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,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,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,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,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,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,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
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,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,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,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
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,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,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,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,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,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,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,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,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,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,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,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,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,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
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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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
61402,SRR12708439,SRX9187374,SRS7423749,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,,XFN2,GSM4802466,,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,XFN2,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 ,GSM4802466,GSM4802466: XFN2; Danio rerio; RNA Seq,GSM4802466,,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:GSM4802466,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP285315,,,XFN2_R1_001.fastq.gz XFN2_R2_001.fastq.gz,fastq fastq,11313005400.0,37710018.0,GSM4802466 r1,0:150 1:150,A:2996096346;C:2703585714;G:2550898118;T:3061720444;N:704778,150,150,,,2996096346,2703585714,2550898118,3061720444,704778,SRX9187374,SRS7423749,SRA1131319,GEO,"White, Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center",2,0.88653,0.88127,0.06171,0.06088,0.74856,0.75252,0.51699,0.51503,150,150,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
61403,SRR12708438,SRX9187373,SRS7423748,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,,XFG2,GSM4802465,,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,XFG2,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+,GSM4802465,GSM4802465: XFG2; Danio rerio; RNA Seq,GSM4802465,,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:GSM4802465,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP285315,,,XFG2_R1_001.fastq.gz XFG2_R2_001.fastq.gz,fastq fastq,11921269800.0,39737566.0,GSM4802465 r1,0:150 1:150,A:3191695537;C:2823855056;G:2636104989;T:3268877243;N:736975,150,150,,,3191695537,2823855056,2636104989,3268877243,736975,SRX9187373,SRS7423748,SRA1131319,GEO,"White, Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center",2,0.89811,0.89304,0.06734,0.0674,0.7391,0.74261,0.51932,0.45328,150,150,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
61406,SRR12708435,SRX9187370,SRS7423745,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,,MFN1,GSM4802462,,tissue:Zebrafish fins|strain:Wildtype melanocyte model Caspers with MiniCoopR eGFP|anatomic location:Fin,MFN1,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 ,GSM4802462,GSM4802462: MFN1; Danio rerio; RNA Seq,GSM4802462,,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:GSM4802462,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP285315,,,MFN1_R1_001.fastq.gz MFN1_R2_001.fastq.gz,fastq fastq,12560283900.0,41867613.0,GSM4802462 r1,0:150 1:150,A:3295279231;C:3013386640;G:2898979550;T:3351847365;N:791114,150,150,,,3295279231,3013386640,2898979550,3351847365,791114,SRX9187370,SRS7423745,SRA1131319,GEO,"White, Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center",2,0.89681,0.89104,0.06566,0.06589,0.74272,0.74791,0.51645,0.51902,150,150,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
61407,SRR12708434,SRX9187369,SRS7423744,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,,MFG1,GSM4802461,,tissue:Zebrafish fins|strain:Wildtype melanocyte model Caspers with MiniCoopR eGFP|anatomic location:Fin,MFG1,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+,GSM4802461,GSM4802461: MFG1; Danio rerio; RNA Seq,GSM4802461,,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:GSM4802461,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP285315,,,MFG1_R1_001.fastq.gz MFG1_R2_001.fastq.gz,fastq fastq,11317873500.0,37726245.0,GSM4802461 r1,0:150 1:150,A:2947830189;C:2733463243;G:2616872694;T:3018996791;N:710583,150,150,,,2947830189,2733463243,2616872694,3018996791,710583,SRX9187369,SRS7423744,SRA1131319,GEO,"White, Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center",2,0.90788,0.90139,0.06383,0.06478,0.74268,0.74686,0.50725,0.50595,150,150,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
61410,SRR12708431,SRX9187366,SRS7423741,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,,XFN1,GSM4802458,,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,XFN1,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 ,GSM4802458,GSM4802458: XFN1; Danio rerio; RNA Seq,GSM4802458,,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:GSM4802458,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP285315,,,XFN1_R1_001.fastq.gz XFN1_R2_001.fastq.gz,fastq fastq,11573931900.0,38579773.0,GSM4802458 r1,0:150 1:150,A:2999184334;C:2801583964;G:2672180906;T:3100254047;N:728649,150,150,,,2999184334,2801583964,2672180906,3100254047,728649,SRX9187366,SRS7423741,SRA1131319,GEO,"White, Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center",2,0.8962,0.88921,0.05791,0.05848,0.74097,0.7471,0.50594,0.5107,150,150,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
61411,SRR12708430,SRX9187365,SRS7423740,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,,XFG1,GSM4802457,,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,XFG1,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+,GSM4802457,GSM4802457: XFG1; Danio rerio; RNA Seq,GSM4802457,,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:GSM4802457,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP285315,,,XFG1_R1_001.fastq.gz XFG1_R2_001.fastq.gz,fastq fastq,11738198700.0,39127329.0,GSM4802457 r1,0:150 1:150,A:3083667179;C:2816699592;G:2648683281;T:3188411465;N:737183,150,150,,,3083667179,2816699592,2648683281,3188411465,737183,SRX9187365,SRS7423740,SRA1131319,GEO,"White, Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center",2,0.90455,0.89777,0.05668,0.05707,0.74631,0.75057,0.49373,0.48957,150,150,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
61815,SRR12992438,SRX9443938,SRS7657861,SRP291307,PRJNA674824,Research on Molecular Mechanism of Zebrafish Caudal Fin Regeneration Based on Whole Transcriptome Technology,GSE160909,Transcriptome Analysis,Background/Aims:The ability of regeneration varies widely from invertebrates to vertebrates. Some animals  for example  flatworms  newts  salamanders  and lower vertebrates have the outstanding ability to regenerate all the organs even the whole individual. Unfortunately  the regenerative capacity of humans extremely attenuates along with the biological evolution and this makes it difficult for humans to recover from damaged or missing organs or tissues  and even cause serious loss of function or death. However  the research on regeneration mechanisms is limited and incomplete so far. Here  we investigated the biological mechanisms of zebrafish caudal fin regeneration. Methods:The zebrafish was used as the research object to analyze the differences of mRNA and ncRNA expressed in new tissues at 0d  3d  and 7d post caudal fin removal  and analyzed the molecular mechanism of caudal fin regeneration from the perspective of the whole transcriptome. Results: We observed that the amputated caudal fin went through a complex genetic change  especially at 3 dpa. This result showed that genes related to response to cell cycle and wounding might play a role in caudal fin regeneration.The up regulated DEGs at 3 dpa blastema outgrowth stage were dramatically enriched in 20 Biological Processes FDR < 0.05  three of which were cell cycle GO:0007049  mitotic cell cycle GO:0000278  and cell cycle process GO:0022402  one was response to wounding GO:0009611  etc. Conclusion: Taken together  the results revealed that the DEGs were enriched in numerous biological processes  molecular function  cellular component  and signaling pathways  suggesting that the caudal fin regeneration is a highly complicated process of the molecular mechanism. Overall design: Caudal fin RNA profiles of  test and control samples were generated by deep sequencing  using Illumina HiSeq 4000.,,pubmed:33186559;pubmed:36012210,,T7dpa 3,GSM4885971,,source name:caudal fin|treatment:caudal fin removal|time:7dpa|tissue:caudal fin regenerating,T7dpa 3,Basecalls performed using  Solexa pipeline v1.8 The trimmed reads trimmed 5’ 3’ adaptor bases using cutadapt were aligned to reference genome using tophat2 version 2.0.3.12software The transcript abundances for each sample was estimated with RSEM the FPKM value for gene and transcript level were calculated with R package edgeR The circRNA reads were aligned to reference genome using tophat2detecting backesplicec junction reads with find circ Genome build: Homo sapiens hg38 Supplementary files format and content: circRNA matrix.txt  lncRNA matrix.txt  mRNA matrix.txt,caudal fin,Wild type zebrafish were kept in a closed recirculating