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
34143,SRR31364121,SRX26737888,SRS23227909,SRP545529,PRJNA1186739,Agouti and BMP signaling drive a naturally occurring fate conversion of melanophores to leucophores in zebrafish,GSE282061,Transcriptome Analysis,The often prominent pigment patterns of vertebrates are varied in form and function and depend on several types of pigment cells derived from embryonic neural crest or latent stem cells of neural crest origin. These cells and the patterns they produce have been useful for uncovering features of differentiation and morphogenesis that underlie adult phenotypes  and they offer opportunities to discover how patterns and the cell types themselves have diversified. In zebrafish  a body pattern of stripes arises by self organizing interactions among three types of pigment cells. Yet these fish also exhibit white ornamentation on their fins that depends on the transdifferentiation of black melanophores to white cells  “melanoleucophores.” To identify mechanisms underlying this conversion we used ultrastrustructural  transcriptomic  mutational and other approaches. Overall design: Zerbrafish dorsal fins were collected from different developmental stages  different fin positions  or post different pharmacological treatments. Cells were isolated and sorted for the presence or absence of tyrp1b:palmmcherry  and analyzed by 10x scRNA seq.,,pubmed:40305763,,dataset3 BMPi LDN RFP,GSM8635057,,source name:dorsal fin|tissue:dorsal fin|genotype:wild type|treatment:LDN|geo loc name:missing|collection date:missing,dataset3 BMPi LDN RFP,We built a zebrafish STAR genome index using Lawson Lab zebrafish transcriptome annotation 46 plus manually annotated entries for mCherry transcript  filtered for protein coding genes. Final cellular barcodes and Unique Molecular Identifiers UMIs were determined using Cell Ranger 6.0.1 10X Genomics and cells were filtered to include only high quality cells. Cell Ranger defaults for selecting cell associated barcodes versus barcodes associated with empty partitions were used. Assembly: GRCz11 Supplementary files format and content: bam and monocle3 RDS,dorsal fin,,Fins were choped to small pieces and isolated with liberase. Digestion was stopped by adding FBS and lysate was filtered and washed with 1xPBS before loading into chips. Cells were captured in a Chromium controller 10X Genomics. Single cell mRNA libraries were prepared using the single cell 3’ solution V3 kit 10X Genomics. Quality control and quantification assays were performed using a Qubit fluorometer ThermoFisher and a 2100 Bioanalyzer Agilent. Libraries were sequenced on an Illumina NextSeq 550 using 75 cycle  high output kits read 1: 26 cycles  i7 Index: 8 cycles  read 2: 57 cycles.,,tissue:dorsal fin|genotype:wild type|treatment:LDN,GSM8635057,GSM8635057: dataset3 BMPi LDN RFP; Danio rerio; RNA Seq,GSM8635057 r1,GSM8635057,1,Fins were choped to small pieces and isolated with liberase. Digestion was stopped by adding FBS and lysate was filtered and washed with 1xPBS before loading into chips. Cells were captured in a Chromium controller 10X Genomics. Single cell mRNA libraries were prepared using the single cell three prime solution V3 kit 10X Genomics. Quality control and quantification assays were performed using a Qubit fluorometer ThermoFisher and a 2100 Bioanalyzer Agilent. Libraries were sequenced on an Illumina NextSeq 550 using 75 cycle  high output kits read 1: 26 cycles  i7 Index: 8 cycles  read 2: 57 cycles.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP545529,,loader:fastq load.py,LDN_RFP_S4_L001_I1_001.fastq.gz LDN_RFP_S4_L001_I2_001.fastq.gz LDN_RFP_S4_L001_R1_001.fastq.gz LDN_RFP_S4_L001_R2_001.fastq.gz,fastq fastq fastq fastq,4755245952.0,34458304.0,GSM8635057 r1,0:10 1:10 2:28 3:90,A:926644119;C:661476939;G:733308280;T:779560094;N:257928,10,10,28,90,926644119,661476939,733308280,779560094,257928,SRX26737888,SRS23227909,SRA2016042,UVA,UVA,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Unknown,2024-11-15,Undetermined,Embryo,Fin,Surface Structure
34144,SRR31364122,SRX26737887,SRS23227908,SRP545529,PRJNA1186739,Agouti and BMP signaling drive a naturally occurring fate conversion of melanophores to leucophores in zebrafish,GSE282061,Transcriptome Analysis,The often prominent pigment patterns of vertebrates are varied in form and function and depend on several types of pigment cells derived from embryonic neural crest or latent stem cells of neural crest origin. These cells and the patterns they produce have been useful for uncovering features of differentiation and morphogenesis that underlie adult phenotypes  and they offer opportunities to discover how patterns and the cell types themselves have diversified. In zebrafish  a body pattern of stripes arises by self organizing interactions among three types of pigment cells. Yet these fish also exhibit white ornamentation on their fins that depends on the transdifferentiation of black melanophores to white cells  “melanoleucophores.” To identify mechanisms underlying this conversion we used ultrastrustructural  transcriptomic  mutational and other approaches. Overall design: Zerbrafish dorsal fins were collected from different developmental stages  different fin positions  or post different pharmacological treatments. Cells were isolated and sorted for the presence or absence of tyrp1b:palmmcherry  and analyzed by 10x scRNA seq.,,pubmed:40305763,,dataset3 BMPi LDN no RFP,GSM8635056,,source name:dorsal fin|tissue:dorsal fin|genotype:wild type|treatment:LDN|geo loc name:missing|collection date:missing,dataset3 BMPi LDN no RFP,We built a zebrafish STAR genome index using Lawson Lab zebrafish transcriptome annotation 46 plus manually annotated entries for mCherry transcript  filtered for protein coding genes. Final cellular barcodes and Unique Molecular Identifiers UMIs were determined using Cell Ranger 6.0.1 10X Genomics and cells were filtered to include only high quality cells. Cell Ranger defaults for selecting cell associated barcodes versus barcodes associated with empty partitions were used. Assembly: GRCz11 Supplementary files format and content: bam and monocle3 RDS,dorsal fin,,Fins were choped to small pieces and isolated with liberase. Digestion was stopped by adding FBS and lysate was filtered and washed with 1xPBS before loading into chips. Cells were captured in a Chromium controller 10X Genomics. Single cell mRNA libraries were prepared using the single cell 3’ solution V3 kit 10X Genomics. Quality control and quantification assays were performed using a Qubit fluorometer ThermoFisher and a 2100 Bioanalyzer Agilent. Libraries were sequenced on an Illumina NextSeq 550 using 75 cycle  high output kits read 1: 26 cycles  i7 Index: 8 cycles  read 2: 57 cycles.,,tissue:dorsal fin|genotype:wild type|treatment:LDN,GSM8635056,GSM8635056: dataset3 BMPi LDN no RFP; Danio rerio; RNA Seq,GSM8635056 r1,GSM8635056,1,Fins were choped to small pieces and isolated with liberase. Digestion was stopped by adding FBS and lysate was filtered and washed with 1xPBS before loading into chips. Cells were captured in a Chromium controller 10X Genomics. Single cell mRNA libraries were prepared using the single cell three prime solution V3 kit 10X Genomics. Quality control and quantification assays were performed using a Qubit fluorometer ThermoFisher and a 2100 Bioanalyzer Agilent. Libraries were sequenced on an Illumina NextSeq 550 using 75 cycle  high output kits read 1: 26 cycles  i7 Index: 8 cycles  read 2: 57 cycles.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP545529,,loader:fastq load.py,LDN_noRFP_S3_L001_I1_001.fastq.gz LDN_noRFP_S3_L001_I2_001.fastq.gz LDN_noRFP_S3_L001_R1_001.fastq.gz LDN_noRFP_S3_L001_R2_001.fastq.gz,fastq fastq fastq fastq,5062759908.0,36686666.0,GSM8635056 r1,0:10 1:10 2:28 3:90,A:992393338;C:660757137;G:728422640;T:919955090;N:271735,10,10,28,90,992393338,660757137,728422640,919955090,271735,SRX26737887,SRS23227908,SRA2016042,UVA,UVA,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Unknown,2024-11-15,Undetermined,Embryo,Fin,Surface Structure
34145,SRR31364123,SRX26737886,SRS23227906,SRP545529,PRJNA1186739,Agouti and BMP signaling drive a naturally occurring fate conversion of melanophores to leucophores in zebrafish,GSE282061,Transcriptome Analysis,The often prominent pigment patterns of vertebrates are varied in form and function and depend on several types of pigment cells derived from embryonic neural crest or latent stem cells of neural crest origin. These cells and the patterns they produce have been useful for uncovering features of differentiation and morphogenesis that underlie adult phenotypes  and they offer opportunities to discover how patterns and the cell types themselves have diversified. In zebrafish  a body pattern of stripes arises by self organizing interactions among three types of pigment cells. Yet these fish also exhibit white ornamentation on their fins that depends on the transdifferentiation of black melanophores to white cells  “melanoleucophores.” To identify mechanisms underlying this conversion we used ultrastrustructural  transcriptomic  mutational and other approaches. Overall design: Zerbrafish dorsal fins were collected from different developmental stages  different fin positions  or post different pharmacological treatments. Cells were isolated and sorted for the presence or absence of tyrp1b:palmmcherry  and analyzed by 10x scRNA seq.,,pubmed:40305763,,dataset3 BMPi DMSO RFP,GSM8635055,,source name:dorsal fin|tissue:dorsal fin|genotype:wild type|treatment:DMSO|geo loc name:missing|collection date:missing,dataset3 BMPi DMSO RFP,We built a zebrafish STAR genome index using Lawson Lab zebrafish transcriptome annotation 46 plus manually annotated entries for mCherry transcript  filtered for protein coding genes. Final cellular barcodes and Unique Molecular Identifiers UMIs were determined using Cell Ranger 6.0.1 10X Genomics and cells were filtered to include only high quality cells. Cell Ranger defaults for selecting cell associated barcodes versus barcodes associated with empty partitions were used. Assembly: GRCz11 Supplementary files format and content: bam and monocle3 RDS,dorsal fin,,Fins were choped to small pieces and isolated with liberase. Digestion was stopped by adding FBS and lysate was filtered and washed with 1xPBS before loading into chips. Cells were captured in a Chromium controller 10X Genomics. Single cell mRNA libraries were prepared using the single cell 3’ solution V3 kit 10X Genomics. Quality control and quantification assays were performed using a Qubit fluorometer ThermoFisher and a 2100 Bioanalyzer Agilent. Libraries were sequenced on an Illumina NextSeq 550 using 75 cycle  high output kits read 1: 26 cycles  i7 Index: 8 cycles  read 2: 57 cycles.,,tissue:dorsal fin|genotype:wild type|treatment:DMSO,GSM8635055,GSM8635055: dataset3 BMPi DMSO RFP; Danio rerio; RNA Seq,GSM8635055 r1,GSM8635055,1,Fins were choped to small pieces and isolated with liberase. Digestion was stopped by adding FBS and lysate was filtered and washed with 1xPBS before loading into chips. Cells were captured in a Chromium controller 10X Genomics. Single cell mRNA libraries were prepared using the single cell three prime solution V3 kit 10X Genomics. Quality control and quantification assays were performed using a Qubit fluorometer ThermoFisher and a 2100 Bioanalyzer Agilent. Libraries were sequenced on an Illumina NextSeq 550 using 75 cycle  high output kits read 1: 26 cycles  i7 Index: 8 cycles  read 2: 57 cycles.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP545529,,loader:fastq load.py,DMSO_RFP_S2_L001_I1_001.fastq.gz DMSO_RFP_S2_L001_I2_001.fastq.gz DMSO_RFP_S2_L001_R1_001.fastq.gz DMSO_RFP_S2_L001_R2_001.fastq.gz,fastq fastq fastq fastq,4298328228.0,31147306.0,GSM8635055 r1,0:10 1:10 2:28 3:90,A:816881516;C:611689038;G:673484940;T:700975488;N:226558,10,10,28,90,816881516,611689038,673484940,700975488,226558,SRX26737886,SRS23227906,SRA2016042,UVA,UVA,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Unknown,2024-11-15,Undetermined,Embryo,Fin,Surface Structure
34146,SRR31364124,SRX26737885,SRS23227907,SRP545529,PRJNA1186739,Agouti and BMP signaling drive a naturally occurring fate conversion of melanophores to leucophores in zebrafish,GSE282061,Transcriptome Analysis,The often prominent pigment patterns of vertebrates are varied in form and function and depend on several types of pigment cells derived from embryonic neural crest or latent stem cells of neural crest origin. These cells and the patterns they produce have been useful for uncovering features of differentiation and morphogenesis that underlie adult phenotypes  and they offer opportunities to discover how patterns and the cell types themselves have diversified. In zebrafish  a body pattern of stripes arises by self organizing interactions among three types of pigment cells. Yet these fish also exhibit white ornamentation on their fins that depends on the transdifferentiation of black melanophores to white cells  “melanoleucophores.” To identify mechanisms underlying this conversion we used ultrastrustructural  transcriptomic  mutational and other approaches. Overall design: Zerbrafish dorsal fins were collected from different developmental stages  different fin positions  or post different pharmacological treatments. Cells were isolated and sorted for the presence or absence of tyrp1b:palmmcherry  and analyzed by 10x scRNA seq.,,pubmed:40305763,,dataset3 BMPi DMSO no RFP,GSM8635054,,source name:dorsal fin|tissue:dorsal fin|genotype:wild type|treatment:DMSO|geo loc name:missing|collection date:missing,dataset3 BMPi DMSO no RFP,We built a zebrafish STAR genome index using Lawson Lab zebrafish transcriptome annotation 46 plus manually annotated entries for mCherry transcript  filtered for protein coding genes. Final cellular barcodes and Unique Molecular Identifiers UMIs were determined using Cell Ranger 6.0.1 10X Genomics and cells were filtered to include only high quality cells. Cell Ranger defaults for selecting cell associated barcodes versus barcodes associated with empty partitions were used. Assembly: GRCz11 Supplementary files format and content: bam and monocle3 RDS,dorsal fin,,Fins were choped to small pieces and isolated with liberase. Digestion was stopped by adding FBS and lysate was filtered and washed with 1xPBS before loading into chips. Cells were captured in a Chromium controller 10X Genomics. Single cell mRNA libraries were prepared using the single cell 3’ solution V3 kit 10X Genomics. Quality control and quantification assays were performed using a Qubit fluorometer ThermoFisher and a 2100 Bioanalyzer Agilent. Libraries were sequenced on an Illumina NextSeq 550 using 75 cycle  high output kits read 1: 26 cycles  i7 Index: 8 cycles  read 2: 57 cycles.,,tissue:dorsal fin|genotype:wild type|treatment:DMSO,GSM8635054,GSM8635054: dataset3 BMPi DMSO no RFP; Danio rerio; RNA Seq,GSM8635054 r1,GSM8635054,1,Fins were choped to small pieces and isolated with liberase. Digestion was stopped by adding FBS and lysate was filtered and washed with 1xPBS before loading into chips. Cells were captured in a Chromium controller 10X Genomics. Single cell mRNA libraries were prepared using the single cell three prime solution V3 kit 10X Genomics. Quality control and quantification assays were performed using a Qubit fluorometer ThermoFisher and a 2100 Bioanalyzer Agilent. Libraries were sequenced on an Illumina NextSeq 550 using 75 cycle  high output kits read 1: 26 cycles  i7 Index: 8 cycles  read 2: 57 cycles.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP545529,,loader:fastq load.py,DMSO_noRFP_S1_L001_I1_001.fastq.gz DMSO_noRFP_S1_L001_I2_001.fastq.gz DMSO_noRFP_S1_L001_R1_001.fastq.gz DMSO_noRFP_S1_L001_R2_001.fastq.gz,fastq fastq fastq fastq,4086026820.0,29608890.0,GSM8635054 r1,0:10 1:10 2:28 3:90,A:794711851;C:543564325;G:594229898;T:732076441;N:217585,10,10,28,90,794711851,543564325,594229898,732076441,217585,SRX26737885,SRS23227907,SRA2016042,UVA,UVA,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Unknown,2024-11-15,Undetermined,Embryo,Fin,Surface Structure
34147,SRR31364125,SRX26737884,SRS23227904,SRP545529,PRJNA1186739,Agouti and BMP signaling drive a naturally occurring fate conversion of melanophores to leucophores in zebrafish,GSE282061,Transcriptome Analysis,The often prominent pigment patterns of vertebrates are varied in form and function and depend on several types of pigment cells derived from embryonic neural crest or latent stem cells of neural crest origin. These cells and the patterns they produce have been useful for uncovering features of differentiation and morphogenesis that underlie adult phenotypes  and they offer opportunities to discover how patterns and the cell types themselves have diversified. In zebrafish  a body pattern of stripes arises by self organizing interactions among three types of pigment cells. Yet these fish also exhibit white ornamentation on their fins that depends on the transdifferentiation of black melanophores to white cells  “melanoleucophores.” To identify mechanisms underlying this conversion we used ultrastrustructural  transcriptomic  mutational and other approaches. Overall design: Zerbrafish dorsal fins were collected from different developmental stages  different fin positions  or post different pharmacological treatments. Cells were isolated and sorted for the presence or absence of tyrp1b:palmmcherry  and analyzed by 10x scRNA seq.,,pubmed:40305763,,dataset2 positions base,GSM8635053,,source name:dorsal fin|tissue:dorsal fin|genotype:wild type|geo loc name:missing|collection date:missing,dataset2 positions base,We built a zebrafish STAR genome index using Lawson Lab zebrafish transcriptome annotation 46 plus manually annotated entries for mCherry transcript  filtered for protein coding genes. Final cellular barcodes and Unique Molecular Identifiers UMIs were determined using Cell Ranger 6.0.1 10X Genomics and cells were filtered to include only high quality cells. Cell Ranger defaults for selecting cell associated barcodes versus barcodes associated with empty partitions were used. Assembly: GRCz11 Supplementary files format and content: bam and monocle3 RDS,dorsal fin,,Fins were choped to small pieces and isolated with liberase. Digestion was stopped by adding FBS and lysate was filtered and washed with 1xPBS before loading into chips. Cells were captured in a Chromium controller 10X Genomics. Single cell mRNA libraries were prepared using the single cell 3’ solution V3 kit 10X Genomics. Quality control and quantification assays were performed using a Qubit fluorometer ThermoFisher and a 2100 Bioanalyzer Agilent. Libraries were sequenced on an Illumina NextSeq 550 using 75 cycle  high output kits read 1: 26 cycles  i7 Index: 8 cycles  read 2: 57 cycles.,,tissue:dorsal fin|genotype:wild type,GSM8635053,GSM8635053: dataset2 positions base; Danio rerio; RNA Seq,GSM8635053 r1,GSM8635053,1,Fins were choped to small pieces and isolated with liberase. Digestion was stopped by adding FBS and lysate was filtered and washed with 1xPBS before loading into chips. Cells were captured in a Chromium controller 10X Genomics. Single cell mRNA libraries were prepared using the single cell three prime solution V3 kit 10X Genomics. Quality control and quantification assays were performed using a Qubit fluorometer ThermoFisher and a 2100 Bioanalyzer Agilent. Libraries were sequenced on an Illumina NextSeq 550 using 75 cycle  high output kits read 1: 26 cycles  i7 Index: 8 cycles  read 2: 57 cycles.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP545529,,loader:fastq load.py,tip_rest_S3_L001_I1_001.fastq.gz tip_rest_S3_L001_R1_001.fastq.gz tip_rest_S3_L001_R2_001.fastq.gz,fastq fastq fastq,2562938024.0,27858022.0,GSM8635053 r1,0:8 1:28 2:56,A:465025810;C:315982726;G:357090865;T:420656906;N:1292925,8,28,56,,465025810,315982726,357090865,420656906,1292925,SRX26737884,SRS23227904,SRA2016042,UVA,UVA,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Unknown,2024-11-15,Undetermined,Embryo,Fin,Surface Structure
34148,SRR31364126,SRX26737883,SRS23227905,SRP545529,PRJNA1186739,Agouti and BMP signaling drive a naturally occurring fate conversion of melanophores to leucophores in zebrafish,GSE282061,Transcriptome Analysis,The often prominent pigment patterns of vertebrates are varied in form and function and depend on several types of pigment cells derived from embryonic neural crest or latent stem cells of neural crest origin. These cells and the patterns they produce have been useful for uncovering features of differentiation and morphogenesis that underlie adult phenotypes  and they offer opportunities to discover how patterns and the cell types themselves have diversified. In zebrafish  a body pattern of stripes arises by self organizing interactions among three types of pigment cells. Yet these fish also exhibit white ornamentation on their fins that depends on the transdifferentiation of black melanophores to white cells  “melanoleucophores.” To identify mechanisms underlying this conversion we used ultrastrustructural  transcriptomic  mutational and other approaches. Overall design: Zerbrafish dorsal fins were collected from different developmental stages  different fin positions  or post different pharmacological treatments. Cells were isolated and sorted for the presence or absence of tyrp1b:palmmcherry  and analyzed by 10x scRNA seq.,,pubmed:40305763,,dataset2 positions edge,GSM8635052,,source name:dorsal fin|tissue:dorsal fin|genotype:wild type|geo loc name:missing|collection date:missing,dataset2 positions edge,We built a zebrafish STAR genome index using Lawson Lab zebrafish transcriptome annotation 46 plus manually annotated entries for mCherry transcript  filtered for protein coding genes. Final cellular barcodes and Unique Molecular Identifiers UMIs were determined using Cell Ranger 6.0.1 10X Genomics and cells were filtered to include only high quality cells. Cell Ranger defaults for selecting cell associated barcodes versus barcodes associated with empty partitions were used. Assembly: GRCz11 Supplementary files format and content: bam and monocle3 RDS,dorsal fin,,Fins were choped to small pieces and isolated with liberase. Digestion was stopped by adding FBS and lysate was filtered and washed with 1xPBS before loading into chips. Cells were captured in a Chromium controller 10X Genomics. Single cell mRNA libraries were prepared using the single cell 3’ solution V3 kit 10X Genomics. Quality control and quantification assays were performed using a Qubit fluorometer ThermoFisher and a 2100 Bioanalyzer Agilent. Libraries were sequenced on an Illumina NextSeq 550 using 75 cycle  high output kits read 1: 26 cycles  i7 Index: 8 cycles  read 2: 57 cycles.,,tissue:dorsal fin|genotype:wild type,GSM8635052,GSM8635052: dataset2 positions edge; Danio rerio; RNA Seq,GSM8635052 r1,GSM8635052,1,Fins were choped to small pieces and isolated with liberase. Digestion was stopped by adding FBS and lysate was filtered and washed with 1xPBS before loading into chips. Cells were captured in a Chromium controller 10X Genomics. Single cell mRNA libraries were prepared using the single cell three prime solution V3 kit 10X Genomics. Quality control and quantification assays were performed using a Qubit fluorometer ThermoFisher and a 2100 Bioanalyzer Agilent. Libraries were sequenced on an Illumina NextSeq 550 using 75 cycle  high output kits read 1: 26 cycles  i7 Index: 8 cycles  read 2: 57 cycles.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP545529,,loader:fastq load.py,tip_white_S2_L001_I1_001.fastq.gz tip_white_S2_L001_R1_001.fastq.gz tip_white_S2_L001_R2_001.fastq.gz,fastq fastq fastq,3561960136.0,38716958.0,GSM8635052 r1,0:8 1:28 2:56,A:640222776;C:444619403;G:502208963;T:579280385;N:1818121,8,28,56,,640222776,444619403,502208963,579280385,1818121,SRX26737883,SRS23227905,SRA2016042,UVA,UVA,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Unknown,2024-11-15,Undetermined,Embryo,Fin,Surface Structure
34149,SRR31364127,SRX26737882,SRS23227903,SRP545529,PRJNA1186739,Agouti and BMP signaling drive a naturally occurring fate conversion of melanophores to leucophores in zebrafish,GSE282061,Transcriptome Analysis,The often prominent pigment patterns of vertebrates are varied in form and function and depend on several types of pigment cells derived from embryonic neural crest or latent stem cells of neural crest origin. These cells and the patterns they produce have been useful for uncovering features of differentiation and morphogenesis that underlie adult phenotypes  and they offer opportunities to discover how patterns and the cell types themselves have diversified. In zebrafish  a body pattern of stripes arises by self organizing interactions among three types of pigment cells. Yet these fish also exhibit white ornamentation on their fins that depends on the transdifferentiation of black melanophores to white cells  “melanoleucophores.” To identify mechanisms underlying this conversion we used ultrastrustructural  transcriptomic  mutational and other approaches. Overall design: Zerbrafish dorsal fins were collected from different developmental stages  different fin positions  or post different pharmacological treatments. Cells were isolated and sorted for the presence or absence of tyrp1b:palmmcherry  and analyzed by 10x scRNA seq.,,pubmed:40305763,,dataset1 stages rep4,GSM8635051,,source name:dorsal fin|tissue:dorsal fin|genotype:wild type|geo loc name:missing|collection date:missing,dataset1 stages rep4,We built a zebrafish STAR genome index using Lawson Lab zebrafish transcriptome annotation 46 plus manually annotated entries for mCherry transcript  filtered for protein coding genes. Final cellular barcodes and Unique Molecular Identifiers UMIs were determined using Cell Ranger 6.0.1 10X Genomics and cells were filtered to include only high quality cells. Cell Ranger defaults for selecting cell associated barcodes versus barcodes associated with empty partitions were used. Assembly: GRCz11 Supplementary files format and content: bam and monocle3 RDS,dorsal fin,,Fins were choped to small pieces and isolated with liberase. Digestion was stopped by adding FBS and lysate was filtered and washed with 1xPBS before loading into chips. Cells were captured in a Chromium controller 10X Genomics. Single cell mRNA libraries were prepared using the single cell 3’ solution V3 kit 10X Genomics. Quality control and quantification assays were performed using a Qubit fluorometer ThermoFisher and a 2100 Bioanalyzer Agilent. Libraries were sequenced on an Illumina NextSeq 550 using 75 cycle  high output kits read 1: 26 cycles  i7 Index: 8 cycles  read 2: 57 cycles.,,tissue:dorsal fin|genotype:wild type,GSM8635051,GSM8635051: dataset1 stages rep4; Danio rerio; RNA Seq,GSM8635051 r1,GSM8635051,1,Fins were choped to small pieces and isolated with liberase. Digestion was stopped by adding FBS and lysate was filtered and washed with 1xPBS before loading into chips. Cells were captured in a Chromium controller 10X Genomics. Single cell mRNA libraries were prepared using the single cell three prime solution V3 kit 10X Genomics. Quality control and quantification assays were performed using a Qubit fluorometer ThermoFisher and a 2100 Bioanalyzer Agilent. Libraries were sequenced on an Illumina NextSeq 550 using 75 cycle  high output kits read 1: 26 cycles  i7 Index: 8 cycles  read 2: 57 cycles.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP545529,,loader:fastq load.py,dorsal_4_S4_L001_I1_001.fastq.gz dorsal_4_S4_L001_R1_001.fastq.gz dorsal_4_S4_L001_R2_001.fastq.gz,fastq fastq fastq,2719423400.0,29558950.0,GSM8635051 r1,0:8 1:28 2:56,A:491347530;C:348666057;G:386184840;T:428683151;N:419622,8,28,56,,491347530,348666057,386184840,428683151,419622,SRX26737882,SRS23227903,SRA2016042,UVA,UVA,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Unknown,2024-11-15,Undetermined,Embryo,Fin,Surface Structure
34150,SRR31364128,SRX26737881,SRS23227902,SRP545529,PRJNA1186739,Agouti and BMP signaling drive a naturally occurring fate conversion of melanophores to leucophores in zebrafish,GSE282061,Transcriptome Analysis,The often prominent pigment patterns of vertebrates are varied in form and function and depend on several types of pigment cells derived from embryonic neural crest or latent stem cells of neural crest origin. These cells and the patterns they produce have been useful for uncovering features of differentiation and morphogenesis that underlie adult phenotypes  and they offer opportunities to discover how patterns and the cell types themselves have diversified. In zebrafish  a body pattern of stripes arises by self organizing interactions among three types of pigment cells. Yet these fish also exhibit white ornamentation on their fins that depends on the transdifferentiation of black melanophores to white cells  “melanoleucophores.” To identify mechanisms underlying this conversion we used ultrastrustructural  transcriptomic  mutational and other approaches. Overall design: Zerbrafish dorsal fins were collected from different developmental stages  different fin positions  or post different pharmacological treatments. Cells were isolated and sorted for the presence or absence of tyrp1b:palmmcherry  and analyzed by 10x scRNA seq.,,pubmed:40305763,,dataset1 stages rep3,GSM8635050,,source name:dorsal fin|tissue:dorsal fin|genotype:wild type|geo loc name:missing|collection date:missing,dataset1 stages rep3,We built a zebrafish STAR genome index using Lawson Lab zebrafish transcriptome annotation 46 plus manually annotated entries for mCherry transcript  filtered for protein coding genes. Final cellular barcodes and Unique Molecular Identifiers UMIs were determined using Cell Ranger 6.0.1 10X Genomics and cells were filtered to include only high quality cells. Cell Ranger defaults for selecting cell associated barcodes versus barcodes associated with empty partitions were used. Assembly: GRCz11 Supplementary files format and content: bam and monocle3 RDS,dorsal fin,,Fins were choped to small pieces and isolated with liberase. Digestion was stopped by adding FBS and lysate was filtered and washed with 1xPBS before loading into chips. Cells were captured in a Chromium controller 10X Genomics. Single cell mRNA libraries were prepared using the single cell 3’ solution V3 kit 10X Genomics. Quality control and quantification assays were performed using a Qubit fluorometer ThermoFisher and a 2100 Bioanalyzer Agilent. Libraries were sequenced on an Illumina NextSeq 550 using 75 cycle  high output kits read 1: 26 cycles  i7 Index: 8 cycles  read 2: 57 cycles.,,tissue:dorsal fin|genotype:wild type,GSM8635050,GSM8635050: dataset1 stages rep3; Danio rerio; RNA Seq,GSM8635050 r1,GSM8635050,1,Fins were choped to small pieces and isolated with liberase. Digestion was stopped by adding FBS and lysate was filtered and washed with 1xPBS before loading into chips. Cells were captured in a Chromium controller 10X Genomics. Single cell mRNA libraries were prepared using the single cell three prime solution V3 kit 10X Genomics. Quality control and quantification assays were performed using a Qubit fluorometer ThermoFisher and a 2100 Bioanalyzer Agilent. Libraries were sequenced on an Illumina NextSeq 550 using 75 cycle  high output kits read 1: 26 cycles  i7 Index: 8 cycles  read 2: 57 cycles.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP545529,,loader:fastq load.py,dorsal_3_S3_L001_I1_001.fastq.gz dorsal_3_S3_L001_R1_001.fastq.gz dorsal_3_S3_L001_R2_001.fastq.gz,fastq fastq fastq,2602160384.0,28284352.0,GSM8635050 r1,0:8 1:28 2:56,A:469841004;C:333542050;G:367823398;T:412316065;N:401195,8,28,56,,469841004,333542050,367823398,412316065,401195,SRX26737881,SRS23227902,SRA2016042,UVA,UVA,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Unknown,2024-11-15,Undetermined,Embryo,Fin,Surface Structure
34151,SRR31364129,SRX26737880,SRS23227901,SRP545529,PRJNA1186739,Agouti and BMP signaling drive a naturally occurring fate conversion of melanophores to leucophores in zebrafish,GSE282061,Transcriptome Analysis,The often prominent pigment patterns of vertebrates are varied in form and function and depend on several types of pigment cells derived from embryonic neural crest or latent stem cells of neural crest origin. These cells and the patterns they produce have been useful for uncovering features of differentiation and morphogenesis that underlie adult phenotypes  and they offer opportunities to discover how patterns and the cell types themselves have diversified. In zebrafish  a body pattern of stripes arises by self organizing interactions among three types of pigment cells. Yet these fish also exhibit white ornamentation on their fins that depends on the transdifferentiation of black melanophores to white cells  “melanoleucophores.” To identify mechanisms underlying this conversion we used ultrastrustructural  transcriptomic  mutational and other approaches. Overall design: Zerbrafish dorsal fins were collected from different developmental stages  different fin positions  or post different pharmacological treatments. Cells were isolated and sorted for the presence or absence of tyrp1b:palmmcherry  and analyzed by 10x scRNA seq.,,pubmed:40305763,,dataset1 stages rep2,GSM8635049,,source name:dorsal fin|tissue:dorsal fin|genotype:wild type|geo loc name:missing|collection date:missing,dataset1 stages rep2,We built a zebrafish STAR genome index using Lawson Lab zebrafish transcriptome annotation 46 plus manually annotated entries for mCherry transcript  filtered for protein coding genes. Final cellular barcodes and Unique Molecular Identifiers UMIs were determined using Cell Ranger 6.0.1 10X Genomics and cells were filtered to include only high quality cells. Cell Ranger defaults for selecting cell associated barcodes versus barcodes associated with empty partitions were used. Assembly: GRCz11 Supplementary files format and content: bam and monocle3 RDS,dorsal fin,,Fins were choped to small pieces and isolated with liberase. Digestion was stopped by adding FBS and lysate was filtered and washed with 1xPBS before loading into chips. Cells were captured in a Chromium controller 10X Genomics. Single cell mRNA libraries were prepared using the single cell 3’ solution V3 kit 10X Genomics. Quality control and quantification assays were performed using a Qubit fluorometer ThermoFisher and a 2100 Bioanalyzer Agilent. Libraries were sequenced on an Illumina NextSeq 550 using 75 cycle  high output kits read 1: 26 cycles  i7 Index: 8 cycles  read 2: 57 cycles.,,tissue:dorsal fin|genotype:wild type,GSM8635049,GSM8635049: dataset1 stages rep2; Danio rerio; RNA Seq,GSM8635049 r1,GSM8635049,1,Fins were choped to small pieces and isolated with liberase. Digestion was stopped by adding FBS and lysate was filtered and washed with 1xPBS before loading into chips. Cells were captured in a Chromium controller 10X Genomics. Single cell mRNA libraries were prepared using the single cell three prime solution V3 kit 10X Genomics. Quality control and quantification assays were performed using a Qubit fluorometer ThermoFisher and a 2100 Bioanalyzer Agilent. Libraries were sequenced on an Illumina NextSeq 550 using 75 cycle  high output kits read 1: 26 cycles  i7 Index: 8 cycles  read 2: 57 cycles.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP545529,,loader:fastq load.py,dorsal_2_S2_L001_I1_001.fastq.gz dorsal_2_S2_L001_R1_001.fastq.gz dorsal_2_S2_L001_R2_001.fastq.gz,fastq fastq fastq,3187245056.0,34643968.0,GSM8635049 r1,0:8 1:28 2:56,A:584729856;C:395297406;G:447424733;T:512111292;N:498921,8,28,56,,584729856,395297406,447424733,512111292,498921,SRX26737880,SRS23227901,SRA2016042,UVA,UVA,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Unknown,2024-11-15,Undetermined,Embryo,Fin,Surface Structure
