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
59497,SRR11924327,SRX8469999,SRS6770650,SRP265951,PRJNA637293,The shift from early to late types of ribosomes in zebrafish development involves changes at a subset of rRNA 2' O Me sites,GSE151797,Other,A sequencing based profiling method RiboMeth seq for ribose methylations was used to study methylation patterns during Zebrafish Danio rerio development Overall design: All samples were analyzed in biological triplicates  except for adult tail trunk that was in duplicate.,,pubmed:32912962,,small RNA oblong 2,GSM4591066,,source name:oblong|tissue:oblong|rna fraction:whole cell RNA depleted for rRNA and size selected for RNA < 200 nt,small RNA oblong 2,Library strategy: RiboMeth seq Barcode separation using python script Adaptor trimming using Cutadapt v. 2.0 Mapping to rRNA reference sequence using Bowtie2 v. 2.3.4.1 Counting read ends and calculating RiboMeth seq scores using python scripts The output FASTA files from small RNA seq were merged and used as the basis of the SNORD search and rRNA interaction prediction. Initially  SNORDs were identified by running the merged FASTA file through snoScan Schattner et al. 2005 against zebrafish early  and late rRNA reference sequences Locati et al. 2017. Genome build: early and late zebrafish rRNA locati et al. The reference sequences are available in the FASTA file on the series record. Supplementary files format and content: MS Excel file contains five prime and three prime read count and calculated RiboMeth seq score at all positions in the rRNA sequence.,oblong,,Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. For small RNA library construction  one  ug of whole cell RNA was subjected to rRNA depletion using the RiboMinusT Eukaryote System v2 Invitrogen  and small RNA libraries were constructed using Ion Total RNA Seq Kit v2 ThermoFisher Scientific with minor modifications. In short  the rRNA depleted RNA samples were enriched for small RNA <200 nt using the magnetic bead clean up module supplied with the kit or MonarchR RNA Cleanup Kit New England Biolabs  adapters diluted 1:2 were ligated to the RNA for 2 h and the RNA subsequently reverse transcribed using Superscript IV ThermoFisher Scientific. The cDNA was purified using the magnetic bead clean up module  without xxx selection. Amplification of cDNA and purification was performed according to the manufacturer. Manual template preparation of libraries was carried out on the Ion OneTouchTM 2 System ThermoFisher Scientific and sequenced on Ion 540TM chips the Ion GeneStudio S5 System.,,tissue:oblong|rna fraction:whole cell RNA depleted for rRNA and size selected for RNA < 200 nt,GSM4591066,GSM4591066: small RNA oblong 2; Danio rerio; OTHER,GSM4591066,,1,Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. For small RNA library construction  one  ug of whole cell RNA was subjected to rRNA depletion using the RiboMinusT Eukaryote System v2 Invitrogen  and small RNA libraries were constructed using Ion Total RNA Seq Kit v2 ThermoFisher Scientific with minor modifications. In short  the rRNA depleted RNA samples were enriched for small RNA <200 nt using the magnetic bead clean up module supplied with the kit or MonarchR RNA Cleanup Kit New England Biolabs  adapters diluted 1:2 were ligated to the RNA for 2 h and the RNA subsequently reverse transcribed using Superscript IV ThermoFisher Scientific. The cDNA was purified using the magnetic bead clean up module  without xxx selection. Amplification of cDNA and purification was performed according to the manufacturer. Manual template preparation of libraries was carried out on the Ion OneTouchTM 2 System ThermoFisher Scientific and sequenced on Ion 540TM chips the Ion GeneStudio S5 System.,GEO Accession:GSM4591066,OTHER,TRANSCRIPTOMIC,other,SINGLE,ION_TORRENT,Ion Torrent S5,,SRP265951,,,small_RNA_oblong_stage_2.fastq,fastq,131762340.0,2740821.0,GSM4591066 r1,0:48.07,A:36963883;C:35740715;G:33446415;T:25611327;N:0,48,,,,36963883,35740715,33446415,25611327,0,SRX8469999,SRS6770650,SRA1083099,GEO,"RNA Group - Prof. Henrik Nielsen, Department of Cellular and Molecular Medicine, University of Copenhagen",1,0.5346,,0.11052,,0.8967,,0.64134,,72,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,rrna_depletion,unknown,bulk,unknown,unknown,,Denmark,2020-06-04,Blastula,Embryo,Undetermined,Embryo Imprecise
59498,SRR11924326,SRX8469998,SRS6770649,SRP265951,PRJNA637293,The shift from early to late types of ribosomes in zebrafish development involves changes at a subset of rRNA 2' O Me sites,GSE151797,Other,A sequencing based profiling method RiboMeth seq for ribose methylations was used to study methylation patterns during Zebrafish Danio rerio development Overall design: All samples were analyzed in biological triplicates  except for adult tail trunk that was in duplicate.,,pubmed:32912962,,small RNA oblong 1,GSM4591065,,source name:oblong|tissue:oblong|rna fraction:whole cell RNA depleted for rRNA and size selected for RNA < 200 nt,small RNA oblong 1,Library strategy: RiboMeth seq Barcode separation using python script Adaptor trimming using Cutadapt v. 2.0 Mapping to rRNA reference sequence using Bowtie2 v. 2.3.4.1 Counting read ends and calculating RiboMeth seq scores using python scripts The output FASTA files from small RNA seq were merged and used as the basis of the SNORD search and rRNA interaction prediction. Initially  SNORDs were identified by running the merged FASTA file through snoScan Schattner et al. 2005 against zebrafish early  and late rRNA reference sequences Locati et al. 2017. Genome build: early and late zebrafish rRNA locati et al. The reference sequences are available in the FASTA file on the series record. Supplementary files format and content: MS Excel file contains five prime and three prime read count and calculated RiboMeth seq score at all positions in the rRNA sequence.,oblong,,Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. For small RNA library construction  one  ug of whole cell RNA was subjected to rRNA depletion using the RiboMinusT Eukaryote System v2 Invitrogen  and small RNA libraries were constructed using Ion Total RNA Seq Kit v2 ThermoFisher Scientific with minor modifications. In short  the rRNA depleted RNA samples were enriched for small RNA <200 nt using the magnetic bead clean up module supplied with the kit or MonarchR RNA Cleanup Kit New England Biolabs  adapters diluted 1:2 were ligated to the RNA for 2 h and the RNA subsequently reverse transcribed using Superscript IV ThermoFisher Scientific. The cDNA was purified using the magnetic bead clean up module  without xxx selection. Amplification of cDNA and purification was performed according to the manufacturer. Manual template preparation of libraries was carried out on the Ion OneTouchTM 2 System ThermoFisher Scientific and sequenced on Ion 540TM chips the Ion GeneStudio S5 System.,,tissue:oblong|rna fraction:whole cell RNA depleted for rRNA and size selected for RNA < 200 nt,GSM4591065,GSM4591065: small RNA oblong 1; Danio rerio; OTHER,GSM4591065,,1,Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. For small RNA library construction  one  ug of whole cell RNA was subjected to rRNA depletion using the RiboMinusT Eukaryote System v2 Invitrogen  and small RNA libraries were constructed using Ion Total RNA Seq Kit v2 ThermoFisher Scientific with minor modifications. In short  the rRNA depleted RNA samples were enriched for small RNA <200 nt using the magnetic bead clean up module supplied with the kit or MonarchR RNA Cleanup Kit New England Biolabs  adapters diluted 1:2 were ligated to the RNA for 2 h and the RNA subsequently reverse transcribed using Superscript IV ThermoFisher Scientific. The cDNA was purified using the magnetic bead clean up module  without xxx selection. Amplification of cDNA and purification was performed according to the manufacturer. Manual template preparation of libraries was carried out on the Ion OneTouchTM 2 System ThermoFisher Scientific and sequenced on Ion 540TM chips the Ion GeneStudio S5 System.,GEO Accession:GSM4591065,OTHER,TRANSCRIPTOMIC,other,SINGLE,ION_TORRENT,Ion Torrent S5,,SRP265951,,,small_RNA_oblong_stage_1.fastq,fastq,90701340.0,2141489.0,GSM4591065 r1,0:42.35,A:25203959;C:24291162;G:23143516;T:18062703;N:0,42,,,,25203959,24291162,23143516,18062703,0,SRX8469998,SRS6770649,SRA1083099,GEO,"RNA Group - Prof. Henrik Nielsen, Department of Cellular and Molecular Medicine, University of Copenhagen",1,0.48132,,0.15952,,0.8756,,0.56134,,29,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,rrna_depletion,unknown,bulk,unknown,unknown,,Denmark,2020-06-04,Blastula,Embryo,Undetermined,Embryo Imprecise