aquacultural system.The intact caudal fins CK0dpa were used as control and the regenerated caudal fins at corresponding stages T3dpa and T7dpa were used as treatment group.,RNA quality and quantity was measured by using nanodrop spectrophotometer ND 1000  Nanodrop Technologies and RNA Integrity was determined by gel electrophoresis Total RNA of each sample was used to prepare the RNA sequencing library 1RNA fragment；2Random primed first strand cDNA synthesis；3dUTP based second strand cDNA synthesis;4Adaptor ligation and PCR amplification.,Wild type zebrafish were kept in a closed recirculating aquacultural system.,treatment:caudal fin removal|time:7dpa|tissue:caudal fin regenerating,GSM4885971,GSM4885971: T7dpa 3; Danio rerio; RNA Seq,GSM4885971,,1,RNA quality and quantity was measured by using nanodrop spectrophotometer ND 1000  Nanodrop Technologies and RNA Integrity was determined by gel electrophoresis Total RNA of each sample was used to prepare the RNA sequencing library 1RNA fragment；2Random primed first strand cDNA synthesis；3dUTP based second strand cDNA synthesis;4Adaptor ligation and PCR amplification.,GEO Accession:GSM4885971,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP291307,,,S264_genedenovo-A_R1811235_AHC7LKDSXX_S264_L004_R1_001.fastq.gz S264_genedenovo-A_R1811235_AHC7LKDSXX_S264_L004_R2_001.fastq.gz,fastq fastq,12837992700.0,42793309.0,GSM4885971 r1,0:150 1:150,A:2967571445;C:3402582572;G:3367407968;T:3100298259;N:132456,150,150,,,2967571445,3402582572,3367407968,3100298259,132456,SRX9443938,SRS7657861,SRA1154680,GEO,henan normal university,2,0.92162,0.92273,0.24841,0.2408,0.74259,0.74134,0.57104,0.55898,150,150,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,bulk,unknown,unknown,,China,2020-11-05,Undetermined,Undetermined,Fin,Surface Structure
61816,SRR12992437,SRX9443937,SRS7657862,SRP291307,PRJNA674824,Research on Molecular Mechanism of Zebrafish Caudal Fin Regeneration Based on Whole Transcriptome Technology,GSE160909,Transcriptome Analysis,Background/Aims:The ability of regeneration varies widely from invertebrates to vertebrates. Some animals  for example  flatworms  newts  salamanders  and lower vertebrates have the outstanding ability to regenerate all the organs even the whole individual. Unfortunately  the regenerative capacity of humans extremely attenuates along with the biological evolution and this makes it difficult for humans to recover from damaged or missing organs or tissues  and even cause serious loss of function or death. However  the research on regeneration mechanisms is limited and incomplete so far. Here  we investigated the biological mechanisms of zebrafish caudal fin regeneration. Methods:The zebrafish was used as the research object to analyze the differences of mRNA and ncRNA expressed in new tissues at 0d  3d  and 7d post caudal fin removal  and analyzed the molecular mechanism of caudal fin regeneration from the perspective of the whole transcriptome. Results: We observed that the amputated caudal fin went through a complex genetic change  especially at 3 dpa. This result showed that genes related to response to cell cycle and wounding might play a role in caudal fin regeneration.The up regulated DEGs at 3 dpa blastema outgrowth stage were dramatically enriched in 20 Biological Processes FDR < 0.05  three of which were cell cycle GO:0007049  mitotic cell cycle GO:0000278  and cell cycle process GO:0022402  one was response to wounding GO:0009611  etc. Conclusion: Taken together  the results revealed that the DEGs were enriched in numerous biological processes  molecular function  cellular component  and signaling pathways  suggesting that the caudal fin regeneration is a highly complicated process of the molecular mechanism. Overall design: Caudal fin RNA profiles of  test and control samples were generated by deep sequencing  using Illumina HiSeq 4000.,,pubmed:33186559;pubmed:36012210,,T7dpa 2,GSM4885970,,source name:caudal fin|treatment:caudal fin removal|time:7dpa|tissue:caudal fin regenerating,T7dpa 2,Basecalls performed using  Solexa pipeline v1.8 The trimmed reads trimmed 5’ 3’ adaptor bases using cutadapt were aligned to reference genome using tophat2 version 2.0.3.12software The transcript abundances for each sample was estimated with RSEM the FPKM value for gene and transcript level were calculated with R package edgeR The circRNA reads were aligned to reference genome using tophat2detecting backesplicec junction reads with find circ Genome build: Homo sapiens hg38 Supplementary files format and content: circRNA matrix.txt  lncRNA matrix.txt  mRNA matrix.txt,caudal fin,Wild type zebrafish were kept in a closed recirculating aquacultural system.The intact caudal fins CK0dpa were used as control and the regenerated caudal fins at corresponding stages T3dpa and T7dpa were used as treatment group.,RNA quality and quantity was measured by using nanodrop spectrophotometer ND 1000  Nanodrop Technologies and RNA Integrity was determined by gel electrophoresis Total RNA of each sample was used to prepare the RNA sequencing library 1RNA fragment；2Random primed first strand cDNA synthesis；3dUTP based second strand cDNA synthesis;4Adaptor ligation and PCR amplification.,Wild type zebrafish were kept in a closed recirculating aquacultural system.,treatment:caudal fin removal|time:7dpa|tissue:caudal fin regenerating,GSM4885970,GSM4885970: T7dpa 2; Danio rerio; RNA Seq,GSM4885970,,1,RNA quality and quantity was measured by using nanodrop spectrophotometer ND 1000  Nanodrop Technologies and RNA Integrity was determined by gel electrophoresis Total RNA of each sample was used to prepare the RNA sequencing library 1RNA fragment；2Random primed first strand cDNA synthesis；3dUTP based second strand cDNA synthesis;4Adaptor ligation and PCR amplification.,GEO Accession:GSM4885970,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP291307,,,S263_genedenovo-A_R1811233_AHC7LKDSXX_S263_L004_R1_001.fastq.gz S263_genedenovo-A_R1811233_AHC7LKDSXX_S263_L004_R2_001.fastq.gz,fastq fastq,12553836900.0,41846123.0,GSM4885970 r1,0:150 1:150,A:2974063075;C:3268655930;G:3245156586;T:3065829642;N:131667,150,150,,,2974063075,3268655930,3245156586,3065829642,131667,SRX9443937,SRS7657862,SRA1154680,GEO,henan normal university,2,0.92648,0.92763,0.23042,0.22406,0.73919,0.73896,0.56022,0.55741,150,150,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,bulk,unknown,unknown,,China,2020-11-05,Undetermined,Undetermined,Fin,Surface Structure
61817,SRR12992436,SRX9443936,SRS7657860,SRP291307,PRJNA674824,Research on Molecular Mechanism of Zebrafish Caudal Fin Regeneration Based on Whole Transcriptome Technology,GSE160909,Transcriptome Analysis,Background/Aims:The ability of regeneration varies widely from invertebrates to vertebrates. Some animals  for example  flatworms  newts  salamanders  and lower vertebrates have the outstanding ability to regenerate all the organs even the whole individual. Unfortunately  the regenerative capacity of humans extremely attenuates along with the biological evolution and this makes it difficult for humans to recover from damaged or missing organs or tissues  and even cause serious loss of function or death. However  the research on regeneration mechanisms is limited and incomplete so far. Here  we investigated the biological mechanisms of zebrafish caudal fin regeneration. Methods:The zebrafish was used as the research object to analyze the differences of mRNA and ncRNA expressed in new tissues at 0d  3d  and 7d post caudal fin removal  and analyzed the molecular mechanism of caudal fin regeneration from the perspective of the whole transcriptome. Results: We observed that the amputated caudal fin went through a complex genetic change  especially at 3 dpa. This result showed that genes related to response to cell cycle and wounding might play a role in caudal fin regeneration.The up regulated DEGs at 3 dpa blastema outgrowth stage were dramatically enriched in 20 Biological Processes FDR < 0.05  three of which were cell cycle GO:0007049  mitotic cell cycle GO:0000278  and cell cycle process GO:0022402  one was response to wounding GO:0009611  etc. Conclusion: Taken together  the results revealed that the DEGs were enriched in numerous biological processes  molecular function  cellular component  and signaling pathways  suggesting that the caudal fin regeneration is a highly complicated process of the molecular mechanism. Overall design: Caudal fin RNA profiles of  test and control samples were generated by deep sequencing  using Illumina HiSeq 4000.,,pubmed:33186559;pubmed:36012210,,T7dpa 1,GSM4885969,,source name:caudal fin|treatment:caudal fin removal|time:7dpa|tissue:caudal fin regenerating,T7dpa 1,Basecalls performed using  Solexa pipeline v1.8 The trimmed reads trimmed 5’ 3’ adaptor bases using cutadapt were aligned to reference genome using tophat2 version 2.0.3.12software The transcript abundances for each sample was estimated with RSEM the FPKM value for gene and transcript level were calculated with R package edgeR The circRNA reads were aligned to reference genome using tophat2detecting backesplicec junction reads with find circ Genome build: Homo sapiens hg38 Supplementary files format and content: circRNA matrix.txt  lncRNA matrix.txt  mRNA matrix.txt,caudal fin,Wild type zebrafish were kept in a closed recirculating aquacultural system.The intact caudal fins CK0dpa were used as control and the regenerated caudal fins at corresponding stages T3dpa and T7dpa were used as treatment group.,RNA quality and quantity was measured by using nanodrop spectrophotometer ND 1000  Nanodrop Technologies and RNA Integrity was determined by gel electrophoresis Total RNA of each sample was used to prepare the RNA sequencing library 1RNA fragment；2Random primed first strand cDNA synthesis；3dUTP based second strand cDNA synthesis;4Adaptor ligation and PCR amplification.,Wild type zebrafish were kept in a closed recirculating aquacultural system.,treatment:caudal fin removal|time:7dpa|tissue:caudal fin regenerating,GSM4885969,GSM4885969: T7dpa 1; Danio rerio; RNA Seq,GSM4885969,,1,RNA quality and quantity was measured by using nanodrop spectrophotometer ND 1000  Nanodrop Technologies and RNA Integrity was determined by gel electrophoresis Total RNA of each sample was used to prepare the RNA sequencing library 1RNA fragment；2Random primed first strand cDNA synthesis；3dUTP based second strand cDNA synthesis;4Adaptor ligation and PCR amplification.,GEO Accession:GSM4885969,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP291307,,,S262_genedenovo-A_R1811232_AHC7LKDSXX_S262_L004_R1_001.fastq.gz S262_genedenovo-A_R1811232_AHC7LKDSXX_S262_L004_R2_001.fastq.gz,fastq fastq,12867986100.0,42893287.0,GSM4885969 r1,0:150 1:150,A:3030197180;C:3372068802;G:3344406440;T:3121182317;N:131361,150,150,,,3030197180,3372068802,3344406440,3121182317,131361,SRX9443936,SRS7657860,SRA1154680,GEO,henan normal university,2,0.92201,0.92284,0.23167,0.22408,0.73852,0.73687,0.5658,0.57391,150,150,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,bulk,unknown,unknown,,China,2020-11-05,Undetermined,Undetermined,Fin,Surface Structure
