell mock R2,,strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:1 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|treatment:mock|BioSampleModel:Model organism or animal,,,,,,,,,tRAM seq of zebrafish: embryo 1 hpf  mock  rep2,EV04003,EV04003,RNA was extracted with Trizol  tRNA isolated by size selection on denaturing polyacrylamide gel  range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment  three prime adapter ligated with T4 RNA ligase 2  reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase  using NEB Next indexed primers.,,,OTHER,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,NextSeq 500,,SRP482074,,,EV04003.R1.fastq.gz,fastq,664112120.0,4743658.0,EV04003.R1.fastq.gz,0:140,A:163711695;C:142612940;G:211194350;T:146562626;N:30509,140,,,,163711695,142612940,211194350,146562626,30509,SRX23139229,SRS20090274,SRA1781872,Medical University of Vienna|Cell and Developmental Biology,Medical University of Vienna,1,2e-05,,0.0,,0.99997,,1.0,,140,,T,,under 1.2% mapping rate,illumina,nextseq,unknown,size_fractionation,nebnext,bulk,unknown,unknown,,Austria,2024-01-09,Cleavage,Embryo,Whole Organism,All anatomical structures
29747,SRR27467680,SRX23139226,SRS20090267,SRP482074,PRJNA1061456,tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development,PRJNA1061456,Other,,,,,,24h BS R2,,strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:24 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|treatment:BS|BioSampleModel:Model organism or animal,,,,,,,,,tRAM seq of zebrafish: embryo 24 hpf  BS  rep2,EV03009,EV03009,RNA was extracted with Trizol  tRNA isolated by size selection on denaturing polyacrylamide gel  range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment  three prime adapter ligated with T4 RNA ligase 2  reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase  using NEB Next indexed primers.,,,OTHER,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,NextSeq 500,,SRP482074,,,EV03009.R1.fastq.gz,fastq,168931280.0,2222780.0,EV03009.R1.fastq.gz,0:76,A:49803604;C:36479774;G:37758990;T:44874154;N:14758,76,,,,49803604,36479774,37758990,44874154,14758,SRX23139226,SRS20090267,SRA1781872,Medical University of Vienna|Cell and Developmental Biology,Medical University of Vienna,1,0.00034,,0.0002,,0.99965,,0.5,,76,,T,,under 1.2% mapping rate,illumina,nextseq,unknown,size_fractionation,nebnext,bulk,unknown,unknown,,Austria,2024-01-09,Pharyngula,Embryo,Whole Organism,All anatomical structures
29748,SRR27467681,SRX23139225,SRS20090266,SRP482074,PRJNA1061456,tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development,PRJNA1061456,Other,,,,,,24h DM R2,,strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:24 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|treatment:DM|BioSampleModel:Model organism or animal,,,,,,,,,tRAM seq of zebrafish: embryo 24 hpf  DM  rep2,EV03008,EV03008,RNA was extracted with Trizol  tRNA isolated by size selection on denaturing polyacrylamide gel  range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment  three prime adapter ligated with T4 RNA ligase 2  reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase  using NEB Next indexed primers.,,,OTHER,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,NextSeq 500,,SRP482074,,,EV03008.R1.fastq.gz,fastq,200878792.0,2643142.0,EV03008.R1.fastq.gz,0:76,A:46955288;C:54746275;G:55887832;T:43270561;N:18836,76,,,,46955288,54746275,55887832,43270561,18836,SRX23139225,SRS20090266,SRA1781872,Medical University of Vienna|Cell and Developmental Biology,Medical University of Vienna,1,0.29408,,0.00737,,0.91823,,0.54549,,76,,B,,usable mapping rate,illumina,nextseq,unknown,size_fractionation,nebnext,bulk,unknown,unknown,,Austria,2024-01-09,Pharyngula,Embryo,Whole Organism,All anatomical structures
29749,SRR27467682,SRX23139224,SRS20090269,SRP482074,PRJNA1061456,tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development,PRJNA1061456,Other,,,,,,24h mock R2,,strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:24 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|treatment:mock|BioSampleModel:Model organism or animal,,,,,,,,,tRAM seq of zebrafish: embryo 24 hpf  mock  rep2,EV03007,EV03007,RNA was extracted with Trizol  tRNA isolated by size selection on denaturing polyacrylamide gel  range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment  three prime adapter ligated with T4 RNA ligase 2  reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase  using NEB Next indexed primers.,,,OTHER,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,NextSeq 500,,SRP482074,,,EV03007.R1.fastq.gz,fastq,175642840.0,2311090.0,EV03007.R1.fastq.gz,0:76,A:44745275;C:48908904;G:44862157;T:37111895;N:14609,76,,,,44745275,48908904,44862157,37111895,14609,SRX23139224,SRS20090269,SRA1781872,Medical University of Vienna|Cell and Developmental Biology,Medical University of Vienna,1,0.06887,,0.00273,,0.96623,,0.48721,,76,,B,,usable mapping rate,illumina,nextseq,unknown,size_fractionation,nebnext,bulk,unknown,unknown,,Austria,2024-01-09,Pharyngula,Embryo,Whole Organism,All anatomical structures
29750,SRR27467683,SRX23139223,SRS20090265,SRP482074,PRJNA1061456,tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development,PRJNA1061456,Other,,,,,,Bud BS R2,,strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:10 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|treatment:BS|BioSampleModel:Model organism or animal,,,,,,,,,tRAM seq of zebrafish: embryo 10 hpf  BS  rep2,EV04014,EV04014,RNA was extracted with Trizol  tRNA isolated by size selection on denaturing polyacrylamide gel  range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment  three prime adapter ligated with T4 RNA ligase 2  reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase  using NEB Next indexed primers.,,,OTHER,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,NextSeq 500,,SRP482074,,,EV04014.R1.fastq.gz,fastq,774901260.0,5535009.0,EV04014.R1.fastq.gz,0:140,A:193865579;C:138861953;G:251102013;T:191036071;N:35644,140,,,,193865579,138861953,251102013,191036071,35644,SRX23139223,SRS20090265,SRA1781872,Medical University of Vienna|Cell and Developmental Biology,Medical University of Vienna,1,0.0,,0.0,,1.0,,,,140,,T,,under 1.2% mapping rate,illumina,nextseq,unknown,size_fractionation,nebnext,bulk,unknown,unknown,,Austria,2024-01-09,Gastrula,Embryo,Whole Organism,All anatomical structures
29751,SRR27467684,SRX23139222,SRS20090264,SRP482074,PRJNA1061456,tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development,PRJNA1061456,Other,,,,,,Bud DM R2,,strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:10 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|treatment:DM|BioSampleModel:Model organism or animal,,,,,,,,,tRAM seq of zebrafish: embryo 10 hpf  DM  rep2,EV04013,EV04013,RNA was extracted with Trizol  tRNA isolated by size selection on denaturing polyacrylamide gel  range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment  three prime adapter ligated with T4 RNA ligase 2  reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase  using NEB Next indexed primers.,,,OTHER,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,NextSeq 500,,SRP482074,,,EV04013.R1.fastq.gz,fastq,666372840.0,4759806.0,EV04013.R1.fastq.gz,0:140,A:172923134;C:142243998;G:211584978;T:139591020;N:29710,140,,,,172923134,142243998,211584978,139591020,29710,SRX23139222,SRS20090264,SRA1781872,Medical University of Vienna|Cell and Developmental Biology,Medical University of Vienna,1,3e-05,,0.0,,0.99991,,1.0,,140,,T,,under 1.2% mapping rate,illumina,nextseq,unknown,size_fractionation,nebnext,bulk,unknown,unknown,,Austria,2024-01-09,Gastrula,Embryo,Whole Organism,All anatomical structures
29752,SRR27467685,SRX23139221,SRS20090262,SRP482074,PRJNA1061456,tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development,PRJNA1061456,Other,,,,,,Bud mock R2,,strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:10 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|treatment:mock|BioSampleModel:Model organism or animal,,,,,,,,,tRAM seq of zebrafish: embryo 10 hpf  mock  rep2,EV04012,EV04012,RNA was extracted with Trizol  tRNA isolated by size selection on denaturing polyacrylamide gel  range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment  three prime adapter ligated with T4 RNA ligase 2  reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase  using NEB Next indexed primers.,,,OTHER,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,NextSeq 500,,SRP482074,,,EV04012.R1.fastq.gz,fastq,628769540.0,4491211.0,EV04012.R1.fastq.gz,0:140,A:160925901;C:143204697;G:183224867;T:141385307;N:28768,140,,,,160925901,143204697,183224867,141385307,28768,SRX23139221,SRS20090262,SRA1781872,Medical University of Vienna|Cell and Developmental Biology,Medical University of Vienna,1,1e-05,,0.0,,0.99997,,1.0,,140,,T,,under 1.2% mapping rate,illumina,nextseq,unknown,size_fractionation,nebnext,bulk,unknown,unknown,,Austria,2024-01-09,Gastrula,Embryo,Whole Organism,All anatomical structures
29753,SRR27467686,SRX23139220,SRS20090263,SRP482074,PRJNA1061456,tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development,PRJNA1061456,Other,,,,,,Dome BS R2,,strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:5 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|treatment:BS|BioSampleModel:Model organism or animal,,,,,,,,,tRAM seq of zebrafish: embryo 5 hpf  BS  rep2,EV04011,EV04011,RNA was extracted with Trizol  tRNA isolated by size selection on denaturing polyacrylamide gel  range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment  three prime adapter ligated with T4 RNA ligase 2  reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase  using NEB Next indexed primers.,,,OTHER,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,NextSeq 500,,SRP482074,,,EV04011.R1.fastq.gz,fastq,720913200.0,5149380.0,EV04011.R1.fastq.gz,0:140,A:185414155;C:126110104;G:238649631;T:170706590;N:32720,140,,,,185414155,126110104,238649631,170706590,32720,SRX23139220,SRS20090263,SRA1781872,Medical University of Vienna|Cell and Developmental Biology,Medical University of Vienna,1,0.0,,0.0,,1.0,,,,140,,T,,under 1.2% mapping rate,illumina,nextseq,unknown,size_fractionation,nebnext,bulk,unknown,unknown,,Austria,2024-01-09,Blastula,Embryo,Whole Organism,All anatomical structures
29754,SRR27467687,SRX23139219,SRS20090259,SRP482074,PRJNA1061456,tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development,PRJNA1061456,Other,,,,,,Dome DM R2,,strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:5 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|treatment:DM|BioSampleModel:Model organism or animal,,,,,,,,,tRAM seq of zebrafish: embryo 5 hpf  DM  rep2,EV04010,EV04010,RNA was extracted with Trizol  tRNA isolated by size selection on denaturing polyacrylamide gel  range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment  three prime adapter ligated with T4 RNA ligase 2  reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase  using NEB Next indexed primers.,,,OTHER,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,NextSeq 500,,SRP482074,,,EV04010.R1.fastq.gz,fastq,443650200.0,3168930.0,EV04010.R1.fastq.gz,0:140,A:114663509;C:102512276;G:135709753;T:90744641;N:20021,140,,,,114663509,102512276,135709753,90744641,20021,SRX23139219,SRS20090259,SRA1781872,Medical University of Vienna|Cell and Developmental Biology,Medical University of Vienna,1,1e-05,,0.0,,0.99997,,1.0,,140,,T,,under 1.2% mapping rate,illumina,nextseq,unknown,size_fractionation,nebnext,bulk,unknown,unknown,,Austria,2024-01-09,Blastula,Embryo,Whole Organism,All anatomical structures
29757,SRR27437477,SRX23109820,SRS20064574,SRP482074,PRJNA1061456,tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development,PRJNA1061456,Other,,,,,,1K cell mock R3,,strain:TLAB fish|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|dev stage:3 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|treatment:mock|BioSampleModel:Model organism or animal,,,,,,,,,tRAM seq of zebrafish: embryo 3 hpf  mock  rep3,EV07007,EV07007,RNA was extracted with Trizol  tRNA isolated by size selection on denaturing polyacrylamide gel  range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment  three prime adapter ligated with T4 RNA ligase 2  reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase  using NEB Next indexed primers.,,,OTHER,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,NextSeq 500,,SRP482074,,,EV07007.R1.fastq.gz,fastq,479994620.0,3428533.0,EV07007.R1.fastq.gz,0:140,A:124628886;C:116843590;G:123136721;T:115372734;N:12689,140,,,,124628886,116843590,123136721,115372734,12689,SRX23109820,SRS20064574,SRA1780298,Medical University of Vienna|Cell and Developmental Biology,Medical University of Vienna,1,6e-05,,1e-05,,0.99989,,1.0,,140,,T,,under 1.2% mapping rate,illumina,nextseq,unknown,size_fractionation,nebnext,bulk,unknown,unknown,,Austria,2024-01-06,Blastula,Embryo,Whole Organism,All anatomical structures
29758,SRR27437478,SRX23109819,SRS20064573,SRP482074,PRJNA1061456,tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development,PRJNA1061456,Other,,,,,,4 cell BS R3,,strain:TLAB fish|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|dev stage:1 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|treatment:BS|BioSampleModel:Model organism or animal,,,,,,,,,tRAM seq of zebrafish: embryo 1 hpf  BS  rep3,EV07006,EV07006,RNA was extracted with Trizol  tRNA isolated by size selection on denaturing polyacrylamide gel  range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment  three prime adapter ligated with T4 RNA ligase 2  reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase  using NEB Next indexed primers.,,,OTHER,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,NextSeq 500,,SRP482074,,,EV07006.R1.fastq.gz,fastq,2584527680.0,18460912.0,EV07006.R1.fastq.gz,0:140,A:685107500;C:367766834;G:717359848;T:814224206;N:69292,140,,,,685107500,367766834,717359848,814224206,69292,SRX23109819,SRS20064573,SRA1780298,Medical University of Vienna|Cell and Developmental Biology,Medical University of Vienna,1,2e-05,,1e-05,,1.0,,,,140,,T,,under 1.2% mapping rate,illumina,nextseq,unknown,size_fractionation,nebnext,bulk,unknown,unknown,,Austria,2024-01-06,Cleavage,Embryo,Whole Organism,All anatomical structures
29759,SRR27437479,SRX23109818,SRS20064571,SRP482074,PRJNA1061456,tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development,PRJNA1061456,Other,,,,,,4 cell DM R3,,strain:TLAB fish|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|dev stage:1 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|treatment:DM|BioSampleModel:Model organism or animal,,,,,,,,,tRAM seq of zebrafish: embryo 1 hpf  DM  rep3,EV07005,EV07005,RNA was extracted with Trizol  tRNA isolated by size selection on denaturing polyacrylamide gel  range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment  three prime adapter ligated with T4 RNA ligase 2  reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase  using NEB Next indexed primers.,,,OTHER,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,NextSeq 500,,SRP482074,,,EV07005.R1.fastq.gz,fastq,713829480.0,5098782.0,EV07005.R1.fastq.gz,0:140,A:183575304;C:168886779;G:213156258;T:148191838;N:19301,140,,,,183575304,168886779,213156258,148191838,19301,SRX23109818,SRS20064571,SRA1780298,Medical University of Vienna|Cell and Developmental Biology,Medical University of Vienna,1,5e-05,,0.0,,0.99989,,1.0,,140,,T,,under 1.2% mapping rate,illumina,nextseq,unknown,size_fractionation,nebnext,bulk,unknown,unknown,,Austria,2024-01-06,Cleavage,Embryo,Whole Organism,All anatomical structures
29760,SRR27437480,SRX23109817,SRS20064572,SRP482074,PRJNA1061456,tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development,PRJNA1061456,Other,,,,,,4 cell mock R3,,strain:TLAB fish|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|dev stage:1 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|treatment:mock|BioSampleModel:Model organism or animal,,,,,,,,,tRAM seq of zebrafish: embryo 1 hpf  mock  rep3,EV07004,EV07004,RNA was extracted with Trizol  tRNA isolated by size selection on denaturing polyacrylamide gel  range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment  three prime adapter ligated with T4 RNA ligase 2  reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase  using NEB Next indexed primers.,,,OTHER,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,NextSeq 500,,SRP482074,,,EV07004.R1.fastq.gz,fastq,517336680.0,3695262.0,EV07004.R1.fastq.gz,0:140,A:136783049;C:131207858;G:139873280;T:109458276;N:14217,140,,,,136783049,131207858,139873280,109458276,14217,SRX23109817,SRS20064572,SRA1780298,Medical University of Vienna|Cell and Developmental Biology,Medical University of Vienna,1,7e-05,,0.0,,0.99981,,0.7,,140,,T,,under 1.2% mapping rate,illumina,nextseq,unknown,size_fractionation,nebnext,bulk,unknown,unknown,,Austria,2024-01-06,Cleavage,Embryo,Whole Organism,All anatomical structures
29764,SRR27437484,SRX23109813,SRS20064567,SRP482074,PRJNA1061456,tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development,PRJNA1061456,Other,,,,,,24h BS R3,,strain:TLAB fish|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|dev stage:24 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|treatment:BS|BioSampleModel:Model organism or animal,,,,,,,,,tRAM seq of zebrafish: embryo 24 hpf  BS  rep3,EV07018,EV07018,RNA was extracted with Trizol  tRNA isolated by size selection on denaturing polyacrylamide gel  range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment  three prime adapter ligated with T4 RNA ligase 2  reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase  using NEB Next indexed primers.,,,OTHER,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,NextSeq 500,,SRP482074,,,EV07018.R1.fastq.gz,fastq,887731180.0,6340937.0,EV07018.R1.fastq.gz,0:140,A:204102176;C:148262233;G:350287017;T:185056779;N:22975,140,,,,204102176,148262233,350287017,185056779,22975,SRX23109813,SRS20064567,SRA1780298,Medical University of Vienna|Cell and Developmental Biology,Medical University of Vienna,1,0.0,,0.0,,1.0,,,,140,,T,,under 1.2% mapping rate,illumina,nextseq,unknown,size_fractionation,nebnext,bulk,unknown,unknown,,Austria,2024-01-06,Pharyngula,Embryo,Whole Organism,All anatomical structures
