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144 rows where devstage_curation_coarse = "Undetermined" and tissue_curation_coarse = "Surface Structure"

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experiment.library_selection 5

tissue_curation 4

technology 4

experiment.platform 2

experiment.library_source 2

experiment.library_layout 2

tissue_curation_coarse 1

  • Surface Structure · 144 ✖

experiment.library_strategy 1

devstage_curation_coarse 1

  • Undetermined · 144 ✖

devstage_curation 1

Link 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
95 95 DRR050167 DRX045209 DRS025834 DRP003043 PRJDB4416 Transcriptome analysis in ES1 expressing rods of zebrafish DRP003043 Transcriptome Analysis Transcriptome analysis using next generation sequencing system for isolated rods from zebrafish of wild type T?bingen long fin TL line. Transgenic zebrafish expressing ES1 and/or EGFP in rods were used.     Zebrafish rods expressing ES1 and EGFP ES1 3 SAMD00044057   sample name:ES1 EGFP rod 003|strain:Tubingen long fin|cell type:rod                 Ion Torrent PGM sequencing of SAMD00044057 DRX045209 1 1 1   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ION_TORRENT Ion Torrent PGM <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>105</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> DRP003043 Ion Torrent PGM sequencing of SAMD00044057       371748120.0 3469843.0 DRR050167 0:107.14 A:107190409;C:79475572;G:83520360;T:101561779;N:0 107       107190409 79475572 83520360 101561779 0 DRX045209 DRS025834 DRA004229 OSAKA_FB|Kawamura lab., Frontier Biology, Osaka univ. Osaka university 1 0.81026   0.26715   0.86953   0.52321   51   B   usable mapping rate ion_torrent ion_torrent unknown cdna_unspecified unknown bulk unknown unknown   Japan 2016-03-09 Undetermined Undetermined Fin Surface Structure
96 96 DRR050166 DRX045208 DRS025833 DRP003043 PRJDB4416 Transcriptome analysis in ES1 expressing rods of zebrafish DRP003043 Transcriptome Analysis Transcriptome analysis using next generation sequencing system for isolated rods from zebrafish of wild type T?bingen long fin TL line. Transgenic zebrafish expressing ES1 and/or EGFP in rods were used.     Zebrafish rods expressing ES1 and EGFP ES1 2 SAMD00044056   sample name:ES1 EGFP rod 002|strain:Tubingen long fin|cell type:rod                 Ion Torrent PGM sequencing of SAMD00044056 DRX045208 1 1 1   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ION_TORRENT Ion Torrent PGM <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>128</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> DRP003043 Ion Torrent PGM sequencing of SAMD00044056       425549011.0 3275261.0 DRR050166 0:129.93 A:126640704;C:86415371;G:90822163;T:121670773;N:0 129       126640704 86415371 90822163 121670773 0 DRX045208 DRS025833 DRA004229 OSAKA_FB|Kawamura lab., Frontier Biology, Osaka univ. Osaka university 1 0.80223   0.31429   0.85861   0.5272   57   B   usable mapping rate ion_torrent ion_torrent unknown cdna_unspecified unknown bulk unknown unknown   Japan 2016-03-09 Undetermined Undetermined Fin Surface Structure
97 97 DRR050165 DRX045207 DRS025832 DRP003043 PRJDB4416 Transcriptome analysis in ES1 expressing rods of zebrafish DRP003043 Transcriptome Analysis Transcriptome analysis using next generation sequencing system for isolated rods from zebrafish of wild type T?bingen long fin TL line. Transgenic zebrafish expressing ES1 and/or EGFP in rods were used.     Zebrafish rods expressing ES1 and EGFP ES1 1 SAMD00044055   sample name:ES1 EGFP rod 001|strain:Tubingen long fin|cell type:rod                 Ion Torrent PGM sequencing of SAMD00044055 DRX045207 1 1 1   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ION_TORRENT Ion Torrent PGM <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>147</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> DRP003043 Ion Torrent PGM sequencing of SAMD00044055       584599765.0 3941083.0 DRR050165 0:148.33 A:164329030;C:129885620;G:136727379;T:153657736;N:0 148       164329030 129885620 136727379 153657736 0 DRX045207 DRS025832 DRA004229 OSAKA_FB|Kawamura lab., Frontier Biology, Osaka univ. Osaka university 1 0.83769   0.25395   0.83116   0.52784   185   B   usable mapping rate ion_torrent ion_torrent unknown cdna_unspecified unknown bulk unknown unknown   Japan 2016-03-09 Undetermined Undetermined Fin Surface Structure
98 98 DRR050164 DRX045206 DRS025831 DRP003043 PRJDB4416 Transcriptome analysis in ES1 expressing rods of zebrafish DRP003043 Transcriptome Analysis Transcriptome analysis using next generation sequencing system for isolated rods from zebrafish of wild type T?bingen long fin TL line. Transgenic zebrafish expressing ES1 and/or EGFP in rods were used.     Zebrafish rods expressing EGFP EGFP 3 SAMD00044054   sample name:EGFP rod 003|strain:Tubingen long fin|cell type:rod                 Ion Torrent PGM sequencing of SAMD00044054 DRX045206 1 1 1   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ION_TORRENT Ion Torrent PGM <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>88</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> DRP003043 Ion Torrent PGM sequencing of SAMD00044054       343014114.0 3827762.0 DRR050164 0:89.61 A:99421434;C:73070267;G:77738821;T:92783592;N:0 89       99421434 73070267 77738821 92783592 0 DRX045206 DRS025831 DRA004229 OSAKA_FB|Kawamura lab., Frontier Biology, Osaka univ. Osaka university 1 0.78953   0.25529   0.87367   0.52148   24   B   usable mapping rate ion_torrent ion_torrent unknown cdna_unspecified unknown bulk unknown unknown   Japan 2016-03-09 Undetermined Undetermined Fin Surface Structure
99 99 DRR050163 DRX045205 DRS025830 DRP003043 PRJDB4416 Transcriptome analysis in ES1 expressing rods of zebrafish DRP003043 Transcriptome Analysis Transcriptome analysis using next generation sequencing system for isolated rods from zebrafish of wild type T?bingen long fin TL line. Transgenic zebrafish expressing ES1 and/or EGFP in rods were used.     Zebrafish rods expressing EGFP EGFP 2 SAMD00044053   sample name:EGFP rod 002|strain:Tubingen long fin|cell type:rod                 Ion Torrent PGM sequencing of SAMD00044053 DRX045205 1 1 1   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ION_TORRENT Ion Torrent PGM <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>137</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> DRP003043 Ion Torrent PGM sequencing of SAMD00044053       533069427.0 3824140.0 DRR050163 0:139.40 A:152608173;C:113928273;G:120051739;T:146481242;N:0 139       152608173 113928273 120051739 146481242 0 DRX045205 DRS025830 DRA004229 OSAKA_FB|Kawamura lab., Frontier Biology, Osaka univ. Osaka university 1 0.80412   0.26768   0.85338   0.52255   245   B   usable mapping rate ion_torrent ion_torrent unknown cdna_unspecified unknown bulk unknown unknown   Japan 2016-03-09 Undetermined Undetermined Fin Surface Structure
100 100 DRR050162 DRX045204 DRS025829 DRP003043 PRJDB4416 Transcriptome analysis in ES1 expressing rods of zebrafish DRP003043 Transcriptome Analysis Transcriptome analysis using next generation sequencing system for isolated rods from zebrafish of wild type T?bingen long fin TL line. Transgenic zebrafish expressing ES1 and/or EGFP in rods were used.     Zebrafish rods expressing EGFP EGFP 1 SAMD00044052   sample name:EGFP rod 001|strain:Tubingen long fin|cell type:rod                 Ion Torrent PGM sequencing of SAMD00044052 DRX045204 1 1 1   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ION_TORRENT Ion Torrent PGM <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>113</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> DRP003043 Ion Torrent PGM sequencing of SAMD00044052       478262965.0 4224064.0 DRR050162 0:113.22 A:136348264;C:104872341;G:113114502;T:123927858;N:0 113       136348264 104872341 113114502 123927858 0 DRX045204 DRS025829 DRA004229 OSAKA_FB|Kawamura lab., Frontier Biology, Osaka univ. Osaka university 1 0.86947   0.29839   0.83317   0.51453   80   B   usable mapping rate ion_torrent ion_torrent unknown cdna_unspecified unknown bulk unknown unknown   Japan 2016-03-09 Undetermined Undetermined Fin Surface Structure
11148 11148 ERR10034072 ERX9574476 ERS12562187 ERP140005 PRJEB55122 Danio developmental transcriptomes ca4a518e-aaf7-42d9-9758-352aac808809 Other Transcriptomic analysis of four different developmental stages of four Danio species D. rerio D. aesculapii Danio aff. kyathit striped also known as Danio quagga and D. albolineatus. Five biological replicates were sampled for every developmental stage of a species. ENA FIRST PUBLIC:2022 08 05|ENA LAST UPDATE:2022 08 08   Metamorphic tissue without xxx from Danio rerio Drerio metamorphic 5 SAMEA110464159 max planck institute for biology ENA FIRST PUBLIC:2022 08 08|ENA LAST UPDATE:2022 08 08|External Id:SAMEA110464159|INSDC center alias:MAX PLANCK INSTITUTE FOR BIOLOGY|INSDC center name:max planck institute for biology|INSDC first public:2022 08 08T04:26:46Z|INSDC last update:2022 08 08T04:26:46Z|INSDC status:public|Submitter Id:SAMPLE25|collected by:Marco Podobnik|collection date:2018 06 27|common name:zebrafish|dev stage:Metamorphic|identified by:Marco Podobnik|sample name:SAMPLE25|sex:not provided|tissue type:whole body without xxx                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 05 08 2022 14:25:08:835 19178 unspecified 1 Illumina TruSeq DNA Nano Kit   RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   ERP140005 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2022 08 08|ENA LAST UPDATE:2022 08 08 S879Nr25.1.fastq.gz S879Nr25.2.fastq.gz fastq fastq 10120435126.0 50403985.0 ena RUN TAB 05 08 2022 14:25:08:835 19179 0:100.39 1:100.39 A:2679131890;C:2420708190;G:2483153503;T:2537307238;N:134305 100 100     2679131890 2420708190 2483153503 2537307238 134305 ERX9574476 ERS12562187 ERA16814395 max planck institute for biology|European Nucleotide Archive max planck institute for biology 2 0.96973 0.97106 0.04979 0.04949 0.71252 0.71654 0.4806 0.49338 101 101 B B biological fallback assumption illumina novaseq_era unknown poly_a trueseq bulk unknown unknown   Germany 2022-08-05 Undetermined Undetermined Trunk Surface Structure
11149 11149 ERR10034071 ERX9574475 ERS12562186 ERP140005 PRJEB55122 Danio developmental transcriptomes ca4a518e-aaf7-42d9-9758-352aac808809 Other Transcriptomic analysis of four different developmental stages of four Danio species D. rerio D. aesculapii Danio aff. kyathit striped also known as Danio quagga and D. albolineatus. Five biological replicates were sampled for every developmental stage of a species. ENA FIRST PUBLIC:2022 08 05|ENA LAST UPDATE:2022 08 08   Metamorphic tissue without xxx from Danio rerio Drerio metamorphic 4 SAMEA110464158 max planck institute for biology ENA FIRST PUBLIC:2022 08 08|ENA LAST UPDATE:2022 08 08|External Id:SAMEA110464158|INSDC center alias:MAX PLANCK INSTITUTE FOR BIOLOGY|INSDC center name:max planck institute for biology|INSDC first public:2022 08 08T04:26:46Z|INSDC last update:2022 08 08T04:26:46Z|INSDC status:public|Submitter Id:SAMPLE24|collected by:Marco Podobnik|collection date:2018 06 27|common name:zebrafish|dev stage:Metamorphic|identified by:Marco Podobnik|sample name:SAMPLE24|sex:not provided|tissue type:whole body without xxx                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 05 08 2022 14:25:08:835 19176 unspecified 1 Illumina TruSeq DNA Nano Kit   RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   ERP140005 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2022 08 08|ENA LAST UPDATE:2022 08 08 S879Nr24.1.fastq.gz S879Nr24.2.fastq.gz fastq fastq 7845661906.0 39121993.0 ena RUN TAB 05 08 2022 14:25:08:835 19177 0:100.27 1:100.27 A:2096079479;C:1862247618;G:1929220494;T:1958006859;N:107456 100 100     2096079479 1862247618 1929220494 1958006859 107456 ERX9574475 ERS12562186 ERA16814395 max planck institute for biology|European Nucleotide Archive max planck institute for biology 2 0.96989 0.96986 0.04901 0.04902 0.71599 0.72301 0.48965 0.48827 101 101 B B biological fallback assumption illumina novaseq_era unknown poly_a trueseq bulk unknown unknown   Germany 2022-08-05 Undetermined Undetermined Trunk Surface Structure
11150 11150 ERR10034070 ERX9574474 ERS12562185 ERP140005 PRJEB55122 Danio developmental transcriptomes ca4a518e-aaf7-42d9-9758-352aac808809 Other Transcriptomic analysis of four different developmental stages of four Danio species D. rerio D. aesculapii Danio aff. kyathit striped also known as Danio quagga and D. albolineatus. Five biological replicates were sampled for every developmental stage of a species. ENA FIRST PUBLIC:2022 08 05|ENA LAST UPDATE:2022 08 08   Metamorphic tissue without xxx from Danio rerio Drerio metamorphic 3 SAMEA110464157 max planck institute for biology ENA FIRST PUBLIC:2022 08 08|ENA LAST UPDATE:2022 08 08|External Id:SAMEA110464157|INSDC center alias:MAX PLANCK INSTITUTE FOR BIOLOGY|INSDC center name:max planck institute for biology|INSDC first public:2022 08 08T04:26:46Z|INSDC last update:2022 08 08T04:26:46Z|INSDC status:public|Submitter Id:SAMPLE23|collected by:Marco Podobnik|collection date:2018 06 27|common name:zebrafish|dev stage:Metamorphic|identified by:Marco Podobnik|sample name:SAMPLE23|sex:not provided|tissue type:whole body without xxx                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 05 08 2022 14:25:08:835 19174 unspecified 1 Illumina TruSeq DNA Nano Kit   RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   ERP140005 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2022 08 08|ENA LAST UPDATE:2022 08 08 S879Nr23.1.fastq.gz S879Nr23.2.fastq.gz fastq fastq 8270390422.0 41338131.0 ena RUN TAB 05 08 2022 14:25:08:835 19175 0:100.03 1:100.03 A:2156060704;C:1998612686;G:2055201244;T:2060404840;N:110948 100 100     2156060704 1998612686 2055201244 2060404840 110948 ERX9574474 ERS12562185 ERA16814395 max planck institute for biology|European Nucleotide Archive max planck institute for biology 2 0.97085 0.97083 0.04232 0.04236 0.7219 0.72671 0.47325 0.4807 101 101 B B biological fallback assumption illumina novaseq_era unknown poly_a trueseq bulk unknown unknown   Germany 2022-08-05 Undetermined Undetermined Trunk Surface Structure
11151 11151 ERR10034069 ERX9574473 ERS12562184 ERP140005 PRJEB55122 Danio developmental transcriptomes ca4a518e-aaf7-42d9-9758-352aac808809 Other Transcriptomic analysis of four different developmental stages of four Danio species D. rerio D. aesculapii Danio aff. kyathit striped also known as Danio quagga and D. albolineatus. Five biological replicates were sampled for every developmental stage of a species. ENA FIRST PUBLIC:2022 08 05|ENA LAST UPDATE:2022 08 08   Metamorphic tissue without xxx from Danio rerio Drerio metamorphic 2 SAMEA110464156 max planck institute for biology ENA FIRST PUBLIC:2022 08 08|ENA LAST UPDATE:2022 08 08|External Id:SAMEA110464156|INSDC center alias:MAX PLANCK INSTITUTE FOR BIOLOGY|INSDC center name:max planck institute for biology|INSDC first public:2022 08 08T04:26:46Z|INSDC last update:2022 08 08T04:26:46Z|INSDC status:public|Submitter Id:SAMPLE22|collected by:Marco Podobnik|collection date:2018 06 27|common name:zebrafish|dev stage:Metamorphic|identified by:Marco Podobnik|sample name:SAMPLE22|sex:not provided|tissue type:whole body without xxx                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 05 08 2022 14:25:08:834 19172 unspecified 1 Illumina TruSeq DNA Nano Kit   RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   ERP140005 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2022 08 08|ENA LAST UPDATE:2022 08 08 S879Nr22.1.fastq.gz S879Nr22.2.fastq.gz fastq fastq 10977356920.0 54380062.0 ena RUN TAB 05 08 2022 14:25:08:834 19173 0:100.93 1:100.93 A:2852856166;C:2671616791;G:2798184312;T:2654546853;N:152798 100 100     2852856166 2671616791 2798184312 2654546853 152798 ERX9574473 ERS12562184 ERA16814395 max planck institute for biology|European Nucleotide Archive max planck institute for biology 2 0.9765 0.97629 0.03531 0.03529 0.72025 0.72705 0.47808 0.46326 101 101 B B biological fallback assumption illumina novaseq_era unknown poly_a trueseq bulk unknown unknown   Germany 2022-08-05 Undetermined Undetermined Trunk Surface Structure
11152 11152 ERR10034068 ERX9574472 ERS12562183 ERP140005 PRJEB55122 Danio developmental transcriptomes ca4a518e-aaf7-42d9-9758-352aac808809 Other Transcriptomic analysis of four different developmental stages of four Danio species D. rerio D. aesculapii Danio aff. kyathit striped also known as Danio quagga and D. albolineatus. Five biological replicates were sampled for every developmental stage of a species. ENA FIRST PUBLIC:2022 08 05|ENA LAST UPDATE:2022 08 08   Metamorphic tissue without xxx from Danio rerio Drerio metamorphic 1 SAMEA110464155 max planck institute for biology ENA FIRST PUBLIC:2022 08 08|ENA LAST UPDATE:2022 08 08|External Id:SAMEA110464155|INSDC center alias:MAX PLANCK INSTITUTE FOR BIOLOGY|INSDC center name:max planck institute for biology|INSDC first public:2022 08 08T04:26:46Z|INSDC last update:2022 08 08T04:26:46Z|INSDC status:public|Submitter Id:SAMPLE21|collected by:Marco Podobnik|collection date:2018 06 27|common name:zebrafish|dev stage:Metamorphic|identified by:Marco Podobnik|sample name:SAMPLE21|sex:not provided|tissue type:whole body without xxx                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 05 08 2022 14:25:08:834 19170 unspecified 1 Illumina TruSeq DNA Nano Kit   RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   ERP140005 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2022 08 08|ENA LAST UPDATE:2022 08 08 S879Nr21.1.fastq.gz S879Nr21.2.fastq.gz fastq fastq 11346084502.0 56210802.0 ena RUN TAB 05 08 2022 14:25:08:834 19171 0:100.92 1:100.92 A:2950787998;C:2755514202;G:2902131288;T:2737495846;N:155168 100 100     2950787998 2755514202 2902131288 2737495846 155168 ERX9574472 ERS12562183 ERA16814395 max planck institute for biology|European Nucleotide Archive max planck institute for biology 2 0.9732 0.97208 0.02959 0.02983 0.72322 0.73135 0.47796 0.47326 101 101 B B biological fallback assumption illumina novaseq_era unknown poly_a trueseq bulk unknown unknown   Germany 2022-08-05 Undetermined Undetermined Trunk Surface Structure
28893 28893 SRR26821448 SRX22518177 SRS19529846 SRP471728 PRJNA1040136 Gene expression analysis in the zebrafish fractured scale exposed to ELF EMFs GSE247669 Transcriptome Analysis The zebrafish scale is a thin membranous bone embedded in the skin and consists of osteoblasts osteoclasts and bone matrix providing an elegant model to understand bone metabolisms. we developed an in vivo model system using zebrafish scales to investigate the effect of extremely low frequency electromagnetic fields ELF EMFs on fracture healing. In this study we have performed RNA seq analysis on intact scales fractured scales not exposed to ELF EMFs and fractured scales exposed ttwo xxx militesra mT of ELF EMFs. Overall design: mRNA profiles of zebrafish scales were generated by Lasy seq using Illumina NovaSeq X.   pubmed:38385024   10mT fractured 3 GSM7898626   source name:Whole scales|tissue:Whole scales|genotype:Wild type|treatment:Fractured scales exposed to 10 mT ELF EMFs|geo loc name:missing|collection date:missing 10mT fractured 3 Illumina RTA software was used for base calling. Sequence reads were mapped to the zebrafish reference genome GRCz11 using BWA mem ver. 0.7.17 r1188. Unique molecular identifier UMI counts of each transcript in each sample were calculated using salmon ver. 1.4.0 Assembly: GRCz11 Supplementary files format and content: Reads per million RPM values for each sample. Whole scales   Total RNAs were extracted from scales using RNeasy Mini Kit QIAGEN. three prime RNA seq was performed according to the Lasy Seq Ver 1.1 method Kamitani et al. 2019; Kashima et al. 2022. Total RNA was extracted from zebrafish scales using RNeasy Mini Kit QIAGEN. Reverse transcription RT was performed using Super Script IV Thermo Fisher Scientific and an RT primer containing oligo dT the index sequence and 9 bases unique molecular identifiers UMIs. RNA/cDNA hybrids were purified using AMpure XP beads Beckman Coulter and second strand DNA was synthesized using DNA polymerase I Enzymatics. dsDNAs were fragmented using WGS Fragmentation Mix Enzymatics and ligated into customized adapters with WGS Ligase Enzymatics. Adapter ligated dsDNAs were amplified with KAPA HiFi ReadyMix Nippon Genetics and SE PCR primers. Next generation sequencing of cDNA libraries was performed by Novogene using an Illumina NovaSeq X illumina.   tissue:Whole scales|genotype:Wild type|treatment:Fractured scales exposed to 10 mT ELF EMFs GSM7898626 GSM7898626: 10mT fractured 3; Danio rerio; RNA Seq GSM7898626 r1 GSM7898626 1 Total RNAs were extracted from scales using RNeasy Mini Kit QIAGEN. three prime RNA seq was performed according to the Lasy Seq Ver 1.1 method Kamitani et al. 2019; Kashima et al. 2022. Total RNA was extracted from zebrafish scales using RNeasy Mini Kit QIAGEN. Reverse transcription RT was performed using Super Script IV Thermo Fisher Scientific and an RT primer containing oligo dT the index sequence and 9 bases unique molecular identifiers UMIs. RNA/cDNA hybrids were purified using AMpure XP beads Beckman Coulter and second strand DNA was synthesized using DNA polymerase I Enzymatics. dsDNAs were fragmented using WGS Fragmentation Mix Enzymatics and ligated into customized adapters with WGS Ligase Enzymatics. Adapter ligated dsDNAs were amplified with KAPA HiFi ReadyMix Nippon Genetics and SE PCR primers. Next generation sequencing of cDNA libraries was performed by Novogene using an Illumina NovaSeq X illumina.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP471728     10mT_fractured_3_R2.fq.gz 10mT_fractured_3_R1.fq.gz fastq fastq 1301482800.0 4338276.0 GSM7898626 r1 0:150 1:150 A:335087662;C:232566321;G:385245929;T:348358361;N:224527 150 150     335087662 232566321 385245929 348358361 224527 SRX22518177 SRS19529846 SRA1750892 Kanazawa University Kanazawa University 2 0.67547 0.04621 0.23296 0.03359 0.78279 0.99648 0.54124 0.52153 150 150 B T mate2 technical by mapping diff illumina novaseq_era unknown poly_a unknown bulk unknown unknown   Japan 2023-11-14 Undetermined Undetermined Scale Surface Structure
28894 28894 SRR26821449 SRX22518176 SRS19529845 SRP471728 PRJNA1040136 Gene expression analysis in the zebrafish fractured scale exposed to ELF EMFs GSE247669 Transcriptome Analysis The zebrafish scale is a thin membranous bone embedded in the skin and consists of osteoblasts osteoclasts and bone matrix providing an elegant model to understand bone metabolisms. we developed an in vivo model system using zebrafish scales to investigate the effect of extremely low frequency electromagnetic fields ELF EMFs on fracture healing. In this study we have performed RNA seq analysis on intact scales fractured scales not exposed to ELF EMFs and fractured scales exposed ttwo xxx militesra mT of ELF EMFs. Overall design: mRNA profiles of zebrafish scales were generated by Lasy seq using Illumina NovaSeq X.   pubmed:38385024   10mT fractured 2 GSM7898625   source name:Whole scales|tissue:Whole scales|genotype:Wild type|treatment:Fractured scales exposed to 10 mT ELF EMFs|geo loc name:missing|collection date:missing 10mT fractured 2 Illumina RTA software was used for base calling. Sequence reads were mapped to the zebrafish reference genome GRCz11 using BWA mem ver. 0.7.17 r1188. Unique molecular identifier UMI counts of each transcript in each sample were calculated using salmon ver. 1.4.0 Assembly: GRCz11 Supplementary files format and content: Reads per million RPM values for each sample. Whole scales   Total RNAs were extracted from scales using RNeasy Mini Kit QIAGEN. three prime RNA seq was performed according to the Lasy Seq Ver 1.1 method Kamitani et al. 2019; Kashima et al. 2022. Total RNA was extracted from zebrafish scales using RNeasy Mini Kit QIAGEN. Reverse transcription RT was performed using Super Script IV Thermo Fisher Scientific and an RT primer containing oligo dT the index sequence and 9 bases unique molecular identifiers UMIs. RNA/cDNA hybrids were purified using AMpure XP beads Beckman Coulter and second strand DNA was synthesized using DNA polymerase I Enzymatics. dsDNAs were fragmented using WGS Fragmentation Mix Enzymatics and ligated into customized adapters with WGS Ligase Enzymatics. Adapter ligated dsDNAs were amplified with KAPA HiFi ReadyMix Nippon Genetics and SE PCR primers. Next generation sequencing of cDNA libraries was performed by Novogene using an Illumina NovaSeq X illumina.   tissue:Whole scales|genotype:Wild type|treatment:Fractured scales exposed to 10 mT ELF EMFs GSM7898625 GSM7898625: 10mT fractured 2; Danio rerio; RNA Seq GSM7898625 r1 GSM7898625 1 Total RNAs were extracted from scales using RNeasy Mini Kit QIAGEN. three prime RNA seq was performed according to the Lasy Seq Ver 1.1 method Kamitani et al. 2019; Kashima et al. 2022. Total RNA was extracted from zebrafish scales using RNeasy Mini Kit QIAGEN. Reverse transcription RT was performed using Super Script IV Thermo Fisher Scientific and an RT primer containing oligo dT the index sequence and 9 bases unique molecular identifiers UMIs. RNA/cDNA hybrids were purified using AMpure XP beads Beckman Coulter and second strand DNA was synthesized using DNA polymerase I Enzymatics. dsDNAs were fragmented using WGS Fragmentation Mix Enzymatics and ligated into customized adapters with WGS Ligase Enzymatics. Adapter ligated dsDNAs were amplified with KAPA HiFi ReadyMix Nippon Genetics and SE PCR primers. Next generation sequencing of cDNA libraries was performed by Novogene using an Illumina NovaSeq X illumina.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP471728     10mT_fractured_2_R1.fq.gz 10mT_fractured_2_R2.fq.gz fastq fastq 1507967100.0 5026557.0 GSM7898625 r1 0:150 1:150 A:390969189;C:278659472;G:444481407;T:393553558;N:303474 150 150     390969189 278659472 444481407 393553558 303474 SRX22518176 SRS19529845 SRA1750892 Kanazawa University Kanazawa University 2 0.68061 0.08614 0.31496 0.0705 0.77001 0.99513 0.53747 0.57677 150 150 B T mate2 technical by mapping diff illumina novaseq_era unknown poly_a unknown bulk unknown unknown   Japan 2023-11-14 Undetermined Undetermined Scale Surface Structure
28895 28895 SRR26821450 SRX22518175 SRS19529844 SRP471728 PRJNA1040136 Gene expression analysis in the zebrafish fractured scale exposed to ELF EMFs GSE247669 Transcriptome Analysis The zebrafish scale is a thin membranous bone embedded in the skin and consists of osteoblasts osteoclasts and bone matrix providing an elegant model to understand bone metabolisms. we developed an in vivo model system using zebrafish scales to investigate the effect of extremely low frequency electromagnetic fields ELF EMFs on fracture healing. In this study we have performed RNA seq analysis on intact scales fractured scales not exposed to ELF EMFs and fractured scales exposed ttwo xxx militesra mT of ELF EMFs. Overall design: mRNA profiles of zebrafish scales were generated by Lasy seq using Illumina NovaSeq X.   pubmed:38385024   10mT fractured 1 GSM7898624   source name:Whole scales|tissue:Whole scales|genotype:Wild type|treatment:Fractured scales exposed to 10 mT ELF EMFs|geo loc name:missing|collection date:missing 10mT fractured 1 Illumina RTA software was used for base calling. Sequence reads were mapped to the zebrafish reference genome GRCz11 using BWA mem ver. 0.7.17 r1188. Unique molecular identifier UMI counts of each transcript in each sample were calculated using salmon ver. 1.4.0 Assembly: GRCz11 Supplementary files format and content: Reads per million RPM values for each sample. Whole scales   Total RNAs were extracted from scales using RNeasy Mini Kit QIAGEN. three prime RNA seq was performed according to the Lasy Seq Ver 1.1 method Kamitani et al. 2019; Kashima et al. 2022. Total RNA was extracted from zebrafish scales using RNeasy Mini Kit QIAGEN. Reverse transcription RT was performed using Super Script IV Thermo Fisher Scientific and an RT primer containing oligo dT the index sequence and 9 bases unique molecular identifiers UMIs. RNA/cDNA hybrids were purified using AMpure XP beads Beckman Coulter and second strand DNA was synthesized using DNA polymerase I Enzymatics. dsDNAs were fragmented using WGS Fragmentation Mix Enzymatics and ligated into customized adapters with WGS Ligase Enzymatics. Adapter ligated dsDNAs were amplified with KAPA HiFi ReadyMix Nippon Genetics and SE PCR primers. Next generation sequencing of cDNA libraries was performed by Novogene using an Illumina NovaSeq X illumina.   tissue:Whole scales|genotype:Wild type|treatment:Fractured scales exposed to 10 mT ELF EMFs GSM7898624 GSM7898624: 10mT fractured 1; Danio rerio; RNA Seq GSM7898624 r1 GSM7898624 1 Total RNAs were extracted from scales using RNeasy Mini Kit QIAGEN. three prime RNA seq was performed according to the Lasy Seq Ver 1.1 method Kamitani et al. 2019; Kashima et al. 2022. Total RNA was extracted from zebrafish scales using RNeasy Mini Kit QIAGEN. Reverse transcription RT was performed using Super Script IV Thermo Fisher Scientific and an RT primer containing oligo dT the index sequence and 9 bases unique molecular identifiers UMIs. RNA/cDNA hybrids were purified using AMpure XP beads Beckman Coulter and second strand DNA was synthesized using DNA polymerase I Enzymatics. dsDNAs were fragmented using WGS Fragmentation Mix Enzymatics and ligated into customized adapters with WGS Ligase Enzymatics. Adapter ligated dsDNAs were amplified with KAPA HiFi ReadyMix Nippon Genetics and SE PCR primers. Next generation sequencing of cDNA libraries was performed by Novogene using an Illumina NovaSeq X illumina.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP471728     10mT_fractured_1_R2.fq.gz 10mT_fractured_1_R1.fq.gz fastq fastq 1718495100.0 5728317.0 GSM7898624 r1 0:150 1:150 A:452779669;C:319880075;G:491162181;T:454320323;N:352852 150 150     452779669 319880075 491162181 454320323 352852 SRX22518175 SRS19529844 SRA1750892 Kanazawa University Kanazawa University 2 0.67153 0.10745 0.32942 0.08781 0.76775 0.99427 0.53417 0.5895 150 150 B T mate2 technical by mapping diff illumina novaseq_era unknown poly_a unknown bulk unknown unknown   Japan 2023-11-14 Undetermined Undetermined Scale Surface Structure
28896 28896 SRR26821451 SRX22518174 SRS19529843 SRP471728 PRJNA1040136 Gene expression analysis in the zebrafish fractured scale exposed to ELF EMFs GSE247669 Transcriptome Analysis The zebrafish scale is a thin membranous bone embedded in the skin and consists of osteoblasts osteoclasts and bone matrix providing an elegant model to understand bone metabolisms. we developed an in vivo model system using zebrafish scales to investigate the effect of extremely low frequency electromagnetic fields ELF EMFs on fracture healing. In this study we have performed RNA seq analysis on intact scales fractured scales not exposed to ELF EMFs and fractured scales exposed ttwo xxx militesra mT of ELF EMFs. Overall design: mRNA profiles of zebrafish scales were generated by Lasy seq using Illumina NovaSeq X.   pubmed:38385024   0mT fractured 3 GSM7898623   source name:Whole scales|tissue:Whole scales|genotype:Wild type|treatment:Fractured scales not exposed to ELF EMFs|geo loc name:missing|collection date:missing 0mT fractured 3 Illumina RTA software was used for base calling. Sequence reads were mapped to the zebrafish reference genome GRCz11 using BWA mem ver. 0.7.17 r1188. Unique molecular identifier UMI counts of each transcript in each sample were calculated using salmon ver. 1.4.0 Assembly: GRCz11 Supplementary files format and content: Reads per million RPM values for each sample. Whole scales   Total RNAs were extracted from scales using RNeasy Mini Kit QIAGEN. three prime RNA seq was performed according to the Lasy Seq Ver 1.1 method Kamitani et al. 2019; Kashima et al. 2022. Total RNA was extracted from zebrafish scales using RNeasy Mini Kit QIAGEN. Reverse transcription RT was performed using Super Script IV Thermo Fisher Scientific and an RT primer containing oligo dT the index sequence and 9 bases unique molecular identifiers UMIs. RNA/cDNA hybrids were purified using AMpure XP beads Beckman Coulter and second strand DNA was synthesized using DNA polymerase I Enzymatics. dsDNAs were fragmented using WGS Fragmentation Mix Enzymatics and ligated into customized adapters with WGS Ligase Enzymatics. Adapter ligated dsDNAs were amplified with KAPA HiFi ReadyMix Nippon Genetics and SE PCR primers. Next generation sequencing of cDNA libraries was performed by Novogene using an Illumina NovaSeq X illumina.   tissue:Whole scales|genotype:Wild type|treatment:Fractured scales not exposed to ELF EMFs GSM7898623 GSM7898623: 0mT fractured 3; Danio rerio; RNA Seq GSM7898623 r1 GSM7898623 1 Total RNAs were extracted from scales using RNeasy Mini Kit QIAGEN. three prime RNA seq was performed according to the Lasy Seq Ver 1.1 method Kamitani et al. 2019; Kashima et al. 2022. Total RNA was extracted from zebrafish scales using RNeasy Mini Kit QIAGEN. Reverse transcription RT was performed using Super Script IV Thermo Fisher Scientific and an RT primer containing oligo dT the index sequence and 9 bases unique molecular identifiers UMIs. RNA/cDNA hybrids were purified using AMpure XP beads Beckman Coulter and second strand DNA was synthesized using DNA polymerase I Enzymatics. dsDNAs were fragmented using WGS Fragmentation Mix Enzymatics and ligated into customized adapters with WGS Ligase Enzymatics. Adapter ligated dsDNAs were amplified with KAPA HiFi ReadyMix Nippon Genetics and SE PCR primers. Next generation sequencing of cDNA libraries was performed by Novogene using an Illumina NovaSeq X illumina.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP471728     0mT_fractured_3_R1.fq.gz 0mT_fractured_3_R2.fq.gz fastq fastq 1468748700.0 4895829.0 GSM7898623 r1 0:150 1:150 A:378980971;C:273130967;G:441424422;T:374917129;N:295211 150 150     378980971 273130967 441424422 374917129 295211 SRX22518174 SRS19529843 SRA1750892 Kanazawa University Kanazawa University 2 0.67867 0.10573 0.35963 0.0899 0.75982 0.99508 0.53209 0.48863 150 150 B T mate2 technical by mapping diff illumina novaseq_era unknown poly_a unknown bulk unknown unknown   Japan 2023-11-14 Undetermined Undetermined Scale Surface Structure
28897 28897 SRR26821452 SRX22518173 SRS19529842 SRP471728 PRJNA1040136 Gene expression analysis in the zebrafish fractured scale exposed to ELF EMFs GSE247669 Transcriptome Analysis The zebrafish scale is a thin membranous bone embedded in the skin and consists of osteoblasts osteoclasts and bone matrix providing an elegant model to understand bone metabolisms. we developed an in vivo model system using zebrafish scales to investigate the effect of extremely low frequency electromagnetic fields ELF EMFs on fracture healing. In this study we have performed RNA seq analysis on intact scales fractured scales not exposed to ELF EMFs and fractured scales exposed ttwo xxx militesra mT of ELF EMFs. Overall design: mRNA profiles of zebrafish scales were generated by Lasy seq using Illumina NovaSeq X.   pubmed:38385024   0mT fractured 2 GSM7898622   source name:Whole scales|tissue:Whole scales|genotype:Wild type|treatment:Fractured scales not exposed to ELF EMFs|geo loc name:missing|collection date:missing 0mT fractured 2 Illumina RTA software was used for base calling. Sequence reads were mapped to the zebrafish reference genome GRCz11 using BWA mem ver. 0.7.17 r1188. Unique molecular identifier UMI counts of each transcript in each sample were calculated using salmon ver. 1.4.0 Assembly: GRCz11 Supplementary files format and content: Reads per million RPM values for each sample. Whole scales   Total RNAs were extracted from scales using RNeasy Mini Kit QIAGEN. three prime RNA seq was performed according to the Lasy Seq Ver 1.1 method Kamitani et al. 2019; Kashima et al. 2022. Total RNA was extracted from zebrafish scales using RNeasy Mini Kit QIAGEN. Reverse transcription RT was performed using Super Script IV Thermo Fisher Scientific and an RT primer containing oligo dT the index sequence and 9 bases unique molecular identifiers UMIs. RNA/cDNA hybrids were purified using AMpure XP beads Beckman Coulter and second strand DNA was synthesized using DNA polymerase I Enzymatics. dsDNAs were fragmented using WGS Fragmentation Mix Enzymatics and ligated into customized adapters with WGS Ligase Enzymatics. Adapter ligated dsDNAs were amplified with KAPA HiFi ReadyMix Nippon Genetics and SE PCR primers. Next generation sequencing of cDNA libraries was performed by Novogene using an Illumina NovaSeq X illumina.   tissue:Whole scales|genotype:Wild type|treatment:Fractured scales not exposed to ELF EMFs GSM7898622 GSM7898622: 0mT fractured 2; Danio rerio; RNA Seq GSM7898622 r1 GSM7898622 1 Total RNAs were extracted from scales using RNeasy Mini Kit QIAGEN. three prime RNA seq was performed according to the Lasy Seq Ver 1.1 method Kamitani et al. 2019; Kashima et al. 2022. Total RNA was extracted from zebrafish scales using RNeasy Mini Kit QIAGEN. Reverse transcription RT was performed using Super Script IV Thermo Fisher Scientific and an RT primer containing oligo dT the index sequence and 9 bases unique molecular identifiers UMIs. RNA/cDNA hybrids were purified using AMpure XP beads Beckman Coulter and second strand DNA was synthesized using DNA polymerase I Enzymatics. dsDNAs were fragmented using WGS Fragmentation Mix Enzymatics and ligated into customized adapters with WGS Ligase Enzymatics. Adapter ligated dsDNAs were amplified with KAPA HiFi ReadyMix Nippon Genetics and SE PCR primers. Next generation sequencing of cDNA libraries was performed by Novogene using an Illumina NovaSeq X illumina.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP471728     0mT_fractured_2_R1.fq.gz 0mT_fractured_2_R2.fq.gz fastq fastq 2406885600.0 8022952.0 GSM7898622 r1 0:150 1:150 A:646926387;C:366751040;G:726614721;T:666425874;N:167578 150 150     646926387 366751040 726614721 666425874 167578 SRX22518173 SRS19529842 SRA1750892 Kanazawa University Kanazawa University 2 0.67096 0.06177 0.27169 0.04875 0.77492 0.99805 0.55512 0.62711 150 150 B T mate2 technical by mapping diff illumina novaseq_era unknown poly_a unknown bulk unknown unknown   Japan 2023-11-14 Undetermined Undetermined Scale Surface Structure