61818,SRR12992435,SRX9443935,SRS7657859,SRP291307,PRJNA674824,Research on Molecular Mechanism of Zebrafish Caudal Fin Regeneration Based on Whole Transcriptome Technology,GSE160909,Transcriptome Analysis,Background/Aims:The ability of regeneration varies widely from invertebrates to vertebrates. Some animals  for example  flatworms  newts  salamanders  and lower vertebrates have the outstanding ability to regenerate all the organs even the whole individual. Unfortunately  the regenerative capacity of humans extremely attenuates along with the biological evolution and this makes it difficult for humans to recover from damaged or missing organs or tissues  and even cause serious loss of function or death. However  the research on regeneration mechanisms is limited and incomplete so far. Here  we investigated the biological mechanisms of zebrafish caudal fin regeneration. Methods:The zebrafish was used as the research object to analyze the differences of mRNA and ncRNA expressed in new tissues at 0d  3d  and 7d post caudal fin removal  and analyzed the molecular mechanism of caudal fin regeneration from the perspective of the whole transcriptome. Results: We observed that the amputated caudal fin went through a complex genetic change  especially at 3 dpa. This result showed that genes related to response to cell cycle and wounding might play a role in caudal fin regeneration.The up regulated DEGs at 3 dpa blastema outgrowth stage were dramatically enriched in 20 Biological Processes FDR < 0.05  three of which were cell cycle GO:0007049  mitotic cell cycle GO:0000278  and cell cycle process GO:0022402  one was response to wounding GO:0009611  etc. Conclusion: Taken together  the results revealed that the DEGs were enriched in numerous biological processes  molecular function  cellular component  and signaling pathways  suggesting that the caudal fin regeneration is a highly complicated process of the molecular mechanism. Overall design: Caudal fin RNA profiles of  test and control samples were generated by deep sequencing  using Illumina HiSeq 4000.,,pubmed:33186559;pubmed:36012210,,T3dpa 3,GSM4885968,,source name:caudal fin|treatment:caudal fin removal|time:3dpa|tissue:caudal fin regenerating,T3dpa 3,Basecalls performed using  Solexa pipeline v1.8 The trimmed reads trimmed 5’ 3’ adaptor bases using cutadapt were aligned to reference genome using tophat2 version 2.0.3.12software The transcript abundances for each sample was estimated with RSEM the FPKM value for gene and transcript level were calculated with R package edgeR The circRNA reads were aligned to reference genome using tophat2detecting backesplicec junction reads with find circ Genome build: Homo sapiens hg38 Supplementary files format and content: circRNA matrix.txt  lncRNA matrix.txt  mRNA matrix.txt,caudal fin,Wild type zebrafish were kept in a closed recirculating aquacultural system.The intact caudal fins CK0dpa were used as control and the regenerated caudal fins at corresponding stages T3dpa and T7dpa were used as treatment group.,RNA quality and quantity was measured by using nanodrop spectrophotometer ND 1000  Nanodrop Technologies and RNA Integrity was determined by gel electrophoresis Total RNA of each sample was used to prepare the RNA sequencing library 1RNA fragment；2Random primed first strand cDNA synthesis；3dUTP based second strand cDNA synthesis;4Adaptor ligation and PCR amplification.,Wild type zebrafish were kept in a closed recirculating aquacultural system.,treatment:caudal fin removal|time:3dpa|tissue:caudal fin regenerating,GSM4885968,GSM4885968: T3dpa 3; Danio rerio; RNA Seq,GSM4885968,,1,RNA quality and quantity was measured by using nanodrop spectrophotometer ND 1000  Nanodrop Technologies and RNA Integrity was determined by gel electrophoresis Total RNA of each sample was used to prepare the RNA sequencing library 1RNA fragment；2Random primed first strand cDNA synthesis；3dUTP based second strand cDNA synthesis;4Adaptor ligation and PCR amplification.,GEO Accession:GSM4885968,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP291307,,,S261_genedenovo-A_R1811231_AHC7LKDSXX_S261_L004_R1_001.fastq.gz S261_genedenovo-A_R1811231_AHC7LKDSXX_S261_L004_R2_001.fastq.gz,fastq fastq,13404565200.0,44681884.0,GSM4885968 r1,0:150 1:150,A:3165812694;C:3493599548;G:3480697330;T:3264316492;N:139136,150,150,,,3165812694,3493599548,3480697330,3264316492,139136,SRX9443935,SRS7657859,SRA1154680,GEO,henan normal university,2,0.87706,0.87858,0.2108,0.20461,0.7405,0.74048,0.53977,0.5707,150,150,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,bulk,unknown,unknown,,China,2020-11-05,Undetermined,Undetermined,Fin,Surface Structure
61819,SRR12992434,SRX9443934,SRS7657858,SRP291307,PRJNA674824,Research on Molecular Mechanism of Zebrafish Caudal Fin Regeneration Based on Whole Transcriptome Technology,GSE160909,Transcriptome Analysis,Background/Aims:The ability of regeneration varies widely from invertebrates to vertebrates. Some animals  for example  flatworms  newts  salamanders  and lower vertebrates have the outstanding ability to regenerate all the organs even the whole individual. Unfortunately  the regenerative capacity of humans extremely attenuates along with the biological evolution and this makes it difficult for humans to recover from damaged or missing organs or tissues  and even cause serious loss of function or death. However  the research on regeneration mechanisms is limited and incomplete so far. Here  we investigated the biological mechanisms of zebrafish caudal fin regeneration. Methods:The zebrafish was used as the research object to analyze the differences of mRNA and ncRNA expressed in new tissues at 0d  3d  and 7d post caudal fin removal  and analyzed the molecular mechanism of caudal fin regeneration from the perspective of the whole transcriptome. Results: We observed that the amputated caudal fin went through a complex genetic change  especially at 3 dpa. This result showed that genes related to response to cell cycle and wounding might play a role in caudal fin regeneration.The up regulated DEGs at 3 dpa blastema outgrowth stage were dramatically enriched in 20 Biological Processes FDR < 0.05  three of which were cell cycle GO:0007049  mitotic cell cycle GO:0000278  and cell cycle process GO:0022402  one was response to wounding GO:0009611  etc. Conclusion: Taken together  the results revealed that the DEGs were enriched in numerous biological processes  molecular function  cellular component  and signaling pathways  suggesting that the caudal fin regeneration is a highly complicated process of the molecular mechanism. Overall design: Caudal fin RNA profiles of  test and control samples were generated by deep sequencing  using Illumina HiSeq 4000.,,pubmed:33186559;pubmed:36012210,,T3dpa 2,GSM4885967,,source name:caudal fin|treatment:caudal fin removal|time:3dpa|tissue:caudal fin regenerating,T3dpa 2,Basecalls performed using  Solexa pipeline v1.8 The trimmed reads trimmed 5’ 3’ adaptor bases using cutadapt were aligned to reference genome using tophat2 version 2.0.3.12software The transcript abundances for each sample was estimated with RSEM the FPKM value for gene and transcript level were calculated with R package edgeR The circRNA reads were aligned to reference genome using tophat2detecting backesplicec junction reads with find circ Genome build: Homo sapiens hg38 Supplementary files format and content: circRNA matrix.txt  lncRNA matrix.txt  mRNA matrix.txt,caudal fin,Wild type zebrafish were kept in a closed recirculating aquacultural system.The intact caudal fins CK0dpa were used as control and the regenerated caudal fins at corresponding stages T3dpa and T7dpa were used as treatment group.,RNA quality and quantity was measured by using nanodrop spectrophotometer ND 1000  Nanodrop Technologies and RNA Integrity was determined by gel electrophoresis Total RNA of each sample was used to prepare the RNA sequencing library 1RNA fragment；2Random primed first strand cDNA synthesis；3dUTP based second strand cDNA synthesis;4Adaptor ligation and PCR amplification.,Wild type zebrafish were kept in a closed recirculating aquacultural system.,treatment:caudal fin removal|time:3dpa|tissue:caudal fin regenerating,GSM4885967,GSM4885967: T3dpa 2; Danio rerio; RNA Seq,GSM4885967,,1,RNA quality and quantity was measured by using nanodrop spectrophotometer ND 1000  Nanodrop Technologies and RNA Integrity was determined by gel electrophoresis Total RNA of each sample was used to prepare the RNA sequencing library 1RNA fragment；2Random primed first strand cDNA synthesis；3dUTP based second strand cDNA synthesis;4Adaptor ligation and PCR amplification.,GEO Accession:GSM4885967,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP291307,,,S260_genedenovo-A_R1811230_AHC7LKDSXX_S260_L004_R1_001.fastq.gz S260_genedenovo-A_R1811230_AHC7LKDSXX_S260_L004_R2_001.fastq.gz,fastq fastq,13176502500.0,43921675.0,GSM4885967 r1,0:150 1:150,A:3157569406;C:3397758315;G:3357831176;T:3263205252;N:138351,150,150,,,3157569406,3397758315,3357831176,3263205252,138351,SRX9443934,SRS7657858,SRA1154680,GEO,henan normal university,2,0.91253,0.91362,0.26776,0.26094,0.73679,0.73484,0.56223,0.57213,150,150,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,bulk,unknown,unknown,,China,2020-11-05,Undetermined,Undetermined,Fin,Surface Structure