34152,SRR31364130,SRX26737879,SRS23227900,SRP545529,PRJNA1186739,Agouti and BMP signaling drive a naturally occurring fate conversion of melanophores to leucophores in zebrafish,GSE282061,Transcriptome Analysis,The often prominent pigment patterns of vertebrates are varied in form and function and depend on several types of pigment cells derived from embryonic neural crest or latent stem cells of neural crest origin. These cells and the patterns they produce have been useful for uncovering features of differentiation and morphogenesis that underlie adult phenotypes  and they offer opportunities to discover how patterns and the cell types themselves have diversified. In zebrafish  a body pattern of stripes arises by self organizing interactions among three types of pigment cells. Yet these fish also exhibit white ornamentation on their fins that depends on the transdifferentiation of black melanophores to white cells  “melanoleucophores.” To identify mechanisms underlying this conversion we used ultrastrustructural  transcriptomic  mutational and other approaches. Overall design: Zerbrafish dorsal fins were collected from different developmental stages  different fin positions  or post different pharmacological treatments. Cells were isolated and sorted for the presence or absence of tyrp1b:palmmcherry  and analyzed by 10x scRNA seq.,,pubmed:40305763,,dataset1 stages rep1,GSM8635048,,source name:dorsal fin|tissue:dorsal fin|genotype:wild type|geo loc name:missing|collection date:missing,dataset1 stages rep1,We built a zebrafish STAR genome index using Lawson Lab zebrafish transcriptome annotation 46 plus manually annotated entries for mCherry transcript  filtered for protein coding genes. Final cellular barcodes and Unique Molecular Identifiers UMIs were determined using Cell Ranger 6.0.1 10X Genomics and cells were filtered to include only high quality cells. Cell Ranger defaults for selecting cell associated barcodes versus barcodes associated with empty partitions were used. Assembly: GRCz11 Supplementary files format and content: bam and monocle3 RDS,dorsal fin,,Fins were choped to small pieces and isolated with liberase. Digestion was stopped by adding FBS and lysate was filtered and washed with 1xPBS before loading into chips. Cells were captured in a Chromium controller 10X Genomics. Single cell mRNA libraries were prepared using the single cell 3’ solution V3 kit 10X Genomics. Quality control and quantification assays were performed using a Qubit fluorometer ThermoFisher and a 2100 Bioanalyzer Agilent. Libraries were sequenced on an Illumina NextSeq 550 using 75 cycle  high output kits read 1: 26 cycles  i7 Index: 8 cycles  read 2: 57 cycles.,,tissue:dorsal fin|genotype:wild type,GSM8635048,GSM8635048: dataset1 stages rep1; Danio rerio; RNA Seq,GSM8635048 r1,GSM8635048,1,Fins were choped to small pieces and isolated with liberase. Digestion was stopped by adding FBS and lysate was filtered and washed with 1xPBS before loading into chips. Cells were captured in a Chromium controller 10X Genomics. Single cell mRNA libraries were prepared using the single cell three prime solution V3 kit 10X Genomics. Quality control and quantification assays were performed using a Qubit fluorometer ThermoFisher and a 2100 Bioanalyzer Agilent. Libraries were sequenced on an Illumina NextSeq 550 using 75 cycle  high output kits read 1: 26 cycles  i7 Index: 8 cycles  read 2: 57 cycles.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP545529,,loader:fastq load.py,dorsal_1_S1_L001_I1_001.fastq.gz dorsal_1_S1_L001_R1_001.fastq.gz dorsal_1_S1_L001_R2_001.fastq.gz,fastq fastq fastq,2963326992.0,32210076.0,GSM8635048 r1,0:8 1:28 2:56,A:550098255;C:357880179;G:398034107;T:497290530;N:461185,8,28,56,,550098255,357880179,398034107,497290530,461185,SRX26737879,SRS23227900,SRA2016042,UVA,UVA,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Unknown,2024-11-15,Undetermined,Embryo,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
41278,SRR6039223,SRX3187382,SRS2515225,SRP082370,PRJNA339266,Single cell sequencing reveals dissociation induced gene expression in tissue subpopulations,GSE85755,Other,"In many gene expression studies  cells are extracted by tissue dissociation and Fluorescence Activated Cell Sorting FACS  but the effect of these protocols on cellular transcriptomes is not well characterized and often ignored. Here  we applied single cell mRNA sequencing scRNA seq to muscle stem cells  and unexpectedly found a subpopulation that is strongly affected by the widely used dissociation protocol that we employed. One implication of this finding is that several published transcriptomics studies may need to be reinterpreted. Importantly  we detected similar subpopulations in other single cell datasets  suggesting that cells from other tissues might be affected by this artefact as well. Overall design: Mouse satellite cells and zebrafish fin cells were extracted from Tibialis Anterior muscles of Pax7nGFP mice and wildtype zebrafish fins  respectively. For cell extraction  traditional Supplementary Methods dissociation protocols that combine mechanical and enzymatic dissociation were employed  and live cells were subsequently sorted into plates using FACS. Next  single cell mRNA sequencing CEL Seq or SORT Seq robotized version of CEL Seq2 was applied  and data was analyzed with RaceID2 to identify clusters. CEL Seq samples: Manual CEL Seq; Satellite cells unstained; Male Pax7nGFP mice 5 mpf 7 mpf; 1h collagenase treated default dissociation protocol; 96 cells per plate with 96 different barcodes see ""Cel seq barcodes 96.csv""; some primes numbers are bulk samples see ""BulkSamples BarcodesAndNrOfCellsUsed perCEL Seq1 library""; Spike ins included see ""ERCC92.fa""; No mitochondrial reads in count tables; Sequencing lanes not concatenated in fastq files uploaded here; ""Merged CEL Seq AllMiceAndLibrariesMerged.csv"" file is count table with reads from all mice and libraries merged Annotation of columns: Zx.y  where Z = mouse  x = library and y = cell barcode; bulk samples are not included any more in this file; See Supplementary Methods for details. SORT Seq 1h and 2h dissociated samples: Robotized CEL Seq2; Satellite cells unstained; Male Pax7nGFP mice 5 mpf 7 mpf; 8 muscles from 4 mice; One plate of 1h default dissociation protocol and one plate of 2h collagenase treated cells; 384 cells per plate with each of the 96 barcodes see ""Cel seq barcodes 96.csv"" used 4 times per plate therefore  each plate has 4 libraries; No bulk samples included; Spike ins included see ""ERCC92.fa""; No mitochondrial reads in count table; In some wells  we sorted no cell internal negative control; barcodes #95 and #96 were used for empty wells; Sequencing lanes not concatenated in fastq files uploaded here; ""Merged SORT Seq DissociationTimecourse.csv"" file is count table were reads from all dissociation timepoints are merged Annotation columns: DZhx y  where Z = 1 or 2 hours collagenase treated  x = library and y = cell barcode; See Supplementary Methods for details. SORT Seq MitoTracker stained samples pilot and repeat: Robotized CEL Seq2 samples; Satellite cells stained with MitoTracker; Female Pax7nGFP mice 1 4.7 mpf mouse for pilot experiment; 3 mpf 6 mpf mice for repeat experiment; 1h collagenase treated default dissociation protocol; 384 cells per plate with each of the 384 barcodes see ""Cel seq barcodes 384.csv"" used 1 times per plate therefore  each plate has 1 library; Note: pilot experiment has 263 cells so plate was partly empty  repeat experiment done with 4 full plates; No bulk samples included; Spike ins included see ""ERCC92.fa""; Mitochondrial reads rows named ""*  chrM"" included in count tables these were removed prior to RaceID2; In some wells  we sorted no cell barcodes #357 #360 and #381 #384 were used for empty wells; Sequencing lanes concatenated in fastq files uploaded here; No merged file was generated for pilot experiment as only one library  ""Merged MitoTracker Repeat.csv"" file is count table were reads from all plates of repeat experiment were merged Annotation of columns: Plx Welly  where x = plate number 1 4 and x = cell barcode; See Supplementary Methods for details. SORT Seq zebrafish fin samples: Robotized CEL Seq2; Fin cells unstained; all live cells; Wildtype zebrafish; Dissociated using default fin dissociation protocol Supplementary Methods; 384 cells per plate with each of the 384 barcodes see ""Cel seq barcodes 384.csv"" used 1 times per plate therefore  each plate has 1 library; Note: only merged count table file ""fin C E count table.csv""  Annotation columns: Xx.py.prim.finZ  where x = cell barcode  y = plate number and Z is fish C or E and no individual library count table files were uploaded to GEO for zebrafish fin data; No bulk samples included; Spike ins not included in merged count tables file; Mitochondrial reads not included in merged count tables file; In some wells  we sorted no cell barcodes #357 #360 and #381 #384 were used for empty wells; Sequencing lanes concatenated in fastq files uploaded here; See Supplementary Methods for details.",,pubmed:28960196,,SORT Seq zebrafish fin merged,GSM2781033,,tissue:All cells from caudal fin|strain:Wildtype,SORT Seq zebrafish fin merged,"Reads 2 were mapped to the reference transcriptome created from the genomes downloaded from the UCSC genome browser; ERCC Spike in sequences and mitochondrial sequences were added in sense direction using bwa version 0.6.2 r126 with default parameters. All isoforms of the same gene were merged to a single gene locus and reads mapping to multiple loci in the transcriptome were discarded. Reads 1 contains the cel specific barcode information first 8 bases followed by a UMI sequence 4bp for unstained satellite cell data; 6bp for MitoTracker Stained satellite cells and zebrafish data and a polyT stretch. Reads 1 were thus used to extract the cell barcode sequences see “Cel seq barcodes 96.csv” file for sequences used for unstained satellite cell data and see ""Cel seq barcodes 384"" for MitoTracker stained satellite cells and zebrafish data and UMIs; see Supplementary Methods for details. post mapping  a UMI correction was applied to the read and barcode counts files to generate unique transcript count tables as described before see Supplementary Methods section for details. Note that processed files for satellite cell data here still contain ERCC Spike in molecules  bulk samples bulk samples are only included in CEL Seq experiments; see “BulkSamples BarcodesAndNrOfCellsUsed perCEL Seq1 library” file for description of how many cells were used as bulk and which primer barcode sequence was used for bulk sample in each library and mitochondrial reads only for MitoTracker stained satellite cells. Genome build: mus musculus: mm10; danio rerio: Zv9 Ensembl release 74; both were extended with spike ins see ""ERCC92.fa"" Supplementary files format and content: *.coutt.csv  *TranscriptCounts.tsv and *count table.csv: tab separated data files listing how many reads of which transcripts were detected in all sequenced cells post UMI correction. Column names refer to cells sequenced in this library numbers refer the the CEL Seq primer barcode used for that cell. The first column lists official gene symbols followed by the chromosome name  separated by a double underscore. Note that processed files for satellite cell data here still contain ERCC Spike in molecules  bulk samples bulk samples are only included in CEL Seq experiments; see “BulkSamples BarcodesAndNrOfCellsUsed perCEL Seq1 library” file for description of how many cells were used as bulk and which primer barcode sequence was used for bulk sample in each library and mitochondrial reads only for MitoTracker stained satellite cells.",All cells from caudal fin,,Cells were sorted into Vapor Lock Qiagen containing a droplet with primers and dNTPs. Cells were lysed at 65 degrees Celsius  post which SORT Seq Muraro et al.  2016  with minor modifications as desribed in Supplementary Methods of van den Brink et al.  2017 was applied. As in SORT Seq protocol Muraro et al.  2016  with minor modifications as desribed in Supplementary Methods of van den Brink et al.  2017.,,strain:Wildtype,GSM2781033,GSM2781033: SORT Seq zebrafish fin merged; Danio rerio; RNA Seq,GSM2781033,,1,Cells were sorted into Vapor Lock Qiagen containing a droplet with primers and dNTPs. Cells were lysed at 65 degrees Celsius  post which SORT Seq Muraro et al.  2016  with minor modifications as desribed in Supplementary Methods of van den Brink et al.  2017 was applied. As in SORT Seq protocol Muraro et al.  2016  with minor modifications as desribed in Supplementary Methods of van den Brink et al.  2017.,GEO Accession:GSM2781033,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP082370,,,FinC_plate01_R1.fastq.gz FinC_plate01_R2.fastq.gz,fastq fastq,4156649914.0,27498834.0,GSM2781033 r1,0:75.66 1:75.50,A:1184667722;C:812111779;G:946047137;T:1213491214;N:332062,75,75,,,1184667722,812111779,946047137,1213491214,332062,SRX3187382,SRS2515225,SRA453335,GEO,"Alexander van Oudenaarden, Hubrecht Institute",2,0.13191,0.2761,0.11086,0.21281,0.97997,0.9586,0.48699,0.512,76,76,B,B,mate1-mate2 similar by mapping diff,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Netherlands,2017-09-12,Undetermined,Adult,Fin,Surface Structure
41279,SRR6039224,SRX3187382,SRS2515225,SRP082370,PRJNA339266,Single cell sequencing reveals dissociation induced gene expression in tissue subpopulations,GSE85755,Other,"In many gene expression studies  cells are extracted by tissue dissociation and Fluorescence Activated Cell Sorting FACS  but the effect of these protocols on cellular transcriptomes is not well characterized and often ignored. Here  we applied single cell mRNA sequencing scRNA seq to muscle stem cells  and unexpectedly found a subpopulation that is strongly affected by the widely used dissociation protocol that we employed. One implication of this finding is that several published transcriptomics studies may need to be reinterpreted. Importantly  we detected similar subpopulations in other single cell datasets  suggesting that cells from other tissues might be affected by this artefact as well. Overall design: Mouse satellite cells and zebrafish fin cells were extracted from Tibialis Anterior muscles of Pax7nGFP mice and wildtype zebrafish fins  respectively. For cell extraction  traditional Supplementary Methods dissociation protocols that combine mechanical and enzymatic dissociation were employed  and live cells were subsequently sorted into plates using FACS. Next  single cell mRNA sequencing CEL Seq or SORT Seq robotized version of CEL Seq2 was applied  and data was analyzed with RaceID2 to identify clusters. CEL Seq samples: Manual CEL Seq; Satellite cells unstained; Male Pax7nGFP mice 5 mpf 7 mpf; 1h collagenase treated default dissociation protocol; 96 cells per plate with 96 different barcodes see ""Cel seq barcodes 96.csv""; some primes numbers are bulk samples see ""BulkSamples BarcodesAndNrOfCellsUsed perCEL Seq1 library""; Spike ins included see ""ERCC92.fa""; No mitochondrial reads in count tables; Sequencing lanes not concatenated in fastq files uploaded here; ""Merged CEL Seq AllMiceAndLibrariesMerged.csv"" file is count table with reads from all mice and libraries merged Annotation of columns: Zx.y  where Z = mouse  x = library and y = cell barcode; bulk samples are not included any more in this file; See Supplementary Methods for details. SORT Seq 1h and 2h dissociated samples: Robotized CEL Seq2; Satellite cells unstained; Male Pax7nGFP mice 5 mpf 7 mpf; 8 muscles from 4 mice; One plate of 1h default dissociation protocol and one plate of 2h collagenase treated cells; 384 cells per plate with each of the 96 barcodes see ""Cel seq barcodes 96.csv"" used 4 times per plate therefore  each plate has 4 libraries; No bulk samples included; Spike ins included see ""ERCC92.fa""; No mitochondrial reads in count table; In some wells  we sorted no cell internal negative control; barcodes #95 and #96 were used for empty wells; Sequencing lanes not concatenated in fastq files uploaded here; ""Merged SORT Seq DissociationTimecourse.csv"" file is count table were reads from all dissociation timepoints are merged Annotation columns: DZhx y  where Z = 1 or 2 hours collagenase treated  x = library and y = cell barcode; See Supplementary Methods for details. SORT Seq MitoTracker stained samples pilot and repeat: Robotized CEL Seq2 samples; Satellite cells stained with MitoTracker; Female Pax7nGFP mice 1 4.7 mpf mouse for pilot experiment; 3 mpf 6 mpf mice for repeat experiment; 1h collagenase treated default dissociation protocol; 384 cells per plate with each of the 384 barcodes see ""Cel seq barcodes 384.csv"" used 1 times per plate therefore  each plate has 1 library; Note: pilot experiment has 263 cells so plate was partly empty  repeat experiment done with 4 full plates; No bulk samples included; Spike ins included see ""ERCC92.fa""; Mitochondrial reads rows named ""*  chrM"" included in count tables these were removed prior to RaceID2; In some wells  we sorted no cell barcodes #357 #360 and #381 #384 were used for empty wells; Sequencing lanes concatenated in fastq files uploaded here; No merged file was generated for pilot experiment as only one library  ""Merged MitoTracker Repeat.csv"" file is count table were reads from all plates of repeat experiment were merged Annotation of columns: Plx Welly  where x = plate number 1 4 and x = cell barcode; See Supplementary Methods for details. SORT Seq zebrafish fin samples: Robotized CEL Seq2; Fin cells unstained; all live cells; Wildtype zebrafish; Dissociated using default fin dissociation protocol Supplementary Methods; 384 cells per plate with each of the 384 barcodes see ""Cel seq barcodes 384.csv"" used 1 times per plate therefore  each plate has 1 library; Note: only merged count table file ""fin C E count table.csv""  Annotation columns: Xx.py.prim.finZ  where x = cell barcode  y = plate number and Z is fish C or E and no individual library count table files were uploaded to GEO for zebrafish fin data; No bulk samples included; Spike ins not included in merged count tables file; Mitochondrial reads not included in merged count tables file; In some wells  we sorted no cell barcodes #357 #360 and #381 #384 were used for empty wells; Sequencing lanes concatenated in fastq files uploaded here; See Supplementary Methods for details.",,pubmed:28960196,,SORT Seq zebrafish fin merged,GSM2781033,,tissue:All cells from caudal fin|strain:Wildtype,SORT Seq zebrafish fin merged,"Reads 2 were mapped to the reference transcriptome created from the genomes downloaded from the UCSC genome browser; ERCC Spike in sequences and mitochondrial sequences were added in sense direction using bwa version 0.6.2 r126 with default parameters. All isoforms of the same gene were merged to a single gene locus and reads mapping to multiple loci in the transcriptome were discarded. Reads 1 contains the cel specific barcode information first 8 bases followed by a UMI sequence 4bp for unstained satellite cell data; 6bp for MitoTracker Stained satellite cells and zebrafish data and a polyT stretch. Reads 1 were thus used to extract the cell barcode sequences see “Cel seq barcodes 96.csv” file for sequences used for unstained satellite cell data and see ""Cel seq barcodes 384"" for MitoTracker stained satellite cells and zebrafish data and UMIs; see Supplementary Methods for details. post mapping  a UMI correction was applied to the read and barcode counts files to generate unique transcript count tables as described before see Supplementary Methods section for details. Note that processed files for satellite cell data here still contain ERCC Spike in molecules  bulk samples bulk samples are only included in CEL Seq experiments; see “BulkSamples BarcodesAndNrOfCellsUsed perCEL Seq1 library” file for description of how many cells were used as bulk and which primer barcode sequence was used for bulk sample in each library and mitochondrial reads only for MitoTracker stained satellite cells. Genome build: mus musculus: mm10; danio rerio: Zv9 Ensembl release 74; both were extended with spike ins see ""ERCC92.fa"" Supplementary files format and content: *.coutt.csv  *TranscriptCounts.tsv and *count table.csv: tab separated data files listing how many reads of which transcripts were detected in all sequenced cells post UMI correction. Column names refer to cells sequenced in this library numbers refer the the CEL Seq primer barcode used for that cell. The first column lists official gene symbols followed by the chromosome name  separated by a double underscore. Note that processed files for satellite cell data here still contain ERCC Spike in molecules  bulk samples bulk samples are only included in CEL Seq experiments; see “BulkSamples BarcodesAndNrOfCellsUsed perCEL Seq1 library” file for description of how many cells were used as bulk and which primer barcode sequence was used for bulk sample in each library and mitochondrial reads only for MitoTracker stained satellite cells.",All cells from caudal fin,,Cells were sorted into Vapor Lock Qiagen containing a droplet with primers and dNTPs. Cells were lysed at 65 degrees Celsius  post which SORT Seq Muraro et al.  2016  with minor modifications as desribed in Supplementary Methods of van den Brink et al.  2017 was applied. As in SORT Seq protocol Muraro et al.  2016  with minor modifications as desribed in Supplementary Methods of van den Brink et al.  2017.,,strain:Wildtype,GSM2781033,GSM2781033: SORT Seq zebrafish fin merged; Danio rerio; RNA Seq,GSM2781033,,1,Cells were sorted into Vapor Lock Qiagen containing a droplet with primers and dNTPs. Cells were lysed at 65 degrees Celsius  post which SORT Seq Muraro et al.  2016  with minor modifications as desribed in Supplementary Methods of van den Brink et al.  2017 was applied. As in SORT Seq protocol Muraro et al.  2016  with minor modifications as desribed in Supplementary Methods of van den Brink et al.  2017.,GEO Accession:GSM2781033,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP082370,,,FinE_plate07_R1.fastq.gz FinE_plate07_R2.fastq.gz,fastq fastq,7045442122.0,46667895.0,GSM2781033 r10,0:75.65 1:75.32,A:1992737539;C:1481998828;G:1584855122;T:1984679859;N:1170774,75,75,,,1992737539,1481998828,1584855122,1984679859,1170774,SRX3187382,SRS2515225,SRA453335,GEO,"Alexander van Oudenaarden, Hubrecht Institute",2,0.08863,0.2093,0.07731,0.18045,0.97934,0.95655,0.51176,0.52167,76,76,B,B,mate1-mate2 similar by mapping diff,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Netherlands,2017-09-12,Undetermined,Adult,Fin,Surface Structure
41280,SRR6039225,SRX3187382,SRS2515225,SRP082370,PRJNA339266,Single cell sequencing reveals dissociation induced gene expression in tissue subpopulations,GSE85755,Other,"In many gene expression studies  cells are extracted by tissue dissociation and Fluorescence Activated Cell Sorting FACS  but the effect of these protocols on cellular transcriptomes is not well characterized and often ignored. Here  we applied single cell mRNA sequencing scRNA seq to muscle stem cells  and unexpectedly found a subpopulation that is strongly affected by the widely used dissociation protocol that we employed. One implication of this finding is that several published transcriptomics studies may need to be reinterpreted. Importantly  we detected similar subpopulations in other single cell datasets  suggesting that cells from other tissues might be affected by this artefact as well. Overall design: Mouse satellite cells and zebrafish fin cells were extracted from Tibialis Anterior muscles of Pax7nGFP mice and wildtype zebrafish fins  respectively. For cell extraction  traditional Supplementary Methods dissociation protocols that combine mechanical and enzymatic dissociation were employed  and live cells were subsequently sorted into plates using FACS. Next  single cell mRNA sequencing CEL Seq or SORT Seq robotized version of CEL Seq2 was applied  and data was analyzed with RaceID2 to identify clusters. CEL Seq samples: Manual CEL Seq; Satellite cells unstained; Male Pax7nGFP mice 5 mpf 7 mpf; 1h collagenase treated default dissociation protocol; 96 cells per plate with 96 different barcodes see ""Cel seq barcodes 96.csv""; some primes numbers are bulk samples see ""BulkSamples BarcodesAndNrOfCellsUsed perCEL Seq1 library""; Spike ins included see ""ERCC92.fa""; No mitochondrial reads in count tables; Sequencing lanes not concatenated in fastq files uploaded here; ""Merged CEL Seq AllMiceAndLibrariesMerged.csv"" file is count table with reads from all mice and libraries merged Annotation of columns: Zx.y  where Z = mouse  x = library and y = cell barcode; bulk samples are not included any more in this file; See Supplementary Methods for details. SORT Seq 1h and 2h dissociated samples: Robotized CEL Seq2; Satellite cells unstained; Male Pax7nGFP mice 5 mpf 7 mpf; 8 muscles from 4 mice; One plate of 1h default dissociation protocol and one plate of 2h collagenase treated cells; 384 cells per plate with each of the 96 barcodes see ""Cel seq barcodes 96.csv"" used 4 times per plate therefore  each plate has 4 libraries; No bulk samples included; Spike ins included see ""ERCC92.fa""; No mitochondrial reads in count table; In some wells  we sorted no cell internal negative control; barcodes #95 and #96 were used for empty wells; Sequencing lanes not concatenated in fastq files uploaded here; ""Merged SORT Seq DissociationTimecourse.csv"" file is count table were reads from all dissociation timepoints are merged Annotation columns: DZhx y  where Z = 1 or 2 hours collagenase treated  x = library and y = cell barcode; See Supplementary Methods for details. SORT Seq MitoTracker stained samples pilot and repeat: Robotized CEL Seq2 samples; Satellite cells stained with MitoTracker; Female Pax7nGFP mice 1 4.7 mpf mouse for pilot experiment; 3 mpf 6 mpf mice for repeat experiment; 1h collagenase treated default dissociation protocol; 384 cells per plate with each of the 384 barcodes see ""Cel seq barcodes 384.csv"" used 1 times per plate therefore  each plate has 1 library; Note: pilot experiment has 263 cells so plate was partly empty  repeat experiment done with 4 full plates; No bulk samples included; Spike ins included see ""ERCC92.fa""; Mitochondrial reads rows named ""*  chrM"" included in count tables these were removed prior to RaceID2; In some wells  we sorted no cell barcodes #357 #360 and #381 #384 were used for empty wells; Sequencing lanes concatenated in fastq files uploaded here; No merged file was generated for pilot experiment as only one library  ""Merged MitoTracker Repeat.csv"" file is count table were reads from all plates of repeat experiment were merged Annotation of columns: Plx Welly  where x = plate number 1 4 and x = cell barcode; See Supplementary Methods for details. SORT Seq zebrafish fin samples: Robotized CEL Seq2; Fin cells unstained; all live cells; Wildtype zebrafish; Dissociated using default fin dissociation protocol Supplementary Methods; 384 cells per plate with each of the 384 barcodes see ""Cel seq barcodes 384.csv"" used 1 times per plate therefore  each plate has 1 library; Note: only merged count table file ""fin C E count table.csv""  Annotation columns: Xx.py.prim.finZ  where x = cell barcode  y = plate number and Z is fish C or E and no individual library count table files were uploaded to GEO for zebrafish fin data; No bulk samples included; Spike ins not included in merged count tables file; Mitochondrial reads not included in merged count tables file; In some wells  we sorted no cell barcodes #357 #360 and #381 #384 were used for empty wells; Sequencing lanes concatenated in fastq files uploaded here; See Supplementary Methods for details.",,pubmed:28960196,,SORT Seq zebrafish fin merged,GSM2781033,,tissue:All cells from caudal fin|strain:Wildtype,SORT Seq zebrafish fin merged,"Reads 2 were mapped to the reference transcriptome created from the genomes downloaded from the UCSC genome browser; ERCC Spike in sequences and mitochondrial sequences were added in sense direction using bwa version 0.6.2 r126 with default parameters. All isoforms of the same gene were merged to a single gene locus and reads mapping to multiple loci in the transcriptome were discarded. Reads 1 contains the cel specific barcode information first 8 bases followed by a UMI sequence 4bp for unstained satellite cell data; 6bp for MitoTracker Stained satellite cells and zebrafish data and a polyT stretch. Reads 1 were thus used to extract the cell barcode sequences see “Cel seq barcodes 96.csv” file for sequences used for unstained satellite cell data and see ""Cel seq barcodes 384"" for MitoTracker stained satellite cells and zebrafish data and UMIs; see Supplementary Methods for details. post mapping  a UMI correction was applied to the read and barcode counts files to generate unique transcript count tables as described before see Supplementary Methods section for details. Note that processed files for satellite cell data here still contain ERCC Spike in molecules  bulk samples bulk samples are only included in CEL Seq experiments; see “BulkSamples BarcodesAndNrOfCellsUsed perCEL Seq1 library” file for description of how many cells were used as bulk and which primer barcode sequence was used for bulk sample in each library and mitochondrial reads only for MitoTracker stained satellite cells. Genome build: mus musculus: mm10; danio rerio: Zv9 Ensembl release 74; both were extended with spike ins see ""ERCC92.fa"" Supplementary files format and content: *.coutt.csv  *TranscriptCounts.tsv and *count table.csv: tab separated data files listing how many reads of which transcripts were detected in all sequenced cells post UMI correction. Column names refer to cells sequenced in this library numbers refer the the CEL Seq primer barcode used for that cell. The first column lists official gene symbols followed by the chromosome name  separated by a double underscore. Note that processed files for satellite cell data here still contain ERCC Spike in molecules  bulk samples bulk samples are only included in CEL Seq experiments; see “BulkSamples BarcodesAndNrOfCellsUsed perCEL Seq1 library” file for description of how many cells were used as bulk and which primer barcode sequence was used for bulk sample in each library and mitochondrial reads only for MitoTracker stained satellite cells.",All cells from caudal fin,,Cells were sorted into Vapor Lock Qiagen containing a droplet with primers and dNTPs. Cells were lysed at 65 degrees Celsius  post which SORT Seq Muraro et al.  2016  with minor modifications as desribed in Supplementary Methods of van den Brink et al.  2017 was applied. As in SORT Seq protocol Muraro et al.  2016  with minor modifications as desribed in Supplementary Methods of van den Brink et al.  2017.,,strain:Wildtype,GSM2781033,GSM2781033: SORT Seq zebrafish fin merged; Danio rerio; RNA Seq,GSM2781033,,1,Cells were sorted into Vapor Lock Qiagen containing a droplet with primers and dNTPs. Cells were lysed at 65 degrees Celsius  post which SORT Seq Muraro et al.  2016  with minor modifications as desribed in Supplementary Methods of van den Brink et al.  2017 was applied. As in SORT Seq protocol Muraro et al.  2016  with minor modifications as desribed in Supplementary Methods of van den Brink et al.  2017.,GEO Accession:GSM2781033,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP082370,,,FinE_plate08_R1.fastq.gz FinE_plate08_R2.fastq.gz,fastq fastq,18530449971.0,122665653.0,GSM2781033 r11,0:75.68 1:75.38,A:4667348302;C:4333487274;G:4681098112;T:4848415162;N:101121,75,75,,,4667348302,4333487274,4681098112,4848415162,101121,SRX3187382,SRS2515225,SRA453335,GEO,"Alexander van Oudenaarden, Hubrecht Institute",2,0.05595,0.12249,0.04637,0.10243,0.98415,0.96451,0.51093,0.52879,75,75,B,B,mate1-mate2 similar by mapping diff,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Netherlands,2017-09-12,Undetermined,Adult,Fin,Surface Structure