29766,SRR27437486,SRX23109811,SRS20064565,SRP482074,PRJNA1061456,tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development,PRJNA1061456,Other,,,,,,24h DM R3,,strain:TLAB fish|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|dev stage:24 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|treatment:DM|BioSampleModel:Model organism or animal,,,,,,,,,tRAM seq of zebrafish: embryo 24 hpf  DM  rep3,EV07017,EV07017,RNA was extracted with Trizol  tRNA isolated by size selection on denaturing polyacrylamide gel  range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment  three prime adapter ligated with T4 RNA ligase 2  reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase  using NEB Next indexed primers.,,,OTHER,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,NextSeq 500,,SRP482074,,,EV07017.R1.fastq.gz,fastq,466089960.0,3329214.0,EV07017.R1.fastq.gz,0:140,A:117818387;C:108651920;G:144753443;T:94853810;N:12400,140,,,,117818387,108651920,144753443,94853810,12400,SRX23109811,SRS20064565,SRA1780298,Medical University of Vienna|Cell and Developmental Biology,Medical University of Vienna,1,0.0,,0.0,,1.0,,,,140,,T,,under 1.2% mapping rate,illumina,nextseq,unknown,size_fractionation,nebnext,bulk,unknown,unknown,,Austria,2024-01-06,Pharyngula,Embryo,Whole Organism,All anatomical structures
29767,SRR27437487,SRX23109810,SRS20064563,SRP482074,PRJNA1061456,tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development,PRJNA1061456,Other,,,,,,24h mock R3,,strain:TLAB fish|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|dev stage:24 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|treatment:mock|BioSampleModel:Model organism or animal,,,,,,,,,tRAM seq of zebrafish: embryo 24 hpf  mock  rep3,EV07016,EV07016,RNA was extracted with Trizol  tRNA isolated by size selection on denaturing polyacrylamide gel  range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment  three prime adapter ligated with T4 RNA ligase 2  reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase  using NEB Next indexed primers.,,,OTHER,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,NextSeq 500,,SRP482074,,,EV07016.R1.fastq.gz,fastq,638674120.0,4561958.0,EV07016.R1.fastq.gz,0:140,A:159572532;C:147135537;G:186885553;T:145063254;N:17244,140,,,,159572532,147135537,186885553,145063254,17244,SRX23109810,SRS20064563,SRA1780298,Medical University of Vienna|Cell and Developmental Biology,Medical University of Vienna,1,4e-05,,0.0,,0.99993,,0.0,,140,,T,,under 1.2% mapping rate,illumina,nextseq,unknown,size_fractionation,nebnext,bulk,unknown,unknown,,Austria,2024-01-06,Pharyngula,Embryo,Whole Organism,All anatomical structures
29768,SRR27437488,SRX23109809,SRS20064564,SRP482074,PRJNA1061456,tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development,PRJNA1061456,Other,,,,,,Bud BS R3,,strain:TLAB fish|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|dev stage:10 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|treatment:BS|BioSampleModel:Model organism or animal,,,,,,,,,tRAM seq of zebrafish: embryo 10 hpf  BS  rep3,EV07015,EV07015,RNA was extracted with Trizol  tRNA isolated by size selection on denaturing polyacrylamide gel  range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment  three prime adapter ligated with T4 RNA ligase 2  reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase  using NEB Next indexed primers.,,,OTHER,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,NextSeq 500,,SRP482074,,,EV07015.R1.fastq.gz,fastq,598389400.0,4274210.0,EV07015.R1.fastq.gz,0:140,A:150315140;C:106310211;G:186765596;T:154982225;N:16228,140,,,,150315140,106310211,186765596,154982225,16228,SRX23109809,SRS20064564,SRA1780298,Medical University of Vienna|Cell and Developmental Biology,Medical University of Vienna,1,0.0,,0.0,,1.0,,,,140,,T,,under 1.2% mapping rate,illumina,nextseq,unknown,size_fractionation,nebnext,bulk,unknown,unknown,,Austria,2024-01-06,Gastrula,Embryo,Whole Organism,All anatomical structures
29769,SRR27437489,SRX23109808,SRS20064562,SRP482074,PRJNA1061456,tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development,PRJNA1061456,Other,,,,,,Bud DM R3,,strain:TLAB fish|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|dev stage:10 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|treatment:DM|BioSampleModel:Model organism or animal,,,,,,,,,tRAM seq of zebrafish: embryo 10 hpf  DM  rep3,EV07014,EV07014,RNA was extracted with Trizol  tRNA isolated by size selection on denaturing polyacrylamide gel  range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment  three prime adapter ligated with T4 RNA ligase 2  reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase  using NEB Next indexed primers.,,,OTHER,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,NextSeq 500,,SRP482074,,,EV07014.R1.fastq.gz,fastq,739056780.0,5278977.0,EV07014.R1.fastq.gz,0:140,A:197948890;C:178761090;G:200265458;T:162060992;N:20350,140,,,,197948890,178761090,200265458,162060992,20350,SRX23109808,SRS20064562,SRA1780298,Medical University of Vienna|Cell and Developmental Biology,Medical University of Vienna,1,3e-05,,0.0,,0.99995,,0.5,,140,,T,,under 1.2% mapping rate,illumina,nextseq,unknown,size_fractionation,nebnext,bulk,unknown,unknown,,Austria,2024-01-06,Gastrula,Embryo,Whole Organism,All anatomical structures
29770,SRR27437490,SRX23109807,SRS20064561,SRP482074,PRJNA1061456,tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development,PRJNA1061456,Other,,,,,,Bud mock R3,,strain:TLAB fish|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|dev stage:10 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|treatment:mock|BioSampleModel:Model organism or animal,,,,,,,,,tRAM seq of zebrafish: embryo 10 hpf  mock  rep3,EV07013,EV07013,RNA was extracted with Trizol  tRNA isolated by size selection on denaturing polyacrylamide gel  range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment  three prime adapter ligated with T4 RNA ligase 2  reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase  using NEB Next indexed primers.,,,OTHER,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,NextSeq 500,,SRP482074,,,EV07013.R1.fastq.gz,fastq,844338040.0,6030986.0,EV07013.R1.fastq.gz,0:140,A:217780710;C:182517044;G:251974206;T:192043675;N:22405,140,,,,217780710,182517044,251974206,192043675,22405,SRX23109807,SRS20064561,SRA1780298,Medical University of Vienna|Cell and Developmental Biology,Medical University of Vienna,1,4e-05,,0.0,,0.99993,,1.0,,140,,T,,under 1.2% mapping rate,illumina,nextseq,unknown,size_fractionation,nebnext,bulk,unknown,unknown,,Austria,2024-01-06,Gastrula,Embryo,Whole Organism,All anatomical structures
29771,SRR27437491,SRX23109806,SRS20064560,SRP482074,PRJNA1061456,tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development,PRJNA1061456,Other,,,,,,Dome BS R3,,strain:TLAB fish|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|dev stage:5 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|treatment:BS|BioSampleModel:Model organism or animal,,,,,,,,,tRAM seq of zebrafish: embryo 5 hpf  BS  rep3,EV07011,EV07011,RNA was extracted with Trizol  tRNA isolated by size selection on denaturing polyacrylamide gel  range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment  three prime adapter ligated with T4 RNA ligase 2  reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase  using NEB Next indexed primers.,,,OTHER,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,NextSeq 500,,SRP482074,,,EV07011.R1.fastq.gz,fastq,893528580.0,6382347.0,EV07011.R1.fastq.gz,0:140,A:240101890;C:155985797;G:262065322;T:235351334;N:24237,140,,,,240101890,155985797,262065322,235351334,24237,SRX23109806,SRS20064560,SRA1780298,Medical University of Vienna|Cell and Developmental Biology,Medical University of Vienna,1,0.0,,0.0,,1.0,,,,140,,T,,under 1.2% mapping rate,illumina,nextseq,unknown,size_fractionation,nebnext,bulk,unknown,unknown,,Austria,2024-01-06,Blastula,Embryo,Whole Organism,All anatomical structures
29772,SRR27437492,SRX23109805,SRS20064559,SRP482074,PRJNA1061456,tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development,PRJNA1061456,Other,,,,,,Dome DM R3,,strain:TLAB fish|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|dev stage:5 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|treatment:DM|BioSampleModel:Model organism or animal,,,,,,,,,tRAM seq of zebrafish: embryo 5 hpf  DM  rep3,EV07012,EV07012,RNA was extracted with Trizol  tRNA isolated by size selection on denaturing polyacrylamide gel  range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment  three prime adapter ligated with T4 RNA ligase 2  reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase  using NEB Next indexed primers.,,,OTHER,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,NextSeq 500,,SRP482074,,,EV07012.R1.fastq.gz,fastq,797662600.0,5697590.0,EV07012.R1.fastq.gz,0:140,A:201908589;C:182656132;G:249672167;T:163404182;N:21530,140,,,,201908589,182656132,249672167,163404182,21530,SRX23109805,SRS20064559,SRA1780298,Medical University of Vienna|Cell and Developmental Biology,Medical University of Vienna,1,3e-05,,0.0,,0.99991,,0.75,,140,,T,,under 1.2% mapping rate,illumina,nextseq,unknown,size_fractionation,nebnext,bulk,unknown,unknown,,Austria,2024-01-06,Blastula,Embryo,Whole Organism,All anatomical structures
29773,SRR27437493,SRX23109804,SRS20064558,SRP482074,PRJNA1061456,tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development,PRJNA1061456,Other,,,,,,Dome mock R3,,strain:TLAB fish|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|dev stage:5 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|treatment:mock|BioSampleModel:Model organism or animal,,,,,,,,,tRAM seq of zebrafish: embryo 5 hpf  mock  rep3,EV07010,EV07010,RNA was extracted with Trizol  tRNA isolated by size selection on denaturing polyacrylamide gel  range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment  three prime adapter ligated with T4 RNA ligase 2  reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase  using NEB Next indexed primers.,,,OTHER,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,NextSeq 500,,SRP482074,,,EV07010.R1.fastq.gz,fastq,467593280.0,3339952.0,EV07010.R1.fastq.gz,0:140,A:122604957;C:118747514;G:124074466;T:102153374;N:12969,140,,,,122604957,118747514,124074466,102153374,12969,SRX23109804,SRS20064558,SRA1780298,Medical University of Vienna|Cell and Developmental Biology,Medical University of Vienna,1,4e-05,,0.0,,0.99993,,1.0,,140,,T,,under 1.2% mapping rate,illumina,nextseq,unknown,size_fractionation,nebnext,bulk,unknown,unknown,,Austria,2024-01-06,Blastula,Embryo,Whole Organism,All anatomical structures
29774,SRR27437494,SRX23109803,SRS20064557,SRP482074,PRJNA1061456,tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development,PRJNA1061456,Other,,,,,,1K cell BS R3,,strain:TLAB fish|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|dev stage:3 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|treatment:BS|BioSampleModel:Model organism or animal,,,,,,,,,tRAM seq of zebrafish: embryo 3 hpf  BS  rep3,EV07008,EV07008,RNA was extracted with Trizol  tRNA isolated by size selection on denaturing polyacrylamide gel  range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment  three prime adapter ligated with T4 RNA ligase 2  reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase  using NEB Next indexed primers.,,,OTHER,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,NextSeq 500,,SRP482074,,,EV07008.R1.fastq.gz,fastq,705682040.0,5040586.0,EV07008.R1.fastq.gz,0:140,A:194506527;C:127442743;G:192893716;T:190818958;N:20096,140,,,,194506527,127442743,192893716,190818958,20096,SRX23109803,SRS20064557,SRA1780298,Medical University of Vienna|Cell and Developmental Biology,Medical University of Vienna,1,0.0,,0.0,,1.0,,,,140,,T,,under 1.2% mapping rate,illumina,nextseq,unknown,size_fractionation,nebnext,bulk,unknown,unknown,,Austria,2024-01-06,Blastula,Embryo,Whole Organism,All anatomical structures
29775,SRR27437495,SRX23109802,SRS20064556,SRP482074,PRJNA1061456,tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development,PRJNA1061456,Other,,,,,,1K cell DM R3,,strain:TLAB fish|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|dev stage:3 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|treatment:DM|BioSampleModel:Model organism or animal,,,,,,,,,tRAM seq of zebrafish: embryo 3 hpf  DM  rep3,EV07009,EV07009,RNA was extracted with Trizol  tRNA isolated by size selection on denaturing polyacrylamide gel  range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment  three prime adapter ligated with T4 RNA ligase 2  reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase  using NEB Next indexed primers.,,,OTHER,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,NextSeq 500,,SRP482074,,,EV07009.R1.fastq.gz,fastq,380716280.0,2719402.0,EV07009.R1.fastq.gz,0:140,A:95351632;C:89558330;G:115625953;T:80169603;N:10762,140,,,,95351632,89558330,115625953,80169603,10762,SRX23109802,SRS20064556,SRA1780298,Medical University of Vienna|Cell and Developmental Biology,Medical University of Vienna,1,6e-05,,1e-05,,0.99991,,0.75,,140,,T,,under 1.2% mapping rate,illumina,nextseq,unknown,size_fractionation,nebnext,bulk,unknown,unknown,,Austria,2024-01-06,Blastula,Embryo,Whole Organism,All anatomical structures
29778,SRR27435863,SRX23108233,SRS20063070,SRP482074,PRJNA1061456,tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development,PRJNA1061456,Other,,,,,,1K cell mock R4,,strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:3 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|treatment:mock|BioSampleModel:Model organism or animal,,,,,,,,,tRAM seq of zebrafish: embryo 3 hpf  mock  rep4,EV08010,EV08010,RNA was extracted with Trizol  tRNA isolated by size selection on denaturing polyacrylamide gel  range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment  three prime adapter ligated with T4 RNA ligase 2  reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase  using NEB Next indexed primers.,,,OTHER,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,NextSeq 500,,SRP482074,,,EV08010.R1.fastq.gz,fastq,678729520.0,4848068.0,EV08010.R1.fastq.gz,0:140,A:170672553;C:182320916;G:171865707;T:153824163;N:46181,140,,,,170672553,182320916,171865707,153824163,46181,SRX23108233,SRS20063070,SRA1780265,Medical University of Vienna|Cell and Developmental Biology,Medical University of Vienna,1,0.0006,,4e-05,,0.99878,,0.79069,,140,,T,,under 1.2% mapping rate,illumina,nextseq,unknown,size_fractionation,nebnext,bulk,unknown,unknown,,Austria,2024-01-05,Blastula,Embryo,Whole Organism,All anatomical structures
29779,SRR27435864,SRX23108232,SRS20063068,SRP482074,PRJNA1061456,tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development,PRJNA1061456,Other,,,,,,4 cell BS R4,,strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:1 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|treatment:BS|BioSampleModel:Model organism or animal,,,,,,,,,tRAM seq of zebrafish: embryo 1 hpf  BS  rep4,EV08009,EV08009,RNA was extracted with Trizol  tRNA isolated by size selection on denaturing polyacrylamide gel  range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment  three prime adapter ligated with T4 RNA ligase 2  reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase  using NEB Next indexed primers.,,,OTHER,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,NextSeq 500,,SRP482074,,,EV08009.R1.fastq.gz,fastq,756964460.0,5406889.0,EV08009.R1.fastq.gz,0:140,A:191381054;C:111783194;G:185694475;T:268052883;N:52854,140,,,,191381054,111783194,185694475,268052883,52854,SRX23108232,SRS20063068,SRA1780265,Medical University of Vienna|Cell and Developmental Biology,Medical University of Vienna,1,1e-05,,0.0,,0.99997,,1.0,,140,,T,,under 1.2% mapping rate,illumina,nextseq,unknown,size_fractionation,nebnext,bulk,unknown,unknown,,Austria,2024-01-05,Cleavage,Embryo,Whole Organism,All anatomical structures
29780,SRR27435865,SRX23108231,SRS20063069,SRP482074,PRJNA1061456,tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development,PRJNA1061456,Other,,,,,,4 cell DM R4,,strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:1 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|treatment:DM|BioSampleModel:Model organism or animal,,,,,,,,,tRAM seq of zebrafish: embryo 1 hpf  DM  rep4,EV08008,EV08008,RNA was extracted with Trizol  tRNA isolated by size selection on denaturing polyacrylamide gel  range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment  three prime adapter ligated with T4 RNA ligase 2  reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase  using NEB Next indexed primers.,,,OTHER,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,NextSeq 500,,SRP482074,,,EV08008.R1.fastq.gz,fastq,751794680.0,5369962.0,EV08008.R1.fastq.gz,0:140,A:194845808;C:197389162;G:194749636;T:164756481;N:53593,140,,,,194845808,197389162,194749636,164756481,53593,SRX23108231,SRS20063069,SRA1780265,Medical University of Vienna|Cell and Developmental Biology,Medical University of Vienna,1,0.00124,,0.00029,,0.99853,,0.77083,,140,,T,,under 1.2% mapping rate,illumina,nextseq,unknown,size_fractionation,nebnext,bulk,unknown,unknown,,Austria,2024-01-05,Cleavage,Embryo,Whole Organism,All anatomical structures