59499,SRR11924325,SRX8469997,SRS6770648,SRP265951,PRJNA637293,The shift from early to late types of ribosomes in zebrafish development involves changes at a subset of rRNA 2' O Me sites,GSE151797,Other,A sequencing based profiling method RiboMeth seq for ribose methylations was used to study methylation patterns during Zebrafish Danio rerio development Overall design: All samples were analyzed in biological triplicates  except for adult tail trunk that was in duplicate.,,pubmed:32912962,,small RNA 32 cell,GSM4591064,,source name:32 cell stage|tissue:32 cell stage|rna fraction:whole cell RNA depleted for rRNA and size selected for RNA < 200 nt,small RNA 32 cell,Library strategy: RiboMeth seq Barcode separation using python script Adaptor trimming using Cutadapt v. 2.0 Mapping to rRNA reference sequence using Bowtie2 v. 2.3.4.1 Counting read ends and calculating RiboMeth seq scores using python scripts The output FASTA files from small RNA seq were merged and used as the basis of the SNORD search and rRNA interaction prediction. Initially  SNORDs were identified by running the merged FASTA file through snoScan Schattner et al. 2005 against zebrafish early  and late rRNA reference sequences Locati et al. 2017. Genome build: early and late zebrafish rRNA locati et al. The reference sequences are available in the FASTA file on the series record. Supplementary files format and content: MS Excel file contains five prime and three prime read count and calculated RiboMeth seq score at all positions in the rRNA sequence.,32 cell stage,,Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. For small RNA library construction  one  ug of whole cell RNA was subjected to rRNA depletion using the RiboMinusT Eukaryote System v2 Invitrogen  and small RNA libraries were constructed using Ion Total RNA Seq Kit v2 ThermoFisher Scientific with minor modifications. In short  the rRNA depleted RNA samples were enriched for small RNA <200 nt using the magnetic bead clean up module supplied with the kit or MonarchR RNA Cleanup Kit New England Biolabs  adapters diluted 1:2 were ligated to the RNA for 2 h and the RNA subsequently reverse transcribed using Superscript IV ThermoFisher Scientific. The cDNA was purified using the magnetic bead clean up module  without xxx selection. Amplification of cDNA and purification was performed according to the manufacturer. Manual template preparation of libraries was carried out on the Ion OneTouchTM 2 System ThermoFisher Scientific and sequenced on Ion 540TM chips the Ion GeneStudio S5 System.,,tissue:32 cell stage|rna fraction:whole cell RNA depleted for rRNA and size selected for RNA < 200 nt,GSM4591064,GSM4591064: small RNA 32 cell; Danio rerio; OTHER,GSM4591064,,1,Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. For small RNA library construction  one  ug of whole cell RNA was subjected to rRNA depletion using the RiboMinusT Eukaryote System v2 Invitrogen  and small RNA libraries were constructed using Ion Total RNA Seq Kit v2 ThermoFisher Scientific with minor modifications. In short  the rRNA depleted RNA samples were enriched for small RNA <200 nt using the magnetic bead clean up module supplied with the kit or MonarchR RNA Cleanup Kit New England Biolabs  adapters diluted 1:2 were ligated to the RNA for 2 h and the RNA subsequently reverse transcribed using Superscript IV ThermoFisher Scientific. The cDNA was purified using the magnetic bead clean up module  without xxx selection. Amplification of cDNA and purification was performed according to the manufacturer. Manual template preparation of libraries was carried out on the Ion OneTouchTM 2 System ThermoFisher Scientific and sequenced on Ion 540TM chips the Ion GeneStudio S5 System.,GEO Accession:GSM4591064,OTHER,TRANSCRIPTOMIC,other,SINGLE,ION_TORRENT,Ion Torrent S5,,SRP265951,,,small_RNA_32_cell_stage.fastq,fastq,275040056.0,6091077.0,GSM4591064 r1,0:45.15,A:69136092;C:69806677;G:72527986;T:63569301;N:0,45,,,,69136092,69806677,72527986,63569301,0,SRX8469997,SRS6770648,SRA1083099,GEO,"RNA Group - Prof. Henrik Nielsen, Department of Cellular and Molecular Medicine, University of Copenhagen",1,0.67676,,0.30881,,0.86636,,0.63482,,22,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,rrna_depletion,unknown,bulk,unknown,unknown,,Denmark,2020-06-04,Cleavage,Embryo,Undetermined,Embryo Imprecise
59500,SRR11924324,SRX8469996,SRS6770647,SRP265951,PRJNA637293,The shift from early to late types of ribosomes in zebrafish development involves changes at a subset of rRNA 2' O Me sites,GSE151797,Other,A sequencing based profiling method RiboMeth seq for ribose methylations was used to study methylation patterns during Zebrafish Danio rerio development Overall design: All samples were analyzed in biological triplicates  except for adult tail trunk that was in duplicate.,,pubmed:32912962,,small RNA 15E,GSM4591063,,source name:zfs:0000015|tissue:zfs:0000015|rna fraction:whole cell RNA depleted for rRNA and size selected for RNA < 200 nt,small RNA 15E,Library strategy: RiboMeth seq Barcode separation using python script Adaptor trimming using Cutadapt v. 2.0 Mapping to rRNA reference sequence using Bowtie2 v. 2.3.4.1 Counting read ends and calculating RiboMeth seq scores using python scripts The output FASTA files from small RNA seq were merged and used as the basis of the SNORD search and rRNA interaction prediction. Initially  SNORDs were identified by running the merged FASTA file through snoScan Schattner et al. 2005 against zebrafish early  and late rRNA reference sequences Locati et al. 2017. Genome build: early and late zebrafish rRNA locati et al. The reference sequences are available in the FASTA file on the series record. Supplementary files format and content: MS Excel file contains five prime and three prime read count and calculated RiboMeth seq score at all positions in the rRNA sequence.,zfs:0000015,,Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. For small RNA library construction  one  ug of whole cell RNA was subjected to rRNA depletion using the RiboMinusT Eukaryote System v2 Invitrogen  and small RNA libraries were constructed using Ion Total RNA Seq Kit v2 ThermoFisher Scientific with minor modifications. In short  the rRNA depleted RNA samples were enriched for small RNA <200 nt using the magnetic bead clean up module supplied with the kit or MonarchR RNA Cleanup Kit New England Biolabs  adapters diluted 1:2 were ligated to the RNA for 2 h and the RNA subsequently reverse transcribed using Superscript IV ThermoFisher Scientific. The cDNA was purified using the magnetic bead clean up module  without xxx selection. Amplification of cDNA and purification was performed according to the manufacturer. Manual template preparation of libraries was carried out on the Ion OneTouchTM 2 System ThermoFisher Scientific and sequenced on Ion 540TM chips the Ion GeneStudio S5 System.,,tissue:zfs:0000015|rna fraction:whole cell RNA depleted for rRNA and size selected for RNA < 200 nt,GSM4591063,GSM4591063: small RNA 15E; Danio rerio; OTHER,GSM4591063,,1,Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. For small RNA library construction  one  ug of whole cell RNA was subjected to rRNA depletion using the RiboMinusT Eukaryote System v2 Invitrogen  and small RNA libraries were constructed using Ion Total RNA Seq Kit v2 ThermoFisher Scientific with minor modifications. In short  the rRNA depleted RNA samples were enriched for small RNA <200 nt using the magnetic bead clean up module supplied with the kit or MonarchR RNA Cleanup Kit New England Biolabs  adapters diluted 1:2 were ligated to the RNA for 2 h and the RNA subsequently reverse transcribed using Superscript IV ThermoFisher Scientific. The cDNA was purified using the magnetic bead clean up module  without xxx selection. Amplification of cDNA and purification was performed according to the manufacturer. Manual template preparation of libraries was carried out on the Ion OneTouchTM 2 System ThermoFisher Scientific and sequenced on Ion 540TM chips the Ion GeneStudio S5 System.,GEO Accession:GSM4591063,OTHER,TRANSCRIPTOMIC,other,SINGLE,ION_TORRENT,Ion Torrent S5,,SRP265951,,,small_RNA_15E_stage.fastq,fastq,264453879.0,5777826.0,GSM4591063 r1,0:45.77,A:63859672;C:67381369;G:71681258;T:61531580;N:0,45,,,,63859672,67381369,71681258,61531580,0,SRX8469996,SRS6770647,SRA1083099,GEO,"RNA Group - Prof. Henrik Nielsen, Department of Cellular and Molecular Medicine, University of Copenhagen",1,0.60375,,0.23463,,0.87606,,0.58681,,40,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,rrna_depletion,unknown,bulk,unknown,unknown,,Denmark,2020-06-04,Blastula,Embryo,Undetermined,Embryo Imprecise