41281,SRR6039226,SRX3187382,SRS2515225,SRP082370,PRJNA339266,Single cell sequencing reveals dissociation induced gene expression in tissue subpopulations,GSE85755,Other,"In many gene expression studies  cells are extracted by tissue dissociation and Fluorescence Activated Cell Sorting FACS  but the effect of these protocols on cellular transcriptomes is not well characterized and often ignored. Here  we applied single cell mRNA sequencing scRNA seq to muscle stem cells  and unexpectedly found a subpopulation that is strongly affected by the widely used dissociation protocol that we employed. One implication of this finding is that several published transcriptomics studies may need to be reinterpreted. Importantly  we detected similar subpopulations in other single cell datasets  suggesting that cells from other tissues might be affected by this artefact as well. Overall design: Mouse satellite cells and zebrafish fin cells were extracted from Tibialis Anterior muscles of Pax7nGFP mice and wildtype zebrafish fins  respectively. For cell extraction  traditional Supplementary Methods dissociation protocols that combine mechanical and enzymatic dissociation were employed  and live cells were subsequently sorted into plates using FACS. Next  single cell mRNA sequencing CEL Seq or SORT Seq robotized version of CEL Seq2 was applied  and data was analyzed with RaceID2 to identify clusters. CEL Seq samples: Manual CEL Seq; Satellite cells unstained; Male Pax7nGFP mice 5 mpf 7 mpf; 1h collagenase treated default dissociation protocol; 96 cells per plate with 96 different barcodes see ""Cel seq barcodes 96.csv""; some primes numbers are bulk samples see ""BulkSamples BarcodesAndNrOfCellsUsed perCEL Seq1 library""; Spike ins included see ""ERCC92.fa""; No mitochondrial reads in count tables; Sequencing lanes not concatenated in fastq files uploaded here; ""Merged CEL Seq AllMiceAndLibrariesMerged.csv"" file is count table with reads from all mice and libraries merged Annotation of columns: Zx.y  where Z = mouse  x = library and y = cell barcode; bulk samples are not included any more in this file; See Supplementary Methods for details. SORT Seq 1h and 2h dissociated samples: Robotized CEL Seq2; Satellite cells unstained; Male Pax7nGFP mice 5 mpf 7 mpf; 8 muscles from 4 mice; One plate of 1h default dissociation protocol and one plate of 2h collagenase treated cells; 384 cells per plate with each of the 96 barcodes see ""Cel seq barcodes 96.csv"" used 4 times per plate therefore  each plate has 4 libraries; No bulk samples included; Spike ins included see ""ERCC92.fa""; No mitochondrial reads in count table; In some wells  we sorted no cell internal negative control; barcodes #95 and #96 were used for empty wells; Sequencing lanes not concatenated in fastq files uploaded here; ""Merged SORT Seq DissociationTimecourse.csv"" file is count table were reads from all dissociation timepoints are merged Annotation columns: DZhx y  where Z = 1 or 2 hours collagenase treated  x = library and y = cell barcode; See Supplementary Methods for details. SORT Seq MitoTracker stained samples pilot and repeat: Robotized CEL Seq2 samples; Satellite cells stained with MitoTracker; Female Pax7nGFP mice 1 4.7 mpf mouse for pilot experiment; 3 mpf 6 mpf mice for repeat experiment; 1h collagenase treated default dissociation protocol; 384 cells per plate with each of the 384 barcodes see ""Cel seq barcodes 384.csv"" used 1 times per plate therefore  each plate has 1 library; Note: pilot experiment has 263 cells so plate was partly empty  repeat experiment done with 4 full plates; No bulk samples included; Spike ins included see ""ERCC92.fa""; Mitochondrial reads rows named ""*  chrM"" included in count tables these were removed prior to RaceID2; In some wells  we sorted no cell barcodes #357 #360 and #381 #384 were used for empty wells; Sequencing lanes concatenated in fastq files uploaded here; No merged file was generated for pilot experiment as only one library  ""Merged MitoTracker Repeat.csv"" file is count table were reads from all plates of repeat experiment were merged Annotation of columns: Plx Welly  where x = plate number 1 4 and x = cell barcode; See Supplementary Methods for details. SORT Seq zebrafish fin samples: Robotized CEL Seq2; Fin cells unstained; all live cells; Wildtype zebrafish; Dissociated using default fin dissociation protocol Supplementary Methods; 384 cells per plate with each of the 384 barcodes see ""Cel seq barcodes 384.csv"" used 1 times per plate therefore  each plate has 1 library; Note: only merged count table file ""fin C E count table.csv""  Annotation columns: Xx.py.prim.finZ  where x = cell barcode  y = plate number and Z is fish C or E and no individual library count table files were uploaded to GEO for zebrafish fin data; No bulk samples included; Spike ins not included in merged count tables file; Mitochondrial reads not included in merged count tables file; In some wells  we sorted no cell barcodes #357 #360 and #381 #384 were used for empty wells; Sequencing lanes concatenated in fastq files uploaded here; See Supplementary Methods for details.",,pubmed:28960196,,SORT Seq zebrafish fin merged,GSM2781033,,tissue:All cells from caudal fin|strain:Wildtype,SORT Seq zebrafish fin merged,"Reads 2 were mapped to the reference transcriptome created from the genomes downloaded from the UCSC genome browser; ERCC Spike in sequences and mitochondrial sequences were added in sense direction using bwa version 0.6.2 r126 with default parameters. All isoforms of the same gene were merged to a single gene locus and reads mapping to multiple loci in the transcriptome were discarded. Reads 1 contains the cel specific barcode information first 8 bases followed by a UMI sequence 4bp for unstained satellite cell data; 6bp for MitoTracker Stained satellite cells and zebrafish data and a polyT stretch. Reads 1 were thus used to extract the cell barcode sequences see “Cel seq barcodes 96.csv” file for sequences used for unstained satellite cell data and see ""Cel seq barcodes 384"" for MitoTracker stained satellite cells and zebrafish data and UMIs; see Supplementary Methods for details. post mapping  a UMI correction was applied to the read and barcode counts files to generate unique transcript count tables as described before see Supplementary Methods section for details. Note that processed files for satellite cell data here still contain ERCC Spike in molecules  bulk samples bulk samples are only included in CEL Seq experiments; see “BulkSamples BarcodesAndNrOfCellsUsed perCEL Seq1 library” file for description of how many cells were used as bulk and which primer barcode sequence was used for bulk sample in each library and mitochondrial reads only for MitoTracker stained satellite cells. Genome build: mus musculus: mm10; danio rerio: Zv9 Ensembl release 74; both were extended with spike ins see ""ERCC92.fa"" Supplementary files format and content: *.coutt.csv  *TranscriptCounts.tsv and *count table.csv: tab separated data files listing how many reads of which transcripts were detected in all sequenced cells post UMI correction. Column names refer to cells sequenced in this library numbers refer the the CEL Seq primer barcode used for that cell. The first column lists official gene symbols followed by the chromosome name  separated by a double underscore. Note that processed files for satellite cell data here still contain ERCC Spike in molecules  bulk samples bulk samples are only included in CEL Seq experiments; see “BulkSamples BarcodesAndNrOfCellsUsed perCEL Seq1 library” file for description of how many cells were used as bulk and which primer barcode sequence was used for bulk sample in each library and mitochondrial reads only for MitoTracker stained satellite cells.",All cells from caudal fin,,Cells were sorted into Vapor Lock Qiagen containing a droplet with primers and dNTPs. Cells were lysed at 65 degrees Celsius  post which SORT Seq Muraro et al.  2016  with minor modifications as desribed in Supplementary Methods of van den Brink et al.  2017 was applied. As in SORT Seq protocol Muraro et al.  2016  with minor modifications as desribed in Supplementary Methods of van den Brink et al.  2017.,,strain:Wildtype,GSM2781033,GSM2781033: SORT Seq zebrafish fin merged; Danio rerio; RNA Seq,GSM2781033,,1,Cells were sorted into Vapor Lock Qiagen containing a droplet with primers and dNTPs. Cells were lysed at 65 degrees Celsius  post which SORT Seq Muraro et al.  2016  with minor modifications as desribed in Supplementary Methods of van den Brink et al.  2017 was applied. As in SORT Seq protocol Muraro et al.  2016  with minor modifications as desribed in Supplementary Methods of van den Brink et al.  2017.,GEO Accession:GSM2781033,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP082370,,,FinC_plate02_R1.fastq.gz FinC_plate02_R2.fastq.gz,fastq fastq,5961095878.0,39431358.0,GSM2781033 r2,0:75.66 1:75.51,A:1678045732;C:1185915367;G:1391829821;T:1704836561;N:468397,75,75,,,1678045732,1185915367,1391829821,1704836561,468397,SRX3187382,SRS2515225,SRA453335,GEO,"Alexander van Oudenaarden, Hubrecht Institute",2,0.13015,0.27027,0.11023,0.2177,0.97985,0.95964,0.5491,0.51821,76,76,B,B,mate1-mate2 similar by mapping diff,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Netherlands,2017-09-12,Undetermined,Adult,Fin,Surface Structure
41282,SRR6039227,SRX3187382,SRS2515225,SRP082370,PRJNA339266,Single cell sequencing reveals dissociation induced gene expression in tissue subpopulations,GSE85755,Other,"In many gene expression studies  cells are extracted by tissue dissociation and Fluorescence Activated Cell Sorting FACS  but the effect of these protocols on cellular transcriptomes is not well characterized and often ignored. Here  we applied single cell mRNA sequencing scRNA seq to muscle stem cells  and unexpectedly found a subpopulation that is strongly affected by the widely used dissociation protocol that we employed. One implication of this finding is that several published transcriptomics studies may need to be reinterpreted. Importantly  we detected similar subpopulations in other single cell datasets  suggesting that cells from other tissues might be affected by this artefact as well. Overall design: Mouse satellite cells and zebrafish fin cells were extracted from Tibialis Anterior muscles of Pax7nGFP mice and wildtype zebrafish fins  respectively. For cell extraction  traditional Supplementary Methods dissociation protocols that combine mechanical and enzymatic dissociation were employed  and live cells were subsequently sorted into plates using FACS. Next  single cell mRNA sequencing CEL Seq or SORT Seq robotized version of CEL Seq2 was applied  and data was analyzed with RaceID2 to identify clusters. CEL Seq samples: Manual CEL Seq; Satellite cells unstained; Male Pax7nGFP mice 5 mpf 7 mpf; 1h collagenase treated default dissociation protocol; 96 cells per plate with 96 different barcodes see ""Cel seq barcodes 96.csv""; some primes numbers are bulk samples see ""BulkSamples BarcodesAndNrOfCellsUsed perCEL Seq1 library""; Spike ins included see ""ERCC92.fa""; No mitochondrial reads in count tables; Sequencing lanes not concatenated in fastq files uploaded here; ""Merged CEL Seq AllMiceAndLibrariesMerged.csv"" file is count table with reads from all mice and libraries merged Annotation of columns: Zx.y  where Z = mouse  x = library and y = cell barcode; bulk samples are not included any more in this file; See Supplementary Methods for details. SORT Seq 1h and 2h dissociated samples: Robotized CEL Seq2; Satellite cells unstained; Male Pax7nGFP mice 5 mpf 7 mpf; 8 muscles from 4 mice; One plate of 1h default dissociation protocol and one plate of 2h collagenase treated cells; 384 cells per plate with each of the 96 barcodes see ""Cel seq barcodes 96.csv"" used 4 times per plate therefore  each plate has 4 libraries; No bulk samples included; Spike ins included see ""ERCC92.fa""; No mitochondrial reads in count table; In some wells  we sorted no cell internal negative control; barcodes #95 and #96 were used for empty wells; Sequencing lanes not concatenated in fastq files uploaded here; ""Merged SORT Seq DissociationTimecourse.csv"" file is count table were reads from all dissociation timepoints are merged Annotation columns: DZhx y  where Z = 1 or 2 hours collagenase treated  x = library and y = cell barcode; See Supplementary Methods for details. SORT Seq MitoTracker stained samples pilot and repeat: Robotized CEL Seq2 samples; Satellite cells stained with MitoTracker; Female Pax7nGFP mice 1 4.7 mpf mouse for pilot experiment; 3 mpf 6 mpf mice for repeat experiment; 1h collagenase treated default dissociation protocol; 384 cells per plate with each of the 384 barcodes see ""Cel seq barcodes 384.csv"" used 1 times per plate therefore  each plate has 1 library; Note: pilot experiment has 263 cells so plate was partly empty  repeat experiment done with 4 full plates; No bulk samples included; Spike ins included see ""ERCC92.fa""; Mitochondrial reads rows named ""*  chrM"" included in count tables these were removed prior to RaceID2; In some wells  we sorted no cell barcodes #357 #360 and #381 #384 were used for empty wells; Sequencing lanes concatenated in fastq files uploaded here; No merged file was generated for pilot experiment as only one library  ""Merged MitoTracker Repeat.csv"" file is count table were reads from all plates of repeat experiment were merged Annotation of columns: Plx Welly  where x = plate number 1 4 and x = cell barcode; See Supplementary Methods for details. SORT Seq zebrafish fin samples: Robotized CEL Seq2; Fin cells unstained; all live cells; Wildtype zebrafish; Dissociated using default fin dissociation protocol Supplementary Methods; 384 cells per plate with each of the 384 barcodes see ""Cel seq barcodes 384.csv"" used 1 times per plate therefore  each plate has 1 library; Note: only merged count table file ""fin C E count table.csv""  Annotation columns: Xx.py.prim.finZ  where x = cell barcode  y = plate number and Z is fish C or E and no individual library count table files were uploaded to GEO for zebrafish fin data; No bulk samples included; Spike ins not included in merged count tables file; Mitochondrial reads not included in merged count tables file; In some wells  we sorted no cell barcodes #357 #360 and #381 #384 were used for empty wells; Sequencing lanes concatenated in fastq files uploaded here; See Supplementary Methods for details.",,pubmed:28960196,,SORT Seq zebrafish fin merged,GSM2781033,,tissue:All cells from caudal fin|strain:Wildtype,SORT Seq zebrafish fin merged,"Reads 2 were mapped to the reference transcriptome created from the genomes downloaded from the UCSC genome browser; ERCC Spike in sequences and mitochondrial sequences were added in sense direction using bwa version 0.6.2 r126 with default parameters. All isoforms of the same gene were merged to a single gene locus and reads mapping to multiple loci in the transcriptome were discarded. Reads 1 contains the cel specific barcode information first 8 bases followed by a UMI sequence 4bp for unstained satellite cell data; 6bp for MitoTracker Stained satellite cells and zebrafish data and a polyT stretch. Reads 1 were thus used to extract the cell barcode sequences see “Cel seq barcodes 96.csv” file for sequences used for unstained satellite cell data and see ""Cel seq barcodes 384"" for MitoTracker stained satellite cells and zebrafish data and UMIs; see Supplementary Methods for details. post mapping  a UMI correction was applied to the read and barcode counts files to generate unique transcript count tables as described before see Supplementary Methods section for details. Note that processed files for satellite cell data here still contain ERCC Spike in molecules  bulk samples bulk samples are only included in CEL Seq experiments; see “BulkSamples BarcodesAndNrOfCellsUsed perCEL Seq1 library” file for description of how many cells were used as bulk and which primer barcode sequence was used for bulk sample in each library and mitochondrial reads only for MitoTracker stained satellite cells. Genome build: mus musculus: mm10; danio rerio: Zv9 Ensembl release 74; both were extended with spike ins see ""ERCC92.fa"" Supplementary files format and content: *.coutt.csv  *TranscriptCounts.tsv and *count table.csv: tab separated data files listing how many reads of which transcripts were detected in all sequenced cells post UMI correction. Column names refer to cells sequenced in this library numbers refer the the CEL Seq primer barcode used for that cell. The first column lists official gene symbols followed by the chromosome name  separated by a double underscore. Note that processed files for satellite cell data here still contain ERCC Spike in molecules  bulk samples bulk samples are only included in CEL Seq experiments; see “BulkSamples BarcodesAndNrOfCellsUsed perCEL Seq1 library” file for description of how many cells were used as bulk and which primer barcode sequence was used for bulk sample in each library and mitochondrial reads only for MitoTracker stained satellite cells.",All cells from caudal fin,,Cells were sorted into Vapor Lock Qiagen containing a droplet with primers and dNTPs. Cells were lysed at 65 degrees Celsius  post which SORT Seq Muraro et al.  2016  with minor modifications as desribed in Supplementary Methods of van den Brink et al.  2017 was applied. As in SORT Seq protocol Muraro et al.  2016  with minor modifications as desribed in Supplementary Methods of van den Brink et al.  2017.,,strain:Wildtype,GSM2781033,GSM2781033: SORT Seq zebrafish fin merged; Danio rerio; RNA Seq,GSM2781033,,1,Cells were sorted into Vapor Lock Qiagen containing a droplet with primers and dNTPs. Cells were lysed at 65 degrees Celsius  post which SORT Seq Muraro et al.  2016  with minor modifications as desribed in Supplementary Methods of van den Brink et al.  2017 was applied. As in SORT Seq protocol Muraro et al.  2016  with minor modifications as desribed in Supplementary Methods of van den Brink et al.  2017.,GEO Accession:GSM2781033,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP082370,,,FinC_plate03_R1.fastq.gz FinC_plate03_R2.fastq.gz,fastq fastq,6170232577.0,40846092.0,GSM2781033 r3,0:75.56 1:75.50,A:1866777846;C:1148020988;G:1151073641;T:2003993265;N:366837,75,75,,,1866777846,1148020988,1151073641,2003993265,366837,SRX3187382,SRS2515225,SRA453335,GEO,"Alexander van Oudenaarden, Hubrecht Institute",2,0.21215,0.40881,0.18316,0.33198,0.95919,0.91102,0.49711,0.53044,75,76,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Netherlands,2017-09-12,Undetermined,Adult,Fin,Surface Structure
41283,SRR6039228,SRX3187382,SRS2515225,SRP082370,PRJNA339266,Single cell sequencing reveals dissociation induced gene expression in tissue subpopulations,GSE85755,Other,"In many gene expression studies  cells are extracted by tissue dissociation and Fluorescence Activated Cell Sorting FACS  but the effect of these protocols on cellular transcriptomes is not well characterized and often ignored. Here  we applied single cell mRNA sequencing scRNA seq to muscle stem cells  and unexpectedly found a subpopulation that is strongly affected by the widely used dissociation protocol that we employed. One implication of this finding is that several published transcriptomics studies may need to be reinterpreted. Importantly  we detected similar subpopulations in other single cell datasets  suggesting that cells from other tissues might be affected by this artefact as well. Overall design: Mouse satellite cells and zebrafish fin cells were extracted from Tibialis Anterior muscles of Pax7nGFP mice and wildtype zebrafish fins  respectively. For cell extraction  traditional Supplementary Methods dissociation protocols that combine mechanical and enzymatic dissociation were employed  and live cells were subsequently sorted into plates using FACS. Next  single cell mRNA sequencing CEL Seq or SORT Seq robotized version of CEL Seq2 was applied  and data was analyzed with RaceID2 to identify clusters. CEL Seq samples: Manual CEL Seq; Satellite cells unstained; Male Pax7nGFP mice 5 mpf 7 mpf; 1h collagenase treated default dissociation protocol; 96 cells per plate with 96 different barcodes see ""Cel seq barcodes 96.csv""; some primes numbers are bulk samples see ""BulkSamples BarcodesAndNrOfCellsUsed perCEL Seq1 library""; Spike ins included see ""ERCC92.fa""; No mitochondrial reads in count tables; Sequencing lanes not concatenated in fastq files uploaded here; ""Merged CEL Seq AllMiceAndLibrariesMerged.csv"" file is count table with reads from all mice and libraries merged Annotation of columns: Zx.y  where Z = mouse  x = library and y = cell barcode; bulk samples are not included any more in this file; See Supplementary Methods for details. SORT Seq 1h and 2h dissociated samples: Robotized CEL Seq2; Satellite cells unstained; Male Pax7nGFP mice 5 mpf 7 mpf; 8 muscles from 4 mice; One plate of 1h default dissociation protocol and one plate of 2h collagenase treated cells; 384 cells per plate with each of the 96 barcodes see ""Cel seq barcodes 96.csv"" used 4 times per plate therefore  each plate has 4 libraries; No bulk samples included; Spike ins included see ""ERCC92.fa""; No mitochondrial reads in count table; In some wells  we sorted no cell internal negative control; barcodes #95 and #96 were used for empty wells; Sequencing lanes not concatenated in fastq files uploaded here; ""Merged SORT Seq DissociationTimecourse.csv"" file is count table were reads from all dissociation timepoints are merged Annotation columns: DZhx y  where Z = 1 or 2 hours collagenase treated  x = library and y = cell barcode; See Supplementary Methods for details. SORT Seq MitoTracker stained samples pilot and repeat: Robotized CEL Seq2 samples; Satellite cells stained with MitoTracker; Female Pax7nGFP mice 1 4.7 mpf mouse for pilot experiment; 3 mpf 6 mpf mice for repeat experiment; 1h collagenase treated default dissociation protocol; 384 cells per plate with each of the 384 barcodes see ""Cel seq barcodes 384.csv"" used 1 times per plate therefore  each plate has 1 library; Note: pilot experiment has 263 cells so plate was partly empty  repeat experiment done with 4 full plates; No bulk samples included; Spike ins included see ""ERCC92.fa""; Mitochondrial reads rows named ""*  chrM"" included in count tables these were removed prior to RaceID2; In some wells  we sorted no cell barcodes #357 #360 and #381 #384 were used for empty wells; Sequencing lanes concatenated in fastq files uploaded here; No merged file was generated for pilot experiment as only one library  ""Merged MitoTracker Repeat.csv"" file is count table were reads from all plates of repeat experiment were merged Annotation of columns: Plx Welly  where x = plate number 1 4 and x = cell barcode; See Supplementary Methods for details. SORT Seq zebrafish fin samples: Robotized CEL Seq2; Fin cells unstained; all live cells; Wildtype zebrafish; Dissociated using default fin dissociation protocol Supplementary Methods; 384 cells per plate with each of the 384 barcodes see ""Cel seq barcodes 384.csv"" used 1 times per plate therefore  each plate has 1 library; Note: only merged count table file ""fin C E count table.csv""  Annotation columns: Xx.py.prim.finZ  where x = cell barcode  y = plate number and Z is fish C or E and no individual library count table files were uploaded to GEO for zebrafish fin data; No bulk samples included; Spike ins not included in merged count tables file; Mitochondrial reads not included in merged count tables file; In some wells  we sorted no cell barcodes #357 #360 and #381 #384 were used for empty wells; Sequencing lanes concatenated in fastq files uploaded here; See Supplementary Methods for details.",,pubmed:28960196,,SORT Seq zebrafish fin merged,GSM2781033,,tissue:All cells from caudal fin|strain:Wildtype,SORT Seq zebrafish fin merged,"Reads 2 were mapped to the reference transcriptome created from the genomes downloaded from the UCSC genome browser; ERCC Spike in sequences and mitochondrial sequences were added in sense direction using bwa version 0.6.2 r126 with default parameters. All isoforms of the same gene were merged to a single gene locus and reads mapping to multiple loci in the transcriptome were discarded. Reads 1 contains the cel specific barcode information first 8 bases followed by a UMI sequence 4bp for unstained satellite cell data; 6bp for MitoTracker Stained satellite cells and zebrafish data and a polyT stretch. Reads 1 were thus used to extract the cell barcode sequences see “Cel seq barcodes 96.csv” file for sequences used for unstained satellite cell data and see ""Cel seq barcodes 384"" for MitoTracker stained satellite cells and zebrafish data and UMIs; see Supplementary Methods for details. post mapping  a UMI correction was applied to the read and barcode counts files to generate unique transcript count tables as described before see Supplementary Methods section for details. Note that processed files for satellite cell data here still contain ERCC Spike in molecules  bulk samples bulk samples are only included in CEL Seq experiments; see “BulkSamples BarcodesAndNrOfCellsUsed perCEL Seq1 library” file for description of how many cells were used as bulk and which primer barcode sequence was used for bulk sample in each library and mitochondrial reads only for MitoTracker stained satellite cells. Genome build: mus musculus: mm10; danio rerio: Zv9 Ensembl release 74; both were extended with spike ins see ""ERCC92.fa"" Supplementary files format and content: *.coutt.csv  *TranscriptCounts.tsv and *count table.csv: tab separated data files listing how many reads of which transcripts were detected in all sequenced cells post UMI correction. Column names refer to cells sequenced in this library numbers refer the the CEL Seq primer barcode used for that cell. The first column lists official gene symbols followed by the chromosome name  separated by a double underscore. Note that processed files for satellite cell data here still contain ERCC Spike in molecules  bulk samples bulk samples are only included in CEL Seq experiments; see “BulkSamples BarcodesAndNrOfCellsUsed perCEL Seq1 library” file for description of how many cells were used as bulk and which primer barcode sequence was used for bulk sample in each library and mitochondrial reads only for MitoTracker stained satellite cells.",All cells from caudal fin,,Cells were sorted into Vapor Lock Qiagen containing a droplet with primers and dNTPs. Cells were lysed at 65 degrees Celsius  post which SORT Seq Muraro et al.  2016  with minor modifications as desribed in Supplementary Methods of van den Brink et al.  2017 was applied. As in SORT Seq protocol Muraro et al.  2016  with minor modifications as desribed in Supplementary Methods of van den Brink et al.  2017.,,strain:Wildtype,GSM2781033,GSM2781033: SORT Seq zebrafish fin merged; Danio rerio; RNA Seq,GSM2781033,,1,Cells were sorted into Vapor Lock Qiagen containing a droplet with primers and dNTPs. Cells were lysed at 65 degrees Celsius  post which SORT Seq Muraro et al.  2016  with minor modifications as desribed in Supplementary Methods of van den Brink et al.  2017 was applied. As in SORT Seq protocol Muraro et al.  2016  with minor modifications as desribed in Supplementary Methods of van den Brink et al.  2017.,GEO Accession:GSM2781033,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP082370,,,FinC_plate04_R1.fastq.gz FinC_plate04_R2.fastq.gz,fastq fastq,11725606474.0,77611342.0,GSM2781033 r4,0:75.62 1:75.46,A:3255674293;C:2567072026;G:2847190480;T:3054954945;N:714730,75,75,,,3255674293,2567072026,2847190480,3054954945,714730,SRX3187382,SRS2515225,SRA453335,GEO,"Alexander van Oudenaarden, Hubrecht Institute",2,0.06975,0.13988,0.05976,0.119,0.98533,0.97165,0.50512,0.46229,75,75,B,B,mate1-mate2 similar by mapping diff,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Netherlands,2017-09-12,Undetermined,Adult,Fin,Surface Structure
41284,SRR6039229,SRX3187382,SRS2515225,SRP082370,PRJNA339266,Single cell sequencing reveals dissociation induced gene expression in tissue subpopulations,GSE85755,Other,"In many gene expression studies  cells are extracted by tissue dissociation and Fluorescence Activated Cell Sorting FACS  but the effect of these protocols on cellular transcriptomes is not well characterized and often ignored. Here  we applied single cell mRNA sequencing scRNA seq to muscle stem cells  and unexpectedly found a subpopulation that is strongly affected by the widely used dissociation protocol that we employed. One implication of this finding is that several published transcriptomics studies may need to be reinterpreted. Importantly  we detected similar subpopulations in other single cell datasets  suggesting that cells from other tissues might be affected by this artefact as well. Overall design: Mouse satellite cells and zebrafish fin cells were extracted from Tibialis Anterior muscles of Pax7nGFP mice and wildtype zebrafish fins  respectively. For cell extraction  traditional Supplementary Methods dissociation protocols that combine mechanical and enzymatic dissociation were employed  and live cells were subsequently sorted into plates using FACS. Next  single cell mRNA sequencing CEL Seq or SORT Seq robotized version of CEL Seq2 was applied  and data was analyzed with RaceID2 to identify clusters. CEL Seq samples: Manual CEL Seq; Satellite cells unstained; Male Pax7nGFP mice 5 mpf 7 mpf; 1h collagenase treated default dissociation protocol; 96 cells per plate with 96 different barcodes see ""Cel seq barcodes 96.csv""; some primes numbers are bulk samples see ""BulkSamples BarcodesAndNrOfCellsUsed perCEL Seq1 library""; Spike ins included see ""ERCC92.fa""; No mitochondrial reads in count tables; Sequencing lanes not concatenated in fastq files uploaded here; ""Merged CEL Seq AllMiceAndLibrariesMerged.csv"" file is count table with reads from all mice and libraries merged Annotation of columns: Zx.y  where Z = mouse  x = library and y = cell barcode; bulk samples are not included any more in this file; See Supplementary Methods for details. SORT Seq 1h and 2h dissociated samples: Robotized CEL Seq2; Satellite cells unstained; Male Pax7nGFP mice 5 mpf 7 mpf; 8 muscles from 4 mice; One plate of 1h default dissociation protocol and one plate of 2h collagenase treated cells; 384 cells per plate with each of the 96 barcodes see ""Cel seq barcodes 96.csv"" used 4 times per plate therefore  each plate has 4 libraries; No bulk samples included; Spike ins included see ""ERCC92.fa""; No mitochondrial reads in count table; In some wells  we sorted no cell internal negative control; barcodes #95 and #96 were used for empty wells; Sequencing lanes not concatenated in fastq files uploaded here; ""Merged SORT Seq DissociationTimecourse.csv"" file is count table were reads from all dissociation timepoints are merged Annotation columns: DZhx y  where Z = 1 or 2 hours collagenase treated  x = library and y = cell barcode; See Supplementary Methods for details. SORT Seq MitoTracker stained samples pilot and repeat: Robotized CEL Seq2 samples; Satellite cells stained with MitoTracker; Female Pax7nGFP mice 1 4.7 mpf mouse for pilot experiment; 3 mpf 6 mpf mice for repeat experiment; 1h collagenase treated default dissociation protocol; 384 cells per plate with each of the 384 barcodes see ""Cel seq barcodes 384.csv"" used 1 times per plate therefore  each plate has 1 library; Note: pilot experiment has 263 cells so plate was partly empty  repeat experiment done with 4 full plates; No bulk samples included; Spike ins included see ""ERCC92.fa""; Mitochondrial reads rows named ""*  chrM"" included in count tables these were removed prior to RaceID2; In some wells  we sorted no cell barcodes #357 #360 and #381 #384 were used for empty wells; Sequencing lanes concatenated in fastq files uploaded here; No merged file was generated for pilot experiment as only one library  ""Merged MitoTracker Repeat.csv"" file is count table were reads from all plates of repeat experiment were merged Annotation of columns: Plx Welly  where x = plate number 1 4 and x = cell barcode; See Supplementary Methods for details. SORT Seq zebrafish fin samples: Robotized CEL Seq2; Fin cells unstained; all live cells; Wildtype zebrafish; Dissociated using default fin dissociation protocol Supplementary Methods; 384 cells per plate with each of the 384 barcodes see ""Cel seq barcodes 384.csv"" used 1 times per plate therefore  each plate has 1 library; Note: only merged count table file ""fin C E count table.csv""  Annotation columns: Xx.py.prim.finZ  where x = cell barcode  y = plate number and Z is fish C or E and no individual library count table files were uploaded to GEO for zebrafish fin data; No bulk samples included; Spike ins not included in merged count tables file; Mitochondrial reads not included in merged count tables file; In some wells  we sorted no cell barcodes #357 #360 and #381 #384 were used for empty wells; Sequencing lanes concatenated in fastq files uploaded here; See Supplementary Methods for details.",,pubmed:28960196,,SORT Seq zebrafish fin merged,GSM2781033,,tissue:All cells from caudal fin|strain:Wildtype,SORT Seq zebrafish fin merged,"Reads 2 were mapped to the reference transcriptome created from the genomes downloaded from the UCSC genome browser; ERCC Spike in sequences and mitochondrial sequences were added in sense direction using bwa version 0.6.2 r126 with default parameters. All isoforms of the same gene were merged to a single gene locus and reads mapping to multiple loci in the transcriptome were discarded. Reads 1 contains the cel specific barcode information first 8 bases followed by a UMI sequence 4bp for unstained satellite cell data; 6bp for MitoTracker Stained satellite cells and zebrafish data and a polyT stretch. Reads 1 were thus used to extract the cell barcode sequences see “Cel seq barcodes 96.csv” file for sequences used for unstained satellite cell data and see ""Cel seq barcodes 384"" for MitoTracker stained satellite cells and zebrafish data and UMIs; see Supplementary Methods for details. post mapping  a UMI correction was applied to the read and barcode counts files to generate unique transcript count tables as described before see Supplementary Methods section for details. Note that processed files for satellite cell data here still contain ERCC Spike in molecules  bulk samples bulk samples are only included in CEL Seq experiments; see “BulkSamples BarcodesAndNrOfCellsUsed perCEL Seq1 library” file for description of how many cells were used as bulk and which primer barcode sequence was used for bulk sample in each library and mitochondrial reads only for MitoTracker stained satellite cells. Genome build: mus musculus: mm10; danio rerio: Zv9 Ensembl release 74; both were extended with spike ins see ""ERCC92.fa"" Supplementary files format and content: *.coutt.csv  *TranscriptCounts.tsv and *count table.csv: tab separated data files listing how many reads of which transcripts were detected in all sequenced cells post UMI correction. Column names refer to cells sequenced in this library numbers refer the the CEL Seq primer barcode used for that cell. The first column lists official gene symbols followed by the chromosome name  separated by a double underscore. Note that processed files for satellite cell data here still contain ERCC Spike in molecules  bulk samples bulk samples are only included in CEL Seq experiments; see “BulkSamples BarcodesAndNrOfCellsUsed perCEL Seq1 library” file for description of how many cells were used as bulk and which primer barcode sequence was used for bulk sample in each library and mitochondrial reads only for MitoTracker stained satellite cells.",All cells from caudal fin,,Cells were sorted into Vapor Lock Qiagen containing a droplet with primers and dNTPs. Cells were lysed at 65 degrees Celsius  post which SORT Seq Muraro et al.  2016  with minor modifications as desribed in Supplementary Methods of van den Brink et al.  2017 was applied. As in SORT Seq protocol Muraro et al.  2016  with minor modifications as desribed in Supplementary Methods of van den Brink et al.  2017.,,strain:Wildtype,GSM2781033,GSM2781033: SORT Seq zebrafish fin merged; Danio rerio; RNA Seq,GSM2781033,,1,Cells were sorted into Vapor Lock Qiagen containing a droplet with primers and dNTPs. Cells were lysed at 65 degrees Celsius  post which SORT Seq Muraro et al.  2016  with minor modifications as desribed in Supplementary Methods of van den Brink et al.  2017 was applied. As in SORT Seq protocol Muraro et al.  2016  with minor modifications as desribed in Supplementary Methods of van den Brink et al.  2017.,GEO Accession:GSM2781033,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP082370,,,FinC_plate05_R1.fastq.gz FinC_plate05_R2.fastq.gz,fastq fastq,10721896827.0,71080622.0,GSM2781033 r5,0:75.44 1:75.41,A:3568478635;C:1747554798;G:1675757438;T:3729472140;N:633816,75,75,,,3568478635,1747554798,1675757438,3729472140,633816,SRX3187382,SRS2515225,SRA453335,GEO,"Alexander van Oudenaarden, Hubrecht Institute",2,0.32303,0.52716,0.2796,0.43703,0.94276,0.90057,0.51543,0.52404,75,75,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Netherlands,2017-09-12,Undetermined,Adult,Fin,Surface Structure