61820,SRR12992433,SRX9443933,SRS7657857,SRP291307,PRJNA674824,Research on Molecular Mechanism of Zebrafish Caudal Fin Regeneration Based on Whole Transcriptome Technology,GSE160909,Transcriptome Analysis,Background/Aims:The ability of regeneration varies widely from invertebrates to vertebrates. Some animals  for example  flatworms  newts  salamanders  and lower vertebrates have the outstanding ability to regenerate all the organs even the whole individual. Unfortunately  the regenerative capacity of humans extremely attenuates along with the biological evolution and this makes it difficult for humans to recover from damaged or missing organs or tissues  and even cause serious loss of function or death. However  the research on regeneration mechanisms is limited and incomplete so far. Here  we investigated the biological mechanisms of zebrafish caudal fin regeneration. Methods:The zebrafish was used as the research object to analyze the differences of mRNA and ncRNA expressed in new tissues at 0d  3d  and 7d post caudal fin removal  and analyzed the molecular mechanism of caudal fin regeneration from the perspective of the whole transcriptome. Results: We observed that the amputated caudal fin went through a complex genetic change  especially at 3 dpa. This result showed that genes related to response to cell cycle and wounding might play a role in caudal fin regeneration.The up regulated DEGs at 3 dpa blastema outgrowth stage were dramatically enriched in 20 Biological Processes FDR < 0.05  three of which were cell cycle GO:0007049  mitotic cell cycle GO:0000278  and cell cycle process GO:0022402  one was response to wounding GO:0009611  etc. Conclusion: Taken together  the results revealed that the DEGs were enriched in numerous biological processes  molecular function  cellular component  and signaling pathways  suggesting that the caudal fin regeneration is a highly complicated process of the molecular mechanism. Overall design: Caudal fin RNA profiles of  test and control samples were generated by deep sequencing  using Illumina HiSeq 4000.,,pubmed:33186559;pubmed:36012210,,T3dpa 1,GSM4885966,,source name:caudal fin|treatment:caudal fin removal|time:3dpa|tissue:caudal fin regenerating,T3dpa 1,Basecalls performed using  Solexa pipeline v1.8 The trimmed reads trimmed 5’ 3’ adaptor bases using cutadapt were aligned to reference genome using tophat2 version 2.0.3.12software The transcript abundances for each sample was estimated with RSEM the FPKM value for gene and transcript level were calculated with R package edgeR The circRNA reads were aligned to reference genome using tophat2detecting backesplicec junction reads with find circ Genome build: Homo sapiens hg38 Supplementary files format and content: circRNA matrix.txt  lncRNA matrix.txt  mRNA matrix.txt,caudal fin,Wild type zebrafish were kept in a closed recirculating aquacultural system.The intact caudal fins CK0dpa were used as control and the regenerated caudal fins at corresponding stages T3dpa and T7dpa were used as treatment group.,RNA quality and quantity was measured by using nanodrop spectrophotometer ND 1000  Nanodrop Technologies and RNA Integrity was determined by gel electrophoresis Total RNA of each sample was used to prepare the RNA sequencing library 1RNA fragment；2Random primed first strand cDNA synthesis；3dUTP based second strand cDNA synthesis;4Adaptor ligation and PCR amplification.,Wild type zebrafish were kept in a closed recirculating aquacultural system.,treatment:caudal fin removal|time:3dpa|tissue:caudal fin regenerating,GSM4885966,GSM4885966: T3dpa 1; Danio rerio; RNA Seq,GSM4885966,,1,RNA quality and quantity was measured by using nanodrop spectrophotometer ND 1000  Nanodrop Technologies and RNA Integrity was determined by gel electrophoresis Total RNA of each sample was used to prepare the RNA sequencing library 1RNA fragment；2Random primed first strand cDNA synthesis；3dUTP based second strand cDNA synthesis;4Adaptor ligation and PCR amplification.,GEO Accession:GSM4885966,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP291307,,,S259_genedenovo-A_R1811229_AHC7LKDSXX_S259_L004_R1_001.fastq.gz S259_genedenovo-A_R1811229_AHC7LKDSXX_S259_L004_R2_001.fastq.gz,fastq fastq,13480211400.0,44934038.0,GSM4885966 r1,0:150 1:150,A:3210397485;C:3465436442;G:3477077735;T:3327162280;N:137458,150,150,,,3210397485,3465436442,3477077735,3327162280,137458,SRX9443933,SRS7657857,SRA1154680,GEO,henan normal university,2,0.90619,0.90739,0.26762,0.26385,0.73783,0.73701,0.58215,0.59258,150,150,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,bulk,unknown,unknown,,China,2020-11-05,Undetermined,Undetermined,Fin,Surface Structure
61821,SRR12992432,SRX9443932,SRS7657856,SRP291307,PRJNA674824,Research on Molecular Mechanism of Zebrafish Caudal Fin Regeneration Based on Whole Transcriptome Technology,GSE160909,Transcriptome Analysis,Background/Aims:The ability of regeneration varies widely from invertebrates to vertebrates. Some animals  for example  flatworms  newts  salamanders  and lower vertebrates have the outstanding ability to regenerate all the organs even the whole individual. Unfortunately  the regenerative capacity of humans extremely attenuates along with the biological evolution and this makes it difficult for humans to recover from damaged or missing organs or tissues  and even cause serious loss of function or death. However  the research on regeneration mechanisms is limited and incomplete so far. Here  we investigated the biological mechanisms of zebrafish caudal fin regeneration. Methods:The zebrafish was used as the research object to analyze the differences of mRNA and ncRNA expressed in new tissues at 0d  3d  and 7d post caudal fin removal  and analyzed the molecular mechanism of caudal fin regeneration from the perspective of the whole transcriptome. Results: We observed that the amputated caudal fin went through a complex genetic change  especially at 3 dpa. This result showed that genes related to response to cell cycle and wounding might play a role in caudal fin regeneration.The up regulated DEGs at 3 dpa blastema outgrowth stage were dramatically enriched in 20 Biological Processes FDR < 0.05  three of which were cell cycle GO:0007049  mitotic cell cycle GO:0000278  and cell cycle process GO:0022402  one was response to wounding GO:0009611  etc. Conclusion: Taken together  the results revealed that the DEGs were enriched in numerous biological processes  molecular function  cellular component  and signaling pathways  suggesting that the caudal fin regeneration is a highly complicated process of the molecular mechanism. Overall design: Caudal fin RNA profiles of  test and control samples were generated by deep sequencing  using Illumina HiSeq 4000.,,pubmed:33186559;pubmed:36012210,,CK0dpa 3,GSM4885965,,source name:caudal fin|treatment:control|time:0dpa|tissue:caudal fin,CK0dpa 3,Basecalls performed using  Solexa pipeline v1.8 The trimmed reads trimmed 5’ 3’ adaptor bases using cutadapt were aligned to reference genome using tophat2 version 2.0.3.12software The transcript abundances for each sample was estimated with RSEM the FPKM value for gene and transcript level were calculated with R package edgeR The circRNA reads were aligned to reference genome using tophat2detecting backesplicec junction reads with find circ Genome build: Homo sapiens hg38 Supplementary files format and content: circRNA matrix.txt  lncRNA matrix.txt  mRNA matrix.txt,caudal fin,Wild type zebrafish were kept in a closed recirculating aquacultural system.The intact caudal fins CK0dpa were used as control and the regenerated caudal fins at corresponding stages T3dpa and T7dpa were used as treatment group.,RNA quality and quantity was measured by using nanodrop spectrophotometer ND 1000  Nanodrop Technologies and RNA Integrity was determined by gel electrophoresis Total RNA of each sample was used to prepare the RNA sequencing library 1RNA fragment；2Random primed first strand cDNA synthesis；3dUTP based second strand cDNA synthesis;4Adaptor ligation and PCR amplification.,Wild type zebrafish were kept in a closed recirculating aquacultural system.,treatment:control|time:0dpa|tissue:caudal fin,GSM4885965,GSM4885965: CK0dpa 3; Danio rerio; RNA Seq,GSM4885965,,1,RNA quality and quantity was measured by using nanodrop spectrophotometer ND 1000  Nanodrop Technologies and RNA Integrity was determined by gel electrophoresis Total RNA of each sample was used to prepare the RNA sequencing library 1RNA fragment；2Random primed first strand cDNA synthesis；3dUTP based second strand cDNA synthesis;4Adaptor ligation and PCR amplification.,GEO Accession:GSM4885965,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP291307,,,S258_genedenovo-A_R1811228_AHC7LKDSXX_S258_L004_R1_001.fastq.gz S258_genedenovo-A_R1811228_AHC7LKDSXX_S258_L004_R2_001.fastq.gz,fastq fastq,12742695600.0,42475652.0,GSM4885965 r1,0:150 1:150,A:2969763948;C:3366446465;G:3332669632;T:3073684859;N:130696,150,150,,,2969763948,3366446465,3332669632,3073684859,130696,SRX9443932,SRS7657856,SRA1154680,GEO,henan normal university,2,0.9139,0.91439,0.25211,0.24406,0.74004,0.73848,0.58121,0.59455,150,150,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,bulk,unknown,unknown,,China,2020-11-05,Undetermined,Undetermined,Fin,Surface Structure