29781,SRR27435866,SRX23108230,SRS20063066,SRP482074,PRJNA1061456,tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development,PRJNA1061456,Other,,,,,,4 cell mock R4,,strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:1 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|treatment:mock|BioSampleModel:Model organism or animal,,,,,,,,,tRAM seq of zebrafish: embryo 1 hpf  mock  rep4,EV08007,EV08007,RNA was extracted with Trizol  tRNA isolated by size selection on denaturing polyacrylamide gel  range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment  three prime adapter ligated with T4 RNA ligase 2  reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase  using NEB Next indexed primers.,,,OTHER,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,NextSeq 500,,SRP482074,,,EV08007.R1.fastq.gz,fastq,761961760.0,5442584.0,EV08007.R1.fastq.gz,0:140,A:194053323;C:191169414;G:194452160;T:182234253;N:52610,140,,,,194053323,191169414,194452160,182234253,52610,SRX23108230,SRS20063066,SRA1780265,Medical University of Vienna|Cell and Developmental Biology,Medical University of Vienna,1,0.00242,,0.00062,,0.99803,,0.81818,,140,,T,,under 1.2% mapping rate,illumina,nextseq,unknown,size_fractionation,nebnext,bulk,unknown,unknown,,Austria,2024-01-05,Cleavage,Embryo,Whole Organism,All anatomical structures
29785,SRR27435870,SRX23108226,SRS20063064,SRP482074,PRJNA1061456,tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development,PRJNA1061456,Other,,,,,,24h BS R4,,strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:24 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|treatment:BS|BioSampleModel:Model organism or animal,,,,,,,,,tRAM seq of zebrafish: embryo 24 hpf  BS  rep4,EV08021,EV08021,RNA was extracted with Trizol  tRNA isolated by size selection on denaturing polyacrylamide gel  range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment  three prime adapter ligated with T4 RNA ligase 2  reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase  using NEB Next indexed primers.,,,OTHER,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,NextSeq 500,,SRP482074,,,EV08021.R1.fastq.gz,fastq,747571860.0,5339799.0,EV08021.R1.fastq.gz,0:140,A:185666613;C:121868156;G:181153824;T:258830310;N:52957,140,,,,185666613,121868156,181153824,258830310,52957,SRX23108226,SRS20063064,SRA1780265,Medical University of Vienna|Cell and Developmental Biology,Medical University of Vienna,1,0.0,,0.0,,1.0,,,,140,,T,,under 1.2% mapping rate,illumina,nextseq,unknown,size_fractionation,nebnext,bulk,unknown,unknown,,Austria,2024-01-05,Pharyngula,Embryo,Whole Organism,All anatomical structures
29787,SRR27435872,SRX23108224,SRS20063061,SRP482074,PRJNA1061456,tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development,PRJNA1061456,Other,,,,,,24h DM R4,,strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:24 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|treatment:DM|BioSampleModel:Model organism or animal,,,,,,,,,tRAM seq of zebrafish: embryo 24 hpf  DM  rep4,EV08020,EV08020,RNA was extracted with Trizol  tRNA isolated by size selection on denaturing polyacrylamide gel  range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment  three prime adapter ligated with T4 RNA ligase 2  reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase  using NEB Next indexed primers.,,,OTHER,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,NextSeq 500,,SRP482074,,,EV08020.R1.fastq.gz,fastq,775090400.0,5536360.0,EV08020.R1.fastq.gz,0:140,A:198131068;C:205114604;G:198783890;T:173006366;N:54472,140,,,,198131068,205114604,198783890,173006366,54472,SRX23108224,SRS20063061,SRA1780265,Medical University of Vienna|Cell and Developmental Biology,Medical University of Vienna,1,0.00056,,4e-05,,0.9989,,0.71052,,140,,T,,under 1.2% mapping rate,illumina,nextseq,unknown,size_fractionation,nebnext,bulk,unknown,unknown,,Austria,2024-01-05,Pharyngula,Embryo,Whole Organism,All anatomical structures
29788,SRR27435873,SRX23108223,SRS20063060,SRP482074,PRJNA1061456,tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development,PRJNA1061456,Other,,,,,,24h mock R4,,strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:24 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|treatment:mock|BioSampleModel:Model organism or animal,,,,,,,,,tRAM seq of zebrafish: embryo 24 hpf  mock  rep4,EV08019,EV08019,RNA was extracted with Trizol  tRNA isolated by size selection on denaturing polyacrylamide gel  range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment  three prime adapter ligated with T4 RNA ligase 2  reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase  using NEB Next indexed primers.,,,OTHER,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,NextSeq 500,,SRP482074,,,EV08019.R1.fastq.gz,fastq,763233240.0,5451666.0,EV08019.R1.fastq.gz,0:140,A:189362337;C:199268270;G:198509945;T:176040551;N:52137,140,,,,189362337,199268270,198509945,176040551,52137,SRX23108223,SRS20063060,SRA1780265,Medical University of Vienna|Cell and Developmental Biology,Medical University of Vienna,1,0.00036,,6e-05,,0.99939,,0.85365,,140,,T,,under 1.2% mapping rate,illumina,nextseq,unknown,size_fractionation,nebnext,bulk,unknown,unknown,,Austria,2024-01-05,Pharyngula,Embryo,Whole Organism,All anatomical structures
29789,SRR27435874,SRX23108222,SRS20063057,SRP482074,PRJNA1061456,tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development,PRJNA1061456,Other,,,,,,Bud BS R4,,strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:10 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|treatment:BS|BioSampleModel:Model organism or animal,,,,,,,,,tRAM seq of zebrafish: embryo 10 hpf  BS  rep4,EV08018,EV08018,RNA was extracted with Trizol  tRNA isolated by size selection on denaturing polyacrylamide gel  range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment  three prime adapter ligated with T4 RNA ligase 2  reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase  using NEB Next indexed primers.,,,OTHER,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,NextSeq 500,,SRP482074,,,EV08018.R1.fastq.gz,fastq,809203080.0,5780022.0,EV08018.R1.fastq.gz,0:140,A:209714496;C:130623600;G:197912909;T:270895413;N:56662,140,,,,209714496,130623600,197912909,270895413,56662,SRX23108222,SRS20063057,SRA1780265,Medical University of Vienna|Cell and Developmental Biology,Medical University of Vienna,1,0.0,,0.0,,1.0,,,,140,,T,,under 1.2% mapping rate,illumina,nextseq,unknown,size_fractionation,nebnext,bulk,unknown,unknown,,Austria,2024-01-05,Gastrula,Embryo,Whole Organism,All anatomical structures
29790,SRR27435875,SRX23108221,SRS20063059,SRP482074,PRJNA1061456,tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development,PRJNA1061456,Other,,,,,,Bud DM R4,,strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:10 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|treatment:DM|BioSampleModel:Model organism or animal,,,,,,,,,tRAM seq of zebrafish: embryo 10 hpf  DM  rep4,EV08017,EV08017,RNA was extracted with Trizol  tRNA isolated by size selection on denaturing polyacrylamide gel  range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment  three prime adapter ligated with T4 RNA ligase 2  reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase  using NEB Next indexed primers.,,,OTHER,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,NextSeq 500,,SRP482074,,,EV08017.R1.fastq.gz,fastq,722137500.0,5158125.0,EV08017.R1.fastq.gz,0:140,A:176408094;C:195907583;G:188487109;T:161283055;N:51659,140,,,,176408094,195907583,188487109,161283055,51659,SRX23108221,SRS20063059,SRA1780265,Medical University of Vienna|Cell and Developmental Biology,Medical University of Vienna,1,0.00053,,3e-05,,0.999,,0.70422,,140,,T,,under 1.2% mapping rate,illumina,nextseq,unknown,size_fractionation,nebnext,bulk,unknown,unknown,,Austria,2024-01-05,Gastrula,Embryo,Whole Organism,All anatomical structures
29791,SRR27435876,SRX23108220,SRS20063058,SRP482074,PRJNA1061456,tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development,PRJNA1061456,Other,,,,,,Bud mock R4,,strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:10 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|treatment:mock|BioSampleModel:Model organism or animal,,,,,,,,,tRAM seq of zebrafish: embryo 10 hpf  mock  rep4,EV08016,EV08016,RNA was extracted with Trizol  tRNA isolated by size selection on denaturing polyacrylamide gel  range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment  three prime adapter ligated with T4 RNA ligase 2  reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase  using NEB Next indexed primers.,,,OTHER,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,NextSeq 500,,SRP482074,,,EV08016.R1.fastq.gz,fastq,827605660.0,5911469.0,EV08016.R1.fastq.gz,0:140,A:204173663;C:224596562;G:206999037;T:191779555;N:56843,140,,,,204173663,224596562,206999037,191779555,56843,SRX23108220,SRS20063058,SRA1780265,Medical University of Vienna|Cell and Developmental Biology,Medical University of Vienna,1,0.00037,,2e-05,,0.99908,,0.7037,,140,,T,,under 1.2% mapping rate,illumina,nextseq,unknown,size_fractionation,nebnext,bulk,unknown,unknown,,Austria,2024-01-05,Gastrula,Embryo,Whole Organism,All anatomical structures
29792,SRR27435877,SRX23108219,SRS20063056,SRP482074,PRJNA1061456,tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development,PRJNA1061456,Other,,,,,,Dome BS R4,,strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:5 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|treatment:BS|BioSampleModel:Model organism or animal,,,,,,,,,tRAM seq of zebrafish: embryo 5 hpf  BS  rep4,EV08015,EV08015,RNA was extracted with Trizol  tRNA isolated by size selection on denaturing polyacrylamide gel  range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment  three prime adapter ligated with T4 RNA ligase 2  reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase  using NEB Next indexed primers.,,,OTHER,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,NextSeq 500,,SRP482074,,,EV08015.R1.fastq.gz,fastq,804598200.0,5747130.0,EV08015.R1.fastq.gz,0:140,A:215467427;C:134937180;G:189531758;T:264604493;N:57342,140,,,,215467427,134937180,189531758,264604493,57342,SRX23108219,SRS20063056,SRA1780265,Medical University of Vienna|Cell and Developmental Biology,Medical University of Vienna,1,2e-05,,0.0,,0.99995,,1.0,,140,,T,,under 1.2% mapping rate,illumina,nextseq,unknown,size_fractionation,nebnext,bulk,unknown,unknown,,Austria,2024-01-05,Blastula,Embryo,Whole Organism,All anatomical structures
29793,SRR27435878,SRX23108218,SRS20063055,SRP482074,PRJNA1061456,tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development,PRJNA1061456,Other,,,,,,Dome DM R4,,strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:5 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|treatment:DM|BioSampleModel:Model organism or animal,,,,,,,,,tRAM seq of zebrafish: embryo 5 hpf  DM  rep4,EV08014,EV08014,RNA was extracted with Trizol  tRNA isolated by size selection on denaturing polyacrylamide gel  range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment  three prime adapter ligated with T4 RNA ligase 2  reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase  using NEB Next indexed primers.,,,OTHER,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,NextSeq 500,,SRP482074,,,EV08014.R1.fastq.gz,fastq,662443740.0,4731741.0,EV08014.R1.fastq.gz,0:140,A:164941700;C:167025964;G:177255084;T:153175163;N:45829,140,,,,164941700,167025964,177255084,153175163,45829,SRX23108218,SRS20063055,SRA1780265,Medical University of Vienna|Cell and Developmental Biology,Medical University of Vienna,1,0.00069,,0.0001,,0.9992,,0.83076,,140,,T,,under 1.2% mapping rate,illumina,nextseq,unknown,size_fractionation,nebnext,bulk,unknown,unknown,,Austria,2024-01-05,Blastula,Embryo,Whole Organism,All anatomical structures
29794,SRR27435879,SRX23108217,SRS20063052,SRP482074,PRJNA1061456,tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development,PRJNA1061456,Other,,,,,,Dome mock R4,,strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:5 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|treatment:mock|BioSampleModel:Model organism or animal,,,,,,,,,tRAM seq of zebrafish: embryo 5 hpf  mock  rep4,EV08013,EV08013,RNA was extracted with Trizol  tRNA isolated by size selection on denaturing polyacrylamide gel  range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment  three prime adapter ligated with T4 RNA ligase 2  reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase  using NEB Next indexed primers.,,,OTHER,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,NextSeq 500,,SRP482074,,,EV08013.R1.fastq.gz,fastq,794760540.0,5676861.0,EV08013.R1.fastq.gz,0:140,A:197361776;C:210230329;G:205734036;T:181380205;N:54194,140,,,,197361776,210230329,205734036,181380205,54194,SRX23108217,SRS20063052,SRA1780265,Medical University of Vienna|Cell and Developmental Biology,Medical University of Vienna,1,0.00066,,9e-05,,0.99894,,0.78378,,140,,T,,under 1.2% mapping rate,illumina,nextseq,unknown,size_fractionation,nebnext,bulk,unknown,unknown,,Austria,2024-01-05,Blastula,Embryo,Whole Organism,All anatomical structures
29795,SRR27435880,SRX23108216,SRS20063054,SRP482074,PRJNA1061456,tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development,PRJNA1061456,Other,,,,,,1K cell BS R4,,strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:3 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|treatment:BS|BioSampleModel:Model organism or animal,,,,,,,,,tRAM seq of zebrafish: embryo 3 hpf  BS  rep4,EV08012,EV08012,RNA was extracted with Trizol  tRNA isolated by size selection on denaturing polyacrylamide gel  range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment  three prime adapter ligated with T4 RNA ligase 2  reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase  using NEB Next indexed primers.,,,OTHER,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,NextSeq 500,,SRP482074,,,EV08012.R1.fastq.gz,fastq,722593200.0,5161380.0,EV08012.R1.fastq.gz,0:140,A:188475497;C:119550806;G:173208825;T:241306038;N:52034,140,,,,188475497,119550806,173208825,241306038,52034,SRX23108216,SRS20063054,SRA1780265,Medical University of Vienna|Cell and Developmental Biology,Medical University of Vienna,1,0.0,,0.0,,1.0,,,,140,,T,,under 1.2% mapping rate,illumina,nextseq,unknown,size_fractionation,nebnext,bulk,unknown,unknown,,Austria,2024-01-05,Blastula,Embryo,Whole Organism,All anatomical structures
29796,SRR27435881,SRX23108215,SRS20063053,SRP482074,PRJNA1061456,tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development,PRJNA1061456,Other,,,,,,1K cell DM R4,,strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:3 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|treatment:DM|BioSampleModel:Model organism or animal,,,,,,,,,tRAM seq of zebrafish: embryo 3 hpf  DM  rep4,EV08011,EV08011,RNA was extracted with Trizol  tRNA isolated by size selection on denaturing polyacrylamide gel  range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment  three prime adapter ligated with T4 RNA ligase 2  reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase  using NEB Next indexed primers.,,,OTHER,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,NextSeq 500,,SRP482074,,,EV08011.R1.fastq.gz,fastq,753783380.0,5384167.0,EV08011.R1.fastq.gz,0:140,A:190029713;C:193734250;G:194752855;T:175212145;N:54417,140,,,,190029713,193734250,194752855,175212145,54417,SRX23108215,SRS20063053,SRA1780265,Medical University of Vienna|Cell and Developmental Biology,Medical University of Vienna,1,0.00076,,5e-05,,0.99859,,0.70873,,140,,T,,under 1.2% mapping rate,illumina,nextseq,unknown,size_fractionation,nebnext,bulk,unknown,unknown,,Austria,2024-01-05,Blastula,Embryo,Whole Organism,All anatomical structures
36195,SRR042434,SRX020028,SRS066219,SRP002411,PRJNA126003,A novel miRNA processing pathway independent of Dicer requires Argonaute2 catalytic activity,GSE21503,Transcriptome Analysis,Here we identify a Dicer independent miRNA biogenesis pathway that employs the slicer catalytic activity of Argonaute2 Ago2. To uncover Dicer independent miRNAs  we sequenced  small RNAs in wild type  maternal zygotic dicer MZdicer and MZago2 mutants  using zebrafish as a model system. We find that  in contrast to other miRNAs  miR 451 levels were increased in MZdicer but drastically reduced in the MZago2 mutants. We show that pre miR 451 processing requires Ago2 catalytic activity in vivo. MZago2 mutant embryos display delayed erythrocyte maturation that can be rescued by wild type Ago2 or miR 451 duplex but not catalytically dead Ago2. We propose that Ago2 mediated cleavage of a subset of pre miRNAs  followed by uridylation and trimming  generates functional miRNAs in a Dicer independent manner. Overall design: Examination of small RNAs 18 to 35 nucleotides in 3 different zebrafish genotypes wild type  MZago2  MZdicer at 48 hpf,,pubmed:20448148,,MZago2 mutant YΔ90,GSM540646,,tissue:48hpf embryo  MZago2 mutant|strain:mixed AB  TU  TL TLF background|developmental stage:48hpf embryo|genotype:MZago2 Δ90/Δ90,MZago2 mutant YΔ90,Alignment: Sequence reads were mapped to Zebrafish Zv8/danRer6 precursor miRNA sequences using Bowtie software version 0.12.1 with maximal two mismatches within first 20 nucleotides. Alignments are available in the supplementary *out.txt file.,48hpf embryo  MZago2 mutant,,Total RNA from frozen embryos was extracted with Trizol reagent and phenol/chloroform. Libraries were prepared according to Illumina's instructions Part # 1004239 Rev. A accompanying the small RNA Sample Kit. Briefly  total RNA samples were run in a denaturing PAGE and the band corresponding to the RNAs of 18 35 nucletides was excised. RNA 5’ and 3’ adapters were ligated sequentially. Reverse transcription followed by PCR amplified cDNA constructs with both adapters. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.,Embryos were collected from breeding tanks and kept at 28C in p60 plates with water and 0.2 mg/L methylene blue. At 48 hpf  embryos were hand dechorionated and 40 embryos per sample were flash frozen in liquid nitrogen.,strain:mixed AB  TU  TL TLF background|developmental stage:48hpf embryo|genotype:MZago2 Δ90/Δ90,GSM540646,GSM540646: MZago2 mutant YΔ90,GSM540646: MZago2 mutant YΔ90,GSM540646: MZago2 mutant YΔ90,1,,GEO Accession:GSM540646,RNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina Genome Analyzer,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP002411,,,Ago2_ydelta90.fastq,fastq,437752008.0,12159778.0,GSM540646 1,0:36,A:96750665;C:83495585;G:119239752;T:138073795;N:192211,36,,,,96750665,83495585,119239752,138073795,192211,SRX020028,SRS066219,SRA012683,GEO,"Giraldez Lab, Genetics, Yale University",1,0.03964,,0.0,,0.99985,,0.00052,,36,,B,,usable mapping rate,illumina,early_illumina,unknown,size_fractionation,unknown,bulk,unknown,unknown,,United States,2010-05-04,Hatching,Embryo,Embryo Imprecise,All anatomical structures