41285,SRR6039230,SRX3187382,SRS2515225,SRP082370,PRJNA339266,Single cell sequencing reveals dissociation induced gene expression in tissue subpopulations,GSE85755,Other,"In many gene expression studies  cells are extracted by tissue dissociation and Fluorescence Activated Cell Sorting FACS  but the effect of these protocols on cellular transcriptomes is not well characterized and often ignored. Here  we applied single cell mRNA sequencing scRNA seq to muscle stem cells  and unexpectedly found a subpopulation that is strongly affected by the widely used dissociation protocol that we employed. One implication of this finding is that several published transcriptomics studies may need to be reinterpreted. Importantly  we detected similar subpopulations in other single cell datasets  suggesting that cells from other tissues might be affected by this artefact as well. Overall design: Mouse satellite cells and zebrafish fin cells were extracted from Tibialis Anterior muscles of Pax7nGFP mice and wildtype zebrafish fins  respectively. For cell extraction  traditional Supplementary Methods dissociation protocols that combine mechanical and enzymatic dissociation were employed  and live cells were subsequently sorted into plates using FACS. Next  single cell mRNA sequencing CEL Seq or SORT Seq robotized version of CEL Seq2 was applied  and data was analyzed with RaceID2 to identify clusters. CEL Seq samples: Manual CEL Seq; Satellite cells unstained; Male Pax7nGFP mice 5 mpf 7 mpf; 1h collagenase treated default dissociation protocol; 96 cells per plate with 96 different barcodes see ""Cel seq barcodes 96.csv""; some primes numbers are bulk samples see ""BulkSamples BarcodesAndNrOfCellsUsed perCEL Seq1 library""; Spike ins included see ""ERCC92.fa""; No mitochondrial reads in count tables; Sequencing lanes not concatenated in fastq files uploaded here; ""Merged CEL Seq AllMiceAndLibrariesMerged.csv"" file is count table with reads from all mice and libraries merged Annotation of columns: Zx.y  where Z = mouse  x = library and y = cell barcode; bulk samples are not included any more in this file; See Supplementary Methods for details. SORT Seq 1h and 2h dissociated samples: Robotized CEL Seq2; Satellite cells unstained; Male Pax7nGFP mice 5 mpf 7 mpf; 8 muscles from 4 mice; One plate of 1h default dissociation protocol and one plate of 2h collagenase treated cells; 384 cells per plate with each of the 96 barcodes see ""Cel seq barcodes 96.csv"" used 4 times per plate therefore  each plate has 4 libraries; No bulk samples included; Spike ins included see ""ERCC92.fa""; No mitochondrial reads in count table; In some wells  we sorted no cell internal negative control; barcodes #95 and #96 were used for empty wells; Sequencing lanes not concatenated in fastq files uploaded here; ""Merged SORT Seq DissociationTimecourse.csv"" file is count table were reads from all dissociation timepoints are merged Annotation columns: DZhx y  where Z = 1 or 2 hours collagenase treated  x = library and y = cell barcode; See Supplementary Methods for details. SORT Seq MitoTracker stained samples pilot and repeat: Robotized CEL Seq2 samples; Satellite cells stained with MitoTracker; Female Pax7nGFP mice 1 4.7 mpf mouse for pilot experiment; 3 mpf 6 mpf mice for repeat experiment; 1h collagenase treated default dissociation protocol; 384 cells per plate with each of the 384 barcodes see ""Cel seq barcodes 384.csv"" used 1 times per plate therefore  each plate has 1 library; Note: pilot experiment has 263 cells so plate was partly empty  repeat experiment done with 4 full plates; No bulk samples included; Spike ins included see ""ERCC92.fa""; Mitochondrial reads rows named ""*  chrM"" included in count tables these were removed prior to RaceID2; In some wells  we sorted no cell barcodes #357 #360 and #381 #384 were used for empty wells; Sequencing lanes concatenated in fastq files uploaded here; No merged file was generated for pilot experiment as only one library  ""Merged MitoTracker Repeat.csv"" file is count table were reads from all plates of repeat experiment were merged Annotation of columns: Plx Welly  where x = plate number 1 4 and x = cell barcode; See Supplementary Methods for details. SORT Seq zebrafish fin samples: Robotized CEL Seq2; Fin cells unstained; all live cells; Wildtype zebrafish; Dissociated using default fin dissociation protocol Supplementary Methods; 384 cells per plate with each of the 384 barcodes see ""Cel seq barcodes 384.csv"" used 1 times per plate therefore  each plate has 1 library; Note: only merged count table file ""fin C E count table.csv""  Annotation columns: Xx.py.prim.finZ  where x = cell barcode  y = plate number and Z is fish C or E and no individual library count table files were uploaded to GEO for zebrafish fin data; No bulk samples included; Spike ins not included in merged count tables file; Mitochondrial reads not included in merged count tables file; In some wells  we sorted no cell barcodes #357 #360 and #381 #384 were used for empty wells; Sequencing lanes concatenated in fastq files uploaded here; See Supplementary Methods for details.",,pubmed:28960196,,SORT Seq zebrafish fin merged,GSM2781033,,tissue:All cells from caudal fin|strain:Wildtype,SORT Seq zebrafish fin merged,"Reads 2 were mapped to the reference transcriptome created from the genomes downloaded from the UCSC genome browser; ERCC Spike in sequences and mitochondrial sequences were added in sense direction using bwa version 0.6.2 r126 with default parameters. All isoforms of the same gene were merged to a single gene locus and reads mapping to multiple loci in the transcriptome were discarded. Reads 1 contains the cel specific barcode information first 8 bases followed by a UMI sequence 4bp for unstained satellite cell data; 6bp for MitoTracker Stained satellite cells and zebrafish data and a polyT stretch. Reads 1 were thus used to extract the cell barcode sequences see “Cel seq barcodes 96.csv” file for sequences used for unstained satellite cell data and see ""Cel seq barcodes 384"" for MitoTracker stained satellite cells and zebrafish data and UMIs; see Supplementary Methods for details. post mapping  a UMI correction was applied to the read and barcode counts files to generate unique transcript count tables as described before see Supplementary Methods section for details. Note that processed files for satellite cell data here still contain ERCC Spike in molecules  bulk samples bulk samples are only included in CEL Seq experiments; see “BulkSamples BarcodesAndNrOfCellsUsed perCEL Seq1 library” file for description of how many cells were used as bulk and which primer barcode sequence was used for bulk sample in each library and mitochondrial reads only for MitoTracker stained satellite cells. Genome build: mus musculus: mm10; danio rerio: Zv9 Ensembl release 74; both were extended with spike ins see ""ERCC92.fa"" Supplementary files format and content: *.coutt.csv  *TranscriptCounts.tsv and *count table.csv: tab separated data files listing how many reads of which transcripts were detected in all sequenced cells post UMI correction. Column names refer to cells sequenced in this library numbers refer the the CEL Seq primer barcode used for that cell. The first column lists official gene symbols followed by the chromosome name  separated by a double underscore. Note that processed files for satellite cell data here still contain ERCC Spike in molecules  bulk samples bulk samples are only included in CEL Seq experiments; see “BulkSamples BarcodesAndNrOfCellsUsed perCEL Seq1 library” file for description of how many cells were used as bulk and which primer barcode sequence was used for bulk sample in each library and mitochondrial reads only for MitoTracker stained satellite cells.",All cells from caudal fin,,Cells were sorted into Vapor Lock Qiagen containing a droplet with primers and dNTPs. Cells were lysed at 65 degrees Celsius  post which SORT Seq Muraro et al.  2016  with minor modifications as desribed in Supplementary Methods of van den Brink et al.  2017 was applied. As in SORT Seq protocol Muraro et al.  2016  with minor modifications as desribed in Supplementary Methods of van den Brink et al.  2017.,,strain:Wildtype,GSM2781033,GSM2781033: SORT Seq zebrafish fin merged; Danio rerio; RNA Seq,GSM2781033,,1,Cells were sorted into Vapor Lock Qiagen containing a droplet with primers and dNTPs. Cells were lysed at 65 degrees Celsius  post which SORT Seq Muraro et al.  2016  with minor modifications as desribed in Supplementary Methods of van den Brink et al.  2017 was applied. As in SORT Seq protocol Muraro et al.  2016  with minor modifications as desribed in Supplementary Methods of van den Brink et al.  2017.,GEO Accession:GSM2781033,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP082370,,,FinC_plate06_R1.fastq.gz FinC_plate06_R2.fastq.gz,fastq fastq,4861560177.0,32218130.0,GSM2781033 r6,0:75.46 1:75.44,A:1606516776;C:766379277;G:687731226;T:1800636189;N:296709,75,75,,,1606516776,766379277,687731226,1800636189,296709,SRX3187382,SRS2515225,SRA453335,GEO,"Alexander van Oudenaarden, Hubrecht Institute",2,0.40204,0.66185,0.35053,0.55748,0.94637,0.89148,0.48866,0.50482,75,75,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Netherlands,2017-09-12,Undetermined,Adult,Fin,Surface Structure
41286,SRR6039231,SRX3187382,SRS2515225,SRP082370,PRJNA339266,Single cell sequencing reveals dissociation induced gene expression in tissue subpopulations,GSE85755,Other,"In many gene expression studies  cells are extracted by tissue dissociation and Fluorescence Activated Cell Sorting FACS  but the effect of these protocols on cellular transcriptomes is not well characterized and often ignored. Here  we applied single cell mRNA sequencing scRNA seq to muscle stem cells  and unexpectedly found a subpopulation that is strongly affected by the widely used dissociation protocol that we employed. One implication of this finding is that several published transcriptomics studies may need to be reinterpreted. Importantly  we detected similar subpopulations in other single cell datasets  suggesting that cells from other tissues might be affected by this artefact as well. Overall design: Mouse satellite cells and zebrafish fin cells were extracted from Tibialis Anterior muscles of Pax7nGFP mice and wildtype zebrafish fins  respectively. For cell extraction  traditional Supplementary Methods dissociation protocols that combine mechanical and enzymatic dissociation were employed  and live cells were subsequently sorted into plates using FACS. Next  single cell mRNA sequencing CEL Seq or SORT Seq robotized version of CEL Seq2 was applied  and data was analyzed with RaceID2 to identify clusters. CEL Seq samples: Manual CEL Seq; Satellite cells unstained; Male Pax7nGFP mice 5 mpf 7 mpf; 1h collagenase treated default dissociation protocol; 96 cells per plate with 96 different barcodes see ""Cel seq barcodes 96.csv""; some primes numbers are bulk samples see ""BulkSamples BarcodesAndNrOfCellsUsed perCEL Seq1 library""; Spike ins included see ""ERCC92.fa""; No mitochondrial reads in count tables; Sequencing lanes not concatenated in fastq files uploaded here; ""Merged CEL Seq AllMiceAndLibrariesMerged.csv"" file is count table with reads from all mice and libraries merged Annotation of columns: Zx.y  where Z = mouse  x = library and y = cell barcode; bulk samples are not included any more in this file; See Supplementary Methods for details. SORT Seq 1h and 2h dissociated samples: Robotized CEL Seq2; Satellite cells unstained; Male Pax7nGFP mice 5 mpf 7 mpf; 8 muscles from 4 mice; One plate of 1h default dissociation protocol and one plate of 2h collagenase treated cells; 384 cells per plate with each of the 96 barcodes see ""Cel seq barcodes 96.csv"" used 4 times per plate therefore  each plate has 4 libraries; No bulk samples included; Spike ins included see ""ERCC92.fa""; No mitochondrial reads in count table; In some wells  we sorted no cell internal negative control; barcodes #95 and #96 were used for empty wells; Sequencing lanes not concatenated in fastq files uploaded here; ""Merged SORT Seq DissociationTimecourse.csv"" file is count table were reads from all dissociation timepoints are merged Annotation columns: DZhx y  where Z = 1 or 2 hours collagenase treated  x = library and y = cell barcode; See Supplementary Methods for details. SORT Seq MitoTracker stained samples pilot and repeat: Robotized CEL Seq2 samples; Satellite cells stained with MitoTracker; Female Pax7nGFP mice 1 4.7 mpf mouse for pilot experiment; 3 mpf 6 mpf mice for repeat experiment; 1h collagenase treated default dissociation protocol; 384 cells per plate with each of the 384 barcodes see ""Cel seq barcodes 384.csv"" used 1 times per plate therefore  each plate has 1 library; Note: pilot experiment has 263 cells so plate was partly empty  repeat experiment done with 4 full plates; No bulk samples included; Spike ins included see ""ERCC92.fa""; Mitochondrial reads rows named ""*  chrM"" included in count tables these were removed prior to RaceID2; In some wells  we sorted no cell barcodes #357 #360 and #381 #384 were used for empty wells; Sequencing lanes concatenated in fastq files uploaded here; No merged file was generated for pilot experiment as only one library  ""Merged MitoTracker Repeat.csv"" file is count table were reads from all plates of repeat experiment were merged Annotation of columns: Plx Welly  where x = plate number 1 4 and x = cell barcode; See Supplementary Methods for details. SORT Seq zebrafish fin samples: Robotized CEL Seq2; Fin cells unstained; all live cells; Wildtype zebrafish; Dissociated using default fin dissociation protocol Supplementary Methods; 384 cells per plate with each of the 384 barcodes see ""Cel seq barcodes 384.csv"" used 1 times per plate therefore  each plate has 1 library; Note: only merged count table file ""fin C E count table.csv""  Annotation columns: Xx.py.prim.finZ  where x = cell barcode  y = plate number and Z is fish C or E and no individual library count table files were uploaded to GEO for zebrafish fin data; No bulk samples included; Spike ins not included in merged count tables file; Mitochondrial reads not included in merged count tables file; In some wells  we sorted no cell barcodes #357 #360 and #381 #384 were used for empty wells; Sequencing lanes concatenated in fastq files uploaded here; See Supplementary Methods for details.",,pubmed:28960196,,SORT Seq zebrafish fin merged,GSM2781033,,tissue:All cells from caudal fin|strain:Wildtype,SORT Seq zebrafish fin merged,"Reads 2 were mapped to the reference transcriptome created from the genomes downloaded from the UCSC genome browser; ERCC Spike in sequences and mitochondrial sequences were added in sense direction using bwa version 0.6.2 r126 with default parameters. All isoforms of the same gene were merged to a single gene locus and reads mapping to multiple loci in the transcriptome were discarded. Reads 1 contains the cel specific barcode information first 8 bases followed by a UMI sequence 4bp for unstained satellite cell data; 6bp for MitoTracker Stained satellite cells and zebrafish data and a polyT stretch. Reads 1 were thus used to extract the cell barcode sequences see “Cel seq barcodes 96.csv” file for sequences used for unstained satellite cell data and see ""Cel seq barcodes 384"" for MitoTracker stained satellite cells and zebrafish data and UMIs; see Supplementary Methods for details. post mapping  a UMI correction was applied to the read and barcode counts files to generate unique transcript count tables as described before see Supplementary Methods section for details. Note that processed files for satellite cell data here still contain ERCC Spike in molecules  bulk samples bulk samples are only included in CEL Seq experiments; see “BulkSamples BarcodesAndNrOfCellsUsed perCEL Seq1 library” file for description of how many cells were used as bulk and which primer barcode sequence was used for bulk sample in each library and mitochondrial reads only for MitoTracker stained satellite cells. Genome build: mus musculus: mm10; danio rerio: Zv9 Ensembl release 74; both were extended with spike ins see ""ERCC92.fa"" Supplementary files format and content: *.coutt.csv  *TranscriptCounts.tsv and *count table.csv: tab separated data files listing how many reads of which transcripts were detected in all sequenced cells post UMI correction. Column names refer to cells sequenced in this library numbers refer the the CEL Seq primer barcode used for that cell. The first column lists official gene symbols followed by the chromosome name  separated by a double underscore. Note that processed files for satellite cell data here still contain ERCC Spike in molecules  bulk samples bulk samples are only included in CEL Seq experiments; see “BulkSamples BarcodesAndNrOfCellsUsed perCEL Seq1 library” file for description of how many cells were used as bulk and which primer barcode sequence was used for bulk sample in each library and mitochondrial reads only for MitoTracker stained satellite cells.",All cells from caudal fin,,Cells were sorted into Vapor Lock Qiagen containing a droplet with primers and dNTPs. Cells were lysed at 65 degrees Celsius  post which SORT Seq Muraro et al.  2016  with minor modifications as desribed in Supplementary Methods of van den Brink et al.  2017 was applied. As in SORT Seq protocol Muraro et al.  2016  with minor modifications as desribed in Supplementary Methods of van den Brink et al.  2017.,,strain:Wildtype,GSM2781033,GSM2781033: SORT Seq zebrafish fin merged; Danio rerio; RNA Seq,GSM2781033,,1,Cells were sorted into Vapor Lock Qiagen containing a droplet with primers and dNTPs. Cells were lysed at 65 degrees Celsius  post which SORT Seq Muraro et al.  2016  with minor modifications as desribed in Supplementary Methods of van den Brink et al.  2017 was applied. As in SORT Seq protocol Muraro et al.  2016  with minor modifications as desribed in Supplementary Methods of van den Brink et al.  2017.,GEO Accession:GSM2781033,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP082370,,,FinE_plate02_R1.fastq.gz FinE_plate02_R2.fastq.gz,fastq fastq,7812360278.0,51697480.0,GSM2781033 r7,0:75.54 1:75.58,A:2098454376;C:1641311761;G:1943503636;T:2128270555;N:819950,75,75,,,2098454376,1641311761,1943503636,2128270555,819950,SRX3187382,SRS2515225,SRA453335,GEO,"Alexander van Oudenaarden, Hubrecht Institute",2,0.0105,0.02592,0.00852,0.02011,0.99626,0.98754,0.33762,0.53206,76,75,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Netherlands,2017-09-12,Undetermined,Adult,Fin,Surface Structure
41287,SRR6039232,SRX3187382,SRS2515225,SRP082370,PRJNA339266,Single cell sequencing reveals dissociation induced gene expression in tissue subpopulations,GSE85755,Other,"In many gene expression studies  cells are extracted by tissue dissociation and Fluorescence Activated Cell Sorting FACS  but the effect of these protocols on cellular transcriptomes is not well characterized and often ignored. Here  we applied single cell mRNA sequencing scRNA seq to muscle stem cells  and unexpectedly found a subpopulation that is strongly affected by the widely used dissociation protocol that we employed. One implication of this finding is that several published transcriptomics studies may need to be reinterpreted. Importantly  we detected similar subpopulations in other single cell datasets  suggesting that cells from other tissues might be affected by this artefact as well. Overall design: Mouse satellite cells and zebrafish fin cells were extracted from Tibialis Anterior muscles of Pax7nGFP mice and wildtype zebrafish fins  respectively. For cell extraction  traditional Supplementary Methods dissociation protocols that combine mechanical and enzymatic dissociation were employed  and live cells were subsequently sorted into plates using FACS. Next  single cell mRNA sequencing CEL Seq or SORT Seq robotized version of CEL Seq2 was applied  and data was analyzed with RaceID2 to identify clusters. CEL Seq samples: Manual CEL Seq; Satellite cells unstained; Male Pax7nGFP mice 5 mpf 7 mpf; 1h collagenase treated default dissociation protocol; 96 cells per plate with 96 different barcodes see ""Cel seq barcodes 96.csv""; some primes numbers are bulk samples see ""BulkSamples BarcodesAndNrOfCellsUsed perCEL Seq1 library""; Spike ins included see ""ERCC92.fa""; No mitochondrial reads in count tables; Sequencing lanes not concatenated in fastq files uploaded here; ""Merged CEL Seq AllMiceAndLibrariesMerged.csv"" file is count table with reads from all mice and libraries merged Annotation of columns: Zx.y  where Z = mouse  x = library and y = cell barcode; bulk samples are not included any more in this file; See Supplementary Methods for details. SORT Seq 1h and 2h dissociated samples: Robotized CEL Seq2; Satellite cells unstained; Male Pax7nGFP mice 5 mpf 7 mpf; 8 muscles from 4 mice; One plate of 1h default dissociation protocol and one plate of 2h collagenase treated cells; 384 cells per plate with each of the 96 barcodes see ""Cel seq barcodes 96.csv"" used 4 times per plate therefore  each plate has 4 libraries; No bulk samples included; Spike ins included see ""ERCC92.fa""; No mitochondrial reads in count table; In some wells  we sorted no cell internal negative control; barcodes #95 and #96 were used for empty wells; Sequencing lanes not concatenated in fastq files uploaded here; ""Merged SORT Seq DissociationTimecourse.csv"" file is count table were reads from all dissociation timepoints are merged Annotation columns: DZhx y  where Z = 1 or 2 hours collagenase treated  x = library and y = cell barcode; See Supplementary Methods for details. SORT Seq MitoTracker stained samples pilot and repeat: Robotized CEL Seq2 samples; Satellite cells stained with MitoTracker; Female Pax7nGFP mice 1 4.7 mpf mouse for pilot experiment; 3 mpf 6 mpf mice for repeat experiment; 1h collagenase treated default dissociation protocol; 384 cells per plate with each of the 384 barcodes see ""Cel seq barcodes 384.csv"" used 1 times per plate therefore  each plate has 1 library; Note: pilot experiment has 263 cells so plate was partly empty  repeat experiment done with 4 full plates; No bulk samples included; Spike ins included see ""ERCC92.fa""; Mitochondrial reads rows named ""*  chrM"" included in count tables these were removed prior to RaceID2; In some wells  we sorted no cell barcodes #357 #360 and #381 #384 were used for empty wells; Sequencing lanes concatenated in fastq files uploaded here; No merged file was generated for pilot experiment as only one library  ""Merged MitoTracker Repeat.csv"" file is count table were reads from all plates of repeat experiment were merged Annotation of columns: Plx Welly  where x = plate number 1 4 and x = cell barcode; See Supplementary Methods for details. SORT Seq zebrafish fin samples: Robotized CEL Seq2; Fin cells unstained; all live cells; Wildtype zebrafish; Dissociated using default fin dissociation protocol Supplementary Methods; 384 cells per plate with each of the 384 barcodes see ""Cel seq barcodes 384.csv"" used 1 times per plate therefore  each plate has 1 library; Note: only merged count table file ""fin C E count table.csv""  Annotation columns: Xx.py.prim.finZ  where x = cell barcode  y = plate number and Z is fish C or E and no individual library count table files were uploaded to GEO for zebrafish fin data; No bulk samples included; Spike ins not included in merged count tables file; Mitochondrial reads not included in merged count tables file; In some wells  we sorted no cell barcodes #357 #360 and #381 #384 were used for empty wells; Sequencing lanes concatenated in fastq files uploaded here; See Supplementary Methods for details.",,pubmed:28960196,,SORT Seq zebrafish fin merged,GSM2781033,,tissue:All cells from caudal fin|strain:Wildtype,SORT Seq zebrafish fin merged,"Reads 2 were mapped to the reference transcriptome created from the genomes downloaded from the UCSC genome browser; ERCC Spike in sequences and mitochondrial sequences were added in sense direction using bwa version 0.6.2 r126 with default parameters. All isoforms of the same gene were merged to a single gene locus and reads mapping to multiple loci in the transcriptome were discarded. Reads 1 contains the cel specific barcode information first 8 bases followed by a UMI sequence 4bp for unstained satellite cell data; 6bp for MitoTracker Stained satellite cells and zebrafish data and a polyT stretch. Reads 1 were thus used to extract the cell barcode sequences see “Cel seq barcodes 96.csv” file for sequences used for unstained satellite cell data and see ""Cel seq barcodes 384"" for MitoTracker stained satellite cells and zebrafish data and UMIs; see Supplementary Methods for details. post mapping  a UMI correction was applied to the read and barcode counts files to generate unique transcript count tables as described before see Supplementary Methods section for details. Note that processed files for satellite cell data here still contain ERCC Spike in molecules  bulk samples bulk samples are only included in CEL Seq experiments; see “BulkSamples BarcodesAndNrOfCellsUsed perCEL Seq1 library” file for description of how many cells were used as bulk and which primer barcode sequence was used for bulk sample in each library and mitochondrial reads only for MitoTracker stained satellite cells. Genome build: mus musculus: mm10; danio rerio: Zv9 Ensembl release 74; both were extended with spike ins see ""ERCC92.fa"" Supplementary files format and content: *.coutt.csv  *TranscriptCounts.tsv and *count table.csv: tab separated data files listing how many reads of which transcripts were detected in all sequenced cells post UMI correction. Column names refer to cells sequenced in this library numbers refer the the CEL Seq primer barcode used for that cell. The first column lists official gene symbols followed by the chromosome name  separated by a double underscore. Note that processed files for satellite cell data here still contain ERCC Spike in molecules  bulk samples bulk samples are only included in CEL Seq experiments; see “BulkSamples BarcodesAndNrOfCellsUsed perCEL Seq1 library” file for description of how many cells were used as bulk and which primer barcode sequence was used for bulk sample in each library and mitochondrial reads only for MitoTracker stained satellite cells.",All cells from caudal fin,,Cells were sorted into Vapor Lock Qiagen containing a droplet with primers and dNTPs. Cells were lysed at 65 degrees Celsius  post which SORT Seq Muraro et al.  2016  with minor modifications as desribed in Supplementary Methods of van den Brink et al.  2017 was applied. As in SORT Seq protocol Muraro et al.  2016  with minor modifications as desribed in Supplementary Methods of van den Brink et al.  2017.,,strain:Wildtype,GSM2781033,GSM2781033: SORT Seq zebrafish fin merged; Danio rerio; RNA Seq,GSM2781033,,1,Cells were sorted into Vapor Lock Qiagen containing a droplet with primers and dNTPs. Cells were lysed at 65 degrees Celsius  post which SORT Seq Muraro et al.  2016  with minor modifications as desribed in Supplementary Methods of van den Brink et al.  2017 was applied. As in SORT Seq protocol Muraro et al.  2016  with minor modifications as desribed in Supplementary Methods of van den Brink et al.  2017.,GEO Accession:GSM2781033,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP082370,,,FinE_plate03_R1.fastq.gz FinE_plate03_R2.fastq.gz,fastq fastq,6704494628.0,44436630.0,GSM2781033 r8,0:75.49 1:75.39,A:2087008571;C:1124579474;G:1252171872;T:2240541544;N:193167,75,75,,,2087008571,1124579474,1252171872,2240541544,193167,SRX3187382,SRS2515225,SRA453335,GEO,"Alexander van Oudenaarden, Hubrecht Institute",2,0.24968,0.47949,0.2198,0.40276,0.95154,0.89238,0.48976,0.54355,75,75,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Netherlands,2017-09-12,Undetermined,Adult,Fin,Surface Structure
41288,SRR6039233,SRX3187382,SRS2515225,SRP082370,PRJNA339266,Single cell sequencing reveals dissociation induced gene expression in tissue subpopulations,GSE85755,Other,"In many gene expression studies  cells are extracted by tissue dissociation and Fluorescence Activated Cell Sorting FACS  but the effect of these protocols on cellular transcriptomes is not well characterized and often ignored. Here  we applied single cell mRNA sequencing scRNA seq to muscle stem cells  and unexpectedly found a subpopulation that is strongly affected by the widely used dissociation protocol that we employed. One implication of this finding is that several published transcriptomics studies may need to be reinterpreted. Importantly  we detected similar subpopulations in other single cell datasets  suggesting that cells from other tissues might be affected by this artefact as well. Overall design: Mouse satellite cells and zebrafish fin cells were extracted from Tibialis Anterior muscles of Pax7nGFP mice and wildtype zebrafish fins  respectively. For cell extraction  traditional Supplementary Methods dissociation protocols that combine mechanical and enzymatic dissociation were employed  and live cells were subsequently sorted into plates using FACS. Next  single cell mRNA sequencing CEL Seq or SORT Seq robotized version of CEL Seq2 was applied  and data was analyzed with RaceID2 to identify clusters. CEL Seq samples: Manual CEL Seq; Satellite cells unstained; Male Pax7nGFP mice 5 mpf 7 mpf; 1h collagenase treated default dissociation protocol; 96 cells per plate with 96 different barcodes see ""Cel seq barcodes 96.csv""; some primes numbers are bulk samples see ""BulkSamples BarcodesAndNrOfCellsUsed perCEL Seq1 library""; Spike ins included see ""ERCC92.fa""; No mitochondrial reads in count tables; Sequencing lanes not concatenated in fastq files uploaded here; ""Merged CEL Seq AllMiceAndLibrariesMerged.csv"" file is count table with reads from all mice and libraries merged Annotation of columns: Zx.y  where Z = mouse  x = library and y = cell barcode; bulk samples are not included any more in this file; See Supplementary Methods for details. SORT Seq 1h and 2h dissociated samples: Robotized CEL Seq2; Satellite cells unstained; Male Pax7nGFP mice 5 mpf 7 mpf; 8 muscles from 4 mice; One plate of 1h default dissociation protocol and one plate of 2h collagenase treated cells; 384 cells per plate with each of the 96 barcodes see ""Cel seq barcodes 96.csv"" used 4 times per plate therefore  each plate has 4 libraries; No bulk samples included; Spike ins included see ""ERCC92.fa""; No mitochondrial reads in count table; In some wells  we sorted no cell internal negative control; barcodes #95 and #96 were used for empty wells; Sequencing lanes not concatenated in fastq files uploaded here; ""Merged SORT Seq DissociationTimecourse.csv"" file is count table were reads from all dissociation timepoints are merged Annotation columns: DZhx y  where Z = 1 or 2 hours collagenase treated  x = library and y = cell barcode; See Supplementary Methods for details. SORT Seq MitoTracker stained samples pilot and repeat: Robotized CEL Seq2 samples; Satellite cells stained with MitoTracker; Female Pax7nGFP mice 1 4.7 mpf mouse for pilot experiment; 3 mpf 6 mpf mice for repeat experiment; 1h collagenase treated default dissociation protocol; 384 cells per plate with each of the 384 barcodes see ""Cel seq barcodes 384.csv"" used 1 times per plate therefore  each plate has 1 library; Note: pilot experiment has 263 cells so plate was partly empty  repeat experiment done with 4 full plates; No bulk samples included; Spike ins included see ""ERCC92.fa""; Mitochondrial reads rows named ""*  chrM"" included in count tables these were removed prior to RaceID2; In some wells  we sorted no cell barcodes #357 #360 and #381 #384 were used for empty wells; Sequencing lanes concatenated in fastq files uploaded here; No merged file was generated for pilot experiment as only one library  ""Merged MitoTracker Repeat.csv"" file is count table were reads from all plates of repeat experiment were merged Annotation of columns: Plx Welly  where x = plate number 1 4 and x = cell barcode; See Supplementary Methods for details. SORT Seq zebrafish fin samples: Robotized CEL Seq2; Fin cells unstained; all live cells; Wildtype zebrafish; Dissociated using default fin dissociation protocol Supplementary Methods; 384 cells per plate with each of the 384 barcodes see ""Cel seq barcodes 384.csv"" used 1 times per plate therefore  each plate has 1 library; Note: only merged count table file ""fin C E count table.csv""  Annotation columns: Xx.py.prim.finZ  where x = cell barcode  y = plate number and Z is fish C or E and no individual library count table files were uploaded to GEO for zebrafish fin data; No bulk samples included; Spike ins not included in merged count tables file; Mitochondrial reads not included in merged count tables file; In some wells  we sorted no cell barcodes #357 #360 and #381 #384 were used for empty wells; Sequencing lanes concatenated in fastq files uploaded here; See Supplementary Methods for details.",,pubmed:28960196,,SORT Seq zebrafish fin merged,GSM2781033,,tissue:All cells from caudal fin|strain:Wildtype,SORT Seq zebrafish fin merged,"Reads 2 were mapped to the reference transcriptome created from the genomes downloaded from the UCSC genome browser; ERCC Spike in sequences and mitochondrial sequences were added in sense direction using bwa version 0.6.2 r126 with default parameters. All isoforms of the same gene were merged to a single gene locus and reads mapping to multiple loci in the transcriptome were discarded. Reads 1 contains the cel specific barcode information first 8 bases followed by a UMI sequence 4bp for unstained satellite cell data; 6bp for MitoTracker Stained satellite cells and zebrafish data and a polyT stretch. Reads 1 were thus used to extract the cell barcode sequences see “Cel seq barcodes 96.csv” file for sequences used for unstained satellite cell data and see ""Cel seq barcodes 384"" for MitoTracker stained satellite cells and zebrafish data and UMIs; see Supplementary Methods for details. post mapping  a UMI correction was applied to the read and barcode counts files to generate unique transcript count tables as described before see Supplementary Methods section for details. Note that processed files for satellite cell data here still contain ERCC Spike in molecules  bulk samples bulk samples are only included in CEL Seq experiments; see “BulkSamples BarcodesAndNrOfCellsUsed perCEL Seq1 library” file for description of how many cells were used as bulk and which primer barcode sequence was used for bulk sample in each library and mitochondrial reads only for MitoTracker stained satellite cells. Genome build: mus musculus: mm10; danio rerio: Zv9 Ensembl release 74; both were extended with spike ins see ""ERCC92.fa"" Supplementary files format and content: *.coutt.csv  *TranscriptCounts.tsv and *count table.csv: tab separated data files listing how many reads of which transcripts were detected in all sequenced cells post UMI correction. Column names refer to cells sequenced in this library numbers refer the the CEL Seq primer barcode used for that cell. The first column lists official gene symbols followed by the chromosome name  separated by a double underscore. Note that processed files for satellite cell data here still contain ERCC Spike in molecules  bulk samples bulk samples are only included in CEL Seq experiments; see “BulkSamples BarcodesAndNrOfCellsUsed perCEL Seq1 library” file for description of how many cells were used as bulk and which primer barcode sequence was used for bulk sample in each library and mitochondrial reads only for MitoTracker stained satellite cells.",All cells from caudal fin,,Cells were sorted into Vapor Lock Qiagen containing a droplet with primers and dNTPs. Cells were lysed at 65 degrees Celsius  post which SORT Seq Muraro et al.  2016  with minor modifications as desribed in Supplementary Methods of van den Brink et al.  2017 was applied. As in SORT Seq protocol Muraro et al.  2016  with minor modifications as desribed in Supplementary Methods of van den Brink et al.  2017.,,strain:Wildtype,GSM2781033,GSM2781033: SORT Seq zebrafish fin merged; Danio rerio; RNA Seq,GSM2781033,,1,Cells were sorted into Vapor Lock Qiagen containing a droplet with primers and dNTPs. Cells were lysed at 65 degrees Celsius  post which SORT Seq Muraro et al.  2016  with minor modifications as desribed in Supplementary Methods of van den Brink et al.  2017 was applied. As in SORT Seq protocol Muraro et al.  2016  with minor modifications as desribed in Supplementary Methods of van den Brink et al.  2017.,GEO Accession:GSM2781033,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP082370,,,FinE_plate04_R2.fastq.gz FinE_plate04_R1.fastq.gz,fastq fastq,8402262674.0,55692887.0,GSM2781033 r9,0:75.48 1:75.39,A:2618499207;C:1444061167;G:1613776766;T:2725680678;N:244856,75,75,,,2618499207,1444061167,1613776766,2725680678,244856,SRX3187382,SRS2515225,SRA453335,GEO,"Alexander van Oudenaarden, Hubrecht Institute",2,0.26069,0.43322,0.23296,0.36903,0.95663,0.90542,0.50653,0.52921,76,75,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Netherlands,2017-09-12,Undetermined,Adult,Fin,Surface Structure
41724,SRR5125792,SRX2440183,SRS1874770,SRP095533,PRJNA358533,Transcriptomic  Proteomic  and Metabolomic Landscape of Positional Memory in the Caudal Fin of Zebrafish,GSE92760,Transcriptome Analysis,Regeneration requires cells to regulate proliferation and patterning according to their spatial position. Positional memory is a property that enables regenerating cells to recall spatial information from the uninjured tissue. Positional memory is hypothesized to rely on gradients of molecules  few of which have been identified. Here  we quantified the global abundance of transcripts  proteins and metabolites along the proximodistal axis of caudal fins of uninjured and regenerating adult zebrafish. Using this approach  we uncovered complex overlapping expression patterns for hundreds of molecules involved in diverse cellular functions  including developmental and bioelectric signaling as well as amino acid and lipid metabolism. Moreover  32 genes differentially expressed at the RNA level had concomitant differential expression of the encoded proteins. Thus  the identification of proximodistal differences in levels of RNAs  proteins  and metabolites will facilitate future functional studies of positional memory during appendage regeneration. Overall design: RNA seq was performed on 5 biological replicates for each of 3 positions along the proximodistal axis of the caudal fin; proximal  middle and distal 15 total samples. Each biological replicate was a pool of fin regions cut from 2 male and 2 female zebrafish.,,pubmed:28096348,,Dist 5,GSM2436989,,tissue:Distal region of caudal fin|strain:AB WT|position:distal|barcode sample name for sequencing:US 1584765,Dist 5,FASTQ reads were aligned to Zebrafish GRCz10 using Tophat 2.0.13 with default settings. HTSeq count was used to get read counts for each sample. Ensembl GRCz10 gene annotation file was used for gene expression quantification Differential analysis was performed with DESeq. Genome build: Zebrafish GRCz10 Supplementary files format and content: tab delimited text files include RPM values for each Sample,Distal region of caudal fin,,Collected fin regions were flash frozen in liquid nitrogen and stored at  80˚C. Total RNA was extracted from fin samples using TRIzol. Total RNA was rRNA depleted using the Ribo Zero Gold rRNA Removal Kit Illumina  San Diego  CA. Sample libraries were made using TruSeq Constructions Kits and sequenced using the HiSeq platform Illumina  San Diego  CA with 20 30 million 50 base pair  paired end sequences per sample. RNA extraction  rRNA depletion  library construction and sequencing were done by Covance Genomics Laboratory Seattle  WA.,,strain:AB WT|position:distal|barcode sample name for sequencing:US 1584765,GSM2436989,GSM2436989: Dist 5; Danio rerio; RNA Seq,GSM2436989,,1,Collected fin regions were flash frozen in liquid nitrogen and stored at  80˚C. Total RNA was extracted from fin samples using TRIzol. Total RNA was rRNA depleted using the Ribo Zero Gold rRNA Removal Kit Illumina  San Diego  CA. Sample libraries were made using TruSeq Constructions Kits and sequenced using the HiSeq platform Illumina  San Diego  CA with 20 30 million 50 base pair  paired end sequences per sample. RNA extraction  rRNA depletion  library construction and sequencing were done by Covance Genomics Laboratory Seattle  WA.,GEO Accession:GSM2436989,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP095533,,,AC6VTYANXX_US-1584765_TGACCA_L007_R2_001.fastq.gz AC6VTYANXX_US-1584765_TGACCA_L007_R1_001.fastq.gz,fastq fastq,1824126996.0,17883598.0,GSM2436989 r1,0:51 1:51,A:458490550;C:446154110;G:453403149;T:464348421;N:1730766,51,51,,,458490550,446154110,453403149,464348421,1730766,SRX2440183,SRS1874770,SRA507993,GEO,University of Washington,2,0.87537,0.88573,0.26699,0.27236,0.7529,0.75597,0.56789,0.57196,51,51,B,B,biological fallback assumption,illumina,hiseq_era,unknown,rrna_depletion,ribozero,bulk,unknown,unknown,,United States,2016-12-22,Undetermined,Adult,Fin,Surface Structure