61822,SRR12992431,SRX9443931,SRS7657855,SRP291307,PRJNA674824,Research on Molecular Mechanism of Zebrafish Caudal Fin Regeneration Based on Whole Transcriptome Technology,GSE160909,Transcriptome Analysis,Background/Aims:The ability of regeneration varies widely from invertebrates to vertebrates. Some animals  for example  flatworms  newts  salamanders  and lower vertebrates have the outstanding ability to regenerate all the organs even the whole individual. Unfortunately  the regenerative capacity of humans extremely attenuates along with the biological evolution and this makes it difficult for humans to recover from damaged or missing organs or tissues  and even cause serious loss of function or death. However  the research on regeneration mechanisms is limited and incomplete so far. Here  we investigated the biological mechanisms of zebrafish caudal fin regeneration. Methods:The zebrafish was used as the research object to analyze the differences of mRNA and ncRNA expressed in new tissues at 0d  3d  and 7d post caudal fin removal  and analyzed the molecular mechanism of caudal fin regeneration from the perspective of the whole transcriptome. Results: We observed that the amputated caudal fin went through a complex genetic change  especially at 3 dpa. This result showed that genes related to response to cell cycle and wounding might play a role in caudal fin regeneration.The up regulated DEGs at 3 dpa blastema outgrowth stage were dramatically enriched in 20 Biological Processes FDR < 0.05  three of which were cell cycle GO:0007049  mitotic cell cycle GO:0000278  and cell cycle process GO:0022402  one was response to wounding GO:0009611  etc. Conclusion: Taken together  the results revealed that the DEGs were enriched in numerous biological processes  molecular function  cellular component  and signaling pathways  suggesting that the caudal fin regeneration is a highly complicated process of the molecular mechanism. Overall design: Caudal fin RNA profiles of  test and control samples were generated by deep sequencing  using Illumina HiSeq 4000.,,pubmed:33186559;pubmed:36012210,,CK0dpa 2,GSM4885964,,source name:caudal fin|treatment:control|time:0dpa|tissue:caudal fin,CK0dpa 2,Basecalls performed using  Solexa pipeline v1.8 The trimmed reads trimmed 5’ 3’ adaptor bases using cutadapt were aligned to reference genome using tophat2 version 2.0.3.12software The transcript abundances for each sample was estimated with RSEM the FPKM value for gene and transcript level were calculated with R package edgeR The circRNA reads were aligned to reference genome using tophat2detecting backesplicec junction reads with find circ Genome build: Homo sapiens hg38 Supplementary files format and content: circRNA matrix.txt  lncRNA matrix.txt  mRNA matrix.txt,caudal fin,Wild type zebrafish were kept in a closed recirculating aquacultural system.The intact caudal fins CK0dpa were used as control and the regenerated caudal fins at corresponding stages T3dpa and T7dpa were used as treatment group.,RNA quality and quantity was measured by using nanodrop spectrophotometer ND 1000  Nanodrop Technologies and RNA Integrity was determined by gel electrophoresis Total RNA of each sample was used to prepare the RNA sequencing library 1RNA fragment；2Random primed first strand cDNA synthesis；3dUTP based second strand cDNA synthesis;4Adaptor ligation and PCR amplification.,Wild type zebrafish were kept in a closed recirculating aquacultural system.,treatment:control|time:0dpa|tissue:caudal fin,GSM4885964,GSM4885964: CK0dpa 2; Danio rerio; RNA Seq,GSM4885964,,1,RNA quality and quantity was measured by using nanodrop spectrophotometer ND 1000  Nanodrop Technologies and RNA Integrity was determined by gel electrophoresis Total RNA of each sample was used to prepare the RNA sequencing library 1RNA fragment；2Random primed first strand cDNA synthesis；3dUTP based second strand cDNA synthesis;4Adaptor ligation and PCR amplification.,GEO Accession:GSM4885964,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP291307,,,S224_genedenovo-A_R1811236_AHC7LKDSXX_S224_L003_R1_001.fastq.gz S224_genedenovo-A_R1811236_AHC7LKDSXX_S224_L003_R2_001.fastq.gz,fastq fastq,11646387000.0,38821290.0,GSM4885964 r1,0:150 1:150,A:2714196007;C:3087288491;G:3040814103;T:2787181254;N:16907145,150,150,,,2714196007,3087288491,3040814103,2787181254,16907145,SRX9443931,SRS7657855,SRA1154680,GEO,henan normal university,2,0.92159,0.9116,0.24217,0.23137,0.74085,0.74675,0.58904,0.59851,150,150,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,bulk,unknown,unknown,,China,2020-11-05,Undetermined,Undetermined,Fin,Surface Structure
61823,SRR12992430,SRX9443930,SRS7657854,SRP291307,PRJNA674824,Research on Molecular Mechanism of Zebrafish Caudal Fin Regeneration Based on Whole Transcriptome Technology,GSE160909,Transcriptome Analysis,Background/Aims:The ability of regeneration varies widely from invertebrates to vertebrates. Some animals  for example  flatworms  newts  salamanders  and lower vertebrates have the outstanding ability to regenerate all the organs even the whole individual. Unfortunately  the regenerative capacity of humans extremely attenuates along with the biological evolution and this makes it difficult for humans to recover from damaged or missing organs or tissues  and even cause serious loss of function or death. However  the research on regeneration mechanisms is limited and incomplete so far. Here  we investigated the biological mechanisms of zebrafish caudal fin regeneration. Methods:The zebrafish was used as the research object to analyze the differences of mRNA and ncRNA expressed in new tissues at 0d  3d  and 7d post caudal fin removal  and analyzed the molecular mechanism of caudal fin regeneration from the perspective of the whole transcriptome. Results: We observed that the amputated caudal fin went through a complex genetic change  especially at 3 dpa. This result showed that genes related to response to cell cycle and wounding might play a role in caudal fin regeneration.The up regulated DEGs at 3 dpa blastema outgrowth stage were dramatically enriched in 20 Biological Processes FDR < 0.05  three of which were cell cycle GO:0007049  mitotic cell cycle GO:0000278  and cell cycle process GO:0022402  one was response to wounding GO:0009611  etc. Conclusion: Taken together  the results revealed that the DEGs were enriched in numerous biological processes  molecular function  cellular component  and signaling pathways  suggesting that the caudal fin regeneration is a highly complicated process of the molecular mechanism. Overall design: Caudal fin RNA profiles of  test and control samples were generated by deep sequencing  using Illumina HiSeq 4000.,,pubmed:33186559;pubmed:36012210,,CK0dpa 1,GSM4885963,,source name:caudal fin|treatment:control|time:0dpa|tissue:caudal fin,CK0dpa 1,Basecalls performed using  Solexa pipeline v1.8 The trimmed reads trimmed 5’ 3’ adaptor bases using cutadapt were aligned to reference genome using tophat2 version 2.0.3.12software The transcript abundances for each sample was estimated with RSEM the FPKM value for gene and transcript level were calculated with R package edgeR The circRNA reads were aligned to reference genome using tophat2detecting backesplicec junction reads with find circ Genome build: Homo sapiens hg38 Supplementary files format and content: circRNA matrix.txt  lncRNA matrix.txt  mRNA matrix.txt,caudal fin,Wild type zebrafish were kept in a closed recirculating aquacultural system.The intact caudal fins CK0dpa were used as control and the regenerated caudal fins at corresponding stages T3dpa and T7dpa were used as treatment group.,RNA quality and quantity was measured by using nanodrop spectrophotometer ND 1000  Nanodrop Technologies and RNA Integrity was determined by gel electrophoresis Total RNA of each sample was used to prepare the RNA sequencing library 1RNA fragment；2Random primed first strand cDNA synthesis；3dUTP based second strand cDNA synthesis;4Adaptor ligation and PCR amplification.,Wild type zebrafish were kept in a closed recirculating aquacultural system.,treatment:control|time:0dpa|tissue:caudal fin,GSM4885963,GSM4885963: CK0dpa 1; Danio rerio; RNA Seq,GSM4885963,,1,RNA quality and quantity was measured by using nanodrop spectrophotometer ND 1000  Nanodrop Technologies and RNA Integrity was determined by gel electrophoresis Total RNA of each sample was used to prepare the RNA sequencing library 1RNA fragment；2Random primed first strand cDNA synthesis；3dUTP based second strand cDNA synthesis;4Adaptor ligation and PCR amplification.,GEO Accession:GSM4885963,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP291307,,,S007_genedenovo-A_R1811234_BHCC73DSXX_S7_L001_R1_001.fastq.gz S007_genedenovo-A_R1811234_BHCC73DSXX_S7_L001_R2_001.fastq.gz,fastq fastq,12627858000.0,42092860.0,GSM4885963 r1,0:150 1:150,A:2888575589;C:3404253059;G:3330717549;T:3004195375;N:116428,150,150,,,2888575589,3404253059,3330717549,3004195375,116428,SRX9443930,SRS7657854,SRA1154680,GEO,henan normal university,2,0.91825,0.91794,0.23296,0.22408,0.73981,0.74052,0.59202,0.58426,150,150,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,bulk,unknown,unknown,,China,2020-11-05,Undetermined,Undetermined,Fin,Surface Structure