59501,SRR11924323,SRX8469995,SRS6770646,SRP265951,PRJNA637293,The shift from early to late types of ribosomes in zebrafish development involves changes at a subset of rRNA 2' O Me sites,GSE151797,Other,A sequencing based profiling method RiboMeth seq for ribose methylations was used to study methylation patterns during Zebrafish Danio rerio development Overall design: All samples were analyzed in biological triplicates  except for adult tail trunk that was in duplicate.,,pubmed:32912962,,Adult tail 2,GSM4591062,,source name:adult tail trunk|tissue:adult tail trunk|rna fraction:size fractionated 20 40 nt whole cell RNA,Adult tail 2,Library strategy: RiboMeth seq Barcode separation using python script Adaptor trimming using Cutadapt v. 2.0 Mapping to rRNA reference sequence using Bowtie2 v. 2.3.4.1 Counting read ends and calculating RiboMeth seq scores using python scripts The output FASTA files from small RNA seq were merged and used as the basis of the SNORD search and rRNA interaction prediction. Initially  SNORDs were identified by running the merged FASTA file through snoScan Schattner et al. 2005 against zebrafish early  and late rRNA reference sequences Locati et al. 2017. Genome build: early and late zebrafish rRNA locati et al. The reference sequences are available in the FASTA file on the series record. Supplementary files format and content: MS Excel file contains five prime and three prime read count and calculated RiboMeth seq score at all positions in the rRNA sequence.,adult tail trunk,,Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. RiboMeth seq: 5 10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20 40 nt was purified on gels and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2' three prime cyclic phosphate and five prime phosphate ends. The library fragments were then sequenced on the Ion Proton platform. See Birkedal U  Christensen Dalsgaard M  Krogh N  Sabarinathan R  Gorodkin J  Nielsen H. Profiling of ribose methylations in RNA by high throughput sequencing. Angewandte Chemie. 2015;542:451 5 for detailed description,,tissue:adult tail trunk|rna fraction:size fractionated 20 40 nt whole cell RNA,GSM4591062,GSM4591062: Adult tail 2; Danio rerio; OTHER,GSM4591062,,1,Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. RiboMeth seq: 5 10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20 40 nt was purified on gels and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2' three prime cyclic phosphate and five prime phosphate ends. The library fragments were then sequenced on the Ion Proton platform. See Birkedal U  Christensen Dalsgaard M  Krogh N  Sabarinathan R  Gorodkin J  Nielsen H. Profiling of ribose methylations in RNA by high throughput sequencing. Angewandte Chemie. 2015;542:451 5 for detailed description,GEO Accession:GSM4591062,OTHER,TRANSCRIPTOMIC,other,SINGLE,ION_TORRENT,Ion Torrent Proton,,SRP265951,,intentional duplicate,Adult_tail_2.bam GSE151797_Reference_sequence.fa,bam bam,156647953.0,5517527.0,GSM4591062 r1,0:28.39,A:32903673;C:49609293;G:39096775;T:35038212;N:0,28,,,,32903673,49609293,39096775,35038212,0,SRX8469995,SRS6770646,SRA1083099,GEO,"RNA Group - Prof. Henrik Nielsen, Department of Cellular and Molecular Medicine, University of Copenhagen",1,0.80662,,0.20653,,0.88722,,0.58074,,37,,B,,usable mapping rate,ion_torrent,ion_torrent,5prime,small_rna,unknown,bulk,unknown,unknown,,Denmark,2020-06-04,Adult,Adult,Multi-tissue,Multi-system
59502,SRR11924321,SRX8469994,SRS6770645,SRP265951,PRJNA637293,The shift from early to late types of ribosomes in zebrafish development involves changes at a subset of rRNA 2' O Me sites,GSE151797,Other,A sequencing based profiling method RiboMeth seq for ribose methylations was used to study methylation patterns during Zebrafish Danio rerio development Overall design: All samples were analyzed in biological triplicates  except for adult tail trunk that was in duplicate.,,pubmed:32912962,,Adult tail 1,GSM4591061,,source name:adult tail trunk|tissue:adult tail trunk|rna fraction:size fractionated 20 40 nt whole cell RNA,Adult tail 1,Library strategy: RiboMeth seq Barcode separation using python script Adaptor trimming using Cutadapt v. 2.0 Mapping to rRNA reference sequence using Bowtie2 v. 2.3.4.1 Counting read ends and calculating RiboMeth seq scores using python scripts The output FASTA files from small RNA seq were merged and used as the basis of the SNORD search and rRNA interaction prediction. Initially  SNORDs were identified by running the merged FASTA file through snoScan Schattner et al. 2005 against zebrafish early  and late rRNA reference sequences Locati et al. 2017. Genome build: early and late zebrafish rRNA locati et al. The reference sequences are available in the FASTA file on the series record. Supplementary files format and content: MS Excel file contains five prime and three prime read count and calculated RiboMeth seq score at all positions in the rRNA sequence.,adult tail trunk,,Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. RiboMeth seq: 5 10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20 40 nt was purified on gels and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2' three prime cyclic phosphate and five prime phosphate ends. The library fragments were then sequenced on the Ion Proton platform. See Birkedal U  Christensen Dalsgaard M  Krogh N  Sabarinathan R  Gorodkin J  Nielsen H. Profiling of ribose methylations in RNA by high throughput sequencing. Angewandte Chemie. 2015;542:451 5 for detailed description,,tissue:adult tail trunk|rna fraction:size fractionated 20 40 nt whole cell RNA,GSM4591061,GSM4591061: Adult tail 1; Danio rerio; OTHER,GSM4591061,,1,Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. RiboMeth seq: 5 10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20 40 nt was purified on gels and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2' three prime cyclic phosphate and five prime phosphate ends. The library fragments were then sequenced on the Ion Proton platform. See Birkedal U  Christensen Dalsgaard M  Krogh N  Sabarinathan R  Gorodkin J  Nielsen H. Profiling of ribose methylations in RNA by high throughput sequencing. Angewandte Chemie. 2015;542:451 5 for detailed description,GEO Accession:GSM4591061,OTHER,TRANSCRIPTOMIC,other,SINGLE,ION_TORRENT,Ion Torrent Proton,,SRP265951,,intentional duplicate,Adult_tail_1.bam GSE151797_Reference_sequence.fa,bam bam,50029636.0,1968329.0,GSM4591061 r1,0:25.42,A:9571393;C:14825016;G:13276309;T:12356918;N:0,25,,,,9571393,14825016,13276309,12356918,0,SRX8469994,SRS6770645,SRA1083099,GEO,"RNA Group - Prof. Henrik Nielsen, Department of Cellular and Molecular Medicine, University of Copenhagen",1,0.46312,,0.12127,,0.91806,,0.67424,,44,,B,,usable mapping rate,ion_torrent,ion_torrent,5prime,small_rna,unknown,bulk,unknown,unknown,,Denmark,2020-06-04,Adult,Adult,Multi-tissue,Multi-system