41725,SRR5125793,SRX2440183,SRS1874770,SRP095533,PRJNA358533,Transcriptomic  Proteomic  and Metabolomic Landscape of Positional Memory in the Caudal Fin of Zebrafish,GSE92760,Transcriptome Analysis,Regeneration requires cells to regulate proliferation and patterning according to their spatial position. Positional memory is a property that enables regenerating cells to recall spatial information from the uninjured tissue. Positional memory is hypothesized to rely on gradients of molecules  few of which have been identified. Here  we quantified the global abundance of transcripts  proteins and metabolites along the proximodistal axis of caudal fins of uninjured and regenerating adult zebrafish. Using this approach  we uncovered complex overlapping expression patterns for hundreds of molecules involved in diverse cellular functions  including developmental and bioelectric signaling as well as amino acid and lipid metabolism. Moreover  32 genes differentially expressed at the RNA level had concomitant differential expression of the encoded proteins. Thus  the identification of proximodistal differences in levels of RNAs  proteins  and metabolites will facilitate future functional studies of positional memory during appendage regeneration. Overall design: RNA seq was performed on 5 biological replicates for each of 3 positions along the proximodistal axis of the caudal fin; proximal  middle and distal 15 total samples. Each biological replicate was a pool of fin regions cut from 2 male and 2 female zebrafish.,,pubmed:28096348,,Dist 5,GSM2436989,,tissue:Distal region of caudal fin|strain:AB WT|position:distal|barcode sample name for sequencing:US 1584765,Dist 5,FASTQ reads were aligned to Zebrafish GRCz10 using Tophat 2.0.13 with default settings. HTSeq count was used to get read counts for each sample. Ensembl GRCz10 gene annotation file was used for gene expression quantification Differential analysis was performed with DESeq. Genome build: Zebrafish GRCz10 Supplementary files format and content: tab delimited text files include RPM values for each Sample,Distal region of caudal fin,,Collected fin regions were flash frozen in liquid nitrogen and stored at  80˚C. Total RNA was extracted from fin samples using TRIzol. Total RNA was rRNA depleted using the Ribo Zero Gold rRNA Removal Kit Illumina  San Diego  CA. Sample libraries were made using TruSeq Constructions Kits and sequenced using the HiSeq platform Illumina  San Diego  CA with 20 30 million 50 base pair  paired end sequences per sample. RNA extraction  rRNA depletion  library construction and sequencing were done by Covance Genomics Laboratory Seattle  WA.,,strain:AB WT|position:distal|barcode sample name for sequencing:US 1584765,GSM2436989,GSM2436989: Dist 5; Danio rerio; RNA Seq,GSM2436989,,1,Collected fin regions were flash frozen in liquid nitrogen and stored at  80˚C. Total RNA was extracted from fin samples using TRIzol. Total RNA was rRNA depleted using the Ribo Zero Gold rRNA Removal Kit Illumina  San Diego  CA. Sample libraries were made using TruSeq Constructions Kits and sequenced using the HiSeq platform Illumina  San Diego  CA with 20 30 million 50 base pair  paired end sequences per sample. RNA extraction  rRNA depletion  library construction and sequencing were done by Covance Genomics Laboratory Seattle  WA.,GEO Accession:GSM2436989,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP095533,,,AC6VTYANXX_US-1584765_TGACCA_L008_R2_001.fastq.gz AC6VTYANXX_US-1584765_TGACCA_L008_R1_001.fastq.gz,fastq fastq,1708520298.0,16750199.0,GSM2436989 r2,0:51 1:51,A:429281773;C:417979070;G:424912195;T:434759639;N:1587621,51,51,,,429281773,417979070,424912195,434759639,1587621,SRX2440183,SRS1874770,SRA507993,GEO,University of Washington,2,0.87424,0.88047,0.26549,0.27043,0.75404,0.75846,0.56471,0.56674,51,51,B,B,biological fallback assumption,illumina,hiseq_era,unknown,rrna_depletion,ribozero,bulk,unknown,unknown,,United States,2016-12-22,Undetermined,Adult,Fin,Surface Structure
41726,SRR5125790,SRX2440182,SRS1874769,SRP095533,PRJNA358533,Transcriptomic  Proteomic  and Metabolomic Landscape of Positional Memory in the Caudal Fin of Zebrafish,GSE92760,Transcriptome Analysis,Regeneration requires cells to regulate proliferation and patterning according to their spatial position. Positional memory is a property that enables regenerating cells to recall spatial information from the uninjured tissue. Positional memory is hypothesized to rely on gradients of molecules  few of which have been identified. Here  we quantified the global abundance of transcripts  proteins and metabolites along the proximodistal axis of caudal fins of uninjured and regenerating adult zebrafish. Using this approach  we uncovered complex overlapping expression patterns for hundreds of molecules involved in diverse cellular functions  including developmental and bioelectric signaling as well as amino acid and lipid metabolism. Moreover  32 genes differentially expressed at the RNA level had concomitant differential expression of the encoded proteins. Thus  the identification of proximodistal differences in levels of RNAs  proteins  and metabolites will facilitate future functional studies of positional memory during appendage regeneration. Overall design: RNA seq was performed on 5 biological replicates for each of 3 positions along the proximodistal axis of the caudal fin; proximal  middle and distal 15 total samples. Each biological replicate was a pool of fin regions cut from 2 male and 2 female zebrafish.,,pubmed:28096348,,Dist 4,GSM2436988,,tissue:Distal region of caudal fin|strain:AB WT|position:distal|barcode sample name for sequencing:US 1584754,Dist 4,FASTQ reads were aligned to Zebrafish GRCz10 using Tophat 2.0.13 with default settings. HTSeq count was used to get read counts for each sample. Ensembl GRCz10 gene annotation file was used for gene expression quantification Differential analysis was performed with DESeq. Genome build: Zebrafish GRCz10 Supplementary files format and content: tab delimited text files include RPM values for each Sample,Distal region of caudal fin,,Collected fin regions were flash frozen in liquid nitrogen and stored at  80˚C. Total RNA was extracted from fin samples using TRIzol. Total RNA was rRNA depleted using the Ribo Zero Gold rRNA Removal Kit Illumina  San Diego  CA. Sample libraries were made using TruSeq Constructions Kits and sequenced using the HiSeq platform Illumina  San Diego  CA with 20 30 million 50 base pair  paired end sequences per sample. RNA extraction  rRNA depletion  library construction and sequencing were done by Covance Genomics Laboratory Seattle  WA.,,strain:AB WT|position:distal|barcode sample name for sequencing:US 1584754,GSM2436988,GSM2436988: Dist 4; Danio rerio; RNA Seq,GSM2436988,,1,Collected fin regions were flash frozen in liquid nitrogen and stored at  80˚C. Total RNA was extracted from fin samples using TRIzol. Total RNA was rRNA depleted using the Ribo Zero Gold rRNA Removal Kit Illumina  San Diego  CA. Sample libraries were made using TruSeq Constructions Kits and sequenced using the HiSeq platform Illumina  San Diego  CA with 20 30 million 50 base pair  paired end sequences per sample. RNA extraction  rRNA depletion  library construction and sequencing were done by Covance Genomics Laboratory Seattle  WA.,GEO Accession:GSM2436988,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP095533,,,AC6VTYANXX_US-1584754_TTAGGC_L007_R1_001.fastq.gz AC6VTYANXX_US-1584754_TTAGGC_L007_R2_001.fastq.gz,fastq fastq,2045322258.0,20052179.0,GSM2436988 r1,0:51 1:51,A:499536380;C:517757411;G:519456007;T:506603070;N:1969390,51,51,,,499536380,517757411,519456007,506603070,1969390,SRX2440182,SRS1874769,SRA507993,GEO,University of Washington,2,0.89693,0.90206,0.2612,0.25781,0.76743,0.76995,0.60642,0.61298,51,51,B,B,biological fallback assumption,illumina,hiseq_era,unknown,rrna_depletion,ribozero,bulk,unknown,unknown,,United States,2016-12-22,Undetermined,Adult,Fin,Surface Structure
41727,SRR5125791,SRX2440182,SRS1874769,SRP095533,PRJNA358533,Transcriptomic  Proteomic  and Metabolomic Landscape of Positional Memory in the Caudal Fin of Zebrafish,GSE92760,Transcriptome Analysis,Regeneration requires cells to regulate proliferation and patterning according to their spatial position. Positional memory is a property that enables regenerating cells to recall spatial information from the uninjured tissue. Positional memory is hypothesized to rely on gradients of molecules  few of which have been identified. Here  we quantified the global abundance of transcripts  proteins and metabolites along the proximodistal axis of caudal fins of uninjured and regenerating adult zebrafish. Using this approach  we uncovered complex overlapping expression patterns for hundreds of molecules involved in diverse cellular functions  including developmental and bioelectric signaling as well as amino acid and lipid metabolism. Moreover  32 genes differentially expressed at the RNA level had concomitant differential expression of the encoded proteins. Thus  the identification of proximodistal differences in levels of RNAs  proteins  and metabolites will facilitate future functional studies of positional memory during appendage regeneration. Overall design: RNA seq was performed on 5 biological replicates for each of 3 positions along the proximodistal axis of the caudal fin; proximal  middle and distal 15 total samples. Each biological replicate was a pool of fin regions cut from 2 male and 2 female zebrafish.,,pubmed:28096348,,Dist 4,GSM2436988,,tissue:Distal region of caudal fin|strain:AB WT|position:distal|barcode sample name for sequencing:US 1584754,Dist 4,FASTQ reads were aligned to Zebrafish GRCz10 using Tophat 2.0.13 with default settings. HTSeq count was used to get read counts for each sample. Ensembl GRCz10 gene annotation file was used for gene expression quantification Differential analysis was performed with DESeq. Genome build: Zebrafish GRCz10 Supplementary files format and content: tab delimited text files include RPM values for each Sample,Distal region of caudal fin,,Collected fin regions were flash frozen in liquid nitrogen and stored at  80˚C. Total RNA was extracted from fin samples using TRIzol. Total RNA was rRNA depleted using the Ribo Zero Gold rRNA Removal Kit Illumina  San Diego  CA. Sample libraries were made using TruSeq Constructions Kits and sequenced using the HiSeq platform Illumina  San Diego  CA with 20 30 million 50 base pair  paired end sequences per sample. RNA extraction  rRNA depletion  library construction and sequencing were done by Covance Genomics Laboratory Seattle  WA.,,strain:AB WT|position:distal|barcode sample name for sequencing:US 1584754,GSM2436988,GSM2436988: Dist 4; Danio rerio; RNA Seq,GSM2436988,,1,Collected fin regions were flash frozen in liquid nitrogen and stored at  80˚C. Total RNA was extracted from fin samples using TRIzol. Total RNA was rRNA depleted using the Ribo Zero Gold rRNA Removal Kit Illumina  San Diego  CA. Sample libraries were made using TruSeq Constructions Kits and sequenced using the HiSeq platform Illumina  San Diego  CA with 20 30 million 50 base pair  paired end sequences per sample. RNA extraction  rRNA depletion  library construction and sequencing were done by Covance Genomics Laboratory Seattle  WA.,GEO Accession:GSM2436988,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP095533,,,AC6VTYANXX_US-1584754_TTAGGC_L008_R1_001.fastq.gz AC6VTYANXX_US-1584754_TTAGGC_L008_R2_001.fastq.gz,fastq fastq,1913367714.0,18758507.0,GSM2436988 r2,0:51 1:51,A:467226131;C:484410903;G:486223507;T:473745423;N:1761750,51,51,,,467226131,484410903,486223507,473745423,1761750,SRX2440182,SRS1874769,SRA507993,GEO,University of Washington,2,0.8959,0.89643,0.26147,0.2566,0.76725,0.77049,0.58923,0.6072,51,51,B,B,biological fallback assumption,illumina,hiseq_era,unknown,rrna_depletion,ribozero,bulk,unknown,unknown,,United States,2016-12-22,Undetermined,Adult,Fin,Surface Structure
41728,SRR5125788,SRX2440181,SRS1874768,SRP095533,PRJNA358533,Transcriptomic  Proteomic  and Metabolomic Landscape of Positional Memory in the Caudal Fin of Zebrafish,GSE92760,Transcriptome Analysis,Regeneration requires cells to regulate proliferation and patterning according to their spatial position. Positional memory is a property that enables regenerating cells to recall spatial information from the uninjured tissue. Positional memory is hypothesized to rely on gradients of molecules  few of which have been identified. Here  we quantified the global abundance of transcripts  proteins and metabolites along the proximodistal axis of caudal fins of uninjured and regenerating adult zebrafish. Using this approach  we uncovered complex overlapping expression patterns for hundreds of molecules involved in diverse cellular functions  including developmental and bioelectric signaling as well as amino acid and lipid metabolism. Moreover  32 genes differentially expressed at the RNA level had concomitant differential expression of the encoded proteins. Thus  the identification of proximodistal differences in levels of RNAs  proteins  and metabolites will facilitate future functional studies of positional memory during appendage regeneration. Overall design: RNA seq was performed on 5 biological replicates for each of 3 positions along the proximodistal axis of the caudal fin; proximal  middle and distal 15 total samples. Each biological replicate was a pool of fin regions cut from 2 male and 2 female zebrafish.,,pubmed:28096348,,Dist 3,GSM2436987,,tissue:Distal region of caudal fin|strain:AB WT|position:distal|barcode sample name for sequencing:US 1584712,Dist 3,FASTQ reads were aligned to Zebrafish GRCz10 using Tophat 2.0.13 with default settings. HTSeq count was used to get read counts for each sample. Ensembl GRCz10 gene annotation file was used for gene expression quantification Differential analysis was performed with DESeq. Genome build: Zebrafish GRCz10 Supplementary files format and content: tab delimited text files include RPM values for each Sample,Distal region of caudal fin,,Collected fin regions were flash frozen in liquid nitrogen and stored at  80˚C. Total RNA was extracted from fin samples using TRIzol. Total RNA was rRNA depleted using the Ribo Zero Gold rRNA Removal Kit Illumina  San Diego  CA. Sample libraries were made using TruSeq Constructions Kits and sequenced using the HiSeq platform Illumina  San Diego  CA with 20 30 million 50 base pair  paired end sequences per sample. RNA extraction  rRNA depletion  library construction and sequencing were done by Covance Genomics Laboratory Seattle  WA.,,strain:AB WT|position:distal|barcode sample name for sequencing:US 1584712,GSM2436987,GSM2436987: Dist 3; Danio rerio; RNA Seq,GSM2436987,,1,Collected fin regions were flash frozen in liquid nitrogen and stored at  80˚C. Total RNA was extracted from fin samples using TRIzol. Total RNA was rRNA depleted using the Ribo Zero Gold rRNA Removal Kit Illumina  San Diego  CA. Sample libraries were made using TruSeq Constructions Kits and sequenced using the HiSeq platform Illumina  San Diego  CA with 20 30 million 50 base pair  paired end sequences per sample. RNA extraction  rRNA depletion  library construction and sequencing were done by Covance Genomics Laboratory Seattle  WA.,GEO Accession:GSM2436987,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP095533,,,AC6VTYANXX_US-1584712_ACTTGA_L007_R1_001.fastq.gz AC6VTYANXX_US-1584712_ACTTGA_L007_R2_001.fastq.gz,fastq fastq,1609928016.0,15783608.0,GSM2436987 r1,0:51 1:51,A:417907004;C:380315213;G:385600713;T:424550260;N:1554826,51,51,,,417907004,380315213,385600713,424550260,1554826,SRX2440181,SRS1874768,SRA507993,GEO,University of Washington,2,0.8685,0.87825,0.27674,0.27998,0.74038,0.74596,0.53899,0.54008,51,51,B,B,biological fallback assumption,illumina,hiseq_era,unknown,rrna_depletion,ribozero,bulk,unknown,unknown,,United States,2016-12-22,Undetermined,Adult,Fin,Surface Structure
41729,SRR5125789,SRX2440181,SRS1874768,SRP095533,PRJNA358533,Transcriptomic  Proteomic  and Metabolomic Landscape of Positional Memory in the Caudal Fin of Zebrafish,GSE92760,Transcriptome Analysis,Regeneration requires cells to regulate proliferation and patterning according to their spatial position. Positional memory is a property that enables regenerating cells to recall spatial information from the uninjured tissue. Positional memory is hypothesized to rely on gradients of molecules  few of which have been identified. Here  we quantified the global abundance of transcripts  proteins and metabolites along the proximodistal axis of caudal fins of uninjured and regenerating adult zebrafish. Using this approach  we uncovered complex overlapping expression patterns for hundreds of molecules involved in diverse cellular functions  including developmental and bioelectric signaling as well as amino acid and lipid metabolism. Moreover  32 genes differentially expressed at the RNA level had concomitant differential expression of the encoded proteins. Thus  the identification of proximodistal differences in levels of RNAs  proteins  and metabolites will facilitate future functional studies of positional memory during appendage regeneration. Overall design: RNA seq was performed on 5 biological replicates for each of 3 positions along the proximodistal axis of the caudal fin; proximal  middle and distal 15 total samples. Each biological replicate was a pool of fin regions cut from 2 male and 2 female zebrafish.,,pubmed:28096348,,Dist 3,GSM2436987,,tissue:Distal region of caudal fin|strain:AB WT|position:distal|barcode sample name for sequencing:US 1584712,Dist 3,FASTQ reads were aligned to Zebrafish GRCz10 using Tophat 2.0.13 with default settings. HTSeq count was used to get read counts for each sample. Ensembl GRCz10 gene annotation file was used for gene expression quantification Differential analysis was performed with DESeq. Genome build: Zebrafish GRCz10 Supplementary files format and content: tab delimited text files include RPM values for each Sample,Distal region of caudal fin,,Collected fin regions were flash frozen in liquid nitrogen and stored at  80˚C. Total RNA was extracted from fin samples using TRIzol. Total RNA was rRNA depleted using the Ribo Zero Gold rRNA Removal Kit Illumina  San Diego  CA. Sample libraries were made using TruSeq Constructions Kits and sequenced using the HiSeq platform Illumina  San Diego  CA with 20 30 million 50 base pair  paired end sequences per sample. RNA extraction  rRNA depletion  library construction and sequencing were done by Covance Genomics Laboratory Seattle  WA.,,strain:AB WT|position:distal|barcode sample name for sequencing:US 1584712,GSM2436987,GSM2436987: Dist 3; Danio rerio; RNA Seq,GSM2436987,,1,Collected fin regions were flash frozen in liquid nitrogen and stored at  80˚C. Total RNA was extracted from fin samples using TRIzol. Total RNA was rRNA depleted using the Ribo Zero Gold rRNA Removal Kit Illumina  San Diego  CA. Sample libraries were made using TruSeq Constructions Kits and sequenced using the HiSeq platform Illumina  San Diego  CA with 20 30 million 50 base pair  paired end sequences per sample. RNA extraction  rRNA depletion  library construction and sequencing were done by Covance Genomics Laboratory Seattle  WA.,GEO Accession:GSM2436987,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP095533,,,AC6VTYANXX_US-1584712_ACTTGA_L008_R1_001.fastq.gz AC6VTYANXX_US-1584712_ACTTGA_L008_R2_001.fastq.gz,fastq fastq,1506730944.0,14771872.0,GSM2436987 r2,0:51 1:51,A:391092462;C:355992751;G:361056075;T:397182080;N:1407576,51,51,,,391092462,355992751,361056075,397182080,1407576,SRX2440181,SRS1874768,SRA507993,GEO,University of Washington,2,0.8689,0.87283,0.276,0.27796,0.74103,0.74533,0.5395,0.53898,51,51,B,B,biological fallback assumption,illumina,hiseq_era,unknown,rrna_depletion,ribozero,bulk,unknown,unknown,,United States,2016-12-22,Undetermined,Adult,Fin,Surface Structure
41730,SRR5125786,SRX2440180,SRS1874767,SRP095533,PRJNA358533,Transcriptomic  Proteomic  and Metabolomic Landscape of Positional Memory in the Caudal Fin of Zebrafish,GSE92760,Transcriptome Analysis,Regeneration requires cells to regulate proliferation and patterning according to their spatial position. Positional memory is a property that enables regenerating cells to recall spatial information from the uninjured tissue. Positional memory is hypothesized to rely on gradients of molecules  few of which have been identified. Here  we quantified the global abundance of transcripts  proteins and metabolites along the proximodistal axis of caudal fins of uninjured and regenerating adult zebrafish. Using this approach  we uncovered complex overlapping expression patterns for hundreds of molecules involved in diverse cellular functions  including developmental and bioelectric signaling as well as amino acid and lipid metabolism. Moreover  32 genes differentially expressed at the RNA level had concomitant differential expression of the encoded proteins. Thus  the identification of proximodistal differences in levels of RNAs  proteins  and metabolites will facilitate future functional studies of positional memory during appendage regeneration. Overall design: RNA seq was performed on 5 biological replicates for each of 3 positions along the proximodistal axis of the caudal fin; proximal  middle and distal 15 total samples. Each biological replicate was a pool of fin regions cut from 2 male and 2 female zebrafish.,,pubmed:28096348,,Dist 2,GSM2436986,,tissue:Distal region of caudal fin|strain:AB WT|position:distal|barcode sample name for sequencing:US 1584722,Dist 2,FASTQ reads were aligned to Zebrafish GRCz10 using Tophat 2.0.13 with default settings. HTSeq count was used to get read counts for each sample. Ensembl GRCz10 gene annotation file was used for gene expression quantification Differential analysis was performed with DESeq. Genome build: Zebrafish GRCz10 Supplementary files format and content: tab delimited text files include RPM values for each Sample,Distal region of caudal fin,,Collected fin regions were flash frozen in liquid nitrogen and stored at  80˚C. Total RNA was extracted from fin samples using TRIzol. Total RNA was rRNA depleted using the Ribo Zero Gold rRNA Removal Kit Illumina  San Diego  CA. Sample libraries were made using TruSeq Constructions Kits and sequenced using the HiSeq platform Illumina  San Diego  CA with 20 30 million 50 base pair  paired end sequences per sample. RNA extraction  rRNA depletion  library construction and sequencing were done by Covance Genomics Laboratory Seattle  WA.,,strain:AB WT|position:distal|barcode sample name for sequencing:US 1584722,GSM2436986,GSM2436986: Dist 2; Danio rerio; RNA Seq,GSM2436986,,1,Collected fin regions were flash frozen in liquid nitrogen and stored at  80˚C. Total RNA was extracted from fin samples using TRIzol. Total RNA was rRNA depleted using the Ribo Zero Gold rRNA Removal Kit Illumina  San Diego  CA. Sample libraries were made using TruSeq Constructions Kits and sequenced using the HiSeq platform Illumina  San Diego  CA with 20 30 million 50 base pair  paired end sequences per sample. RNA extraction  rRNA depletion  library construction and sequencing were done by Covance Genomics Laboratory Seattle  WA.,GEO Accession:GSM2436986,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP095533,,,AC6VTYANXX_US-1584722_ATCACG_L007_R1_001.fastq.gz AC6VTYANXX_US-1584722_ATCACG_L007_R2_001.fastq.gz,fastq fastq,1647116502.0,16148201.0,GSM2436986 r1,0:51 1:51,A:413638524;C:404763796;G:406748454;T:420389489;N:1576239,51,51,,,413638524,404763796,406748454,420389489,1576239,SRX2440180,SRS1874767,SRA507993,GEO,University of Washington,2,0.88515,0.89382,0.2804,0.28244,0.75199,0.75629,0.53197,0.54698,51,51,B,B,biological fallback assumption,illumina,hiseq_era,unknown,rrna_depletion,ribozero,bulk,unknown,unknown,,United States,2016-12-22,Undetermined,Adult,Fin,Surface Structure
41731,SRR5125787,SRX2440180,SRS1874767,SRP095533,PRJNA358533,Transcriptomic  Proteomic  and Metabolomic Landscape of Positional Memory in the Caudal Fin of Zebrafish,GSE92760,Transcriptome Analysis,Regeneration requires cells to regulate proliferation and patterning according to their spatial position. Positional memory is a property that enables regenerating cells to recall spatial information from the uninjured tissue. Positional memory is hypothesized to rely on gradients of molecules  few of which have been identified. Here  we quantified the global abundance of transcripts  proteins and metabolites along the proximodistal axis of caudal fins of uninjured and regenerating adult zebrafish. Using this approach  we uncovered complex overlapping expression patterns for hundreds of molecules involved in diverse cellular functions  including developmental and bioelectric signaling as well as amino acid and lipid metabolism. Moreover  32 genes differentially expressed at the RNA level had concomitant differential expression of the encoded proteins. Thus  the identification of proximodistal differences in levels of RNAs  proteins  and metabolites will facilitate future functional studies of positional memory during appendage regeneration. Overall design: RNA seq was performed on 5 biological replicates for each of 3 positions along the proximodistal axis of the caudal fin; proximal  middle and distal 15 total samples. Each biological replicate was a pool of fin regions cut from 2 male and 2 female zebrafish.,,pubmed:28096348,,Dist 2,GSM2436986,,tissue:Distal region of caudal fin|strain:AB WT|position:distal|barcode sample name for sequencing:US 1584722,Dist 2,FASTQ reads were aligned to Zebrafish GRCz10 using Tophat 2.0.13 with default settings. HTSeq count was used to get read counts for each sample. Ensembl GRCz10 gene annotation file was used for gene expression quantification Differential analysis was performed with DESeq. Genome build: Zebrafish GRCz10 Supplementary files format and content: tab delimited text files include RPM values for each Sample,Distal region of caudal fin,,Collected fin regions were flash frozen in liquid nitrogen and stored at  80˚C. Total RNA was extracted from fin samples using TRIzol. Total RNA was rRNA depleted using the Ribo Zero Gold rRNA Removal Kit Illumina  San Diego  CA. Sample libraries were made using TruSeq Constructions Kits and sequenced using the HiSeq platform Illumina  San Diego  CA with 20 30 million 50 base pair  paired end sequences per sample. RNA extraction  rRNA depletion  library construction and sequencing were done by Covance Genomics Laboratory Seattle  WA.,,strain:AB WT|position:distal|barcode sample name for sequencing:US 1584722,GSM2436986,GSM2436986: Dist 2; Danio rerio; RNA Seq,GSM2436986,,1,Collected fin regions were flash frozen in liquid nitrogen and stored at  80˚C. Total RNA was extracted from fin samples using TRIzol. Total RNA was rRNA depleted using the Ribo Zero Gold rRNA Removal Kit Illumina  San Diego  CA. Sample libraries were made using TruSeq Constructions Kits and sequenced using the HiSeq platform Illumina  San Diego  CA with 20 30 million 50 base pair  paired end sequences per sample. RNA extraction  rRNA depletion  library construction and sequencing were done by Covance Genomics Laboratory Seattle  WA.,GEO Accession:GSM2436986,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP095533,,,AC6VTYANXX_US-1584722_ATCACG_L008_R1_001.fastq.gz AC6VTYANXX_US-1584722_ATCACG_L008_R2_001.fastq.gz,fastq fastq,1543008978.0,15127539.0,GSM2436986 r2,0:51 1:51,A:387375312;C:379224284;G:381235778;T:393748369;N:1425235,51,51,,,387375312,379224284,381235778,393748369,1425235,SRX2440180,SRS1874767,SRA507993,GEO,University of Washington,2,0.8857,0.88907,0.28174,0.28123,0.75546,0.75832,0.55536,0.55843,51,51,B,B,biological fallback assumption,illumina,hiseq_era,unknown,rrna_depletion,ribozero,bulk,unknown,unknown,,United States,2016-12-22,Undetermined,Adult,Fin,Surface Structure
41732,SRR5125784,SRX2440179,SRS1874766,SRP095533,PRJNA358533,Transcriptomic  Proteomic  and Metabolomic Landscape of Positional Memory in the Caudal Fin of Zebrafish,GSE92760,Transcriptome Analysis,Regeneration requires cells to regulate proliferation and patterning according to their spatial position. Positional memory is a property that enables regenerating cells to recall spatial information from the uninjured tissue. Positional memory is hypothesized to rely on gradients of molecules  few of which have been identified. Here  we quantified the global abundance of transcripts  proteins and metabolites along the proximodistal axis of caudal fins of uninjured and regenerating adult zebrafish. Using this approach  we uncovered complex overlapping expression patterns for hundreds of molecules involved in diverse cellular functions  including developmental and bioelectric signaling as well as amino acid and lipid metabolism. Moreover  32 genes differentially expressed at the RNA level had concomitant differential expression of the encoded proteins. Thus  the identification of proximodistal differences in levels of RNAs  proteins  and metabolites will facilitate future functional studies of positional memory during appendage regeneration. Overall design: RNA seq was performed on 5 biological replicates for each of 3 positions along the proximodistal axis of the caudal fin; proximal  middle and distal 15 total samples. Each biological replicate was a pool of fin regions cut from 2 male and 2 female zebrafish.,,pubmed:28096348,,Dist 1,GSM2436985,,tissue:Distal region of caudal fin|strain:AB WT|position:distal|barcode sample name for sequencing:US 1584738,Dist 1,FASTQ reads were aligned to Zebrafish GRCz10 using Tophat 2.0.13 with default settings. HTSeq count was used to get read counts for each sample. Ensembl GRCz10 gene annotation file was used for gene expression quantification Differential analysis was performed with DESeq. Genome build: Zebrafish GRCz10 Supplementary files format and content: tab delimited text files include RPM values for each Sample,Distal region of caudal fin,,Collected fin regions were flash frozen in liquid nitrogen and stored at  80˚C. Total RNA was extracted from fin samples using TRIzol. Total RNA was rRNA depleted using the Ribo Zero Gold rRNA Removal Kit Illumina  San Diego  CA. Sample libraries were made using TruSeq Constructions Kits and sequenced using the HiSeq platform Illumina  San Diego  CA with 20 30 million 50 base pair  paired end sequences per sample. RNA extraction  rRNA depletion  library construction and sequencing were done by Covance Genomics Laboratory Seattle  WA.,,strain:AB WT|position:distal|barcode sample name for sequencing:US 1584738,GSM2436985,GSM2436985: Dist 1; Danio rerio; RNA Seq,GSM2436985,,1,Collected fin regions were flash frozen in liquid nitrogen and stored at  80˚C. Total RNA was extracted from fin samples using TRIzol. Total RNA was rRNA depleted using the Ribo Zero Gold rRNA Removal Kit Illumina  San Diego  CA. Sample libraries were made using TruSeq Constructions Kits and sequenced using the HiSeq platform Illumina  San Diego  CA with 20 30 million 50 base pair  paired end sequences per sample. RNA extraction  rRNA depletion  library construction and sequencing were done by Covance Genomics Laboratory Seattle  WA.,GEO Accession:GSM2436985,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP095533,,,AC6VTYANXX_US-1584738_CGATGT_L007_R1_001.fastq.gz AC6VTYANXX_US-1584738_CGATGT_L007_R2_001.fastq.gz,fastq fastq,1814632530.0,17790515.0,GSM2436985 r1,0:51 1:51,A:463656511;C:436464599;G:441736231;T:471007688;N:1767501,51,51,,,463656511,436464599,441736231,471007688,1767501,SRX2440179,SRS1874766,SRA507993,GEO,University of Washington,2,0.8699,0.88038,0.2672,0.27638,0.74253,0.74734,0.54231,0.52713,51,51,B,B,biological fallback assumption,illumina,hiseq_era,unknown,rrna_depletion,ribozero,bulk,unknown,unknown,,United States,2016-12-22,Undetermined,Adult,Fin,Surface Structure
41733,SRR5125785,SRX2440179,SRS1874766,SRP095533,PRJNA358533,Transcriptomic  Proteomic  and Metabolomic Landscape of Positional Memory in the Caudal Fin of Zebrafish,GSE92760,Transcriptome Analysis,Regeneration requires cells to regulate proliferation and patterning according to their spatial position. Positional memory is a property that enables regenerating cells to recall spatial information from the uninjured tissue. Positional memory is hypothesized to rely on gradients of molecules  few of which have been identified. Here  we quantified the global abundance of transcripts  proteins and metabolites along the proximodistal axis of caudal fins of uninjured and regenerating adult zebrafish. Using this approach  we uncovered complex overlapping expression patterns for hundreds of molecules involved in diverse cellular functions  including developmental and bioelectric signaling as well as amino acid and lipid metabolism. Moreover  32 genes differentially expressed at the RNA level had concomitant differential expression of the encoded proteins. Thus  the identification of proximodistal differences in levels of RNAs  proteins  and metabolites will facilitate future functional studies of positional memory during appendage regeneration. Overall design: RNA seq was performed on 5 biological replicates for each of 3 positions along the proximodistal axis of the caudal fin; proximal  middle and distal 15 total samples. Each biological replicate was a pool of fin regions cut from 2 male and 2 female zebrafish.,,pubmed:28096348,,Dist 1,GSM2436985,,tissue:Distal region of caudal fin|strain:AB WT|position:distal|barcode sample name for sequencing:US 1584738,Dist 1,FASTQ reads were aligned to Zebrafish GRCz10 using Tophat 2.0.13 with default settings. HTSeq count was used to get read counts for each sample. Ensembl GRCz10 gene annotation file was used for gene expression quantification Differential analysis was performed with DESeq. Genome build: Zebrafish GRCz10 Supplementary files format and content: tab delimited text files include RPM values for each Sample,Distal region of caudal fin,,Collected fin regions were flash frozen in liquid nitrogen and stored at  80˚C. Total RNA was extracted from fin samples using TRIzol. Total RNA was rRNA depleted using the Ribo Zero Gold rRNA Removal Kit Illumina  San Diego  CA. Sample libraries were made using TruSeq Constructions Kits and sequenced using the HiSeq platform Illumina  San Diego  CA with 20 30 million 50 base pair  paired end sequences per sample. RNA extraction  rRNA depletion  library construction and sequencing were done by Covance Genomics Laboratory Seattle  WA.,,strain:AB WT|position:distal|barcode sample name for sequencing:US 1584738,GSM2436985,GSM2436985: Dist 1; Danio rerio; RNA Seq,GSM2436985,,1,Collected fin regions were flash frozen in liquid nitrogen and stored at  80˚C. Total RNA was extracted from fin samples using TRIzol. Total RNA was rRNA depleted using the Ribo Zero Gold rRNA Removal Kit Illumina  San Diego  CA. Sample libraries were made using TruSeq Constructions Kits and sequenced using the HiSeq platform Illumina  San Diego  CA with 20 30 million 50 base pair  paired end sequences per sample. RNA extraction  rRNA depletion  library construction and sequencing were done by Covance Genomics Laboratory Seattle  WA.,GEO Accession:GSM2436985,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP095533,,,AC6VTYANXX_US-1584738_CGATGT_L008_R2_001.fastq.gz AC6VTYANXX_US-1584738_CGATGT_L008_R1_001.fastq.gz,fastq fastq,1698958920.0,16656460.0,GSM2436985 r2,0:51 1:51,A:434006394;C:408694425;G:413809330;T:440873225;N:1575546,51,51,,,434006394,408694425,413809330,440873225,1575546,SRX2440179,SRS1874766,SRA507993,GEO,University of Washington,2,0.86958,0.86928,0.27305,0.26876,0.74209,0.74742,0.55057,0.54378,51,51,B,B,biological fallback assumption,illumina,hiseq_era,unknown,rrna_depletion,ribozero,bulk,unknown,unknown,,United States,2016-12-22,Undetermined,Adult,Fin,Surface Structure