36196,SRR042433,SRX020027,SRS066218,SRP002411,PRJNA126003,A novel miRNA processing pathway independent of Dicer requires Argonaute2 catalytic activity,GSE21503,Transcriptome Analysis,Here we identify a Dicer independent miRNA biogenesis pathway that employs the slicer catalytic activity of Argonaute2 Ago2. To uncover Dicer independent miRNAs  we sequenced  small RNAs in wild type  maternal zygotic dicer MZdicer and MZago2 mutants  using zebrafish as a model system. We find that  in contrast to other miRNAs  miR 451 levels were increased in MZdicer but drastically reduced in the MZago2 mutants. We show that pre miR 451 processing requires Ago2 catalytic activity in vivo. MZago2 mutant embryos display delayed erythrocyte maturation that can be rescued by wild type Ago2 or miR 451 duplex but not catalytically dead Ago2. We propose that Ago2 mediated cleavage of a subset of pre miRNAs  followed by uridylation and trimming  generates functional miRNAs in a Dicer independent manner. Overall design: Examination of small RNAs 18 to 35 nucleotides in 3 different zebrafish genotypes wild type  MZago2  MZdicer at 48 hpf,,pubmed:20448148,,WT2,GSM540645,,tissue:48hpf embryo  WT|strain:mixed AB  TU  TL TLF background|developmental stage:48hpf embryo|genotype:wild type,WT2,Alignment: Sequence reads were mapped to Zebrafish Zv8/danRer6 precursor miRNA sequences using Bowtie software version 0.12.1 with maximal two mismatches within first 20 nucleotides. Alignments are available in the supplementary *out.txt file.,48hpf embryo  WT,,Total RNA from frozen embryos was extracted with Trizol reagent and phenol/chloroform. Libraries were prepared according to Illumina's instructions Part # 1004239 Rev. A accompanying the small RNA Sample Kit. Briefly  total RNA samples were run in a denaturing PAGE and the band corresponding to the RNAs of 18 35 nucletides was excised. RNA 5’ and 3’ adapters were ligated sequentially. Reverse transcription followed by PCR amplified cDNA constructs with both adapters. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.,Embryos were collected from breeding tanks and kept at 28C in p60 plates with water and 0.2 mg/L methylene blue. At 48 hpf  embryos were hand dechorionated and 40 embryos per sample were flash frozen in liquid nitrogen.,strain:mixed AB  TU  TL TLF background|developmental stage:48hpf embryo|genotype:wild type,GSM540645,GSM540645: WT2,GSM540645: WT2,GSM540645: WT2,1,,GEO Accession:GSM540645,RNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina Genome Analyzer,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP002411,,,WT2.fastq,fastq,59530030.0,1700858.0,GSM540645 1,0:35,A:12981942;C:11521313;G:16378279;T:18609524;N:38972,35,,,,12981942,11521313,16378279,18609524,38972,SRX020027,SRS066218,SRA012683,GEO,"Giraldez Lab, Genetics, Yale University",1,0.06435,,0.0,,0.99995,,0.0,,35,,B,,usable mapping rate,illumina,early_illumina,unknown,size_fractionation,unknown,bulk,unknown,unknown,,United States,2010-05-04,Hatching,Embryo,Embryo Imprecise,All anatomical structures
36197,SRR042432,SRX020026,SRS066217,SRP002411,PRJNA126003,A novel miRNA processing pathway independent of Dicer requires Argonaute2 catalytic activity,GSE21503,Transcriptome Analysis,Here we identify a Dicer independent miRNA biogenesis pathway that employs the slicer catalytic activity of Argonaute2 Ago2. To uncover Dicer independent miRNAs  we sequenced  small RNAs in wild type  maternal zygotic dicer MZdicer and MZago2 mutants  using zebrafish as a model system. We find that  in contrast to other miRNAs  miR 451 levels were increased in MZdicer but drastically reduced in the MZago2 mutants. We show that pre miR 451 processing requires Ago2 catalytic activity in vivo. MZago2 mutant embryos display delayed erythrocyte maturation that can be rescued by wild type Ago2 or miR 451 duplex but not catalytically dead Ago2. We propose that Ago2 mediated cleavage of a subset of pre miRNAs  followed by uridylation and trimming  generates functional miRNAs in a Dicer independent manner. Overall design: Examination of small RNAs 18 to 35 nucleotides in 3 different zebrafish genotypes wild type  MZago2  MZdicer at 48 hpf,,pubmed:20448148,,MZdicer mutant2 hu896,GSM540644,,tissue:48hpf embryo  Mzdicer mutant|strain:mixed AB  TU  TL TLF background|developmental stage:48hpf embryo|genotype:MZdicer hu896/hu896,MZdicer mutant2 hu896,Alignment: Sequence reads were mapped to Zebrafish Zv8/danRer6 precursor miRNA sequences using Bowtie software version 0.12.1 with maximal two mismatches within first 20 nucleotides. Alignments are available in the supplementary *out.txt file.,48hpf embryo  Mzdicer mutant,,Total RNA from frozen embryos was extracted with Trizol reagent and phenol/chloroform. Libraries were prepared according to Illumina's instructions Part # 1004239 Rev. A accompanying the small RNA Sample Kit. Briefly  total RNA samples were run in a denaturing PAGE and the band corresponding to the RNAs of 18 35 nucletides was excised. RNA 5’ and 3’ adapters were ligated sequentially. Reverse transcription followed by PCR amplified cDNA constructs with both adapters. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.,Embryos were collected from breeding tanks and kept at 28C in p60 plates with water and 0.2 mg/L methylene blue. At 48 hpf  embryos were hand dechorionated and 40 embryos per sample were flash frozen in liquid nitrogen.,strain:mixed AB  TU  TL TLF background|developmental stage:48hpf embryo|genotype:MZdicer hu896/hu896,GSM540644,GSM540644: MZdicer mutant2 hu896,GSM540644: MZdicer mutant2 hu896,GSM540644: MZdicer mutant2 hu896,1,,GEO Accession:GSM540644,RNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina Genome Analyzer,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP002411,,,MZdicer2_hu896.fastq,fastq,4268740.0,121964.0,GSM540644 1,0:35,A:813936;C:1034356;G:1131604;T:1280756;N:8088,35,,,,813936,1034356,1131604,1280756,8088,SRX020026,SRS066217,SRA012683,GEO,"Giraldez Lab, Genetics, Yale University",1,0.03836,,0.0009,,0.99849,,0.3021,,35,,B,,usable mapping rate,illumina,early_illumina,unknown,size_fractionation,unknown,bulk,unknown,unknown,,United States,2010-05-04,Hatching,Embryo,Embryo Imprecise,All anatomical structures
36198,SRR042431,SRX020025,SRS066216,SRP002411,PRJNA126003,A novel miRNA processing pathway independent of Dicer requires Argonaute2 catalytic activity,GSE21503,Transcriptome Analysis,Here we identify a Dicer independent miRNA biogenesis pathway that employs the slicer catalytic activity of Argonaute2 Ago2. To uncover Dicer independent miRNAs  we sequenced  small RNAs in wild type  maternal zygotic dicer MZdicer and MZago2 mutants  using zebrafish as a model system. We find that  in contrast to other miRNAs  miR 451 levels were increased in MZdicer but drastically reduced in the MZago2 mutants. We show that pre miR 451 processing requires Ago2 catalytic activity in vivo. MZago2 mutant embryos display delayed erythrocyte maturation that can be rescued by wild type Ago2 or miR 451 duplex but not catalytically dead Ago2. We propose that Ago2 mediated cleavage of a subset of pre miRNAs  followed by uridylation and trimming  generates functional miRNAs in a Dicer independent manner. Overall design: Examination of small RNAs 18 to 35 nucleotides in 3 different zebrafish genotypes wild type  MZago2  MZdicer at 48 hpf,,pubmed:20448148,,WT1,GSM540643,,tissue:48hpf embryo  WT|strain:mixed AB  TU  TL TLF background|developmental stage:48hpf embryo|genotype:wild type,WT1,Alignment: Sequence reads were mapped to Zebrafish Zv8/danRer6 precursor miRNA sequences using Bowtie software version 0.12.1 with maximal two mismatches within first 20 nucleotides. Alignments are available in the supplementary *out.txt file.,48hpf embryo  WT,,Total RNA from frozen embryos was extracted with Trizol reagent and phenol/chloroform. Libraries were prepared according to Illumina's instructions Part # 1004239 Rev. A accompanying the small RNA Sample Kit. Briefly  total RNA samples were run in a denaturing PAGE and the band corresponding to the RNAs of 18 35 nucletides was excised. RNA 5’ and 3’ adapters were ligated sequentially. Reverse transcription followed by PCR amplified cDNA constructs with both adapters. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.,Embryos were collected from breeding tanks and kept at 28C in p60 plates with water and 0.2 mg/L methylene blue. At 48 hpf  embryos were hand dechorionated and 40 embryos per sample were flash frozen in liquid nitrogen.,strain:mixed AB  TU  TL TLF background|developmental stage:48hpf embryo|genotype:wild type,GSM540643,GSM540643: WT1,GSM540643: WT1,GSM540643: WT1,1,,GEO Accession:GSM540643,RNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina Genome Analyzer,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP002411,,quality book char:@|quality scoring system:log odds,WT1.fastq,fastq,26959392.0,748872.0,GSM540643 1,0:36,A:6097309;C:6093948;G:6950185;T:7813829;N:4121,36,,,,6097309,6093948,6950185,7813829,4121,SRX020025,SRS066216,SRA012683,GEO,"Giraldez Lab, Genetics, Yale University",1,0.0022,,0.0,,0.99993,,0.0,,36,,T,,under 1.2% mapping rate,illumina,early_illumina,unknown,size_fractionation,unknown,bulk,unknown,unknown,,United States,2010-05-04,Hatching,Embryo,Embryo Imprecise,All anatomical structures
36199,SRR042430,SRX020024,SRS066215,SRP002411,PRJNA126003,A novel miRNA processing pathway independent of Dicer requires Argonaute2 catalytic activity,GSE21503,Transcriptome Analysis,Here we identify a Dicer independent miRNA biogenesis pathway that employs the slicer catalytic activity of Argonaute2 Ago2. To uncover Dicer independent miRNAs  we sequenced  small RNAs in wild type  maternal zygotic dicer MZdicer and MZago2 mutants  using zebrafish as a model system. We find that  in contrast to other miRNAs  miR 451 levels were increased in MZdicer but drastically reduced in the MZago2 mutants. We show that pre miR 451 processing requires Ago2 catalytic activity in vivo. MZago2 mutant embryos display delayed erythrocyte maturation that can be rescued by wild type Ago2 or miR 451 duplex but not catalytically dead Ago2. We propose that Ago2 mediated cleavage of a subset of pre miRNAs  followed by uridylation and trimming  generates functional miRNAs in a Dicer independent manner. Overall design: Examination of small RNAs 18 to 35 nucleotides in 3 different zebrafish genotypes wild type  MZago2  MZdicer at 48 hpf,,pubmed:20448148,,MZdicer mutant1 hu715,GSM540642,,tissue:48hpf embryo  Mzdicer mutant|strain:mixed AB  TU  TL TLF background|developmental stage:48hpf embryo|genotype:MZdicer hu715/hu715,MZdicer mutant1 hu715,Alignment: Sequence reads were mapped to Zebrafish Zv8/danRer6 precursor miRNA sequences using Bowtie software version 0.12.1 with maximal two mismatches within first 20 nucleotides. Alignments are available in the supplementary *out.txt file.,48hpf embryo  Mzdicer mutant,,Total RNA from frozen embryos was extracted with Trizol reagent and phenol/chloroform. Libraries were prepared according to Illumina's instructions Part # 1004239 Rev. A accompanying the small RNA Sample Kit. Briefly  total RNA samples were run in a denaturing PAGE and the band corresponding to the RNAs of 18 35 nucletides was excised. RNA 5’ and 3’ adapters were ligated sequentially. Reverse transcription followed by PCR amplified cDNA constructs with both adapters. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.,Embryos were collected from breeding tanks and kept at 28C in p60 plates with water and 0.2 mg/L methylene blue. At 48 hpf  embryos were hand dechorionated and 40 embryos per sample were flash frozen in liquid nitrogen.,strain:mixed AB  TU  TL TLF background|developmental stage:48hpf embryo|genotype:MZdicer hu715/hu715,GSM540642,GSM540642: MZdicer mutant1 hu715,GSM540642: MZdicer mutant1 hu715,GSM540642: MZdicer mutant1 hu715,1,,GEO Accession:GSM540642,RNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina Genome Analyzer,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP002411,,quality book char:@|quality scoring system:log odds,MZdicer1_hu715.fastq,fastq,11972772.0,332577.0,GSM540642 1,0:36,A:2703131;C:3062840;G:3338413;T:2867600;N:788,36,,,,2703131,3062840,3338413,2867600,788,SRX020024,SRS066215,SRA012683,GEO,"Giraldez Lab, Genetics, Yale University",1,0.00678,,0.00073,,0.99847,,0.3421,,36,,T,,under 1.2% mapping rate,illumina,early_illumina,unknown,size_fractionation,unknown,bulk,unknown,unknown,,United States,2010-05-04,Hatching,Embryo,Embryo Imprecise,All anatomical structures
36266,SRR953577,SRX336218,SRS471213,SRP028895,PRJNA138095,Transcriptome wide analysis of small RNA expression in early zebrafish development,GSE27722,Transcriptome Analysis,During early vertebrate development  a large number of noncoding RNAs are maternally inherited or expressed upon activation of zygotic transcription.  The exact identity  expression levels  and function during early vertebrate development for most of these noncoding RNAs remains largely unknown.  miRNAs microRNAs and piRNAs piwi interacting RNAs are two classes of small non coding RNAs that play important roles in gene regulation during early embryonic development.  Here  we utilized Illumina next generation sequencing technology to determine temporal expression patterns for both miRNAs and piRNAs during four distinct stages of early vertebrate development using zebrafish as a model system.  For miRNAs  the expression patterns for 192 known miRNAs and 12 novel miRNAs within 123 different miRNA families were determined.  Significant sequence variation was observed at the five prime' and three prime' ends of miRNAs with a large number of extra nucleotides added in a non template directed manner.  We also identified a large and diverse set of piRNAs expressed during early development  far beyond that expected if piRNA expression is restricted to germ cells.  Our analyses represent the deepest investigation to date of small RNA expression during early vertebrate development and suggest important novel functions for small RNAs during embryogenesis. Overall design: Identify the expression of small RNAs in zebrafish embryos of four different developmental stages using high through put sequencing,,pubmed:22408181,,embryo 1dpf rep1,GSM686385,,source name:the whole embryo|strain:AB*WT|developmental stage:1dpf|tissue:the whole embryos,embryo 1dpf rep1,"fasta: Initial reads were processed to remove linker sequences using a dynamic alignment algorithm  which allows one mismatch in the linker sequences. All the sequence with N inside was removed as well. The unique sequences were retained with the counts indicating thier abundance. The header of each sequence is composed of a unique sequence ID followed by a "" x"" and the reads counts. e.g. unique ID x counts. alignment: Initial reads were processed to remove linker sequences using a dynamic alignment algorithm  which allows one mismatch in the linker sequences.  Small RNAs with perfect matches to the zebrafish genome Zv8 from Ensembl http://www.ensembl.org were retrieved using megaBLAST http://www.ncbi.nlm.nih.gov/blast/megablast.shtml and Bowtie http://bowtie bio.sourceforge.net/tutorial.shtml. To identify piRNAs  consensus sequences from zebrafish repetitive elements were retrieved from Repbase http://www.girinst.org/repbase/index.html and Repeat Maskers using the UCSC genome browser http://genome.ucsc.edu.  Small RNAs perfectly mapping to these consensus sequences and their genomic flanking regions were sorted into piRNA libraries with up to 3 genomic mapping positions for each unique RNA sequence. fasta files description: small RNA 15 30 nt alignment file description: piRNA map to repetitive elements",the whole embryo,,Zebrafish embryos were collected at the 256 cell stage  sphere stage  shield stage  and 1dpf.  Total RNA was isolated from embryos using Trizol.  RNAs were fractionated on 15% denaturing polyacrylamide gels and small RNAs between 15 30 nucleotides were excised and purified.  cDNA libraries were generated using specific linkers and RT/PCR  as previously described.  Libraries were sequenced in the Genome Technology Core of Vanderbilt University using the Illumina sequencing platform.,Embryos were raised at 28°C in egg water 0.03% Instant Ocean marine salt mix for the initial several hours of development,strain:AB*WT|developmental stage:1dpf|tissue:the whole embryos,GSM686385,GSM686385: embryo 1dpf rep1; Danio rerio; ncRNA Seq,GSM686385,,1,Zebrafish embryos were collected at the 256 cell stage  sphere stage  shield stage  and 1dpf.  Total RNA was isolated from embryos using Trizol.  RNAs were fractionated on 15% denaturing polyacrylamide gels and small RNAs between 15 30 nucleotides were excised and purified.  cDNA libraries were generated using specific linkers and RT/PCR  as previously described.  Libraries were sequenced in the Genome Technology Core of Vanderbilt University using the Illumina sequencing platform.,GEO Accession:GSM686385,ncRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina Genome Analyzer II,,SRP028895,,,GSM686385_1dpf_Raw.txt,fastq,293700240.0,8158340.0,GSM686385 r1,0:36,A:74642033;C:62153879;G:83836688;T:69542606;N:3525034,36,,,,74642033,62153879,83836688,69542606,3525034,SRX336218,SRS471213,SRA098146,GEO,"Lee Lab, Molecular Biology, Mass General Hospital",1,0.00386,,0.00274,,0.99758,,0.53623,,36,,T,,under 1.2% mapping rate,illumina,early_illumina,5prime,size_fractionation,unknown,bulk,unknown,unknown,,United States,2011-03-07,Pharyngula,Embryo,Whole Organism,All anatomical structures