59503,SRR11924320,SRX8469993,SRS6770644,SRP265951,PRJNA637293,The shift from early to late types of ribosomes in zebrafish development involves changes at a subset of rRNA 2' O Me sites,GSE151797,Other,A sequencing based profiling method RiboMeth seq for ribose methylations was used to study methylation patterns during Zebrafish Danio rerio development Overall design: All samples were analyzed in biological triplicates  except for adult tail trunk that was in duplicate.,,pubmed:32912962,,PM 3,GSM4591060,,source name:protruding mouth stage|tissue:protruding mouth stage|rna fraction:size fractionated 20 40 nt whole cell RNA,PM 3,Library strategy: RiboMeth seq Barcode separation using python script Adaptor trimming using Cutadapt v. 2.0 Mapping to rRNA reference sequence using Bowtie2 v. 2.3.4.1 Counting read ends and calculating RiboMeth seq scores using python scripts The output FASTA files from small RNA seq were merged and used as the basis of the SNORD search and rRNA interaction prediction. Initially  SNORDs were identified by running the merged FASTA file through snoScan Schattner et al. 2005 against zebrafish early  and late rRNA reference sequences Locati et al. 2017. Genome build: early and late zebrafish rRNA locati et al. The reference sequences are available in the FASTA file on the series record. Supplementary files format and content: MS Excel file contains five prime and three prime read count and calculated RiboMeth seq score at all positions in the rRNA sequence.,protruding mouth stage,,Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. RiboMeth seq: 5 10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20 40 nt was purified on gels and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2' three prime cyclic phosphate and five prime phosphate ends. The library fragments were then sequenced on the Ion Proton platform. See Birkedal U  Christensen Dalsgaard M  Krogh N  Sabarinathan R  Gorodkin J  Nielsen H. Profiling of ribose methylations in RNA by high throughput sequencing. Angewandte Chemie. 2015;542:451 5 for detailed description,,tissue:protruding mouth stage|rna fraction:size fractionated 20 40 nt whole cell RNA,GSM4591060,GSM4591060: PM 3; Danio rerio; OTHER,GSM4591060,,1,Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. RiboMeth seq: 5 10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20 40 nt was purified on gels and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2' three prime cyclic phosphate and five prime phosphate ends. The library fragments were then sequenced on the Ion Proton platform. See Birkedal U  Christensen Dalsgaard M  Krogh N  Sabarinathan R  Gorodkin J  Nielsen H. Profiling of ribose methylations in RNA by high throughput sequencing. Angewandte Chemie. 2015;542:451 5 for detailed description,GEO Accession:GSM4591060,OTHER,TRANSCRIPTOMIC,other,SINGLE,ION_TORRENT,Ion Torrent Proton,,SRP265951,,intentional duplicate,GSE151797_Reference_sequence.fa PM_3.bam,bam bam,215125332.0,6403488.0,GSM4591060 r1,0:33.60,A:50202267;C:65116674;G:52637331;T:47169060;N:0,33,,,,50202267,65116674,52637331,47169060,0,SRX8469993,SRS6770644,SRA1083099,GEO,"RNA Group - Prof. Henrik Nielsen, Department of Cellular and Molecular Medicine, University of Copenhagen",1,0.73594,,0.21617,,0.86251,,0.68892,,42,,B,,usable mapping rate,ion_torrent,ion_torrent,5prime,small_rna,unknown,bulk,unknown,unknown,,Denmark,2020-06-04,Larval,Larval,Undetermined,Undetermined
59504,SRR11924318,SRX8469992,SRS6770643,SRP265951,PRJNA637293,The shift from early to late types of ribosomes in zebrafish development involves changes at a subset of rRNA 2' O Me sites,GSE151797,Other,A sequencing based profiling method RiboMeth seq for ribose methylations was used to study methylation patterns during Zebrafish Danio rerio development Overall design: All samples were analyzed in biological triplicates  except for adult tail trunk that was in duplicate.,,pubmed:32912962,,PM 2,GSM4591059,,source name:protruding mouth stage|tissue:protruding mouth stage|rna fraction:size fractionated 20 40 nt whole cell RNA,PM 2,Library strategy: RiboMeth seq Barcode separation using python script Adaptor trimming using Cutadapt v. 2.0 Mapping to rRNA reference sequence using Bowtie2 v. 2.3.4.1 Counting read ends and calculating RiboMeth seq scores using python scripts The output FASTA files from small RNA seq were merged and used as the basis of the SNORD search and rRNA interaction prediction. Initially  SNORDs were identified by running the merged FASTA file through snoScan Schattner et al. 2005 against zebrafish early  and late rRNA reference sequences Locati et al. 2017. Genome build: early and late zebrafish rRNA locati et al. The reference sequences are available in the FASTA file on the series record. Supplementary files format and content: MS Excel file contains five prime and three prime read count and calculated RiboMeth seq score at all positions in the rRNA sequence.,protruding mouth stage,,Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. RiboMeth seq: 5 10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20 40 nt was purified on gels and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2' three prime cyclic phosphate and five prime phosphate ends. The library fragments were then sequenced on the Ion Proton platform. See Birkedal U  Christensen Dalsgaard M  Krogh N  Sabarinathan R  Gorodkin J  Nielsen H. Profiling of ribose methylations in RNA by high throughput sequencing. Angewandte Chemie. 2015;542:451 5 for detailed description,,tissue:protruding mouth stage|rna fraction:size fractionated 20 40 nt whole cell RNA,GSM4591059,GSM4591059: PM 2; Danio rerio; OTHER,GSM4591059,,1,Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. RiboMeth seq: 5 10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20 40 nt was purified on gels and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2' three prime cyclic phosphate and five prime phosphate ends. The library fragments were then sequenced on the Ion Proton platform. See Birkedal U  Christensen Dalsgaard M  Krogh N  Sabarinathan R  Gorodkin J  Nielsen H. Profiling of ribose methylations in RNA by high throughput sequencing. Angewandte Chemie. 2015;542:451 5 for detailed description,GEO Accession:GSM4591059,OTHER,TRANSCRIPTOMIC,other,SINGLE,ION_TORRENT,Ion Torrent Proton,,SRP265951,,intentional duplicate,GSE151797_Reference_sequence.fa PM_2.bam,bam bam,426315355.0,12915702.0,GSM4591059 r1,0:33.01,A:92276988;C:141702085;G:104175159;T:88161123;N:0,33,,,,92276988,141702085,104175159,88161123,0,SRX8469992,SRS6770643,SRA1083099,GEO,"RNA Group - Prof. Henrik Nielsen, Department of Cellular and Molecular Medicine, University of Copenhagen",1,0.76385,,0.1921,,0.87207,,0.71495,,40,,B,,usable mapping rate,ion_torrent,ion_torrent,5prime,small_rna,unknown,bulk,unknown,unknown,,Denmark,2020-06-04,Larval,Larval,Undetermined,Undetermined
59505,SRR11924317,SRX8469990,SRS6770641,SRP265951,PRJNA637293,The shift from early to late types of ribosomes in zebrafish development involves changes at a subset of rRNA 2' O Me sites,GSE151797,Other,A sequencing based profiling method RiboMeth seq for ribose methylations was used to study methylation patterns during Zebrafish Danio rerio development Overall design: All samples were analyzed in biological triplicates  except for adult tail trunk that was in duplicate.,,pubmed:32912962,,PM 1,GSM4591058,,source name:protruding mouth stage|tissue:protruding mouth stage|rna fraction:size fractionated 20 40 nt whole cell RNA,PM 1,Library strategy: RiboMeth seq Barcode separation using python script Adaptor trimming using Cutadapt v. 2.0 Mapping to rRNA reference sequence using Bowtie2 v. 2.3.4.1 Counting read ends and calculating RiboMeth seq scores using python scripts The output FASTA files from small RNA seq were merged and used as the basis of the SNORD search and rRNA interaction prediction. Initially  SNORDs were identified by running the merged FASTA file through snoScan Schattner et al. 2005 against zebrafish early  and late rRNA reference sequences Locati et al. 2017. Genome build: early and late zebrafish rRNA locati et al. The reference sequences are available in the FASTA file on the series record. Supplementary files format and content: MS Excel file contains five prime and three prime read count and calculated RiboMeth seq score at all positions in the rRNA sequence.,protruding mouth stage,,Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. RiboMeth seq: 5 10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20 40 nt was purified on gels and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2' three prime cyclic phosphate and five prime phosphate ends. The library fragments were then sequenced on the Ion Proton platform. See Birkedal U  Christensen Dalsgaard M  Krogh N  Sabarinathan R  Gorodkin J  Nielsen H. Profiling of ribose methylations in RNA by high throughput sequencing. Angewandte Chemie. 