41734,SRR5125782,SRX2440178,SRS1874765,SRP095533,PRJNA358533,Transcriptomic  Proteomic  and Metabolomic Landscape of Positional Memory in the Caudal Fin of Zebrafish,GSE92760,Transcriptome Analysis,Regeneration requires cells to regulate proliferation and patterning according to their spatial position. Positional memory is a property that enables regenerating cells to recall spatial information from the uninjured tissue. Positional memory is hypothesized to rely on gradients of molecules  few of which have been identified. Here  we quantified the global abundance of transcripts  proteins and metabolites along the proximodistal axis of caudal fins of uninjured and regenerating adult zebrafish. Using this approach  we uncovered complex overlapping expression patterns for hundreds of molecules involved in diverse cellular functions  including developmental and bioelectric signaling as well as amino acid and lipid metabolism. Moreover  32 genes differentially expressed at the RNA level had concomitant differential expression of the encoded proteins. Thus  the identification of proximodistal differences in levels of RNAs  proteins  and metabolites will facilitate future functional studies of positional memory during appendage regeneration. Overall design: RNA seq was performed on 5 biological replicates for each of 3 positions along the proximodistal axis of the caudal fin; proximal  middle and distal 15 total samples. Each biological replicate was a pool of fin regions cut from 2 male and 2 female zebrafish.,,pubmed:28096348,,Mid 5,GSM2436984,,tissue:Middle region of caudal fin|strain:AB WT|position:middle|barcode sample name for sequencing:US 1584753,Mid 5,FASTQ reads were aligned to Zebrafish GRCz10 using Tophat 2.0.13 with default settings. HTSeq count was used to get read counts for each sample. Ensembl GRCz10 gene annotation file was used for gene expression quantification Differential analysis was performed with DESeq. Genome build: Zebrafish GRCz10 Supplementary files format and content: tab delimited text files include RPM values for each Sample,Middle region of caudal fin,,Collected fin regions were flash frozen in liquid nitrogen and stored at  80˚C. Total RNA was extracted from fin samples using TRIzol. Total RNA was rRNA depleted using the Ribo Zero Gold rRNA Removal Kit Illumina  San Diego  CA. Sample libraries were made using TruSeq Constructions Kits and sequenced using the HiSeq platform Illumina  San Diego  CA with 20 30 million 50 base pair  paired end sequences per sample. RNA extraction  rRNA depletion  library construction and sequencing were done by Covance Genomics Laboratory Seattle  WA.,,strain:AB WT|position:middle|barcode sample name for sequencing:US 1584753,GSM2436984,GSM2436984: Mid 5; Danio rerio; RNA Seq,GSM2436984,,1,Collected fin regions were flash frozen in liquid nitrogen and stored at  80˚C. Total RNA was extracted from fin samples using TRIzol. Total RNA was rRNA depleted using the Ribo Zero Gold rRNA Removal Kit Illumina  San Diego  CA. Sample libraries were made using TruSeq Constructions Kits and sequenced using the HiSeq platform Illumina  San Diego  CA with 20 30 million 50 base pair  paired end sequences per sample. RNA extraction  rRNA depletion  library construction and sequencing were done by Covance Genomics Laboratory Seattle  WA.,GEO Accession:GSM2436984,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP095533,,,AC6VTYANXX_US-1584753_AGTTCC_L007_R1_001.fastq.gz AC6VTYANXX_US-1584753_AGTTCC_L007_R2_001.fastq.gz,fastq fastq,1858978356.0,18225278.0,GSM2436984 r1,0:51 1:51,A:468201713;C:450985541;G:463343415;T:474678077;N:1769610,51,51,,,468201713,450985541,463343415,474678077,1769610,SRX2440178,SRS1874765,SRA507993,GEO,University of Washington,2,0.84797,0.85932,0.24983,0.2554,0.74501,0.74998,0.55196,0.555,51,51,B,B,biological fallback assumption,illumina,hiseq_era,unknown,rrna_depletion,ribozero,bulk,unknown,unknown,,United States,2016-12-22,Undetermined,Adult,Fin,Surface Structure
41735,SRR5125783,SRX2440178,SRS1874765,SRP095533,PRJNA358533,Transcriptomic  Proteomic  and Metabolomic Landscape of Positional Memory in the Caudal Fin of Zebrafish,GSE92760,Transcriptome Analysis,Regeneration requires cells to regulate proliferation and patterning according to their spatial position. Positional memory is a property that enables regenerating cells to recall spatial information from the uninjured tissue. Positional memory is hypothesized to rely on gradients of molecules  few of which have been identified. Here  we quantified the global abundance of transcripts  proteins and metabolites along the proximodistal axis of caudal fins of uninjured and regenerating adult zebrafish. Using this approach  we uncovered complex overlapping expression patterns for hundreds of molecules involved in diverse cellular functions  including developmental and bioelectric signaling as well as amino acid and lipid metabolism. Moreover  32 genes differentially expressed at the RNA level had concomitant differential expression of the encoded proteins. Thus  the identification of proximodistal differences in levels of RNAs  proteins  and metabolites will facilitate future functional studies of positional memory during appendage regeneration. Overall design: RNA seq was performed on 5 biological replicates for each of 3 positions along the proximodistal axis of the caudal fin; proximal  middle and distal 15 total samples. Each biological replicate was a pool of fin regions cut from 2 male and 2 female zebrafish.,,pubmed:28096348,,Mid 5,GSM2436984,,tissue:Middle region of caudal fin|strain:AB WT|position:middle|barcode sample name for sequencing:US 1584753,Mid 5,FASTQ reads were aligned to Zebrafish GRCz10 using Tophat 2.0.13 with default settings. HTSeq count was used to get read counts for each sample. Ensembl GRCz10 gene annotation file was used for gene expression quantification Differential analysis was performed with DESeq. Genome build: Zebrafish GRCz10 Supplementary files format and content: tab delimited text files include RPM values for each Sample,Middle region of caudal fin,,Collected fin regions were flash frozen in liquid nitrogen and stored at  80˚C. Total RNA was extracted from fin samples using TRIzol. Total RNA was rRNA depleted using the Ribo Zero Gold rRNA Removal Kit Illumina  San Diego  CA. Sample libraries were made using TruSeq Constructions Kits and sequenced using the HiSeq platform Illumina  San Diego  CA with 20 30 million 50 base pair  paired end sequences per sample. RNA extraction  rRNA depletion  library construction and sequencing were done by Covance Genomics Laboratory Seattle  WA.,,strain:AB WT|position:middle|barcode sample name for sequencing:US 1584753,GSM2436984,GSM2436984: Mid 5; Danio rerio; RNA Seq,GSM2436984,,1,Collected fin regions were flash frozen in liquid nitrogen and stored at  80˚C. Total RNA was extracted from fin samples using TRIzol. Total RNA was rRNA depleted using the Ribo Zero Gold rRNA Removal Kit Illumina  San Diego  CA. Sample libraries were made using TruSeq Constructions Kits and sequenced using the HiSeq platform Illumina  San Diego  CA with 20 30 million 50 base pair  paired end sequences per sample. RNA extraction  rRNA depletion  library construction and sequencing were done by Covance Genomics Laboratory Seattle  WA.,GEO Accession:GSM2436984,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP095533,,,AC6VTYANXX_US-1584753_AGTTCC_L008_R1_001.fastq.gz AC6VTYANXX_US-1584753_AGTTCC_L008_R2_001.fastq.gz,fastq fastq,1740939876.0,17068038.0,GSM2436984 r2,0:51 1:51,A:438384306;C:422379693;G:434157681;T:444403650;N:1614546,51,51,,,438384306,422379693,434157681,444403650,1614546,SRX2440178,SRS1874765,SRA507993,GEO,University of Washington,2,0.84891,0.85466,0.25179,0.25434,0.7488,0.75243,0.55251,0.55446,51,51,B,B,biological fallback assumption,illumina,hiseq_era,unknown,rrna_depletion,ribozero,bulk,unknown,unknown,,United States,2016-12-22,Undetermined,Adult,Fin,Surface Structure
41736,SRR5125780,SRX2440177,SRS1874764,SRP095533,PRJNA358533,Transcriptomic  Proteomic  and Metabolomic Landscape of Positional Memory in the Caudal Fin of Zebrafish,GSE92760,Transcriptome Analysis,Regeneration requires cells to regulate proliferation and patterning according to their spatial position. Positional memory is a property that enables regenerating cells to recall spatial information from the uninjured tissue. Positional memory is hypothesized to rely on gradients of molecules  few of which have been identified. Here  we quantified the global abundance of transcripts  proteins and metabolites along the proximodistal axis of caudal fins of uninjured and regenerating adult zebrafish. Using this approach  we uncovered complex overlapping expression patterns for hundreds of molecules involved in diverse cellular functions  including developmental and bioelectric signaling as well as amino acid and lipid metabolism. Moreover  32 genes differentially expressed at the RNA level had concomitant differential expression of the encoded proteins. Thus  the identification of proximodistal differences in levels of RNAs  proteins  and metabolites will facilitate future functional studies of positional memory during appendage regeneration. Overall design: RNA seq was performed on 5 biological replicates for each of 3 positions along the proximodistal axis of the caudal fin; proximal  middle and distal 15 total samples. Each biological replicate was a pool of fin regions cut from 2 male and 2 female zebrafish.,,pubmed:28096348,,Mid 4,GSM2436983,,tissue:Middle region of caudal fin|strain:AB WT|position:middle|barcode sample name for sequencing:US 1584744,Mid 4,FASTQ reads were aligned to Zebrafish GRCz10 using Tophat 2.0.13 with default settings. HTSeq count was used to get read counts for each sample. Ensembl GRCz10 gene annotation file was used for gene expression quantification Differential analysis was performed with DESeq. Genome build: Zebrafish GRCz10 Supplementary files format and content: tab delimited text files include RPM values for each Sample,Middle region of caudal fin,,Collected fin regions were flash frozen in liquid nitrogen and stored at  80˚C. Total RNA was extracted from fin samples using TRIzol. Total RNA was rRNA depleted using the Ribo Zero Gold rRNA Removal Kit Illumina  San Diego  CA. Sample libraries were made using TruSeq Constructions Kits and sequenced using the HiSeq platform Illumina  San Diego  CA with 20 30 million 50 base pair  paired end sequences per sample. RNA extraction  rRNA depletion  library construction and sequencing were done by Covance Genomics Laboratory Seattle  WA.,,strain:AB WT|position:middle|barcode sample name for sequencing:US 1584744,GSM2436983,GSM2436983: Mid 4; Danio rerio; RNA Seq,GSM2436983,,1,Collected fin regions were flash frozen in liquid nitrogen and stored at  80˚C. Total RNA was extracted from fin samples using TRIzol. Total RNA was rRNA depleted using the Ribo Zero Gold rRNA Removal Kit Illumina  San Diego  CA. Sample libraries were made using TruSeq Constructions Kits and sequenced using the HiSeq platform Illumina  San Diego  CA with 20 30 million 50 base pair  paired end sequences per sample. RNA extraction  rRNA depletion  library construction and sequencing were done by Covance Genomics Laboratory Seattle  WA.,GEO Accession:GSM2436983,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP095533,,,AC6VTYANXX_US-1584744_CTTGTA_L007_R1_001.fastq.gz AC6VTYANXX_US-1584744_CTTGTA_L007_R2_001.fastq.gz,fastq fastq,1820375334.0,17846817.0,GSM2436983 r1,0:51 1:51,A:455740495;C:443198245;G:456775278;T:462913660;N:1747656,51,51,,,455740495,443198245,456775278,462913660,1747656,SRX2440177,SRS1874764,SRA507993,GEO,University of Washington,2,0.84713,0.85929,0.2552,0.25743,0.74454,0.7488,0.54757,0.54151,51,51,B,B,biological fallback assumption,illumina,hiseq_era,unknown,rrna_depletion,ribozero,bulk,unknown,unknown,,United States,2016-12-22,Undetermined,Adult,Fin,Surface Structure
41737,SRR5125781,SRX2440177,SRS1874764,SRP095533,PRJNA358533,Transcriptomic  Proteomic  and Metabolomic Landscape of Positional Memory in the Caudal Fin of Zebrafish,GSE92760,Transcriptome Analysis,Regeneration requires cells to regulate proliferation and patterning according to their spatial position. Positional memory is a property that enables regenerating cells to recall spatial information from the uninjured tissue. Positional memory is hypothesized to rely on gradients of molecules  few of which have been identified. Here  we quantified the global abundance of transcripts  proteins and metabolites along the proximodistal axis of caudal fins of uninjured and regenerating adult zebrafish. Using this approach  we uncovered complex overlapping expression patterns for hundreds of molecules involved in diverse cellular functions  including developmental and bioelectric signaling as well as amino acid and lipid metabolism. Moreover  32 genes differentially expressed at the RNA level had concomitant differential expression of the encoded proteins. Thus  the identification of proximodistal differences in levels of RNAs  proteins  and metabolites will facilitate future functional studies of positional memory during appendage regeneration. Overall design: RNA seq was performed on 5 biological replicates for each of 3 positions along the proximodistal axis of the caudal fin; proximal  middle and distal 15 total samples. Each biological replicate was a pool of fin regions cut from 2 male and 2 female zebrafish.,,pubmed:28096348,,Mid 4,GSM2436983,,tissue:Middle region of caudal fin|strain:AB WT|position:middle|barcode sample name for sequencing:US 1584744,Mid 4,FASTQ reads were aligned to Zebrafish GRCz10 using Tophat 2.0.13 with default settings. HTSeq count was used to get read counts for each sample. Ensembl GRCz10 gene annotation file was used for gene expression quantification Differential analysis was performed with DESeq. Genome build: Zebrafish GRCz10 Supplementary files format and content: tab delimited text files include RPM values for each Sample,Middle region of caudal fin,,Collected fin regions were flash frozen in liquid nitrogen and stored at  80˚C. Total RNA was extracted from fin samples using TRIzol. Total RNA was rRNA depleted using the Ribo Zero Gold rRNA Removal Kit Illumina  San Diego  CA. Sample libraries were made using TruSeq Constructions Kits and sequenced using the HiSeq platform Illumina  San Diego  CA with 20 30 million 50 base pair  paired end sequences per sample. RNA extraction  rRNA depletion  library construction and sequencing were done by Covance Genomics Laboratory Seattle  WA.,,strain:AB WT|position:middle|barcode sample name for sequencing:US 1584744,GSM2436983,GSM2436983: Mid 4; Danio rerio; RNA Seq,GSM2436983,,1,Collected fin regions were flash frozen in liquid nitrogen and stored at  80˚C. Total RNA was extracted from fin samples using TRIzol. Total RNA was rRNA depleted using the Ribo Zero Gold rRNA Removal Kit Illumina  San Diego  CA. Sample libraries were made using TruSeq Constructions Kits and sequenced using the HiSeq platform Illumina  San Diego  CA with 20 30 million 50 base pair  paired end sequences per sample. RNA extraction  rRNA depletion  library construction and sequencing were done by Covance Genomics Laboratory Seattle  WA.,GEO Accession:GSM2436983,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP095533,,,AC6VTYANXX_US-1584744_CTTGTA_L008_R1_001.fastq.gz AC6VTYANXX_US-1584744_CTTGTA_L008_R2_001.fastq.gz,fastq fastq,1703742210.0,16703355.0,GSM2436983 r2,0:51 1:51,A:426426904;C:414863943;G:427689847;T:433160710;N:1600806,51,51,,,426426904,414863943,427689847,433160710,1600806,SRX2440177,SRS1874764,SRA507993,GEO,University of Washington,2,0.84597,0.85285,0.25443,0.25668,0.74375,0.74878,0.54642,0.55378,51,51,B,B,biological fallback assumption,illumina,hiseq_era,unknown,rrna_depletion,ribozero,bulk,unknown,unknown,,United States,2016-12-22,Undetermined,Adult,Fin,Surface Structure
41738,SRR5125778,SRX2440176,SRS1874763,SRP095533,PRJNA358533,Transcriptomic  Proteomic  and Metabolomic Landscape of Positional Memory in the Caudal Fin of Zebrafish,GSE92760,Transcriptome Analysis,Regeneration requires cells to regulate proliferation and patterning according to their spatial position. Positional memory is a property that enables regenerating cells to recall spatial information from the uninjured tissue. Positional memory is hypothesized to rely on gradients of molecules  few of which have been identified. Here  we quantified the global abundance of transcripts  proteins and metabolites along the proximodistal axis of caudal fins of uninjured and regenerating adult zebrafish. Using this approach  we uncovered complex overlapping expression patterns for hundreds of molecules involved in diverse cellular functions  including developmental and bioelectric signaling as well as amino acid and lipid metabolism. Moreover  32 genes differentially expressed at the RNA level had concomitant differential expression of the encoded proteins. Thus  the identification of proximodistal differences in levels of RNAs  proteins  and metabolites will facilitate future functional studies of positional memory during appendage regeneration. Overall design: RNA seq was performed on 5 biological replicates for each of 3 positions along the proximodistal axis of the caudal fin; proximal  middle and distal 15 total samples. Each biological replicate was a pool of fin regions cut from 2 male and 2 female zebrafish.,,pubmed:28096348,,Mid 3,GSM2436982,,tissue:Middle region of caudal fin|strain:AB WT|position:middle|barcode sample name for sequencing:US 1584700,Mid 3,FASTQ reads were aligned to Zebrafish GRCz10 using Tophat 2.0.13 with default settings. HTSeq count was used to get read counts for each sample. Ensembl GRCz10 gene annotation file was used for gene expression quantification Differential analysis was performed with DESeq. Genome build: Zebrafish GRCz10 Supplementary files format and content: tab delimited text files include RPM values for each Sample,Middle region of caudal fin,,Collected fin regions were flash frozen in liquid nitrogen and stored at  80˚C. Total RNA was extracted from fin samples using TRIzol. Total RNA was rRNA depleted using the Ribo Zero Gold rRNA Removal Kit Illumina  San Diego  CA. Sample libraries were made using TruSeq Constructions Kits and sequenced using the HiSeq platform Illumina  San Diego  CA with 20 30 million 50 base pair  paired end sequences per sample. RNA extraction  rRNA depletion  library construction and sequencing were done by Covance Genomics Laboratory Seattle  WA.,,strain:AB WT|position:middle|barcode sample name for sequencing:US 1584700,GSM2436982,GSM2436982: Mid 3; Danio rerio; RNA Seq,GSM2436982,,1,Collected fin regions were flash frozen in liquid nitrogen and stored at  80˚C. Total RNA was extracted from fin samples using TRIzol. Total RNA was rRNA depleted using the Ribo Zero Gold rRNA Removal Kit Illumina  San Diego  CA. Sample libraries were made using TruSeq Constructions Kits and sequenced using the HiSeq platform Illumina  San Diego  CA with 20 30 million 50 base pair  paired end sequences per sample. RNA extraction  rRNA depletion  library construction and sequencing were done by Covance Genomics Laboratory Seattle  WA.,GEO Accession:GSM2436982,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP095533,,,AC6VTYANXX_US-1584700_GCCAAT_L007_R1_001.fastq.gz AC6VTYANXX_US-1584700_GCCAAT_L007_R2_001.fastq.gz,fastq fastq,1761929028.0,17273814.0,GSM2436982 r1,0:51 1:51,A:453256285;C:420273911;G:426872473;T:459853327;N:1673032,51,51,,,453256285,420273911,426872473,459853327,1673032,SRX2440176,SRS1874763,SRA507993,GEO,University of Washington,2,0.85925,0.86931,0.27083,0.27384,0.74065,0.74511,0.55984,0.55914,51,51,B,B,biological fallback assumption,illumina,hiseq_era,unknown,rrna_depletion,ribozero,bulk,unknown,unknown,,United States,2016-12-22,Undetermined,Adult,Fin,Surface Structure
41739,SRR5125779,SRX2440176,SRS1874763,SRP095533,PRJNA358533,Transcriptomic  Proteomic  and Metabolomic Landscape of Positional Memory in the Caudal Fin of Zebrafish,GSE92760,Transcriptome Analysis,Regeneration requires cells to regulate proliferation and patterning according to their spatial position. Positional memory is a property that enables regenerating cells to recall spatial information from the uninjured tissue. Positional memory is hypothesized to rely on gradients of molecules  few of which have been identified. Here  we quantified the global abundance of transcripts  proteins and metabolites along the proximodistal axis of caudal fins of uninjured and regenerating adult zebrafish. Using this approach  we uncovered complex overlapping expression patterns for hundreds of molecules involved in diverse cellular functions  including developmental and bioelectric signaling as well as amino acid and lipid metabolism. Moreover  32 genes differentially expressed at the RNA level had concomitant differential expression of the encoded proteins. Thus  the identification of proximodistal differences in levels of RNAs  proteins  and metabolites will facilitate future functional studies of positional memory during appendage regeneration. Overall design: RNA seq was performed on 5 biological replicates for each of 3 positions along the proximodistal axis of the caudal fin; proximal  middle and distal 15 total samples. Each biological replicate was a pool of fin regions cut from 2 male and 2 female zebrafish.,,pubmed:28096348,,Mid 3,GSM2436982,,tissue:Middle region of caudal fin|strain:AB WT|position:middle|barcode sample name for sequencing:US 1584700,Mid 3,FASTQ reads were aligned to Zebrafish GRCz10 using Tophat 2.0.13 with default settings. HTSeq count was used to get read counts for each sample. Ensembl GRCz10 gene annotation file was used for gene expression quantification Differential analysis was performed with DESeq. Genome build: Zebrafish GRCz10 Supplementary files format and content: tab delimited text files include RPM values for each Sample,Middle region of caudal fin,,Collected fin regions were flash frozen in liquid nitrogen and stored at  80˚C. Total RNA was extracted from fin samples using TRIzol. Total RNA was rRNA depleted using the Ribo Zero Gold rRNA Removal Kit Illumina  San Diego  CA. Sample libraries were made using TruSeq Constructions Kits and sequenced using the HiSeq platform Illumina  San Diego  CA with 20 30 million 50 base pair  paired end sequences per sample. RNA extraction  rRNA depletion  library construction and sequencing were done by Covance Genomics Laboratory Seattle  WA.,,strain:AB WT|position:middle|barcode sample name for sequencing:US 1584700,GSM2436982,GSM2436982: Mid 3; Danio rerio; RNA Seq,GSM2436982,,1,Collected fin regions were flash frozen in liquid nitrogen and stored at  80˚C. Total RNA was extracted from fin samples using TRIzol. Total RNA was rRNA depleted using the Ribo Zero Gold rRNA Removal Kit Illumina  San Diego  CA. Sample libraries were made using TruSeq Constructions Kits and sequenced using the HiSeq platform Illumina  San Diego  CA with 20 30 million 50 base pair  paired end sequences per sample. RNA extraction  rRNA depletion  library construction and sequencing were done by Covance Genomics Laboratory Seattle  WA.,GEO Accession:GSM2436982,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP095533,,,AC6VTYANXX_US-1584700_GCCAAT_L008_R1_001.fastq.gz AC6VTYANXX_US-1584700_GCCAAT_L008_R2_001.fastq.gz,fastq fastq,1648588770.0,16162635.0,GSM2436982 r2,0:51 1:51,A:423980826;C:393302880;G:399604174;T:430181926;N:1518964,51,51,,,423980826,393302880,399604174,430181926,1518964,SRX2440176,SRS1874763,SRA507993,GEO,University of Washington,2,0.85877,0.86273,0.27043,0.27224,0.73969,0.74501,0.55101,0.55748,51,51,B,B,biological fallback assumption,illumina,hiseq_era,unknown,rrna_depletion,ribozero,bulk,unknown,unknown,,United States,2016-12-22,Undetermined,Adult,Fin,Surface Structure
41740,SRR5125776,SRX2440175,SRS1874762,SRP095533,PRJNA358533,Transcriptomic  Proteomic  and Metabolomic Landscape of Positional Memory in the Caudal Fin of Zebrafish,GSE92760,Transcriptome Analysis,Regeneration requires cells to regulate proliferation and patterning according to their spatial position. Positional memory is a property that enables regenerating cells to recall spatial information from the uninjured tissue. Positional memory is hypothesized to rely on gradients of molecules  few of which have been identified. Here  we quantified the global abundance of transcripts  proteins and metabolites along the proximodistal axis of caudal fins of uninjured and regenerating adult zebrafish. Using this approach  we uncovered complex overlapping expression patterns for hundreds of molecules involved in diverse cellular functions  including developmental and bioelectric signaling as well as amino acid and lipid metabolism. Moreover  32 genes differentially expressed at the RNA level had concomitant differential expression of the encoded proteins. Thus  the identification of proximodistal differences in levels of RNAs  proteins  and metabolites will facilitate future functional studies of positional memory during appendage regeneration. Overall design: RNA seq was performed on 5 biological replicates for each of 3 positions along the proximodistal axis of the caudal fin; proximal  middle and distal 15 total samples. Each biological replicate was a pool of fin regions cut from 2 male and 2 female zebrafish.,,pubmed:28096348,,Mid 2,GSM2436981,,tissue:Middle region of caudal fin|strain:AB WT|position:middle|barcode sample name for sequencing:US 1584706,Mid 2,FASTQ reads were aligned to Zebrafish GRCz10 using Tophat 2.0.13 with default settings. HTSeq count was used to get read counts for each sample. Ensembl GRCz10 gene annotation file was used for gene expression quantification Differential analysis was performed with DESeq. Genome build: Zebrafish GRCz10 Supplementary files format and content: tab delimited text files include RPM values for each Sample,Middle region of caudal fin,,Collected fin regions were flash frozen in liquid nitrogen and stored at  80˚C. Total RNA was extracted from fin samples using TRIzol. Total RNA was rRNA depleted using the Ribo Zero Gold rRNA Removal Kit Illumina  San Diego  CA. Sample libraries were made using TruSeq Constructions Kits and sequenced using the HiSeq platform Illumina  San Diego  CA with 20 30 million 50 base pair  paired end sequences per sample. RNA extraction  rRNA depletion  library construction and sequencing were done by Covance Genomics Laboratory Seattle  WA.,,strain:AB WT|position:middle|barcode sample name for sequencing:US 1584706,GSM2436981,GSM2436981: Mid 2; Danio rerio; RNA Seq,GSM2436981,,1,Collected fin regions were flash frozen in liquid nitrogen and stored at  80˚C. Total RNA was extracted from fin samples using TRIzol. Total RNA was rRNA depleted using the Ribo Zero Gold rRNA Removal Kit Illumina  San Diego  CA. Sample libraries were made using TruSeq Constructions Kits and sequenced using the HiSeq platform Illumina  San Diego  CA with 20 30 million 50 base pair  paired end sequences per sample. RNA extraction  rRNA depletion  library construction and sequencing were done by Covance Genomics Laboratory Seattle  WA.,GEO Accession:GSM2436981,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP095533,,,AC6VTYANXX_US-1584706_CAGATC_L007_R1_001.fastq.gz AC6VTYANXX_US-1584706_CAGATC_L007_R2_001.fastq.gz,fastq fastq,1723911588.0,16901094.0,GSM2436981 r1,0:51 1:51,A:438651645;C:415621609;G:422843398;T:445158324;N:1636612,51,51,,,438651645,415621609,422843398,445158324,1636612,SRX2440175,SRS1874762,SRA507993,GEO,University of Washington,2,0.85774,0.86799,0.26362,0.26733,0.73766,0.74119,0.45691,0.46044,51,51,B,B,biological fallback assumption,illumina,hiseq_era,unknown,rrna_depletion,ribozero,bulk,unknown,unknown,,United States,2016-12-22,Undetermined,Adult,Fin,Surface Structure
41741,SRR5125777,SRX2440175,SRS1874762,SRP095533,PRJNA358533,Transcriptomic  Proteomic  and Metabolomic Landscape of Positional Memory in the Caudal Fin of Zebrafish,GSE92760,Transcriptome Analysis,Regeneration requires cells to regulate proliferation and patterning according to their spatial position. Positional memory is a property that enables regenerating cells to recall spatial information from the uninjured tissue. Positional memory is hypothesized to rely on gradients of molecules  few of which have been identified. Here  we quantified the global abundance of transcripts  proteins and metabolites along the proximodistal axis of caudal fins of uninjured and regenerating adult zebrafish. Using this approach  we uncovered complex overlapping expression patterns for hundreds of molecules involved in diverse cellular functions  including developmental and bioelectric signaling as well as amino acid and lipid metabolism. Moreover  32 genes differentially expressed at the RNA level had concomitant differential expression of the encoded proteins. Thus  the identification of proximodistal differences in levels of RNAs  proteins  and metabolites will facilitate future functional studies of positional memory during appendage regeneration. Overall design: RNA seq was performed on 5 biological replicates for each of 3 positions along the proximodistal axis of the caudal fin; proximal  middle and distal 15 total samples. Each biological replicate was a pool of fin regions cut from 2 male and 2 female zebrafish.,,pubmed:28096348,,Mid 2,GSM2436981,,tissue:Middle region of caudal fin|strain:AB WT|position:middle|barcode sample name for sequencing:US 1584706,Mid 2,FASTQ reads were aligned to Zebrafish GRCz10 using Tophat 2.0.13 with default settings. HTSeq count was used to get read counts for each sample. Ensembl GRCz10 gene annotation file was used for gene expression quantification Differential analysis was performed with DESeq. Genome build: Zebrafish GRCz10 Supplementary files format and content: tab delimited text files include RPM values for each Sample,Middle region of caudal fin,,Collected fin regions were flash frozen in liquid nitrogen and stored at  80˚C. Total RNA was extracted from fin samples using TRIzol. Total RNA was rRNA depleted using the Ribo Zero Gold rRNA Removal Kit Illumina  San Diego  CA. Sample libraries were made using TruSeq Constructions Kits and sequenced using the HiSeq platform Illumina  San Diego  CA with 20 30 million 50 base pair  paired end sequences per sample. RNA extraction  rRNA depletion  library construction and sequencing were done by Covance Genomics Laboratory Seattle  WA.,,strain:AB WT|position:middle|barcode sample name for sequencing:US 1584706,GSM2436981,GSM2436981: Mid 2; Danio rerio; RNA Seq,GSM2436981,,1,Collected fin regions were flash frozen in liquid nitrogen and stored at  80˚C. Total RNA was extracted from fin samples using TRIzol. Total RNA was rRNA depleted using the Ribo Zero Gold rRNA Removal Kit Illumina  San Diego  CA. Sample libraries were made using TruSeq Constructions Kits and sequenced using the HiSeq platform Illumina  San Diego  CA with 20 30 million 50 base pair  paired end sequences per sample. RNA extraction  rRNA depletion  library construction and sequencing were done by Covance Genomics Laboratory Seattle  WA.,GEO Accession:GSM2436981,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP095533,,,AC6VTYANXX_US-1584706_CAGATC_L008_R1_001.fastq.gz AC6VTYANXX_US-1584706_CAGATC_L008_R2_001.fastq.gz,fastq fastq,1612114386.0,15805043.0,GSM2436981 r2,0:51 1:51,A:410075621;C:388711900;G:395668085;T:416164606;N:1494174,51,51,,,410075621,388711900,395668085,416164606,1494174,SRX2440175,SRS1874762,SRA507993,GEO,University of Washington,2,0.85782,0.86318,0.26533,0.2667,0.7374,0.74115,0.54561,0.45873,51,51,B,B,biological fallback assumption,illumina,hiseq_era,unknown,rrna_depletion,ribozero,bulk,unknown,unknown,,United States,2016-12-22,Undetermined,Adult,Fin,Surface Structure
41742,SRR5125774,SRX2440174,SRS1874761,SRP095533,PRJNA358533,Transcriptomic  Proteomic  and Metabolomic Landscape of Positional Memory in the Caudal Fin of Zebrafish,GSE92760,Transcriptome Analysis,Regeneration requires cells to regulate proliferation and patterning according to their spatial position. Positional memory is a property that enables regenerating cells to recall spatial information from the uninjured tissue. Positional memory is hypothesized to rely on gradients of molecules  few of which have been identified. Here  we quantified the global abundance of transcripts  proteins and metabolites along the proximodistal axis of caudal fins of uninjured and regenerating adult zebrafish. Using this approach  we uncovered complex overlapping expression patterns for hundreds of molecules involved in diverse cellular functions  including developmental and bioelectric signaling as well as amino acid and lipid metabolism. Moreover  32 genes differentially expressed at the RNA level had concomitant differential expression of the encoded proteins. Thus  the identification of proximodistal differences in levels of RNAs  proteins  and metabolites will facilitate future functional studies of positional memory during appendage regeneration. Overall design: RNA seq was performed on 5 biological replicates for each of 3 positions along the proximodistal axis of the caudal fin; proximal  middle and distal 15 total samples. Each biological replicate was a pool of fin regions cut from 2 male and 2 female zebrafish.,,pubmed:28096348,,Mid 1,GSM2436980,,tissue:Middle region of caudal fin|strain:AB WT|position:middle|barcode sample name for sequencing:US 1584725,Mid 1,FASTQ reads were aligned to Zebrafish GRCz10 using Tophat 2.0.13 with default settings. HTSeq count was used to get read counts for each sample. Ensembl GRCz10 gene annotation file was used for gene expression quantification Differential analysis was performed with DESeq. Genome build: Zebrafish GRCz10 Supplementary files format and content: tab delimited text files include RPM values for each Sample,Middle region of caudal fin,,Collected fin regions were flash frozen in liquid nitrogen and stored at  80˚C. Total RNA was extracted from fin samples using TRIzol. Total RNA was rRNA depleted using the Ribo Zero Gold rRNA Removal Kit Illumina  San Diego  CA. Sample libraries were made using TruSeq Constructions Kits and sequenced using the HiSeq platform Illumina  San Diego  CA with 20 30 million 50 base pair  paired end sequences per sample. RNA extraction  rRNA depletion  library construction and sequencing were done by Covance Genomics Laboratory Seattle  WA.,,strain:AB WT|position:middle|barcode sample name for sequencing:US 1584725,GSM2436980,GSM2436980: Mid 1; Danio rerio; RNA Seq,GSM2436980,,1,Collected fin regions were flash frozen in liquid nitrogen and stored at  80˚C. Total RNA was extracted from fin samples using TRIzol. Total RNA was rRNA depleted using the Ribo Zero Gold rRNA Removal Kit Illumina  San Diego  CA. Sample libraries were made using TruSeq Constructions Kits and sequenced using the HiSeq platform Illumina  San Diego  CA with 20 30 million 50 base pair  paired end sequences per sample. RNA extraction  rRNA depletion  library construction and sequencing were done by Covance Genomics Laboratory Seattle  WA.,GEO Accession:GSM2436980,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP095533,,,AC6VTYANXX_US-1584725_TAGCTT_L007_R1_001.fastq.gz AC6VTYANXX_US-1584725_TAGCTT_L007_R2_001.fastq.gz,fastq fastq,1913312634.0,18757967.0,GSM2436980 r1,0:51 1:51,A:492780448;C:454166657;G:462802006;T:501720327;N:1843196,51,51,,,492780448,454166657,462802006,501720327,1843196,SRX2440174,SRS1874761,SRA507993,GEO,University of Washington,2,0.86908,0.87713,0.26839,0.26807,0.73685,0.7433,0.46738,0.45371,51,51,B,B,biological fallback assumption,illumina,hiseq_era,unknown,rrna_depletion,ribozero,bulk,unknown,unknown,,United States,2016-12-22,Undetermined,Adult,Fin,Surface Structure