36267,SRR953576,SRX336217,SRS471211,SRP028895,PRJNA138095,Transcriptome wide analysis of small RNA expression in early zebrafish development,GSE27722,Transcriptome Analysis,During early vertebrate development  a large number of noncoding RNAs are maternally inherited or expressed upon activation of zygotic transcription.  The exact identity  expression levels  and function during early vertebrate development for most of these noncoding RNAs remains largely unknown.  miRNAs microRNAs and piRNAs piwi interacting RNAs are two classes of small non coding RNAs that play important roles in gene regulation during early embryonic development.  Here  we utilized Illumina next generation sequencing technology to determine temporal expression patterns for both miRNAs and piRNAs during four distinct stages of early vertebrate development using zebrafish as a model system.  For miRNAs  the expression patterns for 192 known miRNAs and 12 novel miRNAs within 123 different miRNA families were determined.  Significant sequence variation was observed at the five prime' and three prime' ends of miRNAs with a large number of extra nucleotides added in a non template directed manner.  We also identified a large and diverse set of piRNAs expressed during early development  far beyond that expected if piRNA expression is restricted to germ cells.  Our analyses represent the deepest investigation to date of small RNA expression during early vertebrate development and suggest important novel functions for small RNAs during embryogenesis. Overall design: Identify the expression of small RNAs in zebrafish embryos of four different developmental stages using high through put sequencing,,pubmed:22408181,,embryo Shield rep1,GSM686384,,source name:the whole embryo|strain:AB*WT|developmental stage:Shield|tissue:the whole embryos,embryo Shield rep1,"fasta: Initial reads were processed to remove linker sequences using a dynamic alignment algorithm  which allows one mismatch in the linker sequences. All the sequence with N inside was removed as well. The unique sequences were retained with the counts indicating thier abundance. The header of each sequence is composed of a unique sequence ID followed by a "" x"" and the reads counts. e.g. unique ID x counts. alignment: Initial reads were processed to remove linker sequences using a dynamic alignment algorithm  which allows one mismatch in the linker sequences.  Small RNAs with perfect matches to the zebrafish genome Zv8 from Ensembl http://www.ensembl.org were retrieved using megaBLAST http://www.ncbi.nlm.nih.gov/blast/megablast.shtml and Bowtie http://bowtie bio.sourceforge.net/tutorial.shtml. To identify piRNAs  consensus sequences from zebrafish repetitive elements were retrieved from Repbase http://www.girinst.org/repbase/index.html and Repeat Maskers using the UCSC genome browser http://genome.ucsc.edu.  Small RNAs perfectly mapping to these consensus sequences and their genomic flanking regions were sorted into piRNA libraries with up to 3 genomic mapping positions for each unique RNA sequence. fasta files description: small RNA 15 30 nt alignment file description: piRNA map to repetitive elements",the whole embryo,,Zebrafish embryos were collected at the 256 cell stage  sphere stage  shield stage  and 1dpf.  Total RNA was isolated from embryos using Trizol.  RNAs were fractionated on 15% denaturing polyacrylamide gels and small RNAs between 15 30 nucleotides were excised and purified.  cDNA libraries were generated using specific linkers and RT/PCR  as previously described.  Libraries were sequenced in the Genome Technology Core of Vanderbilt University using the Illumina sequencing platform.,Embryos were raised at 28°C in egg water 0.03% Instant Ocean marine salt mix for the initial several hours of development,strain:AB*WT|developmental stage:Shield|tissue:the whole embryos,GSM686384,GSM686384: embryo Shield rep1; Danio rerio; ncRNA Seq,GSM686384,,1,Zebrafish embryos were collected at the 256 cell stage  sphere stage  shield stage  and 1dpf.  Total RNA was isolated from embryos using Trizol.  RNAs were fractionated on 15% denaturing polyacrylamide gels and small RNAs between 15 30 nucleotides were excised and purified.  cDNA libraries were generated using specific linkers and RT/PCR  as previously described.  Libraries were sequenced in the Genome Technology Core of Vanderbilt University using the Illumina sequencing platform.,GEO Accession:GSM686384,ncRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina Genome Analyzer II,,SRP028895,,,GSM686384_Shield_Raw.txt,fastq,115067916.0,3196331.0,GSM686384 r1,0:36,A:28435718;C:21893278;G:31779352;T:26635839;N:6323729,36,,,,28435718,21893278,31779352,26635839,6323729,SRX336217,SRS471211,SRA098146,GEO,"Lee Lab, Molecular Biology, Mass General Hospital",1,0.00278,,0.00217,,0.99933,,0.60606,,36,,T,,under 1.2% mapping rate,illumina,early_illumina,5prime,size_fractionation,unknown,bulk,unknown,unknown,,United States,2011-03-07,Gastrula,Embryo,Whole Organism,All anatomical structures
36268,SRR953575,SRX336216,SRS471212,SRP028895,PRJNA138095,Transcriptome wide analysis of small RNA expression in early zebrafish development,GSE27722,Transcriptome Analysis,During early vertebrate development  a large number of noncoding RNAs are maternally inherited or expressed upon activation of zygotic transcription.  The exact identity  expression levels  and function during early vertebrate development for most of these noncoding RNAs remains largely unknown.  miRNAs microRNAs and piRNAs piwi interacting RNAs are two classes of small non coding RNAs that play important roles in gene regulation during early embryonic development.  Here  we utilized Illumina next generation sequencing technology to determine temporal expression patterns for both miRNAs and piRNAs during four distinct stages of early vertebrate development using zebrafish as a model system.  For miRNAs  the expression patterns for 192 known miRNAs and 12 novel miRNAs within 123 different miRNA families were determined.  Significant sequence variation was observed at the five prime' and three prime' ends of miRNAs with a large number of extra nucleotides added in a non template directed manner.  We also identified a large and diverse set of piRNAs expressed during early development  far beyond that expected if piRNA expression is restricted to germ cells.  Our analyses represent the deepest investigation to date of small RNA expression during early vertebrate development and suggest important novel functions for small RNAs during embryogenesis. Overall design: Identify the expression of small RNAs in zebrafish embryos of four different developmental stages using high through put sequencing,,pubmed:22408181,,embryo sphere rep2,GSM686383,,source name:the whole embryo|strain:AB*WT|developmental stage:sphere|tissue:the whole embryos,embryo sphere rep2,"fasta: Initial reads were processed to remove linker sequences using a dynamic alignment algorithm  which allows one mismatch in the linker sequences. All the sequence with N inside was removed as well. The unique sequences were retained with the counts indicating thier abundance. The header of each sequence is composed of a unique sequence ID followed by a "" x"" and the reads counts. e.g. unique ID x counts. alignment: Initial reads were processed to remove linker sequences using a dynamic alignment algorithm  which allows one mismatch in the linker sequences.  Small RNAs with perfect matches to the zebrafish genome Zv8 from Ensembl http://www.ensembl.org were retrieved using megaBLAST http://www.ncbi.nlm.nih.gov/blast/megablast.shtml and Bowtie http://bowtie bio.sourceforge.net/tutorial.shtml. To identify piRNAs  consensus sequences from zebrafish repetitive elements were retrieved from Repbase http://www.girinst.org/repbase/index.html and Repeat Maskers using the UCSC genome browser http://genome.ucsc.edu.  Small RNAs perfectly mapping to these consensus sequences and their genomic flanking regions were sorted into piRNA libraries with up to 3 genomic mapping positions for each unique RNA sequence. fasta files description: small RNA 15 30 nt alignment file description: piRNA map to repetitive elements",the whole embryo,,Zebrafish embryos were collected at the 256 cell stage  sphere stage  shield stage  and 1dpf.  Total RNA was isolated from embryos using Trizol.  RNAs were fractionated on 15% denaturing polyacrylamide gels and small RNAs between 15 30 nucleotides were excised and purified.  cDNA libraries were generated using specific linkers and RT/PCR  as previously described.  Libraries were sequenced in the Genome Technology Core of Vanderbilt University using the Illumina sequencing platform.,Embryos were raised at 28°C in egg water 0.03% Instant Ocean marine salt mix for the initial several hours of development,strain:AB*WT|developmental stage:sphere|tissue:the whole embryos,GSM686383,GSM686383: embryo sphere rep2; Danio rerio; ncRNA Seq,GSM686383,,1,Zebrafish embryos were collected at the 256 cell stage  sphere stage  shield stage  and 1dpf.  Total RNA was isolated from embryos using Trizol.  RNAs were fractionated on 15% denaturing polyacrylamide gels and small RNAs between 15 30 nucleotides were excised and purified.  cDNA libraries were generated using specific linkers and RT/PCR  as previously described.  Libraries were sequenced in the Genome Technology Core of Vanderbilt University using the Illumina sequencing platform.,GEO Accession:GSM686383,ncRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina Genome Analyzer II,,SRP028895,,,GSM686383_Sphere_2_Raw.txt,fastq,369741456.0,10270596.0,GSM686383 r1,0:36,A:89854472;C:70044086;G:109552597;T:100266590;N:23711,36,,,,89854472,70044086,109552597,100266590,23711,SRX336216,SRS471212,SRA098146,GEO,"Lee Lab, Molecular Biology, Mass General Hospital",1,0.00421,,0.00367,,0.99924,,0.51111,,36,,T,,under 1.2% mapping rate,illumina,early_illumina,5prime,size_fractionation,unknown,bulk,unknown,unknown,,United States,2011-03-07,Blastula,Embryo,Whole Organism,All anatomical structures
36269,SRR953574,SRX336215,SRS471209,SRP028895,PRJNA138095,Transcriptome wide analysis of small RNA expression in early zebrafish development,GSE27722,Transcriptome Analysis,During early vertebrate development  a large number of noncoding RNAs are maternally inherited or expressed upon activation of zygotic transcription.  The exact identity  expression levels  and function during early vertebrate development for most of these noncoding RNAs remains largely unknown.  miRNAs microRNAs and piRNAs piwi interacting RNAs are two classes of small non coding RNAs that play important roles in gene regulation during early embryonic development.  Here  we utilized Illumina next generation sequencing technology to determine temporal expression patterns for both miRNAs and piRNAs during four distinct stages of early vertebrate development using zebrafish as a model system.  For miRNAs  the expression patterns for 192 known miRNAs and 12 novel miRNAs within 123 different miRNA families were determined.  Significant sequence variation was observed at the five prime' and three prime' ends of miRNAs with a large number of extra nucleotides added in a non template directed manner.  We also identified a large and diverse set of piRNAs expressed during early development  far beyond that expected if piRNA expression is restricted to germ cells.  Our analyses represent the deepest investigation to date of small RNA expression during early vertebrate development and suggest important novel functions for small RNAs during embryogenesis. Overall design: Identify the expression of small RNAs in zebrafish embryos of four different developmental stages using high through put sequencing,,pubmed:22408181,,embryo sphere rep1,GSM686382,,source name:the whole embryo|strain:AB*WT|developmental stage:sphere|tissue:the whole embryos,embryo sphere rep1,"fasta: Initial reads were processed to remove linker sequences using a dynamic alignment algorithm  which allows one mismatch in the linker sequences. All the sequence with N inside was removed as well. The unique sequences were retained with the counts indicating thier abundance. The header of each sequence is composed of a unique sequence ID followed by a "" x"" and the reads counts. e.g. unique ID x counts. alignment: Initial reads were processed to remove linker sequences using a dynamic alignment algorithm  which allows one mismatch in the linker sequences.  Small RNAs with perfect matches to the zebrafish genome Zv8 from Ensembl http://www.ensembl.org were retrieved using megaBLAST http://www.ncbi.nlm.nih.gov/blast/megablast.shtml and Bowtie http://bowtie bio.sourceforge.net/tutorial.shtml. To identify piRNAs  consensus sequences from zebrafish repetitive elements were retrieved from Repbase http://www.girinst.org/repbase/index.html and Repeat Maskers using the UCSC genome browser http://genome.ucsc.edu.  Small RNAs perfectly mapping to these consensus sequences and their genomic flanking regions were sorted into piRNA libraries with up to 3 genomic mapping positions for each unique RNA sequence. fasta files description: small RNA 15 30 nt alignment file description: piRNA map to repetitive elements",the whole embryo,,Zebrafish embryos were collected at the 256 cell stage  sphere stage  shield stage  and 1dpf.  Total RNA was isolated from embryos using Trizol.  RNAs were fractionated on 15% denaturing polyacrylamide gels and small RNAs between 15 30 nucleotides were excised and purified.  cDNA libraries were generated using specific linkers and RT/PCR  as previously described.  Libraries were sequenced in the Genome Technology Core of Vanderbilt University using the Illumina sequencing platform.,Embryos were raised at 28°C in egg water 0.03% Instant Ocean marine salt mix for the initial several hours of development,strain:AB*WT|developmental stage:sphere|tissue:the whole embryos,GSM686382,GSM686382: embryo sphere rep1; Danio rerio; ncRNA Seq,GSM686382,,1,Zebrafish embryos were collected at the 256 cell stage  sphere stage  shield stage  and 1dpf.  Total RNA was isolated from embryos using Trizol.  RNAs were fractionated on 15% denaturing polyacrylamide gels and small RNAs between 15 30 nucleotides were excised and purified.  cDNA libraries were generated using specific linkers and RT/PCR  as previously described.  Libraries were sequenced in the Genome Technology Core of Vanderbilt University using the Illumina sequencing platform.,GEO Accession:GSM686382,ncRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina Genome Analyzer II,,SRP028895,,,GSM686382_Sphere_1_Raw.txt,fastq,492502284.0,13680619.0,GSM686382 r1,0:36,A:114418890;C:99502519;G:142841794;T:135061742;N:677339,36,,,,114418890,99502519,142841794,135061742,677339,SRX336215,SRS471209,SRA098146,GEO,"Lee Lab, Molecular Biology, Mass General Hospital",1,0.00828,,0.00636,,0.9964,,0.54822,,36,,T,,under 1.2% mapping rate,illumina,early_illumina,5prime,size_fractionation,unknown,bulk,unknown,unknown,,United States,2011-03-07,Blastula,Embryo,Whole Organism,All anatomical structures