28898 28898 SRR26821453 SRX22518172 SRS19529841 SRP471728 PRJNA1040136 Gene expression analysis in the zebrafish fractured scale exposed to ELF EMFs GSE247669 Transcriptome Analysis The zebrafish scale is a thin membranous bone embedded in the skin and consists of osteoblasts osteoclasts and bone matrix providing an elegant model to understand bone metabolisms. we developed an in vivo model system using zebrafish scales to investigate the effect of extremely low frequency electromagnetic fields ELF EMFs on fracture healing. In this study we have performed RNA seq analysis on intact scales fractured scales not exposed to ELF EMFs and fractured scales exposed ttwo xxx militesra mT of ELF EMFs. Overall design: mRNA profiles of zebrafish scales were generated by Lasy seq using Illumina NovaSeq X.   pubmed:38385024   0mT fractured 1 GSM7898621   source name:Whole scales|tissue:Whole scales|genotype:Wild type|treatment:Fractured scales not exposed to ELF EMFs|geo loc name:missing|collection date:missing 0mT fractured 1 Illumina RTA software was used for base calling. Sequence reads were mapped to the zebrafish reference genome GRCz11 using BWA mem ver. 0.7.17 r1188. Unique molecular identifier UMI counts of each transcript in each sample were calculated using salmon ver. 1.4.0 Assembly: GRCz11 Supplementary files format and content: Reads per million RPM values for each sample. Whole scales   Total RNAs were extracted from scales using RNeasy Mini Kit QIAGEN. three prime RNA seq was performed according to the Lasy Seq Ver 1.1 method Kamitani et al. 2019; Kashima et al. 2022. Total RNA was extracted from zebrafish scales using RNeasy Mini Kit QIAGEN. Reverse transcription RT was performed using Super Script IV Thermo Fisher Scientific and an RT primer containing oligo dT the index sequence and 9 bases unique molecular identifiers UMIs. RNA/cDNA hybrids were purified using AMpure XP beads Beckman Coulter and second strand DNA was synthesized using DNA polymerase I Enzymatics. dsDNAs were fragmented using WGS Fragmentation Mix Enzymatics and ligated into customized adapters with WGS Ligase Enzymatics. Adapter ligated dsDNAs were amplified with KAPA HiFi ReadyMix Nippon Genetics and SE PCR primers. Next generation sequencing of cDNA libraries was performed by Novogene using an Illumina NovaSeq X illumina.   tissue:Whole scales|genotype:Wild type|treatment:Fractured scales not exposed to ELF EMFs GSM7898621 GSM7898621: 0mT fractured 1; Danio rerio; RNA Seq GSM7898621 r1 GSM7898621 1 Total RNAs were extracted from scales using RNeasy Mini Kit QIAGEN. three prime RNA seq was performed according to the Lasy Seq Ver 1.1 method Kamitani et al. 2019; Kashima et al. 2022. Total RNA was extracted from zebrafish scales using RNeasy Mini Kit QIAGEN. Reverse transcription RT was performed using Super Script IV Thermo Fisher Scientific and an RT primer containing oligo dT the index sequence and 9 bases unique molecular identifiers UMIs. RNA/cDNA hybrids were purified using AMpure XP beads Beckman Coulter and second strand DNA was synthesized using DNA polymerase I Enzymatics. dsDNAs were fragmented using WGS Fragmentation Mix Enzymatics and ligated into customized adapters with WGS Ligase Enzymatics. Adapter ligated dsDNAs were amplified with KAPA HiFi ReadyMix Nippon Genetics and SE PCR primers. Next generation sequencing of cDNA libraries was performed by Novogene using an Illumina NovaSeq X illumina.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP471728     0mT_fractured_1_R1.fq.gz 0mT_fractured_1_R2.fq.gz fastq fastq 2084550000.0 6948500.0 GSM7898621 r1 0:150 1:150 A:567504433;C:327104215;G:627285267;T:562454734;N:201351 150 150     567504433 327104215 627285267 562454734 201351 SRX22518172 SRS19529841 SRA1750892 Kanazawa University Kanazawa University 2 0.68491 0.14639 0.35327 0.12371 0.76459 0.99584 0.52889 0.52678 150 150 B T mate2 technical by mapping diff illumina novaseq_era unknown poly_a unknown bulk unknown unknown   Japan 2023-11-14 Undetermined Undetermined Scale Surface Structure
28899 28899 SRR26821454 SRX22518171 SRS19529840 SRP471728 PRJNA1040136 Gene expression analysis in the zebrafish fractured scale exposed to ELF EMFs GSE247669 Transcriptome Analysis The zebrafish scale is a thin membranous bone embedded in the skin and consists of osteoblasts osteoclasts and bone matrix providing an elegant model to understand bone metabolisms. we developed an in vivo model system using zebrafish scales to investigate the effect of extremely low frequency electromagnetic fields ELF EMFs on fracture healing. In this study we have performed RNA seq analysis on intact scales fractured scales not exposed to ELF EMFs and fractured scales exposed ttwo xxx militesra mT of ELF EMFs. Overall design: mRNA profiles of zebrafish scales were generated by Lasy seq using Illumina NovaSeq X.   pubmed:38385024   Int 3 GSM7898620   source name:Whole scales|tissue:Whole scales|genotype:Wild type|treatment:Intact scales|geo loc name:missing|collection date:missing Int 3 Illumina RTA software was used for base calling. Sequence reads were mapped to the zebrafish reference genome GRCz11 using BWA mem ver. 0.7.17 r1188. Unique molecular identifier UMI counts of each transcript in each sample were calculated using salmon ver. 1.4.0 Assembly: GRCz11 Supplementary files format and content: Reads per million RPM values for each sample. Whole scales   Total RNAs were extracted from scales using RNeasy Mini Kit QIAGEN. three prime RNA seq was performed according to the Lasy Seq Ver 1.1 method Kamitani et al. 2019; Kashima et al. 2022. Total RNA was extracted from zebrafish scales using RNeasy Mini Kit QIAGEN. Reverse transcription RT was performed using Super Script IV Thermo Fisher Scientific and an RT primer containing oligo dT the index sequence and 9 bases unique molecular identifiers UMIs. RNA/cDNA hybrids were purified using AMpure XP beads Beckman Coulter and second strand DNA was synthesized using DNA polymerase I Enzymatics. dsDNAs were fragmented using WGS Fragmentation Mix Enzymatics and ligated into customized adapters with WGS Ligase Enzymatics. Adapter ligated dsDNAs were amplified with KAPA HiFi ReadyMix Nippon Genetics and SE PCR primers. Next generation sequencing of cDNA libraries was performed by Novogene using an Illumina NovaSeq X illumina.   tissue:Whole scales|genotype:Wild type|treatment:Intact scales GSM7898620 GSM7898620: Int 3; Danio rerio; RNA Seq GSM7898620 r1 GSM7898620 1 Total RNAs were extracted from scales using RNeasy Mini Kit QIAGEN. three prime RNA seq was performed according to the Lasy Seq Ver 1.1 method Kamitani et al. 2019; Kashima et al. 2022. Total RNA was extracted from zebrafish scales using RNeasy Mini Kit QIAGEN. Reverse transcription RT was performed using Super Script IV Thermo Fisher Scientific and an RT primer containing oligo dT the index sequence and 9 bases unique molecular identifiers UMIs. RNA/cDNA hybrids were purified using AMpure XP beads Beckman Coulter and second strand DNA was synthesized using DNA polymerase I Enzymatics. dsDNAs were fragmented using WGS Fragmentation Mix Enzymatics and ligated into customized adapters with WGS Ligase Enzymatics. Adapter ligated dsDNAs were amplified with KAPA HiFi ReadyMix Nippon Genetics and SE PCR primers. Next generation sequencing of cDNA libraries was performed by Novogene using an Illumina NovaSeq X illumina.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP471728     Int_3_R1.fq.gz Int_3_R2.fq.gz fastq fastq 2081211600.0 6937372.0 GSM7898620 r1 0:150 1:150 A:561341589;C:327618433;G:629445558;T:562620891;N:185129 150 150     561341589 327618433 629445558 562620891 185129 SRX22518171 SRS19529840 SRA1750892 Kanazawa University Kanazawa University 2 0.68553 0.11302 0.32184 0.0937 0.7654 0.99646 0.53135 0.50819 150 150 B T mate2 technical by mapping diff illumina novaseq_era unknown poly_a unknown bulk unknown unknown   Japan 2023-11-14 Undetermined Undetermined Scale Surface Structure
28900 28900 SRR26821455 SRX22518170 SRS19529839 SRP471728 PRJNA1040136 Gene expression analysis in the zebrafish fractured scale exposed to ELF EMFs GSE247669 Transcriptome Analysis The zebrafish scale is a thin membranous bone embedded in the skin and consists of osteoblasts osteoclasts and bone matrix providing an elegant model to understand bone metabolisms. we developed an in vivo model system using zebrafish scales to investigate the effect of extremely low frequency electromagnetic fields ELF EMFs on fracture healing. In this study we have performed RNA seq analysis on intact scales fractured scales not exposed to ELF EMFs and fractured scales exposed ttwo xxx militesra mT of ELF EMFs. Overall design: mRNA profiles of zebrafish scales were generated by Lasy seq using Illumina NovaSeq X.   pubmed:38385024   Int 2 GSM7898619   source name:Whole scales|tissue:Whole scales|genotype:Wild type|treatment:Intact scales|geo loc name:missing|collection date:missing Int 2 Illumina RTA software was used for base calling. Sequence reads were mapped to the zebrafish reference genome GRCz11 using BWA mem ver. 0.7.17 r1188. Unique molecular identifier UMI counts of each transcript in each sample were calculated using salmon ver. 1.4.0 Assembly: GRCz11 Supplementary files format and content: Reads per million RPM values for each sample. Whole scales   Total RNAs were extracted from scales using RNeasy Mini Kit QIAGEN. three prime RNA seq was performed according to the Lasy Seq Ver 1.1 method Kamitani et al. 2019; Kashima et al. 2022. Total RNA was extracted from zebrafish scales using RNeasy Mini Kit QIAGEN. Reverse transcription RT was performed using Super Script IV Thermo Fisher Scientific and an RT primer containing oligo dT the index sequence and 9 bases unique molecular identifiers UMIs. RNA/cDNA hybrids were purified using AMpure XP beads Beckman Coulter and second strand DNA was synthesized using DNA polymerase I Enzymatics. dsDNAs were fragmented using WGS Fragmentation Mix Enzymatics and ligated into customized adapters with WGS Ligase Enzymatics. Adapter ligated dsDNAs were amplified with KAPA HiFi ReadyMix Nippon Genetics and SE PCR primers. Next generation sequencing of cDNA libraries was performed by Novogene using an Illumina NovaSeq X illumina.   tissue:Whole scales|genotype:Wild type|treatment:Intact scales GSM7898619 GSM7898619: Int 2; Danio rerio; RNA Seq GSM7898619 r1 GSM7898619 1 Total RNAs were extracted from scales using RNeasy Mini Kit QIAGEN. three prime RNA seq was performed according to the Lasy Seq Ver 1.1 method Kamitani et al. 2019; Kashima et al. 2022. Total RNA was extracted from zebrafish scales using RNeasy Mini Kit QIAGEN. Reverse transcription RT was performed using Super Script IV Thermo Fisher Scientific and an RT primer containing oligo dT the index sequence and 9 bases unique molecular identifiers UMIs. RNA/cDNA hybrids were purified using AMpure XP beads Beckman Coulter and second strand DNA was synthesized using DNA polymerase I Enzymatics. dsDNAs were fragmented using WGS Fragmentation Mix Enzymatics and ligated into customized adapters with WGS Ligase Enzymatics. Adapter ligated dsDNAs were amplified with KAPA HiFi ReadyMix Nippon Genetics and SE PCR primers. Next generation sequencing of cDNA libraries was performed by Novogene using an Illumina NovaSeq X illumina.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP471728     Int_2_R1.fq.gz Int_2_R2.fq.gz fastq fastq 1639167900.0 5463893.0 GSM7898619 r1 0:150 1:150 A:445245908;C:275437900;G:483637484;T:434649575;N:197033 150 150     445245908 275437900 483637484 434649575 197033 SRX22518170 SRS19529839 SRA1750892 Kanazawa University Kanazawa University 2 0.68102 0.1645 0.41429 0.1457 0.76641 0.9964 0.53665 0.50264 150 150 B T mate2 technical by mapping diff illumina novaseq_era unknown poly_a unknown bulk unknown unknown   Japan 2023-11-14 Undetermined Undetermined Scale Surface Structure
28901 28901 SRR26821456 SRX22518169 SRS19529838 SRP471728 PRJNA1040136 Gene expression analysis in the zebrafish fractured scale exposed to ELF EMFs GSE247669 Transcriptome Analysis The zebrafish scale is a thin membranous bone embedded in the skin and consists of osteoblasts osteoclasts and bone matrix providing an elegant model to understand bone metabolisms. we developed an in vivo model system using zebrafish scales to investigate the effect of extremely low frequency electromagnetic fields ELF EMFs on fracture healing. In this study we have performed RNA seq analysis on intact scales fractured scales not exposed to ELF EMFs and fractured scales exposed ttwo xxx militesra mT of ELF EMFs. Overall design: mRNA profiles of zebrafish scales were generated by Lasy seq using Illumina NovaSeq X.   pubmed:38385024   Int 1 GSM7898618   source name:Whole scales|tissue:Whole scales|genotype:Wild type|treatment:Intact scales|geo loc name:missing|collection date:missing Int 1 Illumina RTA software was used for base calling. Sequence reads were mapped to the zebrafish reference genome GRCz11 using BWA mem ver. 0.7.17 r1188. Unique molecular identifier UMI counts of each transcript in each sample were calculated using salmon ver. 1.4.0 Assembly: GRCz11 Supplementary files format and content: Reads per million RPM values for each sample. Whole scales   Total RNAs were extracted from scales using RNeasy Mini Kit QIAGEN. three prime RNA seq was performed according to the Lasy Seq Ver 1.1 method Kamitani et al. 2019; Kashima et al. 2022. Total RNA was extracted from zebrafish scales using RNeasy Mini Kit QIAGEN. Reverse transcription RT was performed using Super Script IV Thermo Fisher Scientific and an RT primer containing oligo dT the index sequence and 9 bases unique molecular identifiers UMIs. RNA/cDNA hybrids were purified using AMpure XP beads Beckman Coulter and second strand DNA was synthesized using DNA polymerase I Enzymatics. dsDNAs were fragmented using WGS Fragmentation Mix Enzymatics and ligated into customized adapters with WGS Ligase Enzymatics. Adapter ligated dsDNAs were amplified with KAPA HiFi ReadyMix Nippon Genetics and SE PCR primers. Next generation sequencing of cDNA libraries was performed by Novogene using an Illumina NovaSeq X illumina.   tissue:Whole scales|genotype:Wild type|treatment:Intact scales GSM7898618 GSM7898618: Int 1; Danio rerio; RNA Seq GSM7898618 r1 GSM7898618 1 Total RNAs were extracted from scales using RNeasy Mini Kit QIAGEN. three prime RNA seq was performed according to the Lasy Seq Ver 1.1 method Kamitani et al. 2019; Kashima et al. 2022. Total RNA was extracted from zebrafish scales using RNeasy Mini Kit QIAGEN. Reverse transcription RT was performed using Super Script IV Thermo Fisher Scientific and an RT primer containing oligo dT the index sequence and 9 bases unique molecular identifiers UMIs. RNA/cDNA hybrids were purified using AMpure XP beads Beckman Coulter and second strand DNA was synthesized using DNA polymerase I Enzymatics. dsDNAs were fragmented using WGS Fragmentation Mix Enzymatics and ligated into customized adapters with WGS Ligase Enzymatics. Adapter ligated dsDNAs were amplified with KAPA HiFi ReadyMix Nippon Genetics and SE PCR primers. Next generation sequencing of cDNA libraries was performed by Novogene using an Illumina NovaSeq X illumina.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP471728     Int_1_R1.fq.gz Int_1_R2.fq.gz fastq fastq 2309186700.0 7697289.0 GSM7898618 r1 0:150 1:150 A:625174483;C:362587163;G:697384210;T:623845956;N:194888 150 150     625174483 362587163 697384210 623845956 194888 SRX22518169 SRS19529838 SRA1750892 Kanazawa University Kanazawa University 2 0.68814 0.09858 0.30026 0.08284 0.77315 0.99768 0.53387 0.50406 150 150 B T mate2 technical by mapping diff illumina novaseq_era unknown poly_a unknown bulk unknown unknown   Japan 2023-11-14 Undetermined Undetermined Scale Surface Structure
29197 29197 SRR27321690 SRX22998813 SRS19963383 SRP479569 PRJNA1055522 Compartmentalization and synergy of osteoblasts drive bone formation in the regenerating fin GSE251828 Transcriptome Analysis This study investigated the cell composition and lineage relationships of FACS fluorescence activated cell sorting enriched epidermal bone forming osteoblast and non osteoblast blastemal fin regenerate cells by single cell sc RNA sequencing. The repetitive cell harvesting in four week intervals revealed a constant gene regulation over four successive regeneration rounds in the early outgrowth stage. In addition the sc RNA dataset uncovered a potential lineage relationship between distal blastema cells and osteoblasts during fin regeneration. These findings together with the identification of novel fin regenerate markers advance our understanding of complex tissue regeneration in zebrafish. Overall design: To study potentially underrepresented cell populations during zebrafish fin regeneration we harvested single cells and FACS enriched for siam+ shha+ osterix+ RUNX2+ cells via respective mCherry and GFP reporter fluorophores. We performed gene expression analysis using data obtained from RNA seq of enriched cells from 4 successive regeneration stages at 3 dpa.   pubmed:38318374   4th round of regeneration GSM7988809   source name:Fin|tissue:Fin|cell type:siam+ shha+ osterix+ RUNX2+ fin regenerate cells|genotype:Tg7xTCF Xla.Sia:NLS mCherryia5 x Tg 2.7shha:GFPt10 x TgOla.Sp7:CreERT2 p2a mCherrytud8 x TgHsa.RUNX2 Mmu.Fos:EGFPzf259|treatment stg:3 dy post amputation|geo loc name:missing|collection date:missing 4th round of regeneration A reference based on GRCz10 Ensembl annotation e98 was created by first adding the sequences of gfp and mCherry as separate chromosomes to the fa file and the gtf file and then building the cellranger reference using cellranger mkref v3.0.0 fastq files were processed with `cellranger count` from 10X genomics version 3.0.0 Assembly: GRCz10 Supplementary files format and content: HDF5 Feature Barcode Matrix Format. Fin Fin regenerates of quadruple transgenic fish [Tg7xTCF Xla.Sia:NLS mCherryia5 x Tg 2.7shha:GFPt10 x TgOla.Sp7:CreERT2 p2a mCherrytud8 x TgHsa.RUNX2 Mmu.Fos:EGFPzf259] were harvested at 3 dpa cut into small pieces with a scalpel and transferred into 1 ml collagenase dispase solution 1 mg/ml in PBS Roche #10269638001 for 10 min at 28°C. The sample was pipetted slowly up and down with an elongated flame polished Pasteur pipette. The procedure was repeated 4 times with decreasing inner tip diameters of the Pasteur pipettes until a homogenous solution was obtained. The dissociates were poured onto an equilibrated 70 µm cell strainer and collected in 10 ml HBSS solution without xxx and MgCl2 Gibco #12082739. post centrifugation 15 minutes 1800 rpm 4°C the supernatant was discarded and the remaining cell pellet resuspended in 500 µl 2% BSA in PBS. Calcein violet 1µl 10mM Invitrogen #C34858 was added to the cell solution and incubated for 30 minutes. Calcein violet GFP and mCherry+ cells were collected in 50 µl 2% BSA in PBS via fluorescence activated cell sorting BD LSR Fortessa and processed for single cell RNA sequencing analysis based on 10X Genomics 10X Chromium system 10X library preparation according to the manufacturer's instructions. For each experiment about 8000 cells from zebrafish fin regenerates were flow sorted into BSA coated PCR tubes containing 1 µl of PBS with 0.04 % BSA. All cells were carefully mixed with reverse transcription mix before loading them in a Chromium Single Cell A Chip on the 10X Genomics Chromium controller and processed further following the guidelines of the 10X Genomics user manual for single cell 3’ RNA seq v2. In short the droplets were directly subjected to reverse transcription the emulsion was broken and cDNA was purified using silane beads. post amplification of cDNA with 12 cycles it underwent a purification with 0.6 volume of SPRI select beads. post quality check and quantification using the Fragment Analyzer Agilent 30 ng cDNA were used to prepare sc RNA seq libraries involving fragmentation dA Tailing adapter ligation and a 12 cycles indexing PCR based on manufacturer’s guidelines. post quantification both libraries were sequenced on an Illumina Nextseq500 system in paired end mode with 26 bp/57 bp for read 1 and 2 respectively thus generating 60 90 mio. fragments for the transcriptome library on average.   tissue:Fin|cell type:siam+ shha+ osterix+ RUNX2+ fin regenerate cells|genotype:Tg7xTCF Xla.Sia:NLS mCherryia5 x Tg 2.7shha:GFPt10 x TgOla.Sp7:CreERT2 p2a mCherrytud8 x TgHsa.RUNX2 Mmu.Fos:EGFPzf259|treatment stg:3 dy post amputation GSM7988809 GSM7988809: 4th round of regeneration; Danio rerio; RNA Seq GSM7988809 r1 GSM7988809 1 For each experiment about 8000 cells from zebrafish fin regenerates were flow sorted into BSA coated PCR tubes containing 1 µl of PBS with 0.04 % BSA. All cells were carefully mixed with reverse transcription mix before loading them in a Chromium Single Cell A Chip on the 10X Genomics Chromium controller and processed further following the guidelines of the 10X Genomics user manual for single cell three prime RNA seq v2. In short the droplets were directly subjected to reverse transcription the emulsion was broken and cDNA was purified using silane beads. post amplification of cDNA with 12 cycles it underwent a purification with 0.6 volume of SPRI select beads. post quality check and quantification using the Fragment Analyzer Agilent 30 ng cDNA were used to prepare sc RNA seq libraries involving fragmentation dA Tailing adapter ligation and a 12 cycles indexing PCR based on manufacturer's guidelines. post quantification both libraries were sequenced on an Illumina Nextseq500 system in paired end mode with 26 bp/57 bp for read 1 and 2 respectively thus generating 60 90 mio. fragments for the transcriptome library on average.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 500   SRP479569     L33268_osteoblasts_reg4_R2.fastq.gz L33268_osteoblasts_reg4_R1.fastq.gz fastq fastq 7429523805.0 89512335.0 GSM7988809 r1 0:26 1:57 A:2056160949;C:1638835280;G:1683264344;T:2047119393;N:4143839 26 57     2056160949 1638835280 1683264344 2047119393 4143839 SRX22998813 SRS19963383 SRA1774238 Dresden-concept Genome Center (DcGC), Center for Molecular and Cellular Bioengineering (CMCB), TU Dresden Dresden-concept Genome Center (DcGC), Center for Molecular and Cellular Bioengineering (CMCB), TU Dresden 2 0.00833 0.93478 0.00199 0.12451 0.9849 0.82418 0.46227 0.53386 26 57 T B sc-like readlen illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   Germany 2023-12-21 Undetermined Undetermined Fin Surface Structure
29198 29198 SRR27321691 SRX22998812 SRS19963382 SRP479569 PRJNA1055522 Compartmentalization and synergy of osteoblasts drive bone formation in the regenerating fin GSE251828 Transcriptome Analysis This study investigated the cell composition and lineage relationships of FACS fluorescence activated cell sorting enriched epidermal bone forming osteoblast and non osteoblast blastemal fin regenerate cells by single cell sc RNA sequencing. The repetitive cell harvesting in four week intervals revealed a constant gene regulation over four successive regeneration rounds in the early outgrowth stage. In addition the sc RNA dataset uncovered a potential lineage relationship between distal blastema cells and osteoblasts during fin regeneration. These findings together with the identification of novel fin regenerate markers advance our understanding of complex tissue regeneration in zebrafish. Overall design: To study potentially underrepresented cell populations during zebrafish fin regeneration we harvested single cells and FACS enriched for siam+ shha+ osterix+ RUNX2+ cells via respective mCherry and GFP reporter fluorophores. We performed gene expression analysis using data obtained from RNA seq of enriched cells from 4 successive regeneration stages at 3 dpa.   pubmed:38318374   3rd round of regeneration GSM7988808   source name:Fin|tissue:Fin|cell type:siam+ shha+ osterix+ RUNX2+ fin regenerate cells|genotype:Tg7xTCF Xla.Sia:NLS mCherryia5 x Tg 2.7shha:GFPt10 x TgOla.Sp7:CreERT2 p2a mCherrytud8 x TgHsa.RUNX2 Mmu.Fos:EGFPzf259|treatment stg:3 dy post amputation|geo loc name:missing|collection date:missing 3rd round of regeneration A reference based on GRCz10 Ensembl annotation e98 was created by first adding the sequences of gfp and mCherry as separate chromosomes to the fa file and the gtf file and then building the cellranger reference using cellranger mkref v3.0.0 fastq files were processed with `cellranger count` from 10X genomics version 3.0.0 Assembly: GRCz10 Supplementary files format and content: HDF5 Feature Barcode Matrix Format. Fin Fin regenerates of quadruple transgenic fish [Tg7xTCF Xla.Sia:NLS mCherryia5 x Tg 2.7shha:GFPt10 x TgOla.Sp7:CreERT2 p2a mCherrytud8 x TgHsa.RUNX2 Mmu.Fos:EGFPzf259] were harvested at 3 dpa cut into small pieces with a scalpel and transferred into 1 ml collagenase dispase solution 1 mg/ml in PBS Roche #10269638001 for 10 min at 28°C. The sample was pipetted slowly up and down with an elongated flame polished Pasteur pipette. The procedure was repeated 4 times with decreasing inner tip diameters of the Pasteur pipettes until a homogenous solution was obtained. The dissociates were poured onto an equilibrated 70 µm cell strainer and collected in 10 ml HBSS solution without xxx and MgCl2 Gibco #12082739. post centrifugation 15 minutes 1800 rpm 4°C the supernatant was discarded and the remaining cell pellet resuspended in 500 µl 2% BSA in PBS. Calcein violet 1µl 10mM Invitrogen #C34858 was added to the cell solution and incubated for 30 minutes. Calcein violet GFP and mCherry+ cells were collected in 50 µl 2% BSA in PBS via fluorescence activated cell sorting BD LSR Fortessa and processed for single cell RNA sequencing analysis based on 10X Genomics 10X Chromium system 10X library preparation according to the manufacturer's instructions. For each experiment about 8000 cells from zebrafish fin regenerates were flow sorted into BSA coated PCR tubes containing 1 µl of PBS with 0.04 % BSA. All cells were carefully mixed with reverse transcription mix before loading them in a Chromium Single Cell A Chip on the 10X Genomics Chromium controller and processed further following the guidelines of the 10X Genomics user manual for single cell 3’ RNA seq v2. In short the droplets were directly subjected to reverse transcription the emulsion was broken and cDNA was purified using silane beads. post amplification of cDNA with 12 cycles it underwent a purification with 0.6 volume of SPRI select beads. post quality check and quantification using the Fragment Analyzer Agilent 30 ng cDNA were used to prepare sc RNA seq libraries involving fragmentation dA Tailing adapter ligation and a 12 cycles indexing PCR based on manufacturer’s guidelines. post quantification both libraries were sequenced on an Illumina Nextseq500 system in paired end mode with 26 bp/57 bp for read 1 and 2 respectively thus generating 60 90 mio. fragments for the transcriptome library on average.   tissue:Fin|cell type:siam+ shha+ osterix+ RUNX2+ fin regenerate cells|genotype:Tg7xTCF Xla.Sia:NLS mCherryia5 x Tg 2.7shha:GFPt10 x TgOla.Sp7:CreERT2 p2a mCherrytud8 x TgHsa.RUNX2 Mmu.Fos:EGFPzf259|treatment stg:3 dy post amputation GSM7988808 GSM7988808: 3rd round of regeneration; Danio rerio; RNA Seq GSM7988808 r1 GSM7988808 1 For each experiment about 8000 cells from zebrafish fin regenerates were flow sorted into BSA coated PCR tubes containing 1 µl of PBS with 0.04 % BSA. All cells were carefully mixed with reverse transcription mix before loading them in a Chromium Single Cell A Chip on the 10X Genomics Chromium controller and processed further following the guidelines of the 10X Genomics user manual for single cell three prime RNA seq v2. In short the droplets were directly subjected to reverse transcription the emulsion was broken and cDNA was purified using silane beads. post amplification of cDNA with 12 cycles it underwent a purification with 0.6 volume of SPRI select beads. post quality check and quantification using the Fragment Analyzer Agilent 30 ng cDNA were used to prepare sc RNA seq libraries involving fragmentation dA Tailing adapter ligation and a 12 cycles indexing PCR based on manufacturer's guidelines. post quantification both libraries were sequenced on an Illumina Nextseq500 system in paired end mode with 26 bp/57 bp for read 1 and 2 respectively thus generating 60 90 mio. fragments for the transcriptome library on average.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 500   SRP479569     L33267_osteoblasts_reg3_R1.fastq.gz L33267_osteoblasts_reg3_R2.fastq.gz fastq fastq 5171923722.0 62312334.0 GSM7988808 r1 0:26 1:57 A:1429339406;C:1125953827;G:1205184308;T:1408611366;N:2834815 26 57     1429339406 1125953827 1205184308 1408611366 2834815 SRX22998812 SRS19963382 SRA1774238 Dresden-concept Genome Center (DcGC), Center for Molecular and Cellular Bioengineering (CMCB), TU Dresden Dresden-concept Genome Center (DcGC), Center for Molecular and Cellular Bioengineering (CMCB), TU Dresden 2 0.01041 0.92057 0.00236 0.13516 0.98198 0.82244 0.45267 0.53338 26 57 T B sc-like readlen illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   Germany 2023-12-21 Undetermined Undetermined Fin Surface Structure
29199 29199 SRR27321692 SRX22998811 SRS19963381 SRP479569 PRJNA1055522 Compartmentalization and synergy of osteoblasts drive bone formation in the regenerating fin GSE251828 Transcriptome Analysis This study investigated the cell composition and lineage relationships of FACS fluorescence activated cell sorting enriched epidermal bone forming osteoblast and non osteoblast blastemal fin regenerate cells by single cell sc RNA sequencing. The repetitive cell harvesting in four week intervals revealed a constant gene regulation over four successive regeneration rounds in the early outgrowth stage. In addition the sc RNA dataset uncovered a potential lineage relationship between distal blastema cells and osteoblasts during fin regeneration. These findings together with the identification of novel fin regenerate markers advance our understanding of complex tissue regeneration in zebrafish. Overall design: To study potentially underrepresented cell populations during zebrafish fin regeneration we harvested single cells and FACS enriched for siam+ shha+ osterix+ RUNX2+ cells via respective mCherry and GFP reporter fluorophores. We performed gene expression analysis using data obtained from RNA seq of enriched cells from 4 successive regeneration stages at 3 dpa.   pubmed:38318374   2nd round of regeneration GSM7988807   source name:Fin|tissue:Fin|cell type:siam+ shha+ osterix+ RUNX2+ fin regenerate cells|genotype:Tg7xTCF Xla.Sia:NLS mCherryia5 x Tg 2.7shha:GFPt10 x TgOla.Sp7:CreERT2 p2a mCherrytud8 x TgHsa.RUNX2 Mmu.Fos:EGFPzf259|treatment stg:3 dy post amputation|geo loc name:missing|collection date:missing 2nd round of regeneration A reference based on GRCz10 Ensembl annotation e98 was created by first adding the sequences of gfp and mCherry as separate chromosomes to the fa file and the gtf file and then building the cellranger reference using cellranger mkref v3.0.0 fastq files were processed with `cellranger count` from 10X genomics version 3.0.0 Assembly: GRCz10 Supplementary files format and content: HDF5 Feature Barcode Matrix Format. Fin Fin regenerates of quadruple transgenic fish [Tg7xTCF Xla.Sia:NLS mCherryia5 x Tg 2.7shha:GFPt10 x TgOla.Sp7:CreERT2 p2a mCherrytud8 x TgHsa.RUNX2 Mmu.Fos:EGFPzf259] were harvested at 3 dpa cut into small pieces with a scalpel and transferred into 1 ml collagenase dispase solution 1 mg/ml in PBS Roche #10269638001 for 10 min at 28°C. The sample was pipetted slowly up and down with an elongated flame polished Pasteur pipette. The procedure was repeated 4 times with decreasing inner tip diameters of the Pasteur pipettes until a homogenous solution was obtained. The dissociates were poured onto an equilibrated 70 µm cell strainer and collected in 10 ml HBSS solution without xxx and MgCl2 Gibco #12082739. post centrifugation 15 minutes 1800 rpm 4°C the supernatant was discarded and the remaining cell pellet resuspended in 500 µl 2% BSA in PBS. Calcein violet 1µl 10mM Invitrogen #C34858 was added to the cell solution and incubated for 30 minutes. Calcein violet GFP and mCherry+ cells were collected in 50 µl 2% BSA in PBS via fluorescence activated cell sorting BD LSR Fortessa and processed for single cell RNA sequencing analysis based on 10X Genomics 10X Chromium system 10X library preparation according to the manufacturer's instructions. For each experiment about 8000 cells from zebrafish fin regenerates were flow sorted into BSA coated PCR tubes containing 1 µl of PBS with 0.04 % BSA. All cells were carefully mixed with reverse transcription mix before loading them in a Chromium Single Cell A Chip on the 10X Genomics Chromium controller and processed further following the guidelines of the 10X Genomics user manual for single cell 3’ RNA seq v2. In short the droplets were directly subjected to reverse transcription the emulsion was broken and cDNA was purified using silane beads. post amplification of cDNA with 12 cycles it underwent a purification with 0.6 volume of SPRI select beads. post quality check and quantification using the Fragment Analyzer Agilent 30 ng cDNA were used to prepare sc RNA seq libraries involving fragmentation dA Tailing adapter ligation and a 12 cycles indexing PCR based on manufacturer’s guidelines. post quantification both libraries were sequenced on an Illumina Nextseq500 system in paired end mode with 26 bp/57 bp for read 1 and 2 respectively thus generating 60 90 mio. fragments for the transcriptome library on average.   tissue:Fin|cell type:siam+ shha+ osterix+ RUNX2+ fin regenerate cells|genotype:Tg7xTCF Xla.Sia:NLS mCherryia5 x Tg 2.7shha:GFPt10 x TgOla.Sp7:CreERT2 p2a mCherrytud8 x TgHsa.RUNX2 Mmu.Fos:EGFPzf259|treatment stg:3 dy post amputation GSM7988807 GSM7988807: 2nd round of regeneration; Danio rerio; RNA Seq GSM7988807 r1 GSM7988807 1 For each experiment about 8000 cells from zebrafish fin regenerates were flow sorted into BSA coated PCR tubes containing 1 µl of PBS with 0.04 % BSA. All cells were carefully mixed with reverse transcription mix before loading them in a Chromium Single Cell A Chip on the 10X Genomics Chromium controller and processed further following the guidelines of the 10X Genomics user manual for single cell three prime RNA seq v2. In short the droplets were directly subjected to reverse transcription the emulsion was broken and cDNA was purified using silane beads. post amplification of cDNA with 12 cycles it underwent a purification with 0.6 volume of SPRI select beads. post quality check and quantification using the Fragment Analyzer Agilent 30 ng cDNA were used to prepare sc RNA seq libraries involving fragmentation dA Tailing adapter ligation and a 12 cycles indexing PCR based on manufacturer's guidelines. post quantification both libraries were sequenced on an Illumina Nextseq500 system in paired end mode with 26 bp/57 bp for read 1 and 2 respectively thus generating 60 90 mio. fragments for the transcriptome library on average.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 500   SRP479569     L32508_osteoblasts_reg2_R1.fastq.gz L32508_osteoblasts_reg2_R2.fastq.gz fastq fastq 6922720659.0 83406273.0 GSM7988807 r1 0:26 1:57 A:1901173243;C:1540845413;G:1598673449;T:1877295749;N:4732805 26 57     1901173243 1540845413 1598673449 1877295749 4732805 SRX22998811 SRS19963381 SRA1774238 Dresden-concept Genome Center (DcGC), Center for Molecular and Cellular Bioengineering (CMCB), TU Dresden Dresden-concept Genome Center (DcGC), Center for Molecular and Cellular Bioengineering (CMCB), TU Dresden 2 0.00257 0.93924 0.00083 0.10412 0.99474 0.83023 0.47435 0.51839 26 57 T B sc-like readlen illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   Germany 2023-12-21 Undetermined Undetermined Fin Surface Structure