66795,SRR16604670,SRX12805808,SRS10751269,SRP343527,PRJNA775662,Regulation of fin regeneration by a voltage gated sodium channel,GSE186729,Transcriptome Analysis,We compare the brain and fin RNA seq profiles of wild type and scn8ab mutant zebrafish  which exhibit locomotion and fin regeneration defects. Overall design: Biological duplicate brain and fin profiles of adult wild type sibling and scn8abtemca mutant zebrafish. Corresponding sample pools include: whole brain of wild type siblings and temca mutants and uninjured and 36 hpa fins of wild type siblings and temca mutants at the restrictive temperature 33 degrees,,,,Fin uninjured control 2,GSM5660160,,source name:Fin uninjured control|strain:Ekkwill|genotype:wild type|treatment:Uninjured|protocol:33°C for 36 hours|tissue:Uninjured fin,Fin uninjured control 2,Cutadapt to remove adapter sequences and short reads less than 10bp HISAT2 to align to zebrafish GRCz11 reference genome FeatureCount Genome build: GRCz11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample,Fin uninjured control,,Tissues were homogenized in immediately post dissection and RNA was extracted using Trizol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols,,strain:Ekkwill|genotype:wild type|treatment:Uninjured|protocol:33°C for 36 hours|tissue:Uninjured fin,GSM5660160,GSM5660160: Fin uninjured control 2; Danio rerio; RNA Seq,GSM5660160,,1,Tissues were homogenized in immediately post dissection and RNA was extracted using Trizol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM5660160,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP343527,,loader:fastq load.py,UN-HET3_S2_L001_R1_001.fastq.gz UN-HET3_S2_L001_R2_001.fastq.gz,fastq fastq,19459866186.0,64436643.0,GSM5660160 r1,0:151 1:151,A:5049939022;C:4684311321;G:4882183554;T:4843199884;N:232405,151,151,,,5049939022,4684311321,4882183554,4843199884,232405,SRX12805808,SRS10751269,SRA1318866,GEO,"Junsu Kang Lab, Cell and Regenerative Biology, University of Wisconsin-Madison",2,0.94988,0.95024,0.04948,0.04916,0.73736,0.73821,0.44082,0.43999,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2021-10-27,Undetermined,Undetermined,Fin,Surface Structure
66796,SRR16604669,SRX12805807,SRS10751268,SRP343527,PRJNA775662,Regulation of fin regeneration by a voltage gated sodium channel,GSE186729,Transcriptome Analysis,We compare the brain and fin RNA seq profiles of wild type and scn8ab mutant zebrafish  which exhibit locomotion and fin regeneration defects. Overall design: Biological duplicate brain and fin profiles of adult wild type sibling and scn8abtemca mutant zebrafish. Corresponding sample pools include: whole brain of wild type siblings and temca mutants and uninjured and 36 hpa fins of wild type siblings and temca mutants at the restrictive temperature 33 degrees,,,,Fin uninjured control 1,GSM5660159,,source name:Fin uninjured control|strain:Ekkwill|genotype:wild type|treatment:Uninjured|protocol:33°C for 36 hours|tissue:Uninjured fin,Fin uninjured control 1,Cutadapt to remove adapter sequences and short reads less than 10bp HISAT2 to align to zebrafish GRCz11 reference genome FeatureCount Genome build: GRCz11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample,Fin uninjured control,,Tissues were homogenized in immediately post dissection and RNA was extracted using Trizol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols,,strain:Ekkwill|genotype:wild type|treatment:Uninjured|protocol:33°C for 36 hours|tissue:Uninjured fin,GSM5660159,GSM5660159: Fin uninjured control 1; Danio rerio; RNA Seq,GSM5660159,,1,Tissues were homogenized in immediately post dissection and RNA was extracted using Trizol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM5660159,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP343527,,loader:fastq load.py,UN-HET2_S1_L001_R2_001.fastq.gz UN-HET2_S1_L001_R1_001.fastq.gz,fastq fastq,27479475884.0,90991642.0,GSM5660159 r1,0:151 1:151,A:7093156924;C:6670638365;G:6882029592;T:6833331180;N:319823,151,151,,,7093156924,6670638365,6882029592,6833331180,319823,SRX12805807,SRS10751268,SRA1318866,GEO,"Junsu Kang Lab, Cell and Regenerative Biology, University of Wisconsin-Madison",2,0.94831,0.83016,0.04913,0.04202,0.74079,0.75262,0.454,0.44756,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2021-10-27,Undetermined,Undetermined,Fin,Surface Structure
66797,SRR16604668,SRX12805806,SRS10751267,SRP343527,PRJNA775662,Regulation of fin regeneration by a voltage gated sodium channel,GSE186729,Transcriptome Analysis,We compare the brain and fin RNA seq profiles of wild type and scn8ab mutant zebrafish  which exhibit locomotion and fin regeneration defects. Overall design: Biological duplicate brain and fin profiles of adult wild type sibling and scn8abtemca mutant zebrafish. Corresponding sample pools include: whole brain of wild type siblings and temca mutants and uninjured and 36 hpa fins of wild type siblings and temca mutants at the restrictive temperature 33 degrees,,,,Fin uninjured mutant 2,GSM5660158,,source name:Fin uninjured mutant|strain:Ekkwill|genotype:scn8abtemca  / |treatment:Uninjured|protocol:33°C for 36 hours|tissue:Uninjured fin,Fin uninjured mutant 2,Cutadapt to remove adapter sequences and short reads less than 10bp HISAT2 to align to zebrafish GRCz11 reference genome FeatureCount Genome build: GRCz11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample,Fin uninjured mutant,,Tissues were homogenized in immediately post dissection and RNA was extracted using Trizol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols,,strain:Ekkwill|genotype:scn8abtemca  / |treatment:Uninjured|protocol:33°C for 36 hours|tissue:Uninjured fin,GSM5660158,GSM5660158: Fin uninjured mutant 2; Danio rerio; RNA Seq,GSM5660158,,1,Tissues were homogenized in immediately post dissection and RNA was extracted using Trizol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM5660158,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP343527,,loader:fastq load.py,UN-MUT4_S4_L001_R1_001.fastq.gz UN-MUT4_S4_L001_R2_001.fastq.gz,fastq fastq,24620270046.0,81524073.0,GSM5660158 r1,0:151 1:151,A:6316714614;C:6018428543;G:6199001287;T:6085843801;N:281801,151,151,,,6316714614,6018428543,6199001287,6085843801,281801,SRX12805806,SRS10751267,SRA1318866,GEO,"Junsu Kang Lab, Cell and Regenerative Biology, University of Wisconsin-Madison",2,0.95069,0.95088,0.04728,0.04688,0.739,0.73904,0.43884,0.44078,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2021-10-27,Undetermined,Undetermined,Fin,Surface Structure
66798,SRR16604667,SRX12805805,SRS10751266,SRP343527,PRJNA775662,Regulation of fin regeneration by a voltage gated sodium channel,GSE186729,Transcriptome Analysis,We compare the brain and fin RNA seq profiles of wild type and scn8ab mutant zebrafish  which exhibit locomotion and fin regeneration defects. Overall design: Biological duplicate brain and fin profiles of adult wild type sibling and scn8abtemca mutant zebrafish. Corresponding sample pools include: whole brain of wild type siblings and temca mutants and uninjured and 36 hpa fins of wild type siblings and temca mutants at the restrictive temperature 33 degrees,,,,Fin uninjured mutant 1,GSM5660157,,source name:Fin uninjured mutant|strain:Ekkwill|genotype:scn8abtemca  / |treatment:Uninjured|protocol:33°C for 36 hours|tissue:Uninjured fin,Fin uninjured mutant 1,Cutadapt to remove adapter sequences and short reads less than 10bp HISAT2 to align to zebrafish GRCz11 reference genome FeatureCount Genome build: GRCz11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample,Fin uninjured mutant,,Tissues were homogenized in immediately post dissection and RNA was extracted using Trizol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols,,strain:Ekkwill|genotype:scn8abtemca  / |treatment:Uninjured|protocol:33°C for 36 hours|tissue:Uninjured fin,GSM5660157,GSM5660157: Fin uninjured mutant 1; Danio rerio; RNA Seq,GSM5660157,,1,Tissues were homogenized in immediately post dissection and RNA was extracted using Trizol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM5660157,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP343527,,loader:fastq load.py,UN-MUT2_S3_L001_R1_001.fastq.gz UN-MUT2_S3_L001_R2_001.fastq.gz,fastq fastq,24670868636.0,81691618.0,GSM5660157 r1,0:151 1:151,A:6315706878;C:5985978585;G:6229426117;T:6139464652;N:292404,151,151,,,6315706878,5985978585,6229426117,6139464652,292404,SRX12805805,SRS10751266,SRA1318866,GEO,"Junsu Kang Lab, Cell and Regenerative Biology, University of Wisconsin-Madison",2,0.94924,0.94781,0.05071,0.04959,0.73089,0.73129,0.44532,0.44696,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2021-10-27,Undetermined,Undetermined,Fin,Surface Structure