36270,SRR953573,SRX336214,SRS471210,SRP028895,PRJNA138095,Transcriptome wide analysis of small RNA expression in early zebrafish development,GSE27722,Transcriptome Analysis,During early vertebrate development  a large number of noncoding RNAs are maternally inherited or expressed upon activation of zygotic transcription.  The exact identity  expression levels  and function during early vertebrate development for most of these noncoding RNAs remains largely unknown.  miRNAs microRNAs and piRNAs piwi interacting RNAs are two classes of small non coding RNAs that play important roles in gene regulation during early embryonic development.  Here  we utilized Illumina next generation sequencing technology to determine temporal expression patterns for both miRNAs and piRNAs during four distinct stages of early vertebrate development using zebrafish as a model system.  For miRNAs  the expression patterns for 192 known miRNAs and 12 novel miRNAs within 123 different miRNA families were determined.  Significant sequence variation was observed at the five prime' and three prime' ends of miRNAs with a large number of extra nucleotides added in a non template directed manner.  We also identified a large and diverse set of piRNAs expressed during early development  far beyond that expected if piRNA expression is restricted to germ cells.  Our analyses represent the deepest investigation to date of small RNA expression during early vertebrate development and suggest important novel functions for small RNAs during embryogenesis. Overall design: Identify the expression of small RNAs in zebrafish embryos of four different developmental stages using high through put sequencing,,pubmed:22408181,,embryo 256 cell rep1,GSM686381,,source name:the whole embryo|strain:AB* WT|developmental stage:256 cell|tissue:the whole embryos,embryo 256 cell rep1,"fasta: Initial reads were processed to remove linker sequences using a dynamic alignment algorithm  which allows one mismatch in the linker sequences. All the sequence with N inside was removed as well. The unique sequences were retained with the counts indicating thier abundance. The header of each sequence is composed of a unique sequence ID followed by a "" x"" and the reads counts. e.g. unique ID x counts. alignment: Initial reads were processed to remove linker sequences using a dynamic alignment algorithm  which allows one mismatch in the linker sequences.  Small RNAs with perfect matches to the zebrafish genome Zv8 from Ensembl http://www.ensembl.org were retrieved using megaBLAST http://www.ncbi.nlm.nih.gov/blast/megablast.shtml and Bowtie http://bowtie bio.sourceforge.net/tutorial.shtml. To identify piRNAs  consensus sequences from zebrafish repetitive elements were retrieved from Repbase http://www.girinst.org/repbase/index.html and Repeat Maskers using the UCSC genome browser http://genome.ucsc.edu.  Small RNAs perfectly mapping to these consensus sequences and their genomic flanking regions were sorted into piRNA libraries with up to 3 genomic mapping positions for each unique RNA sequence. fasta files description: small RNA 15 30 nt alignment file description: piRNA map to repetitive elements",the whole embryo,,Zebrafish embryos were collected at the 256 cell stage  sphere stage  shield stage  and 1dpf.  Total RNA was isolated from embryos using Trizol.  RNAs were fractionated on 15% denaturing polyacrylamide gels and small RNAs between 15 30 nucleotides were excised and purified.  cDNA libraries were generated using specific linkers and RT/PCR  as previously described.  Libraries were sequenced in the Genome Technology Core of Vanderbilt University using the Illumina sequencing platform.,Embryos were raised at 28°C in egg water 0.03% Instant Ocean marine salt mix for the initial several hours of development,strain:AB* WT|developmental stage:256 cell|tissue:the whole embryos,GSM686381,GSM686381: embryo 256 cell rep1; Danio rerio; ncRNA Seq,GSM686381,,1,Zebrafish embryos were collected at the 256 cell stage  sphere stage  shield stage  and 1dpf.  Total RNA was isolated from embryos using Trizol.  RNAs were fractionated on 15% denaturing polyacrylamide gels and small RNAs between 15 30 nucleotides were excised and purified.  cDNA libraries were generated using specific linkers and RT/PCR  as previously described.  Libraries were sequenced in the Genome Technology Core of Vanderbilt University using the Illumina sequencing platform.,GEO Accession:GSM686381,ncRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina Genome Analyzer II,,SRP028895,,,GSM686381_256-cell_Raw.txt,fastq,177430716.0,4928631.0,GSM686381 r1,0:36,A:46047586;C:39494059;G:46591098;T:42305117;N:2992856,36,,,,46047586,39494059,46591098,42305117,2992856,SRX336214,SRS471210,SRA098146,GEO,"Lee Lab, Molecular Biology, Mass General Hospital",1,0.01914,,0.01515,,0.99164,,0.52579,,36,,B,,usable mapping rate,illumina,early_illumina,5prime,size_fractionation,unknown,bulk,unknown,unknown,,United States,2011-03-07,Blastula,Embryo,Whole Organism,All anatomical structures
36278,SRR352486,SRX100938,SRS266977,SRP008845,PRJNA146609,Conserved Function of lincRNAs in Vertebrate Embryonic Development Despite Rapid Sequence Evolution,GSE32880,Other,Thousands of large intervening non coding RNAs lincRNAs have been identified in mammals. To better understand the evolution and functions of these enigmatic RNAs  we used chromatin marks  polyA site mapping and RNA Seq data  to identify more than 550 distinct lincRNAs in zebrafish. Although these shared many characteristics with mammalian lincRNAs  only 29 had detectable sequence similarity with putative mammalian orthologs  typically restricted to a single short region of high conservation. Other lincRNAs had conserved genomic locations without xxx sequence conservation. Antisense reagents targeting conserved regions of two zebrafish lincRNAs caused developmental defects. Reagents targeting splice sites caused the same defects and were rescued by adding either the mature lincRNA or its human or mouse ortholog. Our study provides a roadmap for identification and analysis of lincRNAs in model organisms and shows that lincRNAs play crucial biological roles during embryonic development with functionality conserved despite limited sequence conservation. Overall design: H3K4me3  H3K36me3 chromatin maps  3P Seq and RNA Seq were used to identify lincRNAs in the zebrafish genome,,pubmed:22196729,,3P Seq Adult,GSM813764,,source name:mixed gender adults|tissue:whole adult|developmental stage:mixed gender adults|genotype:wt,3P Seq Adult,Reads were reverse complemented and aligned to the D. rerio genome Zv9/danRer7 using Bowtie. Reads that aligned to up to four genomic locus and had one or more mismatches at their three prime end within a terminal adenylate run were carried forward as 3P tags. Reads mapping to the same locus with the same number of terminal adenylates were consolidated in the processed data file. GSE24924,mixed gender adults,For adult fish  anesthetized fish were homogenized in the TissueRuptor Qiagen. Formaldehyde was quenched by adding 1/20 volume 2.5 M glycine. Cells were pelleted at 400 x g for 5 min. The supernatant was removed  and pellets were rinsed twice with PBS  flash frozen in liquid nitrogen and stored at –80C.,3P Seq; see http://web.wi.mit.edu/bartel/pub/protocols.html,Zebrafish embryos or adults grown under standard condition,tissue:whole adult|developmental stage:mixed gender adults|genotype:wt,GSM813764,GSM813764: 3P Seq Adult,GSM813764: 3P Seq Adult,GSM813764: 3P Seq Adult,1,,GEO Accession:GSM813764,RNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina Genome Analyzer II,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP008845,,read name barcode proc directive:ignore,3P_Seq_Adult.fastq,fastq,824962572.0,22915627.0,GSM813764 1,0:36,A:230176177;C:144743199;G:130818857;T:314618483;N:4605856,36,,,,230176177,144743199,130818857,314618483,4605856,SRX100938,SRS266977,SRA047033,GEO,Whitehead Institute for Biomedical Research,1,0.64306,,0.03985,,0.78102,,0.46237,,36,,B,,usable mapping rate,illumina,early_illumina,3prime,size_fractionation,unknown,bulk,unknown,unknown,,United States,2011-10-11,Adult,Adult,Whole Organism,All anatomical structures
36279,SRR352485,SRX100937,SRS266976,SRP008845,PRJNA146609,Conserved Function of lincRNAs in Vertebrate Embryonic Development Despite Rapid Sequence Evolution,GSE32880,Other,Thousands of large intervening non coding RNAs lincRNAs have been identified in mammals. To better understand the evolution and functions of these enigmatic RNAs  we used chromatin marks  polyA site mapping and RNA Seq data  to identify more than 550 distinct lincRNAs in zebrafish. Although these shared many characteristics with mammalian lincRNAs  only 29 had detectable sequence similarity with putative mammalian orthologs  typically restricted to a single short region of high conservation. Other lincRNAs had conserved genomic locations without xxx sequence conservation. Antisense reagents targeting conserved regions of two zebrafish lincRNAs caused developmental defects. Reagents targeting splice sites caused the same defects and were rescued by adding either the mature lincRNA or its human or mouse ortholog. Our study provides a roadmap for identification and analysis of lincRNAs in model organisms and shows that lincRNAs play crucial biological roles during embryonic development with functionality conserved despite limited sequence conservation. Overall design: H3K4me3  H3K36me3 chromatin maps  3P Seq and RNA Seq were used to identify lincRNAs in the zebrafish genome,,pubmed:22196729,,3P Seq 72 hpf,GSM813763,,tissue:whole embryo at 72 hpf embryo|developmental stage:72 hpf,3P Seq 72 hpf,Reads were reverse complemented and aligned to the D. rerio genome Zv9/danRer7 using Bowtie. Reads that aligned to up to four genomic locus and had one or more mismatches at their three prime end within a terminal adenylate run were carried forward as 3P tags. Reads mapping to the same locus with the same number of terminal adenylates were consolidated in the processed data file. GSE24924,whole embryo at 72 hpf,Anesthetized 24 hpf and 72 hpf decorioneted embryos were washed three times in PBS 137 mM NaCl  2.7 mM KCl  1.5 mM KH2PO4  8 mM Na2HP04  pH 7.4 and suspended in PBS containing 1% freshly added formaldehyde. Embryos were transferred to a dounce homogenizer  dounced several times and incubated at room temperature for 15 min. Formaldehyde was quenched by adding 1/20 volume 2.5 M glycine. Cells were pelleted at 400 x g for 5 min. The supernatant was removed  and pellets were rinsed twice with PBS  flash frozen in liquid nitrogen and stored at –80C.,3P Seq; see http://web.wi.mit.edu/bartel/pub/protocols.html,Zebrafish embryos or adults grown under standard condition,tissue:whole embryo|developmental stage:72 hpf,GSM813763,GSM813763: 3P Seq 72 hpf,GSM813763: 3P Seq 72 hpf,GSM813763: 3P Seq 72 hpf,1,,GEO Accession:GSM813763,RNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina Genome Analyzer II,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP008845,,read name barcode proc directive:ignore,3P_Seq_72hpf.fastq,fastq,875542968.0,24320638.0,GSM813763 1,0:36,A:246098313;C:139311840;G:129654215;T:353566279;N:6912321,36,,,,246098313,139311840,129654215,353566279,6912321,SRX100937,SRS266976,SRA047033,GEO,Whitehead Institute for Biomedical Research,1,0.72092,,0.09355,,0.7601,,0.4422,,36,,B,,usable mapping rate,illumina,early_illumina,3prime,size_fractionation,unknown,bulk,unknown,unknown,,United States,2011-10-11,Larval,Larval,Whole Organism,All anatomical structures
36280,SRR352484,SRX100936,SRS266975,SRP008845,PRJNA146609,Conserved Function of lincRNAs in Vertebrate Embryonic Development Despite Rapid Sequence Evolution,GSE32880,Other,Thousands of large intervening non coding RNAs lincRNAs have been identified in mammals. To better understand the evolution and functions of these enigmatic RNAs  we used chromatin marks  polyA site mapping and RNA Seq data  to identify more than 550 distinct lincRNAs in zebrafish. Although these shared many characteristics with mammalian lincRNAs  only 29 had detectable sequence similarity with putative mammalian orthologs  typically restricted to a single short region of high conservation. Other lincRNAs had conserved genomic locations without xxx sequence conservation. Antisense reagents targeting conserved regions of two zebrafish lincRNAs caused developmental defects. Reagents targeting splice sites caused the same defects and were rescued by adding either the mature lincRNA or its human or mouse ortholog. Our study provides a roadmap for identification and analysis of lincRNAs in model organisms and shows that lincRNAs play crucial biological roles during embryonic development with functionality conserved despite limited sequence conservation. Overall design: H3K4me3  H3K36me3 chromatin maps  3P Seq and RNA Seq were used to identify lincRNAs in the zebrafish genome,,pubmed:22196729,,3P Seq 24 hpf,GSM813762,,tissue:whole embryo at 24 hpf embryo|developmental stage:24 hpf,3P Seq 24 hpf,Reads were reverse complemented and aligned to the D. rerio genome Zv9/danRer7 using Bowtie. Reads that aligned to up to four genomic locus and had one or more mismatches at their three prime end within a terminal adenylate run were carried forward as 3P tags. Reads mapping to the same locus with the same number of terminal adenylates were consolidated in the processed data file. The BED file is as in Jan et al. GSE24924,whole embryo at 24 hpf,Anesthetized 24 hpf and 72 hpf decorioneted embryos were washed three times in PBS 137 mM NaCl  2.7 mM KCl  1.5 mM KH2PO4  8 mM Na2HP04  pH 7.4 and suspended in PBS containing 1% freshly added formaldehyde. Embryos were transferred to a dounce homogenizer  dounced several times and incubated at room temperature for 15 min. Formaldehyde was quenched by adding 1/20 volume 2.5 M glycine. Cells were pelleted at 400 x g for 5 min. The supernatant was removed  and pellets were rinsed twice with PBS  flash frozen in liquid nitrogen and stored at –80C.,3P Seq; see http://web.wi.mit.edu/bartel/pub/protocols.html,Zebrafish embryos or adults grown under standard condition,tissue:whole embryo|developmental stage:24 hpf,GSM813762,GSM813762: 3P Seq 24 hpf,GSM813762: 3P Seq 24 hpf,GSM813762: 3P Seq 24 hpf,1,,GEO Accession:GSM813762,RNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina Genome Analyzer II,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP008845,,read name barcode proc directive:ignore,3P_Seq_24hpf.fastq,fastq,951095592.0,26419322.0,GSM813762 1,0:36,A:261158914;C:169001356;G:163312440;T:350565754;N:7057128,36,,,,261158914,169001356,163312440,350565754,7057128,SRX100936,SRS266975,SRA047033,GEO,Whitehead Institute for Biomedical Research,,,,,,,,,,,,B,,usable mapping rate,illumina,early_illumina,3prime,size_fractionation,unknown,bulk,unknown,unknown,,United States,2011-10-11,Pharyngula,Embryo,Whole Organism,All anatomical structures
36281,SRR352482,SRX100935,SRS266974,SRP008845,PRJNA146609,Conserved Function of lincRNAs in Vertebrate Embryonic Development Despite Rapid Sequence Evolution,GSE32880,Other,Thousands of large intervening non coding RNAs lincRNAs have been identified in mammals. To better understand the evolution and functions of these enigmatic RNAs  we used chromatin marks  polyA site mapping and RNA Seq data  to identify more than 550 distinct lincRNAs in zebrafish. Although these shared many characteristics with mammalian lincRNAs  only 29 had detectable sequence similarity with putative mammalian orthologs  typically restricted to a single short region of high conservation. Other lincRNAs had conserved genomic locations without xxx sequence conservation. Antisense reagents targeting conserved regions of two zebrafish lincRNAs caused developmental defects. Reagents targeting splice sites caused the same defects and were rescued by adding either the mature lincRNA or its human or mouse ortholog. Our study provides a roadmap for identification and analysis of lincRNAs in model organisms and shows that lincRNAs play crucial biological roles during embryonic development with functionality conserved despite limited sequence conservation. Overall design: H3K4me3  H3K36me3 chromatin maps  3P Seq and RNA Seq were used to identify lincRNAs in the zebrafish genome,,pubmed:22196729,,Strand specific RNA Seq 72 hpf,GSM813761,,tissue:whole embryo at 72 hpf embryo|developmental stage:72 hpf,Strand specific RNA Seq 72 hpf,Reads were aligned to the zebrafish danRer7 genome assembly using Bowtie  allowing for up to one mismatch and up to 4 genomic matches.,whole embryo at 72 hpf,Anesthetized 24 hpf and 72 hpf decorioneted embryos were washed three times in PBS 137 mM NaCl  2.7 mM KCl  1.5 mM KH2PO4  8 mM Na2HP04  pH 7.4 and suspended in PBS containing 1% freshly added formaldehyde. Embryos were transferred to a dounce homogenizer  dounced several times and incubated at room temperature for 15 min. Formaldehyde was quenched by adding 1/20 volume 2.5 M glycine. Cells were pelleted at 400 x g for 5 min. The supernatant was removed  and pellets were rinsed twice with PBS  flash frozen in liquid nitrogen and stored at –80C.,polyA selected RNA was amplified using RiboAmp Plus RNA Amplification kit  randomly fragmented by partial alkaline hydrolysis. Size selected RNA fragments 25 45 nt were used for library preparation. Libraries were prepared as in Guo et al  2010 GSE21992,Zebrafish embryos or adults grown under standard condition,tissue:whole embryo|developmental stage:72 hpf,GSM813761,GSM813761: Strand specific RNA Seq 72 hpf,GSM813761: Strand specific RNA Seq 72 hpf,GSM813761: Strand specific RNA Seq 72 hpf,1,,GEO Accession:GSM813761,RNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina Genome Analyzer II,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP008845,,read name barcode proc directive:ignore,RNA_Seq_72hpf.1.fastq,fastq,734147136.0,20392976.0,GSM813761 1,0:36,A:175662892;C:172216317;G:208650086;T:171852136;N:5765705,36,,,,175662892,172216317,208650086,171852136,5765705,SRX100935,SRS266974,SRA047033,GEO,Whitehead Institute for Biomedical Research,1,0.4603,,0.10593,,0.88274,,0.59195,,36,,B,,usable mapping rate,illumina,early_illumina,unknown,size_fractionation,unknown,bulk,unknown,unknown,,United States,2011-10-11,Larval,Larval,Whole Organism,All anatomical structures
36282,SRR352483,SRX100935,SRS266974,SRP008845,PRJNA146609,Conserved Function of lincRNAs in Vertebrate Embryonic Development Despite Rapid Sequence Evolution,GSE32880,Other,Thousands of large intervening non coding RNAs lincRNAs have been identified in mammals. To better understand the evolution and functions of these enigmatic RNAs  we used chromatin marks  polyA site mapping and RNA Seq data  to identify more than 550 distinct lincRNAs in zebrafish. Although these shared many characteristics with mammalian lincRNAs  only 29 had detectable sequence similarity with putative mammalian orthologs  typically restricted to a single short region of high conservation. Other lincRNAs had conserved genomic locations without xxx sequence conservation. Antisense reagents targeting conserved regions of two zebrafish lincRNAs caused developmental defects. Reagents targeting splice sites caused the same defects and were rescued by adding either the mature lincRNA or its human or mouse ortholog. Our study provides a roadmap for identification and analysis of lincRNAs in model organisms and shows that lincRNAs play crucial biological roles during embryonic development with functionality conserved despite limited sequence conservation. Overall design: H3K4me3  H3K36me3 chromatin maps  3P Seq and RNA Seq were used to identify lincRNAs in the zebrafish genome,,pubmed:22196729,,Strand specific RNA Seq 72 hpf,GSM813761,,tissue:whole embryo at 72 hpf embryo|developmental stage:72 hpf,Strand specific RNA Seq 72 hpf,Reads were aligned to the zebrafish danRer7 genome assembly using Bowtie  allowing for up to one mismatch and up to 4 genomic matches.,whole embryo at 72 hpf,Anesthetized 24 hpf and 72 hpf decorioneted embryos were washed three times in PBS 137 mM NaCl  2.7 mM KCl  1.5 mM KH2PO4  8 mM Na2HP04  pH 7.4 and suspended in PBS containing 1% freshly added formaldehyde. Embryos were transferred to a dounce homogenizer  dounced several times and incubated at room temperature for 15 min. Formaldehyde was quenched by adding 1/20 volume 2.5 M glycine. Cells were pelleted at 400 x g for 5 min. The supernatant was removed  and pellets were rinsed twice with PBS  flash frozen in liquid nitrogen and stored at –80C.,polyA selected RNA was amplified using RiboAmp Plus RNA Amplification kit  randomly fragmented by partial alkaline hydrolysis. Size selected RNA fragments 25 45 nt were used for library preparation. Libraries were prepared as in Guo et al  2010 GSE21992,Zebrafish embryos or adults grown under standard condition,tissue:whole embryo|developmental stage:72 hpf,GSM813761,GSM813761: Strand specific RNA Seq 72 hpf,GSM813761: Strand specific RNA Seq 72 hpf,GSM813761: Strand specific RNA Seq 72 hpf,1,,GEO Accession:GSM813761,RNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina Genome Analyzer II,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP008845,,read name barcode proc directive:ignore,RNA_Seq_72hpf.2.fastq,fastq,924879168.0,25691088.0,GSM813761 2,0:36,A:218871678;C:217000200;G:266487098;T:214411336;N:8108856,36,,,,218871678,217000200,266487098,214411336,8108856,SRX100935,SRS266974,SRA047033,GEO,Whitehead Institute for Biomedical Research,1,0.47296,,0.10988,,0.86397,,0.59423,,36,,B,,usable mapping rate,illumina,early_illumina,unknown,size_fractionation,unknown,bulk,unknown,unknown,,United States,2011-10-11,Larval,Larval,Whole Organism,All anatomical structures