2015;542:451 5 for detailed description,,tissue:protruding mouth stage|rna fraction:size fractionated 20 40 nt whole cell RNA,GSM4591058,GSM4591058: PM 1; Danio rerio; OTHER,GSM4591058,,1,Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. RiboMeth seq: 5 10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20 40 nt was purified on gels and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2' three prime cyclic phosphate and five prime phosphate ends. The library fragments were then sequenced on the Ion Proton platform. See Birkedal U  Christensen Dalsgaard M  Krogh N  Sabarinathan R  Gorodkin J  Nielsen H. Profiling of ribose methylations in RNA by high throughput sequencing. Angewandte Chemie. 2015;542:451 5 for detailed description,GEO Accession:GSM4591058,OTHER,TRANSCRIPTOMIC,other,SINGLE,ION_TORRENT,Ion Torrent Proton,,SRP265951,,intentional duplicate,GSE151797_Reference_sequence.fa PM_1.bam,bam bam,130388595.0,5124384.0,GSM4591058 r1,0:25.44,A:27290253;C:42592303;G:31075292;T:29430747;N:0,25,,,,27290253,42592303,31075292,29430747,0,SRX8469990,SRS6770641,SRA1083099,GEO,"RNA Group - Prof. Henrik Nielsen, Department of Cellular and Molecular Medicine, University of Copenhagen",1,0.78884,,0.23004,,0.85113,,0.67571,,38,,B,,usable mapping rate,ion_torrent,ion_torrent,5prime,small_rna,unknown,bulk,unknown,unknown,,Denmark,2020-06-04,Larval,Larval,Undetermined,Undetermined
59506,SRR11924315,SRX8469989,SRS6770640,SRP265951,PRJNA637293,The shift from early to late types of ribosomes in zebrafish development involves changes at a subset of rRNA 2' O Me sites,GSE151797,Other,A sequencing based profiling method RiboMeth seq for ribose methylations was used to study methylation patterns during Zebrafish Danio rerio development Overall design: All samples were analyzed in biological triplicates  except for adult tail trunk that was in duplicate.,,pubmed:32912962,,12 somite 3,GSM4591057,,source name:12 somite stage|tissue:12 somite stage|rna fraction:size fractionated 20 40 nt whole cell RNA,12 somite 3,Library strategy: RiboMeth seq Barcode separation using python script Adaptor trimming using Cutadapt v. 2.0 Mapping to rRNA reference sequence using Bowtie2 v. 2.3.4.1 Counting read ends and calculating RiboMeth seq scores using python scripts The output FASTA files from small RNA seq were merged and used as the basis of the SNORD search and rRNA interaction prediction. Initially  SNORDs were identified by running the merged FASTA file through snoScan Schattner et al. 2005 against zebrafish early  and late rRNA reference sequences Locati et al. 2017. Genome build: early and late zebrafish rRNA locati et al. The reference sequences are available in the FASTA file on the series record. Supplementary files format and content: MS Excel file contains five prime and three prime read count and calculated RiboMeth seq score at all positions in the rRNA sequence.,12 somite stage,,Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. RiboMeth seq: 5 10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20 40 nt was purified on gels and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2' three prime cyclic phosphate and five prime phosphate ends. The library fragments were then sequenced on the Ion Proton platform. See Birkedal U  Christensen Dalsgaard M  Krogh N  Sabarinathan R  Gorodkin J  Nielsen H. Profiling of ribose methylations in RNA by high throughput sequencing. Angewandte Chemie. 2015;542:451 5 for detailed description,,tissue:12 somite stage|rna fraction:size fractionated 20 40 nt whole cell RNA,GSM4591057,GSM4591057: 12 somite 3; Danio rerio; OTHER,GSM4591057,,1,Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. RiboMeth seq: 5 10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20 40 nt was purified on gels and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2' three prime cyclic phosphate and five prime phosphate ends. The library fragments were then sequenced on the Ion Proton platform. See Birkedal U  Christensen Dalsgaard M  Krogh N  Sabarinathan R  Gorodkin J  Nielsen H. Profiling of ribose methylations in RNA by high throughput sequencing. Angewandte Chemie. 2015;542:451 5 for detailed description,GEO Accession:GSM4591057,OTHER,TRANSCRIPTOMIC,other,SINGLE,ION_TORRENT,Ion Torrent Proton,,SRP265951,,intentional duplicate,12_somite_3.bam GSE151797_Reference_sequence.fa,bam bam,105146264.0,3189309.0,GSM4591057 r1,0:32.97,A:24684898;C:33906144;G:26247070;T:20308152;N:0,32,,,,24684898,33906144,26247070,20308152,0,SRX8469989,SRS6770640,SRA1083099,GEO,"RNA Group - Prof. Henrik Nielsen, Department of Cellular and Molecular Medicine, University of Copenhagen",1,0.83304,,0.22816,,0.88325,,0.69597,,43,,B,,usable mapping rate,ion_torrent,ion_torrent,5prime,small_rna,unknown,bulk,unknown,unknown,,Denmark,2020-06-04,Segmentation,Embryo,Undetermined,Embryo Imprecise
59507,SRR11924314,SRX8469988,SRS6770639,SRP265951,PRJNA637293,The shift from early to late types of ribosomes in zebrafish development involves changes at a subset of rRNA 2' O Me sites,GSE151797,Other,A sequencing based profiling method RiboMeth seq for ribose methylations was used to study methylation patterns during Zebrafish Danio rerio development Overall design: All samples were analyzed in biological triplicates  except for adult tail trunk that was in duplicate.,,pubmed:32912962,,12 somite 2,GSM4591056,,source name:12 somite stage|tissue:12 somite stage|rna fraction:size fractionated 20 40 nt whole cell RNA,12 somite 2,Library strategy: RiboMeth seq Barcode separation using python script Adaptor trimming using Cutadapt v. 2.0 Mapping to rRNA reference sequence using Bowtie2 v. 2.3.4.1 Counting read ends and calculating RiboMeth seq scores using python scripts The output FASTA files from small RNA seq were merged and used as the basis of the SNORD search and rRNA interaction prediction. Initially  SNORDs were identified by running the merged FASTA file through snoScan Schattner et al. 2005 against zebrafish early  and late rRNA reference sequences Locati et al. 2017. Genome build: early and late zebrafish rRNA locati et al. The reference sequences are available in the FASTA file on the series record. Supplementary files format and content: MS Excel file contains five prime and three prime read count and calculated RiboMeth seq score at all positions in the rRNA sequence.,12 somite stage,,Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. RiboMeth seq: 5 10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20 40 nt was purified on gels and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2' three prime cyclic phosphate and five prime phosphate ends. The library fragments were then sequenced on the Ion Proton platform. See Birkedal U  Christensen Dalsgaard M  Krogh N  Sabarinathan R  Gorodkin J  Nielsen H. Profiling of ribose methylations in RNA by high throughput sequencing. Angewandte Chemie. 2015;542:451 5 for detailed description,,tissue:12 somite stage|rna fraction:size fractionated 20 40 nt whole cell RNA,GSM4591056,GSM4591056: 12 somite 2; Danio rerio; OTHER,GSM4591056,,1,Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. RiboMeth seq: 5 10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20 40 nt was purified on gels and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2' three prime cyclic phosphate and five prime phosphate ends. The library fragments were then sequenced on the Ion Proton platform. See Birkedal U  Christensen Dalsgaard M  Krogh N  Sabarinathan R  Gorodkin J  Nielsen H. Profiling of ribose methylations in RNA by high throughput sequencing. Angewandte Chemie. 2015;542:451 5 for detailed description,GEO Accession:GSM4591056,OTHER,TRANSCRIPTOMIC,other,SINGLE,ION_TORRENT,Ion Torrent Proton,,SRP265951,,intentional duplicate,12_somite_2.bam GSE151797_Reference_sequence.fa,bam bam,255844263.0,7971494.0,GSM4591056 r1,0:32.09,A:53703561;C:85057062;G:64342817;T:52740823;N:0,32,,,,53703561,85057062,64342817,52740823,0,SRX8469988,SRS6770639,SRA1083099,GEO,"RNA Group - Prof. Henrik Nielsen, Department of Cellular and Molecular Medicine, University of Copenhagen",1,0.79601,,0.23342,,0.90281,,0.75464,,40,,B,,usable mapping rate,ion_torrent,ion_torrent,5prime,small_rna,unknown,bulk,unknown,unknown,,Denmark,2020-06-04,Segmentation,Embryo,Undetermined,Embryo Imprecise