41743,SRR5125775,SRX2440174,SRS1874761,SRP095533,PRJNA358533,Transcriptomic  Proteomic  and Metabolomic Landscape of Positional Memory in the Caudal Fin of Zebrafish,GSE92760,Transcriptome Analysis,Regeneration requires cells to regulate proliferation and patterning according to their spatial position. Positional memory is a property that enables regenerating cells to recall spatial information from the uninjured tissue. Positional memory is hypothesized to rely on gradients of molecules  few of which have been identified. Here  we quantified the global abundance of transcripts  proteins and metabolites along the proximodistal axis of caudal fins of uninjured and regenerating adult zebrafish. Using this approach  we uncovered complex overlapping expression patterns for hundreds of molecules involved in diverse cellular functions  including developmental and bioelectric signaling as well as amino acid and lipid metabolism. Moreover  32 genes differentially expressed at the RNA level had concomitant differential expression of the encoded proteins. Thus  the identification of proximodistal differences in levels of RNAs  proteins  and metabolites will facilitate future functional studies of positional memory during appendage regeneration. Overall design: RNA seq was performed on 5 biological replicates for each of 3 positions along the proximodistal axis of the caudal fin; proximal  middle and distal 15 total samples. Each biological replicate was a pool of fin regions cut from 2 male and 2 female zebrafish.,,pubmed:28096348,,Mid 1,GSM2436980,,tissue:Middle region of caudal fin|strain:AB WT|position:middle|barcode sample name for sequencing:US 1584725,Mid 1,FASTQ reads were aligned to Zebrafish GRCz10 using Tophat 2.0.13 with default settings. HTSeq count was used to get read counts for each sample. Ensembl GRCz10 gene annotation file was used for gene expression quantification Differential analysis was performed with DESeq. Genome build: Zebrafish GRCz10 Supplementary files format and content: tab delimited text files include RPM values for each Sample,Middle region of caudal fin,,Collected fin regions were flash frozen in liquid nitrogen and stored at  80˚C. Total RNA was extracted from fin samples using TRIzol. Total RNA was rRNA depleted using the Ribo Zero Gold rRNA Removal Kit Illumina  San Diego  CA. Sample libraries were made using TruSeq Constructions Kits and sequenced using the HiSeq platform Illumina  San Diego  CA with 20 30 million 50 base pair  paired end sequences per sample. RNA extraction  rRNA depletion  library construction and sequencing were done by Covance Genomics Laboratory Seattle  WA.,,strain:AB WT|position:middle|barcode sample name for sequencing:US 1584725,GSM2436980,GSM2436980: Mid 1; Danio rerio; RNA Seq,GSM2436980,,1,Collected fin regions were flash frozen in liquid nitrogen and stored at  80˚C. Total RNA was extracted from fin samples using TRIzol. Total RNA was rRNA depleted using the Ribo Zero Gold rRNA Removal Kit Illumina  San Diego  CA. Sample libraries were made using TruSeq Constructions Kits and sequenced using the HiSeq platform Illumina  San Diego  CA with 20 30 million 50 base pair  paired end sequences per sample. RNA extraction  rRNA depletion  library construction and sequencing were done by Covance Genomics Laboratory Seattle  WA.,GEO Accession:GSM2436980,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP095533,,,AC6VTYANXX_US-1584725_TAGCTT_L008_R1_001.fastq.gz AC6VTYANXX_US-1584725_TAGCTT_L008_R2_001.fastq.gz,fastq fastq,1790252796.0,17551498.0,GSM2436980 r2,0:51 1:51,A:460917277;C:424988770;G:433244274;T:469439846;N:1662629,51,51,,,460917277,424988770,433244274,469439846,1662629,SRX2440174,SRS1874761,SRA507993,GEO,University of Washington,2,0.86931,0.87173,0.26684,0.26488,0.73831,0.74332,0.46248,0.46193,51,51,B,B,biological fallback assumption,illumina,hiseq_era,unknown,rrna_depletion,ribozero,bulk,unknown,unknown,,United States,2016-12-22,Undetermined,Adult,Fin,Surface Structure
41744,SRR5125772,SRX2440173,SRS1874760,SRP095533,PRJNA358533,Transcriptomic  Proteomic  and Metabolomic Landscape of Positional Memory in the Caudal Fin of Zebrafish,GSE92760,Transcriptome Analysis,Regeneration requires cells to regulate proliferation and patterning according to their spatial position. Positional memory is a property that enables regenerating cells to recall spatial information from the uninjured tissue. Positional memory is hypothesized to rely on gradients of molecules  few of which have been identified. Here  we quantified the global abundance of transcripts  proteins and metabolites along the proximodistal axis of caudal fins of uninjured and regenerating adult zebrafish. Using this approach  we uncovered complex overlapping expression patterns for hundreds of molecules involved in diverse cellular functions  including developmental and bioelectric signaling as well as amino acid and lipid metabolism. Moreover  32 genes differentially expressed at the RNA level had concomitant differential expression of the encoded proteins. Thus  the identification of proximodistal differences in levels of RNAs  proteins  and metabolites will facilitate future functional studies of positional memory during appendage regeneration. Overall design: RNA seq was performed on 5 biological replicates for each of 3 positions along the proximodistal axis of the caudal fin; proximal  middle and distal 15 total samples. Each biological replicate was a pool of fin regions cut from 2 male and 2 female zebrafish.,,pubmed:28096348,,Prox 5,GSM2436979,,tissue:Proximal region of caudal fin|strain:AB WT|position:proximal|barcode sample name for sequencing:US 1584758,Prox 5,FASTQ reads were aligned to Zebrafish GRCz10 using Tophat 2.0.13 with default settings. HTSeq count was used to get read counts for each sample. Ensembl GRCz10 gene annotation file was used for gene expression quantification Differential analysis was performed with DESeq. Genome build: Zebrafish GRCz10 Supplementary files format and content: tab delimited text files include RPM values for each Sample,Proximal region of caudal fin,,Collected fin regions were flash frozen in liquid nitrogen and stored at  80˚C. Total RNA was extracted from fin samples using TRIzol. Total RNA was rRNA depleted using the Ribo Zero Gold rRNA Removal Kit Illumina  San Diego  CA. Sample libraries were made using TruSeq Constructions Kits and sequenced using the HiSeq platform Illumina  San Diego  CA with 20 30 million 50 base pair  paired end sequences per sample. RNA extraction  rRNA depletion  library construction and sequencing were done by Covance Genomics Laboratory Seattle  WA.,,strain:AB WT|position:proximal|barcode sample name for sequencing:US 1584758,GSM2436979,GSM2436979: Prox 5; Danio rerio; RNA Seq,GSM2436979,,1,Collected fin regions were flash frozen in liquid nitrogen and stored at  80˚C. Total RNA was extracted from fin samples using TRIzol. Total RNA was rRNA depleted using the Ribo Zero Gold rRNA Removal Kit Illumina  San Diego  CA. Sample libraries were made using TruSeq Constructions Kits and sequenced using the HiSeq platform Illumina  San Diego  CA with 20 30 million 50 base pair  paired end sequences per sample. RNA extraction  rRNA depletion  library construction and sequencing were done by Covance Genomics Laboratory Seattle  WA.,GEO Accession:GSM2436979,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP095533,,,AC6VTYANXX_US-1584758_ATGTCA_L007_R1_001.fastq.gz AC6VTYANXX_US-1584758_ATGTCA_L007_R2_001.fastq.gz,fastq fastq,1952007150.0,19137325.0,GSM2436979 r1,0:51 1:51,A:479424502;C:486963585;G:496721899;T:486994631;N:1902533,51,51,,,479424502,486963585,496721899,486994631,1902533,SRX2440173,SRS1874760,SRA507993,GEO,University of Washington,2,0.84451,0.85542,0.23953,0.24357,0.75022,0.7545,0.58816,0.47521,51,51,B,B,biological fallback assumption,illumina,hiseq_era,unknown,rrna_depletion,ribozero,bulk,unknown,unknown,,United States,2016-12-22,Undetermined,Adult,Fin,Surface Structure
41745,SRR5125773,SRX2440173,SRS1874760,SRP095533,PRJNA358533,Transcriptomic  Proteomic  and Metabolomic Landscape of Positional Memory in the Caudal Fin of Zebrafish,GSE92760,Transcriptome Analysis,Regeneration requires cells to regulate proliferation and patterning according to their spatial position. Positional memory is a property that enables regenerating cells to recall spatial information from the uninjured tissue. Positional memory is hypothesized to rely on gradients of molecules  few of which have been identified. Here  we quantified the global abundance of transcripts  proteins and metabolites along the proximodistal axis of caudal fins of uninjured and regenerating adult zebrafish. Using this approach  we uncovered complex overlapping expression patterns for hundreds of molecules involved in diverse cellular functions  including developmental and bioelectric signaling as well as amino acid and lipid metabolism. Moreover  32 genes differentially expressed at the RNA level had concomitant differential expression of the encoded proteins. Thus  the identification of proximodistal differences in levels of RNAs  proteins  and metabolites will facilitate future functional studies of positional memory during appendage regeneration. Overall design: RNA seq was performed on 5 biological replicates for each of 3 positions along the proximodistal axis of the caudal fin; proximal  middle and distal 15 total samples. Each biological replicate was a pool of fin regions cut from 2 male and 2 female zebrafish.,,pubmed:28096348,,Prox 5,GSM2436979,,tissue:Proximal region of caudal fin|strain:AB WT|position:proximal|barcode sample name for sequencing:US 1584758,Prox 5,FASTQ reads were aligned to Zebrafish GRCz10 using Tophat 2.0.13 with default settings. HTSeq count was used to get read counts for each sample. Ensembl GRCz10 gene annotation file was used for gene expression quantification Differential analysis was performed with DESeq. Genome build: Zebrafish GRCz10 Supplementary files format and content: tab delimited text files include RPM values for each Sample,Proximal region of caudal fin,,Collected fin regions were flash frozen in liquid nitrogen and stored at  80˚C. Total RNA was extracted from fin samples using TRIzol. Total RNA was rRNA depleted using the Ribo Zero Gold rRNA Removal Kit Illumina  San Diego  CA. Sample libraries were made using TruSeq Constructions Kits and sequenced using the HiSeq platform Illumina  San Diego  CA with 20 30 million 50 base pair  paired end sequences per sample. RNA extraction  rRNA depletion  library construction and sequencing were done by Covance Genomics Laboratory Seattle  WA.,,strain:AB WT|position:proximal|barcode sample name for sequencing:US 1584758,GSM2436979,GSM2436979: Prox 5; Danio rerio; RNA Seq,GSM2436979,,1,Collected fin regions were flash frozen in liquid nitrogen and stored at  80˚C. Total RNA was extracted from fin samples using TRIzol. Total RNA was rRNA depleted using the Ribo Zero Gold rRNA Removal Kit Illumina  San Diego  CA. Sample libraries were made using TruSeq Constructions Kits and sequenced using the HiSeq platform Illumina  San Diego  CA with 20 30 million 50 base pair  paired end sequences per sample. RNA extraction  rRNA depletion  library construction and sequencing were done by Covance Genomics Laboratory Seattle  WA.,GEO Accession:GSM2436979,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP095533,,,AC6VTYANXX_US-1584758_ATGTCA_L008_R1_001.fastq.gz AC6VTYANXX_US-1584758_ATGTCA_L008_R2_001.fastq.gz,fastq fastq,1827926700.0,17920850.0,GSM2436979 r2,0:51 1:51,A:448866466;C:456045219;G:465439820;T:455884892;N:1690303,51,51,,,448866466,456045219,465439820,455884892,1690303,SRX2440173,SRS1874760,SRA507993,GEO,University of Washington,2,0.84542,0.8491,0.2401,0.24279,0.7502,0.75708,0.59047,0.58826,51,51,B,B,biological fallback assumption,illumina,hiseq_era,unknown,rrna_depletion,ribozero,bulk,unknown,unknown,,United States,2016-12-22,Undetermined,Adult,Fin,Surface Structure
41746,SRR5125770,SRX2440172,SRS1874759,SRP095533,PRJNA358533,Transcriptomic  Proteomic  and Metabolomic Landscape of Positional Memory in the Caudal Fin of Zebrafish,GSE92760,Transcriptome Analysis,Regeneration requires cells to regulate proliferation and patterning according to their spatial position. Positional memory is a property that enables regenerating cells to recall spatial information from the uninjured tissue. Positional memory is hypothesized to rely on gradients of molecules  few of which have been identified. Here  we quantified the global abundance of transcripts  proteins and metabolites along the proximodistal axis of caudal fins of uninjured and regenerating adult zebrafish. Using this approach  we uncovered complex overlapping expression patterns for hundreds of molecules involved in diverse cellular functions  including developmental and bioelectric signaling as well as amino acid and lipid metabolism. Moreover  32 genes differentially expressed at the RNA level had concomitant differential expression of the encoded proteins. Thus  the identification of proximodistal differences in levels of RNAs  proteins  and metabolites will facilitate future functional studies of positional memory during appendage regeneration. Overall design: RNA seq was performed on 5 biological replicates for each of 3 positions along the proximodistal axis of the caudal fin; proximal  middle and distal 15 total samples. Each biological replicate was a pool of fin regions cut from 2 male and 2 female zebrafish.,,pubmed:28096348,,Prox 4,GSM2436978,,tissue:Proximal region of caudal fin|strain:AB WT|position:proximal|barcode sample name for sequencing:US 1584693,Prox 4,FASTQ reads were aligned to Zebrafish GRCz10 using Tophat 2.0.13 with default settings. HTSeq count was used to get read counts for each sample. Ensembl GRCz10 gene annotation file was used for gene expression quantification Differential analysis was performed with DESeq. Genome build: Zebrafish GRCz10 Supplementary files format and content: tab delimited text files include RPM values for each Sample,Proximal region of caudal fin,,Collected fin regions were flash frozen in liquid nitrogen and stored at  80˚C. Total RNA was extracted from fin samples using TRIzol. Total RNA was rRNA depleted using the Ribo Zero Gold rRNA Removal Kit Illumina  San Diego  CA. Sample libraries were made using TruSeq Constructions Kits and sequenced using the HiSeq platform Illumina  San Diego  CA with 20 30 million 50 base pair  paired end sequences per sample. RNA extraction  rRNA depletion  library construction and sequencing were done by Covance Genomics Laboratory Seattle  WA.,,strain:AB WT|position:proximal|barcode sample name for sequencing:US 1584693,GSM2436978,GSM2436978: Prox 4; Danio rerio; RNA Seq,GSM2436978,,1,Collected fin regions were flash frozen in liquid nitrogen and stored at  80˚C. Total RNA was extracted from fin samples using TRIzol. Total RNA was rRNA depleted using the Ribo Zero Gold rRNA Removal Kit Illumina  San Diego  CA. Sample libraries were made using TruSeq Constructions Kits and sequenced using the HiSeq platform Illumina  San Diego  CA with 20 30 million 50 base pair  paired end sequences per sample. RNA extraction  rRNA depletion  library construction and sequencing were done by Covance Genomics Laboratory Seattle  WA.,GEO Accession:GSM2436978,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP095533,,,AC6VTYANXX_US-1584693_ACAGTG_L007_R2_001.fastq.gz AC6VTYANXX_US-1584693_ACAGTG_L007_R1_001.fastq.gz,fastq fastq,1900457880.0,18631940.0,GSM2436978 r1,0:51 1:51,A:479961702;C:461532736;G:470280019;T:486828615;N:1854808,51,51,,,479961702,461532736,470280019,486828615,1854808,SRX2440172,SRS1874759,SRA507993,GEO,University of Washington,2,0.8576,0.86993,0.2678,0.27331,0.74278,0.74754,0.57447,0.57758,51,51,B,B,biological fallback assumption,illumina,hiseq_era,unknown,rrna_depletion,ribozero,bulk,unknown,unknown,,United States,2016-12-22,Undetermined,Adult,Fin,Surface Structure
41747,SRR5125771,SRX2440172,SRS1874759,SRP095533,PRJNA358533,Transcriptomic  Proteomic  and Metabolomic Landscape of Positional Memory in the Caudal Fin of Zebrafish,GSE92760,Transcriptome Analysis,Regeneration requires cells to regulate proliferation and patterning according to their spatial position. Positional memory is a property that enables regenerating cells to recall spatial information from the uninjured tissue. Positional memory is hypothesized to rely on gradients of molecules  few of which have been identified. Here  we quantified the global abundance of transcripts  proteins and metabolites along the proximodistal axis of caudal fins of uninjured and regenerating adult zebrafish. Using this approach  we uncovered complex overlapping expression patterns for hundreds of molecules involved in diverse cellular functions  including developmental and bioelectric signaling as well as amino acid and lipid metabolism. Moreover  32 genes differentially expressed at the RNA level had concomitant differential expression of the encoded proteins. Thus  the identification of proximodistal differences in levels of RNAs  proteins  and metabolites will facilitate future functional studies of positional memory during appendage regeneration. Overall design: RNA seq was performed on 5 biological replicates for each of 3 positions along the proximodistal axis of the caudal fin; proximal  middle and distal 15 total samples. Each biological replicate was a pool of fin regions cut from 2 male and 2 female zebrafish.,,pubmed:28096348,,Prox 4,GSM2436978,,tissue:Proximal region of caudal fin|strain:AB WT|position:proximal|barcode sample name for sequencing:US 1584693,Prox 4,FASTQ reads were aligned to Zebrafish GRCz10 using Tophat 2.0.13 with default settings. HTSeq count was used to get read counts for each sample. Ensembl GRCz10 gene annotation file was used for gene expression quantification Differential analysis was performed with DESeq. Genome build: Zebrafish GRCz10 Supplementary files format and content: tab delimited text files include RPM values for each Sample,Proximal region of caudal fin,,Collected fin regions were flash frozen in liquid nitrogen and stored at  80˚C. Total RNA was extracted from fin samples using TRIzol. Total RNA was rRNA depleted using the Ribo Zero Gold rRNA Removal Kit Illumina  San Diego  CA. Sample libraries were made using TruSeq Constructions Kits and sequenced using the HiSeq platform Illumina  San Diego  CA with 20 30 million 50 base pair  paired end sequences per sample. RNA extraction  rRNA depletion  library construction and sequencing were done by Covance Genomics Laboratory Seattle  WA.,,strain:AB WT|position:proximal|barcode sample name for sequencing:US 1584693,GSM2436978,GSM2436978: Prox 4; Danio rerio; RNA Seq,GSM2436978,,1,Collected fin regions were flash frozen in liquid nitrogen and stored at  80˚C. Total RNA was extracted from fin samples using TRIzol. Total RNA was rRNA depleted using the Ribo Zero Gold rRNA Removal Kit Illumina  San Diego  CA. Sample libraries were made using TruSeq Constructions Kits and sequenced using the HiSeq platform Illumina  San Diego  CA with 20 30 million 50 base pair  paired end sequences per sample. RNA extraction  rRNA depletion  library construction and sequencing were done by Covance Genomics Laboratory Seattle  WA.,GEO Accession:GSM2436978,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP095533,,,AC6VTYANXX_US-1584693_ACAGTG_L008_R1_001.fastq.gz AC6VTYANXX_US-1584693_ACAGTG_L008_R2_001.fastq.gz,fastq fastq,1779360012.0,17444706.0,GSM2436978 r2,0:51 1:51,A:449252897;C:432234206;G:440584933;T:455632107;N:1655869,51,51,,,449252897,432234206,440584933,455632107,1655869,SRX2440172,SRS1874759,SRA507993,GEO,University of Washington,2,0.85779,0.86314,0.26773,0.27023,0.74554,0.74951,0.57777,0.57716,51,51,B,B,biological fallback assumption,illumina,hiseq_era,unknown,rrna_depletion,ribozero,bulk,unknown,unknown,,United States,2016-12-22,Undetermined,Adult,Fin,Surface Structure
41748,SRR5125768,SRX2440171,SRS1874758,SRP095533,PRJNA358533,Transcriptomic  Proteomic  and Metabolomic Landscape of Positional Memory in the Caudal Fin of Zebrafish,GSE92760,Transcriptome Analysis,Regeneration requires cells to regulate proliferation and patterning according to their spatial position. Positional memory is a property that enables regenerating cells to recall spatial information from the uninjured tissue. Positional memory is hypothesized to rely on gradients of molecules  few of which have been identified. Here  we quantified the global abundance of transcripts  proteins and metabolites along the proximodistal axis of caudal fins of uninjured and regenerating adult zebrafish. Using this approach  we uncovered complex overlapping expression patterns for hundreds of molecules involved in diverse cellular functions  including developmental and bioelectric signaling as well as amino acid and lipid metabolism. Moreover  32 genes differentially expressed at the RNA level had concomitant differential expression of the encoded proteins. Thus  the identification of proximodistal differences in levels of RNAs  proteins  and metabolites will facilitate future functional studies of positional memory during appendage regeneration. Overall design: RNA seq was performed on 5 biological replicates for each of 3 positions along the proximodistal axis of the caudal fin; proximal  middle and distal 15 total samples. Each biological replicate was a pool of fin regions cut from 2 male and 2 female zebrafish.,,pubmed:28096348,,Prox 3,GSM2436977,,tissue:Proximal region of caudal fin|strain:AB WT|position:proximal|barcode sample name for sequencing:US 1584724,Prox 3,FASTQ reads were aligned to Zebrafish GRCz10 using Tophat 2.0.13 with default settings. HTSeq count was used to get read counts for each sample. Ensembl GRCz10 gene annotation file was used for gene expression quantification Differential analysis was performed with DESeq. Genome build: Zebrafish GRCz10 Supplementary files format and content: tab delimited text files include RPM values for each Sample,Proximal region of caudal fin,,Collected fin regions were flash frozen in liquid nitrogen and stored at  80˚C. Total RNA was extracted from fin samples using TRIzol. Total RNA was rRNA depleted using the Ribo Zero Gold rRNA Removal Kit Illumina  San Diego  CA. Sample libraries were made using TruSeq Constructions Kits and sequenced using the HiSeq platform Illumina  San Diego  CA with 20 30 million 50 base pair  paired end sequences per sample. RNA extraction  rRNA depletion  library construction and sequencing were done by Covance Genomics Laboratory Seattle  WA.,,strain:AB WT|position:proximal|barcode sample name for sequencing:US 1584724,GSM2436977,GSM2436977: Prox 3; Danio rerio; RNA Seq,GSM2436977,,1,Collected fin regions were flash frozen in liquid nitrogen and stored at  80˚C. Total RNA was extracted from fin samples using TRIzol. Total RNA was rRNA depleted using the Ribo Zero Gold rRNA Removal Kit Illumina  San Diego  CA. Sample libraries were made using TruSeq Constructions Kits and sequenced using the HiSeq platform Illumina  San Diego  CA with 20 30 million 50 base pair  paired end sequences per sample. RNA extraction  rRNA depletion  library construction and sequencing were done by Covance Genomics Laboratory Seattle  WA.,GEO Accession:GSM2436977,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP095533,,,AC6VTYANXX_US-1584724_GATCAG_L007_R1_001.fastq.gz AC6VTYANXX_US-1584724_GATCAG_L007_R2_001.fastq.gz,fastq fastq,1880339094.0,18434697.0,GSM2436977 r1,0:51 1:51,A:473465587;C:456210186;G:466222765;T:482640937;N:1799619,51,51,,,473465587,456210186,466222765,482640937,1799619,SRX2440171,SRS1874758,SRA507993,GEO,University of Washington,2,0.86138,0.86928,0.27403,0.27401,0.74292,0.74864,0.57932,0.58297,51,51,B,B,biological fallback assumption,illumina,hiseq_era,unknown,rrna_depletion,ribozero,bulk,unknown,unknown,,United States,2016-12-22,Undetermined,Adult,Fin,Surface Structure
41749,SRR5125769,SRX2440171,SRS1874758,SRP095533,PRJNA358533,Transcriptomic  Proteomic  and Metabolomic Landscape of Positional Memory in the Caudal Fin of Zebrafish,GSE92760,Transcriptome Analysis,Regeneration requires cells to regulate proliferation and patterning according to their spatial position. Positional memory is a property that enables regenerating cells to recall spatial information from the uninjured tissue. Positional memory is hypothesized to rely on gradients of molecules  few of which have been identified. Here  we quantified the global abundance of transcripts  proteins and metabolites along the proximodistal axis of caudal fins of uninjured and regenerating adult zebrafish. Using this approach  we uncovered complex overlapping expression patterns for hundreds of molecules involved in diverse cellular functions  including developmental and bioelectric signaling as well as amino acid and lipid metabolism. Moreover  32 genes differentially expressed at the RNA level had concomitant differential expression of the encoded proteins. Thus  the identification of proximodistal differences in levels of RNAs  proteins  and metabolites will facilitate future functional studies of positional memory during appendage regeneration. Overall design: RNA seq was performed on 5 biological replicates for each of 3 positions along the proximodistal axis of the caudal fin; proximal  middle and distal 15 total samples. Each biological replicate was a pool of fin regions cut from 2 male and 2 female zebrafish.,,pubmed:28096348,,Prox 3,GSM2436977,,tissue:Proximal region of caudal fin|strain:AB WT|position:proximal|barcode sample name for sequencing:US 1584724,Prox 3,FASTQ reads were aligned to Zebrafish GRCz10 using Tophat 2.0.13 with default settings. HTSeq count was used to get read counts for each sample. Ensembl GRCz10 gene annotation file was used for gene expression quantification Differential analysis was performed with DESeq. Genome build: Zebrafish GRCz10 Supplementary files format and content: tab delimited text files include RPM values for each Sample,Proximal region of caudal fin,,Collected fin regions were flash frozen in liquid nitrogen and stored at  80˚C. Total RNA was extracted from fin samples using TRIzol. Total RNA was rRNA depleted using the Ribo Zero Gold rRNA Removal Kit Illumina  San Diego  CA. Sample libraries were made using TruSeq Constructions Kits and sequenced using the HiSeq platform Illumina  San Diego  CA with 20 30 million 50 base pair  paired end sequences per sample. RNA extraction  rRNA depletion  library construction and sequencing were done by Covance Genomics Laboratory Seattle  WA.,,strain:AB WT|position:proximal|barcode sample name for sequencing:US 1584724,GSM2436977,GSM2436977: Prox 3; Danio rerio; RNA Seq,GSM2436977,,1,Collected fin regions were flash frozen in liquid nitrogen and stored at  80˚C. Total RNA was extracted from fin samples using TRIzol. Total RNA was rRNA depleted using the Ribo Zero Gold rRNA Removal Kit Illumina  San Diego  CA. Sample libraries were made using TruSeq Constructions Kits and sequenced using the HiSeq platform Illumina  San Diego  CA with 20 30 million 50 base pair  paired end sequences per sample. RNA extraction  rRNA depletion  library construction and sequencing were done by Covance Genomics Laboratory Seattle  WA.,GEO Accession:GSM2436977,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP095533,,,AC6VTYANXX_US-1584724_GATCAG_L008_R1_001.fastq.gz AC6VTYANXX_US-1584724_GATCAG_L008_R2_001.fastq.gz,fastq fastq,1761776232.0,17272316.0,GSM2436977 r2,0:51 1:51,A:443462809;C:427563081;G:437023021;T:452089133;N:1638188,51,51,,,443462809,427563081,437023021,452089133,1638188,SRX2440171,SRS1874758,SRA507993,GEO,University of Washington,2,0.86003,0.86319,0.27335,0.27199,0.74438,0.74986,0.57998,0.5842,51,51,B,B,biological fallback assumption,illumina,hiseq_era,unknown,rrna_depletion,ribozero,bulk,unknown,unknown,,United States,2016-12-22,Undetermined,Adult,Fin,Surface Structure
41750,SRR5125766,SRX2440170,SRS1874757,SRP095533,PRJNA358533,Transcriptomic  Proteomic  and Metabolomic Landscape of Positional Memory in the Caudal Fin of Zebrafish,GSE92760,Transcriptome Analysis,Regeneration requires cells to regulate proliferation and patterning according to their spatial position. Positional memory is a property that enables regenerating cells to recall spatial information from the uninjured tissue. Positional memory is hypothesized to rely on gradients of molecules  few of which have been identified. Here  we quantified the global abundance of transcripts  proteins and metabolites along the proximodistal axis of caudal fins of uninjured and regenerating adult zebrafish. Using this approach  we uncovered complex overlapping expression patterns for hundreds of molecules involved in diverse cellular functions  including developmental and bioelectric signaling as well as amino acid and lipid metabolism. Moreover  32 genes differentially expressed at the RNA level had concomitant differential expression of the encoded proteins. Thus  the identification of proximodistal differences in levels of RNAs  proteins  and metabolites will facilitate future functional studies of positional memory during appendage regeneration. Overall design: RNA seq was performed on 5 biological replicates for each of 3 positions along the proximodistal axis of the caudal fin; proximal  middle and distal 15 total samples. Each biological replicate was a pool of fin regions cut from 2 male and 2 female zebrafish.,,pubmed:28096348,,Prox 2,GSM2436976,,tissue:Proximal region of caudal fin|strain:AB WT|position:proximal|barcode sample name for sequencing:US 1584732,Prox 2,FASTQ reads were aligned to Zebrafish GRCz10 using Tophat 2.0.13 with default settings. HTSeq count was used to get read counts for each sample. Ensembl GRCz10 gene annotation file was used for gene expression quantification Differential analysis was performed with DESeq. Genome build: Zebrafish GRCz10 Supplementary files format and content: tab delimited text files include RPM values for each Sample,Proximal region of caudal fin,,Collected fin regions were flash frozen in liquid nitrogen and stored at  80˚C. Total RNA was extracted from fin samples using TRIzol. Total RNA was rRNA depleted using the Ribo Zero Gold rRNA Removal Kit Illumina  San Diego  CA. Sample libraries were made using TruSeq Constructions Kits and sequenced using the HiSeq platform Illumina  San Diego  CA with 20 30 million 50 base pair  paired end sequences per sample. RNA extraction  rRNA depletion  library construction and sequencing were done by Covance Genomics Laboratory Seattle  WA.,,strain:AB WT|position:proximal|barcode sample name for sequencing:US 1584732,GSM2436976,GSM2436976: Prox 2; Danio rerio; RNA Seq,GSM2436976,,1,Collected fin regions were flash frozen in liquid nitrogen and stored at  80˚C. Total RNA was extracted from fin samples using TRIzol. Total RNA was rRNA depleted using the Ribo Zero Gold rRNA Removal Kit Illumina  San Diego  CA. Sample libraries were made using TruSeq Constructions Kits and sequenced using the HiSeq platform Illumina  San Diego  CA with 20 30 million 50 base pair  paired end sequences per sample. RNA extraction  rRNA depletion  library construction and sequencing were done by Covance Genomics Laboratory Seattle  WA.,GEO Accession:GSM2436976,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP095533,,,AC6VTYANXX_US-1584732_GGCTAC_L007_R1_001.fastq.gz AC6VTYANXX_US-1584732_GGCTAC_L007_R2_001.fastq.gz,fastq fastq,1940899758.0,19028429.0,GSM2436976 r1,0:51 1:51,A:490621032;C:469829066;G:478454726;T:500137701;N:1857233,51,51,,,490621032,469829066,478454726,500137701,1857233,SRX2440170,SRS1874757,SRA507993,GEO,University of Washington,2,0.86398,0.87296,0.28207,0.2836,0.7416,0.74726,0.56787,0.5472,51,51,B,B,biological fallback assumption,illumina,hiseq_era,unknown,rrna_depletion,ribozero,bulk,unknown,unknown,,United States,2016-12-22,Undetermined,Adult,Fin,Surface Structure
41751,SRR5125767,SRX2440170,SRS1874757,SRP095533,PRJNA358533,Transcriptomic  Proteomic  and Metabolomic Landscape of Positional Memory in the Caudal Fin of Zebrafish,GSE92760,Transcriptome Analysis,Regeneration requires cells to regulate proliferation and patterning according to their spatial position. Positional memory is a property that enables regenerating cells to recall spatial information from the uninjured tissue. Positional memory is hypothesized to rely on gradients of molecules  few of which have been identified. Here  we quantified the global abundance of transcripts  proteins and metabolites along the proximodistal axis of caudal fins of uninjured and regenerating adult zebrafish. Using this approach  we uncovered complex overlapping expression patterns for hundreds of molecules involved in diverse cellular functions  including developmental and bioelectric signaling as well as amino acid and lipid metabolism. Moreover  32 genes differentially expressed at the RNA level had concomitant differential expression of the encoded proteins. Thus  the identification of proximodistal differences in levels of RNAs  proteins  and metabolites will facilitate future functional studies of positional memory during appendage regeneration. Overall design: RNA seq was performed on 5 biological replicates for each of 3 positions along the proximodistal axis of the caudal fin; proximal  middle and distal 15 total samples. Each biological replicate was a pool of fin regions cut from 2 male and 2 female zebrafish.,,pubmed:28096348,,Prox 2,GSM2436976,,tissue:Proximal region of caudal fin|strain:AB WT|position:proximal|barcode sample name for sequencing:US 1584732,Prox 2,FASTQ reads were aligned to Zebrafish GRCz10 using Tophat 2.0.13 with default settings. HTSeq count was used to get read counts for each sample. Ensembl GRCz10 gene annotation file was used for gene expression quantification Differential analysis was performed with DESeq. Genome build: Zebrafish GRCz10 Supplementary files format and content: tab delimited text files include RPM values for each Sample,Proximal region of caudal fin,,Collected fin regions were flash frozen in liquid nitrogen and stored at  80˚C. Total RNA was extracted from fin samples using TRIzol. Total RNA was rRNA depleted using the Ribo Zero Gold rRNA Removal Kit Illumina  San Diego  CA. Sample libraries were made using TruSeq Constructions Kits and sequenced using the HiSeq platform Illumina  San Diego  CA with 20 30 million 50 base pair  paired end sequences per sample. RNA extraction  rRNA depletion  library construction and sequencing were done by Covance Genomics Laboratory Seattle  WA.,,strain:AB WT|position:proximal|barcode sample name for sequencing:US 1584732,GSM2436976,GSM2436976: Prox 2; Danio rerio; RNA Seq,GSM2436976,,1,Collected fin regions were flash frozen in liquid nitrogen and stored at  80˚C. Total RNA was extracted from fin samples using TRIzol. Total RNA was rRNA depleted using the Ribo Zero Gold rRNA Removal Kit Illumina  San Diego  CA. Sample libraries were made using TruSeq Constructions Kits and sequenced using the HiSeq platform Illumina  San Diego  CA with 20 30 million 50 base pair  paired end sequences per sample. RNA extraction  rRNA depletion  library construction and sequencing were done by Covance Genomics Laboratory Seattle  WA.,GEO Accession:GSM2436976,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP095533,,,AC6VTYANXX_US-1584732_GGCTAC_L008_R1_001.fastq.gz AC6VTYANXX_US-1584732_GGCTAC_L008_R2_001.fastq.gz,fastq fastq,1819166634.0,17834967.0,GSM2436976 r2,0:51 1:51,A:459617381;C:440486686;G:448738324;T:468660475;N:1663768,51,51,,,459617381,440486686,448738324,468660475,1663768,SRX2440170,SRS1874757,SRA507993,GEO,University of Washington,2,0.86476,0.86641,0.28029,0.27717,0.74387,0.74811,0.58049,0.57945,51,51,B,B,biological fallback assumption,illumina,hiseq_era,unknown,rrna_depletion,ribozero,bulk,unknown,unknown,,United States,2016-12-22,Undetermined,Adult,Fin,Surface Structure