66799,SRR16604666,SRX12805804,SRS10751265,SRP343527,PRJNA775662,Regulation of fin regeneration by a voltage gated sodium channel,GSE186729,Transcriptome Analysis,We compare the brain and fin RNA seq profiles of wild type and scn8ab mutant zebrafish  which exhibit locomotion and fin regeneration defects. Overall design: Biological duplicate brain and fin profiles of adult wild type sibling and scn8abtemca mutant zebrafish. Corresponding sample pools include: whole brain of wild type siblings and temca mutants and uninjured and 36 hpa fins of wild type siblings and temca mutants at the restrictive temperature 33 degrees,,,,Fin 36hpa control 2,GSM5660156,,source name:Fin 36hpa control|strain:Ekkwill|genotype:wild type|treatment:Amputated|protocol:33°C for 36 hours|tissue:Regenerating fin,Fin 36hpa control 2,Cutadapt to remove adapter sequences and short reads less than 10bp HISAT2 to align to zebrafish GRCz11 reference genome FeatureCount Genome build: GRCz11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample,Fin 36hpa control,,Tissues were homogenized in immediately post dissection and RNA was extracted using Trizol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols,,strain:Ekkwill|genotype:wild type|treatment:Amputated|protocol:33°C for 36 hours|tissue:Regenerating fin,GSM5660156,GSM5660156: Fin 36hpa control 2; Danio rerio; RNA Seq,GSM5660156,,1,Tissues were homogenized in immediately post dissection and RNA was extracted using Trizol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM5660156,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP343527,,loader:fastq load.py,36-HET3_S6_L001_R1_001.fastq.gz 36-HET3_S6_L001_R2_001.fastq.gz,fastq fastq,22566569480.0,74723740.0,GSM5660156 r1,0:151 1:151,A:5767936654;C:5525950628;G:5631828938;T:5640587381;N:265879,151,151,,,5767936654,5525950628,5631828938,5640587381,265879,SRX12805804,SRS10751265,SRA1318866,GEO,"Junsu Kang Lab, Cell and Regenerative Biology, University of Wisconsin-Madison",2,0.9628,0.96333,0.04371,0.0431,0.72914,0.7292,0.46321,0.46573,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2021-10-27,Undetermined,Undetermined,Fin,Surface Structure
66800,SRR16604665,SRX12805803,SRS10751264,SRP343527,PRJNA775662,Regulation of fin regeneration by a voltage gated sodium channel,GSE186729,Transcriptome Analysis,We compare the brain and fin RNA seq profiles of wild type and scn8ab mutant zebrafish  which exhibit locomotion and fin regeneration defects. Overall design: Biological duplicate brain and fin profiles of adult wild type sibling and scn8abtemca mutant zebrafish. Corresponding sample pools include: whole brain of wild type siblings and temca mutants and uninjured and 36 hpa fins of wild type siblings and temca mutants at the restrictive temperature 33 degrees,,,,Fin 36hpa control 1,GSM5660155,,source name:Fin 36hpa control|strain:Ekkwill|genotype:wild type|treatment:Amputated|protocol:33°C for 36 hours|tissue:Regenerating fin,Fin 36hpa control 1,Cutadapt to remove adapter sequences and short reads less than 10bp HISAT2 to align to zebrafish GRCz11 reference genome FeatureCount Genome build: GRCz11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample,Fin 36hpa control,,Tissues were homogenized in immediately post dissection and RNA was extracted using Trizol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols,,strain:Ekkwill|genotype:wild type|treatment:Amputated|protocol:33°C for 36 hours|tissue:Regenerating fin,GSM5660155,GSM5660155: Fin 36hpa control 1; Danio rerio; RNA Seq,GSM5660155,,1,Tissues were homogenized in immediately post dissection and RNA was extracted using Trizol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM5660155,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP343527,,loader:fastq load.py,36-HET2_S5_L001_R1_001.fastq.gz 36-HET2_S5_L001_R2_001.fastq.gz,fastq fastq,24278594192.0,80392696.0,GSM5660155 r1,0:151 1:151,A:6236525751;C:5924143928;G:6044955150;T:6072678922;N:290441,151,151,,,6236525751,5924143928,6044955150,6072678922,290441,SRX12805803,SRS10751264,SRA1318866,GEO,"Junsu Kang Lab, Cell and Regenerative Biology, University of Wisconsin-Madison",2,0.96158,0.96225,0.04444,0.04416,0.72573,0.72634,0.4724,0.47335,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2021-10-27,Undetermined,Undetermined,Fin,Surface Structure
66801,SRR16604664,SRX12805802,SRS10751263,SRP343527,PRJNA775662,Regulation of fin regeneration by a voltage gated sodium channel,GSE186729,Transcriptome Analysis,We compare the brain and fin RNA seq profiles of wild type and scn8ab mutant zebrafish  which exhibit locomotion and fin regeneration defects. Overall design: Biological duplicate brain and fin profiles of adult wild type sibling and scn8abtemca mutant zebrafish. Corresponding sample pools include: whole brain of wild type siblings and temca mutants and uninjured and 36 hpa fins of wild type siblings and temca mutants at the restrictive temperature 33 degrees,,,,Fin 36hpa mutant 2,GSM5660154,,source name:Fin 36hpa mutant|strain:Ekkwill|genotype:scn8abtemca  / |treatment:Amputated|protocol:33°C for 36 hours|tissue:Regenerating fin,Fin 36hpa mutant 2,Cutadapt to remove adapter sequences and short reads less than 10bp HISAT2 to align to zebrafish GRCz11 reference genome FeatureCount Genome build: GRCz11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample,Fin 36hpa mutant,,Tissues were homogenized in immediately post dissection and RNA was extracted using Trizol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols,,strain:Ekkwill|genotype:scn8abtemca  / |treatment:Amputated|protocol:33°C for 36 hours|tissue:Regenerating fin,GSM5660154,GSM5660154: Fin 36hpa mutant 2; Danio rerio; RNA Seq,GSM5660154,,1,Tissues were homogenized in immediately post dissection and RNA was extracted using Trizol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM5660154,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP343527,,loader:fastq load.py,36-MUT4_S8_L001_R1_001.fastq.gz 36-MUT4_S8_L001_R2_001.fastq.gz,fastq fastq,23823079740.0,78884370.0,GSM5660154 r1,0:151 1:151,A:6170278427;C:5759242402;G:5864658841;T:6028619789;N:280281,151,151,,,6170278427,5759242402,5864658841,6028619789,280281,SRX12805802,SRS10751263,SRA1318866,GEO,"Junsu Kang Lab, Cell and Regenerative Biology, University of Wisconsin-Madison",2,0.96165,0.96145,0.04415,0.04364,0.72618,0.7261,0.47788,0.4714,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2021-10-27,Undetermined,Undetermined,Fin,Surface Structure
66802,SRR16604663,SRX12805801,SRS10751262,SRP343527,PRJNA775662,Regulation of fin regeneration by a voltage gated sodium channel,GSE186729,Transcriptome Analysis,We compare the brain and fin RNA seq profiles of wild type and scn8ab mutant zebrafish  which exhibit locomotion and fin regeneration defects. Overall design: Biological duplicate brain and fin profiles of adult wild type sibling and scn8abtemca mutant zebrafish. Corresponding sample pools include: whole brain of wild type siblings and temca mutants and uninjured and 36 hpa fins of wild type siblings and temca mutants at the restrictive temperature 33 degrees,,,,Fin 36hpa mutant 1,GSM5660153,,source name:Fin 36hpa mutant|strain:Ekkwill|genotype:scn8abtemca  / |treatment:Amputated|protocol:33°C for 36 hours|tissue:Regenerating fin,Fin 36hpa mutant 1,Cutadapt to remove adapter sequences and short reads less than 10bp HISAT2 to align to zebrafish GRCz11 reference genome FeatureCount Genome build: GRCz11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample,Fin 36hpa mutant,,Tissues were homogenized in immediately post dissection and RNA was extracted using Trizol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols,,strain:Ekkwill|genotype:scn8abtemca  / |treatment:Amputated|protocol:33°C for 36 hours|tissue:Regenerating fin,GSM5660153,GSM5660153: Fin 36hpa mutant 1; Danio rerio; RNA Seq,GSM5660153,,1,Tissues were homogenized in immediately post dissection and RNA was extracted using Trizol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM5660153,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP343527,,loader:fastq load.py,36-MUT2_S7_L001_R1_001.fastq.gz 36-MUT2_S7_L001_R2_001.fastq.gz,fastq fastq,21653872328.0,71701564.0,GSM5660153 r1,0:151 1:151,A:5580243905;C:5261823509;G:5370184364;T:5441361192;N:259358,151,151,,,5580243905,5261823509,5370184364,5441361192,259358,SRX12805801,SRS10751262,SRA1318866,GEO,"Junsu Kang Lab, Cell and Regenerative Biology, University of Wisconsin-Madison",2,0.96165,0.96176,0.04508,0.04415,0.72839,0.72894,0.4695,0.47129,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2021-10-27,Undetermined,Undetermined,Fin,Surface Structure
70206,SRR19572324,SRX15624358,SRS13324587,SRP378897,PRJNA846701,Fin ray branching is defined by TRAP+ osteolytic tubules in zebrafish,GSE205599,Transcriptome Analysis,Study and define how caudal fin rays mineralize and are shaped during regeneration  providing a detailed perspective about its formation and bifurcation and identifying key roles of OLTs. Overall design: Comparative gene expression analysis of regenerating zebrafish fins between 1 and 3 dy post amputation,,,,5 NGS2016020501P116,GSM6215363,,source name:Danio Rerio caudal fin regenerated tissue Control|tissue:caudal fin regenerated tissue|treatment:Control,5 NGS2016020501P116,CLC Genomics Workbench 9.0.1. Sequence reads were trimmed for adaptor sequence/low quality sequence using CLC genomic benchwork parameter  Quality limit: 0.01 Trimmed sequence reads were mapped to GRCz10 using CLC genomic benchwork parameters  mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.95 similarity fraction: 0.95 Read count extraction and normalization were performed using CLC genomic benchwork Assembly: GRCz10 Supplementary files format and content: tab delimited text files include RPKM values for each Sample,Danio Rerio caudal fin regenerated tissue Control,,The regenerated tissue was homogenized and a phenolic extraction was performed as previously described in Chomczynski and Sacchi  2006 Illumina TruSeq Stranded mRNA Library Preparation Kit,,tissue:caudal fin regenerated tissue|treatment:Control,GSM6215363,GSM6215363: 5 NGS2016020501P116; Danio rerio; RNA Seq,GSM6215363 r1,GSM6215363,1,The regenerated tissue was homogenized and a phenolic extraction was performed as previously described in Chomczynski and Sacchi  2006 Illumina TruSeq Stranded mRNA Library Preparation Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP378897,,loader:fastq load.py,5-NGS2016020501P116_R1.fastq.gz 5-NGS2016020501P116_R2.fastq.gz,fastq fastq,4168972133.0,20866510.0,GSM6215363 r1,0:99.68 1:100.11,A:1111900344;C:972434705;G:950907789;T:1133536284;N:193011,99,100,,,1111900344,972434705,950907789,1133536284,193011,SRX15624358,SRS13324587,SRA1433229,"NGS, STAB VIDA","NGS, STAB VIDA",2,0.94915,0.95043,0.08765,0.08617,0.71167,0.71715,0.46955,0.46253,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Portugal,2022-06-07,Undetermined,Undetermined,Fin,Surface Structure