29200 29200 SRR27321693 SRX22998810 SRS19963380 SRP479569 PRJNA1055522 Compartmentalization and synergy of osteoblasts drive bone formation in the regenerating fin GSE251828 Transcriptome Analysis This study investigated the cell composition and lineage relationships of FACS fluorescence activated cell sorting enriched epidermal bone forming osteoblast and non osteoblast blastemal fin regenerate cells by single cell sc RNA sequencing. The repetitive cell harvesting in four week intervals revealed a constant gene regulation over four successive regeneration rounds in the early outgrowth stage. In addition the sc RNA dataset uncovered a potential lineage relationship between distal blastema cells and osteoblasts during fin regeneration. These findings together with the identification of novel fin regenerate markers advance our understanding of complex tissue regeneration in zebrafish. Overall design: To study potentially underrepresented cell populations during zebrafish fin regeneration we harvested single cells and FACS enriched for siam+ shha+ osterix+ RUNX2+ cells via respective mCherry and GFP reporter fluorophores. We performed gene expression analysis using data obtained from RNA seq of enriched cells from 4 successive regeneration stages at 3 dpa.   pubmed:38318374   1st round of regeneration GSM7988806   source name:Fin|tissue:Fin|cell type:siam+ shha+ osterix+ RUNX2+ fin regenerate cells|genotype:Tg7xTCF Xla.Sia:NLS mCherryia5 x Tg 2.7shha:GFPt10 x TgOla.Sp7:CreERT2 p2a mCherrytud8 x TgHsa.RUNX2 Mmu.Fos:EGFPzf259|treatment stg:3 dy post amputation|geo loc name:missing|collection date:missing 1st round of regeneration A reference based on GRCz10 Ensembl annotation e98 was created by first adding the sequences of gfp and mCherry as separate chromosomes to the fa file and the gtf file and then building the cellranger reference using cellranger mkref v3.0.0 fastq files were processed with `cellranger count` from 10X genomics version 3.0.0 Assembly: GRCz10 Supplementary files format and content: HDF5 Feature Barcode Matrix Format. Fin Fin regenerates of quadruple transgenic fish [Tg7xTCF Xla.Sia:NLS mCherryia5 x Tg 2.7shha:GFPt10 x TgOla.Sp7:CreERT2 p2a mCherrytud8 x TgHsa.RUNX2 Mmu.Fos:EGFPzf259] were harvested at 3 dpa cut into small pieces with a scalpel and transferred into 1 ml collagenase dispase solution 1 mg/ml in PBS Roche #10269638001 for 10 min at 28°C. The sample was pipetted slowly up and down with an elongated flame polished Pasteur pipette. The procedure was repeated 4 times with decreasing inner tip diameters of the Pasteur pipettes until a homogenous solution was obtained. The dissociates were poured onto an equilibrated 70 µm cell strainer and collected in 10 ml HBSS solution without xxx and MgCl2 Gibco #12082739. post centrifugation 15 minutes 1800 rpm 4°C the supernatant was discarded and the remaining cell pellet resuspended in 500 µl 2% BSA in PBS. Calcein violet 1µl 10mM Invitrogen #C34858 was added to the cell solution and incubated for 30 minutes. Calcein violet GFP and mCherry+ cells were collected in 50 µl 2% BSA in PBS via fluorescence activated cell sorting BD LSR Fortessa and processed for single cell RNA sequencing analysis based on 10X Genomics 10X Chromium system 10X library preparation according to the manufacturer's instructions. For each experiment about 8000 cells from zebrafish fin regenerates were flow sorted into BSA coated PCR tubes containing 1 µl of PBS with 0.04 % BSA. All cells were carefully mixed with reverse transcription mix before loading them in a Chromium Single Cell A Chip on the 10X Genomics Chromium controller and processed further following the guidelines of the 10X Genomics user manual for single cell 3’ RNA seq v2. In short the droplets were directly subjected to reverse transcription the emulsion was broken and cDNA was purified using silane beads. post amplification of cDNA with 12 cycles it underwent a purification with 0.6 volume of SPRI select beads. post quality check and quantification using the Fragment Analyzer Agilent 30 ng cDNA were used to prepare sc RNA seq libraries involving fragmentation dA Tailing adapter ligation and a 12 cycles indexing PCR based on manufacturer’s guidelines. post quantification both libraries were sequenced on an Illumina Nextseq500 system in paired end mode with 26 bp/57 bp for read 1 and 2 respectively thus generating 60 90 mio. fragments for the transcriptome library on average.   tissue:Fin|cell type:siam+ shha+ osterix+ RUNX2+ fin regenerate cells|genotype:Tg7xTCF Xla.Sia:NLS mCherryia5 x Tg 2.7shha:GFPt10 x TgOla.Sp7:CreERT2 p2a mCherrytud8 x TgHsa.RUNX2 Mmu.Fos:EGFPzf259|treatment stg:3 dy post amputation GSM7988806 GSM7988806: 1st round of regeneration; Danio rerio; RNA Seq GSM7988806 r1 GSM7988806 1 For each experiment about 8000 cells from zebrafish fin regenerates were flow sorted into BSA coated PCR tubes containing 1 µl of PBS with 0.04 % BSA. All cells were carefully mixed with reverse transcription mix before loading them in a Chromium Single Cell A Chip on the 10X Genomics Chromium controller and processed further following the guidelines of the 10X Genomics user manual for single cell three prime RNA seq v2. In short the droplets were directly subjected to reverse transcription the emulsion was broken and cDNA was purified using silane beads. post amplification of cDNA with 12 cycles it underwent a purification with 0.6 volume of SPRI select beads. post quality check and quantification using the Fragment Analyzer Agilent 30 ng cDNA were used to prepare sc RNA seq libraries involving fragmentation dA Tailing adapter ligation and a 12 cycles indexing PCR based on manufacturer's guidelines. post quantification both libraries were sequenced on an Illumina Nextseq500 system in paired end mode with 26 bp/57 bp for read 1 and 2 respectively thus generating 60 90 mio. fragments for the transcriptome library on average.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 500   SRP479569     L32023_osteoblasts_reg1_R1.fastq.gz L32023_osteoblasts_reg1_R2.fastq.gz fastq fastq 15070528207.0 181572629.0 GSM7988806 r1 0:26 1:57 A:4238593010;C:3314457079;G:3500292725;T:4013398538;N:3786855 26 57     4238593010 3314457079 3500292725 4013398538 3786855 SRX22998810 SRS19963380 SRA1774238 Dresden-concept Genome Center (DcGC), Center for Molecular and Cellular Bioengineering (CMCB), TU Dresden Dresden-concept Genome Center (DcGC), Center for Molecular and Cellular Bioengineering (CMCB), TU Dresden 2 0.01031 0.92947 0.00392 0.17331 0.98526 0.81815 0.4321 0.54688 26 57 T B sc-like readlen illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   Germany 2023-12-21 Undetermined Undetermined Fin Surface Structure
30702 30702 SRR28328136 SRX23936571 SRS20740255 SRP494948 PRJNA1086823 Danio rerio Raw sequence reads PRJNA1086823 Whole Genome Sequencing Study the effects on the body when this gene is lost     Study the effects on the body when this gene is lost Model organism or animal sample from Danio rerio tu   strain:FISH|age:2|collection date:2023 02 28|geo loc name:missing|sex:missing|tissue:missing|biomaterial provider:missing|BioSampleModel:Model organism or animal                 SampleF 6 6 control     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA HiSeq X Ten   SRP494948     tu_3.R1.raw.fastq.gz tu_3.R2.raw.fastq.gz fastq fastq 6836795894.0 22638397.0 tu 3.R1.raw.fastq.gz 0:151 1:151 A:1911756035;C:1496221872;G:1563235044;T:1865509810;N:73133 151 151     1911756035 1496221872 1563235044 1865509810 73133 SRX23936571 SRS20740255 SRA1823374 Hunan Normal University|Hunan Normal University Hunan Normal University                       B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2024-03-13 Undetermined Undetermined Trunk Surface Structure
30703 30703 SRR28328137 SRX23936570 SRS20740255 SRP494948 PRJNA1086823 Danio rerio Raw sequence reads PRJNA1086823 Whole Genome Sequencing Study the effects on the body when this gene is lost     Study the effects on the body when this gene is lost Model organism or animal sample from Danio rerio tu   strain:FISH|age:2|collection date:2023 02 28|geo loc name:missing|sex:missing|tissue:missing|biomaterial provider:missing|BioSampleModel:Model organism or animal                 SampleE 5 5 control     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA HiSeq X Ten   SRP494948     tu_2.R1.raw.fastq.gz tu_2.R2.raw.fastq.gz fastq fastq 6933313282.0 22957991.0 tu 2.R1.raw.fastq.gz 0:151 1:151 A:1895897966;C:1562896362;G:1633152399;T:1841286721;N:79834 151 151     1895897966 1562896362 1633152399 1841286721 79834 SRX23936570 SRS20740255 SRA1823374 Hunan Normal University|Hunan Normal University Hunan Normal University                       B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2024-03-13 Undetermined Undetermined Trunk Surface Structure
30704 30704 SRR28328138 SRX23936569 SRS20740255 SRP494948 PRJNA1086823 Danio rerio Raw sequence reads PRJNA1086823 Whole Genome Sequencing Study the effects on the body when this gene is lost     Study the effects on the body when this gene is lost Model organism or animal sample from Danio rerio tu   strain:FISH|age:2|collection date:2023 02 28|geo loc name:missing|sex:missing|tissue:missing|biomaterial provider:missing|BioSampleModel:Model organism or animal                 SampleD 4 4 control     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA HiSeq X Ten   SRP494948     tu_1.R1.raw.fastq.gz tu_1.R2.raw.fastq.gz fastq fastq 6953463930.0 23024715.0 tu 1.R1.raw.fastq.gz 0:151 1:151 A:1914281996;C:1558685345;G:1630355775;T:1850061551;N:79263 151 151     1914281996 1558685345 1630355775 1850061551 79263 SRX23936569 SRS20740255 SRA1823374 Hunan Normal University|Hunan Normal University Hunan Normal University                       B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2024-03-13 Undetermined Undetermined Trunk Surface Structure
30705 30705 SRR28328139 SRX23936568 SRS20740254 SRP494948 PRJNA1086823 Danio rerio Raw sequence reads PRJNA1086823 Whole Genome Sequencing Study the effects on the body when this gene is lost     Study the effects on the body when this gene is lost Model organism or animal sample from Danio rerio myo7aa   strain:FISH|age:2|collection date:2023 02 28|geo loc name:missing|sex:missing|tissue:missing|BioSampleModel:Model organism or animal                 SampleC 3 3 treatment     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA HiSeq X Ten   SRP494948     myo7aa_3.R1.raw.fastq.gz myo7aa_3.R2.raw.fastq.gz fastq fastq 6793366180.0 22494590.0 myo7aa 3.R1.raw.fastq.gz 0:151 1:151 A:1786353133;C:1602317410;G:1674855786;T:1729822151;N:17700 151 151     1786353133 1602317410 1674855786 1729822151 17700 SRX23936568 SRS20740254 SRA1823374 Hunan Normal University|Hunan Normal University Hunan Normal University                       B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2024-03-13 Undetermined Undetermined Trunk Surface Structure
30706 30706 SRR28328140 SRX23936567 SRS20740254 SRP494948 PRJNA1086823 Danio rerio Raw sequence reads PRJNA1086823 Whole Genome Sequencing Study the effects on the body when this gene is lost     Study the effects on the body when this gene is lost Model organism or animal sample from Danio rerio myo7aa   strain:FISH|age:2|collection date:2023 02 28|geo loc name:missing|sex:missing|tissue:missing|BioSampleModel:Model organism or animal                 SampleB 2 2 treatment     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA HiSeq X Ten   SRP494948     myo7aa_2.R1.raw.fastq.gz myo7aa_2.R2.raw.fastq.gz fastq fastq 6762797438.0 22393369.0 myo7aa 2.R1.raw.fastq.gz 0:151 1:151 A:1816704062;C:1557768239;G:1627373716;T:1760926609;N:24812 151 151     1816704062 1557768239 1627373716 1760926609 24812 SRX23936567 SRS20740254 SRA1823374 Hunan Normal University|Hunan Normal University Hunan Normal University                       B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2024-03-13 Undetermined Undetermined Trunk Surface Structure
30707 30707 SRR28328141 SRX23936566 SRS20740254 SRP494948 PRJNA1086823 Danio rerio Raw sequence reads PRJNA1086823 Whole Genome Sequencing Study the effects on the body when this gene is lost     Study the effects on the body when this gene is lost Model organism or animal sample from Danio rerio myo7aa   strain:FISH|age:2|collection date:2023 02 28|geo loc name:missing|sex:missing|tissue:missing|BioSampleModel:Model organism or animal                 SampleA 1 1 treatment     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA HiSeq X Ten   SRP494948     myo7aa_1.R1.raw.fastq.gz myo7aa_1.R2.raw.fastq.gz fastq fastq 6605710628.0 21873214.0 myo7aa 1.R1.raw.fastq.gz 0:151 1:151 A:1728796843;C:1565920605;G:1629477870;T:1681497978;N:17332 151 151     1728796843 1565920605 1629477870 1681497978 17332 SRX23936566 SRS20740254 SRA1823374 Hunan Normal University|Hunan Normal University Hunan Normal University                       B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2024-03-13 Undetermined Undetermined Trunk Surface Structure
33894 33894 SRR30866028 SRX26263941 SRS22803195 SRP536275 PRJNA1168148 Mgat4b mediated selective N glycosyl modification regulates melanocyte development and melanoma progression [bulk RNA seq] GSE278653 Transcriptome Analysis Dysregulated melanocyte state transitions are a pivotal driver of melanoma development highlighting the need to identify key regulators of these processes. Understanding these factors is key to know how normal melanocyte functions and shift towards initiation of melanoma. Our study identifies Mgat4b a glycosyl transferase involved in selective N glycan branching enriched in pigment progenitors as a key regulator of directional melanocyte migration and establishment of Melanocyte stem cell McSC pool during early development in zebrafish and mammalian melanocytes. Single cell RNA sequencing analysis in zebrafish upon targeted disruption of Mgat4b reveals that a subset of melanocytes marked by aberrant galectin expression are impaired in migration and are lost. Lectin binding proteomic analysis reveals the glycosylation of key melanocyte proteins Gpnmb Kit and Tyrp1 to be under the control of Mgat4b. Additionally mislocalization of Gamma catenin Jup explains the observed defects in cell adhesion and migration to be regulated by mgat4b but not its isozyme mgat4a. Our meta analysis further revealed that melanoma patients with both the BrafV600E mutation and elevated Mgat4b levels have significantly worse survival outcomes compared to those with only the BrafV600E mutation. By leveraging the MAZERATI platform to model BrafV600E driver mutation in vivo we show that Mgat4b mutant cells fail to aggregate and initiate tumors. Our study underscores the importance of selective N glycan branching in both melanocyte development and melanoma initiation suggesting a Mitf controlled Mgat4b as a promising therapeutic target for melanoma treatment. Overall design: To investigate the mechanisms that inhibit mutant cells from initiating melanoma in the absence of mgat4b we utilized mature melanophores and melanoma cells from the skin of five zebrafish including both MAZERATI wild type and MAZERATI zebrafish carrying mgat4b mutations. We then performed gene expression profiling analysis using data obtained from RNA seq of m…       m4b mut melanoma biol rep 2 GSM8552314   source name:skin|tissue:skin|cell type:melanoma|genotype:mgat4b mutant|treatment:MAZERATI|geo loc name:missing|collection date:missing m4b mut melanoma biol rep 2 Raw fastq files were trimmed using trimmomatic to remove adaptors and retain high quality reads. The reads were then aligned with zebrafish reference assembly GRCz11 using STAR. Featurecounts was used to calculate raw counts from the aligned reads. Assembly: GRCz11 Supplementary files format and content: tab delimited text file including raw counts for each sample skin   The cell isolation process involved density gradient centrifugation followed by RNA extraction using Trizol method. Illumina standard total RNA prep kit was used for library construction   tissue:skin|cell type:melanoma|genotype:mgat4b mutant|treatment:MAZERATI GSM8552314 GSM8552314: m4b mut melanoma biol rep 2; Danio rerio; RNA Seq GSM8552314 r1 GSM8552314 1 The cell isolation process involved density gradient centrifugation followed by RNA extraction using Trizol method. Illumina standard total RNA prep kit was used for library construction   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 2000   SRP536275     MKO2_S39_R1_001.fastq.gz MKO2_S39_R2_001.fastq.gz fastq fastq 3705364625.0 14164066.0 GSM8552314 r1 0:126.72 1:134.89 A:785806700;C:949078797;G:1178279032;T:784972987;N:7227109 126 134     785806700 949078797 1178279032 784972987 7227109 SRX26263941 SRS22803195 SRA1984938 Pigment Cell Biology Lab, CSIR-IGIB Pigment Cell Biology Lab, CSIR-IGIB                       B B biological fallback assumption illumina nextseq_v2 unknown cdna_unspecified trueseq sc_generic bulk bulk   India 2024-10-02 Undetermined Undetermined Skin Surface Structure
33895 33895 SRR30866029 SRX26263940 SRS22803194 SRP536275 PRJNA1168148 Mgat4b mediated selective N glycosyl modification regulates melanocyte development and melanoma progression [bulk RNA seq] GSE278653 Transcriptome Analysis Dysregulated melanocyte state transitions are a pivotal driver of melanoma development highlighting the need to identify key regulators of these processes. Understanding these factors is key to know how normal melanocyte functions and shift towards initiation of melanoma. Our study identifies Mgat4b a glycosyl transferase involved in selective N glycan branching enriched in pigment progenitors as a key regulator of directional melanocyte migration and establishment of Melanocyte stem cell McSC pool during early development in zebrafish and mammalian melanocytes. Single cell RNA sequencing analysis in zebrafish upon targeted disruption of Mgat4b reveals that a subset of melanocytes marked by aberrant galectin expression are impaired in migration and are lost. Lectin binding proteomic analysis reveals the glycosylation of key melanocyte proteins Gpnmb Kit and Tyrp1 to be under the control of Mgat4b. Additionally mislocalization of Gamma catenin Jup explains the observed defects in cell adhesion and migration to be regulated by mgat4b but not its isozyme mgat4a. Our meta analysis further revealed that melanoma patients with both the BrafV600E mutation and elevated Mgat4b levels have significantly worse survival outcomes compared to those with only the BrafV600E mutation. By leveraging the MAZERATI platform to model BrafV600E driver mutation in vivo we show that Mgat4b mutant cells fail to aggregate and initiate tumors. Our study underscores the importance of selective N glycan branching in both melanocyte development and melanoma initiation suggesting a Mitf controlled Mgat4b as a promising therapeutic target for melanoma treatment. Overall design: To investigate the mechanisms that inhibit mutant cells from initiating melanoma in the absence of mgat4b we utilized mature melanophores and melanoma cells from the skin of five zebrafish including both MAZERATI wild type and MAZERATI zebrafish carrying mgat4b mutations. We then performed gene expression profiling analysis using data obtained from RNA seq of m…       m4b mut melanoma biol rep 1 GSM8552313   source name:skin|tissue:skin|cell type:melanoma|genotype:mgat4b mutant|treatment:MAZERATI|geo loc name:missing|collection date:missing m4b mut melanoma biol rep 1 Raw fastq files were trimmed using trimmomatic to remove adaptors and retain high quality reads. The reads were then aligned with zebrafish reference assembly GRCz11 using STAR. Featurecounts was used to calculate raw counts from the aligned reads. Assembly: GRCz11 Supplementary files format and content: tab delimited text file including raw counts for each sample skin   The cell isolation process involved density gradient centrifugation followed by RNA extraction using Trizol method. Illumina standard total RNA prep kit was used for library construction   tissue:skin|cell type:melanoma|genotype:mgat4b mutant|treatment:MAZERATI GSM8552313 GSM8552313: m4b mut melanoma biol rep 1; Danio rerio; RNA Seq GSM8552313 r1 GSM8552313 1 The cell isolation process involved density gradient centrifugation followed by RNA extraction using Trizol method. Illumina standard total RNA prep kit was used for library construction   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 2000   SRP536275     MKO1_S38_R1_001.fastq.gz MKO1_S38_R2_001.fastq.gz fastq fastq 4779377372.0 18058294.0 GSM8552313 r1 0:128.72 1:135.94 A:1016908920;C:1236613888;G:1502465334;T:1018053808;N:5335422 128 135     1016908920 1236613888 1502465334 1018053808 5335422 SRX26263940 SRS22803194 SRA1984938 Pigment Cell Biology Lab, CSIR-IGIB Pigment Cell Biology Lab, CSIR-IGIB                       B B biological fallback assumption illumina nextseq_v2 unknown cdna_unspecified trueseq sc_generic bulk bulk   India 2024-10-02 Undetermined Undetermined Skin Surface Structure
33896 33896 SRR30866030 SRX26263939 SRS22803193 SRP536275 PRJNA1168148 Mgat4b mediated selective N glycosyl modification regulates melanocyte development and melanoma progression [bulk RNA seq] GSE278653 Transcriptome Analysis Dysregulated melanocyte state transitions are a pivotal driver of melanoma development highlighting the need to identify key regulators of these processes. Understanding these factors is key to know how normal melanocyte functions and shift towards initiation of melanoma. Our study identifies Mgat4b a glycosyl transferase involved in selective N glycan branching enriched in pigment progenitors as a key regulator of directional melanocyte migration and establishment of Melanocyte stem cell McSC pool during early development in zebrafish and mammalian melanocytes. Single cell RNA sequencing analysis in zebrafish upon targeted disruption of Mgat4b reveals that a subset of melanocytes marked by aberrant galectin expression are impaired in migration and are lost. Lectin binding proteomic analysis reveals the glycosylation of key melanocyte proteins Gpnmb Kit and Tyrp1 to be under the control of Mgat4b. Additionally mislocalization of Gamma catenin Jup explains the observed defects in cell adhesion and migration to be regulated by mgat4b but not its isozyme mgat4a. Our meta analysis further revealed that melanoma patients with both the BrafV600E mutation and elevated Mgat4b levels have significantly worse survival outcomes compared to those with only the BrafV600E mutation. By leveraging the MAZERATI platform to model BrafV600E driver mutation in vivo we show that Mgat4b mutant cells fail to aggregate and initiate tumors. Our study underscores the importance of selective N glycan branching in both melanocyte development and melanoma initiation suggesting a Mitf controlled Mgat4b as a promising therapeutic target for melanoma treatment. Overall design: To investigate the mechanisms that inhibit mutant cells from initiating melanoma in the absence of mgat4b we utilized mature melanophores and melanoma cells from the skin of five zebrafish including both MAZERATI wild type and MAZERATI zebrafish carrying mgat4b mutations. We then performed gene expression profiling analysis using data obtained from RNA seq of m…       wild type melanoma control biol rep 2 GSM8552312   source name:skin|tissue:skin|cell type:melanoma|genotype:WT|treatment:MAZERATI|geo loc name:missing|collection date:missing wild type melanoma control biol rep 2 Raw fastq files were trimmed using trimmomatic to remove adaptors and retain high quality reads. The reads were then aligned with zebrafish reference assembly GRCz11 using STAR. Featurecounts was used to calculate raw counts from the aligned reads. Assembly: GRCz11 Supplementary files format and content: tab delimited text file including raw counts for each sample skin   The cell isolation process involved density gradient centrifugation followed by RNA extraction using Trizol method. Illumina standard total RNA prep kit was used for library construction   tissue:skin|cell type:melanoma|genotype:WT|treatment:MAZERATI GSM8552312 GSM8552312: wild type melanoma control biol rep 2; Danio rerio; RNA Seq GSM8552312 r1 GSM8552312 1 The cell isolation process involved density gradient centrifugation followed by RNA extraction using Trizol method. Illumina standard total RNA prep kit was used for library construction   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 2000   SRP536275     EV2_S37_R1_001.fastq.gz EV2_S37_R2_001.fastq.gz fastq fastq 5427379509.0 19981504.0 GSM8552312 r1 0:133.16 1:138.46 A:1136639418;C:1414638483;G:1736492639;T:1137614638;N:1994331 133 138     1136639418 1414638483 1736492639 1137614638 1994331 SRX26263939 SRS22803193 SRA1984938 Pigment Cell Biology Lab, CSIR-IGIB Pigment Cell Biology Lab, CSIR-IGIB                       B B biological fallback assumption illumina nextseq_v2 unknown cdna_unspecified trueseq sc_generic bulk bulk   India 2024-10-02 Undetermined Undetermined Skin Surface Structure
33897 33897 SRR30866031 SRX26263938 SRS22803192 SRP536275 PRJNA1168148 Mgat4b mediated selective N glycosyl modification regulates melanocyte development and melanoma progression [bulk RNA seq] GSE278653 Transcriptome Analysis Dysregulated melanocyte state transitions are a pivotal driver of melanoma development highlighting the need to identify key regulators of these processes. Understanding these factors is key to know how normal melanocyte functions and shift towards initiation of melanoma. Our study identifies Mgat4b a glycosyl transferase involved in selective N glycan branching enriched in pigment progenitors as a key regulator of directional melanocyte migration and establishment of Melanocyte stem cell McSC pool during early development in zebrafish and mammalian melanocytes. Single cell RNA sequencing analysis in zebrafish upon targeted disruption of Mgat4b reveals that a subset of melanocytes marked by aberrant galectin expression are impaired in migration and are lost. Lectin binding proteomic analysis reveals the glycosylation of key melanocyte proteins Gpnmb Kit and Tyrp1 to be under the control of Mgat4b. Additionally mislocalization of Gamma catenin Jup explains the observed defects in cell adhesion and migration to be regulated by mgat4b but not its isozyme mgat4a. Our meta analysis further revealed that melanoma patients with both the BrafV600E mutation and elevated Mgat4b levels have significantly worse survival outcomes compared to those with only the BrafV600E mutation. By leveraging the MAZERATI platform to model BrafV600E driver mutation in vivo we show that Mgat4b mutant cells fail to aggregate and initiate tumors. Our study underscores the importance of selective N glycan branching in both melanocyte development and melanoma initiation suggesting a Mitf controlled Mgat4b as a promising therapeutic target for melanoma treatment. Overall design: To investigate the mechanisms that inhibit mutant cells from initiating melanoma in the absence of mgat4b we utilized mature melanophores and melanoma cells from the skin of five zebrafish including both MAZERATI wild type and MAZERATI zebrafish carrying mgat4b mutations. We then performed gene expression profiling analysis using data obtained from RNA seq of m…       wild type melanoma control biol rep 1 GSM8552311   source name:skin|tissue:skin|cell type:melanoma|genotype:WT|treatment:MAZERATI|geo loc name:missing|collection date:missing wild type melanoma control biol rep 1 Raw fastq files were trimmed using trimmomatic to remove adaptors and retain high quality reads. The reads were then aligned with zebrafish reference assembly GRCz11 using STAR. Featurecounts was used to calculate raw counts from the aligned reads. Assembly: GRCz11 Supplementary files format and content: tab delimited text file including raw counts for each sample skin   The cell isolation process involved density gradient centrifugation followed by RNA extraction using Trizol method. Illumina standard total RNA prep kit was used for library construction   tissue:skin|cell type:melanoma|genotype:WT|treatment:MAZERATI GSM8552311 GSM8552311: wild type melanoma control biol rep 1; Danio rerio; RNA Seq GSM8552311 r1 GSM8552311 1 The cell isolation process involved density gradient centrifugation followed by RNA extraction using Trizol method. Illumina standard total RNA prep kit was used for library construction   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 2000   SRP536275     EV1_S36_R1_001.fastq.gz EV1_S36_R2_001.fastq.gz fastq fastq 5248108957.0 19087024.0 GSM8552311 r1 0:135.12 1:139.84 A:1112163842;C:1354895660;G:1658732932;T:1120342985;N:1973538 135 139     1112163842 1354895660 1658732932 1120342985 1973538 SRX26263938 SRS22803192 SRA1984938 Pigment Cell Biology Lab, CSIR-IGIB Pigment Cell Biology Lab, CSIR-IGIB                       B B biological fallback assumption illumina nextseq_v2 unknown cdna_unspecified trueseq sc_generic bulk bulk   India 2024-10-02 Undetermined Undetermined Skin Surface Structure
33898 33898 SRR30866032 SRX26263937 SRS22803191 SRP536275 PRJNA1168148 Mgat4b mediated selective N glycosyl modification regulates melanocyte development and melanoma progression [bulk RNA seq] GSE278653 Transcriptome Analysis Dysregulated melanocyte state transitions are a pivotal driver of melanoma development highlighting the need to identify key regulators of these processes. Understanding these factors is key to know how normal melanocyte functions and shift towards initiation of melanoma. Our study identifies Mgat4b a glycosyl transferase involved in selective N glycan branching enriched in pigment progenitors as a key regulator of directional melanocyte migration and establishment of Melanocyte stem cell McSC pool during early development in zebrafish and mammalian melanocytes. Single cell RNA sequencing analysis in zebrafish upon targeted disruption of Mgat4b reveals that a subset of melanocytes marked by aberrant galectin expression are impaired in migration and are lost. Lectin binding proteomic analysis reveals the glycosylation of key melanocyte proteins Gpnmb Kit and Tyrp1 to be under the control of Mgat4b. Additionally mislocalization of Gamma catenin Jup explains the observed defects in cell adhesion and migration to be regulated by mgat4b but not its isozyme mgat4a. Our meta analysis further revealed that melanoma patients with both the BrafV600E mutation and elevated Mgat4b levels have significantly worse survival outcomes compared to those with only the BrafV600E mutation. By leveraging the MAZERATI platform to model BrafV600E driver mutation in vivo we show that Mgat4b mutant cells fail to aggregate and initiate tumors. Our study underscores the importance of selective N glycan branching in both melanocyte development and melanoma initiation suggesting a Mitf controlled Mgat4b as a promising therapeutic target for melanoma treatment. Overall design: To investigate the mechanisms that inhibit mutant cells from initiating melanoma in the absence of mgat4b we utilized mature melanophores and melanoma cells from the skin of five zebrafish including both MAZERATI wild type and MAZERATI zebrafish carrying mgat4b mutations. We then performed gene expression profiling analysis using data obtained from RNA seq of m…       melanophore biol rep 2 GSM8552310   source name:skin|tissue:skin|cell type:melanophore|genotype:WT|treatment:No|geo loc name:missing|collection date:missing melanophore biol rep 2 Raw fastq files were trimmed using trimmomatic to remove adaptors and retain high quality reads. The reads were then aligned with zebrafish reference assembly GRCz11 using STAR. Featurecounts was used to calculate raw counts from the aligned reads. Assembly: GRCz11 Supplementary files format and content: tab delimited text file including raw counts for each sample skin   The cell isolation process involved density gradient centrifugation followed by RNA extraction using Trizol method. Illumina standard total RNA prep kit was used for library construction   tissue:skin|cell type:melanophore|genotype:WT|treatment:No GSM8552310 GSM8552310: melanophore biol rep 2; Danio rerio; RNA Seq GSM8552310 r1 GSM8552310 1 The cell isolation process involved density gradient centrifugation followed by RNA extraction using Trizol method. Illumina standard total RNA prep kit was used for library construction   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 2000   SRP536275     WT2_S41_R1_001.fastq.gz WT2_S41_R2_001.fastq.gz fastq fastq 4636631881.0 16340506.0 GSM8552310 r1 0:140.47 1:143.28 A:1114533149;C:1104066636;G:1293649625;T:1122672029;N:1710442 140 143     1114533149 1104066636 1293649625 1122672029 1710442 SRX26263937 SRS22803191 SRA1984938 Pigment Cell Biology Lab, CSIR-IGIB Pigment Cell Biology Lab, CSIR-IGIB                       B B biological fallback assumption illumina nextseq_v2 unknown cdna_unspecified trueseq sc_generic bulk bulk   India 2024-10-02 Undetermined Undetermined Skin Surface Structure
33899 33899 SRR30866033 SRX26263936 SRS22803190 SRP536275 PRJNA1168148 Mgat4b mediated selective N glycosyl modification regulates melanocyte development and melanoma progression [bulk RNA seq] GSE278653 Transcriptome Analysis Dysregulated melanocyte state transitions are a pivotal driver of melanoma development highlighting the need to identify key regulators of these processes. Understanding these factors is key to know how normal melanocyte functions and shift towards initiation of melanoma. Our study identifies Mgat4b a glycosyl transferase involved in selective N glycan branching enriched in pigment progenitors as a key regulator of directional melanocyte migration and establishment of Melanocyte stem cell McSC pool during early development in zebrafish and mammalian melanocytes. Single cell RNA sequencing analysis in zebrafish upon targeted disruption of Mgat4b reveals that a subset of melanocytes marked by aberrant galectin expression are impaired in migration and are lost. Lectin binding proteomic analysis reveals the glycosylation of key melanocyte proteins Gpnmb Kit and Tyrp1 to be under the control of Mgat4b. Additionally mislocalization of Gamma catenin Jup explains the observed defects in cell adhesion and migration to be regulated by mgat4b but not its isozyme mgat4a. Our meta analysis further revealed that melanoma patients with both the BrafV600E mutation and elevated Mgat4b levels have significantly worse survival outcomes compared to those with only the BrafV600E mutation. By leveraging the MAZERATI platform to model BrafV600E driver mutation in vivo we show that Mgat4b mutant cells fail to aggregate and initiate tumors. Our study underscores the importance of selective N glycan branching in both melanocyte development and melanoma initiation suggesting a Mitf controlled Mgat4b as a promising therapeutic target for melanoma treatment. Overall design: To investigate the mechanisms that inhibit mutant cells from initiating melanoma in the absence of mgat4b we utilized mature melanophores and melanoma cells from the skin of five zebrafish including both MAZERATI wild type and MAZERATI zebrafish carrying mgat4b mutations. We then performed gene expression profiling analysis using data obtained from RNA seq of m…       melanophore biol rep 1 GSM8552309   source name:skin|tissue:skin|cell type:melanophore|genotype:WT|treatment:No|geo loc name:missing|collection date:missing melanophore biol rep 1 Raw fastq files were trimmed using trimmomatic to remove adaptors and retain high quality reads. The reads were then aligned with zebrafish reference assembly GRCz11 using STAR. Featurecounts was used to calculate raw counts from the aligned reads. Assembly: GRCz11 Supplementary files format and content: tab delimited text file including raw counts for each sample skin   The cell isolation process involved density gradient centrifugation followed by RNA extraction using Trizol method. Illumina standard total RNA prep kit was used for library construction   tissue:skin|cell type:melanophore|genotype:WT|treatment:No GSM8552309 GSM8552309: melanophore biol rep 1; Danio rerio; RNA Seq GSM8552309 r1 GSM8552309 1 The cell isolation process involved density gradient centrifugation followed by RNA extraction using Trizol method. Illumina standard total RNA prep kit was used for library construction   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 2000   SRP536275     WT1_S40_R1_001.fastq.gz WT1_S40_R2_001.fastq.gz fastq fastq 5185761246.0 18118534.0 GSM8552309 r1 0:141.81 1:144.40 A:1231235669;C:1235759770;G:1476864583;T:1240636871;N:1264353 141 144     1231235669 1235759770 1476864583 1240636871 1264353 SRX26263936 SRS22803190 SRA1984938 Pigment Cell Biology Lab, CSIR-IGIB Pigment Cell Biology Lab, CSIR-IGIB                       B B biological fallback assumption illumina nextseq_v2 unknown cdna_unspecified trueseq sc_generic bulk bulk   India 2024-10-02 Undetermined Undetermined Skin Surface Structure
36272 36272 SRR298567 SRX079845 SRS212651 SRP007331 PRJNA141525 Tdrd1 acts as a molecular scaffold for Piwi proteins and piRNA targets in zebrafish. GSE29418 Transcriptome Analysis RNA libraries from immunoprecipitates of Tdrd1 Ziwi and Zili total testis RNA total RNA from 3 wpf wild type and tdrd1 mutant gonads. Overall design: Both size selected and non size selected libraries were made. Sequencing was performed using Illumina platform.   pubmed:21743441   ZiliIPTes GSM727524   tissue:RNA obtained from immunoprecipitation with Zili antibody|strain:TL ZiliIPTes three prime adapter sequences were trimmed and inserts longer than 18 nt were mapped to the D. rerio genome Zv9. RNA obtained from immunoprecipitation with Zili antibody   Tissues in IP lysis buffer were sonicated for 2 minutes at 4 oC and centrifuged for 10 minutes at 16000 rpm at 4 oC. Supernatant was used for IP. One IP contains 30 µl Dynabeads Invitrogen 3 or 6 testes and Zili antibody in a total volume of 500 µl. RNA was then size selected 18 35 nucleotides from gel. For cDNA synthesis adaptors were ligated to the three prime and five prime ends of the RNAof the size selected immunoprecipitated fraction. First strand cDNA synthesis was then performed using an oligodT linker primer and M MLVRNase H reverse transcriptase. cDNA was PCR amplified with adapter specific primers and used in Illumina sequencing.   strain:TL GSM727524 GSM727524: ZiliIPTes GSM727524: ZiliIPTes GSM727524: ZiliIPTes 1   GEO Accession:GSM727524 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> SRP007331   read name barcode proc directive:ignore ZiliIPTes.fastq fastq 995759064.0 27659974.0 GSM727524 1 0:36   36                 SRX079845 SRS212651 SRA039167 GEO European Research Institute for the Biology of Ageing, University Medical Center Groningen 1 0.0537   0.03117   0.95856   0.42091   36   B   usable mapping rate illumina early_illumina 5prime size_fractionation unknown bulk unknown unknown   Netherlands 2011-05-20 Undetermined Undetermined Trunk Surface Structure