36283,SRR352480,SRX100934,SRS266973,SRP008845,PRJNA146609,Conserved Function of lincRNAs in Vertebrate Embryonic Development Despite Rapid Sequence Evolution,GSE32880,Other,Thousands of large intervening non coding RNAs lincRNAs have been identified in mammals. To better understand the evolution and functions of these enigmatic RNAs  we used chromatin marks  polyA site mapping and RNA Seq data  to identify more than 550 distinct lincRNAs in zebrafish. Although these shared many characteristics with mammalian lincRNAs  only 29 had detectable sequence similarity with putative mammalian orthologs  typically restricted to a single short region of high conservation. Other lincRNAs had conserved genomic locations without xxx sequence conservation. Antisense reagents targeting conserved regions of two zebrafish lincRNAs caused developmental defects. Reagents targeting splice sites caused the same defects and were rescued by adding either the mature lincRNA or its human or mouse ortholog. Our study provides a roadmap for identification and analysis of lincRNAs in model organisms and shows that lincRNAs play crucial biological roles during embryonic development with functionality conserved despite limited sequence conservation. Overall design: H3K4me3  H3K36me3 chromatin maps  3P Seq and RNA Seq were used to identify lincRNAs in the zebrafish genome,,pubmed:22196729,,Strand specific RNA Seq 24 hpf,GSM813760,,tissue:whole embryo at 24 hpf embryo|developmental stage:24 hpf,Strand specific RNA Seq 24 hpf,Reads were aligned to the zebrafish danRer7 genome assembly using Bowtie  allowing for up to one mismatch and up to 4 genomic matches.,whole embryo at 24 hpf,Anesthetized 24 hpf and 72 hpf decorioneted embryos were washed three times in PBS 137 mM NaCl  2.7 mM KCl  1.5 mM KH2PO4  8 mM Na2HP04  pH 7.4 and suspended in PBS containing 1% freshly added formaldehyde. Embryos were transferred to a dounce homogenizer  dounced several times and incubated at room temperature for 15 min. Formaldehyde was quenched by adding 1/20 volume 2.5 M glycine. Cells were pelleted at 400 x g for 5 min. The supernatant was removed  and pellets were rinsed twice with PBS  flash frozen in liquid nitrogen and stored at –80C.,polyA selected RNA was amplified using RiboAmp Plus RNA Amplification kit  randomly fragmented by partial alkaline hydrolysis. Size selected RNA fragments 25 45 nt were used for library preparation. Libraries were prepared as in Guo et al  2010 GSE21992,Zebrafish embryos or adults grown under standard condition,tissue:whole embryo|developmental stage:24 hpf,GSM813760,GSM813760: Strand specific RNA Seq 24 hpf,GSM813760: Strand specific RNA Seq 24 hpf,GSM813760: Strand specific RNA Seq 24 hpf,1,,GEO Accession:GSM813760,RNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina Genome Analyzer II,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP008845,,read name barcode proc directive:ignore,RNA_Seq_24hpf.1.fastq,fastq,759129588.0,21086933.0,GSM813760 1,0:36,A:169759696;C:187766678;G:221392768;T:174382883;N:5827563,36,,,,169759696,187766678,221392768,174382883,5827563,SRX100934,SRS266973,SRA047033,GEO,Whitehead Institute for Biomedical Research,1,0.52959,,0.10037,,0.87014,,0.61896,,36,,B,,usable mapping rate,illumina,early_illumina,unknown,size_fractionation,unknown,bulk,unknown,unknown,,United States,2011-10-11,Pharyngula,Embryo,Whole Organism,All anatomical structures
36284,SRR352481,SRX100934,SRS266973,SRP008845,PRJNA146609,Conserved Function of lincRNAs in Vertebrate Embryonic Development Despite Rapid Sequence Evolution,GSE32880,Other,Thousands of large intervening non coding RNAs lincRNAs have been identified in mammals. To better understand the evolution and functions of these enigmatic RNAs  we used chromatin marks  polyA site mapping and RNA Seq data  to identify more than 550 distinct lincRNAs in zebrafish. Although these shared many characteristics with mammalian lincRNAs  only 29 had detectable sequence similarity with putative mammalian orthologs  typically restricted to a single short region of high conservation. Other lincRNAs had conserved genomic locations without xxx sequence conservation. Antisense reagents targeting conserved regions of two zebrafish lincRNAs caused developmental defects. Reagents targeting splice sites caused the same defects and were rescued by adding either the mature lincRNA or its human or mouse ortholog. Our study provides a roadmap for identification and analysis of lincRNAs in model organisms and shows that lincRNAs play crucial biological roles during embryonic development with functionality conserved despite limited sequence conservation. Overall design: H3K4me3  H3K36me3 chromatin maps  3P Seq and RNA Seq were used to identify lincRNAs in the zebrafish genome,,pubmed:22196729,,Strand specific RNA Seq 24 hpf,GSM813760,,tissue:whole embryo at 24 hpf embryo|developmental stage:24 hpf,Strand specific RNA Seq 24 hpf,Reads were aligned to the zebrafish danRer7 genome assembly using Bowtie  allowing for up to one mismatch and up to 4 genomic matches.,whole embryo at 24 hpf,Anesthetized 24 hpf and 72 hpf decorioneted embryos were washed three times in PBS 137 mM NaCl  2.7 mM KCl  1.5 mM KH2PO4  8 mM Na2HP04  pH 7.4 and suspended in PBS containing 1% freshly added formaldehyde. Embryos were transferred to a dounce homogenizer  dounced several times and incubated at room temperature for 15 min. Formaldehyde was quenched by adding 1/20 volume 2.5 M glycine. Cells were pelleted at 400 x g for 5 min. The supernatant was removed  and pellets were rinsed twice with PBS  flash frozen in liquid nitrogen and stored at –80C.,polyA selected RNA was amplified using RiboAmp Plus RNA Amplification kit  randomly fragmented by partial alkaline hydrolysis. Size selected RNA fragments 25 45 nt were used for library preparation. Libraries were prepared as in Guo et al  2010 GSE21992,Zebrafish embryos or adults grown under standard condition,tissue:whole embryo|developmental stage:24 hpf,GSM813760,GSM813760: Strand specific RNA Seq 24 hpf,GSM813760: Strand specific RNA Seq 24 hpf,GSM813760: Strand specific RNA Seq 24 hpf,1,,GEO Accession:GSM813760,RNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina Genome Analyzer II,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP008845,,read name barcode proc directive:ignore,RNA_Seq_24hpf.2.fastq,fastq,916505136.0,25458476.0,GSM813760 2,0:36,A:203678661;C:227621613;G:269472018;T:207401580;N:8331264,36,,,,203678661,227621613,269472018,207401580,8331264,SRX100934,SRS266973,SRA047033,GEO,Whitehead Institute for Biomedical Research,1,0.54008,,0.10064,,0.85425,,0.61991,,36,,B,,usable mapping rate,illumina,early_illumina,unknown,size_fractionation,unknown,bulk,unknown,unknown,,United States,2011-10-11,Pharyngula,Embryo,Whole Organism,All anatomical structures
36333,SRR398324,SRX115582,SRS285699,SRP010291,PRJNA150927,miR 221 is required for endothelial tip cell behaviors during vascular development,GSE35078,Transcriptome Analysis,Through deep sequencing and functional screening in zebrafish  we find that miR 221 is essential for angiogenesis. miR 221 knockdown phenocopied defects associated with loss of the tip cell expressed Flt4 receptor.  Furthermore  miR 221 was required for tip cell proliferation and migration  as well as tip cell potential in mosaic blood vessels.  miR 221 knockdown also prevented “hyper angiogenesis” defects associated with Notch deficiency and miR 221 expression was inhibited by Notch signaling.  Finally  miR 221 promoted tip cell behavior through repression of two targets: cyclin dependent kinase inhibitor 1b cdkn1b and phosphoinositide 3 kinase regulatory subunit 1 pik3r1.  These results identify miR 221 as an important regulatory node through which tip cell migration and proliferation are controlled during angiogenesis. Overall design: Identification of endothelial expressed microRNA from FACS isolated zebrafish endothelial cells.,,pubmed:22340502,,kdrl:egfp min microRNA,GSM861786,,tissue:FACS isolated egfp negative cells|genotype:Tgkdrl:egfp|age:24 hpf|development stage:embryo|cell type:non endothelial cells,kdrl:egfp min microRNA,The standard Illumina pipeline was applied for base calls and quality scoring; sequence tags were subsequently analyzed using miR Deep2.,FACS isolated egfp negative cells,Tgkdrl:egfp embryos were dissociated at 24 hpf  followed by fluorescence activated cell sorting to isolate GFP positive and  negative cells.,Small RNAs were isolated by polyacrylamide gel electrophoresis and ligated to RNA adapters  followed by cDNA synthesis and amplification with Illumina primers.,,genotype:Tgkdrl:egfp|age:24 hpf|developmental stage:embryo|cell type:non endothelial cells,GSM861786,GSM861786: kdrl:egfp min microRNA; Danio rerio; RNA Seq,GSM861786 1,GSM861786: kdrl:egfp min microRNA,1,,GEO Accession:GSM861786,RNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina Genome Analyzer,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP010291,,,miRNA_GFP_MINUS.fastq.gz,fastq,206441460.0,5734485.0,GSM861786 r1,0:36,A:53061964;C:48186825;G:47161433;T:53484016;N:4547222,36,,,,53061964,48186825,47161433,53484016,4547222,SRX115582,SRS285699,SRA049243,GEO,"Nathan Lawson Lab, PGFE, Umass Medical School",1,0.01499,,0.01416,,0.99922,,0.4,,36,,B,,usable mapping rate,illumina,early_illumina,unknown,size_fractionation,unknown,bulk,unknown,unknown,,United States,2012-01-12,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
36334,SRR398323,SRX115581,SRS285698,SRP010291,PRJNA150927,miR 221 is required for endothelial tip cell behaviors during vascular development,GSE35078,Transcriptome Analysis,Through deep sequencing and functional screening in zebrafish  we find that miR 221 is essential for angiogenesis. miR 221 knockdown phenocopied defects associated with loss of the tip cell expressed Flt4 receptor.  Furthermore  miR 221 was required for tip cell proliferation and migration  as well as tip cell potential in mosaic blood vessels.  miR 221 knockdown also prevented “hyper angiogenesis” defects associated with Notch deficiency and miR 221 expression was inhibited by Notch signaling.  Finally  miR 221 promoted tip cell behavior through repression of two targets: cyclin dependent kinase inhibitor 1b cdkn1b and phosphoinositide 3 kinase regulatory subunit 1 pik3r1.  These results identify miR 221 as an important regulatory node through which tip cell migration and proliferation are controlled during angiogenesis. Overall design: Identification of endothelial expressed microRNA from FACS isolated zebrafish endothelial cells.,,pubmed:22340502,,kdrl:egfp pos microRNA,GSM861785,,tissue:FACS isolated kdrl:egfp positive cells|genotype:Tgkdrl:egfp|age:24 hpf|development stage:embryo|cell type:endothelial cells,kdrl:egfp pos microRNA,The standard Illumina pipeline was applied for base calls and quality scoring; sequence tags were subsequently analyzed using miR Deep2.,FACS isolated kdrl:egfp positive cells,Tgkdrl:egfp embryos were dissociated at 24 hpf  followed by fluorescence activated cell sorting to isolate GFP positive and  negative cells.,Small RNAs were isolated by polyacrylamide gel electrophoresis and ligated to RNA adapters  followed by cDNA synthesis and amplification with Illumina primers.,,genotype:Tgkdrl:egfp|age:24 hpf|developmental stage:embryo|cell type:endothelial cells,GSM861785,GSM861785: kdrl:egfp pos microRNA; Danio rerio; RNA Seq,GSM861785 1,GSM861785: kdrl:egfp pos microRNA,1,,GEO Accession:GSM861785,RNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina Genome Analyzer,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP010291,,,miRNA_GFP_PLUS.fastq.gz,fastq,265629096.0,7378586.0,GSM861785 r1,0:36,A:67563811;C:62134550;G:62283750;T:67966396;N:5680589,36,,,,67563811,62134550,62283750,67966396,5680589,SRX115581,SRS285698,SRA049243,GEO,"Nathan Lawson Lab, PGFE, Umass Medical School",1,0.01356,,0.01279,,0.99924,,0.3125,,36,,B,,usable mapping rate,illumina,early_illumina,unknown,size_fractionation,unknown,bulk,unknown,unknown,,United States,2012-01-12,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
36482,SRR530894,SRX172598,SRS352620,SRP014646,PRJNA171751,MicroRNA expression profiling post short term exposure to TCDD in zebrafish embryos [miRNA Seq data],GSE39808,Transcriptome Analysis,Although many drugs and environmental chemicals are teratogenic  the mechanisms by which most toxicants disrupt embryonic development are not well understood. microRNAs miRNAs   single stranded RNA molecules of 22 nt that regulate protein expression by inhibiting mRNA translation and promoting mRNA sequestration or degradation  are important regulators of a variety of cellular processes including embryonic development and cellular differentiation.  We hypothesized that exposure to xenobiotics can alter miRNA expression and contribute to the mechanisms by which environmental chemicals disrupt embryonic development. To test this hypothesis for one well known teratogen  we exposed zebrafish embryos to DMSO 0.1% or TCDD 5 nM for 1 hr at 30 hpf and measured microRNA expression using several methods at 36 hpf and 60 hpf. TCDD caused strong induction of CYP1A at 36 hpf 62 fold and 60 hpf 135 fold as determined by qPCR  verifying the  effectiveness of the exposure.  microRNA expression profiles were determined using microarrays Agilent and Exiqon  next generation sequencing SOLiD and real time RT PCR. The two microarray platforms yielded results that were similar but not identical; both showed significant changes in expression of miR 451  23a  23b  24 and 27e at 60 hpf.  Multiple analyses were performed on the SOLiD sequences yielding a total of 16 miRNAs as potentially differentially expressed by TCDD in zebrafish embryos.  However  miR 27e was the only miRNA to be identified as differentially expressed by all three methods both microarrays  SOLiD sequencing  and qPCR.  These results suggest that TCDD exposure causes modest changes in expression of microRNAs  including some miR 451  23a  23b  24 and 27e that are critical for hematopoiesis and cardiovascular development. Overall design: Small RNA profiles were deteremined in TCDD exposed zebrafish embryos using SOLID sequencing,parent bioproject:PRJNA171747,pubmed:22921993,,60hpf TCDD 3,GSM979608,,source name:Embryos|strain:TL wild type|tissue:embryos|time:60 hpf|treatment:TCDD,60hpf TCDD 3,CLC Bio Genomics Work bench version 4.7 was used Adaptor trimming followed by alignining the reads to precursor miRNA sequences downloaded from miRBASE v.16. Remaining reads were mapped to other non coding RNAs downloaded from ncRNA.org Statistical analysis was done using edgeR  a bioconductor package R project Genome build: miRBase version 16 Supplementary files format and content: tab delimited text files,Embryos,,Small RNA libraries were prepared using the small RNA expression kit SREK protocol Applied Biosystems  Foster City  CA. Sequencing was done on a SOLiD V3 system Applied Biosystems.,,strain:TL wild type|tissue:embryos|time:60 hpf|treatment:TCDD,GSM979608,GSM979608: 60hpf TCDD 3; Danio rerio; RNA Seq,GSM979608 1,GSM979608: 60hpf TCDD 3,1,,GEO Accession:GSM979608,RNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ABI_SOLID,AB SOLiD System 3.0,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>35</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP014646,,,,,1007239870.0,28778282.0,GSM979608 r1,0:35,0:284531587;1:248579138;2:213782485;3:258771962;.:1574698,35,,,,,,,,,SRX172598,SRS352620,SRA056525,GEO,"Aluru Lab, Biology, Woods Hole Oceanographic Institution",1,0.04824,,0.03,,0.981,,0.49967,,35,,B,,usable mapping rate,legacy,early,unknown,size_fractionation,unknown,bulk,unknown,unknown,,United States,2012-08-01,Hatching,Embryo,Embryo Imprecise,All anatomical structures