70207,SRR19572325,SRX15624357,SRS13324586,SRP378897,PRJNA846701,Fin ray branching is defined by TRAP+ osteolytic tubules in zebrafish,GSE205599,Transcriptome Analysis,Study and define how caudal fin rays mineralize and are shaped during regeneration  providing a detailed perspective about its formation and bifurcation and identifying key roles of OLTs. Overall design: Comparative gene expression analysis of regenerating zebrafish fins between 1 and 3 dy post amputation,,,,4 NGS2016020501P115,GSM6215362,,source name:Danio Rerio caudal fin regenerated tissue Control|tissue:caudal fin regenerated tissue|treatment:Control,4 NGS2016020501P115,CLC Genomics Workbench 9.0.1. Sequence reads were trimmed for adaptor sequence/low quality sequence using CLC genomic benchwork parameter  Quality limit: 0.01 Trimmed sequence reads were mapped to GRCz10 using CLC genomic benchwork parameters  mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.95 similarity fraction: 0.95 Read count extraction and normalization were performed using CLC genomic benchwork Assembly: GRCz10 Supplementary files format and content: tab delimited text files include RPKM values for each Sample,Danio Rerio caudal fin regenerated tissue Control,,The regenerated tissue was homogenized and a phenolic extraction was performed as previously described in Chomczynski and Sacchi  2006 Illumina TruSeq Stranded mRNA Library Preparation Kit,,tissue:caudal fin regenerated tissue|treatment:Control,GSM6215362,GSM6215362: 4 NGS2016020501P115; Danio rerio; RNA Seq,GSM6215362 r1,GSM6215362,1,The regenerated tissue was homogenized and a phenolic extraction was performed as previously described in Chomczynski and Sacchi  2006 Illumina TruSeq Stranded mRNA Library Preparation Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP378897,,loader:fastq load.py,4-NGS2016020501P115_R1.fastq.gz 4-NGS2016020501P115_R2.fastq.gz,fastq fastq,5106840970.0,25558452.0,GSM6215362 r1,0:99.69 1:100.12,A:1368703272;C:1185689470;G:1163767029;T:1388450304;N:230895,99,100,,,1368703272,1185689470,1163767029,1388450304,230895,SRX15624357,SRS13324586,SRA1433229,"NGS, STAB VIDA","NGS, STAB VIDA",2,0.94362,0.94621,0.09241,0.09066,0.71323,0.71482,0.47513,0.46584,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Portugal,2022-06-07,Undetermined,Undetermined,Fin,Surface Structure
70208,SRR19572326,SRX15624356,SRS13324585,SRP378897,PRJNA846701,Fin ray branching is defined by TRAP+ osteolytic tubules in zebrafish,GSE205599,Transcriptome Analysis,Study and define how caudal fin rays mineralize and are shaped during regeneration  providing a detailed perspective about its formation and bifurcation and identifying key roles of OLTs. Overall design: Comparative gene expression analysis of regenerating zebrafish fins between 1 and 3 dy post amputation,,,,3 NGS2016020501P114,GSM6215361,,source name:Danio Rerio caudal fin regenerated tissue 24h|tissue:caudal fin regenerated tissue|treatment:24h,3 NGS2016020501P114,CLC Genomics Workbench 9.0.1. Sequence reads were trimmed for adaptor sequence/low quality sequence using CLC genomic benchwork parameter  Quality limit: 0.01 Trimmed sequence reads were mapped to GRCz10 using CLC genomic benchwork parameters  mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.95 similarity fraction: 0.95 Read count extraction and normalization were performed using CLC genomic benchwork Assembly: GRCz10 Supplementary files format and content: tab delimited text files include RPKM values for each Sample,Danio Rerio caudal fin regenerated tissue 24h,,The regenerated tissue was homogenized and a phenolic extraction was performed as previously described in Chomczynski and Sacchi  2006 Illumina TruSeq Stranded mRNA Library Preparation Kit,,tissue:caudal fin regenerated tissue|treatment:24h,GSM6215361,GSM6215361: 3 NGS2016020501P114; Danio rerio; RNA Seq,GSM6215361 r1,GSM6215361,1,The regenerated tissue was homogenized and a phenolic extraction was performed as previously described in Chomczynski and Sacchi  2006 Illumina TruSeq Stranded mRNA Library Preparation Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP378897,,loader:fastq load.py,3-NGS2016020501P114_R1.fastq.gz 3-NGS2016020501P114_R2.fastq.gz,fastq fastq,4003530514.0,20036390.0,GSM6215361 r1,0:99.70 1:100.11,A:1077687185;C:925827316;G:905609909;T:1094208566;N:197538,99,100,,,1077687185,925827316,905609909,1094208566,197538,SRX15624356,SRS13324585,SRA1433229,"NGS, STAB VIDA","NGS, STAB VIDA",2,0.94907,0.95225,0.09407,0.09354,0.72476,0.72681,0.48794,0.47815,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Portugal,2022-06-07,Undetermined,Undetermined,Fin,Surface Structure
70209,SRR19572327,SRX15624355,SRS13324583,SRP378897,PRJNA846701,Fin ray branching is defined by TRAP+ osteolytic tubules in zebrafish,GSE205599,Transcriptome Analysis,Study and define how caudal fin rays mineralize and are shaped during regeneration  providing a detailed perspective about its formation and bifurcation and identifying key roles of OLTs. Overall design: Comparative gene expression analysis of regenerating zebrafish fins between 1 and 3 dy post amputation,,,,2 NGS2016020501P113,GSM6215360,,source name:Danio Rerio caudal fin regenerated tissue 24h|tissue:caudal fin regenerated tissue|treatment:24h,2 NGS2016020501P113,CLC Genomics Workbench 9.0.1. Sequence reads were trimmed for adaptor sequence/low quality sequence using CLC genomic benchwork parameter  Quality limit: 0.01 Trimmed sequence reads were mapped to GRCz10 using CLC genomic benchwork parameters  mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.95 similarity fraction: 0.95 Read count extraction and normalization were performed using CLC genomic benchwork Assembly: GRCz10 Supplementary files format and content: tab delimited text files include RPKM values for each Sample,Danio Rerio caudal fin regenerated tissue 24h,,The regenerated tissue was homogenized and a phenolic extraction was performed as previously described in Chomczynski and Sacchi  2006 Illumina TruSeq Stranded mRNA Library Preparation Kit,,tissue:caudal fin regenerated tissue|treatment:24h,GSM6215360,GSM6215360: 2 NGS2016020501P113; Danio rerio; RNA Seq,GSM6215360 r1,GSM6215360,1,The regenerated tissue was homogenized and a phenolic extraction was performed as previously described in Chomczynski and Sacchi  2006 Illumina TruSeq Stranded mRNA Library Preparation Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP378897,,loader:fastq load.py,2-NGS2016020501P113_R1.fastq.gz 2-NGS2016020501P113_R2.fastq.gz,fastq fastq,6010524551.0,30053957.0,GSM6215360 r1,0:99.79 1:100.20,A:1621952736;C:1386940946;G:1353305703;T:1648081487;N:243679,99,100,,,1621952736,1386940946,1353305703,1648081487,243679,SRX15624355,SRS13324583,SRA1433229,"NGS, STAB VIDA","NGS, STAB VIDA",2,0.94314,0.94585,0.09385,0.09216,0.72174,0.72441,0.49514,0.48343,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Portugal,2022-06-07,Undetermined,Undetermined,Fin,Surface Structure
70210,SRR19572328,SRX15624354,SRS13324584,SRP378897,PRJNA846701,Fin ray branching is defined by TRAP+ osteolytic tubules in zebrafish,GSE205599,Transcriptome Analysis,Study and define how caudal fin rays mineralize and are shaped during regeneration  providing a detailed perspective about its formation and bifurcation and identifying key roles of OLTs. Overall design: Comparative gene expression analysis of regenerating zebrafish fins between 1 and 3 dy post amputation,,,,1 NGS2016020501P112,GSM6215359,,source name:Danio Rerio caudal fin regenerated tissue 24h|tissue:caudal fin regenerated tissue|treatment:24h,1 NGS2016020501P112,CLC Genomics Workbench 9.0.1. Sequence reads were trimmed for adaptor sequence/low quality sequence using CLC genomic benchwork parameter  Quality limit: 0.01 Trimmed sequence reads were mapped to GRCz10 using CLC genomic benchwork parameters  mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.95 similarity fraction: 0.95 Read count extraction and normalization were performed using CLC genomic benchwork Assembly: GRCz10 Supplementary files format and content: tab delimited text files include RPKM values for each Sample,Danio Rerio caudal fin regenerated tissue 24h,,The regenerated tissue was homogenized and a phenolic extraction was performed as previously described in Chomczynski and Sacchi  2006 Illumina TruSeq Stranded mRNA Library Preparation Kit,,tissue:caudal fin regenerated tissue|treatment:24h,GSM6215359,GSM6215359: 1 NGS2016020501P112; Danio rerio; RNA Seq,GSM6215359 r1,GSM6215359,1,The regenerated tissue was homogenized and a phenolic extraction was performed as previously described in Chomczynski and Sacchi  2006 Illumina TruSeq Stranded mRNA Library Preparation Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP378897,,loader:fastq load.py,1-NGS2016020501P112_R1.fastq.gz 1-NGS2016020501P112_R2.fastq.gz,fastq fastq,6057446462.0,30269459.0,GSM6215359 r1,0:99.85 1:100.27,A:1647553047;C:1386800169;G:1350820899;T:1671970842;N:301505,99,100,,,1647553047,1386800169,1350820899,1671970842,301505,SRX15624354,SRS13324584,SRA1433229,"NGS, STAB VIDA","NGS, STAB VIDA",2,0.94274,0.94447,0.09517,0.09363,0.7332,0.73499,0.50165,0.50148,101,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Portugal,2022-06-07,Undetermined,Undetermined,Fin,Surface Structure