40334 40334 SRR3086895 SRX1518389 SRS1236744 SRP068114 PRJNA307985 Transcription profiling of zebrafish fin regeneration GSE76564 Transcriptome Analysis We compared transcriptional profiles of regenerating zebrafish caudal fins following fin amputation with profiles from uninjured zebrafish caudal fins Overall design: Examination of whole fin transcriptional profiles from regenerating fins 2 pools of 10 fins and uninjured fins 2 pools of 10 fins   pubmed:27049946   ZF Uninjured Fin 2 GSM2028020   tissue:Uninjured fins|strain:EK|line:Wild type|treatment:N1 ZF Uninjured Fin 2 Base calling with Casava Alignment with TopHat Counts summarized with R using TopHat output Analysis performed with EdgeR package of Bioconductor Genome build: Zv9 Supplementary files format and content: "Regenerate fin counts.txt" and "Uninjured fin Control counts.txt" is a tab delimited text file containing summarized counts for each transcript. This was the dataset entered into edgeR. Uninjured fins Fins were amputated to 50% of their original length using razor blades Either uninjured fins or fins at 4 dy post amputation were collected. 10 fins were dissected rinsed in PBS placed in Trizol and homogenized. RNA was then extracted. Illumina RNA Seq 50 bp Single end libraries   strain:EK|line:Wild type|treatment:N1 GSM2028020 GSM2028020: ZF Uninjured Fin 2; Danio rerio; RNA Seq GSM2028020   1 Either uninjured fins or fins at 4 dy post amputation were collected. 10 fins were dissected rinsed in PBS placed in Trizol and homogenized. RNA was then extracted. Illumina RNA Seq 50 bp Single end libraries GEO Accession:GSM2028020 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina Genome Analyzer II   SRP068114     Un2-1.fastq.gz fastq 800000000.0 16000000.0 GSM2028020 r1 0:50 A:210926663;C:190496048;G:184518152;T:213985916;N:73221 50       210926663 190496048 184518152 213985916 73221 SRX1518389 SRS1236744 SRA329570 GEO Kenneth Poss lab, Department of Cell Biology, Duke University Medical Center 1 0.91126   0.08857   0.72054   0.44807   50   B   usable mapping rate illumina early_illumina full_length random_priming unknown bulk unknown unknown   United States 2016-01-05 Undetermined Undetermined Fin Surface Structure
40335 40335 SRR3086896 SRX1518389 SRS1236744 SRP068114 PRJNA307985 Transcription profiling of zebrafish fin regeneration GSE76564 Transcriptome Analysis We compared transcriptional profiles of regenerating zebrafish caudal fins following fin amputation with profiles from uninjured zebrafish caudal fins Overall design: Examination of whole fin transcriptional profiles from regenerating fins 2 pools of 10 fins and uninjured fins 2 pools of 10 fins   pubmed:27049946   ZF Uninjured Fin 2 GSM2028020   tissue:Uninjured fins|strain:EK|line:Wild type|treatment:N1 ZF Uninjured Fin 2 Base calling with Casava Alignment with TopHat Counts summarized with R using TopHat output Analysis performed with EdgeR package of Bioconductor Genome build: Zv9 Supplementary files format and content: "Regenerate fin counts.txt" and "Uninjured fin Control counts.txt" is a tab delimited text file containing summarized counts for each transcript. This was the dataset entered into edgeR. Uninjured fins Fins were amputated to 50% of their original length using razor blades Either uninjured fins or fins at 4 dy post amputation were collected. 10 fins were dissected rinsed in PBS placed in Trizol and homogenized. RNA was then extracted. Illumina RNA Seq 50 bp Single end libraries   strain:EK|line:Wild type|treatment:N1 GSM2028020 GSM2028020: ZF Uninjured Fin 2; Danio rerio; RNA Seq GSM2028020   1 Either uninjured fins or fins at 4 dy post amputation were collected. 10 fins were dissected rinsed in PBS placed in Trizol and homogenized. RNA was then extracted. Illumina RNA Seq 50 bp Single end libraries GEO Accession:GSM2028020 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina Genome Analyzer II   SRP068114     Un2-2.fastq.gz fastq 800000000.0 16000000.0 GSM2028020 r2 0:50 A:210822728;C:190175530;G:185124231;T:213867287;N:10224 50       210822728 190175530 185124231 213867287 10224 SRX1518389 SRS1236744 SRA329570 GEO Kenneth Poss lab, Department of Cell Biology, Duke University Medical Center 1 0.90559   0.08872   0.7194   0.43319   50   B   usable mapping rate illumina early_illumina full_length random_priming unknown bulk unknown unknown   United States 2016-01-05 Undetermined Undetermined Fin Surface Structure
40336 40336 SRR3086897 SRX1518389 SRS1236744 SRP068114 PRJNA307985 Transcription profiling of zebrafish fin regeneration GSE76564 Transcriptome Analysis We compared transcriptional profiles of regenerating zebrafish caudal fins following fin amputation with profiles from uninjured zebrafish caudal fins Overall design: Examination of whole fin transcriptional profiles from regenerating fins 2 pools of 10 fins and uninjured fins 2 pools of 10 fins   pubmed:27049946   ZF Uninjured Fin 2 GSM2028020   tissue:Uninjured fins|strain:EK|line:Wild type|treatment:N1 ZF Uninjured Fin 2 Base calling with Casava Alignment with TopHat Counts summarized with R using TopHat output Analysis performed with EdgeR package of Bioconductor Genome build: Zv9 Supplementary files format and content: "Regenerate fin counts.txt" and "Uninjured fin Control counts.txt" is a tab delimited text file containing summarized counts for each transcript. This was the dataset entered into edgeR. Uninjured fins Fins were amputated to 50% of their original length using razor blades Either uninjured fins or fins at 4 dy post amputation were collected. 10 fins were dissected rinsed in PBS placed in Trizol and homogenized. RNA was then extracted. Illumina RNA Seq 50 bp Single end libraries   strain:EK|line:Wild type|treatment:N1 GSM2028020 GSM2028020: ZF Uninjured Fin 2; Danio rerio; RNA Seq GSM2028020   1 Either uninjured fins or fins at 4 dy post amputation were collected. 10 fins were dissected rinsed in PBS placed in Trizol and homogenized. RNA was then extracted. Illumina RNA Seq 50 bp Single end libraries GEO Accession:GSM2028020 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina Genome Analyzer II   SRP068114     Un2-3.fastq.gz fastq 46067800.0 921356.0 GSM2028020 r3 0:50 A:12182398;C:10879021;G:10673094;T:12333021;N:266 50       12182398 10879021 10673094 12333021 266 SRX1518389 SRS1236744 SRA329570 GEO Kenneth Poss lab, Department of Cell Biology, Duke University Medical Center 1 0.89253   0.08727   0.72094   0.45046   50   B   usable mapping rate illumina early_illumina full_length random_priming unknown bulk unknown unknown   United States 2016-01-05 Undetermined Undetermined Fin Surface Structure
40337 40337 SRR3086892 SRX1518388 SRS1236746 SRP068114 PRJNA307985 Transcription profiling of zebrafish fin regeneration GSE76564 Transcriptome Analysis We compared transcriptional profiles of regenerating zebrafish caudal fins following fin amputation with profiles from uninjured zebrafish caudal fins Overall design: Examination of whole fin transcriptional profiles from regenerating fins 2 pools of 10 fins and uninjured fins 2 pools of 10 fins   pubmed:27049946   ZF Uninjured Fin 1 GSM2028019   tissue:Uninjured fins|strain:EK|line:Wild type|treatment:N1 ZF Uninjured Fin 1 Base calling with Casava Alignment with TopHat Counts summarized with R using TopHat output Analysis performed with EdgeR package of Bioconductor Genome build: Zv9 Supplementary files format and content: "Regenerate fin counts.txt" and "Uninjured fin Control counts.txt" is a tab delimited text file containing summarized counts for each transcript. This was the dataset entered into edgeR. Uninjured fins Fins were amputated to 50% of their original length using razor blades Either uninjured fins or fins at 4 dy post amputation were collected. 10 fins were dissected rinsed in PBS placed in Trizol and homogenized. RNA was then extracted. Illumina RNA Seq 50 bp Single end libraries   strain:EK|line:Wild type|treatment:N1 GSM2028019 GSM2028019: ZF Uninjured Fin 1; Danio rerio; RNA Seq GSM2028019   1 Either uninjured fins or fins at 4 dy post amputation were collected. 10 fins were dissected rinsed in PBS placed in Trizol and homogenized. RNA was then extracted. Illumina RNA Seq 50 bp Single end libraries GEO Accession:GSM2028019 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina Genome Analyzer II   SRP068114     Un1-1.fastq.gz fastq 800000000.0 16000000.0 GSM2028019 r1 0:50 A:206270357;C:193369997;G:191677237;T:208652195;N:30214 50       206270357 193369997 191677237 208652195 30214 SRX1518388 SRS1236746 SRA329570 GEO Kenneth Poss lab, Department of Cell Biology, Duke University Medical Center 1 0.91334   0.07414   0.73034   0.44343   50   B   usable mapping rate illumina early_illumina full_length random_priming unknown bulk unknown unknown   United States 2016-01-05 Undetermined Undetermined Fin Surface Structure
40338 40338 SRR3086893 SRX1518388 SRS1236746 SRP068114 PRJNA307985 Transcription profiling of zebrafish fin regeneration GSE76564 Transcriptome Analysis We compared transcriptional profiles of regenerating zebrafish caudal fins following fin amputation with profiles from uninjured zebrafish caudal fins Overall design: Examination of whole fin transcriptional profiles from regenerating fins 2 pools of 10 fins and uninjured fins 2 pools of 10 fins   pubmed:27049946   ZF Uninjured Fin 1 GSM2028019   tissue:Uninjured fins|strain:EK|line:Wild type|treatment:N1 ZF Uninjured Fin 1 Base calling with Casava Alignment with TopHat Counts summarized with R using TopHat output Analysis performed with EdgeR package of Bioconductor Genome build: Zv9 Supplementary files format and content: "Regenerate fin counts.txt" and "Uninjured fin Control counts.txt" is a tab delimited text file containing summarized counts for each transcript. This was the dataset entered into edgeR. Uninjured fins Fins were amputated to 50% of their original length using razor blades Either uninjured fins or fins at 4 dy post amputation were collected. 10 fins were dissected rinsed in PBS placed in Trizol and homogenized. RNA was then extracted. Illumina RNA Seq 50 bp Single end libraries   strain:EK|line:Wild type|treatment:N1 GSM2028019 GSM2028019: ZF Uninjured Fin 1; Danio rerio; RNA Seq GSM2028019   1 Either uninjured fins or fins at 4 dy post amputation were collected. 10 fins were dissected rinsed in PBS placed in Trizol and homogenized. RNA was then extracted. Illumina RNA Seq 50 bp Single end libraries GEO Accession:GSM2028019 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina Genome Analyzer II   SRP068114     Un1-2.fastq.gz fastq 493137350.0 9862747.0 GSM2028019 r2 0:50 A:127272457;C:119005858;G:118176094;T:128679179;N:3762 50       127272457 119005858 118176094 128679179 3762 SRX1518388 SRS1236746 SRA329570 GEO Kenneth Poss lab, Department of Cell Biology, Duke University Medical Center 1 0.90901   0.07418   0.73085   0.44107   50   B   usable mapping rate illumina early_illumina full_length random_priming unknown bulk unknown unknown   United States 2016-01-05 Undetermined Undetermined Fin Surface Structure
40339 40339 SRR3086894 SRX1518388 SRS1236746 SRP068114 PRJNA307985 Transcription profiling of zebrafish fin regeneration GSE76564 Transcriptome Analysis We compared transcriptional profiles of regenerating zebrafish caudal fins following fin amputation with profiles from uninjured zebrafish caudal fins Overall design: Examination of whole fin transcriptional profiles from regenerating fins 2 pools of 10 fins and uninjured fins 2 pools of 10 fins   pubmed:27049946   ZF Uninjured Fin 1 GSM2028019   tissue:Uninjured fins|strain:EK|line:Wild type|treatment:N1 ZF Uninjured Fin 1 Base calling with Casava Alignment with TopHat Counts summarized with R using TopHat output Analysis performed with EdgeR package of Bioconductor Genome build: Zv9 Supplementary files format and content: "Regenerate fin counts.txt" and "Uninjured fin Control counts.txt" is a tab delimited text file containing summarized counts for each transcript. This was the dataset entered into edgeR. Uninjured fins Fins were amputated to 50% of their original length using razor blades Either uninjured fins or fins at 4 dy post amputation were collected. 10 fins were dissected rinsed in PBS placed in Trizol and homogenized. RNA was then extracted. Illumina RNA Seq 50 bp Single end libraries   strain:EK|line:Wild type|treatment:N1 GSM2028019 GSM2028019: ZF Uninjured Fin 1; Danio rerio; RNA Seq GSM2028019   1 Either uninjured fins or fins at 4 dy post amputation were collected. 10 fins were dissected rinsed in PBS placed in Trizol and homogenized. RNA was then extracted. Illumina RNA Seq 50 bp Single end libraries GEO Accession:GSM2028019 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina Genome Analyzer II   SRP068114     Un1-3.fastq.gz fastq 800000000.0 16000000.0 GSM2028019 r3 0:50 A:206410293;C:193573258;G:191140232;T:208806339;N:69878 50       206410293 193573258 191140232 208806339 69878 SRX1518388 SRS1236746 SRA329570 GEO Kenneth Poss lab, Department of Cell Biology, Duke University Medical Center 1 0.91744   0.07298   0.72847   0.44383   50   B   usable mapping rate illumina early_illumina full_length random_priming unknown bulk unknown unknown   United States 2016-01-05 Undetermined Undetermined Fin Surface Structure
40340 40340 SRR3086888 SRX1518387 SRS1236747 SRP068114 PRJNA307985 Transcription profiling of zebrafish fin regeneration GSE76564 Transcriptome Analysis We compared transcriptional profiles of regenerating zebrafish caudal fins following fin amputation with profiles from uninjured zebrafish caudal fins Overall design: Examination of whole fin transcriptional profiles from regenerating fins 2 pools of 10 fins and uninjured fins 2 pools of 10 fins   pubmed:27049946   ZF 4dpa Fin 2 GSM2028018   tissue:Fins 4d post amputation|strain:EK|line:Wild type|treatment:Fin Amputation ZF 4dpa Fin 2 Base calling with Casava Alignment with TopHat Counts summarized with R using TopHat output Analysis performed with EdgeR package of Bioconductor Genome build: Zv9 Supplementary files format and content: "Regenerate fin counts.txt" and "Uninjured fin Control counts.txt" is a tab delimited text file containing summarized counts for each transcript. This was the dataset entered into edgeR. Fins 4d post amputation Fins were amputated to 50% of their original length using razor blades Either uninjured fins or fins at 4 dy post amputation were collected. 10 fins were dissected rinsed in PBS placed in Trizol and homogenized. RNA was then extracted. Illumina RNA Seq 50 bp Single end libraries   strain:EK|line:Wild type|treatment:Fin Amputation GSM2028018 GSM2028018: ZF 4dpa Fin 2; Danio rerio; RNA Seq GSM2028018   1 Either uninjured fins or fins at 4 dy post amputation were collected. 10 fins were dissected rinsed in PBS placed in Trizol and homogenized. RNA was then extracted. Illumina RNA Seq 50 bp Single end libraries GEO Accession:GSM2028018 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina Genome Analyzer II   SRP068114     Reg2-1.fastq.gz fastq 800000000.0 16000000.0 GSM2028018 r1 0:50 A:208862526;C:192270727;G:188582591;T:210215639;N:68517 50       208862526 192270727 188582591 210215639 68517 SRX1518387 SRS1236747 SRA329570 GEO Kenneth Poss lab, Department of Cell Biology, Duke University Medical Center 1 0.92514   0.07091   0.70638   0.46239   50   B   usable mapping rate illumina early_illumina full_length random_priming unknown bulk unknown unknown   United States 2016-01-05 Undetermined Undetermined Fin Surface Structure
40341 40341 SRR3086889 SRX1518387 SRS1236747 SRP068114 PRJNA307985 Transcription profiling of zebrafish fin regeneration GSE76564 Transcriptome Analysis We compared transcriptional profiles of regenerating zebrafish caudal fins following fin amputation with profiles from uninjured zebrafish caudal fins Overall design: Examination of whole fin transcriptional profiles from regenerating fins 2 pools of 10 fins and uninjured fins 2 pools of 10 fins   pubmed:27049946   ZF 4dpa Fin 2 GSM2028018   tissue:Fins 4d post amputation|strain:EK|line:Wild type|treatment:Fin Amputation ZF 4dpa Fin 2 Base calling with Casava Alignment with TopHat Counts summarized with R using TopHat output Analysis performed with EdgeR package of Bioconductor Genome build: Zv9 Supplementary files format and content: "Regenerate fin counts.txt" and "Uninjured fin Control counts.txt" is a tab delimited text file containing summarized counts for each transcript. This was the dataset entered into edgeR. Fins 4d post amputation Fins were amputated to 50% of their original length using razor blades Either uninjured fins or fins at 4 dy post amputation were collected. 10 fins were dissected rinsed in PBS placed in Trizol and homogenized. RNA was then extracted. Illumina RNA Seq 50 bp Single end libraries   strain:EK|line:Wild type|treatment:Fin Amputation GSM2028018 GSM2028018: ZF 4dpa Fin 2; Danio rerio; RNA Seq GSM2028018   1 Either uninjured fins or fins at 4 dy post amputation were collected. 10 fins were dissected rinsed in PBS placed in Trizol and homogenized. RNA was then extracted. Illumina RNA Seq 50 bp Single end libraries GEO Accession:GSM2028018 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina Genome Analyzer II   SRP068114     Reg2-2.fastq.gz fastq 800000000.0 16000000.0 GSM2028018 r2 0:50 A:208854177;C:192161932;G:188871135;T:210062448;N:50308 50       208854177 192161932 188871135 210062448 50308 SRX1518387 SRS1236747 SRA329570 GEO Kenneth Poss lab, Department of Cell Biology, Duke University Medical Center 1 0.92252   0.07056   0.70694   0.45392   50   B   usable mapping rate illumina early_illumina full_length random_priming unknown bulk unknown unknown   United States 2016-01-05 Undetermined Undetermined Fin Surface Structure
40342 40342 SRR3086890 SRX1518387 SRS1236747 SRP068114 PRJNA307985 Transcription profiling of zebrafish fin regeneration GSE76564 Transcriptome Analysis We compared transcriptional profiles of regenerating zebrafish caudal fins following fin amputation with profiles from uninjured zebrafish caudal fins Overall design: Examination of whole fin transcriptional profiles from regenerating fins 2 pools of 10 fins and uninjured fins 2 pools of 10 fins   pubmed:27049946   ZF 4dpa Fin 2 GSM2028018   tissue:Fins 4d post amputation|strain:EK|line:Wild type|treatment:Fin Amputation ZF 4dpa Fin 2 Base calling with Casava Alignment with TopHat Counts summarized with R using TopHat output Analysis performed with EdgeR package of Bioconductor Genome build: Zv9 Supplementary files format and content: "Regenerate fin counts.txt" and "Uninjured fin Control counts.txt" is a tab delimited text file containing summarized counts for each transcript. This was the dataset entered into edgeR. Fins 4d post amputation Fins were amputated to 50% of their original length using razor blades Either uninjured fins or fins at 4 dy post amputation were collected. 10 fins were dissected rinsed in PBS placed in Trizol and homogenized. RNA was then extracted. Illumina RNA Seq 50 bp Single end libraries   strain:EK|line:Wild type|treatment:Fin Amputation GSM2028018 GSM2028018: ZF 4dpa Fin 2; Danio rerio; RNA Seq GSM2028018   1 Either uninjured fins or fins at 4 dy post amputation were collected. 10 fins were dissected rinsed in PBS placed in Trizol and homogenized. RNA was then extracted. Illumina RNA Seq 50 bp Single end libraries GEO Accession:GSM2028018 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina Genome Analyzer II   SRP068114     Reg2-3.fastq.gz fastq 800000000.0 16000000.0 GSM2028018 r3 0:50 A:208765699;C:191936198;G:189409194;T:209878960;N:9949 50       208765699 191936198 189409194 209878960 9949 SRX1518387 SRS1236747 SRA329570 GEO Kenneth Poss lab, Department of Cell Biology, Duke University Medical Center 1 0.91451   0.06995   0.70741   0.45822   50   B   usable mapping rate illumina early_illumina full_length random_priming unknown bulk unknown unknown   United States 2016-01-05 Undetermined Undetermined Fin Surface Structure
40343 40343 SRR3086891 SRX1518387 SRS1236747 SRP068114 PRJNA307985 Transcription profiling of zebrafish fin regeneration GSE76564 Transcriptome Analysis We compared transcriptional profiles of regenerating zebrafish caudal fins following fin amputation with profiles from uninjured zebrafish caudal fins Overall design: Examination of whole fin transcriptional profiles from regenerating fins 2 pools of 10 fins and uninjured fins 2 pools of 10 fins   pubmed:27049946   ZF 4dpa Fin 2 GSM2028018   tissue:Fins 4d post amputation|strain:EK|line:Wild type|treatment:Fin Amputation ZF 4dpa Fin 2 Base calling with Casava Alignment with TopHat Counts summarized with R using TopHat output Analysis performed with EdgeR package of Bioconductor Genome build: Zv9 Supplementary files format and content: "Regenerate fin counts.txt" and "Uninjured fin Control counts.txt" is a tab delimited text file containing summarized counts for each transcript. This was the dataset entered into edgeR. Fins 4d post amputation Fins were amputated to 50% of their original length using razor blades Either uninjured fins or fins at 4 dy post amputation were collected. 10 fins were dissected rinsed in PBS placed in Trizol and homogenized. RNA was then extracted. Illumina RNA Seq 50 bp Single end libraries   strain:EK|line:Wild type|treatment:Fin Amputation GSM2028018 GSM2028018: ZF 4dpa Fin 2; Danio rerio; RNA Seq GSM2028018   1 Either uninjured fins or fins at 4 dy post amputation were collected. 10 fins were dissected rinsed in PBS placed in Trizol and homogenized. RNA was then extracted. Illumina RNA Seq 50 bp Single end libraries GEO Accession:GSM2028018 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina Genome Analyzer II   SRP068114     Reg2-4.fastq.gz fastq 123651950.0 2473039.0 GSM2028018 r4 0:50 A:32365652;C:29515195;G:29236871;T:32533508;N:724 50       32365652 29515195 29236871 32533508 724 SRX1518387 SRS1236747 SRA329570 GEO Kenneth Poss lab, Department of Cell Biology, Duke University Medical Center 1 0.91437   0.07079   0.70867   0.46558   50   B   usable mapping rate illumina early_illumina full_length random_priming unknown bulk unknown unknown   United States 2016-01-05 Undetermined Undetermined Fin Surface Structure
40344 40344 SRR3086884 SRX1518386 SRS1236745 SRP068114 PRJNA307985 Transcription profiling of zebrafish fin regeneration GSE76564 Transcriptome Analysis We compared transcriptional profiles of regenerating zebrafish caudal fins following fin amputation with profiles from uninjured zebrafish caudal fins Overall design: Examination of whole fin transcriptional profiles from regenerating fins 2 pools of 10 fins and uninjured fins 2 pools of 10 fins   pubmed:27049946   ZF 4dpa Fin 1 GSM2028017   tissue:Fins 4d post amputation|strain:EK|line:Wild type|treatment:Fin Amputation ZF 4dpa Fin 1 Base calling with Casava Alignment with TopHat Counts summarized with R using TopHat output Analysis performed with EdgeR package of Bioconductor Genome build: Zv9 Supplementary files format and content: "Regenerate fin counts.txt" and "Uninjured fin Control counts.txt" is a tab delimited text file containing summarized counts for each transcript. This was the dataset entered into edgeR. Fins 4d post amputation Fins were amputated to 50% of their original length using razor blades Either uninjured fins or fins at 4 dy post amputation were collected. 10 fins were dissected rinsed in PBS placed in Trizol and homogenized. RNA was then extracted. Illumina RNA Seq 50 bp Single end libraries   strain:EK|line:Wild type|treatment:Fin Amputation GSM2028017 GSM2028017: ZF 4dpa Fin 1; Danio rerio; RNA Seq GSM2028017   1 Either uninjured fins or fins at 4 dy post amputation were collected. 10 fins were dissected rinsed in PBS placed in Trizol and homogenized. RNA was then extracted. Illumina RNA Seq 50 bp Single end libraries GEO Accession:GSM2028017 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina Genome Analyzer II   SRP068114     Reg1-1.fastq.gz fastq 800000000.0 16000000.0 GSM2028017 r1 0:50 A:207070768;C:193619920;G:189688453;T:209552804;N:68055 50       207070768 193619920 189688453 209552804 68055 SRX1518386 SRS1236745 SRA329570 GEO Kenneth Poss lab, Department of Cell Biology, Duke University Medical Center 1 0.92944   0.06242   0.71224   0.46274   50   B   usable mapping rate illumina early_illumina full_length random_priming unknown bulk unknown unknown   United States 2016-01-05 Undetermined Undetermined Fin Surface Structure
40345 40345 SRR3086885 SRX1518386 SRS1236745 SRP068114 PRJNA307985 Transcription profiling of zebrafish fin regeneration GSE76564 Transcriptome Analysis We compared transcriptional profiles of regenerating zebrafish caudal fins following fin amputation with profiles from uninjured zebrafish caudal fins Overall design: Examination of whole fin transcriptional profiles from regenerating fins 2 pools of 10 fins and uninjured fins 2 pools of 10 fins   pubmed:27049946   ZF 4dpa Fin 1 GSM2028017   tissue:Fins 4d post amputation|strain:EK|line:Wild type|treatment:Fin Amputation ZF 4dpa Fin 1 Base calling with Casava Alignment with TopHat Counts summarized with R using TopHat output Analysis performed with EdgeR package of Bioconductor Genome build: Zv9 Supplementary files format and content: "Regenerate fin counts.txt" and "Uninjured fin Control counts.txt" is a tab delimited text file containing summarized counts for each transcript. This was the dataset entered into edgeR. Fins 4d post amputation Fins were amputated to 50% of their original length using razor blades Either uninjured fins or fins at 4 dy post amputation were collected. 10 fins were dissected rinsed in PBS placed in Trizol and homogenized. RNA was then extracted. Illumina RNA Seq 50 bp Single end libraries   strain:EK|line:Wild type|treatment:Fin Amputation GSM2028017 GSM2028017: ZF 4dpa Fin 1; Danio rerio; RNA Seq GSM2028017   1 Either uninjured fins or fins at 4 dy post amputation were collected. 10 fins were dissected rinsed in PBS placed in Trizol and homogenized. RNA was then extracted. Illumina RNA Seq 50 bp Single end libraries GEO Accession:GSM2028017 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina Genome Analyzer II   SRP068114     Reg1-2.fastq.gz fastq 800000000.0 16000000.0 GSM2028017 r2 0:50 A:207042635;C:193500947;G:190015843;T:209392450;N:48125 50       207042635 193500947 190015843 209392450 48125 SRX1518386 SRS1236745 SRA329570 GEO Kenneth Poss lab, Department of Cell Biology, Duke University Medical Center 1 0.92402   0.06138   0.71295   0.46332   50   B   usable mapping rate illumina early_illumina full_length random_priming unknown bulk unknown unknown   United States 2016-01-05 Undetermined Undetermined Fin Surface Structure
40346 40346 SRR3086886 SRX1518386 SRS1236745 SRP068114 PRJNA307985 Transcription profiling of zebrafish fin regeneration GSE76564 Transcriptome Analysis We compared transcriptional profiles of regenerating zebrafish caudal fins following fin amputation with profiles from uninjured zebrafish caudal fins Overall design: Examination of whole fin transcriptional profiles from regenerating fins 2 pools of 10 fins and uninjured fins 2 pools of 10 fins   pubmed:27049946   ZF 4dpa Fin 1 GSM2028017   tissue:Fins 4d post amputation|strain:EK|line:Wild type|treatment:Fin Amputation ZF 4dpa Fin 1 Base calling with Casava Alignment with TopHat Counts summarized with R using TopHat output Analysis performed with EdgeR package of Bioconductor Genome build: Zv9 Supplementary files format and content: "Regenerate fin counts.txt" and "Uninjured fin Control counts.txt" is a tab delimited text file containing summarized counts for each transcript. This was the dataset entered into edgeR. Fins 4d post amputation Fins were amputated to 50% of their original length using razor blades Either uninjured fins or fins at 4 dy post amputation were collected. 10 fins were dissected rinsed in PBS placed in Trizol and homogenized. RNA was then extracted. Illumina RNA Seq 50 bp Single end libraries   strain:EK|line:Wild type|treatment:Fin Amputation GSM2028017 GSM2028017: ZF 4dpa Fin 1; Danio rerio; RNA Seq GSM2028017   1 Either uninjured fins or fins at 4 dy post amputation were collected. 10 fins were dissected rinsed in PBS placed in Trizol and homogenized. RNA was then extracted. Illumina RNA Seq 50 bp Single end libraries GEO Accession:GSM2028017 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina Genome Analyzer II   SRP068114     Reg1-3.fastq.gz fastq 800000000.0 16000000.0 GSM2028017 r3 0:50 A:206941368;C:193232860;G:190532195;T:209283728;N:9849 50       206941368 193232860 190532195 209283728 9849 SRX1518386 SRS1236745 SRA329570 GEO Kenneth Poss lab, Department of Cell Biology, Duke University Medical Center 1 0.91924   0.06196   0.71275   0.46184   50   B   usable mapping rate illumina early_illumina full_length random_priming unknown bulk unknown unknown   United States 2016-01-05 Undetermined Undetermined Fin Surface Structure
40347 40347 SRR3086887 SRX1518386 SRS1236745 SRP068114 PRJNA307985 Transcription profiling of zebrafish fin regeneration GSE76564 Transcriptome Analysis We compared transcriptional profiles of regenerating zebrafish caudal fins following fin amputation with profiles from uninjured zebrafish caudal fins Overall design: Examination of whole fin transcriptional profiles from regenerating fins 2 pools of 10 fins and uninjured fins 2 pools of 10 fins   pubmed:27049946   ZF 4dpa Fin 1 GSM2028017   tissue:Fins 4d post amputation|strain:EK|line:Wild type|treatment:Fin Amputation ZF 4dpa Fin 1 Base calling with Casava Alignment with TopHat Counts summarized with R using TopHat output Analysis performed with EdgeR package of Bioconductor Genome build: Zv9 Supplementary files format and content: "Regenerate fin counts.txt" and "Uninjured fin Control counts.txt" is a tab delimited text file containing summarized counts for each transcript. This was the dataset entered into edgeR. Fins 4d post amputation Fins were amputated to 50% of their original length using razor blades Either uninjured fins or fins at 4 dy post amputation were collected. 10 fins were dissected rinsed in PBS placed in Trizol and homogenized. RNA was then extracted. Illumina RNA Seq 50 bp Single end libraries   strain:EK|line:Wild type|treatment:Fin Amputation GSM2028017 GSM2028017: ZF 4dpa Fin 1; Danio rerio; RNA Seq GSM2028017   1 Either uninjured fins or fins at 4 dy post amputation were collected. 10 fins were dissected rinsed in PBS placed in Trizol and homogenized. RNA was then extracted. Illumina RNA Seq 50 bp Single end libraries GEO Accession:GSM2028017 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina Genome Analyzer II   SRP068114     Reg1-4.fastq.gz fastq 90897750.0 1817955.0 GSM2028017 r4 0:50 A:23579811;C:21833091;G:21640955;T:23843357;N:536 50       23579811 21833091 21640955 23843357 536 SRX1518386 SRS1236745 SRA329570 GEO Kenneth Poss lab, Department of Cell Biology, Duke University Medical Center 1 0.91241   0.06085   0.7152   0.46013   50   B   usable mapping rate illumina early_illumina full_length random_priming unknown bulk unknown unknown   United States 2016-01-05 Undetermined Undetermined Fin Surface Structure
47613 47613 SRR6760977 SRX3733411 SRS2990508 SRP133266 PRJNA434353 Transcriptome assemblies 10 vertebrate species PRJNA434353 Other 2 types of content: a Raw RNA seq files from cell lines of 10 vertebrate species human mouse cow tasmanian devil chicken duck zebra finch xenopus medaka and zebrafish 4 replicates per species. b Refined transcriptomes post combining with paired proteomics data and data curation.     4 replicates   Zebrafish   strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:missing|tissue:scale|cell line:BRF41|cell type:fibroblast|BioSampleModel:Model organism or animal                 Transcriptome assemblies 10 vertebrate species zebrafish replicate2 zebrafish replicate2 Zebrafish sample replicate 2     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 2500   SRP133266     Sample_imb_butter_2014_04_30_zebrafish_B_R2.fastq.gz Sample_imb_butter_2014_04_30_zebrafish_B_R1.fastq.gz fastq fastq 8021078014.0 39708307.0 Sample imb butter 2014 04 30 zebrafish B R2.fastq.gz 0:101 1:101 A:2198831905;C:1810184353;G:1779924959;T:2210094554;N:22042243 101 101     2198831905 1810184353 1779924959 2210094554 22042243 SRX3733411 SRS2990508 SRA660975 Institute of Molecular Biology|Quantitative Proteomics Institute of Molecular Biology 2 0.94194 0.93911 0.07724 0.08406 0.75724 0.75558 0.47712 0.49049 101 101 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Unknown 2019-02-15 Undetermined Undetermined Scale Surface Structure
47614 47614 SRR6760978 SRX3733410 SRS2990508 SRP133266 PRJNA434353 Transcriptome assemblies 10 vertebrate species PRJNA434353 Other 2 types of content: a Raw RNA seq files from cell lines of 10 vertebrate species human mouse cow tasmanian devil chicken duck zebra finch xenopus medaka and zebrafish 4 replicates per species. b Refined transcriptomes post combining with paired proteomics data and data curation.     4 replicates   Zebrafish   strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:missing|tissue:scale|cell line:BRF41|cell type:fibroblast|BioSampleModel:Model organism or animal                 Transcriptome assemblies 10 vertebrate species zebrafish replicate1 zebrafish replicate1 Zebrafish sample replicate 1     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 2500   SRP133266     Sample_imb_butter_2014_04_29_zebrafish_A_R1.fastq.gz Sample_imb_butter_2014_04_29_zebrafish_A_R2.fastq.gz fastq fastq 7117920864.0 35237232.0 Sample imb butter 2014 04 29 zebrafish A R2.fastq.gz 0:101 1:101 A:1980152632;C:1580333689;G:1558362064;T:1979596193;N:19476286 101 101     1980152632 1580333689 1558362064 1979596193 19476286 SRX3733410 SRS2990508 SRA660975 Institute of Molecular Biology|Quantitative Proteomics Institute of Molecular Biology 2 0.9342 0.93044 0.08741 0.09642 0.75674 0.75497 0.49192 0.46492 101 101 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Unknown 2018-02-22 Undetermined Undetermined Scale Surface Structure
47615 47615 SRR6760981 SRX3733407 SRS2990508 SRP133266 PRJNA434353 Transcriptome assemblies 10 vertebrate species PRJNA434353 Other 2 types of content: a Raw RNA seq files from cell lines of 10 vertebrate species human mouse cow tasmanian devil chicken duck zebra finch xenopus medaka and zebrafish 4 replicates per species. b Refined transcriptomes post combining with paired proteomics data and data curation.     4 replicates   Zebrafish   strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:missing|tissue:scale|cell line:BRF41|cell type:fibroblast|BioSampleModel:Model organism or animal                 Transcriptome assemblies 10 vertebrate species zebrafish replicate4 zebrafish replicate4 Zebrafish sample replicate 4     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 2500   SRP133266     Sample_imb_butter_2014_04_32_zebrafish_D_R1.fastq.gz Sample_imb_butter_2014_04_32_zebrafish_D_R2.fastq.gz fastq fastq 8570683654.0 42429127.0 Sample imb butter 2014 04 32 zebrafish D R1.fastq.gz 0:101 1:101 A:2343151377;C:1943560489;G:1909682494;T:2350658549;N:23630745 101 101     2343151377 1943560489 1909682494 2350658549 23630745 SRX3733407 SRS2990508 SRA660975 Institute of Molecular Biology|Quantitative Proteomics Institute of Molecular Biology 2 0.94036 0.94349 0.0838 0.0779 0.75538 0.75737 0.4881 0.48296 101 101 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Unknown 2019-02-15 Undetermined Undetermined Scale Surface Structure
47616 47616 SRR6760982 SRX3733406 SRS2990508 SRP133266 PRJNA434353 Transcriptome assemblies 10 vertebrate species PRJNA434353 Other 2 types of content: a Raw RNA seq files from cell lines of 10 vertebrate species human mouse cow tasmanian devil chicken duck zebra finch xenopus medaka and zebrafish 4 replicates per species. b Refined transcriptomes post combining with paired proteomics data and data curation.     4 replicates   Zebrafish   strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:missing|tissue:scale|cell line:BRF41|cell type:fibroblast|BioSampleModel:Model organism or animal                 Transcriptome assemblies 10 vertebrate species zebrafish replicate3 zebrafish replicate3 Zebrafish sample replicate 3     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 2500   SRP133266     Sample_imb_butter_2014_04_31_zebrafish_C_R1.fastq.gz Sample_imb_butter_2014_04_31_zebrafish_C_R2.fastq.gz fastq fastq 5889796416.0 29157408.0 Sample imb butter 2014 04 31 zebrafish C R1.fastq.gz 0:101 1:101 A:1629550499;C:1313886355;G:1293890602;T:1636478119;N:15990841 101 101     1629550499 1313886355 1293890602 1636478119 15990841 SRX3733406 SRS2990508 SRA660975 Institute of Molecular Biology|Quantitative Proteomics Institute of Molecular Biology 2 0.93285 0.93628 0.09745 0.0871 0.7586 0.7611 0.47374 0.47763 101 101 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Unknown 2018-02-22 Undetermined Undetermined Scale Surface Structure
49175 49175 SRR7764540 SRX4620156 SRS3722694 SRP159053 PRJNA488354 Molecularly distinct models of zebrafish Myc induced B cell leukemia GSE119173 Transcriptome Analysis The goal of this study was to compare transcriptomic profiles of two recent B cell ALL models in zebrafish expressing either mMyc GSE108855 or hMYC transgenes. 13 unique hMYC expressing samples are included. Overall design: 13 zebrafish ALL from the rag2:hMYC; lck:GFP double transgeneic background.   pubmed:30573774   hMYC 14 GSM3360022   tissue:GFP+ FACS purified ALL from total body|strain:rag2:hMYC; lck:eGFP double transgenic line hMYC 14 Illumina bcl2fastq2 was used for basecalling. RNA Seq data were processed as previously described in Garcia et al. 2018 PMID 29749398. Briefly reads were aligned using STAR Dobin et al. 2013 to GRCz10. Picard was used to filter out potential PCR duplicates. Counts were assigned to each gene using featureCounts Liao et al. 2014. Genome build: GRCz10 Supplementary files format and content: tab delimited text file includes count matrix for all samples GFP+ FACS purified ALL from total body   Trizol extraction of total RNA was performed according to the manufacturer's instructions. Illumina TruSeq Stranded RNA Sample Prep Kit Cat#FC 122 1001 was used with 100 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols   strain:rag2:hMYC;lck:eGFP double transgenic line GSM3360022 GSM3360022: hMYC 14; Danio rerio; RNA Seq GSM3360022   1 Trizol extraction of total RNA was performed according to the manufacturer's instructions. Illumina TruSeq Stranded RNA Sample Prep Kit Cat#FC 122 1001 was used with 100 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM3360022 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 3000   SRP159053     MCB_14_d_R2_001.fastq.gz MCB_14_d_R1_001.fastq.gz fastq fastq 8041956188.0 26628994.0 GSM3360022 r1 0:151 1:151 A:2169107009;C:1867732731;G:1838645489;T:2164562982;N:1907977 151 151     2169107009 1867732731 1838645489 2164562982 1907977 SRX4620156 SRS3722694 SRA764101 GEO Pediatrics, University of Oklahoma Health Sciences Center 2 0.90129 0.90181 0.17265 0.16628 0.77914 0.78571 0.51437 0.51601 151 151 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   United States 2018-08-29 Undetermined Undetermined Trunk Surface Structure