59508,SRR11924312,SRX8469987,SRS6770638,SRP265951,PRJNA637293,The shift from early to late types of ribosomes in zebrafish development involves changes at a subset of rRNA 2' O Me sites,GSE151797,Other,A sequencing based profiling method RiboMeth seq for ribose methylations was used to study methylation patterns during Zebrafish Danio rerio development Overall design: All samples were analyzed in biological triplicates  except for adult tail trunk that was in duplicate.,,pubmed:32912962,,12 somite 1,GSM4591055,,source name:12 somite stage|tissue:12 somite stage|rna fraction:size fractionated 20 40 nt whole cell RNA,12 somite 1,Library strategy: RiboMeth seq Barcode separation using python script Adaptor trimming using Cutadapt v. 2.0 Mapping to rRNA reference sequence using Bowtie2 v. 2.3.4.1 Counting read ends and calculating RiboMeth seq scores using python scripts The output FASTA files from small RNA seq were merged and used as the basis of the SNORD search and rRNA interaction prediction. Initially  SNORDs were identified by running the merged FASTA file through snoScan Schattner et al. 2005 against zebrafish early  and late rRNA reference sequences Locati et al. 2017. Genome build: early and late zebrafish rRNA locati et al. The reference sequences are available in the FASTA file on the series record. Supplementary files format and content: MS Excel file contains five prime and three prime read count and calculated RiboMeth seq score at all positions in the rRNA sequence.,12 somite stage,,Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. RiboMeth seq: 5 10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20 40 nt was purified on gels and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2' three prime cyclic phosphate and five prime phosphate ends. The library fragments were then sequenced on the Ion Proton platform. See Birkedal U  Christensen Dalsgaard M  Krogh N  Sabarinathan R  Gorodkin J  Nielsen H. Profiling of ribose methylations in RNA by high throughput sequencing. Angewandte Chemie. 2015;542:451 5 for detailed description,,tissue:12 somite stage|rna fraction:size fractionated 20 40 nt whole cell RNA,GSM4591055,GSM4591055: 12 somite 1; Danio rerio; OTHER,GSM4591055,,1,Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. RiboMeth seq: 5 10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20 40 nt was purified on gels and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2' three prime cyclic phosphate and five prime phosphate ends. The library fragments were then sequenced on the Ion Proton platform. See Birkedal U  Christensen Dalsgaard M  Krogh N  Sabarinathan R  Gorodkin J  Nielsen H. Profiling of ribose methylations in RNA by high throughput sequencing. Angewandte Chemie. 2015;542:451 5 for detailed description,GEO Accession:GSM4591055,OTHER,TRANSCRIPTOMIC,other,SINGLE,ION_TORRENT,Ion Torrent Proton,,SRP265951,,intentional duplicate,12_somite_1.bam GSE151797_Reference_sequence.fa,bam bam,254000103.0,7990851.0,GSM4591055 r1,0:31.79,A:52359510;C:82090735;G:62850013;T:56699845;N:0,31,,,,52359510,82090735,62850013,56699845,0,SRX8469987,SRS6770638,SRA1083099,GEO,"RNA Group - Prof. Henrik Nielsen, Department of Cellular and Molecular Medicine, University of Copenhagen",1,0.69554,,0.21063,,0.88284,,0.72326,,43,,B,,usable mapping rate,ion_torrent,ion_torrent,5prime,small_rna,unknown,bulk,unknown,unknown,,Denmark,2020-06-04,Segmentation,Embryo,Undetermined,Embryo Imprecise
59509,SRR11924311,SRX8469986,SRS6770637,SRP265951,PRJNA637293,The shift from early to late types of ribosomes in zebrafish development involves changes at a subset of rRNA 2' O Me sites,GSE151797,Other,A sequencing based profiling method RiboMeth seq for ribose methylations was used to study methylation patterns during Zebrafish Danio rerio development Overall design: All samples were analyzed in biological triplicates  except for adult tail trunk that was in duplicate.,,pubmed:32912962,,32 cell 3,GSM4591054,,source name:32 cell stage|tissue:32 cell stage|rna fraction:size fractionated 20 40 nt whole cell RNA,32 cell 3,Library strategy: RiboMeth seq Barcode separation using python script Adaptor trimming using Cutadapt v. 2.0 Mapping to rRNA reference sequence using Bowtie2 v. 2.3.4.1 Counting read ends and calculating RiboMeth seq scores using python scripts The output FASTA files from small RNA seq were merged and used as the basis of the SNORD search and rRNA interaction prediction. Initially  SNORDs were identified by running the merged FASTA file through snoScan Schattner et al. 2005 against zebrafish early  and late rRNA reference sequences Locati et al. 2017. Genome build: early and late zebrafish rRNA locati et al. The reference sequences are available in the FASTA file on the series record. Supplementary files format and content: MS Excel file contains five prime and three prime read count and calculated RiboMeth seq score at all positions in the rRNA sequence.,32 cell stage,,Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. RiboMeth seq: 5 10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20 40 nt was purified on gels and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2' three prime cyclic phosphate and five prime phosphate ends. The library fragments were then sequenced on the Ion Proton platform. See Birkedal U  Christensen Dalsgaard M  Krogh N  Sabarinathan R  Gorodkin J  Nielsen H. Profiling of ribose methylations in RNA by high throughput sequencing. Angewandte Chemie. 2015;542:451 5 for detailed description,,tissue:32 cell stage|rna fraction:size fractionated 20 40 nt whole cell RNA,GSM4591054,GSM4591054: 32 cell 3; Danio rerio; OTHER,GSM4591054,,1,Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. RiboMeth seq: 5 10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20 40 nt was purified on gels and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2' three prime cyclic phosphate and five prime phosphate ends. The library fragments were then sequenced on the Ion Proton platform. See Birkedal U  Christensen Dalsgaard M  Krogh N  Sabarinathan R  Gorodkin J  Nielsen H. Profiling of ribose methylations in RNA by high throughput sequencing. Angewandte Chemie. 2015;542:451 5 for detailed description,GEO Accession:GSM4591054,OTHER,TRANSCRIPTOMIC,other,SINGLE,ION_TORRENT,Ion Torrent Proton,,SRP265951,,intentional duplicate,32_cell_3.bam GSE151797_Reference_sequence.fa,bam bam,306452866.0,9472058.0,GSM4591054 r1,0:32.35,A:62923439;C:99486553;G:78734118;T:65308756;N:0,32,,,,62923439,99486553,78734118,65308756,0,SRX8469986,SRS6770637,SRA1083099,GEO,"RNA Group - Prof. Henrik Nielsen, Department of Cellular and Molecular Medicine, University of Copenhagen",1,0.69616,,0.21356,,0.91885,,0.77399,,44,,B,,usable mapping rate,ion_torrent,ion_torrent,5prime,small_rna,unknown,bulk,unknown,unknown,,Denmark,2020-06-04,Cleavage,Embryo,Undetermined,Embryo Imprecise