36483,SRR530893,SRX172597,SRS352619,SRP014646,PRJNA171751,MicroRNA expression profiling post short term exposure to TCDD in zebrafish embryos [miRNA Seq data],GSE39808,Transcriptome Analysis,Although many drugs and environmental chemicals are teratogenic  the mechanisms by which most toxicants disrupt embryonic development are not well understood. microRNAs miRNAs   single stranded RNA molecules of 22 nt that regulate protein expression by inhibiting mRNA translation and promoting mRNA sequestration or degradation  are important regulators of a variety of cellular processes including embryonic development and cellular differentiation.  We hypothesized that exposure to xenobiotics can alter miRNA expression and contribute to the mechanisms by which environmental chemicals disrupt embryonic development. To test this hypothesis for one well known teratogen  we exposed zebrafish embryos to DMSO 0.1% or TCDD 5 nM for 1 hr at 30 hpf and measured microRNA expression using several methods at 36 hpf and 60 hpf. TCDD caused strong induction of CYP1A at 36 hpf 62 fold and 60 hpf 135 fold as determined by qPCR  verifying the  effectiveness of the exposure.  microRNA expression profiles were determined using microarrays Agilent and Exiqon  next generation sequencing SOLiD and real time RT PCR. The two microarray platforms yielded results that were similar but not identical; both showed significant changes in expression of miR 451  23a  23b  24 and 27e at 60 hpf.  Multiple analyses were performed on the SOLiD sequences yielding a total of 16 miRNAs as potentially differentially expressed by TCDD in zebrafish embryos.  However  miR 27e was the only miRNA to be identified as differentially expressed by all three methods both microarrays  SOLiD sequencing  and qPCR.  These results suggest that TCDD exposure causes modest changes in expression of microRNAs  including some miR 451  23a  23b  24 and 27e that are critical for hematopoiesis and cardiovascular development. Overall design: Small RNA profiles were deteremined in TCDD exposed zebrafish embryos using SOLID sequencing,parent bioproject:PRJNA171747,pubmed:22921993,,60hpf TCDD 2,GSM979607,,source name:Embryos|strain:TL wild type|tissue:embryos|time:60 hpf|treatment:TCDD,60hpf TCDD 2,CLC Bio Genomics Work bench version 4.7 was used Adaptor trimming followed by alignining the reads to precursor miRNA sequences downloaded from miRBASE v.16. Remaining reads were mapped to other non coding RNAs downloaded from ncRNA.org Statistical analysis was done using edgeR  a bioconductor package R project Genome build: miRBase version 16 Supplementary files format and content: tab delimited text files,Embryos,,Small RNA libraries were prepared using the small RNA expression kit SREK protocol Applied Biosystems  Foster City  CA. Sequencing was done on a SOLiD V3 system Applied Biosystems.,,strain:TL wild type|tissue:embryos|time:60 hpf|treatment:TCDD,GSM979607,GSM979607: 60hpf TCDD 2; Danio rerio; RNA Seq,GSM979607 1,GSM979607: 60hpf TCDD 2,1,,GEO Accession:GSM979607,RNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ABI_SOLID,AB SOLiD System 3.0,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>35</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP014646,,,MH_0011.csfasta,SOLiD_native,407347325.0,11638495.0,GSM979607 r1,0:35,0:99062820;1:113921998;2:81336108;3:112422342;.:604057,35,,,,,,,,,SRX172597,SRS352619,SRA056525,GEO,"Aluru Lab, Biology, Woods Hole Oceanographic Institution",1,0.04258,,0.02455,,0.98287,,0.5048,,35,,B,,usable mapping rate,legacy,early,unknown,size_fractionation,unknown,bulk,unknown,unknown,,United States,2012-08-01,Hatching,Embryo,Embryo Imprecise,All anatomical structures
36484,SRR530892,SRX172596,SRS352618,SRP014646,PRJNA171751,MicroRNA expression profiling post short term exposure to TCDD in zebrafish embryos [miRNA Seq data],GSE39808,Transcriptome Analysis,Although many drugs and environmental chemicals are teratogenic  the mechanisms by which most toxicants disrupt embryonic development are not well understood. microRNAs miRNAs   single stranded RNA molecules of 22 nt that regulate protein expression by inhibiting mRNA translation and promoting mRNA sequestration or degradation  are important regulators of a variety of cellular processes including embryonic development and cellular differentiation.  We hypothesized that exposure to xenobiotics can alter miRNA expression and contribute to the mechanisms by which environmental chemicals disrupt embryonic development. To test this hypothesis for one well known teratogen  we exposed zebrafish embryos to DMSO 0.1% or TCDD 5 nM for 1 hr at 30 hpf and measured microRNA expression using several methods at 36 hpf and 60 hpf. TCDD caused strong induction of CYP1A at 36 hpf 62 fold and 60 hpf 135 fold as determined by qPCR  verifying the  effectiveness of the exposure.  microRNA expression profiles were determined using microarrays Agilent and Exiqon  next generation sequencing SOLiD and real time RT PCR. The two microarray platforms yielded results that were similar but not identical; both showed significant changes in expression of miR 451  23a  23b  24 and 27e at 60 hpf.  Multiple analyses were performed on the SOLiD sequences yielding a total of 16 miRNAs as potentially differentially expressed by TCDD in zebrafish embryos.  However  miR 27e was the only miRNA to be identified as differentially expressed by all three methods both microarrays  SOLiD sequencing  and qPCR.  These results suggest that TCDD exposure causes modest changes in expression of microRNAs  including some miR 451  23a  23b  24 and 27e that are critical for hematopoiesis and cardiovascular development. Overall design: Small RNA profiles were deteremined in TCDD exposed zebrafish embryos using SOLID sequencing,parent bioproject:PRJNA171747,pubmed:22921993,,60hpf TCDD 1,GSM979606,,source name:Embryos|strain:TL wild type|tissue:embryos|time:60 hpf|treatment:TCDD,60hpf TCDD 1,CLC Bio Genomics Work bench version 4.7 was used Adaptor trimming followed by alignining the reads to precursor miRNA sequences downloaded from miRBASE v.16. Remaining reads were mapped to other non coding RNAs downloaded from ncRNA.org Statistical analysis was done using edgeR  a bioconductor package R project Genome build: miRBase version 16 Supplementary files format and content: tab delimited text files,Embryos,,Small RNA libraries were prepared using the small RNA expression kit SREK protocol Applied Biosystems  Foster City  CA. Sequencing was done on a SOLiD V3 system Applied Biosystems.,,strain:TL wild type|tissue:embryos|time:60 hpf|treatment:TCDD,GSM979606,GSM979606: 60hpf TCDD 1; Danio rerio; RNA Seq,GSM979606 1,GSM979606: 60hpf TCDD 1,1,,GEO Accession:GSM979606,RNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ABI_SOLID,AB SOLiD System 3.0,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>35</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP014646,,,MH_0010.csfasta,SOLiD_native,680837045.0,19452487.0,GSM979606 r1,0:35,0:165079839;1:167219862;2:147812329;3:199659766;.:1065249,35,,,,,,,,,SRX172596,SRS352618,SRA056525,GEO,"Aluru Lab, Biology, Woods Hole Oceanographic Institution",1,0.02295,,0.01479,,0.98884,,0.55191,,35,,B,,usable mapping rate,legacy,early,unknown,size_fractionation,unknown,bulk,unknown,unknown,,United States,2012-08-01,Hatching,Embryo,Embryo Imprecise,All anatomical structures
36485,SRR530891,SRX172595,SRS352617,SRP014646,PRJNA171751,MicroRNA expression profiling post short term exposure to TCDD in zebrafish embryos [miRNA Seq data],GSE39808,Transcriptome Analysis,Although many drugs and environmental chemicals are teratogenic  the mechanisms by which most toxicants disrupt embryonic development are not well understood. microRNAs miRNAs   single stranded RNA molecules of 22 nt that regulate protein expression by inhibiting mRNA translation and promoting mRNA sequestration or degradation  are important regulators of a variety of cellular processes including embryonic development and cellular differentiation.  We hypothesized that exposure to xenobiotics can alter miRNA expression and contribute to the mechanisms by which environmental chemicals disrupt embryonic development. To test this hypothesis for one well known teratogen  we exposed zebrafish embryos to DMSO 0.1% or TCDD 5 nM for 1 hr at 30 hpf and measured microRNA expression using several methods at 36 hpf and 60 hpf. TCDD caused strong induction of CYP1A at 36 hpf 62 fold and 60 hpf 135 fold as determined by qPCR  verifying the  effectiveness of the exposure.  microRNA expression profiles were determined using microarrays Agilent and Exiqon  next generation sequencing SOLiD and real time RT PCR. The two microarray platforms yielded results that were similar but not identical; both showed significant changes in expression of miR 451  23a  23b  24 and 27e at 60 hpf.  Multiple analyses were performed on the SOLiD sequences yielding a total of 16 miRNAs as potentially differentially expressed by TCDD in zebrafish embryos.  However  miR 27e was the only miRNA to be identified as differentially expressed by all three methods both microarrays  SOLiD sequencing  and qPCR.  These results suggest that TCDD exposure causes modest changes in expression of microRNAs  including some miR 451  23a  23b  24 and 27e that are critical for hematopoiesis and cardiovascular development. Overall design: Small RNA profiles were deteremined in TCDD exposed zebrafish embryos using SOLID sequencing,parent bioproject:PRJNA171747,pubmed:22921993,,60hpf DMSO 3,GSM979605,,source name:Embryos|strain:TL wild type|tissue:embryos|time:60 hpf|treatment:DMSO,60hpf DMSO 3,CLC Bio Genomics Work bench version 4.7 was used Adaptor trimming followed by alignining the reads to precursor miRNA sequences downloaded from miRBASE v.16. Remaining reads were mapped to other non coding RNAs downloaded from ncRNA.org Statistical analysis was done using edgeR  a bioconductor package R project Genome build: miRBase version 16 Supplementary files format and content: tab delimited text files,Embryos,,Small RNA libraries were prepared using the small RNA expression kit SREK protocol Applied Biosystems  Foster City  CA. Sequencing was done on a SOLiD V3 system Applied Biosystems.,,strain:TL wild type|tissue:embryos|time:60 hpf|treatment:DMSO,GSM979605,GSM979605: 60hpf DMSO 3; Danio rerio; RNA Seq,GSM979605 1,GSM979605: 60hpf DMSO 3,1,,GEO Accession:GSM979605,RNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ABI_SOLID,AB SOLiD System 3.0,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>35</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP014646,,,MH_0009.csfasta,SOLiD_native,495019840.0,14143424.0,GSM979605 r1,0:35,0:134854583;1:126192934;2:102458221;3:130747961;.:766141,35,,,,,,,,,SRX172595,SRS352617,SRA056525,GEO,"Aluru Lab, Biology, Woods Hole Oceanographic Institution",1,0.06707,,0.04409,,0.97285,,0.5058,,35,,B,,usable mapping rate,legacy,early,unknown,size_fractionation,unknown,bulk,unknown,unknown,,United States,2012-08-01,Hatching,Embryo,Embryo Imprecise,All anatomical structures
36486,SRR530890,SRX172594,SRS352616,SRP014646,PRJNA171751,MicroRNA expression profiling post short term exposure to TCDD in zebrafish embryos [miRNA Seq data],GSE39808,Transcriptome Analysis,Although many drugs and environmental chemicals are teratogenic  the mechanisms by which most toxicants disrupt embryonic development are not well understood. microRNAs miRNAs   single stranded RNA molecules of 22 nt that regulate protein expression by inhibiting mRNA translation and promoting mRNA sequestration or degradation  are important regulators of a variety of cellular processes including embryonic development and cellular differentiation.  We hypothesized that exposure to xenobiotics can alter miRNA expression and contribute to the mechanisms by which environmental chemicals disrupt embryonic development. To test this hypothesis for one well known teratogen  we exposed zebrafish embryos to DMSO 0.1% or TCDD 5 nM for 1 hr at 30 hpf and measured microRNA expression using several methods at 36 hpf and 60 hpf. TCDD caused strong induction of CYP1A at 36 hpf 62 fold and 60 hpf 135 fold as determined by qPCR  verifying the  effectiveness of the exposure.  microRNA expression profiles were determined using microarrays Agilent and Exiqon  next generation sequencing SOLiD and real time RT PCR. The two microarray platforms yielded results that were similar but not identical; both showed significant changes in expression of miR 451  23a  23b  24 and 27e at 60 hpf.  Multiple analyses were performed on the SOLiD sequences yielding a total of 16 miRNAs as potentially differentially expressed by TCDD in zebrafish embryos.  However  miR 27e was the only miRNA to be identified as differentially expressed by all three methods both microarrays  SOLiD sequencing  and qPCR.  These results suggest that TCDD exposure causes modest changes in expression of microRNAs  including some miR 451  23a  23b  24 and 27e that are critical for hematopoiesis and cardiovascular development. Overall design: Small RNA profiles were deteremined in TCDD exposed zebrafish embryos using SOLID sequencing,parent bioproject:PRJNA171747,pubmed:22921993,,60hpf DMSO 2,GSM979604,,source name:Embryos|strain:TL wild type|tissue:embryos|time:60 hpf|treatment:DMSO,60hpf DMSO 2,CLC Bio Genomics Work bench version 4.7 was used Adaptor trimming followed by alignining the reads to precursor miRNA sequences downloaded from miRBASE v.16. Remaining reads were mapped to other non coding RNAs downloaded from ncRNA.org Statistical analysis was done using edgeR  a bioconductor package R project Genome build: miRBase version 16 Supplementary files format and content: tab delimited text files,Embryos,,Small RNA libraries were prepared using the small RNA expression kit SREK protocol Applied Biosystems  Foster City  CA. Sequencing was done on a SOLiD V3 system Applied Biosystems.,,strain:TL wild type|tissue:embryos|time:60 hpf|treatment:DMSO,GSM979604,GSM979604: 60hpf DMSO 2; Danio rerio; RNA Seq,GSM979604 1,GSM979604: 60hpf DMSO 2,1,,GEO Accession:GSM979604,RNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ABI_SOLID,AB SOLiD System 3.0,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>35</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP014646,,,MH_0008.qual,SOLiD_native,440403425.0,12582955.0,GSM979604 r1,0:35,0:110302240;1:106481197;2:104551283;3:118415637;.:653068,35,,,,,,,,,SRX172594,SRS352616,SRA056525,GEO,"Aluru Lab, Biology, Woods Hole Oceanographic Institution",1,0.05778,,0.03522,,0.97423,,0.50884,,35,,B,,usable mapping rate,legacy,early,unknown,size_fractionation,unknown,bulk,unknown,unknown,,United States,2012-08-01,Hatching,Embryo,Embryo Imprecise,All anatomical structures
36487,SRR530889,SRX172593,SRS352615,SRP014646,PRJNA171751,MicroRNA expression profiling post short term exposure to TCDD in zebrafish embryos [miRNA Seq data],GSE39808,Transcriptome Analysis,Although many drugs and environmental chemicals are teratogenic  the mechanisms by which most toxicants disrupt embryonic development are not well understood. microRNAs miRNAs   single stranded RNA molecules of 22 nt that regulate protein expression by inhibiting mRNA translation and promoting mRNA sequestration or degradation  are important regulators of a variety of cellular processes including embryonic development and cellular differentiation.  We hypothesized that exposure to xenobiotics can alter miRNA expression and contribute to the mechanisms by which environmental chemicals disrupt embryonic development. To test this hypothesis for one well known teratogen  we exposed zebrafish embryos to DMSO 0.1% or TCDD 5 nM for 1 hr at 30 hpf and measured microRNA expression using several methods at 36 hpf and 60 hpf. TCDD caused strong induction of CYP1A at 36 hpf 62 fold and 60 hpf 135 fold as determined by qPCR  verifying the  effectiveness of the exposure.  microRNA expression profiles were determined using microarrays Agilent and Exiqon  next generation sequencing SOLiD and real time RT PCR. The two microarray platforms yielded results that were similar but not identical; both showed significant changes in expression of miR 451  23a  23b  24 and 27e at 60 hpf.  Multiple analyses were performed on the SOLiD sequences yielding a total of 16 miRNAs as potentially differentially expressed by TCDD in zebrafish embryos.  However  miR 27e was the only miRNA to be identified as differentially expressed by all three methods both microarrays  SOLiD sequencing  and qPCR.  These results suggest that TCDD exposure causes modest changes in expression of microRNAs  including some miR 451  23a  23b  24 and 27e that are critical for hematopoiesis and cardiovascular development. Overall design: Small RNA profiles were deteremined in TCDD exposed zebrafish embryos using SOLID sequencing,parent bioproject:PRJNA171747,pubmed:22921993,,60hpf DMSO 1,GSM979603,,source name:Embryos|strain:TL wild type|tissue:embryos|time:60 hpf|treatment:DMSO,60hpf DMSO 1,CLC Bio Genomics Work bench version 4.7 was used Adaptor trimming followed by alignining the reads to precursor miRNA sequences downloaded from miRBASE v.16. Remaining reads were mapped to other non coding RNAs downloaded from ncRNA.org Statistical analysis was done using edgeR  a bioconductor package R project Genome build: miRBase version 16 Supplementary files format and content: tab delimited text files,Embryos,,Small RNA libraries were prepared using the small RNA expression kit SREK protocol Applied Biosystems  Foster City  CA. Sequencing was done on a SOLiD V3 system Applied Biosystems.,,strain:TL wild type|tissue:embryos|time:60 hpf|treatment:DMSO,GSM979603,GSM979603: 60hpf DMSO 1; Danio rerio; RNA Seq,GSM979603 1,GSM979603: 60hpf DMSO 1,1,,GEO Accession:GSM979603,RNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ABI_SOLID,AB SOLiD System 3.0,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>35</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP014646,,,MH_0007.csfasta MH_0007.qual,SOLiD_native SOLiD_native,583800490.0,16680014.0,GSM979603 r1,0:35,0:166122108;1:149534173;2:111986455;3:155255262;.:902492,35,,,,,,,,,SRX172593,SRS352615,SRA056525,GEO,"Aluru Lab, Biology, Woods Hole Oceanographic Institution",1,0.05644,,0.03829,,0.9781,,0.4997,,35,,B,,usable mapping rate,legacy,early,unknown,size_fractionation,unknown,bulk,unknown,unknown,,United States,2012-08-01,Hatching,Embryo,Embryo Imprecise,All anatomical structures