49176 49176 SRR7764539 SRX4620155 SRS3722693 SRP159053 PRJNA488354 Molecularly distinct models of zebrafish Myc induced B cell leukemia GSE119173 Transcriptome Analysis The goal of this study was to compare transcriptomic profiles of two recent B cell ALL models in zebrafish expressing either mMyc GSE108855 or hMYC transgenes. 13 unique hMYC expressing samples are included. Overall design: 13 zebrafish ALL from the rag2:hMYC; lck:GFP double transgeneic background.   pubmed:30573774   hMYC 13 GSM3360021   tissue:GFP+ FACS purified ALL from total body|strain:rag2:hMYC; lck:eGFP double transgenic line hMYC 13 Illumina bcl2fastq2 was used for basecalling. RNA Seq data were processed as previously described in Garcia et al. 2018 PMID 29749398. Briefly reads were aligned using STAR Dobin et al. 2013 to GRCz10. Picard was used to filter out potential PCR duplicates. Counts were assigned to each gene using featureCounts Liao et al. 2014. Genome build: GRCz10 Supplementary files format and content: tab delimited text file includes count matrix for all samples GFP+ FACS purified ALL from total body   Trizol extraction of total RNA was performed according to the manufacturer's instructions. Illumina TruSeq Stranded RNA Sample Prep Kit Cat#FC 122 1001 was used with 100 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols   strain:rag2:hMYC;lck:eGFP double transgenic line GSM3360021 GSM3360021: hMYC 13; Danio rerio; RNA Seq GSM3360021   1 Trizol extraction of total RNA was performed according to the manufacturer's instructions. Illumina TruSeq Stranded RNA Sample Prep Kit Cat#FC 122 1001 was used with 100 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM3360021 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 3000   SRP159053     MCB_13_d_R1_001.fastq.gz MCB_13_d_R2_001.fastq.gz fastq fastq 8396214872.0 27802036.0 GSM3360021 r1 0:151 1:151 A:2241185626;C:1969096150;G:1937906595;T:2246030255;N:1996246 151 151     2241185626 1969096150 1937906595 2246030255 1996246 SRX4620155 SRS3722693 SRA764101 GEO Pediatrics, University of Oklahoma Health Sciences Center 2 0.9263 0.92555 0.1672 0.16003 0.7754 0.78143 0.50818 0.50565 151 151 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   United States 2018-08-29 Undetermined Undetermined Trunk Surface Structure
49177 49177 SRR7764538 SRX4620154 SRS3722692 SRP159053 PRJNA488354 Molecularly distinct models of zebrafish Myc induced B cell leukemia GSE119173 Transcriptome Analysis The goal of this study was to compare transcriptomic profiles of two recent B cell ALL models in zebrafish expressing either mMyc GSE108855 or hMYC transgenes. 13 unique hMYC expressing samples are included. Overall design: 13 zebrafish ALL from the rag2:hMYC; lck:GFP double transgeneic background.   pubmed:30573774   hMYC 12 GSM3360020   tissue:GFP+ FACS purified ALL from total body|strain:rag2:hMYC; lck:eGFP double transgenic line hMYC 12 Illumina bcl2fastq2 was used for basecalling. RNA Seq data were processed as previously described in Garcia et al. 2018 PMID 29749398. Briefly reads were aligned using STAR Dobin et al. 2013 to GRCz10. Picard was used to filter out potential PCR duplicates. Counts were assigned to each gene using featureCounts Liao et al. 2014. Genome build: GRCz10 Supplementary files format and content: tab delimited text file includes count matrix for all samples GFP+ FACS purified ALL from total body   Trizol extraction of total RNA was performed according to the manufacturer's instructions. Illumina TruSeq Stranded RNA Sample Prep Kit Cat#FC 122 1001 was used with 100 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols   strain:rag2:hMYC;lck:eGFP double transgenic line GSM3360020 GSM3360020: hMYC 12; Danio rerio; RNA Seq GSM3360020   1 Trizol extraction of total RNA was performed according to the manufacturer's instructions. Illumina TruSeq Stranded RNA Sample Prep Kit Cat#FC 122 1001 was used with 100 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM3360020 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 3000   SRP159053     MCB_12_d_R2_001.fastq.gz MCB_12_d_R1_001.fastq.gz fastq fastq 8640985570.0 28612535.0 GSM3360020 r1 0:151 1:151 A:2320458014;C:2008991633;G:1983687859;T:2325784420;N:2063644 151 151     2320458014 2008991633 1983687859 2325784420 2063644 SRX4620154 SRS3722692 SRA764101 GEO Pediatrics, University of Oklahoma Health Sciences Center 2 0.91667 0.9169 0.20552 0.19745 0.77137 0.77768 0.51563 0.51361 151 151 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   United States 2018-08-29 Undetermined Undetermined Trunk Surface Structure
49178 49178 SRR7764537 SRX4620153 SRS3722691 SRP159053 PRJNA488354 Molecularly distinct models of zebrafish Myc induced B cell leukemia GSE119173 Transcriptome Analysis The goal of this study was to compare transcriptomic profiles of two recent B cell ALL models in zebrafish expressing either mMyc GSE108855 or hMYC transgenes. 13 unique hMYC expressing samples are included. Overall design: 13 zebrafish ALL from the rag2:hMYC; lck:GFP double transgeneic background.   pubmed:30573774   hMYC 11 GSM3360019   tissue:GFP+ FACS purified ALL from total body|strain:rag2:hMYC; lck:eGFP double transgenic line hMYC 11 Illumina bcl2fastq2 was used for basecalling. RNA Seq data were processed as previously described in Garcia et al. 2018 PMID 29749398. Briefly reads were aligned using STAR Dobin et al. 2013 to GRCz10. Picard was used to filter out potential PCR duplicates. Counts were assigned to each gene using featureCounts Liao et al. 2014. Genome build: GRCz10 Supplementary files format and content: tab delimited text file includes count matrix for all samples GFP+ FACS purified ALL from total body   Trizol extraction of total RNA was performed according to the manufacturer's instructions. Illumina TruSeq Stranded RNA Sample Prep Kit Cat#FC 122 1001 was used with 100 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols   strain:rag2:hMYC;lck:eGFP double transgenic line GSM3360019 GSM3360019: hMYC 11; Danio rerio; RNA Seq GSM3360019   1 Trizol extraction of total RNA was performed according to the manufacturer's instructions. Illumina TruSeq Stranded RNA Sample Prep Kit Cat#FC 122 1001 was used with 100 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM3360019 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 3000   SRP159053     MCB_11_d_R1_001.fastq.gz MCB_11_d_R2_001.fastq.gz fastq fastq 10375306338.0 34355319.0 GSM3360019 r1 0:151 1:151 A:2774834850;C:2433110341;G:2384852893;T:2780049207;N:2459047 151 151     2774834850 2433110341 2384852893 2780049207 2459047 SRX4620153 SRS3722691 SRA764101 GEO Pediatrics, University of Oklahoma Health Sciences Center 2 0.92646 0.92634 0.25883 0.24912 0.80667 0.81294 0.52396 0.4604 151 151 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   United States 2018-08-29 Undetermined Undetermined Trunk Surface Structure
49179 49179 SRR7764536 SRX4620152 SRS3722690 SRP159053 PRJNA488354 Molecularly distinct models of zebrafish Myc induced B cell leukemia GSE119173 Transcriptome Analysis The goal of this study was to compare transcriptomic profiles of two recent B cell ALL models in zebrafish expressing either mMyc GSE108855 or hMYC transgenes. 13 unique hMYC expressing samples are included. Overall design: 13 zebrafish ALL from the rag2:hMYC; lck:GFP double transgeneic background.   pubmed:30573774   hMYC 10 GSM3360018   tissue:GFP+ FACS purified ALL from total body|strain:rag2:hMYC; lck:eGFP double transgenic line hMYC 10 Illumina bcl2fastq2 was used for basecalling. RNA Seq data were processed as previously described in Garcia et al. 2018 PMID 29749398. Briefly reads were aligned using STAR Dobin et al. 2013 to GRCz10. Picard was used to filter out potential PCR duplicates. Counts were assigned to each gene using featureCounts Liao et al. 2014. Genome build: GRCz10 Supplementary files format and content: tab delimited text file includes count matrix for all samples GFP+ FACS purified ALL from total body   Trizol extraction of total RNA was performed according to the manufacturer's instructions. Illumina TruSeq Stranded RNA Sample Prep Kit Cat#FC 122 1001 was used with 100 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols   strain:rag2:hMYC;lck:eGFP double transgenic line GSM3360018 GSM3360018: hMYC 10; Danio rerio; RNA Seq GSM3360018   1 Trizol extraction of total RNA was performed according to the manufacturer's instructions. Illumina TruSeq Stranded RNA Sample Prep Kit Cat#FC 122 1001 was used with 100 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM3360018 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 3000   SRP159053     MCB_10_d_R1_001.fastq.gz MCB_10_d_R2_001.fastq.gz fastq fastq 9103054630.0 30142565.0 GSM3360018 r1 0:151 1:151 A:2444515359;C:2120625212;G:2086999932;T:2448748127;N:2166000 151 151     2444515359 2120625212 2086999932 2448748127 2166000 SRX4620152 SRS3722690 SRA764101 GEO Pediatrics, University of Oklahoma Health Sciences Center 2 0.919 0.91974 0.20589 0.19901 0.78169 0.78855 0.51136 0.5163 151 151 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   United States 2018-08-29 Undetermined Undetermined Trunk Surface Structure
49180 49180 SRR7764535 SRX4620151 SRS3722689 SRP159053 PRJNA488354 Molecularly distinct models of zebrafish Myc induced B cell leukemia GSE119173 Transcriptome Analysis The goal of this study was to compare transcriptomic profiles of two recent B cell ALL models in zebrafish expressing either mMyc GSE108855 or hMYC transgenes. 13 unique hMYC expressing samples are included. Overall design: 13 zebrafish ALL from the rag2:hMYC; lck:GFP double transgeneic background.   pubmed:30573774   hMYC 9 GSM3360017   tissue:GFP+ FACS purified ALL from total body|strain:rag2:hMYC; lck:eGFP double transgenic line hMYC 9 Illumina bcl2fastq2 was used for basecalling. RNA Seq data were processed as previously described in Garcia et al. 2018 PMID 29749398. Briefly reads were aligned using STAR Dobin et al. 2013 to GRCz10. Picard was used to filter out potential PCR duplicates. Counts were assigned to each gene using featureCounts Liao et al. 2014. Genome build: GRCz10 Supplementary files format and content: tab delimited text file includes count matrix for all samples GFP+ FACS purified ALL from total body   Trizol extraction of total RNA was performed according to the manufacturer's instructions. Illumina TruSeq Stranded RNA Sample Prep Kit Cat#FC 122 1001 was used with 100 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols   strain:rag2:hMYC;lck:eGFP double transgenic line GSM3360017 GSM3360017: hMYC 9; Danio rerio; RNA Seq GSM3360017   1 Trizol extraction of total RNA was performed according to the manufacturer's instructions. Illumina TruSeq Stranded RNA Sample Prep Kit Cat#FC 122 1001 was used with 100 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM3360017 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 3000   SRP159053     MCB_9_d_R1_001.fastq.gz MCB_9_d_R2_001.fastq.gz fastq fastq 9781069696.0 32387648.0 GSM3360017 r1 0:151 1:151 A:2593768575;C:2312524357;G:2270896742;T:2601565073;N:2314949 151 151     2593768575 2312524357 2270896742 2601565073 2314949 SRX4620151 SRS3722689 SRA764101 GEO Pediatrics, University of Oklahoma Health Sciences Center 2 0.9302 0.9302 0.16677 0.16095 0.78486 0.79105 0.51234 0.50852 151 151 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   United States 2018-08-29 Undetermined Undetermined Trunk Surface Structure
49181 49181 SRR7764534 SRX4620150 SRS3722687 SRP159053 PRJNA488354 Molecularly distinct models of zebrafish Myc induced B cell leukemia GSE119173 Transcriptome Analysis The goal of this study was to compare transcriptomic profiles of two recent B cell ALL models in zebrafish expressing either mMyc GSE108855 or hMYC transgenes. 13 unique hMYC expressing samples are included. Overall design: 13 zebrafish ALL from the rag2:hMYC; lck:GFP double transgeneic background.   pubmed:30573774   hMYC 8 GSM3360016   tissue:GFP+ FACS purified ALL from total body|strain:rag2:hMYC; lck:eGFP double transgenic line hMYC 8 Illumina bcl2fastq2 was used for basecalling. RNA Seq data were processed as previously described in Garcia et al. 2018 PMID 29749398. Briefly reads were aligned using STAR Dobin et al. 2013 to GRCz10. Picard was used to filter out potential PCR duplicates. Counts were assigned to each gene using featureCounts Liao et al. 2014. Genome build: GRCz10 Supplementary files format and content: tab delimited text file includes count matrix for all samples GFP+ FACS purified ALL from total body   Trizol extraction of total RNA was performed according to the manufacturer's instructions. Illumina TruSeq Stranded RNA Sample Prep Kit Cat#FC 122 1001 was used with 100 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols   strain:rag2:hMYC;lck:eGFP double transgenic line GSM3360016 GSM3360016: hMYC 8; Danio rerio; RNA Seq GSM3360016   1 Trizol extraction of total RNA was performed according to the manufacturer's instructions. Illumina TruSeq Stranded RNA Sample Prep Kit Cat#FC 122 1001 was used with 100 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM3360016 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 3000   SRP159053     MCB_8_c_GCCAAT_R1_concat.fastq.gz MCB_8_c_GCCAAT_R2_concat.fastq.gz fastq fastq 5631730306.0 27879853.0 GSM3360016 r1 0:101 1:101 A:1502650481;C:1306810950;G:1314705252;T:1500209887;N:7353736 101 101     1502650481 1306810950 1314705252 1500209887 7353736 SRX4620150 SRS3722687 SRA764101 GEO Pediatrics, University of Oklahoma Health Sciences Center 2 0.93418 0.93562 0.20662 0.20876 0.78175 0.78455 0.51374 0.50871 101 101 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   United States 2018-08-29 Undetermined Undetermined Trunk Surface Structure
49182 49182 SRR7764533 SRX4620149 SRS3722688 SRP159053 PRJNA488354 Molecularly distinct models of zebrafish Myc induced B cell leukemia GSE119173 Transcriptome Analysis The goal of this study was to compare transcriptomic profiles of two recent B cell ALL models in zebrafish expressing either mMyc GSE108855 or hMYC transgenes. 13 unique hMYC expressing samples are included. Overall design: 13 zebrafish ALL from the rag2:hMYC; lck:GFP double transgeneic background.   pubmed:30573774   hMYC 6 GSM3360015   tissue:GFP+ FACS purified ALL from total body|strain:rag2:hMYC; lck:eGFP double transgenic line hMYC 6 Illumina bcl2fastq2 was used for basecalling. RNA Seq data were processed as previously described in Garcia et al. 2018 PMID 29749398. Briefly reads were aligned using STAR Dobin et al. 2013 to GRCz10. Picard was used to filter out potential PCR duplicates. Counts were assigned to each gene using featureCounts Liao et al. 2014. Genome build: GRCz10 Supplementary files format and content: tab delimited text file includes count matrix for all samples GFP+ FACS purified ALL from total body   Trizol extraction of total RNA was performed according to the manufacturer's instructions. Illumina TruSeq Stranded RNA Sample Prep Kit Cat#FC 122 1001 was used with 100 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols   strain:rag2:hMYC;lck:eGFP double transgenic line GSM3360015 GSM3360015: hMYC 6; Danio rerio; RNA Seq GSM3360015   1 Trizol extraction of total RNA was performed according to the manufacturer's instructions. Illumina TruSeq Stranded RNA Sample Prep Kit Cat#FC 122 1001 was used with 100 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM3360015 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 3000   SRP159053     MCB_6_c_TGACCA_R1_concat.fastq.gz MCB_6_c_TGACCA_R2_concat.fastq.gz fastq fastq 5005976120.0 24782060.0 GSM3360015 r1 0:101 1:101 A:1337000499;C:1160240242;G:1164651573;T:1337549504;N:6534302 101 101     1337000499 1160240242 1164651573 1337549504 6534302 SRX4620149 SRS3722688 SRA764101 GEO Pediatrics, University of Oklahoma Health Sciences Center 2 0.93447 0.93694 0.24013 0.24194 0.78569 0.78843 0.51039 0.51234 101 101 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   United States 2018-08-29 Undetermined Undetermined Trunk Surface Structure
49183 49183 SRR7764532 SRX4620148 SRS3722686 SRP159053 PRJNA488354 Molecularly distinct models of zebrafish Myc induced B cell leukemia GSE119173 Transcriptome Analysis The goal of this study was to compare transcriptomic profiles of two recent B cell ALL models in zebrafish expressing either mMyc GSE108855 or hMYC transgenes. 13 unique hMYC expressing samples are included. Overall design: 13 zebrafish ALL from the rag2:hMYC; lck:GFP double transgeneic background.   pubmed:30573774   hMYC 5 GSM3360014   tissue:GFP+ FACS purified ALL from total body|strain:rag2:hMYC; lck:eGFP double transgenic line hMYC 5 Illumina bcl2fastq2 was used for basecalling. RNA Seq data were processed as previously described in Garcia et al. 2018 PMID 29749398. Briefly reads were aligned using STAR Dobin et al. 2013 to GRCz10. Picard was used to filter out potential PCR duplicates. Counts were assigned to each gene using featureCounts Liao et al. 2014. Genome build: GRCz10 Supplementary files format and content: tab delimited text file includes count matrix for all samples GFP+ FACS purified ALL from total body   Trizol extraction of total RNA was performed according to the manufacturer's instructions. Illumina TruSeq Stranded RNA Sample Prep Kit Cat#FC 122 1001 was used with 100 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols   strain:rag2:hMYC;lck:eGFP double transgenic line GSM3360014 GSM3360014: hMYC 5; Danio rerio; RNA Seq GSM3360014   1 Trizol extraction of total RNA was performed according to the manufacturer's instructions. Illumina TruSeq Stranded RNA Sample Prep Kit Cat#FC 122 1001 was used with 100 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM3360014 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 3000   SRP159053     MCB_5_c_TTAGGC_R1_concat.fastq.gz MCB_5_c_TTAGGC_R2_concat.fastq.gz fastq fastq 4977608654.0 24641627.0 GSM3360014 r1 0:101 1:101 A:1314910590;C:1165984454;G:1181974120;T:1308322261;N:6417229 101 101     1314910590 1165984454 1181974120 1308322261 6417229 SRX4620148 SRS3722686 SRA764101 GEO Pediatrics, University of Oklahoma Health Sciences Center 2 0.92362 0.92695 0.10675 0.10794 0.76698 0.76873 0.50174 0.50838 101 101 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   United States 2018-08-29 Undetermined Undetermined Trunk Surface Structure
49184 49184 SRR7764531 SRX4620147 SRS3722684 SRP159053 PRJNA488354 Molecularly distinct models of zebrafish Myc induced B cell leukemia GSE119173 Transcriptome Analysis The goal of this study was to compare transcriptomic profiles of two recent B cell ALL models in zebrafish expressing either mMyc GSE108855 or hMYC transgenes. 13 unique hMYC expressing samples are included. Overall design: 13 zebrafish ALL from the rag2:hMYC; lck:GFP double transgeneic background.   pubmed:30573774   hMYC 4 GSM3360013   tissue:GFP+ FACS purified ALL from total body|strain:rag2:hMYC; lck:eGFP double transgenic line hMYC 4 Illumina bcl2fastq2 was used for basecalling. RNA Seq data were processed as previously described in Garcia et al. 2018 PMID 29749398. Briefly reads were aligned using STAR Dobin et al. 2013 to GRCz10. Picard was used to filter out potential PCR duplicates. Counts were assigned to each gene using featureCounts Liao et al. 2014. Genome build: GRCz10 Supplementary files format and content: tab delimited text file includes count matrix for all samples GFP+ FACS purified ALL from total body   Trizol extraction of total RNA was performed according to the manufacturer's instructions. Illumina TruSeq Stranded RNA Sample Prep Kit Cat#FC 122 1001 was used with 100 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols   strain:rag2:hMYC;lck:eGFP double transgenic line GSM3360013 GSM3360013: hMYC 4; Danio rerio; RNA Seq GSM3360013   1 Trizol extraction of total RNA was performed according to the manufacturer's instructions. Illumina TruSeq Stranded RNA Sample Prep Kit Cat#FC 122 1001 was used with 100 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM3360013 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 3000   SRP159053     MCB_4_c_AGTCAA_R1_concat.fastq.gz MCB_4_c_AGTCAA_R2_concat.fastq.gz fastq fastq 4643314814.0 22986707.0 GSM3360013 r1 0:101 1:101 A:1230639467;C:1085508722;G:1095255741;T:1225853845;N:6057039 101 101     1230639467 1085508722 1095255741 1225853845 6057039 SRX4620147 SRS3722684 SRA764101 GEO Pediatrics, University of Oklahoma Health Sciences Center 2 0.92296 0.92585 0.14279 0.14414 0.76232 0.76392 0.51322 0.51626 101 101 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   United States 2018-08-29 Undetermined Undetermined Trunk Surface Structure
49185 49185 SRR7764530 SRX4620146 SRS3722683 SRP159053 PRJNA488354 Molecularly distinct models of zebrafish Myc induced B cell leukemia GSE119173 Transcriptome Analysis The goal of this study was to compare transcriptomic profiles of two recent B cell ALL models in zebrafish expressing either mMyc GSE108855 or hMYC transgenes. 13 unique hMYC expressing samples are included. Overall design: 13 zebrafish ALL from the rag2:hMYC; lck:GFP double transgeneic background.   pubmed:30573774   hMYC 3 GSM3360012   tissue:GFP+ FACS purified ALL from total body|strain:rag2:hMYC; lck:eGFP double transgenic line hMYC 3 Illumina bcl2fastq2 was used for basecalling. RNA Seq data were processed as previously described in Garcia et al. 2018 PMID 29749398. Briefly reads were aligned using STAR Dobin et al. 2013 to GRCz10. Picard was used to filter out potential PCR duplicates. Counts were assigned to each gene using featureCounts Liao et al. 2014. Genome build: GRCz10 Supplementary files format and content: tab delimited text file includes count matrix for all samples GFP+ FACS purified ALL from total body   Trizol extraction of total RNA was performed according to the manufacturer's instructions. Illumina TruSeq Stranded RNA Sample Prep Kit Cat#FC 122 1001 was used with 100 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols   strain:rag2:hMYC;lck:eGFP double transgenic line GSM3360012 GSM3360012: hMYC 3; Danio rerio; RNA Seq GSM3360012   1 Trizol extraction of total RNA was performed according to the manufacturer's instructions. Illumina TruSeq Stranded RNA Sample Prep Kit Cat#FC 122 1001 was used with 100 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM3360012 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 3000   SRP159053     MCB_3_c_AGTTCC_R1_concat.fastq.gz MCB_3_c_AGTTCC_R2_concat.fastq.gz fastq fastq 4554953954.0 22549277.0 GSM3360012 r1 0:101 1:101 A:1189333550;C:1082661290;G:1094370390;T:1182606305;N:5982419 101 101     1189333550 1082661290 1094370390 1182606305 5982419 SRX4620146 SRS3722683 SRA764101 GEO Pediatrics, University of Oklahoma Health Sciences Center 2 0.92378 0.92708 0.10269 0.10292 0.76051 0.76199 0.51083 0.50811 101 101 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   United States 2018-08-29 Undetermined Undetermined Trunk Surface Structure
49186 49186 SRR7764529 SRX4620145 SRS3722685 SRP159053 PRJNA488354 Molecularly distinct models of zebrafish Myc induced B cell leukemia GSE119173 Transcriptome Analysis The goal of this study was to compare transcriptomic profiles of two recent B cell ALL models in zebrafish expressing either mMyc GSE108855 or hMYC transgenes. 13 unique hMYC expressing samples are included. Overall design: 13 zebrafish ALL from the rag2:hMYC; lck:GFP double transgeneic background.   pubmed:30573774   hMYC 2 GSM3360011   tissue:GFP+ FACS purified ALL from total body|strain:rag2:hMYC; lck:eGFP double transgenic line hMYC 2 Illumina bcl2fastq2 was used for basecalling. RNA Seq data were processed as previously described in Garcia et al. 2018 PMID 29749398. Briefly reads were aligned using STAR Dobin et al. 2013 to GRCz10. Picard was used to filter out potential PCR duplicates. Counts were assigned to each gene using featureCounts Liao et al. 2014. Genome build: GRCz10 Supplementary files format and content: tab delimited text file includes count matrix for all samples GFP+ FACS purified ALL from total body   Trizol extraction of total RNA was performed according to the manufacturer's instructions. Illumina TruSeq Stranded RNA Sample Prep Kit Cat#FC 122 1001 was used with 100 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols   strain:rag2:hMYC;lck:eGFP double transgenic line GSM3360011 GSM3360011: hMYC 2; Danio rerio; RNA Seq GSM3360011   1 Trizol extraction of total RNA was performed according to the manufacturer's instructions. Illumina TruSeq Stranded RNA Sample Prep Kit Cat#FC 122 1001 was used with 100 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM3360011 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 3000   SRP159053     MCB_2_c_CTTGTA_R1_concat.fastq.gz MCB_2_c_CTTGTA_R2_concat.fastq.gz fastq fastq 4765708230.0 23592615.0 GSM3360011 r1 0:101 1:101 A:1281598432;C:1095469903;G:1100358193;T:1282017533;N:6264169 101 101     1281598432 1095469903 1100358193 1282017533 6264169 SRX4620145 SRS3722685 SRA764101 GEO Pediatrics, University of Oklahoma Health Sciences Center 2 0.9366 0.93502 0.29149 0.28598 0.81834 0.81611 0.51036 0.50798 101 101 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   United States 2018-08-29 Undetermined Undetermined Trunk Surface Structure
49187 49187 SRR7764528 SRX4620144 SRS3722682 SRP159053 PRJNA488354 Molecularly distinct models of zebrafish Myc induced B cell leukemia GSE119173 Transcriptome Analysis The goal of this study was to compare transcriptomic profiles of two recent B cell ALL models in zebrafish expressing either mMyc GSE108855 or hMYC transgenes. 13 unique hMYC expressing samples are included. Overall design: 13 zebrafish ALL from the rag2:hMYC; lck:GFP double transgeneic background.   pubmed:30573774   hMYC 1 GSM3360010   tissue:GFP+ FACS purified ALL from total body|strain:rag2:hMYC; lck:eGFP double transgenic line hMYC 1 Illumina bcl2fastq2 was used for basecalling. RNA Seq data were processed as previously described in Garcia et al. 2018 PMID 29749398. Briefly reads were aligned using STAR Dobin et al. 2013 to GRCz10. Picard was used to filter out potential PCR duplicates. Counts were assigned to each gene using featureCounts Liao et al. 2014. Genome build: GRCz10 Supplementary files format and content: tab delimited text file includes count matrix for all samples GFP+ FACS purified ALL from total body   Trizol extraction of total RNA was performed according to the manufacturer's instructions. Illumina TruSeq Stranded RNA Sample Prep Kit Cat#FC 122 1001 was used with 100 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols   strain:rag2:hMYC;lck:eGFP double transgenic line GSM3360010 GSM3360010: hMYC 1; Danio rerio; RNA Seq GSM3360010   1 Trizol extraction of total RNA was performed according to the manufacturer's instructions. Illumina TruSeq Stranded RNA Sample Prep Kit Cat#FC 122 1001 was used with 100 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM3360010 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 3000   SRP159053     MCB_1_c_CGATGT_R1_concan.fastq.gz MCB_1_c_CGATGT_R2_concan.fastq.gz fastq fastq 4646978084.0 23004842.0 GSM3360010 r1 0:101 1:101 A:1211324194;C:1106543328;G:1120164021;T:1202883527;N:6063014 101 101     1211324194 1106543328 1120164021 1202883527 6063014 SRX4620144 SRS3722682 SRA764101 GEO Pediatrics, University of Oklahoma Health Sciences Center 2 0.92808 0.9305 0.10385 0.10435 0.76485 0.76627 0.51885 0.51967 101 101 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   United States 2018-08-29 Undetermined Undetermined Trunk Surface Structure
51072 51072 SRR8503426 SRX5307303 SRS4304843 SRP182846 PRJNA517717 Transpositional scaling and niche transitions restore organ size and shape during zebrafish fin regeneration GSE125859 Transcriptome Analysis Regenerating zebrafish fins have distal progenitor and proximal re differentiation zones. A Wnt producing "niche" population maintains distal cells in progenitor states. We sought to define molecular markers of niche cells to study their origins and fates and how they contribute to fin size and shape restoration. Overall design: We used RNA Seq to compare gene expression between three replicates of microdissected distal vs. proximal regenerating fin tissue as distinguished by distal shha:gfp expression. Each replicate consisted of pooled tissue from four caudal fins.       prox 4 GSM3583370   source name:96 hpa proximal regenerate|transgene:shha:eGFP|tissue:regenerating caudal fin|time:96 hours post amputation prox 4 Basecalling by Illumina Real Time Analysis 2 RTA2. Sequence reads were mapped to GRCz11/danRer11 using TopHat2 Mapped reads were counted using HTSeq Genome build: GRCz11/danRer11 Supplementary files format and content: Tab delimited text files of HTSeq counts for each sample are provided 96 hpa proximal regenerate   Tissue was collected and immediately placed in TRIzol reagent and homogenized. RNA was isolated using manufacturer's instruction. Libraries were prepared from 1ug of isolated RNA using Kapa stranded mRNA Seq kit and protocol.   transgene:shha:eGFP|tissue:regenerating caudal fin|time:96 hours post amputation GSM3583370 GSM3583370: prox 4; Danio rerio; RNA Seq GSM3583370   1 Tissue was collected and immediately placed in TRIzol reagent and homogenized. RNA was isolated using manufacturer's instruction. Libraries were prepared from 1ug of isolated RNA using Kapa stranded mRNA Seq kit and protocol. GEO Accession:GSM3583370 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP182846     P_H4_S10_R1_001.fastq fastq 2542575470.0 30622171.0 GSM3583370 r1 0:83.03 1:0 A:589076767;C:639351667;G:597170951;T:716352530;N:623555 83 0     589076767 639351667 597170951 716352530 623555 SRX5307303 SRS4304843 SRA841050 GEO Stankunas, Biology- Institute of Molecular Biology, University of Oregon 1 0.96003   0.11536   0.73184   0.50861   82   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   United States 2019-01-29 Undetermined Undetermined Fin Surface Structure
51073 51073 SRR8503425 SRX5307302 SRS4304842 SRP182846 PRJNA517717 Transpositional scaling and niche transitions restore organ size and shape during zebrafish fin regeneration GSE125859 Transcriptome Analysis Regenerating zebrafish fins have distal progenitor and proximal re differentiation zones. A Wnt producing "niche" population maintains distal cells in progenitor states. We sought to define molecular markers of niche cells to study their origins and fates and how they contribute to fin size and shape restoration. Overall design: We used RNA Seq to compare gene expression between three replicates of microdissected distal vs. proximal regenerating fin tissue as distinguished by distal shha:gfp expression. Each replicate consisted of pooled tissue from four caudal fins.       prox 3 GSM3583369   source name:96 hpa proximal regenerate|transgene:shha:eGFP|tissue:regenerating caudal fin|time:96 hours post amputation prox 3 Basecalling by Illumina Real Time Analysis 2 RTA2. Sequence reads were mapped to GRCz11/danRer11 using TopHat2 Mapped reads were counted using HTSeq Genome build: GRCz11/danRer11 Supplementary files format and content: Tab delimited text files of HTSeq counts for each sample are provided 96 hpa proximal regenerate   Tissue was collected and immediately placed in TRIzol reagent and homogenized. RNA was isolated using manufacturer's instruction. Libraries were prepared from 1ug of isolated RNA using Kapa stranded mRNA Seq kit and protocol.   transgene:shha:eGFP|tissue:regenerating caudal fin|time:96 hours post amputation GSM3583369 GSM3583369: prox 3; Danio rerio; RNA Seq GSM3583369   1 Tissue was collected and immediately placed in TRIzol reagent and homogenized. RNA was isolated using manufacturer's instruction. Libraries were prepared from 1ug of isolated RNA using Kapa stranded mRNA Seq kit and protocol. GEO Accession:GSM3583369 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP182846     P_H3_S6_R1_001.fastq fastq 2572355378.0 30989968.0 GSM3583369 r1 0:83.01 1:0 A:628074006;C:625169881;G:585755261;T:732650748;N:705482 83 0     628074006 625169881 585755261 732650748 705482 SRX5307302 SRS4304842 SRA841050 GEO Stankunas, Biology- Institute of Molecular Biology, University of Oregon 1 0.95739   0.12653   0.72066   0.49327   84   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   United States 2019-01-29 Undetermined Undetermined Fin Surface Structure
51074 51074 SRR8503424 SRX5307301 SRS4304841 SRP182846 PRJNA517717 Transpositional scaling and niche transitions restore organ size and shape during zebrafish fin regeneration GSE125859 Transcriptome Analysis Regenerating zebrafish fins have distal progenitor and proximal re differentiation zones. A Wnt producing "niche" population maintains distal cells in progenitor states. We sought to define molecular markers of niche cells to study their origins and fates and how they contribute to fin size and shape restoration. Overall design: We used RNA Seq to compare gene expression between three replicates of microdissected distal vs. proximal regenerating fin tissue as distinguished by distal shha:gfp expression. Each replicate consisted of pooled tissue from four caudal fins.       prox 2 GSM3583368   source name:96 hpa proximal regenerate|transgene:shha:eGFP|tissue:regenerating caudal fin|time:96 hours post amputation prox 2 Basecalling by Illumina Real Time Analysis 2 RTA2. Sequence reads were mapped to GRCz11/danRer11 using TopHat2 Mapped reads were counted using HTSeq Genome build: GRCz11/danRer11 Supplementary files format and content: Tab delimited text files of HTSeq counts for each sample are provided 96 hpa proximal regenerate   Tissue was collected and immediately placed in TRIzol reagent and homogenized. RNA was isolated using manufacturer's instruction. Libraries were prepared from 1ug of isolated RNA using Kapa stranded mRNA Seq kit and protocol.   transgene:shha:eGFP|tissue:regenerating caudal fin|time:96 hours post amputation GSM3583368 GSM3583368: prox 2; Danio rerio; RNA Seq GSM3583368   1 Tissue was collected and immediately placed in TRIzol reagent and homogenized. RNA was isolated using manufacturer's instruction. Libraries were prepared from 1ug of isolated RNA using Kapa stranded mRNA Seq kit and protocol. GEO Accession:GSM3583368 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP182846     P_H2_S2_R1_001.fastq fastq 2715018138.0 32683271.0 GSM3583368 r1 0:83.07 1:0 A:650816207;C:672048834;G:625641446;T:765832919;N:678732 83 0     650816207 672048834 625641446 765832919 678732 SRX5307301 SRS4304841 SRA841050 GEO Stankunas, Biology- Institute of Molecular Biology, University of Oregon 1 0.96137   0.11136   0.72299   0.49133   84   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   United States 2019-01-29 Undetermined Undetermined Fin Surface Structure
51075 51075 SRR8503423 SRX5307300 SRS4304840 SRP182846 PRJNA517717 Transpositional scaling and niche transitions restore organ size and shape during zebrafish fin regeneration GSE125859 Transcriptome Analysis Regenerating zebrafish fins have distal progenitor and proximal re differentiation zones. A Wnt producing "niche" population maintains distal cells in progenitor states. We sought to define molecular markers of niche cells to study their origins and fates and how they contribute to fin size and shape restoration. Overall design: We used RNA Seq to compare gene expression between three replicates of microdissected distal vs. proximal regenerating fin tissue as distinguished by distal shha:gfp expression. Each replicate consisted of pooled tissue from four caudal fins.       dist 4 GSM3583367   source name:96 hpa distal regenerate|transgene:shha:eGFP|tissue:regenerating caudal fin|time:96 hours post amputation dist 4 Basecalling by Illumina Real Time Analysis 2 RTA2. Sequence reads were mapped to GRCz11/danRer11 using TopHat2 Mapped reads were counted using HTSeq Genome build: GRCz11/danRer11 Supplementary files format and content: Tab delimited text files of HTSeq counts for each sample are provided 96 hpa distal regenerate   Tissue was collected and immediately placed in TRIzol reagent and homogenized. RNA was isolated using manufacturer's instruction. Libraries were prepared from 1ug of isolated RNA using Kapa stranded mRNA Seq kit and protocol.   transgene:shha:eGFP|tissue:regenerating caudal fin|time:96 hours post amputation GSM3583367 GSM3583367: dist 4; Danio rerio; RNA Seq GSM3583367   1 Tissue was collected and immediately placed in TRIzol reagent and homogenized. RNA was isolated using manufacturer's instruction. Libraries were prepared from 1ug of isolated RNA using Kapa stranded mRNA Seq kit and protocol. GEO Accession:GSM3583367 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP182846     D_H4_S9_R1_001.fastq fastq 2464857182.0 29674986.0 GSM3583367 r1 0:83.06 1:0 A:605468091;C:597283347;G:564251292;T:696611465;N:1242987 83 0     605468091 597283347 564251292 696611465 1242987 SRX5307300 SRS4304840 SRA841050 GEO Stankunas, Biology- Institute of Molecular Biology, University of Oregon 1 0.95564   0.13712   0.72492   0.52324   83   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   United States 2019-01-29 Undetermined Undetermined Fin Surface Structure