59510,SRR11924310,SRX8469985,SRS6770636,SRP265951,PRJNA637293,The shift from early to late types of ribosomes in zebrafish development involves changes at a subset of rRNA 2' O Me sites,GSE151797,Other,A sequencing based profiling method RiboMeth seq for ribose methylations was used to study methylation patterns during Zebrafish Danio rerio development Overall design: All samples were analyzed in biological triplicates  except for adult tail trunk that was in duplicate.,,pubmed:32912962,,32 cell 2,GSM4591053,,source name:32 cell stage|tissue:32 cell stage|rna fraction:size fractionated 20 40 nt whole cell RNA,32 cell 2,Library strategy: RiboMeth seq Barcode separation using python script Adaptor trimming using Cutadapt v. 2.0 Mapping to rRNA reference sequence using Bowtie2 v. 2.3.4.1 Counting read ends and calculating RiboMeth seq scores using python scripts The output FASTA files from small RNA seq were merged and used as the basis of the SNORD search and rRNA interaction prediction. Initially  SNORDs were identified by running the merged FASTA file through snoScan Schattner et al. 2005 against zebrafish early  and late rRNA reference sequences Locati et al. 2017. Genome build: early and late zebrafish rRNA locati et al. The reference sequences are available in the FASTA file on the series record. Supplementary files format and content: MS Excel file contains five prime and three prime read count and calculated RiboMeth seq score at all positions in the rRNA sequence.,32 cell stage,,Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. RiboMeth seq: 5 10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20 40 nt was purified on gels and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2' three prime cyclic phosphate and five prime phosphate ends. The library fragments were then sequenced on the Ion Proton platform. See Birkedal U  Christensen Dalsgaard M  Krogh N  Sabarinathan R  Gorodkin J  Nielsen H. Profiling of ribose methylations in RNA by high throughput sequencing. Angewandte Chemie. 2015;542:451 5 for detailed description,,tissue:32 cell stage|rna fraction:size fractionated 20 40 nt whole cell RNA,GSM4591053,GSM4591053: 32 cell 2; Danio rerio; OTHER,GSM4591053,,1,Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. RiboMeth seq: 5 10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20 40 nt was purified on gels and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2' three prime cyclic phosphate and five prime phosphate ends. The library fragments were then sequenced on the Ion Proton platform. See Birkedal U  Christensen Dalsgaard M  Krogh N  Sabarinathan R  Gorodkin J  Nielsen H. Profiling of ribose methylations in RNA by high throughput sequencing. Angewandte Chemie. 2015;542:451 5 for detailed description,GEO Accession:GSM4591053,OTHER,TRANSCRIPTOMIC,other,SINGLE,ION_TORRENT,Ion Torrent Proton,,SRP265951,,intentional duplicate,32_cell_2.bam GSE151797_Reference_sequence.fa,bam bam,231900531.0,6985149.0,GSM4591053 r1,0:33.20,A:46033127;C:77390842;G:61355372;T:47121190;N:0,33,,,,46033127,77390842,61355372,47121190,0,SRX8469985,SRS6770636,SRA1083099,GEO,"RNA Group - Prof. Henrik Nielsen, Department of Cellular and Molecular Medicine, University of Copenhagen",1,0.83429,,0.25864,,0.9137,,0.78928,,39,,B,,usable mapping rate,ion_torrent,ion_torrent,5prime,small_rna,unknown,bulk,unknown,unknown,,Denmark,2020-06-04,Cleavage,Embryo,Undetermined,Embryo Imprecise
59511,SRR11924308,SRX8469984,SRS6770635,SRP265951,PRJNA637293,The shift from early to late types of ribosomes in zebrafish development involves changes at a subset of rRNA 2' O Me sites,GSE151797,Other,A sequencing based profiling method RiboMeth seq for ribose methylations was used to study methylation patterns during Zebrafish Danio rerio development Overall design: All samples were analyzed in biological triplicates  except for adult tail trunk that was in duplicate.,,pubmed:32912962,,32 cell 1,GSM4591052,,source name:32 cell stage|tissue:32 cell stage|rna fraction:size fractionated 20 40 nt whole cell RNA,32 cell 1,Library strategy: RiboMeth seq Barcode separation using python script Adaptor trimming using Cutadapt v. 2.0 Mapping to rRNA reference sequence using Bowtie2 v. 2.3.4.1 Counting read ends and calculating RiboMeth seq scores using python scripts The output FASTA files from small RNA seq were merged and used as the basis of the SNORD search and rRNA interaction prediction. Initially  SNORDs were identified by running the merged FASTA file through snoScan Schattner et al. 2005 against zebrafish early  and late rRNA reference sequences Locati et al. 2017. Genome build: early and late zebrafish rRNA locati et al. The reference sequences are available in the FASTA file on the series record. Supplementary files format and content: MS Excel file contains five prime and three prime read count and calculated RiboMeth seq score at all positions in the rRNA sequence.,32 cell stage,,Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. RiboMeth seq: 5 10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20 40 nt was purified on gels and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2' three prime cyclic phosphate and five prime phosphate ends. The library fragments were then sequenced on the Ion Proton platform. See Birkedal U  Christensen Dalsgaard M  Krogh N  Sabarinathan R  Gorodkin J  Nielsen H. Profiling of ribose methylations in RNA by high throughput sequencing. Angewandte Chemie. 2015;542:451 5 for detailed description,,tissue:32 cell stage|rna fraction:size fractionated 20 40 nt whole cell RNA,GSM4591052,GSM4591052: 32 cell 1; Danio rerio; OTHER,GSM4591052,,1,Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. RiboMeth seq: 5 10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20 40 nt was purified on gels and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2' three prime cyclic phosphate and five prime phosphate ends. The library fragments were then sequenced on the Ion Proton platform. See Birkedal U  Christensen Dalsgaard M  Krogh N  Sabarinathan R  Gorodkin J  Nielsen H. Profiling of ribose methylations in RNA by high throughput sequencing. Angewandte Chemie. 2015;542:451 5 for detailed description,GEO Accession:GSM4591052,OTHER,TRANSCRIPTOMIC,other,SINGLE,ION_TORRENT,Ion Torrent Proton,,SRP265951,,intentional duplicate,32_cell_1.bam GSE151797_Reference_sequence.fa,bam bam,252107732.0,7470443.0,GSM4591052 r1,0:33.75,A:53056857;C:79089015;G:65131744;T:54830116;N:0,33,,,,53056857,79089015,65131744,54830116,0,SRX8469984,SRS6770635,SRA1083099,GEO,"RNA Group - Prof. Henrik Nielsen, Department of Cellular and Molecular Medicine, University of Copenhagen",1,0.78874,,0.25062,,0.89645,,0.73533,,48,,B,,usable mapping rate,ion_torrent,ion_torrent,5prime,small_rna,unknown,bulk,unknown,unknown,,Denmark,2020-06-04,Cleavage,Embryo,Undetermined,Embryo Imprecise
59512,SRR11924307,SRX8469983,SRS6770634,SRP265951,PRJNA637293,The shift from early to late types of ribosomes in zebrafish development involves changes at a subset of rRNA 2' O Me sites,GSE151797,Other,A sequencing based profiling method RiboMeth seq for ribose methylations was used to study methylation patterns during Zebrafish Danio rerio development Overall design: All samples were analyzed in biological triplicates  except for adult tail trunk that was in duplicate.,,pubmed:32912962,,Unf egg 3,GSM4591051,,source name:unfertilized egg|tissue:unfertilized egg|rna fraction:size fractionated 20 40 nt whole cell RNA,Unf egg 3,Library strategy: RiboMeth seq Barcode separation using python script Adaptor trimming using Cutadapt v. 2.0 Mapping to rRNA reference sequence using Bowtie2 v. 2.3.4.1 Counting read ends and calculating RiboMeth seq scores using python scripts The output FASTA files from small RNA seq were merged and used as the basis of the SNORD search and rRNA interaction prediction. Initially  SNORDs were identified by running the merged FASTA file through snoScan Schattner et al. 2005 against zebrafish early  and late rRNA reference sequences Locati et al. 2017. Genome build: early and late zebrafish rRNA locati et al. The reference sequences are available in the FASTA file on the series record. Supplementary files format and content: MS Excel file contains five prime and three prime read count and calculated RiboMeth seq score at all positions in the rRNA sequence.,unfertilized egg,,Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. RiboMeth seq: 5 10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20 40 nt was purified on gels and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2' three prime cyclic phosphate and five prime phosphate ends. The library fragments were then sequenced on the Ion Proton platform. See Birkedal U  Christensen Dalsgaard M  Krogh N  Sabarinathan R  Gorodkin J  Nielsen H. Profiling of ribose methylations in RNA by high throughput sequencing. Angewandte Chemie. 