41752,SRR5125764,SRX2440169,SRS1874756,SRP095533,PRJNA358533,Transcriptomic  Proteomic  and Metabolomic Landscape of Positional Memory in the Caudal Fin of Zebrafish,GSE92760,Transcriptome Analysis,Regeneration requires cells to regulate proliferation and patterning according to their spatial position. Positional memory is a property that enables regenerating cells to recall spatial information from the uninjured tissue. Positional memory is hypothesized to rely on gradients of molecules  few of which have been identified. Here  we quantified the global abundance of transcripts  proteins and metabolites along the proximodistal axis of caudal fins of uninjured and regenerating adult zebrafish. Using this approach  we uncovered complex overlapping expression patterns for hundreds of molecules involved in diverse cellular functions  including developmental and bioelectric signaling as well as amino acid and lipid metabolism. Moreover  32 genes differentially expressed at the RNA level had concomitant differential expression of the encoded proteins. Thus  the identification of proximodistal differences in levels of RNAs  proteins  and metabolites will facilitate future functional studies of positional memory during appendage regeneration. Overall design: RNA seq was performed on 5 biological replicates for each of 3 positions along the proximodistal axis of the caudal fin; proximal  middle and distal 15 total samples. Each biological replicate was a pool of fin regions cut from 2 male and 2 female zebrafish.,,pubmed:28096348,,Prox 1,GSM2436975,,tissue:Proximal region of caudal fin|strain:AB WT|position:proximal|barcode sample name for sequencing:US 1584752,Prox 1,FASTQ reads were aligned to Zebrafish GRCz10 using Tophat 2.0.13 with default settings. HTSeq count was used to get read counts for each sample. Ensembl GRCz10 gene annotation file was used for gene expression quantification Differential analysis was performed with DESeq. Genome build: Zebrafish GRCz10 Supplementary files format and content: tab delimited text files include RPM values for each Sample,Proximal region of caudal fin,,Collected fin regions were flash frozen in liquid nitrogen and stored at  80˚C. Total RNA was extracted from fin samples using TRIzol. Total RNA was rRNA depleted using the Ribo Zero Gold rRNA Removal Kit Illumina  San Diego  CA. Sample libraries were made using TruSeq Constructions Kits and sequenced using the HiSeq platform Illumina  San Diego  CA with 20 30 million 50 base pair  paired end sequences per sample. RNA extraction  rRNA depletion  library construction and sequencing were done by Covance Genomics Laboratory Seattle  WA.,,strain:AB WT|position:proximal|barcode sample name for sequencing:US 1584752,GSM2436975,GSM2436975: Prox 1; Danio rerio; RNA Seq,GSM2436975,,1,Collected fin regions were flash frozen in liquid nitrogen and stored at  80˚C. Total RNA was extracted from fin samples using TRIzol. Total RNA was rRNA depleted using the Ribo Zero Gold rRNA Removal Kit Illumina  San Diego  CA. Sample libraries were made using TruSeq Constructions Kits and sequenced using the HiSeq platform Illumina  San Diego  CA with 20 30 million 50 base pair  paired end sequences per sample. RNA extraction  rRNA depletion  library construction and sequencing were done by Covance Genomics Laboratory Seattle  WA.,GEO Accession:GSM2436975,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP095533,,,AC6VTYANXX_US-1584752_AGTCAA_L007_R1_001.fastq.gz AC6VTYANXX_US-1584752_AGTCAA_L007_R2_001.fastq.gz,fastq fastq,1890704844.0,18536322.0,GSM2436975 r1,0:51 1:51,A:469162531;C:465995012;G:477596114;T:476134847;N:1816340,51,51,,,469162531,465995012,477596114,476134847,1816340,SRX2440169,SRS1874756,SRA507993,GEO,University of Washington,2,0.85362,0.86447,0.26393,0.26801,0.74588,0.74984,0.58892,0.58892,51,51,B,B,biological fallback assumption,illumina,hiseq_era,unknown,rrna_depletion,ribozero,bulk,unknown,unknown,,United States,2016-12-22,Undetermined,Adult,Fin,Surface Structure
41753,SRR5125765,SRX2440169,SRS1874756,SRP095533,PRJNA358533,Transcriptomic  Proteomic  and Metabolomic Landscape of Positional Memory in the Caudal Fin of Zebrafish,GSE92760,Transcriptome Analysis,Regeneration requires cells to regulate proliferation and patterning according to their spatial position. Positional memory is a property that enables regenerating cells to recall spatial information from the uninjured tissue. Positional memory is hypothesized to rely on gradients of molecules  few of which have been identified. Here  we quantified the global abundance of transcripts  proteins and metabolites along the proximodistal axis of caudal fins of uninjured and regenerating adult zebrafish. Using this approach  we uncovered complex overlapping expression patterns for hundreds of molecules involved in diverse cellular functions  including developmental and bioelectric signaling as well as amino acid and lipid metabolism. Moreover  32 genes differentially expressed at the RNA level had concomitant differential expression of the encoded proteins. Thus  the identification of proximodistal differences in levels of RNAs  proteins  and metabolites will facilitate future functional studies of positional memory during appendage regeneration. Overall design: RNA seq was performed on 5 biological replicates for each of 3 positions along the proximodistal axis of the caudal fin; proximal  middle and distal 15 total samples. Each biological replicate was a pool of fin regions cut from 2 male and 2 female zebrafish.,,pubmed:28096348,,Prox 1,GSM2436975,,tissue:Proximal region of caudal fin|strain:AB WT|position:proximal|barcode sample name for sequencing:US 1584752,Prox 1,FASTQ reads were aligned to Zebrafish GRCz10 using Tophat 2.0.13 with default settings. HTSeq count was used to get read counts for each sample. Ensembl GRCz10 gene annotation file was used for gene expression quantification Differential analysis was performed with DESeq. Genome build: Zebrafish GRCz10 Supplementary files format and content: tab delimited text files include RPM values for each Sample,Proximal region of caudal fin,,Collected fin regions were flash frozen in liquid nitrogen and stored at  80˚C. Total RNA was extracted from fin samples using TRIzol. Total RNA was rRNA depleted using the Ribo Zero Gold rRNA Removal Kit Illumina  San Diego  CA. Sample libraries were made using TruSeq Constructions Kits and sequenced using the HiSeq platform Illumina  San Diego  CA with 20 30 million 50 base pair  paired end sequences per sample. RNA extraction  rRNA depletion  library construction and sequencing were done by Covance Genomics Laboratory Seattle  WA.,,strain:AB WT|position:proximal|barcode sample name for sequencing:US 1584752,GSM2436975,GSM2436975: Prox 1; Danio rerio; RNA Seq,GSM2436975,,1,Collected fin regions were flash frozen in liquid nitrogen and stored at  80˚C. Total RNA was extracted from fin samples using TRIzol. Total RNA was rRNA depleted using the Ribo Zero Gold rRNA Removal Kit Illumina  San Diego  CA. Sample libraries were made using TruSeq Constructions Kits and sequenced using the HiSeq platform Illumina  San Diego  CA with 20 30 million 50 base pair  paired end sequences per sample. RNA extraction  rRNA depletion  library construction and sequencing were done by Covance Genomics Laboratory Seattle  WA.,GEO Accession:GSM2436975,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP095533,,,AC6VTYANXX_US-1584752_AGTCAA_L008_R1_001.fastq.gz AC6VTYANXX_US-1584752_AGTCAA_L008_R2_001.fastq.gz,fastq fastq,1772593842.0,17378371.0,GSM2436975 r2,0:51 1:51,A:439706550;C:436987194;G:448069723;T:446203845;N:1626530,51,51,,,439706550,436987194,448069723,446203845,1626530,SRX2440169,SRS1874756,SRA507993,GEO,University of Washington,2,0.85457,0.86023,0.26486,0.26831,0.7472,0.75219,0.58719,0.59058,51,51,B,B,biological fallback assumption,illumina,hiseq_era,unknown,rrna_depletion,ribozero,bulk,unknown,unknown,,United States,2016-12-22,Undetermined,Adult,Fin,Surface Structure
43472,SRR6888831,SRX3839382,SRS3086668,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,P2 cfin vent Scar,GSM3065988,,tissue:primary fin single cells|cas9 injection:protein|FISH id:P2|organ:primary fin|sorted plates:2,P2 cfin vent Scar,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.,primary fin single cells,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,,cas9 injection:protein|FISH id:P2|organ:primary fin|sorted plates:2,GSM3065988,GSM3065988: P2 cfin vent Scar; Danio rerio; RNA Seq,GSM3065988,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM3065988,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,P2-CFin-Vent-003-Scar_R1.fastq.gz P2-CFin-Vent-003-Scar_R2.fastq.gz,fastq fastq,344793287.0,2269321.0,GSM3065988 r1,0:75.99 1:75.95,A:61565924;C:101344805;G:127059615;T:54785853;N:37090,75,75,,,61565924,101344805,127059615,54785853,37090,SRX3839382,SRS3086668,SRA602108,GEO,"AVO, Hubrecht Institue",2,0.00015,0.00029,0.00012,0.00017,0.99993,0.99977,0.33333,0.58823,76,76,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2018-03-23,Undetermined,Multi-stage,Fin,Surface Structure
43473,SRR6888832,SRX3839382,SRS3086668,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,P2 cfin vent Scar,GSM3065988,,tissue:primary fin single cells|cas9 injection:protein|FISH id:P2|organ:primary fin|sorted plates:2,P2 cfin vent Scar,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.,primary fin single cells,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,,cas9 injection:protein|FISH id:P2|organ:primary fin|sorted plates:2,GSM3065988,GSM3065988: P2 cfin vent Scar; Danio rerio; RNA Seq,GSM3065988,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM3065988,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,P2-CFin-Vent-004-Scar_R1.fastq.gz P2-CFin-Vent-004-Scar_R2.fastq.gz,fastq fastq,110701966.0,728490.0,GSM3065988 r2,0:75.99 1:75.97,A:19507928;C:32552811;G:40930271;T:17699467;N:11489,75,75,,,19507928,32552811,40930271,17699467,11489,SRX3839382,SRS3086668,SRA602108,GEO,"AVO, Hubrecht Institue",2,0.00021,0.0004,0.00015,0.00031,0.99991,0.99981,1.0,0.84615,76,76,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2018-03-23,Undetermined,Multi-stage,Fin,Surface Structure
43474,SRR6888829,SRX3839381,SRS3086670,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,P1 cfin dorsal Scar,GSM3065987,,tissue:primary fin single cells|cas9 injection:protein|FISH id:P2|organ:primary fin|sorted plates:2,P1 cfin dorsal Scar,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.,primary fin single cells,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,,cas9 injection:protein|FISH id:P2|organ:primary fin|sorted plates:2,GSM3065987,GSM3065987: P1 cfin dorsal Scar; Danio rerio; RNA Seq,GSM3065987,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM3065987,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,P2-CFin-Dors-003-Scar_R2.fastq.gz P2-CFin-Dors-003-Scar_R1.fastq.gz,fastq fastq,537943644.0,3539989.0,GSM3065987 r1,0:75.99 1:75.97,A:94708808;C:157878001;G:198461680;T:86838061;N:57094,75,75,,,94708808,157878001,198461680,86838061,57094,SRX3839381,SRS3086670,SRA602108,GEO,"AVO, Hubrecht Institue",2,0.00016,0.00102,0.0001,0.00067,0.99995,0.99995,0.0,1.0,76,76,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2018-03-23,Undetermined,Multi-stage,Fin,Surface Structure
43475,SRR6888830,SRX3839381,SRS3086670,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,P1 cfin dorsal Scar,GSM3065987,,tissue:primary fin single cells|cas9 injection:protein|FISH id:P2|organ:primary fin|sorted plates:2,P1 cfin dorsal Scar,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.,primary fin single cells,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,,cas9 injection:protein|FISH id:P2|organ:primary fin|sorted plates:2,GSM3065987,GSM3065987: P1 cfin dorsal Scar; Danio rerio; RNA Seq,GSM3065987,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM3065987,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,P2-CFin-Dors-004-Scar_R1.fastq.gz P2-CFin-Dors-004-Scar_R2.fastq.gz,fastq fastq,856597590.0,5637115.0,GSM3065987 r2,0:75.99 1:75.97,A:151359975;C:251587454;G:317011744;T:136549208;N:89209,75,75,,,151359975,251587454,317011744,136549208,89209,SRX3839381,SRS3086670,SRA602108,GEO,"AVO, Hubrecht Institue",2,0.00027,0.00065,0.00016,0.00039,0.99975,0.99951,0.29411,0.53658,76,76,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2018-03-23,Undetermined,Multi-stage,Fin,Surface Structure
43476,SRR6020446,SRX3171493,SRS2501302,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,R5 sec Trans,GSM2776988,,source name:secondary fin single cells|cas9 injection:mRNA|FISH id:R5|tissue:secondary fin|sorted plates:6,R5 sec Trans,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.,secondary fin single cells,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,,cas9 injection:mRNA|FISH id:R5|tissue:secondary fin|sorted plates:6,GSM2776988,GSM2776988: R5 sec Trans; Danio rerio; RNA Seq,GSM2776988,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2776988,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,R5_sec_Trans_p01_R1.fastq.gz R5_sec_Trans_p01_R2.fastq.gz,fastq fastq,5031589058.0,33202740.0,GSM2776988 r1,0:75.79 1:75.75,A:1144328847;C:1211156155;G:1480041764;T:1195826451;N:235841,75,75,,,1144328847,1211156155,1480041764,1195826451,235841,SRX3171493,SRS2501302,SRA602108,GEO,"AVO, Hubrecht Institue",2,0.11853,0.24563,0.10636,0.21925,0.96585,0.92555,0.49894,0.48592,75,75,B,B,mate1-mate2 similar by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2017-09-08,Undetermined,Multi-stage,Fin,Surface Structure
43477,SRR6020447,SRX3171493,SRS2501302,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,R5 sec Trans,GSM2776988,,source name:secondary fin single cells|cas9 injection:mRNA|FISH id:R5|tissue:secondary fin|sorted plates:6,R5 sec Trans,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.,secondary fin single cells,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,,cas9 injection:mRNA|FISH id:R5|tissue:secondary fin|sorted plates:6,GSM2776988,GSM2776988: R5 sec Trans; Danio rerio; RNA Seq,GSM2776988,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2776988,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,R5_sec_Trans_p02_R2.fastq.gz R5_sec_Trans_p02_R1.fastq.gz,fastq fastq,5020749563.0,33189212.0,GSM2776988 r2,0:75.66 1:75.61,A:1271180542;C:1081665590;G:1257183505;T:1410487545;N:232381,75,75,,,1271180542,1081665590,1257183505,1410487545,232381,SRX3171493,SRS2501302,SRA602108,GEO,"AVO, Hubrecht Institue",2,0.12477,0.33055,0.10671,0.26254,0.96773,0.90583,0.50071,0.48529,76,76,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2017-09-08,Undetermined,Multi-stage,Fin,Surface Structure
43478,SRR6020448,SRX3171493,SRS2501302,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,R5 sec Trans,GSM2776988,,source name:secondary fin single cells|cas9 injection:mRNA|FISH id:R5|tissue:secondary fin|sorted plates:6,R5 sec Trans,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.,secondary fin single cells,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,,cas9 injection:mRNA|FISH id:R5|tissue:secondary fin|sorted plates:6,GSM2776988,GSM2776988: R5 sec Trans; Danio rerio; RNA Seq,GSM2776988,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2776988,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,R5_sec_Trans_p03_R1.fastq.gz R5_sec_Trans_p03_R2.fastq.gz,fastq fastq,9930849737.0,65769125.0,GSM2776988 r3,0:75.49 1:75.50,A:2771601461;C:1594447174;G:1778419273;T:3786066213;N:315616,75,75,,,2771601461,1594447174,1778419273,3786066213,315616,SRX3171493,SRS2501302,SRA602108,GEO,"AVO, Hubrecht Institue",2,0.31895,0.74881,0.28344,0.57326,0.96546,0.85234,0.4987,0.52017,76,76,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2017-09-08,Undetermined,Multi-stage,Fin,Surface Structure
43479,SRR6020449,SRX3171493,SRS2501302,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,R5 sec Trans,GSM2776988,,source name:secondary fin single cells|cas9 injection:mRNA|FISH id:R5|tissue:secondary fin|sorted plates:6,R5 sec Trans,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.,secondary fin single cells,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,,cas9 injection:mRNA|FISH id:R5|tissue:secondary fin|sorted plates:6,GSM2776988,GSM2776988: R5 sec Trans; Danio rerio; RNA Seq,GSM2776988,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2776988,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,R5_sec_Trans_p04_R1.fastq.gz R5_sec_Trans_p04_R2.fastq.gz,fastq fastq,7297925579.0,48343134.0,GSM2776988 r4,0:75.51 1:75.45,A:2157432534;C:1129186071;G:1200823243;T:2810444585;N:39146,75,75,,,2157432534,1129186071,1200823243,2810444585,39146,SRX3171493,SRS2501302,SRA602108,GEO,"AVO, Hubrecht Institue",2,0.352,0.75293,0.31357,0.60441,0.95828,0.83885,0.50134,0.50535,75,75,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2017-09-08,Undetermined,Multi-stage,Fin,Surface Structure
43480,SRR6020450,SRX3171493,SRS2501302,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,R5 sec Trans,GSM2776988,,source name:secondary fin single cells|cas9 injection:mRNA|FISH id:R5|tissue:secondary fin|sorted plates:6,R5 sec Trans,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.,secondary fin single cells,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,,cas9 injection:mRNA|FISH id:R5|tissue:secondary fin|sorted plates:6,GSM2776988,GSM2776988: R5 sec Trans; Danio rerio; RNA Seq,GSM2776988,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2776988,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,R5_sec_Trans_p05_R2.fastq.gz R5_sec_Trans_p05_R1.fastq.gz,fastq fastq,13855953318.0,91804628.0,GSM2776988 r5,0:75.50 1:75.43,A:4146316683;C:2217362039;G:2391706547;T:5100492721;N:75328,75,75,,,4146316683,2217362039,2391706547,5100492721,75328,SRX3171493,SRS2501302,SRA602108,GEO,"AVO, Hubrecht Institue",2,0.37449,0.68646,0.32985,0.54102,0.95347,0.849,0.49416,0.50708,75,76,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2017-09-08,Undetermined,Multi-stage,Fin,Surface Structure
43481,SRR6020451,SRX3171493,SRS2501302,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,R5 sec Trans,GSM2776988,,source name:secondary fin single cells|cas9 injection:mRNA|FISH id:R5|tissue:secondary fin|sorted plates:6,R5 sec Trans,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.,secondary fin single cells,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,,cas9 injection:mRNA|FISH id:R5|tissue:secondary fin|sorted plates:6,GSM2776988,GSM2776988: R5 sec Trans; Danio rerio; RNA Seq,GSM2776988,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2776988,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,R5_sec_Trans_p06_R1.fastq.gz R5_sec_Trans_p06_R2.fastq.gz,fastq fastq,9723577592.0,64415623.0,GSM2776988 r6,0:75.50 1:75.45,A:2835431401;C:1511580093;G:1616039076;T:3760473139;N:53883,75,75,,,2835431401,1511580093,1616039076,3760473139,53883,SRX3171493,SRS2501302,SRA602108,GEO,"AVO, Hubrecht Institue",2,0.33655,0.77492,0.29229,0.58155,0.95978,0.8454,0.49546,0.51051,76,76,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2017-09-08,Undetermined,Multi-stage,Fin,Surface Structure
43482,SRR6020440,SRX3171492,SRS2501301,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,R5 sec Scar,GSM2776987,,source name:secondary fin single cells|cas9 injection:mRNA|FISH id:R5|tissue:secondary fin|sorted plates:6,R5 sec Scar,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.,secondary fin single cells,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,,cas9 injection:mRNA|FISH id:R5|tissue:secondary fin|sorted plates:6,GSM2776987,GSM2776987: R5 sec Scar; Danio rerio; RNA Seq,GSM2776987,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2776987,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,R5_sec_Scar_p01_R1.fastq.gz R5_sec_Scar_p01_R2.fastq.gz,fastq fastq,361194076.0,2376599.0,GSM2776987 r1,0:75.99 1:75.99,A:63932353;C:105212754;G:137339472;T:54692604;N:16893,75,75,,,63932353,105212754,137339472,54692604,16893,SRX3171492,SRS2501301,SRA602108,GEO,"AVO, Hubrecht Institue",2,7e-05,0.00012,4e-05,9e-05,0.99993,0.99991,0.5,0.75,76,76,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2017-09-08,Undetermined,Multi-stage,Fin,Surface Structure
43483,SRR6020441,SRX3171492,SRS2501301,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,R5 sec Scar,GSM2776987,,source name:secondary fin single cells|cas9 injection:mRNA|FISH id:R5|tissue:secondary fin|sorted plates:6,R5 sec Scar,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.,secondary fin single cells,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,,cas9 injection:mRNA|FISH id:R5|tissue:secondary fin|sorted plates:6,GSM2776987,GSM2776987: R5 sec Scar; Danio rerio; RNA Seq,GSM2776987,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2776987,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,R5_sec_Scar_p02_R1.fastq.gz R5_sec_Scar_p02_R2.fastq.gz,fastq fastq,460055993.0,3027108.0,GSM2776987 r2,0:75.99 1:75.99,A:80579341;C:134185300;G:175364991;T:69904520;N:21841,75,75,,,80579341,134185300,175364991,69904520,21841,SRX3171492,SRS2501301,SRA602108,GEO,"AVO, Hubrecht Institue",2,5e-05,2e-05,2e-05,0.0,0.99997,0.99997,0.0,1.0,76,76,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2017-09-08,Undetermined,Multi-stage,Fin,Surface Structure
43484,SRR6020442,SRX3171492,SRS2501301,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,R5 sec Scar,GSM2776987,,source name:secondary fin single cells|cas9 injection:mRNA|FISH id:R5|tissue:secondary fin|sorted plates:6,R5 sec Scar,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.,secondary fin single cells,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,,cas9 injection:mRNA|FISH id:R5|tissue:secondary fin|sorted plates:6,GSM2776987,GSM2776987: R5 sec Scar; Danio rerio; RNA Seq,GSM2776987,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2776987,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,R5_sec_Scar_p03_R1.fastq.gz R5_sec_Scar_p03_R2.fastq.gz,fastq fastq,466000423.0,3066554.0,GSM2776987 r3,0:75.98 1:75.98,A:81301391;C:136221817;G:177874701;T:70591092;N:11422,75,75,,,81301391,136221817,177874701,70591092,11422,SRX3171492,SRS2501301,SRA602108,GEO,"AVO, Hubrecht Institue",2,0.0001,0.00016,8e-05,0.00011,0.99993,0.99987,0.0,0.66666,76,76,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2017-09-08,Undetermined,Multi-stage,Fin,Surface Structure
43485,SRR6020443,SRX3171492,SRS2501301,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,R5 sec Scar,GSM2776987,,source name:secondary fin single cells|cas9 injection:mRNA|FISH id:R5|tissue:secondary fin|sorted plates:6,R5 sec Scar,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.,secondary fin single cells,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,,cas9 injection:mRNA|FISH id:R5|tissue:secondary fin|sorted plates:6,GSM2776987,GSM2776987: R5 sec Scar; Danio rerio; RNA Seq,GSM2776987,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2776987,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,R5_sec_Scar_p04_R1.fastq.gz R5_sec_Scar_p04_R2.fastq.gz,fastq fastq,203843839.0,1341388.0,GSM2776987 r4,,,,,,,,,,,,SRX3171492,SRS2501301,SRA602108,GEO,"AVO, Hubrecht Institue",2,0.00013,0.00027,9e-05,0.00019,0.99995,0.99977,0.16666,0.66666,76,76,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2017-09-08,Undetermined,Multi-stage,Fin,Surface Structure
43486,SRR6020444,SRX3171492,SRS2501301,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,R5 sec Scar,GSM2776987,,source name:secondary fin single cells|cas9 injection:mRNA|FISH id:R5|tissue:secondary fin|sorted plates:6,R5 sec Scar,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.,secondary fin single cells,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,,cas9 injection:mRNA|FISH id:R5|tissue:secondary fin|sorted plates:6,GSM2776987,GSM2776987: R5 sec Scar; Danio rerio; RNA Seq,GSM2776987,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2776987,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,R5_sec_Scar_p05_R1.fastq.gz R5_sec_Scar_p05_R2.fastq.gz,fastq fastq,305866297.0,2012742.0,GSM2776987 r5,0:75.98 1:75.98,A:53459692;C:89448285;G:116312720;T:46644195;N:1405,75,75,,,53459692,89448285,116312720,46644195,1405,SRX3171492,SRS2501301,SRA602108,GEO,"AVO, Hubrecht Institue",2,6e-05,9e-05,3e-05,5e-05,0.99997,0.99993,0.0,0.5,76,76,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2017-09-08,Undetermined,Multi-stage,Fin,Surface Structure
43487,SRR6020445,SRX3171492,SRS2501301,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,R5 sec Scar,GSM2776987,,source name:secondary fin single cells|cas9 injection:mRNA|FISH id:R5|tissue:secondary fin|sorted plates:6,R5 sec Scar,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.,secondary fin single cells,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,,cas9 injection:mRNA|FISH id:R5|tissue:secondary fin|sorted plates:6,GSM2776987,GSM2776987: R5 sec Scar; Danio rerio; RNA Seq,GSM2776987,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2776987,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,R5_sec_Scar_p06_R1.fastq.gz R5_sec_Scar_p06_R2.fastq.gz,fastq fastq,557494800.0,3670391.0,GSM2776987 r6,0:75.96 1:75.93,A:101252524;C:160223186;G:205832526;T:90183664;N:2900,75,75,,,101252524,160223186,205832526,90183664,2900,SRX3171492,SRS2501301,SRA602108,GEO,"AVO, Hubrecht Institue",2,0.00382,0.00768,0.00317,0.00636,0.99827,0.99673,0.48648,0.5,76,76,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2017-09-08,Undetermined,Multi-stage,Fin,Surface Structure
43488,SRR6020435,SRX3171491,SRS2501300,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,R5 prim Trans,GSM2776986,,source name:primary fin single cells|cas9 injection:mRNA|FISH id:R5|tissue:primary fin|sorted plates:5,R5 prim Trans,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.,primary fin single cells,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,,cas9 injection:mRNA|FISH id:R5|tissue:primary fin|sorted plates:5,GSM2776986,GSM2776986: R5 prim Trans; Danio rerio; RNA Seq,GSM2776986,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2776986,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,R5_prim_Trans_p02_R1.fastq.gz R5_prim_Trans_p02_R2.fastq.gz,fastq fastq,7812360278.0,51697480.0,GSM2776986 r1,0:75.54 1:75.58,A:2098454376;C:1641311761;G:1943503636;T:2128270555;N:819950,75,75,,,2098454376,1641311761,1943503636,2128270555,819950,SRX3171491,SRS2501300,SRA602108,GEO,"AVO, Hubrecht Institue",2,0.01048,0.02593,0.00847,0.02007,0.99614,0.98742,0.33227,0.53419,76,75,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2017-09-08,Undetermined,Multi-stage,Fin,Surface Structure
43489,SRR6020436,SRX3171491,SRS2501300,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,R5 prim Trans,GSM2776986,,source name:primary fin single cells|cas9 injection:mRNA|FISH id:R5|tissue:primary fin|sorted plates:5,R5 prim Trans,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.,primary fin single cells,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,,cas9 injection:mRNA|FISH id:R5|tissue:primary fin|sorted plates:5,GSM2776986,GSM2776986: R5 prim Trans; Danio rerio; RNA Seq,GSM2776986,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2776986,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,R5_prim_Trans_p03_R1.fastq.gz R5_prim_Trans_p03_R2.fastq.gz,fastq fastq,6704494628.0,44436630.0,GSM2776986 r2,0:75.49 1:75.39,A:2087008571;C:1124579474;G:1252171872;T:2240541544;N:193167,75,75,,,2087008571,1124579474,1252171872,2240541544,193167,SRX3171491,SRS2501300,SRA602108,GEO,"AVO, Hubrecht Institue",2,0.24966,0.47946,0.21997,0.40259,0.95162,0.89191,0.48641,0.54514,75,75,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2017-09-08,Undetermined,Multi-stage,Fin,Surface Structure
43490,SRR6020437,SRX3171491,SRS2501300,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,R5 prim Trans,GSM2776986,,source name:primary fin single cells|cas9 injection:mRNA|FISH id:R5|tissue:primary fin|sorted plates:5,R5 prim Trans,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.,primary fin single cells,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,,cas9 injection:mRNA|FISH id:R5|tissue:primary fin|sorted plates:5,GSM2776986,GSM2776986: R5 prim Trans; Danio rerio; RNA Seq,GSM2776986,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2776986,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,R5_prim_Trans_p04_R1.fastq.gz R5_prim_Trans_p04_R2.fastq.gz,fastq fastq,8402262674.0,55692887.0,GSM2776986 r3,0:75.48 1:75.39,A:2618499207;C:1444061167;G:1613776766;T:2725680678;N:244856,75,75,,,2618499207,1444061167,1613776766,2725680678,244856,SRX3171491,SRS2501300,SRA602108,GEO,"AVO, Hubrecht Institue",2,0.26079,0.43317,0.23304,0.36897,0.95686,0.90575,0.50825,0.53432,76,75,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2017-09-08,Undetermined,Multi-stage,Fin,Surface Structure
43491,SRR6020438,SRX3171491,SRS2501300,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,R5 prim Trans,GSM2776986,,source name:primary fin single cells|cas9 injection:mRNA|FISH id:R5|tissue:primary fin|sorted plates:5,R5 prim Trans,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.,primary fin single cells,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,,cas9 injection:mRNA|FISH id:R5|tissue:primary fin|sorted plates:5,GSM2776986,GSM2776986: R5 prim Trans; Danio rerio; RNA Seq,GSM2776986,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2776986,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,R5_prim_Trans_p07_R1.fastq.gz R5_prim_Trans_p07_R2.fastq.gz,fastq fastq,7045442122.0,46667895.0,GSM2776986 r4,0:75.65 1:75.32,A:1992737539;C:1481998828;G:1584855122;T:1984679859;N:1170774,75,75,,,1992737539,1481998828,1584855122,1984679859,1170774,SRX3171491,SRS2501300,SRA602108,GEO,"AVO, Hubrecht Institue",2,0.08866,0.20939,0.07714,0.18048,0.97906,0.95674,0.50746,0.52807,76,76,B,B,mate1-mate2 similar by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2017-09-08,Undetermined,Multi-stage,Fin,Surface Structure
43492,SRR6020439,SRX3171491,SRS2501300,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,R5 prim Trans,GSM2776986,,source name:primary fin single cells|cas9 injection:mRNA|FISH id:R5|tissue:primary fin|sorted plates:5,R5 prim Trans,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.,primary fin single cells,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,,cas9 injection:mRNA|FISH id:R5|tissue:primary fin|sorted plates:5,GSM2776986,GSM2776986: R5 prim Trans; Danio rerio; RNA Seq,GSM2776986,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2776986,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,R5_prim_Trans_p08_R1.fastq.gz R5_prim_Trans_p08_R2.fastq.gz,fastq fastq,18530449971.0,122665653.0,GSM2776986 r5,0:75.68 1:75.38,A:4667348302;C:4333487274;G:4681098112;T:4848415162;N:101121,75,75,,,4667348302,4333487274,4681098112,4848415162,101121,SRX3171491,SRS2501300,SRA602108,GEO,"AVO, Hubrecht Institue",2,0.05599,0.12252,0.04627,0.10255,0.98409,0.96467,0.50898,0.5274,75,75,B,B,mate1-mate2 similar by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2017-09-08,Undetermined,Multi-stage,Fin,Surface Structure
43493,SRR6020429,SRX3171490,SRS2501299,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,R5 prim Scar,GSM2776985,,source name:primary fin single cells|cas9 injection:mRNA|FISH id:R5|tissue:primary fin|sorted plates:6,R5 prim Scar,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.,primary fin single cells,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,,cas9 injection:mRNA|FISH id:R5|tissue:primary fin|sorted plates:6,GSM2776985,GSM2776985: R5 prim Scar; Danio rerio; RNA Seq,GSM2776985,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2776985,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,R5_prim_Scar_p01_R1.fastq.gz R5_prim_Scar_p01_R2.fastq.gz,fastq fastq,24766319.0,163126.0,GSM2776985 r1,0:75.95 1:75.87,A:4693411;C:6959422;G:8727578;T:4381992;N:3916,75,75,,,4693411,6959422,8727578,4381992,3916,SRX3171490,SRS2501299,SRA602108,GEO,"AVO, Hubrecht Institue",2,0.00023,0.00064,0.00018,0.00044,0.99989,0.99969,0.6,0.8,76,76,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2017-09-08,Undetermined,Multi-stage,Fin,Surface Structure
43494,SRR6020430,SRX3171490,SRS2501299,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,R5 prim Scar,GSM2776985,,source name:primary fin single cells|cas9 injection:mRNA|FISH id:R5|tissue:primary fin|sorted plates:6,R5 prim Scar,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.,primary fin single cells,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,,cas9 injection:mRNA|FISH id:R5|tissue:primary fin|sorted plates:6,GSM2776985,GSM2776985: R5 prim Scar; Danio rerio; RNA Seq,GSM2776985,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2776985,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,R5_prim_Scar_p02_R1.fastq.gz R5_prim_Scar_p02_R2.fastq.gz,fastq fastq,1266120923.0,8332017.0,GSM2776985 r2,0:75.98 1:75.98,A:222649072;C:369728088;G:482809574;T:190903334;N:30855,75,75,,,222649072,369728088,482809574,190903334,30855,SRX3171490,SRS2501299,SRA602108,GEO,"AVO, Hubrecht Institue",2,4e-05,2e-05,3e-05,1e-05,0.99997,0.99997,0.0,1.0,76,76,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2017-09-08,Undetermined,Multi-stage,Fin,Surface Structure
43495,SRR6020431,SRX3171490,SRS2501299,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,R5 prim Scar,GSM2776985,,source name:primary fin single cells|cas9 injection:mRNA|FISH id:R5|tissue:primary fin|sorted plates:6,R5 prim Scar,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.,primary fin single cells,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,,cas9 injection:mRNA|FISH id:R5|tissue:primary fin|sorted plates:6,GSM2776985,GSM2776985: R5 prim Scar; Danio rerio; RNA Seq,GSM2776985,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2776985,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,R5_prim_Scar_p03_R1.fastq.gz R5_prim_Scar_p03_R2.fastq.gz,fastq fastq,494949145.0,3257351.0,GSM2776985 r3,0:75.98 1:75.97,A:87163836;C:143707892;G:188542837;T:75522642;N:11938,75,75,,,87163836,143707892,188542837,75522642,11938,SRX3171490,SRS2501299,SRA602108,GEO,"AVO, Hubrecht Institue",2,0.00015,5e-05,9e-05,2e-05,0.99995,0.99993,0.0,0.0,76,76,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2017-09-08,Undetermined,Multi-stage,Fin,Surface Structure
43496,SRR6020432,SRX3171490,SRS2501299,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,R5 prim Scar,GSM2776985,,source name:primary fin single cells|cas9 injection:mRNA|FISH id:R5|tissue:primary fin|sorted plates:6,R5 prim Scar,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.,primary fin single cells,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,,cas9 injection:mRNA|FISH id:R5|tissue:primary fin|sorted plates:6,GSM2776985,GSM2776985: R5 prim Scar; Danio rerio; RNA Seq,GSM2776985,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2776985,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,R5_prim_Scar_p04_R1.fastq.gz R5_prim_Scar_p04_R2.fastq.gz,fastq fastq,376701290.0,2478856.0,GSM2776985 r4,0:75.99 1:75.98,A:66002492;C:109979363;G:143811826;T:56905698;N:1911,75,75,,,66002492,109979363,143811826,56905698,1911,SRX3171490,SRS2501299,SRA602108,GEO,"AVO, Hubrecht Institue",2,4e-05,5e-05,3e-05,4e-05,1.0,1.0,,,76,76,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2017-09-08,Undetermined,Multi-stage,Fin,Surface Structure