51076 51076 SRR8503422 SRX5307299 SRS4304839 SRP182846 PRJNA517717 Transpositional scaling and niche transitions restore organ size and shape during zebrafish fin regeneration GSE125859 Transcriptome Analysis Regenerating zebrafish fins have distal progenitor and proximal re differentiation zones. A Wnt producing "niche" population maintains distal cells in progenitor states. We sought to define molecular markers of niche cells to study their origins and fates and how they contribute to fin size and shape restoration. Overall design: We used RNA Seq to compare gene expression between three replicates of microdissected distal vs. proximal regenerating fin tissue as distinguished by distal shha:gfp expression. Each replicate consisted of pooled tissue from four caudal fins.       dist 3 GSM3583366   source name:96 hpa distal regenerate|transgene:shha:eGFP|tissue:regenerating caudal fin|time:96 hours post amputation dist 3 Basecalling by Illumina Real Time Analysis 2 RTA2. Sequence reads were mapped to GRCz11/danRer11 using TopHat2 Mapped reads were counted using HTSeq Genome build: GRCz11/danRer11 Supplementary files format and content: Tab delimited text files of HTSeq counts for each sample are provided 96 hpa distal regenerate   Tissue was collected and immediately placed in TRIzol reagent and homogenized. RNA was isolated using manufacturer's instruction. Libraries were prepared from 1ug of isolated RNA using Kapa stranded mRNA Seq kit and protocol.   transgene:shha:eGFP|tissue:regenerating caudal fin|time:96 hours post amputation GSM3583366 GSM3583366: dist 3; Danio rerio; RNA Seq GSM3583366   1 Tissue was collected and immediately placed in TRIzol reagent and homogenized. RNA was isolated using manufacturer's instruction. Libraries were prepared from 1ug of isolated RNA using Kapa stranded mRNA Seq kit and protocol. GEO Accession:GSM3583366 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP182846     D_H3_S5_R1_001.fastq fastq 2722788315.0 32775698.0 GSM3583366 r1 0:83.07 1:0 A:668412932;C:661166177;G:622685501;T:770010239;N:513466 83 0     668412932 661166177 622685501 770010239 513466 SRX5307299 SRS4304839 SRA841050 GEO Stankunas, Biology- Institute of Molecular Biology, University of Oregon 1 0.95609   0.14248   0.71855   0.51164   84   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   United States 2019-01-29 Undetermined Undetermined Fin Surface Structure
51077 51077 SRR8503421 SRX5307298 SRS4304838 SRP182846 PRJNA517717 Transpositional scaling and niche transitions restore organ size and shape during zebrafish fin regeneration GSE125859 Transcriptome Analysis Regenerating zebrafish fins have distal progenitor and proximal re differentiation zones. A Wnt producing "niche" population maintains distal cells in progenitor states. We sought to define molecular markers of niche cells to study their origins and fates and how they contribute to fin size and shape restoration. Overall design: We used RNA Seq to compare gene expression between three replicates of microdissected distal vs. proximal regenerating fin tissue as distinguished by distal shha:gfp expression. Each replicate consisted of pooled tissue from four caudal fins.       dist 2 GSM3583365   source name:96 hpa distal regenerate|transgene:shha:eGFP|tissue:regenerating caudal fin|time:96 hours post amputation dist 2 Basecalling by Illumina Real Time Analysis 2 RTA2. Sequence reads were mapped to GRCz11/danRer11 using TopHat2 Mapped reads were counted using HTSeq Genome build: GRCz11/danRer11 Supplementary files format and content: Tab delimited text files of HTSeq counts for each sample are provided 96 hpa distal regenerate   Tissue was collected and immediately placed in TRIzol reagent and homogenized. RNA was isolated using manufacturer's instruction. Libraries were prepared from 1ug of isolated RNA using Kapa stranded mRNA Seq kit and protocol.   transgene:shha:eGFP|tissue:regenerating caudal fin|time:96 hours post amputation GSM3583365 GSM3583365: dist 2; Danio rerio; RNA Seq GSM3583365   1 Tissue was collected and immediately placed in TRIzol reagent and homogenized. RNA was isolated using manufacturer's instruction. Libraries were prepared from 1ug of isolated RNA using Kapa stranded mRNA Seq kit and protocol. GEO Accession:GSM3583365 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP182846     D_H2_S1_R1_001.fastq fastq 2701672782.0 32524371.0 GSM3583365 r1 0:83.07 1:0 A:655498678;C:666854715;G:624383445;T:753418035;N:1517909 83 0     655498678 666854715 624383445 753418035 1517909 SRX5307298 SRS4304838 SRA841050 GEO Stankunas, Biology- Institute of Molecular Biology, University of Oregon 1 0.95937   0.14803   0.72569   0.5327   81   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   United States 2019-01-29 Undetermined Undetermined Fin Surface Structure
51194 51194 SRR8587741 SRX5388280 SRS4376719 SRP186180 PRJNA523009 Regenerating zebrafish fin epigenome is characterized by stable lineage specific DNA methylation and dynamic chromatin accessibility RNA seq GSE126701 Transcriptome Analysis Background: Zebrafish can faithfully regenerate injured fins through the formation of a blastema a mass of proliferative cells that can grow and develop into the lost body part. post amputation various cell types contribute to blastema formation where each cell type retains fate restriction and exclusively contributes to regeneration of its own lineage. Epigenetic changes that are associated with lineage restriction during regeneration remain underexplored. Results: We produce epigenome maps including DNA methylation and chromatin accessibility as well as transcriptomes of osteoblasts and other cells in uninjured and regenerating fins. This effort reveals regeneration as a process of highly dynamic and orchestrated transcriptomic and chromatin accessibility changes coupled with stably maintained lineage specific DNA methylation. The epigenetic signatures also reveal many novel regeneration specific enhancers which are experimentally validated. Regulatory networks important for regeneration are constructed through integrative analysis of the epigenome map and a knockout of a predicted upstream regulator disrupts normal regeneration validating our prediction. Conclusion: Our study shows that lineage specific DNA methylation signatures are stably maintained during regeneration and regeneration enhancers are preset as hypomethylated before injury. In contrast chromatin accessibility is dynamically changed during regeneration. Many enhancers driving regeneration gene expression as well as upstream regulators of regeneration are identified and validated through integrative epigenome analysis. Overall design: mRNA profiles of the uninjured and regenerating fin by deep sequencing in duplicate using Illumina NextSeq. parent bioproject:PRJNA523007 pubmed:32106888   RNA fosl1aKO 4dpa rep2 GSM3611582   tissue:zebrafish fin|cell type:blastema|dy post amputation:4 dpa|genotype/variation:fosl1a KO RNA fosl1aKO 4dpa rep2 Basecalls were performed by the Edison Family Center for Genome Sciences & Systems Biology Sequencing Center using bcl2fastq The raw sequence reads were aligned to zebrafish transcriptome Ensembl release 85 and the zebrafish genome assembly GRCz10 by using STAR aligner version 2.5.2a with the following parameters: sjdbScore 1 clip3pAdapterSeq AGATCGGAAGAGC outWigStrand Unstranded outFilterType BySJout outFilterMultimapNmax 1. The total number of reads overlapping each gene were counted using featureCounts v.1.5.0 with Ensembl release 85 gtf file and the following parameters: F GTF t exon g gene id O s 0 primary p. Genome build: GRCz10 Supplementary files format and content: TXT zebrafish fin   The total RNA was extracted by using TRIzol solution Ambion according to the manufacturer’s instructions with minor modifications. RNA seq libraries were generated by using TruSeq RNA Library Prep Kit v2 Illumina according to the manufacturer’s instructions.   cell type:blastema|dy post amputation:4 dpa|genotype/variation:fosl1a KO GSM3611582 GSM3611582: RNA fosl1aKO 4dpa rep2; Danio rerio; RNA Seq GSM3611582   1 The total RNA was extracted by using TRIzol solution Ambion according to the manufacturer's instructions with minor modifications. RNA seq libraries were generated by using TruSeq RNA Library Prep Kit v2 Illumina according to the manufacturer's instructions. GEO Accession:GSM3611582 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP186180     RNA_fosl1aKO_4dpa_rep2_R1.fastq.gz RNA_fosl1aKO_4dpa_rep2_R2.fastq.gz fastq fastq 4333742700.0 28891618.0 GSM3611582 r1 0:75 1:75 A:1010389064;C:1147530033;G:1144519365;T:1030805675;N:498563 75 75     1010389064 1147530033 1144519365 1030805675 498563 SRX5388280 SRS4376719 SRA850124 GEO Ting Wang, Department of Genetics, Washington University School of Medicine 2 0.95218 0.95027 0.03979 0.03899 0.74452 0.74844 0.44397 0.43644 75 75 B B biological fallback assumption illumina nextseq unknown cdna_unspecified trueseq bulk unknown unknown   United States 2019-02-18 Undetermined Undetermined Fin Surface Structure
51195 51195 SRR8587740 SRX5388279 SRS4376718 SRP186180 PRJNA523009 Regenerating zebrafish fin epigenome is characterized by stable lineage specific DNA methylation and dynamic chromatin accessibility RNA seq GSE126701 Transcriptome Analysis Background: Zebrafish can faithfully regenerate injured fins through the formation of a blastema a mass of proliferative cells that can grow and develop into the lost body part. post amputation various cell types contribute to blastema formation where each cell type retains fate restriction and exclusively contributes to regeneration of its own lineage. Epigenetic changes that are associated with lineage restriction during regeneration remain underexplored. Results: We produce epigenome maps including DNA methylation and chromatin accessibility as well as transcriptomes of osteoblasts and other cells in uninjured and regenerating fins. This effort reveals regeneration as a process of highly dynamic and orchestrated transcriptomic and chromatin accessibility changes coupled with stably maintained lineage specific DNA methylation. The epigenetic signatures also reveal many novel regeneration specific enhancers which are experimentally validated. Regulatory networks important for regeneration are constructed through integrative analysis of the epigenome map and a knockout of a predicted upstream regulator disrupts normal regeneration validating our prediction. Conclusion: Our study shows that lineage specific DNA methylation signatures are stably maintained during regeneration and regeneration enhancers are preset as hypomethylated before injury. In contrast chromatin accessibility is dynamically changed during regeneration. Many enhancers driving regeneration gene expression as well as upstream regulators of regeneration are identified and validated through integrative epigenome analysis. Overall design: mRNA profiles of the uninjured and regenerating fin by deep sequencing in duplicate using Illumina NextSeq. parent bioproject:PRJNA523007 pubmed:32106888   RNA fosl1aKO 4dpa rep1 GSM3611581   tissue:zebrafish fin|cell type:blastema|dy post amputation:4 dpa|genotype/variation:fosl1a KO RNA fosl1aKO 4dpa rep1 Basecalls were performed by the Edison Family Center for Genome Sciences & Systems Biology Sequencing Center using bcl2fastq The raw sequence reads were aligned to zebrafish transcriptome Ensembl release 85 and the zebrafish genome assembly GRCz10 by using STAR aligner version 2.5.2a with the following parameters: sjdbScore 1 clip3pAdapterSeq AGATCGGAAGAGC outWigStrand Unstranded outFilterType BySJout outFilterMultimapNmax 1. The total number of reads overlapping each gene were counted using featureCounts v.1.5.0 with Ensembl release 85 gtf file and the following parameters: F GTF t exon g gene id O s 0 primary p. Genome build: GRCz10 Supplementary files format and content: TXT zebrafish fin   The total RNA was extracted by using TRIzol solution Ambion according to the manufacturer’s instructions with minor modifications. RNA seq libraries were generated by using TruSeq RNA Library Prep Kit v2 Illumina according to the manufacturer’s instructions.   cell type:blastema|dy post amputation:4 dpa|genotype/variation:fosl1a KO GSM3611581 GSM3611581: RNA fosl1aKO 4dpa rep1; Danio rerio; RNA Seq GSM3611581   1 The total RNA was extracted by using TRIzol solution Ambion according to the manufacturer's instructions with minor modifications. RNA seq libraries were generated by using TruSeq RNA Library Prep Kit v2 Illumina according to the manufacturer's instructions. GEO Accession:GSM3611581 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP186180     RNA_fosl1aKO_4dpa_rep1_R1.fastq.gz RNA_fosl1aKO_4dpa_rep1_R2.fastq.gz fastq fastq 4888155000.0 32587700.0 GSM3611581 r1 0:75 1:75 A:1108723318;C:1330619563;G:1323468665;T:1124752996;N:590458 75 75     1108723318 1330619563 1323468665 1124752996 590458 SRX5388279 SRS4376718 SRA850124 GEO Ting Wang, Department of Genetics, Washington University School of Medicine 2 0.96275 0.95975 0.03265 0.03216 0.75243 0.75737 0.43553 0.43982 75 75 B B biological fallback assumption illumina nextseq unknown cdna_unspecified trueseq bulk unknown unknown   United States 2019-02-18 Undetermined Undetermined Fin Surface Structure
51196 51196 SRR8587739 SRX5388278 SRS4376717 SRP186180 PRJNA523009 Regenerating zebrafish fin epigenome is characterized by stable lineage specific DNA methylation and dynamic chromatin accessibility RNA seq GSE126701 Transcriptome Analysis Background: Zebrafish can faithfully regenerate injured fins through the formation of a blastema a mass of proliferative cells that can grow and develop into the lost body part. post amputation various cell types contribute to blastema formation where each cell type retains fate restriction and exclusively contributes to regeneration of its own lineage. Epigenetic changes that are associated with lineage restriction during regeneration remain underexplored. Results: We produce epigenome maps including DNA methylation and chromatin accessibility as well as transcriptomes of osteoblasts and other cells in uninjured and regenerating fins. This effort reveals regeneration as a process of highly dynamic and orchestrated transcriptomic and chromatin accessibility changes coupled with stably maintained lineage specific DNA methylation. The epigenetic signatures also reveal many novel regeneration specific enhancers which are experimentally validated. Regulatory networks important for regeneration are constructed through integrative analysis of the epigenome map and a knockout of a predicted upstream regulator disrupts normal regeneration validating our prediction. Conclusion: Our study shows that lineage specific DNA methylation signatures are stably maintained during regeneration and regeneration enhancers are preset as hypomethylated before injury. In contrast chromatin accessibility is dynamically changed during regeneration. Many enhancers driving regeneration gene expression as well as upstream regulators of regeneration are identified and validated through integrative epigenome analysis. Overall design: mRNA profiles of the uninjured and regenerating fin by deep sequencing in duplicate using Illumina NextSeq. parent bioproject:PRJNA523007 pubmed:32106888   RNA fosl1aKO 1dpa rep2 GSM3611580   tissue:zebrafish fin|cell type:blastema|dy post amputation:1 dpa|genotype/variation:fosl1a KO RNA fosl1aKO 1dpa rep2 Basecalls were performed by the Edison Family Center for Genome Sciences & Systems Biology Sequencing Center using bcl2fastq The raw sequence reads were aligned to zebrafish transcriptome Ensembl release 85 and the zebrafish genome assembly GRCz10 by using STAR aligner version 2.5.2a with the following parameters: sjdbScore 1 clip3pAdapterSeq AGATCGGAAGAGC outWigStrand Unstranded outFilterType BySJout outFilterMultimapNmax 1. The total number of reads overlapping each gene were counted using featureCounts v.1.5.0 with Ensembl release 85 gtf file and the following parameters: F GTF t exon g gene id O s 0 primary p. Genome build: GRCz10 Supplementary files format and content: TXT zebrafish fin   The total RNA was extracted by using TRIzol solution Ambion according to the manufacturer’s instructions with minor modifications. RNA seq libraries were generated by using TruSeq RNA Library Prep Kit v2 Illumina according to the manufacturer’s instructions.   cell type:blastema|dy post amputation:1 dpa|genotype/variation:fosl1a KO GSM3611580 GSM3611580: RNA fosl1aKO 1dpa rep2; Danio rerio; RNA Seq GSM3611580   1 The total RNA was extracted by using TRIzol solution Ambion according to the manufacturer's instructions with minor modifications. RNA seq libraries were generated by using TruSeq RNA Library Prep Kit v2 Illumina according to the manufacturer's instructions. GEO Accession:GSM3611580 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP186180     RNA_fosl1aKO_1dpa_rep2_R1.fastq.gz RNA_fosl1aKO_1dpa_rep2_R2.fastq.gz fastq fastq 3725421150.0 24836141.0 GSM3611580 r1 0:75 1:75 A:926984963;C:922244919;G:923073807;T:952682172;N:435289 75 75     926984963 922244919 923073807 952682172 435289 SRX5388278 SRS4376717 SRA850124 GEO Ting Wang, Department of Genetics, Washington University School of Medicine 2 0.93758 0.92982 0.05286 0.05199 0.74683 0.75114 0.4297 0.42145 75 75 B B biological fallback assumption illumina nextseq unknown cdna_unspecified trueseq bulk unknown unknown   United States 2019-02-18 Undetermined Undetermined Fin Surface Structure
51197 51197 SRR8587738 SRX5388277 SRS4376716 SRP186180 PRJNA523009 Regenerating zebrafish fin epigenome is characterized by stable lineage specific DNA methylation and dynamic chromatin accessibility RNA seq GSE126701 Transcriptome Analysis Background: Zebrafish can faithfully regenerate injured fins through the formation of a blastema a mass of proliferative cells that can grow and develop into the lost body part. post amputation various cell types contribute to blastema formation where each cell type retains fate restriction and exclusively contributes to regeneration of its own lineage. Epigenetic changes that are associated with lineage restriction during regeneration remain underexplored. Results: We produce epigenome maps including DNA methylation and chromatin accessibility as well as transcriptomes of osteoblasts and other cells in uninjured and regenerating fins. This effort reveals regeneration as a process of highly dynamic and orchestrated transcriptomic and chromatin accessibility changes coupled with stably maintained lineage specific DNA methylation. The epigenetic signatures also reveal many novel regeneration specific enhancers which are experimentally validated. Regulatory networks important for regeneration are constructed through integrative analysis of the epigenome map and a knockout of a predicted upstream regulator disrupts normal regeneration validating our prediction. Conclusion: Our study shows that lineage specific DNA methylation signatures are stably maintained during regeneration and regeneration enhancers are preset as hypomethylated before injury. In contrast chromatin accessibility is dynamically changed during regeneration. Many enhancers driving regeneration gene expression as well as upstream regulators of regeneration are identified and validated through integrative epigenome analysis. Overall design: mRNA profiles of the uninjured and regenerating fin by deep sequencing in duplicate using Illumina NextSeq. parent bioproject:PRJNA523007 pubmed:32106888   RNA fosl1aKO 1dpa rep1 GSM3611579   tissue:zebrafish fin|cell type:blastema|dy post amputation:1 dpa|genotype/variation:fosl1a KO RNA fosl1aKO 1dpa rep1 Basecalls were performed by the Edison Family Center for Genome Sciences & Systems Biology Sequencing Center using bcl2fastq The raw sequence reads were aligned to zebrafish transcriptome Ensembl release 85 and the zebrafish genome assembly GRCz10 by using STAR aligner version 2.5.2a with the following parameters: sjdbScore 1 clip3pAdapterSeq AGATCGGAAGAGC outWigStrand Unstranded outFilterType BySJout outFilterMultimapNmax 1. The total number of reads overlapping each gene were counted using featureCounts v.1.5.0 with Ensembl release 85 gtf file and the following parameters: F GTF t exon g gene id O s 0 primary p. Genome build: GRCz10 Supplementary files format and content: TXT zebrafish fin   The total RNA was extracted by using TRIzol solution Ambion according to the manufacturer’s instructions with minor modifications. RNA seq libraries were generated by using TruSeq RNA Library Prep Kit v2 Illumina according to the manufacturer’s instructions.   cell type:blastema|dy post amputation:1 dpa|genotype/variation:fosl1a KO GSM3611579 GSM3611579: RNA fosl1aKO 1dpa rep1; Danio rerio; RNA Seq GSM3611579   1 The total RNA was extracted by using TRIzol solution Ambion according to the manufacturer's instructions with minor modifications. RNA seq libraries were generated by using TruSeq RNA Library Prep Kit v2 Illumina according to the manufacturer's instructions. GEO Accession:GSM3611579 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP186180     RNA_fosl1aKO_1dpa_rep1_R1.fastq.gz RNA_fosl1aKO_1dpa_rep1_R2.fastq.gz fastq fastq 3191604900.0 21277366.0 GSM3611579 r1 0:75 1:75 A:811665055;C:763363145;G:774183657;T:842004197;N:388846 75 75     811665055 763363145 774183657 842004197 388846 SRX5388277 SRS4376716 SRA850124 GEO Ting Wang, Department of Genetics, Washington University School of Medicine 2 0.91616 0.8993 0.05799 0.05685 0.73973 0.74395 0.43716 0.44106 75 75 B B biological fallback assumption illumina nextseq unknown cdna_unspecified trueseq bulk unknown unknown   United States 2019-02-18 Undetermined Undetermined Fin Surface Structure
51198 51198 SRR8587737 SRX5388276 SRS4376715 SRP186180 PRJNA523009 Regenerating zebrafish fin epigenome is characterized by stable lineage specific DNA methylation and dynamic chromatin accessibility RNA seq GSE126701 Transcriptome Analysis Background: Zebrafish can faithfully regenerate injured fins through the formation of a blastema a mass of proliferative cells that can grow and develop into the lost body part. post amputation various cell types contribute to blastema formation where each cell type retains fate restriction and exclusively contributes to regeneration of its own lineage. Epigenetic changes that are associated with lineage restriction during regeneration remain underexplored. Results: We produce epigenome maps including DNA methylation and chromatin accessibility as well as transcriptomes of osteoblasts and other cells in uninjured and regenerating fins. This effort reveals regeneration as a process of highly dynamic and orchestrated transcriptomic and chromatin accessibility changes coupled with stably maintained lineage specific DNA methylation. The epigenetic signatures also reveal many novel regeneration specific enhancers which are experimentally validated. Regulatory networks important for regeneration are constructed through integrative analysis of the epigenome map and a knockout of a predicted upstream regulator disrupts normal regeneration validating our prediction. Conclusion: Our study shows that lineage specific DNA methylation signatures are stably maintained during regeneration and regeneration enhancers are preset as hypomethylated before injury. In contrast chromatin accessibility is dynamically changed during regeneration. Many enhancers driving regeneration gene expression as well as upstream regulators of regeneration are identified and validated through integrative epigenome analysis. Overall design: mRNA profiles of the uninjured and regenerating fin by deep sequencing in duplicate using Illumina NextSeq. parent bioproject:PRJNA523007 pubmed:32106888   RNA fosl1aKO 0dpa rep2 GSM3611578   tissue:zebrafish fin|cell type:fin|dy post amputation:0 dpa|genotype/variation:fosl1a KO RNA fosl1aKO 0dpa rep2 Basecalls were performed by the Edison Family Center for Genome Sciences & Systems Biology Sequencing Center using bcl2fastq The raw sequence reads were aligned to zebrafish transcriptome Ensembl release 85 and the zebrafish genome assembly GRCz10 by using STAR aligner version 2.5.2a with the following parameters: sjdbScore 1 clip3pAdapterSeq AGATCGGAAGAGC outWigStrand Unstranded outFilterType BySJout outFilterMultimapNmax 1. The total number of reads overlapping each gene were counted using featureCounts v.1.5.0 with Ensembl release 85 gtf file and the following parameters: F GTF t exon g gene id O s 0 primary p. Genome build: GRCz10 Supplementary files format and content: TXT zebrafish fin   The total RNA was extracted by using TRIzol solution Ambion according to the manufacturer’s instructions with minor modifications. RNA seq libraries were generated by using TruSeq RNA Library Prep Kit v2 Illumina according to the manufacturer’s instructions.   cell type:fin|dy post amputation:0 dpa|genotype/variation:fosl1a KO GSM3611578 GSM3611578: RNA fosl1aKO 0dpa rep2; Danio rerio; RNA Seq GSM3611578   1 The total RNA was extracted by using TRIzol solution Ambion according to the manufacturer's instructions with minor modifications. RNA seq libraries were generated by using TruSeq RNA Library Prep Kit v2 Illumina according to the manufacturer's instructions. GEO Accession:GSM3611578 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP186180     RNA_fosl1aKO_0dpa_rep2_R1.fastq.gz RNA_fosl1aKO_0dpa_rep2_R2.fastq.gz fastq fastq 4542697500.0 30284650.0 GSM3611578 r1 0:75 1:75 A:1084046634;C:1170171796;G:1176769539;T:1111171698;N:537833 75 75     1084046634 1170171796 1176769539 1111171698 537833 SRX5388276 SRS4376715 SRA850124 GEO Ting Wang, Department of Genetics, Washington University School of Medicine 2 0.94272 0.93585 0.04662 0.04565 0.75063 0.75446 0.40736 0.40407 75 75 B B biological fallback assumption illumina nextseq unknown cdna_unspecified trueseq bulk unknown unknown   United States 2019-02-18 Undetermined Undetermined Fin Surface Structure
51199 51199 SRR8587736 SRX5388275 SRS4376714 SRP186180 PRJNA523009 Regenerating zebrafish fin epigenome is characterized by stable lineage specific DNA methylation and dynamic chromatin accessibility RNA seq GSE126701 Transcriptome Analysis Background: Zebrafish can faithfully regenerate injured fins through the formation of a blastema a mass of proliferative cells that can grow and develop into the lost body part. post amputation various cell types contribute to blastema formation where each cell type retains fate restriction and exclusively contributes to regeneration of its own lineage. Epigenetic changes that are associated with lineage restriction during regeneration remain underexplored. Results: We produce epigenome maps including DNA methylation and chromatin accessibility as well as transcriptomes of osteoblasts and other cells in uninjured and regenerating fins. This effort reveals regeneration as a process of highly dynamic and orchestrated transcriptomic and chromatin accessibility changes coupled with stably maintained lineage specific DNA methylation. The epigenetic signatures also reveal many novel regeneration specific enhancers which are experimentally validated. Regulatory networks important for regeneration are constructed through integrative analysis of the epigenome map and a knockout of a predicted upstream regulator disrupts normal regeneration validating our prediction. Conclusion: Our study shows that lineage specific DNA methylation signatures are stably maintained during regeneration and regeneration enhancers are preset as hypomethylated before injury. In contrast chromatin accessibility is dynamically changed during regeneration. Many enhancers driving regeneration gene expression as well as upstream regulators of regeneration are identified and validated through integrative epigenome analysis. Overall design: mRNA profiles of the uninjured and regenerating fin by deep sequencing in duplicate using Illumina NextSeq. parent bioproject:PRJNA523007 pubmed:32106888   RNA fosl1aKO 0dpa rep1 GSM3611577   tissue:zebrafish fin|cell type:fin|dy post amputation:0 dpa|genotype/variation:fosl1a KO RNA fosl1aKO 0dpa rep1 Basecalls were performed by the Edison Family Center for Genome Sciences & Systems Biology Sequencing Center using bcl2fastq The raw sequence reads were aligned to zebrafish transcriptome Ensembl release 85 and the zebrafish genome assembly GRCz10 by using STAR aligner version 2.5.2a with the following parameters: sjdbScore 1 clip3pAdapterSeq AGATCGGAAGAGC outWigStrand Unstranded outFilterType BySJout outFilterMultimapNmax 1. The total number of reads overlapping each gene were counted using featureCounts v.1.5.0 with Ensembl release 85 gtf file and the following parameters: F GTF t exon g gene id O s 0 primary p. Genome build: GRCz10 Supplementary files format and content: TXT zebrafish fin   The total RNA was extracted by using TRIzol solution Ambion according to the manufacturer’s instructions with minor modifications. RNA seq libraries were generated by using TruSeq RNA Library Prep Kit v2 Illumina according to the manufacturer’s instructions.   cell type:fin|dy post amputation:0 dpa|genotype/variation:fosl1a KO GSM3611577 GSM3611577: RNA fosl1aKO 0dpa rep1; Danio rerio; RNA Seq GSM3611577   1 The total RNA was extracted by using TRIzol solution Ambion according to the manufacturer's instructions with minor modifications. RNA seq libraries were generated by using TruSeq RNA Library Prep Kit v2 Illumina according to the manufacturer's instructions. GEO Accession:GSM3611577 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP186180     RNA_fosl1aKO_0dpa_rep1_R1.fastq.gz RNA_fosl1aKO_0dpa_rep1_R2.fastq.gz fastq fastq 2172914550.0 14486097.0 GSM3611577 r1 0:75 1:75 A:558371871;C:513150289;G:526257237;T:574878263;N:256890 75 75     558371871 513150289 526257237 574878263 256890 SRX5388275 SRS4376714 SRA850124 GEO Ting Wang, Department of Genetics, Washington University School of Medicine 2 0.90582 0.89465 0.07325 0.07242 0.72754 0.73253 0.43067 0.4364 75 75 B B biological fallback assumption illumina nextseq unknown cdna_unspecified trueseq bulk unknown unknown   United States 2019-02-18 Undetermined Undetermined Fin Surface Structure
51200 51200 SRR8587735 SRX5388274 SRS4376713 SRP186180 PRJNA523009 Regenerating zebrafish fin epigenome is characterized by stable lineage specific DNA methylation and dynamic chromatin accessibility RNA seq GSE126701 Transcriptome Analysis Background: Zebrafish can faithfully regenerate injured fins through the formation of a blastema a mass of proliferative cells that can grow and develop into the lost body part. post amputation various cell types contribute to blastema formation where each cell type retains fate restriction and exclusively contributes to regeneration of its own lineage. Epigenetic changes that are associated with lineage restriction during regeneration remain underexplored. Results: We produce epigenome maps including DNA methylation and chromatin accessibility as well as transcriptomes of osteoblasts and other cells in uninjured and regenerating fins. This effort reveals regeneration as a process of highly dynamic and orchestrated transcriptomic and chromatin accessibility changes coupled with stably maintained lineage specific DNA methylation. The epigenetic signatures also reveal many novel regeneration specific enhancers which are experimentally validated. Regulatory networks important for regeneration are constructed through integrative analysis of the epigenome map and a knockout of a predicted upstream regulator disrupts normal regeneration validating our prediction. Conclusion: Our study shows that lineage specific DNA methylation signatures are stably maintained during regeneration and regeneration enhancers are preset as hypomethylated before injury. In contrast chromatin accessibility is dynamically changed during regeneration. Many enhancers driving regeneration gene expression as well as upstream regulators of regeneration are identified and validated through integrative epigenome analysis. Overall design: mRNA profiles of the uninjured and regenerating fin by deep sequencing in duplicate using Illumina NextSeq. parent bioproject:PRJNA523007 pubmed:32106888   RNA fosl1aWT 4dpa rep2 GSM3611576   tissue:zebrafish fin|cell type:blastema|dy post amputation:4 dpa|genotype/variation:fosl1a WT RNA fosl1aWT 4dpa rep2 Basecalls were performed by the Edison Family Center for Genome Sciences & Systems Biology Sequencing Center using bcl2fastq The raw sequence reads were aligned to zebrafish transcriptome Ensembl release 85 and the zebrafish genome assembly GRCz10 by using STAR aligner version 2.5.2a with the following parameters: sjdbScore 1 clip3pAdapterSeq AGATCGGAAGAGC outWigStrand Unstranded outFilterType BySJout outFilterMultimapNmax 1. The total number of reads overlapping each gene were counted using featureCounts v.1.5.0 with Ensembl release 85 gtf file and the following parameters: F GTF t exon g gene id O s 0 primary p. Genome build: GRCz10 Supplementary files format and content: TXT zebrafish fin   The total RNA was extracted by using TRIzol solution Ambion according to the manufacturer’s instructions with minor modifications. RNA seq libraries were generated by using TruSeq RNA Library Prep Kit v2 Illumina according to the manufacturer’s instructions.   cell type:blastema|dy post amputation:4 dpa|genotype/variation:fosl1a WT GSM3611576 GSM3611576: RNA fosl1aWT 4dpa rep2; Danio rerio; RNA Seq GSM3611576   1 The total RNA was extracted by using TRIzol solution Ambion according to the manufacturer's instructions with minor modifications. RNA seq libraries were generated by using TruSeq RNA Library Prep Kit v2 Illumina according to the manufacturer's instructions. GEO Accession:GSM3611576 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP186180     RNA_fosl1aWT_4dpa_rep2_R1.fastq.gz RNA_fosl1aWT_4dpa_rep2_R2.fastq.gz fastq fastq 4393415550.0 29289437.0 GSM3611576 r1 0:75 1:75 A:1081814164;C:1112395765;G:1098941227;T:1099750114;N:514280 75 75     1081814164 1112395765 1098941227 1099750114 514280 SRX5388274 SRS4376713 SRA850124 GEO Ting Wang, Department of Genetics, Washington University School of Medicine 2 0.94536 0.93701 0.04522 0.04477 0.73361 0.73572 0.45358 0.45013 75 75 B B biological fallback assumption illumina nextseq unknown cdna_unspecified trueseq bulk unknown unknown   United States 2019-02-18 Undetermined Undetermined Fin Surface Structure
51201 51201 SRR8587734 SRX5388273 SRS4376712 SRP186180 PRJNA523009 Regenerating zebrafish fin epigenome is characterized by stable lineage specific DNA methylation and dynamic chromatin accessibility RNA seq GSE126701 Transcriptome Analysis Background: Zebrafish can faithfully regenerate injured fins through the formation of a blastema a mass of proliferative cells that can grow and develop into the lost body part. post amputation various cell types contribute to blastema formation where each cell type retains fate restriction and exclusively contributes to regeneration of its own lineage. Epigenetic changes that are associated with lineage restriction during regeneration remain underexplored. Results: We produce epigenome maps including DNA methylation and chromatin accessibility as well as transcriptomes of osteoblasts and other cells in uninjured and regenerating fins. This effort reveals regeneration as a process of highly dynamic and orchestrated transcriptomic and chromatin accessibility changes coupled with stably maintained lineage specific DNA methylation. The epigenetic signatures also reveal many novel regeneration specific enhancers which are experimentally validated. Regulatory networks important for regeneration are constructed through integrative analysis of the epigenome map and a knockout of a predicted upstream regulator disrupts normal regeneration validating our prediction. Conclusion: Our study shows that lineage specific DNA methylation signatures are stably maintained during regeneration and regeneration enhancers are preset as hypomethylated before injury. In contrast chromatin accessibility is dynamically changed during regeneration. Many enhancers driving regeneration gene expression as well as upstream regulators of regeneration are identified and validated through integrative epigenome analysis. Overall design: mRNA profiles of the uninjured and regenerating fin by deep sequencing in duplicate using Illumina NextSeq. parent bioproject:PRJNA523007 pubmed:32106888   RNA fosl1aWT 4dpa rep1 GSM3611575   tissue:zebrafish fin|cell type:blastema|dy post amputation:4 dpa|genotype/variation:fosl1a WT RNA fosl1aWT 4dpa rep1 Basecalls were performed by the Edison Family Center for Genome Sciences & Systems Biology Sequencing Center using bcl2fastq The raw sequence reads were aligned to zebrafish transcriptome Ensembl release 85 and the zebrafish genome assembly GRCz10 by using STAR aligner version 2.5.2a with the following parameters: sjdbScore 1 clip3pAdapterSeq AGATCGGAAGAGC outWigStrand Unstranded outFilterType BySJout outFilterMultimapNmax 1. The total number of reads overlapping each gene were counted using featureCounts v.1.5.0 with Ensembl release 85 gtf file and the following parameters: F GTF t exon g gene id O s 0 primary p. Genome build: GRCz10 Supplementary files format and content: TXT zebrafish fin   The total RNA was extracted by using TRIzol solution Ambion according to the manufacturer’s instructions with minor modifications. RNA seq libraries were generated by using TruSeq RNA Library Prep Kit v2 Illumina according to the manufacturer’s instructions.   cell type:blastema|dy post amputation:4 dpa|genotype/variation:fosl1a WT GSM3611575 GSM3611575: RNA fosl1aWT 4dpa rep1; Danio rerio; RNA Seq GSM3611575   1 The total RNA was extracted by using TRIzol solution Ambion according to the manufacturer's instructions with minor modifications. RNA seq libraries were generated by using TruSeq RNA Library Prep Kit v2 Illumina according to the manufacturer's instructions. GEO Accession:GSM3611575 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP186180     RNA_fosl1aWT_4dpa_rep1_R1.fastq.gz RNA_fosl1aWT_4dpa_rep1_R2.fastq.gz fastq fastq 3896927850.0 25979519.0 GSM3611575 r1 0:75 1:75 A:940364294;C:1005241083;G:990216788;T:960643155;N:462530 75 75     940364294 1005241083 990216788 960643155 462530 SRX5388273 SRS4376712 SRA850124 GEO Ting Wang, Department of Genetics, Washington University School of Medicine 2 0.94564 0.93465 0.04169 0.04145 0.74316 0.74757 0.45882 0.44998 75 75 B B biological fallback assumption illumina nextseq unknown cdna_unspecified trueseq bulk unknown unknown   United States 2019-02-18 Undetermined Undetermined Fin Surface Structure