2015;542:451 5 for detailed description,,tissue:unfertilized egg|rna fraction:size fractionated 20 40 nt whole cell RNA,GSM4591051,GSM4591051: Unf egg 3; Danio rerio; OTHER,GSM4591051,,1,Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. RiboMeth seq: 5 10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20 40 nt was purified on gels and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2' three prime cyclic phosphate and five prime phosphate ends. The library fragments were then sequenced on the Ion Proton platform. See Birkedal U  Christensen Dalsgaard M  Krogh N  Sabarinathan R  Gorodkin J  Nielsen H. Profiling of ribose methylations in RNA by high throughput sequencing. Angewandte Chemie. 2015;542:451 5 for detailed description,GEO Accession:GSM4591051,OTHER,TRANSCRIPTOMIC,other,SINGLE,ION_TORRENT,Ion Torrent Proton,,SRP265951,,intentional duplicate,GSE151797_Reference_sequence.fa Unf_egg_3.bam,bam bam,149835556.0,5777340.0,GSM4591051 r1,0:25.94,A:27873539;C:50837956;G:37710769;T:33413292;N:0,25,,,,27873539,50837956,37710769,33413292,0,SRX8469983,SRS6770634,SRA1083099,GEO,"RNA Group - Prof. Henrik Nielsen, Department of Cellular and Molecular Medicine, University of Copenhagen",1,0.74561,,0.22616,,0.89441,,0.76897,,34,,B,,usable mapping rate,ion_torrent,ion_torrent,5prime,small_rna,unknown,bulk,unknown,unknown,,Denmark,2020-06-04,Zygote,Embryo,Oocyte,Reproductive System
59513,SRR11924305,SRX8469982,SRS6770633,SRP265951,PRJNA637293,The shift from early to late types of ribosomes in zebrafish development involves changes at a subset of rRNA 2' O Me sites,GSE151797,Other,A sequencing based profiling method RiboMeth seq for ribose methylations was used to study methylation patterns during Zebrafish Danio rerio development Overall design: All samples were analyzed in biological triplicates  except for adult tail trunk that was in duplicate.,,pubmed:32912962,,Unf egg 2,GSM4591050,,source name:unfertilized egg|tissue:unfertilized egg|rna fraction:size fractionated 20 40 nt whole cell RNA,Unf egg 2,Library strategy: RiboMeth seq Barcode separation using python script Adaptor trimming using Cutadapt v. 2.0 Mapping to rRNA reference sequence using Bowtie2 v. 2.3.4.1 Counting read ends and calculating RiboMeth seq scores using python scripts The output FASTA files from small RNA seq were merged and used as the basis of the SNORD search and rRNA interaction prediction. Initially  SNORDs were identified by running the merged FASTA file through snoScan Schattner et al. 2005 against zebrafish early  and late rRNA reference sequences Locati et al. 2017. Genome build: early and late zebrafish rRNA locati et al. The reference sequences are available in the FASTA file on the series record. Supplementary files format and content: MS Excel file contains five prime and three prime read count and calculated RiboMeth seq score at all positions in the rRNA sequence.,unfertilized egg,,Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. RiboMeth seq: 5 10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20 40 nt was purified on gels and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2' three prime cyclic phosphate and five prime phosphate ends. The library fragments were then sequenced on the Ion Proton platform. See Birkedal U  Christensen Dalsgaard M  Krogh N  Sabarinathan R  Gorodkin J  Nielsen H. Profiling of ribose methylations in RNA by high throughput sequencing. Angewandte Chemie. 2015;542:451 5 for detailed description,,tissue:unfertilized egg|rna fraction:size fractionated 20 40 nt whole cell RNA,GSM4591050,GSM4591050: Unf egg 2; Danio rerio; OTHER,GSM4591050,,1,Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. RiboMeth seq: 5 10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20 40 nt was purified on gels and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2' three prime cyclic phosphate and five prime phosphate ends. The library fragments were then sequenced on the Ion Proton platform. See Birkedal U  Christensen Dalsgaard M  Krogh N  Sabarinathan R  Gorodkin J  Nielsen H. Profiling of ribose methylations in RNA by high throughput sequencing. Angewandte Chemie. 2015;542:451 5 for detailed description,GEO Accession:GSM4591050,OTHER,TRANSCRIPTOMIC,other,SINGLE,ION_TORRENT,Ion Torrent Proton,,SRP265951,,intentional duplicate,GSE151797_Reference_sequence.fa Unf_egg_2.bam,bam bam,235014832.0,8915586.0,GSM4591050 r1,0:26.36,A:43825969;C:79775479;G:60531219;T:50882165;N:0,26,,,,43825969,79775479,60531219,50882165,0,SRX8469982,SRS6770633,SRA1083099,GEO,"RNA Group - Prof. Henrik Nielsen, Department of Cellular and Molecular Medicine, University of Copenhagen",1,0.78414,,0.23044,,0.90352,,0.76934,,40,,B,,usable mapping rate,ion_torrent,ion_torrent,5prime,small_rna,unknown,bulk,unknown,unknown,,Denmark,2020-06-04,Zygote,Embryo,Oocyte,Reproductive System
59514,SRR11924304,SRX8469981,SRS6770632,SRP265951,PRJNA637293,The shift from early to late types of ribosomes in zebrafish development involves changes at a subset of rRNA 2' O Me sites,GSE151797,Other,A sequencing based profiling method RiboMeth seq for ribose methylations was used to study methylation patterns during Zebrafish Danio rerio development Overall design: All samples were analyzed in biological triplicates  except for adult tail trunk that was in duplicate.,,pubmed:32912962,,Unf egg 1,GSM4591049,,source name:unfertilized egg|tissue:unfertilized egg|rna fraction:size fractionated 20 40 nt whole cell RNA,Unf egg 1,Library strategy: RiboMeth seq Barcode separation using python script Adaptor trimming using Cutadapt v. 2.0 Mapping to rRNA reference sequence using Bowtie2 v. 2.3.4.1 Counting read ends and calculating RiboMeth seq scores using python scripts The output FASTA files from small RNA seq were merged and used as the basis of the SNORD search and rRNA interaction prediction. Initially  SNORDs were identified by running the merged FASTA file through snoScan Schattner et al. 2005 against zebrafish early  and late rRNA reference sequences Locati et al. 2017. Genome build: early and late zebrafish rRNA locati et al. The reference sequences are available in the FASTA file on the series record. Supplementary files format and content: MS Excel file contains five prime and three prime read count and calculated RiboMeth seq score at all positions in the rRNA sequence.,unfertilized egg,,Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. RiboMeth seq: 5 10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20 40 nt was purified on gels and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2' three prime cyclic phosphate and five prime phosphate ends. The library fragments were then sequenced on the Ion Proton platform. See Birkedal U  Christensen Dalsgaard M  Krogh N  Sabarinathan R  Gorodkin J  Nielsen H. Profiling of ribose methylations in RNA by high throughput sequencing. Angewandte Chemie. 2015;542:451 5 for detailed description,,tissue:unfertilized egg|rna fraction:size fractionated 20 40 nt whole cell RNA,GSM4591049,GSM4591049: Unf egg 1; Danio rerio; OTHER,GSM4591049,,1,Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. RiboMeth seq: 5 10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20 40 nt was purified on gels and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2' three prime cyclic phosphate and five prime phosphate ends. The library fragments were then sequenced on the Ion Proton platform. See Birkedal U  Christensen Dalsgaard M  Krogh N  Sabarinathan R  Gorodkin J  Nielsen H. Profiling of ribose methylations in RNA by high throughput sequencing. Angewandte Chemie. 2015;542:451 5 for detailed description,GEO Accession:GSM4591049,OTHER,TRANSCRIPTOMIC,other,SINGLE,ION_TORRENT,Ion Torrent Proton,,SRP265951,,intentional duplicate,GSE151797_Reference_sequence.fa Unf_egg_1.bam,bam bam,245529952.0,9182415.0,GSM4591049 r1,0:26.74,A:46557080;C:80893860;G:66050448;T:52028564;N:0,26,,,,46557080,80893860,66050448,52028564,0,SRX8469981,SRS6770632,SRA1083099,GEO,"RNA Group - Prof. Henrik Nielsen, Department of Cellular and Molecular Medicine, University of Copenhagen",1,0.87423,,0.27943,,0.91721,,0.76816,,37,,B,,usable mapping rate,ion_torrent,ion_torrent,5prime,small_rna,unknown,bulk,unknown,unknown,,Denmark,2020-06-04,Zygote,Embryo,Oocyte,Reproductive System