51202 51202 SRR8587733 SRX5388272 SRS4376711 SRP186180 PRJNA523009 Regenerating zebrafish fin epigenome is characterized by stable lineage specific DNA methylation and dynamic chromatin accessibility RNA seq GSE126701 Transcriptome Analysis Background: Zebrafish can faithfully regenerate injured fins through the formation of a blastema a mass of proliferative cells that can grow and develop into the lost body part. post amputation various cell types contribute to blastema formation where each cell type retains fate restriction and exclusively contributes to regeneration of its own lineage. Epigenetic changes that are associated with lineage restriction during regeneration remain underexplored. Results: We produce epigenome maps including DNA methylation and chromatin accessibility as well as transcriptomes of osteoblasts and other cells in uninjured and regenerating fins. This effort reveals regeneration as a process of highly dynamic and orchestrated transcriptomic and chromatin accessibility changes coupled with stably maintained lineage specific DNA methylation. The epigenetic signatures also reveal many novel regeneration specific enhancers which are experimentally validated. Regulatory networks important for regeneration are constructed through integrative analysis of the epigenome map and a knockout of a predicted upstream regulator disrupts normal regeneration validating our prediction. Conclusion: Our study shows that lineage specific DNA methylation signatures are stably maintained during regeneration and regeneration enhancers are preset as hypomethylated before injury. In contrast chromatin accessibility is dynamically changed during regeneration. Many enhancers driving regeneration gene expression as well as upstream regulators of regeneration are identified and validated through integrative epigenome analysis. Overall design: mRNA profiles of the uninjured and regenerating fin by deep sequencing in duplicate using Illumina NextSeq. parent bioproject:PRJNA523007 pubmed:32106888   RNA fosl1aWT 1dpa rep2 GSM3611574   tissue:zebrafish fin|cell type:blastema|dy post amputation:1 dpa|genotype/variation:fosl1a WT RNA fosl1aWT 1dpa rep2 Basecalls were performed by the Edison Family Center for Genome Sciences & Systems Biology Sequencing Center using bcl2fastq The raw sequence reads were aligned to zebrafish transcriptome Ensembl release 85 and the zebrafish genome assembly GRCz10 by using STAR aligner version 2.5.2a with the following parameters: sjdbScore 1 clip3pAdapterSeq AGATCGGAAGAGC outWigStrand Unstranded outFilterType BySJout outFilterMultimapNmax 1. The total number of reads overlapping each gene were counted using featureCounts v.1.5.0 with Ensembl release 85 gtf file and the following parameters: F GTF t exon g gene id O s 0 primary p. Genome build: GRCz10 Supplementary files format and content: TXT zebrafish fin   The total RNA was extracted by using TRIzol solution Ambion according to the manufacturer’s instructions with minor modifications. RNA seq libraries were generated by using TruSeq RNA Library Prep Kit v2 Illumina according to the manufacturer’s instructions.   cell type:blastema|dy post amputation:1 dpa|genotype/variation:fosl1a WT GSM3611574 GSM3611574: RNA fosl1aWT 1dpa rep2; Danio rerio; RNA Seq GSM3611574   1 The total RNA was extracted by using TRIzol solution Ambion according to the manufacturer's instructions with minor modifications. RNA seq libraries were generated by using TruSeq RNA Library Prep Kit v2 Illumina according to the manufacturer's instructions. GEO Accession:GSM3611574 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP186180     RNA_fosl1aWT_1dpa_rep2_R1.fastq.gz RNA_fosl1aWT_1dpa_rep2_R2.fastq.gz fastq fastq 5146891650.0 34312611.0 GSM3611574 r1 0:75 1:75 A:1266077989;C:1290251013;G:1284774114;T:1305186340;N:602194 75 75     1266077989 1290251013 1284774114 1305186340 602194 SRX5388272 SRS4376711 SRA850124 GEO Ting Wang, Department of Genetics, Washington University School of Medicine 2 0.93588 0.92329 0.04613 0.0466 0.75897 0.7637 0.43843 0.44319 75 75 B B biological fallback assumption illumina nextseq unknown cdna_unspecified trueseq bulk unknown unknown   United States 2019-02-18 Undetermined Undetermined Fin Surface Structure
51203 51203 SRR8587732 SRX5388271 SRS4376710 SRP186180 PRJNA523009 Regenerating zebrafish fin epigenome is characterized by stable lineage specific DNA methylation and dynamic chromatin accessibility RNA seq GSE126701 Transcriptome Analysis Background: Zebrafish can faithfully regenerate injured fins through the formation of a blastema a mass of proliferative cells that can grow and develop into the lost body part. post amputation various cell types contribute to blastema formation where each cell type retains fate restriction and exclusively contributes to regeneration of its own lineage. Epigenetic changes that are associated with lineage restriction during regeneration remain underexplored. Results: We produce epigenome maps including DNA methylation and chromatin accessibility as well as transcriptomes of osteoblasts and other cells in uninjured and regenerating fins. This effort reveals regeneration as a process of highly dynamic and orchestrated transcriptomic and chromatin accessibility changes coupled with stably maintained lineage specific DNA methylation. The epigenetic signatures also reveal many novel regeneration specific enhancers which are experimentally validated. Regulatory networks important for regeneration are constructed through integrative analysis of the epigenome map and a knockout of a predicted upstream regulator disrupts normal regeneration validating our prediction. Conclusion: Our study shows that lineage specific DNA methylation signatures are stably maintained during regeneration and regeneration enhancers are preset as hypomethylated before injury. In contrast chromatin accessibility is dynamically changed during regeneration. Many enhancers driving regeneration gene expression as well as upstream regulators of regeneration are identified and validated through integrative epigenome analysis. Overall design: mRNA profiles of the uninjured and regenerating fin by deep sequencing in duplicate using Illumina NextSeq. parent bioproject:PRJNA523007 pubmed:32106888   RNA fosl1aWT 1dpa rep1 GSM3611573   tissue:zebrafish fin|cell type:blastema|dy post amputation:1 dpa|genotype/variation:fosl1a WT RNA fosl1aWT 1dpa rep1 Basecalls were performed by the Edison Family Center for Genome Sciences & Systems Biology Sequencing Center using bcl2fastq The raw sequence reads were aligned to zebrafish transcriptome Ensembl release 85 and the zebrafish genome assembly GRCz10 by using STAR aligner version 2.5.2a with the following parameters: sjdbScore 1 clip3pAdapterSeq AGATCGGAAGAGC outWigStrand Unstranded outFilterType BySJout outFilterMultimapNmax 1. The total number of reads overlapping each gene were counted using featureCounts v.1.5.0 with Ensembl release 85 gtf file and the following parameters: F GTF t exon g gene id O s 0 primary p. Genome build: GRCz10 Supplementary files format and content: TXT zebrafish fin   The total RNA was extracted by using TRIzol solution Ambion according to the manufacturer’s instructions with minor modifications. RNA seq libraries were generated by using TruSeq RNA Library Prep Kit v2 Illumina according to the manufacturer’s instructions.   cell type:blastema|dy post amputation:1 dpa|genotype/variation:fosl1a WT GSM3611573 GSM3611573: RNA fosl1aWT 1dpa rep1; Danio rerio; RNA Seq GSM3611573   1 The total RNA was extracted by using TRIzol solution Ambion according to the manufacturer's instructions with minor modifications. RNA seq libraries were generated by using TruSeq RNA Library Prep Kit v2 Illumina according to the manufacturer's instructions. GEO Accession:GSM3611573 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP186180     RNA_fosl1aWT_1dpa_rep1_R1.fastq.gz RNA_fosl1aWT_1dpa_rep1_R2.fastq.gz fastq fastq 5700521250.0 38003475.0 GSM3611573 r1 0:75 1:75 A:1433619467;C:1408496030;G:1397469154;T:1460277087;N:659512 75 75     1433619467 1408496030 1397469154 1460277087 659512 SRX5388271 SRS4376710 SRA850124 GEO Ting Wang, Department of Genetics, Washington University School of Medicine 2 0.94134 0.93285 0.0524 0.05148 0.74899 0.75274 0.43666 0.43532 75 75 B B biological fallback assumption illumina nextseq unknown cdna_unspecified trueseq bulk unknown unknown   United States 2019-02-18 Undetermined Undetermined Fin Surface Structure
51204 51204 SRR8587731 SRX5388270 SRS4376709 SRP186180 PRJNA523009 Regenerating zebrafish fin epigenome is characterized by stable lineage specific DNA methylation and dynamic chromatin accessibility RNA seq GSE126701 Transcriptome Analysis Background: Zebrafish can faithfully regenerate injured fins through the formation of a blastema a mass of proliferative cells that can grow and develop into the lost body part. post amputation various cell types contribute to blastema formation where each cell type retains fate restriction and exclusively contributes to regeneration of its own lineage. Epigenetic changes that are associated with lineage restriction during regeneration remain underexplored. Results: We produce epigenome maps including DNA methylation and chromatin accessibility as well as transcriptomes of osteoblasts and other cells in uninjured and regenerating fins. This effort reveals regeneration as a process of highly dynamic and orchestrated transcriptomic and chromatin accessibility changes coupled with stably maintained lineage specific DNA methylation. The epigenetic signatures also reveal many novel regeneration specific enhancers which are experimentally validated. Regulatory networks important for regeneration are constructed through integrative analysis of the epigenome map and a knockout of a predicted upstream regulator disrupts normal regeneration validating our prediction. Conclusion: Our study shows that lineage specific DNA methylation signatures are stably maintained during regeneration and regeneration enhancers are preset as hypomethylated before injury. In contrast chromatin accessibility is dynamically changed during regeneration. Many enhancers driving regeneration gene expression as well as upstream regulators of regeneration are identified and validated through integrative epigenome analysis. Overall design: mRNA profiles of the uninjured and regenerating fin by deep sequencing in duplicate using Illumina NextSeq. parent bioproject:PRJNA523007 pubmed:32106888   RNA fosl1aWT 0dpa rep2 GSM3611572   tissue:zebrafish fin|cell type:fin|dy post amputation:0 dpa|genotype/variation:fosl1a WT RNA fosl1aWT 0dpa rep2 Basecalls were performed by the Edison Family Center for Genome Sciences & Systems Biology Sequencing Center using bcl2fastq The raw sequence reads were aligned to zebrafish transcriptome Ensembl release 85 and the zebrafish genome assembly GRCz10 by using STAR aligner version 2.5.2a with the following parameters: sjdbScore 1 clip3pAdapterSeq AGATCGGAAGAGC outWigStrand Unstranded outFilterType BySJout outFilterMultimapNmax 1. The total number of reads overlapping each gene were counted using featureCounts v.1.5.0 with Ensembl release 85 gtf file and the following parameters: F GTF t exon g gene id O s 0 primary p. Genome build: GRCz10 Supplementary files format and content: TXT zebrafish fin   The total RNA was extracted by using TRIzol solution Ambion according to the manufacturer’s instructions with minor modifications. RNA seq libraries were generated by using TruSeq RNA Library Prep Kit v2 Illumina according to the manufacturer’s instructions.   cell type:fin|dy post amputation:0 dpa|genotype/variation:fosl1a WT GSM3611572 GSM3611572: RNA fosl1aWT 0dpa rep2; Danio rerio; RNA Seq GSM3611572   1 The total RNA was extracted by using TRIzol solution Ambion according to the manufacturer's instructions with minor modifications. RNA seq libraries were generated by using TruSeq RNA Library Prep Kit v2 Illumina according to the manufacturer's instructions. GEO Accession:GSM3611572 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP186180     RNA_fosl1aWT_0dpa_rep2_R1.fastq.gz RNA_fosl1aWT_0dpa_rep2_R2.fastq.gz fastq fastq 4304045700.0 28693638.0 GSM3611572 r1 0:75 1:75 A:1029816293;C:1115426844;G:1110052108;T:1048249658;N:500797 75 75     1029816293 1115426844 1110052108 1048249658 500797 SRX5388270 SRS4376709 SRA850124 GEO Ting Wang, Department of Genetics, Washington University School of Medicine 2 0.9504 0.94568 0.04578 0.04622 0.74093 0.74495 0.41692 0.4085 75 75 B B biological fallback assumption illumina nextseq unknown cdna_unspecified trueseq bulk unknown unknown   United States 2019-02-18 Undetermined Undetermined Fin Surface Structure
51205 51205 SRR8587730 SRX5388269 SRS4376708 SRP186180 PRJNA523009 Regenerating zebrafish fin epigenome is characterized by stable lineage specific DNA methylation and dynamic chromatin accessibility RNA seq GSE126701 Transcriptome Analysis Background: Zebrafish can faithfully regenerate injured fins through the formation of a blastema a mass of proliferative cells that can grow and develop into the lost body part. post amputation various cell types contribute to blastema formation where each cell type retains fate restriction and exclusively contributes to regeneration of its own lineage. Epigenetic changes that are associated with lineage restriction during regeneration remain underexplored. Results: We produce epigenome maps including DNA methylation and chromatin accessibility as well as transcriptomes of osteoblasts and other cells in uninjured and regenerating fins. This effort reveals regeneration as a process of highly dynamic and orchestrated transcriptomic and chromatin accessibility changes coupled with stably maintained lineage specific DNA methylation. The epigenetic signatures also reveal many novel regeneration specific enhancers which are experimentally validated. Regulatory networks important for regeneration are constructed through integrative analysis of the epigenome map and a knockout of a predicted upstream regulator disrupts normal regeneration validating our prediction. Conclusion: Our study shows that lineage specific DNA methylation signatures are stably maintained during regeneration and regeneration enhancers are preset as hypomethylated before injury. In contrast chromatin accessibility is dynamically changed during regeneration. Many enhancers driving regeneration gene expression as well as upstream regulators of regeneration are identified and validated through integrative epigenome analysis. Overall design: mRNA profiles of the uninjured and regenerating fin by deep sequencing in duplicate using Illumina NextSeq. parent bioproject:PRJNA523007 pubmed:32106888   RNA fosl1aWT 0dpa rep1 GSM3611571   tissue:zebrafish fin|cell type:fin|dy post amputation:0 dpa|genotype/variation:fosl1a WT RNA fosl1aWT 0dpa rep1 Basecalls were performed by the Edison Family Center for Genome Sciences & Systems Biology Sequencing Center using bcl2fastq The raw sequence reads were aligned to zebrafish transcriptome Ensembl release 85 and the zebrafish genome assembly GRCz10 by using STAR aligner version 2.5.2a with the following parameters: sjdbScore 1 clip3pAdapterSeq AGATCGGAAGAGC outWigStrand Unstranded outFilterType BySJout outFilterMultimapNmax 1. The total number of reads overlapping each gene were counted using featureCounts v.1.5.0 with Ensembl release 85 gtf file and the following parameters: F GTF t exon g gene id O s 0 primary p. Genome build: GRCz10 Supplementary files format and content: TXT zebrafish fin   The total RNA was extracted by using TRIzol solution Ambion according to the manufacturer’s instructions with minor modifications. RNA seq libraries were generated by using TruSeq RNA Library Prep Kit v2 Illumina according to the manufacturer’s instructions.   cell type:fin|dy post amputation:0 dpa|genotype/variation:fosl1a WT GSM3611571 GSM3611571: RNA fosl1aWT 0dpa rep1; Danio rerio; RNA Seq GSM3611571   1 The total RNA was extracted by using TRIzol solution Ambion according to the manufacturer's instructions with minor modifications. RNA seq libraries were generated by using TruSeq RNA Library Prep Kit v2 Illumina according to the manufacturer's instructions. GEO Accession:GSM3611571 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP186180     RNA_fosl1aWT_0dpa_rep1_R1.fastq.gz RNA_fosl1aWT_0dpa_rep1_R2.fastq.gz fastq fastq 5808520950.0 38723473.0 GSM3611571 r1 0:75 1:75 A:1421129493;C:1469873837;G:1468527263;T:1448319733;N:670624 75 75     1421129493 1469873837 1468527263 1448319733 670624 SRX5388269 SRS4376708 SRA850124 GEO Ting Wang, Department of Genetics, Washington University School of Medicine 2 0.94105 0.93405 0.05359 0.05367 0.73338 0.73708 0.4287 0.42818 75 75 B B biological fallback assumption illumina nextseq unknown cdna_unspecified trueseq bulk unknown unknown   United States 2019-02-18 Undetermined Undetermined Fin Surface Structure
51206 51206 SRR8587729 SRX5388268 SRS4376707 SRP186180 PRJNA523009 Regenerating zebrafish fin epigenome is characterized by stable lineage specific DNA methylation and dynamic chromatin accessibility RNA seq GSE126701 Transcriptome Analysis Background: Zebrafish can faithfully regenerate injured fins through the formation of a blastema a mass of proliferative cells that can grow and develop into the lost body part. post amputation various cell types contribute to blastema formation where each cell type retains fate restriction and exclusively contributes to regeneration of its own lineage. Epigenetic changes that are associated with lineage restriction during regeneration remain underexplored. Results: We produce epigenome maps including DNA methylation and chromatin accessibility as well as transcriptomes of osteoblasts and other cells in uninjured and regenerating fins. This effort reveals regeneration as a process of highly dynamic and orchestrated transcriptomic and chromatin accessibility changes coupled with stably maintained lineage specific DNA methylation. The epigenetic signatures also reveal many novel regeneration specific enhancers which are experimentally validated. Regulatory networks important for regeneration are constructed through integrative analysis of the epigenome map and a knockout of a predicted upstream regulator disrupts normal regeneration validating our prediction. Conclusion: Our study shows that lineage specific DNA methylation signatures are stably maintained during regeneration and regeneration enhancers are preset as hypomethylated before injury. In contrast chromatin accessibility is dynamically changed during regeneration. Many enhancers driving regeneration gene expression as well as upstream regulators of regeneration are identified and validated through integrative epigenome analysis. Overall design: mRNA profiles of the uninjured and regenerating fin by deep sequencing in duplicate using Illumina NextSeq. parent bioproject:PRJNA523007 pubmed:32106888   RNA sp7po4dpa rep2 GSM3611570   tissue:zebrafish fin|strain:Tgsp7:EGFP|cell type:sp7+ cells|dy post amputation:4 dpa RNA sp7po4dpa rep2 Basecalls were performed by the Edison Family Center for Genome Sciences & Systems Biology Sequencing Center using bcl2fastq The raw sequence reads were aligned to zebrafish transcriptome Ensembl release 85 and the zebrafish genome assembly GRCz10 by using STAR aligner version 2.5.2a with the following parameters: sjdbScore 1 clip3pAdapterSeq AGATCGGAAGAGC outWigStrand Unstranded outFilterType BySJout outFilterMultimapNmax 1. The total number of reads overlapping each gene were counted using featureCounts v.1.5.0 with Ensembl release 85 gtf file and the following parameters: F GTF t exon g gene id O s 0 primary p. Genome build: GRCz10 Supplementary files format and content: TXT zebrafish fin   The total RNA was extracted by using TRIzol solution Ambion according to the manufacturer’s instructions with minor modifications. RNA seq libraries were generated by using TruSeq RNA Library Prep Kit v2 Illumina according to the manufacturer’s instructions.   strain:Tgsp7:EGFP|cell type:sp7+ cells|dy post amputation:4 dpa GSM3611570 GSM3611570: RNA sp7po4dpa rep2; Danio rerio; RNA Seq GSM3611570   1 The total RNA was extracted by using TRIzol solution Ambion according to the manufacturer's instructions with minor modifications. RNA seq libraries were generated by using TruSeq RNA Library Prep Kit v2 Illumina according to the manufacturer's instructions. GEO Accession:GSM3611570 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP186180     RNA_sp7po4dpa_rep2_R1.fastq.gz RNA_sp7po4dpa_rep2_R2.fastq.gz fastq fastq 6329971650.0 42199811.0 GSM3611570 r1 0:75 1:75 A:1388641164;C:1777097035;G:1770281560;T:1393138883;N:813008 75 75     1388641164 1777097035 1770281560 1393138883 813008 SRX5388268 SRS4376707 SRA850124 GEO Ting Wang, Department of Genetics, Washington University School of Medicine 2 0.9741 0.97261 0.02314 0.02324 0.80144 0.80562 0.45998 0.4214 75 75 B B biological fallback assumption illumina nextseq unknown cdna_unspecified trueseq bulk unknown unknown   United States 2019-02-18 Undetermined Undetermined Fin Surface Structure
51207 51207 SRR8587728 SRX5388267 SRS4376706 SRP186180 PRJNA523009 Regenerating zebrafish fin epigenome is characterized by stable lineage specific DNA methylation and dynamic chromatin accessibility RNA seq GSE126701 Transcriptome Analysis Background: Zebrafish can faithfully regenerate injured fins through the formation of a blastema a mass of proliferative cells that can grow and develop into the lost body part. post amputation various cell types contribute to blastema formation where each cell type retains fate restriction and exclusively contributes to regeneration of its own lineage. Epigenetic changes that are associated with lineage restriction during regeneration remain underexplored. Results: We produce epigenome maps including DNA methylation and chromatin accessibility as well as transcriptomes of osteoblasts and other cells in uninjured and regenerating fins. This effort reveals regeneration as a process of highly dynamic and orchestrated transcriptomic and chromatin accessibility changes coupled with stably maintained lineage specific DNA methylation. The epigenetic signatures also reveal many novel regeneration specific enhancers which are experimentally validated. Regulatory networks important for regeneration are constructed through integrative analysis of the epigenome map and a knockout of a predicted upstream regulator disrupts normal regeneration validating our prediction. Conclusion: Our study shows that lineage specific DNA methylation signatures are stably maintained during regeneration and regeneration enhancers are preset as hypomethylated before injury. In contrast chromatin accessibility is dynamically changed during regeneration. Many enhancers driving regeneration gene expression as well as upstream regulators of regeneration are identified and validated through integrative epigenome analysis. Overall design: mRNA profiles of the uninjured and regenerating fin by deep sequencing in duplicate using Illumina NextSeq. parent bioproject:PRJNA523007 pubmed:32106888   RNA sp7po4dpa rep1 GSM3611569   tissue:zebrafish fin|strain:Tgsp7:EGFP|cell type:sp7+ cells|dy post amputation:4 dpa RNA sp7po4dpa rep1 Basecalls were performed by the Edison Family Center for Genome Sciences & Systems Biology Sequencing Center using bcl2fastq The raw sequence reads were aligned to zebrafish transcriptome Ensembl release 85 and the zebrafish genome assembly GRCz10 by using STAR aligner version 2.5.2a with the following parameters: sjdbScore 1 clip3pAdapterSeq AGATCGGAAGAGC outWigStrand Unstranded outFilterType BySJout outFilterMultimapNmax 1. The total number of reads overlapping each gene were counted using featureCounts v.1.5.0 with Ensembl release 85 gtf file and the following parameters: F GTF t exon g gene id O s 0 primary p. Genome build: GRCz10 Supplementary files format and content: TXT zebrafish fin   The total RNA was extracted by using TRIzol solution Ambion according to the manufacturer’s instructions with minor modifications. RNA seq libraries were generated by using TruSeq RNA Library Prep Kit v2 Illumina according to the manufacturer’s instructions.   strain:Tgsp7:EGFP|cell type:sp7+ cells|dy post amputation:4 dpa GSM3611569 GSM3611569: RNA sp7po4dpa rep1; Danio rerio; RNA Seq GSM3611569   1 The total RNA was extracted by using TRIzol solution Ambion according to the manufacturer's instructions with minor modifications. RNA seq libraries were generated by using TruSeq RNA Library Prep Kit v2 Illumina according to the manufacturer's instructions. GEO Accession:GSM3611569 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP186180     RNA_sp7po4dpa_rep1_R1.fastq.gz RNA_sp7po4dpa_rep1_R2.fastq.gz fastq fastq 8449550100.0 56330334.0 GSM3611569 r1 0:75 1:75 A:1918679931;C:2308288944;G:2303881576;T:1917610027;N:1089622 75 75     1918679931 2308288944 2303881576 1917610027 1089622 SRX5388267 SRS4376706 SRA850124 GEO Ting Wang, Department of Genetics, Washington University School of Medicine 2 0.97236 0.97243 0.0223 0.02227 0.78835 0.79121 0.45945 0.45935 75 75 B B biological fallback assumption illumina nextseq unknown cdna_unspecified trueseq bulk unknown unknown   United States 2019-02-18 Undetermined Undetermined Fin Surface Structure
51208 51208 SRR8587727 SRX5388266 SRS4376705 SRP186180 PRJNA523009 Regenerating zebrafish fin epigenome is characterized by stable lineage specific DNA methylation and dynamic chromatin accessibility RNA seq GSE126701 Transcriptome Analysis Background: Zebrafish can faithfully regenerate injured fins through the formation of a blastema a mass of proliferative cells that can grow and develop into the lost body part. post amputation various cell types contribute to blastema formation where each cell type retains fate restriction and exclusively contributes to regeneration of its own lineage. Epigenetic changes that are associated with lineage restriction during regeneration remain underexplored. Results: We produce epigenome maps including DNA methylation and chromatin accessibility as well as transcriptomes of osteoblasts and other cells in uninjured and regenerating fins. This effort reveals regeneration as a process of highly dynamic and orchestrated transcriptomic and chromatin accessibility changes coupled with stably maintained lineage specific DNA methylation. The epigenetic signatures also reveal many novel regeneration specific enhancers which are experimentally validated. Regulatory networks important for regeneration are constructed through integrative analysis of the epigenome map and a knockout of a predicted upstream regulator disrupts normal regeneration validating our prediction. Conclusion: Our study shows that lineage specific DNA methylation signatures are stably maintained during regeneration and regeneration enhancers are preset as hypomethylated before injury. In contrast chromatin accessibility is dynamically changed during regeneration. Many enhancers driving regeneration gene expression as well as upstream regulators of regeneration are identified and validated through integrative epigenome analysis. Overall design: mRNA profiles of the uninjured and regenerating fin by deep sequencing in duplicate using Illumina NextSeq. parent bioproject:PRJNA523007 pubmed:32106888   RNA sp7po0dpa rep2 GSM3611568   tissue:zebrafish fin|strain:Tgsp7:EGFP|cell type:sp7+ cells|dy post amputation:0 dpa RNA sp7po0dpa rep2 Basecalls were performed by the Edison Family Center for Genome Sciences & Systems Biology Sequencing Center using bcl2fastq The raw sequence reads were aligned to zebrafish transcriptome Ensembl release 85 and the zebrafish genome assembly GRCz10 by using STAR aligner version 2.5.2a with the following parameters: sjdbScore 1 clip3pAdapterSeq AGATCGGAAGAGC outWigStrand Unstranded outFilterType BySJout outFilterMultimapNmax 1. The total number of reads overlapping each gene were counted using featureCounts v.1.5.0 with Ensembl release 85 gtf file and the following parameters: F GTF t exon g gene id O s 0 primary p. Genome build: GRCz10 Supplementary files format and content: TXT zebrafish fin   The total RNA was extracted by using TRIzol solution Ambion according to the manufacturer’s instructions with minor modifications. RNA seq libraries were generated by using TruSeq RNA Library Prep Kit v2 Illumina according to the manufacturer’s instructions.   strain:Tgsp7:EGFP|cell type:sp7+ cells|dy post amputation:0 dpa GSM3611568 GSM3611568: RNA sp7po0dpa rep2; Danio rerio; RNA Seq GSM3611568   1 The total RNA was extracted by using TRIzol solution Ambion according to the manufacturer's instructions with minor modifications. RNA seq libraries were generated by using TruSeq RNA Library Prep Kit v2 Illumina according to the manufacturer's instructions. GEO Accession:GSM3611568 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP186180     RNA_sp7po0dpa_rep2_R1.fastq.gz RNA_sp7po0dpa_rep2_R2.fastq.gz fastq fastq 5198857200.0 34659048.0 GSM3611568 r1 0:75 1:75 A:1191996037;C:1407488600;G:1411331628;T:1187356971;N:683964 75 75     1191996037 1407488600 1411331628 1187356971 683964 SRX5388266 SRS4376705 SRA850124 GEO Ting Wang, Department of Genetics, Washington University School of Medicine 2 0.96007 0.96273 0.0371 0.03697 0.82136 0.82449 0.46842 0.46757 75 75 B B biological fallback assumption illumina nextseq unknown cdna_unspecified trueseq bulk unknown unknown   United States 2019-02-18 Undetermined Undetermined Fin Surface Structure
51209 51209 SRR8587726 SRX5388265 SRS4376704 SRP186180 PRJNA523009 Regenerating zebrafish fin epigenome is characterized by stable lineage specific DNA methylation and dynamic chromatin accessibility RNA seq GSE126701 Transcriptome Analysis Background: Zebrafish can faithfully regenerate injured fins through the formation of a blastema a mass of proliferative cells that can grow and develop into the lost body part. post amputation various cell types contribute to blastema formation where each cell type retains fate restriction and exclusively contributes to regeneration of its own lineage. Epigenetic changes that are associated with lineage restriction during regeneration remain underexplored. Results: We produce epigenome maps including DNA methylation and chromatin accessibility as well as transcriptomes of osteoblasts and other cells in uninjured and regenerating fins. This effort reveals regeneration as a process of highly dynamic and orchestrated transcriptomic and chromatin accessibility changes coupled with stably maintained lineage specific DNA methylation. The epigenetic signatures also reveal many novel regeneration specific enhancers which are experimentally validated. Regulatory networks important for regeneration are constructed through integrative analysis of the epigenome map and a knockout of a predicted upstream regulator disrupts normal regeneration validating our prediction. Conclusion: Our study shows that lineage specific DNA methylation signatures are stably maintained during regeneration and regeneration enhancers are preset as hypomethylated before injury. In contrast chromatin accessibility is dynamically changed during regeneration. Many enhancers driving regeneration gene expression as well as upstream regulators of regeneration are identified and validated through integrative epigenome analysis. Overall design: mRNA profiles of the uninjured and regenerating fin by deep sequencing in duplicate using Illumina NextSeq. parent bioproject:PRJNA523007 pubmed:32106888   RNA sp7po0dpa rep1 GSM3611567   tissue:zebrafish fin|strain:Tgsp7:EGFP|cell type:sp7+ cells|dy post amputation:0 dpa RNA sp7po0dpa rep1 Basecalls were performed by the Edison Family Center for Genome Sciences & Systems Biology Sequencing Center using bcl2fastq The raw sequence reads were aligned to zebrafish transcriptome Ensembl release 85 and the zebrafish genome assembly GRCz10 by using STAR aligner version 2.5.2a with the following parameters: sjdbScore 1 clip3pAdapterSeq AGATCGGAAGAGC outWigStrand Unstranded outFilterType BySJout outFilterMultimapNmax 1. The total number of reads overlapping each gene were counted using featureCounts v.1.5.0 with Ensembl release 85 gtf file and the following parameters: F GTF t exon g gene id O s 0 primary p. Genome build: GRCz10 Supplementary files format and content: TXT zebrafish fin   The total RNA was extracted by using TRIzol solution Ambion according to the manufacturer’s instructions with minor modifications. RNA seq libraries were generated by using TruSeq RNA Library Prep Kit v2 Illumina according to the manufacturer’s instructions.   strain:Tgsp7:EGFP|cell type:sp7+ cells|dy post amputation:0 dpa GSM3611567 GSM3611567: RNA sp7po0dpa rep1; Danio rerio; RNA Seq GSM3611567   1 The total RNA was extracted by using TRIzol solution Ambion according to the manufacturer's instructions with minor modifications. RNA seq libraries were generated by using TruSeq RNA Library Prep Kit v2 Illumina according to the manufacturer's instructions. GEO Accession:GSM3611567 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP186180     RNA_sp7po0dpa_rep1_R1.fastq.gz RNA_sp7po0dpa_rep1_R2.fastq.gz fastq fastq 5236574700.0 34910498.0 GSM3611567 r1 0:75 1:75 A:1192484238;C:1424507119;G:1427165429;T:1191770780;N:647134 75 75     1192484238 1424507119 1427165429 1191770780 647134 SRX5388265 SRS4376704 SRA850124 GEO Ting Wang, Department of Genetics, Washington University School of Medicine 2 0.96042 0.96268 0.03495 0.03439 0.83236 0.83812 0.47004 0.4629 75 75 B B biological fallback assumption illumina nextseq unknown cdna_unspecified trueseq bulk unknown unknown   United States 2019-02-18 Undetermined Undetermined Fin Surface Structure
51210 51210 SRR8587725 SRX5388264 SRS4376703 SRP186180 PRJNA523009 Regenerating zebrafish fin epigenome is characterized by stable lineage specific DNA methylation and dynamic chromatin accessibility RNA seq GSE126701 Transcriptome Analysis Background: Zebrafish can faithfully regenerate injured fins through the formation of a blastema a mass of proliferative cells that can grow and develop into the lost body part. post amputation various cell types contribute to blastema formation where each cell type retains fate restriction and exclusively contributes to regeneration of its own lineage. Epigenetic changes that are associated with lineage restriction during regeneration remain underexplored. Results: We produce epigenome maps including DNA methylation and chromatin accessibility as well as transcriptomes of osteoblasts and other cells in uninjured and regenerating fins. This effort reveals regeneration as a process of highly dynamic and orchestrated transcriptomic and chromatin accessibility changes coupled with stably maintained lineage specific DNA methylation. The epigenetic signatures also reveal many novel regeneration specific enhancers which are experimentally validated. Regulatory networks important for regeneration are constructed through integrative analysis of the epigenome map and a knockout of a predicted upstream regulator disrupts normal regeneration validating our prediction. Conclusion: Our study shows that lineage specific DNA methylation signatures are stably maintained during regeneration and regeneration enhancers are preset as hypomethylated before injury. In contrast chromatin accessibility is dynamically changed during regeneration. Many enhancers driving regeneration gene expression as well as upstream regulators of regeneration are identified and validated through integrative epigenome analysis. Overall design: mRNA profiles of the uninjured and regenerating fin by deep sequencing in duplicate using Illumina NextSeq. parent bioproject:PRJNA523007 pubmed:32106888   RNA sp7ne4dpa rep2 GSM3611566   tissue:zebrafish fin|strain:Tgsp7:EGFP|cell type:sp7 cells|dy post amputation:4 dpa RNA sp7ne4dpa rep2 Basecalls were performed by the Edison Family Center for Genome Sciences & Systems Biology Sequencing Center using bcl2fastq The raw sequence reads were aligned to zebrafish transcriptome Ensembl release 85 and the zebrafish genome assembly GRCz10 by using STAR aligner version 2.5.2a with the following parameters: sjdbScore 1 clip3pAdapterSeq AGATCGGAAGAGC outWigStrand Unstranded outFilterType BySJout outFilterMultimapNmax 1. The total number of reads overlapping each gene were counted using featureCounts v.1.5.0 with Ensembl release 85 gtf file and the following parameters: F GTF t exon g gene id O s 0 primary p. Genome build: GRCz10 Supplementary files format and content: TXT zebrafish fin   The total RNA was extracted by using TRIzol solution Ambion according to the manufacturer’s instructions with minor modifications. RNA seq libraries were generated by using TruSeq RNA Library Prep Kit v2 Illumina according to the manufacturer’s instructions.   strain:Tgsp7:EGFP|cell type:sp7 cells|dy post amputation:4 dpa GSM3611566 GSM3611566: RNA sp7ne4dpa rep2; Danio rerio; RNA Seq GSM3611566   1 The total RNA was extracted by using TRIzol solution Ambion according to the manufacturer's instructions with minor modifications. RNA seq libraries were generated by using TruSeq RNA Library Prep Kit v2 Illumina according to the manufacturer's instructions. GEO Accession:GSM3611566 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP186180     RNA_sp7ne4dpa_rep2_R1.fastq.gz RNA_sp7ne4dpa_rep2_R2.fastq.gz fastq fastq 7756468350.0 51709789.0 GSM3611566 r1 0:75 1:75 A:1728700539;C:2145281440;G:2145751356;T:1735730929;N:1004086 75 75     1728700539 2145281440 2145751356 1735730929 1004086 SRX5388264 SRS4376703 SRA850124 GEO Ting Wang, Department of Genetics, Washington University School of Medicine 2 0.9699 0.97111 0.01594 0.01634 0.79987 0.8031 0.46708 0.45952 75 75 B B biological fallback assumption illumina nextseq unknown cdna_unspecified trueseq bulk unknown unknown   United States 2019-02-18 Undetermined Undetermined Fin Surface Structure
51211 51211 SRR8587724 SRX5388263 SRS4376702 SRP186180 PRJNA523009 Regenerating zebrafish fin epigenome is characterized by stable lineage specific DNA methylation and dynamic chromatin accessibility RNA seq GSE126701 Transcriptome Analysis Background: Zebrafish can faithfully regenerate injured fins through the formation of a blastema a mass of proliferative cells that can grow and develop into the lost body part. post amputation various cell types contribute to blastema formation where each cell type retains fate restriction and exclusively contributes to regeneration of its own lineage. Epigenetic changes that are associated with lineage restriction during regeneration remain underexplored. Results: We produce epigenome maps including DNA methylation and chromatin accessibility as well as transcriptomes of osteoblasts and other cells in uninjured and regenerating fins. This effort reveals regeneration as a process of highly dynamic and orchestrated transcriptomic and chromatin accessibility changes coupled with stably maintained lineage specific DNA methylation. The epigenetic signatures also reveal many novel regeneration specific enhancers which are experimentally validated. Regulatory networks important for regeneration are constructed through integrative analysis of the epigenome map and a knockout of a predicted upstream regulator disrupts normal regeneration validating our prediction. Conclusion: Our study shows that lineage specific DNA methylation signatures are stably maintained during regeneration and regeneration enhancers are preset as hypomethylated before injury. In contrast chromatin accessibility is dynamically changed during regeneration. Many enhancers driving regeneration gene expression as well as upstream regulators of regeneration are identified and validated through integrative epigenome analysis. Overall design: mRNA profiles of the uninjured and regenerating fin by deep sequencing in duplicate using Illumina NextSeq. parent bioproject:PRJNA523007 pubmed:32106888   RNA sp7ne4dpa rep1 GSM3611565   tissue:zebrafish fin|strain:Tgsp7:EGFP|cell type:sp7 cells|dy post amputation:4 dpa RNA sp7ne4dpa rep1 Basecalls were performed by the Edison Family Center for Genome Sciences & Systems Biology Sequencing Center using bcl2fastq The raw sequence reads were aligned to zebrafish transcriptome Ensembl release 85 and the zebrafish genome assembly GRCz10 by using STAR aligner version 2.5.2a with the following parameters: sjdbScore 1 clip3pAdapterSeq AGATCGGAAGAGC outWigStrand Unstranded outFilterType BySJout outFilterMultimapNmax 1. The total number of reads overlapping each gene were counted using featureCounts v.1.5.0 with Ensembl release 85 gtf file and the following parameters: F GTF t exon g gene id O s 0 primary p. Genome build: GRCz10 Supplementary files format and content: TXT zebrafish fin   The total RNA was extracted by using TRIzol solution Ambion according to the manufacturer’s instructions with minor modifications. RNA seq libraries were generated by using TruSeq RNA Library Prep Kit v2 Illumina according to the manufacturer’s instructions.   strain:Tgsp7:EGFP|cell type:sp7 cells|dy post amputation:4 dpa GSM3611565 GSM3611565: RNA sp7ne4dpa rep1; Danio rerio; RNA Seq GSM3611565   1 The total RNA was extracted by using TRIzol solution Ambion according to the manufacturer's instructions with minor modifications. RNA seq libraries were generated by using TruSeq RNA Library Prep Kit v2 Illumina according to the manufacturer's instructions. GEO Accession:GSM3611565 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP186180     RNA_sp7ne4dpa_rep1_R1.fastq.gz RNA_sp7ne4dpa_rep1_R2.fastq.gz fastq fastq 8439460350.0 56263069.0 GSM3611565 r1 0:75 1:75 A:1887175309;C:2332104703;G:2326716023;T:1892380553;N:1083762 75 75     1887175309 2332104703 2326716023 1892380553 1083762 SRX5388263 SRS4376702 SRA850124 GEO Ting Wang, Department of Genetics, Washington University School of Medicine 2 0.97339 0.97412 0.01837 0.01793 0.7949 0.79691 0.47227 0.47364 75 75 B B biological fallback assumption illumina nextseq unknown cdna_unspecified trueseq bulk unknown unknown   United States 2019-02-18 Undetermined Undetermined Fin Surface Structure
51212 51212 SRR8587723 SRX5388262 SRS4376701 SRP186180 PRJNA523009 Regenerating zebrafish fin epigenome is characterized by stable lineage specific DNA methylation and dynamic chromatin accessibility RNA seq GSE126701 Transcriptome Analysis Background: Zebrafish can faithfully regenerate injured fins through the formation of a blastema a mass of proliferative cells that can grow and develop into the lost body part. post amputation various cell types contribute to blastema formation where each cell type retains fate restriction and exclusively contributes to regeneration of its own lineage. Epigenetic changes that are associated with lineage restriction during regeneration remain underexplored. Results: We produce epigenome maps including DNA methylation and chromatin accessibility as well as transcriptomes of osteoblasts and other cells in uninjured and regenerating fins. This effort reveals regeneration as a process of highly dynamic and orchestrated transcriptomic and chromatin accessibility changes coupled with stably maintained lineage specific DNA methylation. The epigenetic signatures also reveal many novel regeneration specific enhancers which are experimentally validated. Regulatory networks important for regeneration are constructed through integrative analysis of the epigenome map and a knockout of a predicted upstream regulator disrupts normal regeneration validating our prediction. Conclusion: Our study shows that lineage specific DNA methylation signatures are stably maintained during regeneration and regeneration enhancers are preset as hypomethylated before injury. In contrast chromatin accessibility is dynamically changed during regeneration. Many enhancers driving regeneration gene expression as well as upstream regulators of regeneration are identified and validated through integrative epigenome analysis. Overall design: mRNA profiles of the uninjured and regenerating fin by deep sequencing in duplicate using Illumina NextSeq. parent bioproject:PRJNA523007 pubmed:32106888   RNA sp7ne0dpa rep2 GSM3611564   tissue:zebrafish fin|strain:Tgsp7:EGFP|cell type:sp7 cells|dy post amputation:0 dpa RNA sp7ne0dpa rep2 Basecalls were performed by the Edison Family Center for Genome Sciences & Systems Biology Sequencing Center using bcl2fastq The raw sequence reads were aligned to zebrafish transcriptome Ensembl release 85 and the zebrafish genome assembly GRCz10 by using STAR aligner version 2.5.2a with the following parameters: sjdbScore 1 clip3pAdapterSeq AGATCGGAAGAGC outWigStrand Unstranded outFilterType BySJout outFilterMultimapNmax 1. The total number of reads overlapping each gene were counted using featureCounts v.1.5.0 with Ensembl release 85 gtf file and the following parameters: F GTF t exon g gene id O s 0 primary p. Genome build: GRCz10 Supplementary files format and content: TXT zebrafish fin   The total RNA was extracted by using TRIzol solution Ambion according to the manufacturer’s instructions with minor modifications. RNA seq libraries were generated by using TruSeq RNA Library Prep Kit v2 Illumina according to the manufacturer’s instructions.   strain:Tgsp7:EGFP|cell type:sp7 cells|dy post amputation:0 dpa GSM3611564 GSM3611564: RNA sp7ne0dpa rep2; Danio rerio; RNA Seq GSM3611564   1 The total RNA was extracted by using TRIzol solution Ambion according to the manufacturer's instructions with minor modifications. RNA seq libraries were generated by using TruSeq RNA Library Prep Kit v2 Illumina according to the manufacturer's instructions. GEO Accession:GSM3611564 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP186180     RNA_sp7ne0dpa_rep2_R2.fastq.gz RNA_sp7ne0dpa_rep2_R1.fastq.gz fastq fastq 7717072650.0 51447151.0 GSM3611564 r1 0:75 1:75 A:1769886209;C:2081033837;G:2087874484;T:1777287682;N:990438 75 75     1769886209 2081033837 2087874484 1777287682 990438 SRX5388262 SRS4376701 SRA850124 GEO Ting Wang, Department of Genetics, Washington University School of Medicine 2 0.96981 0.9702 0.02436 0.02449 0.81852 0.82091 0.46189 0.46596 75 75 B B biological fallback assumption illumina nextseq unknown cdna_unspecified trueseq bulk unknown unknown   United States 2019-02-18 Undetermined Undetermined Fin Surface Structure
51213 51213 SRR8587722 SRX5388261 SRS4376700 SRP186180 PRJNA523009 Regenerating zebrafish fin epigenome is characterized by stable lineage specific DNA methylation and dynamic chromatin accessibility RNA seq GSE126701 Transcriptome Analysis Background: Zebrafish can faithfully regenerate injured fins through the formation of a blastema a mass of proliferative cells that can grow and develop into the lost body part. post amputation various cell types contribute to blastema formation where each cell type retains fate restriction and exclusively contributes to regeneration of its own lineage. Epigenetic changes that are associated with lineage restriction during regeneration remain underexplored. Results: We produce epigenome maps including DNA methylation and chromatin accessibility as well as transcriptomes of osteoblasts and other cells in uninjured and regenerating fins. This effort reveals regeneration as a process of highly dynamic and orchestrated transcriptomic and chromatin accessibility changes coupled with stably maintained lineage specific DNA methylation. The epigenetic signatures also reveal many novel regeneration specific enhancers which are experimentally validated. Regulatory networks important for regeneration are constructed through integrative analysis of the epigenome map and a knockout of a predicted upstream regulator disrupts normal regeneration validating our prediction. Conclusion: Our study shows that lineage specific DNA methylation signatures are stably maintained during regeneration and regeneration enhancers are preset as hypomethylated before injury. In contrast chromatin accessibility is dynamically changed during regeneration. Many enhancers driving regeneration gene expression as well as upstream regulators of regeneration are identified and validated through integrative epigenome analysis. Overall design: mRNA profiles of the uninjured and regenerating fin by deep sequencing in duplicate using Illumina NextSeq. parent bioproject:PRJNA523007 pubmed:32106888   RNA sp7ne0dpa rep1 GSM3611563   tissue:zebrafish fin|strain:Tgsp7:EGFP|cell type:sp7 cells|dy post amputation:0 dpa RNA sp7ne0dpa rep1 Basecalls were performed by the Edison Family Center for Genome Sciences & Systems Biology Sequencing Center using bcl2fastq The raw sequence reads were aligned to zebrafish transcriptome Ensembl release 85 and the zebrafish genome assembly GRCz10 by using STAR aligner version 2.5.2a with the following parameters: sjdbScore 1 clip3pAdapterSeq AGATCGGAAGAGC outWigStrand Unstranded outFilterType BySJout outFilterMultimapNmax 1. The total number of reads overlapping each gene were counted using featureCounts v.1.5.0 with Ensembl release 85 gtf file and the following parameters: F GTF t exon g gene id O s 0 primary p. Genome build: GRCz10 Supplementary files format and content: TXT zebrafish fin   The total RNA was extracted by using TRIzol solution Ambion according to the manufacturer’s instructions with minor modifications. RNA seq libraries were generated by using TruSeq RNA Library Prep Kit v2 Illumina according to the manufacturer’s instructions.   strain:Tgsp7:EGFP|cell type:sp7 cells|dy post amputation:0 dpa GSM3611563 GSM3611563: RNA sp7ne0dpa rep1; Danio rerio; RNA Seq GSM3611563   1 The total RNA was extracted by using TRIzol solution Ambion according to the manufacturer's instructions with minor modifications. RNA seq libraries were generated by using TruSeq RNA Library Prep Kit v2 Illumina according to the manufacturer's instructions. GEO Accession:GSM3611563 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP186180     RNA_sp7ne0dpa_rep1_R1.fastq.gz RNA_sp7ne0dpa_rep1_R2.fastq.gz fastq fastq 6359572800.0 42397152.0 GSM3611563 r1 0:75 1:75 A:1436300525;C:1737689578;G:1741478191;T:1443303935;N:800571 75 75     1436300525 1737689578 1741478191 1443303935 800571 SRX5388261 SRS4376700 SRA850124 GEO Ting Wang, Department of Genetics, Washington University School of Medicine 2 0.97133 0.97042 0.0204 0.02062 0.82597 0.82791 0.44709 0.44848 75 75 B B biological fallback assumption illumina nextseq unknown cdna_unspecified trueseq bulk unknown unknown   United States 2019-02-18 Undetermined Undetermined Fin Surface Structure
61390 61390 SRR12708451 SRX9187386 SRS7423761 SRP285315 PRJNA665531 Bulk RNA seq of fin and body melanocytes and microenvironments GSE158538 Transcriptome Analysis Broadly we were interested in understanding how fin and body melanocytes were different. The goal of the experiment was to investigate the interaction between three different variables: 1 cell lineage: melanocyte vs bulk microenvironment 2 anatomic location: fin vs body 3 genotype: wildtype vs CRKL GAB2 TERT overexpression with NF1 loss. We found that melanocytes have unique transcriptional programs based on their anatomic location and that these programs can regulate the response to oncogenic drivers like CRKL. Overall design: For this experiment we used two genetic strains of zebrafish. 1 Wildtype melanocyte model stable line was generated by injecting Caspers with MiniCoopR eGFP. 2 Acral melanoma model stable line was generated by injecting Caspers with MiniCoopR eGFP mitfa:hsCRKL mitfa:hsGAB2 mitfa:hsTERT mitfa:Cas9 mCherry;U6 nf1a gRNA mitfa:Cas9 mCherry;U6 nf1b gRNA. Fish were dissected to collect body skin and fins digested using liberase and then FACS sorted for GFP+ melanocytes and GFP microenvironment cells. Each biological replicate constituted a pooling of 2 males and 2 females. There were 2 genetic strainsWT v Acral x 2 anatomic locationsfin v body x 2 sorted conditionsGFP+ v GFP x 3 biological replicates = 24 samples total.   pubmed:35355015   MFN3 GSM4802478   tissue:Zebrafish fins|strain:Wildtype melanocyte model Caspers with MiniCoopR eGFP|anatomic location:Fin MFN3 md5sum to confirm files copied to server without xxx; FastQC for all files; Trimmomatic for all files to remove adaptor sequences and low quality sequences; FastQC for all files; STAR to align to GRCz10 Ensemble version 81 and get both BAM file and counts table as output; SeQC on aligned BAM file for each sample. Genome build: GRCz10 Supplementary files format and content: tab delimited text file for every sample with raw counts for every gene Supplementary files format and content: table with raw counts for every gene and every sample with genes annotated Zebrafish fins   Cells were FACS sorted into TRIZOL LS and snap frozen. Total RNA was extracted using TRIZOL LS protocol. Total RNA varied from 1.2ng to 150ng all having RIN scores > 7. Reverse transcription and cDNA amplification were performed with SMART Seq v4 Ultra Low Input RNA Kit Clontech. Libraries were constructed using Illumina Nextera XT kit and analyzed for concentration Qubit size distribribution Agilent Bioanalyzer.   strain:Wildtype melanocyte model Caspers with MiniCoopR eGFP|anatomic location:Fin|gfp+ or gfp :GFP GSM4802478 GSM4802478: MFN3; Danio rerio; RNA Seq GSM4802478   1 Cells were FACS sorted into TRIZOL LS and snap frozen. Total RNA was extracted using TRIZOL LS protocol. Total RNA varied from 1.2ng to 150ng all having RIN scores > 7. Reverse transcription and cDNA amplification were performed with SMART Seq v4 Ultra Low Input RNA Kit Clontech. Libraries were constructed using Illumina Nextera XT kit and analyzed for concentration Qubit size distribribution Agilent Bioanalyzer. GEO Accession:GSM4802478 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP285315     MFN3_R1_001.fastq.gz MFN3_R2_001.fastq.gz fastq fastq 14558703600.0 48529012.0 GSM4802478 r1 0:150 1:150 A:3871514784;C:3434394240;G:3331911824;T:3919968300;N:914452 150 150     3871514784 3434394240 3331911824 3919968300 914452 SRX9187386 SRS7423761 SRA1131319 GEO White, Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center 2 0.89707 0.89196 0.05724 0.05696 0.75396 0.75597 0.43181 0.41631 150 150 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2020-09-24 Undetermined Undetermined Fin Surface Structure
61391 61391 SRR12708450 SRX9187385 SRS7423760 SRP285315 PRJNA665531 Bulk RNA seq of fin and body melanocytes and microenvironments GSE158538 Transcriptome Analysis Broadly we were interested in understanding how fin and body melanocytes were different. The goal of the experiment was to investigate the interaction between three different variables: 1 cell lineage: melanocyte vs bulk microenvironment 2 anatomic location: fin vs body 3 genotype: wildtype vs CRKL GAB2 TERT overexpression with NF1 loss. We found that melanocytes have unique transcriptional programs based on their anatomic location and that these programs can regulate the response to oncogenic drivers like CRKL. Overall design: For this experiment we used two genetic strains of zebrafish. 1 Wildtype melanocyte model stable line was generated by injecting Caspers with MiniCoopR eGFP. 2 Acral melanoma model stable line was generated by injecting Caspers with MiniCoopR eGFP mitfa:hsCRKL mitfa:hsGAB2 mitfa:hsTERT mitfa:Cas9 mCherry;U6 nf1a gRNA mitfa:Cas9 mCherry;U6 nf1b gRNA. Fish were dissected to collect body skin and fins digested using liberase and then FACS sorted for GFP+ melanocytes and GFP microenvironment cells. Each biological replicate constituted a pooling of 2 males and 2 females. There were 2 genetic strainsWT v Acral x 2 anatomic locationsfin v body x 2 sorted conditionsGFP+ v GFP x 3 biological replicates = 24 samples total.   pubmed:35355015   MFG3 GSM4802477   tissue:Zebrafish fins|strain:Wildtype melanocyte model Caspers with MiniCoopR eGFP|anatomic location:Fin MFG3 md5sum to confirm files copied to server without xxx; FastQC for all files; Trimmomatic for all files to remove adaptor sequences and low quality sequences; FastQC for all files; STAR to align to GRCz10 Ensemble version 81 and get both BAM file and counts table as output; SeQC on aligned BAM file for each sample. Genome build: GRCz10 Supplementary files format and content: tab delimited text file for every sample with raw counts for every gene Supplementary files format and content: table with raw counts for every gene and every sample with genes annotated Zebrafish fins   Cells were FACS sorted into TRIZOL LS and snap frozen. Total RNA was extracted using TRIZOL LS protocol. Total RNA varied from 1.2ng to 150ng all having RIN scores > 7. Reverse transcription and cDNA amplification were performed with SMART Seq v4 Ultra Low Input RNA Kit Clontech. Libraries were constructed using Illumina Nextera XT kit and analyzed for concentration Qubit size distribribution Agilent Bioanalyzer.   strain:Wildtype melanocyte model Caspers with MiniCoopR eGFP|anatomic location:Fin|gfp+ or gfp :GFP+ GSM4802477 GSM4802477: MFG3; Danio rerio; RNA Seq GSM4802477   1 Cells were FACS sorted into TRIZOL LS and snap frozen. Total RNA was extracted using TRIZOL LS protocol. Total RNA varied from 1.2ng to 150ng all having RIN scores > 7. Reverse transcription and cDNA amplification were performed with SMART Seq v4 Ultra Low Input RNA Kit Clontech. Libraries were constructed using Illumina Nextera XT kit and analyzed for concentration Qubit size distribribution Agilent Bioanalyzer. GEO Accession:GSM4802477 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP285315     MFG3_R1_001.fastq.gz MFG3_R2_001.fastq.gz fastq fastq 10045323900.0 33484413.0 GSM4802477 r1 0:150 1:150 A:2619233046;C:2425417526;G:2312268655;T:2687771920;N:632753 150 150     2619233046 2425417526 2312268655 2687771920 632753 SRX9187385 SRS7423760 SRA1131319 GEO White, Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center 2 0.90365 0.90046 0.06439 0.06489 0.75436 0.75641 0.54634 0.54693 150 150 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2020-09-24 Undetermined Undetermined Fin Surface Structure
61394 61394 SRR12708447 SRX9187382 SRS7423757 SRP285315 PRJNA665531 Bulk RNA seq of fin and body melanocytes and microenvironments GSE158538 Transcriptome Analysis Broadly we were interested in understanding how fin and body melanocytes were different. The goal of the experiment was to investigate the interaction between three different variables: 1 cell lineage: melanocyte vs bulk microenvironment 2 anatomic location: fin vs body 3 genotype: wildtype vs CRKL GAB2 TERT overexpression with NF1 loss. We found that melanocytes have unique transcriptional programs based on their anatomic location and that these programs can regulate the response to oncogenic drivers like CRKL. Overall design: For this experiment we used two genetic strains of zebrafish. 1 Wildtype melanocyte model stable line was generated by injecting Caspers with MiniCoopR eGFP. 2 Acral melanoma model stable line was generated by injecting Caspers with MiniCoopR eGFP mitfa:hsCRKL mitfa:hsGAB2 mitfa:hsTERT mitfa:Cas9 mCherry;U6 nf1a gRNA mitfa:Cas9 mCherry;U6 nf1b gRNA. Fish were dissected to collect body skin and fins digested using liberase and then FACS sorted for GFP+ melanocytes and GFP microenvironment cells. Each biological replicate constituted a pooling of 2 males and 2 females. There were 2 genetic strainsWT v Acral x 2 anatomic locationsfin v body x 2 sorted conditionsGFP+ v GFP x 3 biological replicates = 24 samples total.   pubmed:35355015   XFN3 GSM4802474   tissue:Zebrafish fins|strain:Acral melanoma model Caspers with MiniCoopR eGFP mitfa:hsCRKL mitfa:hsGAB2 mitfa:hsTERT mitfa:Cas9 mCherry; U6 nf1a gRNA mitfa:Cas9 mCherry; U6 nf1b gRNA|anatomic location:Fin XFN3 md5sum to confirm files copied to server without xxx; FastQC for all files; Trimmomatic for all files to remove adaptor sequences and low quality sequences; FastQC for all files; STAR to align to GRCz10 Ensemble version 81 and get both BAM file and counts table as output; SeQC on aligned BAM file for each sample. Genome build: GRCz10 Supplementary files format and content: tab delimited text file for every sample with raw counts for every gene Supplementary files format and content: table with raw counts for every gene and every sample with genes annotated Zebrafish fins   Cells were FACS sorted into TRIZOL LS and snap frozen. Total RNA was extracted using TRIZOL LS protocol. Total RNA varied from 1.2ng to 150ng all having RIN scores > 7. Reverse transcription and cDNA amplification were performed with SMART Seq v4 Ultra Low Input RNA Kit Clontech. Libraries were constructed using Illumina Nextera XT kit and analyzed for concentration Qubit size distribribution Agilent Bioanalyzer.   strain:Acral melanoma model Caspers with MiniCoopR eGFP mitfa:hsCRKL mitfa:hsGAB2 mitfa:hsTERT mitfa:Cas9 mCherry;U6 nf1a gRNA mitfa:Cas9 mCherry;U6 nf1b gRNA|anatomic location:Fin|gfp+ or gfp :GFP GSM4802474 GSM4802474: XFN3; Danio rerio; RNA Seq GSM4802474   1 Cells were FACS sorted into TRIZOL LS and snap frozen. Total RNA was extracted using TRIZOL LS protocol. Total RNA varied from 1.2ng to 150ng all having RIN scores > 7. Reverse transcription and cDNA amplification were performed with SMART Seq v4 Ultra Low Input RNA Kit Clontech. Libraries were constructed using Illumina Nextera XT kit and analyzed for concentration Qubit size distribribution Agilent Bioanalyzer. GEO Accession:GSM4802474 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP285315     XFN3_R1_001.fastq.gz XFN3_R2_001.fastq.gz fastq fastq 11204873700.0 37349579.0 GSM4802474 r1 0:150 1:150 A:2943394483;C:2667470839;G:2579644073;T:3013655182;N:709123 150 150     2943394483 2667470839 2579644073 3013655182 709123 SRX9187382 SRS7423757 SRA1131319 GEO White, Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center 2 0.90055 0.89407 0.05457 0.05489 0.74247 0.746 0.48492 0.48602 150 150 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2020-09-24 Undetermined Undetermined Fin Surface Structure
61395 61395 SRR12708446 SRX9187381 SRS7423756 SRP285315 PRJNA665531 Bulk RNA seq of fin and body melanocytes and microenvironments GSE158538 Transcriptome Analysis Broadly we were interested in understanding how fin and body melanocytes were different. The goal of the experiment was to investigate the interaction between three different variables: 1 cell lineage: melanocyte vs bulk microenvironment 2 anatomic location: fin vs body 3 genotype: wildtype vs CRKL GAB2 TERT overexpression with NF1 loss. We found that melanocytes have unique transcriptional programs based on their anatomic location and that these programs can regulate the response to oncogenic drivers like CRKL. Overall design: For this experiment we used two genetic strains of zebrafish. 1 Wildtype melanocyte model stable line was generated by injecting Caspers with MiniCoopR eGFP. 2 Acral melanoma model stable line was generated by injecting Caspers with MiniCoopR eGFP mitfa:hsCRKL mitfa:hsGAB2 mitfa:hsTERT mitfa:Cas9 mCherry;U6 nf1a gRNA mitfa:Cas9 mCherry;U6 nf1b gRNA. Fish were dissected to collect body skin and fins digested using liberase and then FACS sorted for GFP+ melanocytes and GFP microenvironment cells. Each biological replicate constituted a pooling of 2 males and 2 females. There were 2 genetic strainsWT v Acral x 2 anatomic locationsfin v body x 2 sorted conditionsGFP+ v GFP x 3 biological replicates = 24 samples total.   pubmed:35355015   XFG3 GSM4802473   tissue:Zebrafish fins|strain:Acral melanoma model Caspers with MiniCoopR eGFP mitfa:hsCRKL mitfa:hsGAB2 mitfa:hsTERT mitfa:Cas9 mCherry; U6 nf1a gRNA mitfa:Cas9 mCherry; U6 nf1b gRNA|anatomic location:Fin XFG3 md5sum to confirm files copied to server without xxx; FastQC for all files; Trimmomatic for all files to remove adaptor sequences and low quality sequences; FastQC for all files; STAR to align to GRCz10 Ensemble version 81 and get both BAM file and counts table as output; SeQC on aligned BAM file for each sample. Genome build: GRCz10 Supplementary files format and content: tab delimited text file for every sample with raw counts for every gene Supplementary files format and content: table with raw counts for every gene and every sample with genes annotated Zebrafish fins   Cells were FACS sorted into TRIZOL LS and snap frozen. Total RNA was extracted using TRIZOL LS protocol. Total RNA varied from 1.2ng to 150ng all having RIN scores > 7. Reverse transcription and cDNA amplification were performed with SMART Seq v4 Ultra Low Input RNA Kit Clontech. Libraries were constructed using Illumina Nextera XT kit and analyzed for concentration Qubit size distribribution Agilent Bioanalyzer.   strain:Acral melanoma model Caspers with MiniCoopR eGFP mitfa:hsCRKL mitfa:hsGAB2 mitfa:hsTERT mitfa:Cas9 mCherry;U6 nf1a gRNA mitfa:Cas9 mCherry;U6 nf1b gRNA|anatomic location:Fin|gfp+ or gfp :GFP+ GSM4802473 GSM4802473: XFG3; Danio rerio; RNA Seq GSM4802473   1 Cells were FACS sorted into TRIZOL LS and snap frozen. Total RNA was extracted using TRIZOL LS protocol. Total RNA varied from 1.2ng to 150ng all having RIN scores > 7. Reverse transcription and cDNA amplification were performed with SMART Seq v4 Ultra Low Input RNA Kit Clontech. Libraries were constructed using Illumina Nextera XT kit and analyzed for concentration Qubit size distribribution Agilent Bioanalyzer. GEO Accession:GSM4802473 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP285315     XFG3_R1_001.fastq.gz XFG3_R2_001.fastq.gz fastq fastq 11212083000.0 37373610.0 GSM4802473 r1 0:150 1:150 A:2979985262;C:2652925544;G:2513147966;T:3065318302;N:705926 150 150     2979985262 2652925544 2513147966 3065318302 705926 SRX9187381 SRS7423756 SRA1131319 GEO White, Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center 2 0.9056 0.89972 0.06159 0.06165 0.74194 0.74602 0.49523 0.44889 150 150 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2020-09-24 Undetermined Undetermined Fin Surface Structure
61398 61398 SRR12708443 SRX9187378 SRS7423753 SRP285315 PRJNA665531 Bulk RNA seq of fin and body melanocytes and microenvironments GSE158538 Transcriptome Analysis Broadly we were interested in understanding how fin and body melanocytes were different. The goal of the experiment was to investigate the interaction between three different variables: 1 cell lineage: melanocyte vs bulk microenvironment 2 anatomic location: fin vs body 3 genotype: wildtype vs CRKL GAB2 TERT overexpression with NF1 loss. We found that melanocytes have unique transcriptional programs based on their anatomic location and that these programs can regulate the response to oncogenic drivers like CRKL. Overall design: For this experiment we used two genetic strains of zebrafish. 1 Wildtype melanocyte model stable line was generated by injecting Caspers with MiniCoopR eGFP. 2 Acral melanoma model stable line was generated by injecting Caspers with MiniCoopR eGFP mitfa:hsCRKL mitfa:hsGAB2 mitfa:hsTERT mitfa:Cas9 mCherry;U6 nf1a gRNA mitfa:Cas9 mCherry;U6 nf1b gRNA. Fish were dissected to collect body skin and fins digested using liberase and then FACS sorted for GFP+ melanocytes and GFP microenvironment cells. Each biological replicate constituted a pooling of 2 males and 2 females. There were 2 genetic strainsWT v Acral x 2 anatomic locationsfin v body x 2 sorted conditionsGFP+ v GFP x 3 biological replicates = 24 samples total.   pubmed:35355015   MFN2 GSM4802470   tissue:Zebrafish fins|strain:Wildtype melanocyte model Caspers with MiniCoopR eGFP|anatomic location:Fin MFN2 md5sum to confirm files copied to server without xxx; FastQC for all files; Trimmomatic for all files to remove adaptor sequences and low quality sequences; FastQC for all files; STAR to align to GRCz10 Ensemble version 81 and get both BAM file and counts table as output; SeQC on aligned BAM file for each sample. Genome build: GRCz10 Supplementary files format and content: tab delimited text file for every sample with raw counts for every gene Supplementary files format and content: table with raw counts for every gene and every sample with genes annotated Zebrafish fins   Cells were FACS sorted into TRIZOL LS and snap frozen. Total RNA was extracted using TRIZOL LS protocol. Total RNA varied from 1.2ng to 150ng all having RIN scores > 7. Reverse transcription and cDNA amplification were performed with SMART Seq v4 Ultra Low Input RNA Kit Clontech. Libraries were constructed using Illumina Nextera XT kit and analyzed for concentration Qubit size distribribution Agilent Bioanalyzer.   strain:Wildtype melanocyte model Caspers with MiniCoopR eGFP|anatomic location:Fin|gfp+ or gfp :GFP GSM4802470 GSM4802470: MFN2; Danio rerio; RNA Seq GSM4802470   1 Cells were FACS sorted into TRIZOL LS and snap frozen. Total RNA was extracted using TRIZOL LS protocol. Total RNA varied from 1.2ng to 150ng all having RIN scores > 7. Reverse transcription and cDNA amplification were performed with SMART Seq v4 Ultra Low Input RNA Kit Clontech. Libraries were constructed using Illumina Nextera XT kit and analyzed for concentration Qubit size distribribution Agilent Bioanalyzer. GEO Accession:GSM4802470 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP285315     MFN2_R1_001.fastq.gz MFN2_R2_001.fastq.gz fastq fastq 9002969100.0 30009897.0 GSM4802470 r1 0:150 1:150 A:2383579322;C:2152753900;G:2013843514;T:2452228154;N:564210 150 150     2383579322 2152753900 2013843514 2452228154 564210 SRX9187378 SRS7423753 SRA1131319 GEO White, Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center 2 0.89613 0.89129 0.06896 0.06936 0.75235 0.75659 0.51059 0.50763 150 150 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2020-09-24 Undetermined Undetermined Fin Surface Structure
61399 61399 SRR12708442 SRX9187377 SRS7423752 SRP285315 PRJNA665531 Bulk RNA seq of fin and body melanocytes and microenvironments GSE158538 Transcriptome Analysis Broadly we were interested in understanding how fin and body melanocytes were different. The goal of the experiment was to investigate the interaction between three different variables: 1 cell lineage: melanocyte vs bulk microenvironment 2 anatomic location: fin vs body 3 genotype: wildtype vs CRKL GAB2 TERT overexpression with NF1 loss. We found that melanocytes have unique transcriptional programs based on their anatomic location and that these programs can regulate the response to oncogenic drivers like CRKL. Overall design: For this experiment we used two genetic strains of zebrafish. 1 Wildtype melanocyte model stable line was generated by injecting Caspers with MiniCoopR eGFP. 2 Acral melanoma model stable line was generated by injecting Caspers with MiniCoopR eGFP mitfa:hsCRKL mitfa:hsGAB2 mitfa:hsTERT mitfa:Cas9 mCherry;U6 nf1a gRNA mitfa:Cas9 mCherry;U6 nf1b gRNA. Fish were dissected to collect body skin and fins digested using liberase and then FACS sorted for GFP+ melanocytes and GFP microenvironment cells. Each biological replicate constituted a pooling of 2 males and 2 females. There were 2 genetic strainsWT v Acral x 2 anatomic locationsfin v body x 2 sorted conditionsGFP+ v GFP x 3 biological replicates = 24 samples total.   pubmed:35355015   MFG2 GSM4802469   tissue:Zebrafish fins|strain:Wildtype melanocyte model Caspers with MiniCoopR eGFP|anatomic location:Fin MFG2 md5sum to confirm files copied to server without xxx; FastQC for all files; Trimmomatic for all files to remove adaptor sequences and low quality sequences; FastQC for all files; STAR to align to GRCz10 Ensemble version 81 and get both BAM file and counts table as output; SeQC on aligned BAM file for each sample. Genome build: GRCz10 Supplementary files format and content: tab delimited text file for every sample with raw counts for every gene Supplementary files format and content: table with raw counts for every gene and every sample with genes annotated Zebrafish fins   Cells were FACS sorted into TRIZOL LS and snap frozen. Total RNA was extracted using TRIZOL LS protocol. Total RNA varied from 1.2ng to 150ng all having RIN scores > 7. Reverse transcription and cDNA amplification were performed with SMART Seq v4 Ultra Low Input RNA Kit Clontech. Libraries were constructed using Illumina Nextera XT kit and analyzed for concentration Qubit size distribribution Agilent Bioanalyzer.   strain:Wildtype melanocyte model Caspers with MiniCoopR eGFP|anatomic location:Fin|gfp+ or gfp :GFP+ GSM4802469 GSM4802469: MFG2; Danio rerio; RNA Seq GSM4802469   1 Cells were FACS sorted into TRIZOL LS and snap frozen. Total RNA was extracted using TRIZOL LS protocol. Total RNA varied from 1.2ng to 150ng all having RIN scores > 7. Reverse transcription and cDNA amplification were performed with SMART Seq v4 Ultra Low Input RNA Kit Clontech. Libraries were constructed using Illumina Nextera XT kit and analyzed for concentration Qubit size distribribution Agilent Bioanalyzer. GEO Accession:GSM4802469 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP285315     MFG2_R1_001.fastq.gz MFG2_R2_001.fastq.gz fastq fastq 11893039800.0 39643466.0 GSM4802469 r1 0:150 1:150 A:3160384920;C:2834257771;G:2698430613;T:3199226169;N:740327 150 150     3160384920 2834257771 2698430613 3199226169 740327 SRX9187377 SRS7423752 SRA1131319 GEO White, Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center 2 0.90353 0.89813 0.06957 0.06993 0.75183 0.75607 0.46098 0.51543 150 150 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2020-09-24 Undetermined Undetermined Fin Surface Structure

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CREATE TABLE run_metadata("run.accession" VARCHAR, "experiment.accession" VARCHAR, "sample.accession" VARCHAR, "study.accession" VARCHAR, bioproject VARCHAR, "study.title" VARCHAR, "study.alias" VARCHAR, "study.type" VARCHAR, "study.abstract" VARCHAR, "study.attributes" VARCHAR, "study.PMIDs" VARCHAR, "sample.description" VARCHAR, "sample.title" VARCHAR, "sample.alias" VARCHAR, "sample.centername" VARCHAR, "sample.attributes" VARCHAR, "GEOsample.title" VARCHAR, "GEOsample.dataprocessing" VARCHAR, "GEOsample.source" VARCHAR, "GEOsample.treatmentprotocol" VARCHAR, "GEOsample.extractprotocol" VARCHAR, "GEOsample.growthprotocol" VARCHAR, "GEOsample.characteristics" VARCHAR, "GEOsample.accession" VARCHAR, "experiment.title" VARCHAR, "experiment.alias" VARCHAR, "experiment.library_name" VARCHAR, "experiment.design_description" VARCHAR, "experiment.library_construction_protocol" VARCHAR, "experiment.attributes" VARCHAR, "experiment.library_strategy" VARCHAR, "experiment.library_source" VARCHAR, "experiment.library_selection" VARCHAR, "experiment.library_layout" VARCHAR, "experiment.platform" VARCHAR, "experiment.instrument_model" VARCHAR, "experiment.spot_descriptor" VARCHAR, "experiment.study_ref" VARCHAR, "run.title" VARCHAR, "run.attributes" VARCHAR, "run.filename" VARCHAR, "run.semantic_name" VARCHAR, "run.total_bases" DOUBLE, "run.total_spots" DOUBLE, "run.alias" VARCHAR, "run.read_lengths" VARCHAR, "run.base_counts" VARCHAR, "run.r1_length" BIGINT, "run.r2_length" BIGINT, "run.r3_length" BIGINT, "run.r4_length" BIGINT, "run.Acount" BIGINT, "run.Ccount" BIGINT, "run.Gcount" BIGINT, "run.Tcount" BIGINT, "run.Ncount" BIGINT, "run.experiment" VARCHAR, "run.pool_member" VARCHAR, "submission.accession" VARCHAR, "submission.srasource" VARCHAR, "submission.bioprojectsource" VARCHAR, "seqdetective.n_mates" BIGINT, "seqdetective.mapping_rate.mate1" DOUBLE, "seqdetective.mapping_rate.mate2" DOUBLE, "seqdetective.nofeature_rate.mate1" DOUBLE, "seqdetective.nofeature_rate.mate2" DOUBLE, "seqdetective.sparsity.mate1" DOUBLE, "seqdetective.sparsity.mate2" DOUBLE, "seqdetective.pos_strand_rate.mate1" DOUBLE, "seqdetective.pos_strand_rate.mate2" DOUBLE, "seqdetective.readlen.mate1" BIGINT, "seqdetective.readlen.mate2" BIGINT, "seqdetective.judgement.mate1" VARCHAR, "seqdetective.judgement.mate2" VARCHAR, "seqdetective.judgement.reason" VARCHAR, platform_family VARCHAR, instrument_generation VARCHAR, read_bias VARCHAR, selection_class VARCHAR, prep_kit VARCHAR, sc_or_bulk VARCHAR, tech_class VARCHAR, technology VARCHAR, tech_variant VARCHAR, "submission.bioprojectsource.country" VARCHAR, earliest_date DATE, devstage_curation VARCHAR, devstage_curation_coarse VARCHAR, tissue_curation VARCHAR, tissue_curation_coarse VARCHAR);;
CREATE INDEX idx_run_bioproject ON run_metadata(bioproject);;
CREATE INDEX idx_run_run_accession ON run_metadata("run.accession");;